Carrel name: journal-plosOne-cord Creating study carrel named journal-plosOne-cord Initializing database file: cache/cord-000008-3dgjv0x1.json key: cord-000008-3dgjv0x1 authors: Vali, Bahareh; Yue, Feng Yun; Jones, R. Brad; Sheth, Prameet M.; Kaul, Rupert; Betts, Michael R.; Wong, David; Kovacs, Colin; Loutfy, Mona; Common, Andrew; Halpenny, Roberta; Ostrowski, Mario A. title: HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date: 2008-10-20 journal: PLoS One DOI: 10.1371/journal.pone.0003454 sha: doc_id: 8 cord_uid: 3dgjv0x1 file: cache/cord-000006-104sqoxz.json key: cord-000006-104sqoxz authors: Bray, Daniel P.; Bennett, Malcolm; Stockley, Paula; Hurst, Jane L.; Kipar, Anja title: Composition and Function of Haemolymphatic Tissues in the European Common Shrew date: 2008-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0003413 sha: doc_id: 6 cord_uid: 104sqoxz file: cache/cord-000166-36bfeoqv.json key: cord-000166-36bfeoqv authors: Tracht, Samantha M.; Del Valle, Sara Y.; Hyman, James M. title: Mathematical Modeling of the Effectiveness of Facemasks in Reducing the Spread of Novel Influenza A (H1N1) date: 2010-02-10 journal: PLoS One DOI: 10.1371/journal.pone.0009018 sha: doc_id: 166 cord_uid: 36bfeoqv file: cache/cord-000131-ugbwvy6j.json key: cord-000131-ugbwvy6j authors: Jones, James Holland; Salathé, Marcel title: Early Assessment of Anxiety and Behavioral Response to Novel Swine-Origin Influenza A(H1N1) date: 2009-12-03 journal: PLoS One DOI: 10.1371/journal.pone.0008032 sha: doc_id: 131 cord_uid: ugbwvy6j file: cache/cord-000079-533xlisc.json key: cord-000079-533xlisc authors: Huszthy, Peter C.; Giroglou, Tsanan; Tsinkalovsky, Oleg; Euskirchen, Philipp; Skaftnesmo, Kai Ove; Bjerkvig, Rolf; von Laer, Dorothee; Miletic, Hrvoje title: Remission of Invasive, Cancer Stem-Like Glioblastoma Xenografts Using Lentiviral Vector-Mediated Suicide Gene Therapy date: 2009-07-20 journal: PLoS One DOI: 10.1371/journal.pone.0006314 sha: doc_id: 79 cord_uid: 533xlisc file: cache/cord-000082-jy7j8sh0.json key: cord-000082-jy7j8sh0 authors: Huang, Ting; Wang, Wei; Bessaud, Mael; Ren, Peijun; Sheng, Jun; Yan, Huajie; Zhang, Jing; Lin, Xin; Wang, Yongjin; Delpeyroux, Francis; Deubel, Vincent title: Evidence of Recombination and Genetic Diversity in Human Rhinoviruses in Children with Acute Respiratory Infection date: 2009-07-27 journal: PLoS One DOI: 10.1371/journal.pone.0006355 sha: doc_id: 82 cord_uid: jy7j8sh0 file: cache/cord-000050-tfcerilc.json key: cord-000050-tfcerilc authors: Rao, Srinivas; Kong, Wing-Pui; Wei, Chih-Jen; Yang, Zhi-Yong; Nason, Martha; Styles, Darrel; DeTolla, Louis J.; Sorrell, Erin M.; Song, Haichen; Wan, Hongquan; Ramirez-Nieto, Gloria C.; Perez, Daniel; Nabel, Gary J. title: Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date: 2008-06-18 journal: PLoS One DOI: 10.1371/journal.pone.0002432 sha: doc_id: 50 cord_uid: tfcerilc file: cache/cord-000013-pr9i9swk.json key: cord-000013-pr9i9swk authors: Croyle, Maria A.; Patel, Ami; Tran, Kaylie N.; Gray, Michael; Zhang, Yi; Strong, James E.; Feldmann, Heinz; Kobinger, Gary P. title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice date: 2008-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0003548 sha: doc_id: 13 cord_uid: pr9i9swk file: cache/cord-000269-v4jochbe.json key: cord-000269-v4jochbe authors: Wittekindt, Nicola E.; Padhi, Abinash; Schuster, Stephan C.; Qi, Ji; Zhao, Fangqing; Tomsho, Lynn P.; Kasson, Lindsay R.; Packard, Michael; Cross, Paul; Poss, Mary title: Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics date: 2010-10-18 journal: PLoS One DOI: 10.1371/journal.pone.0013432 sha: doc_id: 269 cord_uid: v4jochbe file: cache/cord-000266-xwfptmmv.json key: cord-000266-xwfptmmv authors: Liao, Qiuyan; Cowling, Benjamin; Lam, Wing Tak; Ng, Man Wai; Fielding, Richard title: Situational Awareness and Health Protective Responses to Pandemic Influenza A (H1N1) in Hong Kong: A Cross-Sectional Study date: 2010-10-12 journal: PLoS One DOI: 10.1371/journal.pone.0013350 sha: doc_id: 266 cord_uid: xwfptmmv file: cache/cord-000366-u4649rtx.json key: cord-000366-u4649rtx authors: Shan, Tongling; Lan, Daoliang; Li, Linlin; Wang, Chunmei; Cui, Li; Zhang, Wen; Hua, Xiuguo; Zhu, Caixia; Zhao, Wei; Delwart, Eric title: Genomic Characterization and High Prevalence of Bocaviruses in Swine date: 2011-04-15 journal: PLoS One DOI: 10.1371/journal.pone.0017292 sha: doc_id: 366 cord_uid: u4649rtx file: cache/cord-000063-tex6bgab.json key: cord-000063-tex6bgab authors: Sui, Hong-Yan; Zhao, Guang-Yu; Huang, Jian-Dong; Jin, Dong-Yan; Yuen, Kwok-Yung; Zheng, Bo-Jian title: Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication date: 2009-05-22 journal: PLoS One DOI: 10.1371/journal.pone.0005671 sha: doc_id: 63 cord_uid: tex6bgab file: cache/cord-000540-bbjmcdo5.json key: cord-000540-bbjmcdo5 authors: Hellard, Eléonore; Pontier, Dominique; Sauvage, Frank; Poulet, Hervé; Fouchet, David title: True versus False Parasite Interactions: A Robust Method to Take Risk Factors into Account and Its Application to Feline Viruses date: 2012-01-03 journal: PLoS One DOI: 10.1371/journal.pone.0029618 sha: doc_id: 540 cord_uid: bbjmcdo5 file: cache/cord-000574-7eflwyxk.json key: cord-000574-7eflwyxk authors: Liu, Yanli; Huangfu, Jie; Qi, Feng; Kaleem, Imdad; E, Wenwen; Li, Chun title: Effects of a Non-Conservative Sequence on the Properties of β-glucuronidase from Aspergillus terreus Li-20 date: 2012-02-07 journal: PLoS One DOI: 10.1371/journal.pone.0030998 sha: doc_id: 574 cord_uid: 7eflwyxk file: cache/cord-000255-73nlxqgk.json key: cord-000255-73nlxqgk authors: Hosseini, Parviez; Sokolow, Susanne H.; Vandegrift, Kurt J.; Kilpatrick, A. Marm; Daszak, Peter title: Predictive Power of Air Travel and Socio-Economic Data for Early Pandemic Spread date: 2010-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0012763 sha: doc_id: 255 cord_uid: 73nlxqgk file: cache/cord-000140-5kapn32k.json key: cord-000140-5kapn32k authors: Wang, Pei-Gang; Kudelko, Mateusz; Lo, Joanne; Siu, Lewis Yu Lam; Kwok, Kevin Tsz Hin; Sachse, Martin; Nicholls, John M.; Bruzzone, Roberto; Altmeyer, Ralf M.; Nal, Béatrice title: Efficient Assembly and Secretion of Recombinant Subviral Particles of the Four Dengue Serotypes Using Native prM and E Proteins date: 2009-12-15 journal: PLoS One DOI: 10.1371/journal.pone.0008325 sha: doc_id: 140 cord_uid: 5kapn32k file: cache/cord-000176-z76vjkxg.json key: cord-000176-z76vjkxg authors: Nguyen, Jack T.; Hoopes, Justin D.; Le, Minh H.; Smee, Donald F.; Patick, Amy K.; Faix, Dennis J.; Blair, Patrick J.; de Jong, Menno D.; Prichard, Mark N.; Went, Gregory T. title: Triple Combination of Amantadine, Ribavirin, and Oseltamivir Is Highly Active and Synergistic against Drug Resistant Influenza Virus Strains In Vitro date: 2010-02-22 journal: PLoS One DOI: 10.1371/journal.pone.0009332 sha: doc_id: 176 cord_uid: z76vjkxg file: cache/cord-000143-2xvd5ogf.json key: cord-000143-2xvd5ogf authors: Napthine, Sawsan; Lever, Robert A.; Powell, Michael L.; Jackson, Richard J.; Brown, T. David K.; Brierley, Ian title: Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy date: 2009-12-22 journal: PLoS One DOI: 10.1371/journal.pone.0008390 sha: doc_id: 143 cord_uid: 2xvd5ogf file: cache/cord-000224-2lz03oqb.json key: cord-000224-2lz03oqb authors: Porter, Kristen A.; Kelley, Lauren N.; George, Annette; Harton, Jonathan A.; Duus, Karen M. title: Class II Transactivator (CIITA) Enhances Cytoplasmic Processing of HIV-1 Pr55Gag date: 2010-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0011304 sha: doc_id: 224 cord_uid: 2lz03oqb file: cache/cord-000720-5b936n3g.json key: cord-000720-5b936n3g authors: Nannyonga, Betty; Sumpter, David J. T.; Mugisha, Joseph Y. T.; Luboobi, Livingstone S. title: The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks date: 2012-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0041135 sha: doc_id: 720 cord_uid: 5b936n3g file: cache/cord-000742-0r4z1zea.json key: cord-000742-0r4z1zea authors: Vittecoq, Marion; Grandhomme, Viviane; Champagnon, Jocelyn; Guillemain, Matthieu; Crescenzo-Chaigne, Bernadette; Renaud, François; Thomas, Frédéric; Gauthier-Clerc, Michel; van der Werf, Sylvie title: High Influenza A Virus Infection Rates in Mallards Bred for Hunting in the Camargue, South of France date: 2012-08-27 journal: PLoS One DOI: 10.1371/journal.pone.0043974 sha: doc_id: 742 cord_uid: 0r4z1zea file: cache/cord-000408-pt3b4yc7.json key: cord-000408-pt3b4yc7 authors: Lu, Sydney X.; Kappel, Lucy W.; Charbonneau-Allard, Anne-Marie; Atallah, Renée; Holland, Amanda M.; Turbide, Claire; Hubbard, Vanessa M.; Rotolo, Jimmy A.; Smith, Marsinay; Suh, David; King, Christopher; Rao, Uttam K.; Yim, Nury; Bautista, Johanne L.; Jenq, Robert R.; Penack, Olaf; Na, Il-Kang; Liu, Chen; Murphy, George; Alpdogan, Onder; Blumberg, Richard S.; Macian, Fernando; Holmes, Kathryn V.; Beauchemin, Nicole; van den Brink, Marcel R. M. title: Ceacam1 Separates Graft-versus-Host-Disease from Graft-versus-Tumor Activity after Experimental Allogeneic Bone Marrow Transplantation date: 2011-07-06 journal: PLoS One DOI: 10.1371/journal.pone.0021611 sha: doc_id: 408 cord_uid: pt3b4yc7 file: cache/cord-000588-3wok0n21.json key: cord-000588-3wok0n21 authors: Sainz, Juan; Lupiáñez, Carmen Belén; Segura-Catena, Juana; Vazquez, Lourdes; Ríos, Rafael; Oyonarte, Salvador; Hemminki, Kari; Försti, Asta; Jurado, Manuel title: Dectin-1 and DC-SIGN Polymorphisms Associated with Invasive Pulmonary Aspergillosis Infection date: 2012-02-27 journal: PLoS One DOI: 10.1371/journal.pone.0032273 sha: doc_id: 588 cord_uid: 3wok0n21 file: cache/cord-000765-r7y1cqou.json key: cord-000765-r7y1cqou authors: Chang, Yu-Ming; Chen, Cammy K. -M.; Chang, Yuan-Chih; Jeng, Wen-Yih; Hou, Ming-Hon; Wang, Andrew H. -J. title: Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis date: 2012-09-21 journal: PLoS One DOI: 10.1371/journal.pone.0045665 sha: doc_id: 765 cord_uid: r7y1cqou file: cache/cord-000501-qz68gtd4.json key: cord-000501-qz68gtd4 authors: Greatorex, Jane S.; Digard, Paul; Curran, Martin D.; Moynihan, Robert; Wensley, Harrison; Wreghitt, Tim; Varsani, Harsha; Garcia, Fayna; Enstone, Joanne; Nguyen-Van-Tam, Jonathan S. title: Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date: 2011-11-22 journal: PLoS One DOI: 10.1371/journal.pone.0027932 sha: doc_id: 501 cord_uid: qz68gtd4 file: cache/cord-000077-d441jam3.json key: cord-000077-d441jam3 authors: Zhang, Hao-Jie; Wang, Yong-Xiang; Wu, Hao; Jin, Dong-Yan; Wen, Yu-Mei; Zheng, Bo-Jian title: The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date: 2009-07-03 journal: PLoS One DOI: 10.1371/journal.pone.0006108 sha: doc_id: 77 cord_uid: d441jam3 file: cache/cord-000182-ni6iyzdn.json key: cord-000182-ni6iyzdn authors: He, Zhisong; Zhang, Jian; Shi, Xiao-He; Hu, Le-Le; Kong, Xiangyin; Cai, Yu-Dong; Chou, Kuo-Chen title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features date: 2010-03-11 journal: PLoS One DOI: 10.1371/journal.pone.0009603 sha: doc_id: 182 cord_uid: ni6iyzdn file: cache/cord-000237-mticfoic.json key: cord-000237-mticfoic authors: Guan, Xuhua; Silk, Benjamin J.; Li, Wenkai; Fleischauer, Aaron T.; Xing, Xuesen; Jiang, Xiaoqing; Yu, Hongjie; Olsen, Sonja J.; Cohen, Adam L. title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008 date: 2010-07-23 journal: PLoS One DOI: 10.1371/journal.pone.0011721 sha: doc_id: 237 cord_uid: mticfoic file: cache/cord-000321-ee7q7jhv.json key: cord-000321-ee7q7jhv authors: Powell, Michael L.; Leigh, Kendra E.; Pöyry, Tuija A. A.; Jackson, Richard J.; Brown, T. David K.; Brierley, Ian title: Further Characterisation of the Translational Termination-Reinitiation Signal of the Influenza B Virus Segment 7 RNA date: 2011-02-08 journal: PLoS One DOI: 10.1371/journal.pone.0016822 sha: doc_id: 321 cord_uid: ee7q7jhv file: cache/cord-000460-h3owwjao.json key: cord-000460-h3owwjao authors: Xiong, Jing; Miller, Virginia M.; Hunter, Larry W.; Li, Yunman; Jayachandran, Muthuvel title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide date: 2011-09-26 journal: PLoS One DOI: 10.1371/journal.pone.0025504 sha: doc_id: 460 cord_uid: h3owwjao file: cache/cord-000638-ss1435el.json key: cord-000638-ss1435el authors: Beq, Stephanie; Rozlan, Sandra; Pelletier, Sandy; Willems, Bernard; Bruneau, Julie; Lelievre, Jean-Daniel; Levy, Yves; Shoukry, Naglaa H.; Cheynier, Rémi title: Altered Thymic Function during Interferon Therapy in HCV-Infected Patients date: 2012-04-16 journal: PLoS One DOI: 10.1371/journal.pone.0034326 sha: doc_id: 638 cord_uid: ss1435el file: cache/cord-000556-uu1oz2ei.json key: cord-000556-uu1oz2ei authors: Kumar, Ranjit; Lawrence, Mark L.; Watt, James; Cooksey, Amanda M.; Burgess, Shane C.; Nanduri, Bindu title: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” date: 2012-01-20 journal: PLoS One DOI: 10.1371/journal.pone.0029435 sha: doc_id: 556 cord_uid: uu1oz2ei file: cache/cord-000666-je9t4i6q.json key: cord-000666-je9t4i6q authors: Verbist, Katherine C.; Rose, David L.; Cole, Charles J.; Field, Mary B.; Klonowski, Kimberly D. title: IL-15 Participates in the Respiratory Innate Immune Response to Influenza Virus Infection date: 2012-05-18 journal: PLoS One DOI: 10.1371/journal.pone.0037539 sha: doc_id: 666 cord_uid: je9t4i6q file: cache/cord-000547-adfigzc1.json key: cord-000547-adfigzc1 authors: Beniac, Daniel R.; Melito, Pasquale L.; deVarennes, Shauna L.; Hiebert, Shannon L.; Rabb, Melissa J.; Lamboo, Lindsey L.; Jones, Steven M.; Booth, Timothy F. title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date: 2012-01-11 journal: PLoS One DOI: 10.1371/journal.pone.0029608 sha: doc_id: 547 cord_uid: adfigzc1 file: cache/cord-000736-6f8vyziv.json key: cord-000736-6f8vyziv authors: Pripuzova, Natalia; Wang, Richard; Tsai, Shien; Li, Bingjie; Hung, Guo-Chiuan; Ptak, Roger G.; Lo, Shyh-Ching title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 journal: PLoS One DOI: 10.1371/journal.pone.0043246 sha: doc_id: 736 cord_uid: 6f8vyziv file: cache/cord-000434-ff2zadol.json key: cord-000434-ff2zadol authors: Zhao, Rongmao; Cui, Shujuan; Guo, Li; Wu, Chao; Gonzalez, Richard; Paranhos-Baccalà, Gláucia; Vernet, Guy; Wang, Jianwei; Hung, Tao title: Identification of a Highly Conserved H1 Subtype-Specific Epitope with Diagnostic Potential in the Hemagglutinin Protein of Influenza A Virus date: 2011-08-19 journal: PLoS One DOI: 10.1371/journal.pone.0023374 sha: doc_id: 434 cord_uid: ff2zadol file: cache/cord-000580-dcid9emx.json key: cord-000580-dcid9emx authors: Sällman Almén, Markus; Bringeland, Nathalie; Fredriksson, Robert; Schiöth, Helgi B. title: The Dispanins: A Novel Gene Family of Ancient Origin That Contains 14 Human Members date: 2012-02-20 journal: PLoS One DOI: 10.1371/journal.pone.0031961 sha: doc_id: 580 cord_uid: dcid9emx file: cache/cord-000609-dpcgl6ig.json key: cord-000609-dpcgl6ig authors: Raju, Sammeta V.; Wang, Guoshun title: Suppression of Adenosine-Activated Chloride Transport by Ethanol in Airway Epithelia date: 2012-03-19 journal: PLoS One DOI: 10.1371/journal.pone.0032112 sha: doc_id: 609 cord_uid: dpcgl6ig file: cache/cord-000267-xroo7z7g.json key: cord-000267-xroo7z7g authors: Xiao, Xiaodong; Zhu, Zhongyu; Dankmeyer, Jennifer L.; Wormald, Michael M.; Fast, Randy L.; Worsham, Patricia L.; Cote, Christopher K.; Amemiya, Kei; Dimitrov, Dimiter S. title: Human Anti-Plague Monoclonal Antibodies Protect Mice from Yersinia pestis in a Bubonic Plague Model date: 2010-10-13 journal: PLoS One DOI: 10.1371/journal.pone.0013047 sha: doc_id: 267 cord_uid: xroo7z7g file: cache/cord-000346-9b6yz3f4.json key: cord-000346-9b6yz3f4 authors: Holder, Benjamin P.; Simon, Philippe; Liao, Laura E.; Abed, Yacine; Bouhy, Xavier; Beauchemin, Catherine A. A.; Boivin, Guy title: Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model date: 2011-03-24 journal: PLoS One DOI: 10.1371/journal.pone.0014767 sha: doc_id: 346 cord_uid: 9b6yz3f4 file: cache/cord-000326-a18rch1f.json key: cord-000326-a18rch1f authors: Zhou, Jun-Wei; Tsui, Stephen K. W.; Ng, Maggie C. Y.; Geng, Hua; Li, Sai-Kam; So, Wing-Yee; Ma, Ronald C.; Wang, Ying; Tao, Qian; Chen, Zhen-Yu; Chan, Juliana C. N.; Ho, Yuan-Yuan title: Apolipoprotein M Gene (APOM) Polymorphism Modifies Metabolic and Disease Traits in Type 2 Diabetes date: 2011-02-24 journal: PLoS One DOI: 10.1371/journal.pone.0017324 sha: doc_id: 326 cord_uid: a18rch1f file: cache/cord-000336-57es391o.json key: cord-000336-57es391o authors: Liao, Qiuyan; Cowling, Benjamin J.; Lam, Wendy Wing Tak; Fielding, Richard title: Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study date: 2011-03-11 journal: PLoS One DOI: 10.1371/journal.pone.0017713 sha: doc_id: 336 cord_uid: 57es391o file: cache/cord-000478-88wo4xen.json key: cord-000478-88wo4xen authors: Gowen, Brian B.; Ennis, Jane; Russell, Andrew; Sefing, Eric J.; Wong, Min-Hui; Turner, Jeffrey title: Use of Recombinant Adenovirus Vectored Consensus IFN-α to Avert Severe Arenavirus Infection date: 2011-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0026072 sha: doc_id: 478 cord_uid: 88wo4xen file: cache/cord-000715-zl1s82yi.json key: cord-000715-zl1s82yi authors: Shulman, Lester M.; Hindiyeh, Musa; Muhsen, Khitam; Cohen, Dani; Mendelson, Ella; Sofer, Danit title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 journal: PLoS One DOI: 10.1371/journal.pone.0039455 sha: doc_id: 715 cord_uid: zl1s82yi file: cache/cord-000208-th0wddvc.json key: cord-000208-th0wddvc authors: Cornelissen, Lisette A. H. M.; de Vries, Robert P.; de Boer-Luijtze, Els A.; Rigter, Alan; Rottier, Peter J. M.; de Haan, Cornelis A. M. title: A Single Immunization with Soluble Recombinant Trimeric Hemagglutinin Protects Chickens against Highly Pathogenic Avian Influenza Virus H5N1 date: 2010-05-14 journal: PLoS One DOI: 10.1371/journal.pone.0010645 sha: doc_id: 208 cord_uid: th0wddvc file: cache/cord-000581-ewx5xhrb.json key: cord-000581-ewx5xhrb authors: Rudge, James W.; Hanvoravongchai, Piya; Krumkamp, Ralf; Chavez, Irwin; Adisasmito, Wiku; Ngoc Chau, Pham; Phommasak, Bounlay; Putthasri, Weerasak; Shih, Chin-Shui; Stein, Mart; Timen, Aura; Touch, Sok; Reintjes, Ralf; Coker, Richard title: Health System Resource Gaps and Associated Mortality from Pandemic Influenza across Six Asian Territories date: 2012-02-21 journal: PLoS One DOI: 10.1371/journal.pone.0031800 sha: doc_id: 581 cord_uid: ewx5xhrb file: cache/cord-000725-rafwlw0t.json key: cord-000725-rafwlw0t authors: Hindinger, Claudia; Bergmann, Cornelia C.; Hinton, David R.; Phares, Timothy W.; Parra, Gabriel I.; Hussain, Shabbir; Savarin, Carine; Atkinson, Roscoe D.; Stohlman, Stephen A. title: IFN-γ Signaling to Astrocytes Protects from Autoimmune Mediated Neurological Disability date: 2012-07-27 journal: PLoS One DOI: 10.1371/journal.pone.0042088 sha: doc_id: 725 cord_uid: rafwlw0t file: cache/cord-001045-jm60nxc2.json key: cord-001045-jm60nxc2 authors: DeLisle, Sylvain; Kim, Bernard; Deepak, Janaki; Siddiqui, Tariq; Gundlapalli, Adi; Samore, Matthew; D'Avolio, Leonard title: Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy date: 2013-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0070944 sha: doc_id: 1045 cord_uid: jm60nxc2 file: cache/cord-000265-llilwq1u.json key: cord-000265-llilwq1u authors: Gao, Rongbao; Dong, Libo; Dong, Jie; Wen, Leying; Zhang, Ye; Yu, Hongjie; Feng, Zijian; Chen, Minmei; Tan, Yi; Mo, Zhaojun; Liu, Haiyan; Fan, Yunyan; Li, Kunxiong; Li, Chris Ka-Fai; Li, Dexin; Yang, Weizhong; Shu, Yuelong title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 journal: PLoS One DOI: 10.1371/journal.pone.0013315 sha: doc_id: 265 cord_uid: llilwq1u file: cache/cord-000554-p4ufea6x.json key: cord-000554-p4ufea6x authors: Gao, Wei; Sun, Wenkui; Qu, Bingqian; Cardona, Carol J.; Powell, Kira; Wegner, Marta; Shi, Yi; Xing, Zheng title: Distinct Regulation of Host Responses by ERK and JNK MAP Kinases in Swine Macrophages Infected with Pandemic (H1N1) 2009 Influenza Virus date: 2012-01-18 journal: PLoS One DOI: 10.1371/journal.pone.0030328 sha: doc_id: 554 cord_uid: p4ufea6x file: cache/cord-000721-leedutqo.json key: cord-000721-leedutqo authors: Nawaz, Sameena; Allen, David J.; Aladin, Farah; Gallimore, Christopher; Iturriza-Gómara, Miren title: Human Bocaviruses Are Not Significantly Associated with Gastroenteritis: Results of Retesting Archive DNA from a Case Control Study in the UK date: 2012-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0041346 sha: doc_id: 721 cord_uid: leedutqo file: cache/cord-001014-8yrpcl94.json key: cord-001014-8yrpcl94 authors: Kitagawa, Hiroshi; Kawano, Mitsuo; Yamanaka, Keiichi; Kakeda, Masato; Tsuda, Kenshiro; Inada, Hiroyasu; Yoneda, Misao; Sakaguchi, Tadashi; Nigi, Akina; Nishimura, Koumei; Komada, Hiroshi; Tsurudome, Masato; Yasutomi, Yasuhiro; Nosaka, Tetsuya; Mizutani, Hitoshi title: Intranasally Administered Antigen 85B Gene Vaccine in Non-Replicating Human Parainfluenza Type 2 Virus Vector Ameliorates Mouse Atopic Dermatitis date: 2013-07-03 journal: PLoS One DOI: 10.1371/journal.pone.0066614 sha: doc_id: 1014 cord_uid: 8yrpcl94 file: cache/cord-001007-645zegcv.json key: cord-001007-645zegcv authors: Kim, Hak; Kim, Kisoon; Kim, Dae-Won; Jung, Hee-Dong; Min Cheong, Hyang; Kim, Ki Hwan; Soo Kim, Dong; Kim, You-Jin title: Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections date: 2013-06-27 journal: PLoS One DOI: 10.1371/journal.pone.0068081 sha: doc_id: 1007 cord_uid: 645zegcv file: cache/cord-000413-h2e6h076.json key: cord-000413-h2e6h076 authors: Zhang, Jingyu; Ma, Zhenni; Dong, Ningzheng; Liu, Fang; Su, Jian; Zhao, Yiming; Shen, Fei; Wang, Anyou; Ruan, Changgeng title: A Conformation-Sensitive Monoclonal Antibody against the A2 Domain of von Willebrand Factor Reduces Its Proteolysis by ADAMTS13 date: 2011-07-11 journal: PLoS One DOI: 10.1371/journal.pone.0022157 sha: doc_id: 413 cord_uid: h2e6h076 file: cache/cord-000837-rdpsxb4n.json key: cord-000837-rdpsxb4n authors: Perez-Pepe, Marcelo; Slomiansky, Victoria; Loschi, Mariela; Luchelli, Luciana; Neme, Maximiliano; Thomas, María Gabriela; Boccaccio, Graciela Lidia title: BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis date: 2012-12-20 journal: PLoS One DOI: 10.1371/journal.pone.0051495 sha: doc_id: 837 cord_uid: rdpsxb4n file: cache/cord-000248-zueoyesj.json key: cord-000248-zueoyesj authors: Berretta, Regina; Moscato, Pablo title: Cancer Biomarker Discovery: The Entropic Hallmark date: 2010-08-18 journal: PLoS One DOI: 10.1371/journal.pone.0012262 sha: doc_id: 248 cord_uid: zueoyesj file: cache/cord-000375-fvfl0bn1.json key: cord-000375-fvfl0bn1 authors: Shen, Ching-I; Wang, Ching-Ho; Shen, Shih-Cheng; Lee, Hsiu-Chin; Liao, Jiunn-Wang; Su, Hong-Lin title: The Infection of Chicken Tracheal Epithelial Cells with a H6N1 Avian Influenza Virus date: 2011-05-06 journal: PLoS One DOI: 10.1371/journal.pone.0018894 sha: doc_id: 375 cord_uid: fvfl0bn1 file: cache/cord-000719-o7ttiu97.json key: cord-000719-o7ttiu97 authors: Jonsson, Colleen B.; Camp, Jeremy V.; Wu, Albert; Zheng, Huaiyu; Kraenzle, Jennifer L.; Biller, Ashley E.; Vanover, Carol D.; Chu, Yong-Kyu; Ng, Chin K.; Proctor, Mary; Sherwood, Leslie; Steffen, Marlene C.; Mollura, Daniel J. title: Molecular Imaging Reveals a Progressive Pulmonary Inflammation in Lower Airways in Ferrets Infected with 2009 H1N1 Pandemic Influenza Virus date: 2012-07-20 journal: PLoS One DOI: 10.1371/journal.pone.0040094 sha: doc_id: 719 cord_uid: o7ttiu97 file: cache/cord-000158-d08buwtu.json key: cord-000158-d08buwtu authors: Corti, Davide; Langedijk, Johannes P. M.; Hinz, Andreas; Seaman, Michael S.; Vanzetta, Fabrizia; Fernandez-Rodriguez, Blanca M.; Silacci, Chiara; Pinna, Debora; Jarrossay, David; Balla-Jhagjhoorsingh, Sunita; Willems, Betty; Zekveld, Maria J.; Dreja, Hanna; O'Sullivan, Eithne; Pade, Corinna; Orkin, Chloe; Jeffs, Simon A.; Montefiori, David C.; Davis, David; Weissenhorn, Winfried; McKnight, Áine; Heeney, Jonathan L.; Sallusto, Federica; Sattentau, Quentin J.; Weiss, Robin A.; Lanzavecchia, Antonio title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals date: 2010-01-20 journal: PLoS One DOI: 10.1371/journal.pone.0008805 sha: doc_id: 158 cord_uid: d08buwtu file: cache/cord-000536-0mn1gbll.json key: cord-000536-0mn1gbll authors: Hu, Le-Le; Chen, Chen; Huang, Tao; Cai, Yu-Dong; Chou, Kuo-Chen title: Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions date: 2011-12-29 journal: PLoS One DOI: 10.1371/journal.pone.0029491 sha: doc_id: 536 cord_uid: 0mn1gbll file: cache/cord-000642-mkwpuav6.json key: cord-000642-mkwpuav6 authors: Moreira, Rebeca; Balseiro, Pablo; Planas, Josep V.; Fuste, Berta; Beltran, Sergi; Novoa, Beatriz; Figueras, Antonio title: Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing date: 2012-04-19 journal: PLoS One DOI: 10.1371/journal.pone.0035009 sha: doc_id: 642 cord_uid: mkwpuav6 file: cache/cord-000809-9voqa1oy.json key: cord-000809-9voqa1oy authors: Archer, Brett N.; Tempia, Stefano; White, Laura F.; Pagano, Marcello; Cohen, Cheryl title: Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa date: 2012-11-16 journal: PLoS One DOI: 10.1371/journal.pone.0049482 sha: doc_id: 809 cord_uid: 9voqa1oy file: cache/cord-000813-gagakqw4.json key: cord-000813-gagakqw4 authors: Xue, Mei; Shi, Xingming; Zhang, Jing; Zhao, Yan; Cui, Hongyu; Hu, Shunlei; Gao, Hongbo; Cui, Xianlan; Wang, Yun-Feng title: Identification of a Conserved B-cell Epitope on Reticuloendotheliosis Virus Envelope Protein by Screening a Phage-displayed Random Peptide Library date: 2012-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0049842 sha: doc_id: 813 cord_uid: gagakqw4 file: cache/cord-000851-uylgyhs8.json key: cord-000851-uylgyhs8 authors: Wang, Zhenya; Chai, Weidong; Burwinkel, Michael; Twardziok, Sven; Wrede, Paul; Palissa, Christiane; Esch, Bettina; Schmidt, Michael F. G. title: Inhibitory Influence of Enterococcus faecium on the Propagation of Swine Influenza A Virus In Vitro date: 2013-01-07 journal: PLoS One DOI: 10.1371/journal.pone.0053043 sha: doc_id: 851 cord_uid: uylgyhs8 file: cache/cord-000180-howix091.json key: cord-000180-howix091 authors: MacLeod, Iain J.; Minson, Tony title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 journal: PLoS One DOI: 10.1371/journal.pone.0009560 sha: doc_id: 180 cord_uid: howix091 file: cache/cord-000689-8lvzab4i.json key: cord-000689-8lvzab4i authors: Qi, Yilin; Operario, Darwin J.; Georas, Steve N.; Mosmann, Tim R. title: The Acute Environment, Rather than T Cell Subset Pre-Commitment, Regulates Expression of the Human T Cell Cytokine Amphiregulin date: 2012-06-14 journal: PLoS One DOI: 10.1371/journal.pone.0039072 sha: doc_id: 689 cord_uid: 8lvzab4i file: cache/cord-000877-usz7pnvu.json key: cord-000877-usz7pnvu authors: Abdel-Moneim, Ahmed S.; Kamel, Mahmoud M.; Al-Ghamdi, Abdullhamid S.; Al-Malky, Mater I. R. title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date: 2013-01-30 journal: PLoS One DOI: 10.1371/journal.pone.0055500 sha: doc_id: 877 cord_uid: usz7pnvu file: cache/cord-000726-tonaaft2.json key: cord-000726-tonaaft2 authors: Chang, Binggong; Petersen, Robert; Wisniewski, Thomas; Rubenstein, Richard title: Influence of Mabs on PrP(Sc) Formation Using In Vitro and Cell-Free Systems date: 2012-07-27 journal: PLoS One DOI: 10.1371/journal.pone.0041626 sha: doc_id: 726 cord_uid: tonaaft2 file: cache/cord-000261-ip32y0j5.json key: cord-000261-ip32y0j5 authors: Becker, Pablo D.; Legrand, Nicolas; van Geelen, Caroline M. M.; Noerder, Miriam; Huntington, Nicholas D.; Lim, Annick; Yasuda, Etsuko; Diehl, Sean A.; Scheeren, Ferenc A.; Ott, Michael; Weijer, Kees; Wedemeyer, Heiner; Di Santo, James P.; Beaumont, Tim; Guzman, Carlos A.; Spits, Hergen title: Generation of Human Antigen-Specific Monoclonal IgM Antibodies Using Vaccinated “Human Immune System” Mice date: 2010-10-04 journal: PLoS One DOI: 10.1371/journal.pone.0013137 sha: doc_id: 261 cord_uid: ip32y0j5 file: cache/cord-000425-isw6jeir.json key: cord-000425-isw6jeir authors: Flori, Laurence; Gao, Yu; Laloë, Denis; Lemonnier, Gaëtan; Leplat, Jean-Jacques; Teillaud, Angélique; Cossalter, Anne-Marie; Laffitte, Joëlle; Pinton, Philippe; de Vaureix, Christiane; Bouffaud, Marcel; Mercat, Marie-José; Lefèvre, François; Oswald, Isabelle P.; Bidanel, Jean-Pierre; Rogel-Gaillard, Claire title: Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation date: 2011-07-29 journal: PLoS One DOI: 10.1371/journal.pone.0022717 sha: doc_id: 425 cord_uid: isw6jeir file: cache/cord-000959-nk2thkme.json key: cord-000959-nk2thkme authors: Downer, Eric J.; Jones, Raasay S.; McDonald, Claire L.; Greco, Eleonora; Brennan, Sabina; Connor, Thomas J.; Robertson, Ian H.; Lynch, Marina A. title: Identifying Early Inflammatory Changes in Monocyte-Derived Macrophages from a Population with IQ-Discrepant Episodic Memory date: 2013-05-06 journal: PLoS One DOI: 10.1371/journal.pone.0063194 sha: doc_id: 959 cord_uid: nk2thkme file: cache/cord-000695-g5sum116.json key: cord-000695-g5sum116 authors: Hou, Yanxia; Guo, Yingying; Wu, Chunyan; Shen, Nan; Jiang, Yongping; Wang, Jingfei title: Prediction and Identification of T Cell Epitopes in the H5N1 Influenza Virus Nucleoprotein in Chicken date: 2012-06-20 journal: PLoS One DOI: 10.1371/journal.pone.0039344 sha: doc_id: 695 cord_uid: g5sum116 file: cache/cord-000981-6vloa2w3.json key: cord-000981-6vloa2w3 authors: Bálint, Zoltán; Zabini, Diana; Konya, Viktoria; Nagaraj, Chandran; Végh, Attila G.; Váró, György; Wilhelm, Imola; Fazakas, Csilla; Krizbai, István A.; Heinemann, Akos; Olschewski, Horst; Olschewski, Andrea title: Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells date: 2013-06-03 journal: PLoS One DOI: 10.1371/journal.pone.0063776 sha: doc_id: 981 cord_uid: 6vloa2w3 file: cache/cord-000352-qzkpik3z.json key: cord-000352-qzkpik3z authors: Carvalho, Gabrielle; Poalas, Konstantinos; Demian, Catherine; Hatchi, Emeline; Vazquez, Aimé; Bidère, Nicolas title: Participation of the Cell Polarity Protein PALS1 to T-Cell Receptor-Mediated NF-κB Activation date: 2011-03-30 journal: PLoS One DOI: 10.1371/journal.pone.0018159 sha: doc_id: 352 cord_uid: qzkpik3z file: cache/cord-000833-m6abyuvx.json key: cord-000833-m6abyuvx authors: Sekiguchi, Satoshi; Kimura, Kiminori; Chiyo, Tomoko; Ohtsuki, Takahiro; Tobita, Yoshimi; Tokunaga, Yuko; Yasui, Fumihiko; Tsukiyama-Kohara, Kyoko; Wakita, Takaji; Tanaka, Toshiyuki; Miyasaka, Masayuki; Mizuno, Kyosuke; Hayashi, Yukiko; Hishima, Tsunekazu; Matsushima, Kouji; Kohara, Michinori title: Immunization with a Recombinant Vaccinia Virus That Encodes Nonstructural Proteins of the Hepatitis C Virus Suppresses Viral Protein Levels in Mouse Liver date: 2012-12-17 journal: PLoS One DOI: 10.1371/journal.pone.0051656 sha: doc_id: 833 cord_uid: m6abyuvx file: cache/cord-000895-z5rdf0mi.json key: cord-000895-z5rdf0mi authors: Belalov, Ilya S.; Lukashev, Alexander N. title: Causes and Implications of Codon Usage Bias in RNA Viruses date: 2013-02-25 journal: PLoS One DOI: 10.1371/journal.pone.0056642 sha: doc_id: 895 cord_uid: z5rdf0mi file: cache/cord-000912-6l6c7jpq.json key: cord-000912-6l6c7jpq authors: Vitelli, Alessandra; Quirion, Mary R.; Lo, Chia-Yun; Misplon, Julia A.; Grabowska, Agnieszka K.; Pierantoni, Angiolo; Ammendola, Virginia; Price, Graeme E.; Soboleski, Mark R.; Cortese, Riccardo; Colloca, Stefano; Nicosia, Alfredo; Epstein, Suzanne L. title: Vaccination to Conserved Influenza Antigens in Mice Using a Novel Simian Adenovirus Vector, PanAd3, Derived from the Bonobo Pan paniscus date: 2013-03-11 journal: PLoS One DOI: 10.1371/journal.pone.0055435 sha: doc_id: 912 cord_uid: 6l6c7jpq file: cache/cord-000374-gt2pwc9b.json key: cord-000374-gt2pwc9b authors: Yang, Albert C.; Tsai, Shih-Jen; Hong, Chen-Jee; Wang, Cynthia; Chen, Tai-Jui; Liou, Ying-Jay; Peng, Chung-Kang title: Clustering Heart Rate Dynamics Is Associated with β-Adrenergic Receptor Polymorphisms: Analysis by Information-Based Similarity Index date: 2011-05-04 journal: PLoS One DOI: 10.1371/journal.pone.0019232 sha: doc_id: 374 cord_uid: gt2pwc9b file: cache/cord-000410-av8b8g8c.json key: cord-000410-av8b8g8c authors: Radoshitzky, Sheli R.; Longobardi, Lindsay E.; Kuhn, Jens H.; Retterer, Cary; Dong, Lian; Clester, Jeremiah C.; Kota, Krishna; Carra, John; Bavari, Sina title: Machupo Virus Glycoprotein Determinants for Human Transferrin Receptor 1 Binding and Cell Entry date: 2011-07-07 journal: PLoS One DOI: 10.1371/journal.pone.0021398 sha: doc_id: 410 cord_uid: av8b8g8c file: cache/cord-000539-uh3q65we.json key: cord-000539-uh3q65we authors: Zhang, Yi; Sun, Honglei; Fan, Lihong; Ma, Yuan; Sun, Yipeng; Pu, Juan; Yang, Jun; Qiao, Jian; Ma, Guangpeng; Liu, Jinhua title: Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date: 2012-01-03 journal: PLoS One DOI: 10.1371/journal.pone.0029347 sha: doc_id: 539 cord_uid: uh3q65we file: cache/cord-000341-d3a06n3f.json key: cord-000341-d3a06n3f authors: Xu, Wanghui; Han, Lu; Lin, Zhanglin title: Screening of Random Peptide Library of Hemagglutinin from Pandemic 2009 A(H1N1) Influenza Virus Reveals Unexpected Antigenically Important Regions date: 2011-03-18 journal: PLoS One DOI: 10.1371/journal.pone.0018016 sha: doc_id: 341 cord_uid: d3a06n3f file: cache/cord-000347-gdra8xhj.json key: cord-000347-gdra8xhj authors: Gibbons, Henry S.; Broomall, Stacey M.; McNew, Lauren A.; Daligault, Hajnalka; Chapman, Carol; Bruce, David; Karavis, Mark; Krepps, Michael; McGregor, Paul A.; Hong, Charles; Park, Kyong H.; Akmal, Arya; Feldman, Andrew; Lin, Jeffrey S.; Chang, Wenling E.; Higgs, Brandon W.; Demirev, Plamen; Lindquist, John; Liem, Alvin; Fochler, Ed; Read, Timothy D.; Tapia, Roxanne; Johnson, Shannon; Bishop-Lilly, Kimberly A.; Detter, Chris; Han, Cliff; Sozhamannan, Shanmuga; Rosenzweig, C. Nicole; Skowronski, Evan W. title: Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant date: 2011-03-25 journal: PLoS One DOI: 10.1371/journal.pone.0017836 sha: doc_id: 347 cord_uid: gdra8xhj file: cache/cord-000359-y0m1utug.json key: cord-000359-y0m1utug authors: Walpita, Pramila; Barr, Jennifer; Sherman, Michael; Basler, Christopher F.; Wang, Linfa title: Vaccine Potential of Nipah Virus-Like Particles date: 2011-04-06 journal: PLoS One DOI: 10.1371/journal.pone.0018437 sha: doc_id: 359 cord_uid: y0m1utug file: cache/cord-000868-vnwpzsu8.json key: cord-000868-vnwpzsu8 authors: Eissmann, Kristin; Mueller, Sebastian; Sticht, Heinrich; Jung, Susan; Zou, Peng; Jiang, Shibo; Gross, Andrea; Eichler, Jutta; Fleckenstein, Bernhard; Reil, Heide title: HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop date: 2013-01-22 journal: PLoS One DOI: 10.1371/journal.pone.0054452 sha: doc_id: 868 cord_uid: vnwpzsu8 file: cache/cord-000979-cav9n18w.json key: cord-000979-cav9n18w authors: Hoppe, Sebastian; Bier, Frank F.; Nickisch-Rosenegk, Markus v. title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0065837 sha: doc_id: 979 cord_uid: cav9n18w file: cache/cord-000322-8ctsa9sd.json key: cord-000322-8ctsa9sd authors: Ninove, Laetitia; Nougairede, Antoine; Gazin, Celine; Thirion, Laurence; Delogu, Ilenia; Zandotti, Christine; Charrel, Remi N.; De Lamballerie, Xavier title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date: 2011-02-09 journal: PLoS One DOI: 10.1371/journal.pone.0016142 sha: doc_id: 322 cord_uid: 8ctsa9sd file: cache/cord-000947-psguw47w.json key: cord-000947-psguw47w authors: Feng, Jianyu; Guo, Hong; Li, Sen; Lu, Tun title: A Study of the Mechanism of the Chaperone-like Function of an scFv of Human Creatine Kinase by Computer Simulation date: 2013-04-24 journal: PLoS One DOI: 10.1371/journal.pone.0062147 sha: doc_id: 947 cord_uid: psguw47w file: cache/cord-000723-wo20st5w.json key: cord-000723-wo20st5w authors: Xu, Zhenqiang; Shen, Fangxia; Li, Xiaoguang; Wu, Yan; Chen, Qi; Jie, Xu; Yao, Maosheng title: Molecular and Microscopic Analysis of Bacteria and Viruses in Exhaled Breath Collected Using a Simple Impaction and Condensing Method date: 2012-07-25 journal: PLoS One DOI: 10.1371/journal.pone.0041137 sha: doc_id: 723 cord_uid: wo20st5w file: cache/cord-001039-qocuprwb.json key: cord-001039-qocuprwb authors: Hayasaka, Daisuke; Shirai, Kenji; Aoki, Kotaro; Nagata, Noriyo; Simantini, Dash Sima; Kitaura, Kazutaka; Takamatsu, Yuki; Gould, Ernest; Suzuki, Ryuji; Morita, Kouichi title: TNF-α Acts as an Immunoregulator in the Mouse Brain by Reducing the Incidence of Severe Disease Following Japanese Encephalitis Virus Infection date: 2013-08-05 journal: PLoS One DOI: 10.1371/journal.pone.0071643 sha: doc_id: 1039 cord_uid: qocuprwb file: cache/cord-000905-1rhlu59c.json key: cord-000905-1rhlu59c authors: Cyktor, Joshua C.; Carruthers, Bridget; Beamer, Gillian L.; Turner, Joanne title: Clonal Expansions of CD8(+) T Cells with IL-10 Secreting Capacity Occur during Chronic Mycobacterium tuberculosis Infection date: 2013-03-05 journal: PLoS One DOI: 10.1371/journal.pone.0058612 sha: doc_id: 905 cord_uid: 1rhlu59c file: cache/cord-000786-ofpcgxce.json key: cord-000786-ofpcgxce authors: Chua, Brendon Y.; Johnson, Douglas; Tan, Amabel; Earnest-Silveira, Linda; Sekiya, Toshiki; Chin, Ruth; Torresi, Joseph; Jackson, David C. title: Hepatitis C VLPs Delivered to Dendritic Cells by a TLR2 Targeting Lipopeptide Results in Enhanced Antibody and Cell-Mediated Responses date: 2012-10-16 journal: PLoS One DOI: 10.1371/journal.pone.0047492 sha: doc_id: 786 cord_uid: ofpcgxce file: cache/cord-000937-8vk89i4h.json key: cord-000937-8vk89i4h authors: Law, John; Jovel, Juan; Patterson, Jordan; Ford, Glenn; O’keefe, Sandra; Wang, Weiwei; Meng, Bo; Song, Deyong; Zhang, Yong; Tian, Zhijian; Wasilenko, Shawn T.; Rahbari, Mandana; Mitchell, Troy; Jordan, Tracy; Carpenter, Eric; Mason, Andrew L.; Wong, Gane Ka-Shu title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 journal: PLoS One DOI: 10.1371/journal.pone.0060595 sha: doc_id: 937 cord_uid: 8vk89i4h file: cache/cord-001071-bjx5td52.json key: cord-001071-bjx5td52 authors: Vanhems, Philippe; Barrat, Alain; Cattuto, Ciro; Pinton, Jean-François; Khanafer, Nagham; Régis, Corinne; Kim, Byeul-a; Comte, Brigitte; Voirin, Nicolas title: Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors date: 2013-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0073970 sha: doc_id: 1071 cord_uid: bjx5td52 file: cache/cord-001011-vjxmrmfc.json key: cord-001011-vjxmrmfc authors: Lei, Daoxiong; Li, Faqian; Su, Huabo; Liu, Jinbao; Wei, Ning; Wang, Xuejun title: Hepatic Deficiency of COP9 Signalosome Subunit 8 Induces Ubiquitin-Proteasome System Impairment and Bim-Mediated Apoptosis in Murine Livers date: 2013-07-01 journal: PLoS One DOI: 10.1371/journal.pone.0067793 sha: doc_id: 1011 cord_uid: vjxmrmfc file: cache/cord-001021-nag4at49.json key: cord-001021-nag4at49 authors: Shaheen, Hussam H.; Prinz, Bianka; Chen, Ming-Tang; Pavoor, Tej; Lin, Song; Houston-Cummings, Nga Rewa; Moore, Renee; Stadheim, Terrance A.; Zha, Dongxing title: A Dual-Mode Surface Display System for the Maturation and Production of Monoclonal Antibodies in Glyco-Engineered Pichia pastoris date: 2013-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0070190 sha: doc_id: 1021 cord_uid: nag4at49 file: cache/cord-000866-dr2uow4m.json key: cord-000866-dr2uow4m authors: Picard-Jean, Frédéric; Bougie, Isabelle; Shuto, Satoshi; Bisaillon, Martin title: The Immunosuppressive Agent Mizoribine Monophosphate Is an Inhibitor of the Human RNA Capping Enzyme date: 2013-01-17 journal: PLoS One DOI: 10.1371/journal.pone.0054621 sha: doc_id: 866 cord_uid: dr2uow4m file: cache/cord-001083-vy1nxax2.json key: cord-001083-vy1nxax2 authors: Malagnac, Fabienne; Fabret, Céline; Prigent, Magali; Rousset, Jean-Pierre; Namy, Olivier; Silar, Philippe title: Rab-GDI Complex Dissociation Factor Expressed through Translational Frameshifting in Filamentous Ascomycetes date: 2013-09-19 journal: PLoS One DOI: 10.1371/journal.pone.0073772 sha: doc_id: 1083 cord_uid: vy1nxax2 file: cache/cord-000984-64p3wpav.json key: cord-000984-64p3wpav authors: Huang, Shang-Hui; Zhao, Li-Xiang; Hong, Chao; Duo, Cui-Cui; Guo, Bing-Nan; Zhang, Li-Juan; Gong, Zheng; Xiong, Si-Dong; Gong, Fang-Yuan; Gao, Xiao-Ming title: Self-Oligomerization Is Essential for Enhanced Immunological Activities of Soluble Recombinant Calreticulin date: 2013-06-10 journal: PLoS One DOI: 10.1371/journal.pone.0064951 sha: doc_id: 984 cord_uid: 64p3wpav file: cache/cord-001078-5m29nugu.json key: cord-001078-5m29nugu authors: Chen, Xiaorong; Yang, Zongguo; Lu, Yunfei; Xu, Qingnian; Wang, Qiang; Chen, Liang title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study date: 2013-09-17 journal: PLoS One DOI: 10.1371/journal.pone.0073362 sha: doc_id: 1078 cord_uid: 5m29nugu file: cache/cord-001090-qg2r691d.json key: cord-001090-qg2r691d authors: Twin, Jimmy; Bradshaw, Catriona S.; Garland, Suzanne M.; Fairley, Christopher K.; Fethers, Katherine; Tabrizi, Sepehr N. title: The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis date: 2013-09-27 journal: PLoS One DOI: 10.1371/journal.pone.0076892 sha: doc_id: 1090 cord_uid: qg2r691d file: cache/cord-001065-j4hvyyoi.json key: cord-001065-j4hvyyoi authors: Boncristiani, Humberto F.; Evans, Jay D.; Chen, Yanping; Pettis, Jeff; Murphy, Charles; Lopez, Dawn L.; Simone-Finstrom, Michael; Strand, Micheline; Tarpy, David R.; Rueppell, Olav title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date: 2013-09-05 journal: PLoS One DOI: 10.1371/journal.pone.0073429 sha: doc_id: 1065 cord_uid: j4hvyyoi file: cache/cord-001092-pkps5j8w.json key: cord-001092-pkps5j8w authors: Coleman, Ryan G.; Carchia, Michael; Sterling, Teague; Irwin, John J.; Shoichet, Brian K. title: Ligand Pose and Orientational Sampling in Molecular Docking date: 2013-10-01 journal: PLoS One DOI: 10.1371/journal.pone.0075992 sha: doc_id: 1092 cord_uid: pkps5j8w file: cache/cord-001120-fxd533b4.json key: cord-001120-fxd533b4 authors: Everitt, Aaron R.; Clare, Simon; McDonald, Jacqueline U.; Kane, Leanne; Harcourt, Katherine; Ahras, Malika; Lall, Amar; Hale, Christine; Rodgers, Angela; Young, Douglas B.; Haque, Ashraful; Billker, Oliver; Tregoning, John S.; Dougan, Gordon; Kellam, Paul title: Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date: 2013-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0080723 sha: doc_id: 1120 cord_uid: fxd533b4 file: cache/cord-001123-n2e4s7bu.json key: cord-001123-n2e4s7bu authors: Lin, Yue-Zhi; Yang, Fei; Zhang, Shu-Qin; Sun, Liu-Ke; Wang, Xue-Feng; Du, Cheng; Zhou, Jian-Hua title: The Soluble Form of the EIAV Receptor Encoded by an Alternative Splicing Variant Inhibits EIAV Infection of Target Cells date: 2013-11-22 journal: PLoS One DOI: 10.1371/journal.pone.0079299 sha: doc_id: 1123 cord_uid: n2e4s7bu file: cache/cord-001088-dugsh7mp.json key: cord-001088-dugsh7mp authors: Kim, So-Hee; Kim, Joo Young; Choi, Youngjoo; Nguyen, Huan H.; Song, Man Ki; Chang, Jun title: Mucosal Vaccination with Recombinant Adenovirus Encoding Nucleoprotein Provides Potent Protection against Influenza Virus Infection date: 2013-09-25 journal: PLoS One DOI: 10.1371/journal.pone.0075460 sha: doc_id: 1088 cord_uid: dugsh7mp file: cache/cord-001253-3jnkki5z.json key: cord-001253-3jnkki5z authors: Mohammad, Fahim; Theisen-Toupal, Jesse C.; Arnaout, Ramy title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data date: 2014-04-14 journal: PLoS One DOI: 10.1371/journal.pone.0092199 sha: doc_id: 1253 cord_uid: 3jnkki5z file: cache/cord-001099-jirkkkvy.json key: cord-001099-jirkkkvy authors: Yousuf, Mohammad A.; Zhou, Xiaohong; Mukherjee, Santanu; Chintakuntlawar, Ashish V.; Lee, Jeong Yoon; Ramke, Mirja; Chodosh, James; Rajaiya, Jaya title: Caveolin-1 Associated Adenovirus Entry into Human Corneal Cells date: 2013-10-11 journal: PLoS One DOI: 10.1371/journal.pone.0077462 sha: doc_id: 1099 cord_uid: jirkkkvy file: cache/cord-001199-9khx93c0.json key: cord-001199-9khx93c0 authors: Liu, Fengchen; Enanoria, Wayne T. A.; Ray, Kathryn J.; Coffee, Megan P.; Gordon, Aubree; Aragón, Tomás J.; Yu, Guowei; Cowling, Benjamin J.; Porco, Travis C. title: Effect of the One-Child Policy on Influenza Transmission in China: A Stochastic Transmission Model date: 2014-02-06 journal: PLoS One DOI: 10.1371/journal.pone.0084961 sha: doc_id: 1199 cord_uid: 9khx93c0 file: cache/cord-001186-jkg7qkj6.json key: cord-001186-jkg7qkj6 authors: Skowronski, Danuta M.; Hamelin, Marie-Eve; De Serres, Gaston; Janjua, Naveed Z.; Li, Guiyun; Sabaiduc, Suzana; Bouhy, Xavier; Couture, Christian; Leung, Anders; Kobasa, Darwyn; Embury-Hyatt, Carissa; de Bruin, Erwin; Balshaw, Robert; Lavigne, Sophie; Petric, Martin; Koopmans, Marion; Boivin, Guy title: Randomized Controlled Ferret Study to Assess the Direct Impact of 2008–09 Trivalent Inactivated Influenza Vaccine on A(H1N1)pdm09 Disease Risk date: 2014-01-27 journal: PLoS One DOI: 10.1371/journal.pone.0086555 sha: doc_id: 1186 cord_uid: jkg7qkj6 file: cache/cord-001162-z8cbbit3.json key: cord-001162-z8cbbit3 authors: Yun, Heather C.; Fugate, William H.; Murray, Clinton K.; Cropper, Thomas L.; Lott, Lisa; McDonald, J. Matthew title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection date: 2014-01-08 journal: PLoS One DOI: 10.1371/journal.pone.0085094 sha: doc_id: 1162 cord_uid: z8cbbit3 file: cache/cord-001117-llb4f74a.json key: cord-001117-llb4f74a authors: Ji, Wen-Jie; Ma, Yong-Qiang; Zhou, Xin; Zhang, Yi-Dan; Lu, Rui-Yi; Guo, Zhao-Zeng; Sun, Hai-Ying; Hu, Dao-Chuan; Yang, Guo-Hong; Li, Yu-Ming; Wei, Lu-Qing title: Spironolactone Attenuates Bleomycin-Induced Pulmonary Injury Partially via Modulating Mononuclear Phagocyte Phenotype Switching in Circulating and Alveolar Compartments date: 2013-11-19 journal: PLoS One DOI: 10.1371/journal.pone.0081090 sha: doc_id: 1117 cord_uid: llb4f74a file: cache/cord-001213-gxqufddb.json key: cord-001213-gxqufddb authors: Butt, Azeem Mehmood; Nasrullah, Izza; Tong, Yigang title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses date: 2014-03-04 journal: PLoS One DOI: 10.1371/journal.pone.0090905 sha: doc_id: 1213 cord_uid: gxqufddb file: cache/cord-001251-forh7lw4.json key: cord-001251-forh7lw4 authors: Jank, Johanna M.; Maier, Esther M.; Reiß, Dunja D.; Haslbeck, Martin; Kemter, Kristina F.; Truger, Marietta S.; Sommerhoff, Christian P.; Ferdinandusse, Sacha; Wanders, Ronald J.; Gersting, Søren W.; Muntau, Ania C. title: The Domain-Specific and Temperature-Dependent Protein Misfolding Phenotype of Variant Medium-Chain acyl-CoA Dehydrogenase date: 2014-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0093852 sha: doc_id: 1251 cord_uid: forh7lw4 file: cache/cord-001129-gi2kswai.json key: cord-001129-gi2kswai authors: Lemos de Matos, Ana; McFadden, Grant; Esteves, Pedro J. title: Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals date: 2013-11-27 journal: PLoS One DOI: 10.1371/journal.pone.0081864 sha: doc_id: 1129 cord_uid: gi2kswai file: cache/cord-001207-yjaiybwf.json key: cord-001207-yjaiybwf authors: Sachsenröder, Jana; Twardziok, Sven O.; Scheuch, Matthias; Johne, Reimar title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 journal: PLoS One DOI: 10.1371/journal.pone.0088888 sha: doc_id: 1207 cord_uid: yjaiybwf file: cache/cord-001368-ymp1pj3r.json key: cord-001368-ymp1pj3r authors: Zhang, Chao; He, Xinlong; Gu, Yaping; Zhou, Huayun; Cao, Jun; Gao, Qi title: Recombinant Scorpine Produced Using SUMO Fusion Partner in Escherichia coli Has the Activities against Clinically Isolated Bacteria and Inhibits the Plasmodium falciparum Parasitemia In Vitro date: 2014-07-28 journal: PLoS One DOI: 10.1371/journal.pone.0103456 sha: doc_id: 1368 cord_uid: ymp1pj3r file: cache/cord-001145-hc9ssruz.json key: cord-001145-hc9ssruz authors: Akazawa, Yuko; Isomoto, Hajime; Matsushima, Kayoko; Kanda, Tsutomu; Minami, Hitomi; Yamaghchi, Naoyuki; Taura, Naota; Shiozawa, Ken; Ohnita, Ken; Takeshima, Fuminao; Nakano, Masayuki; Moss, Joel; Hirayama, Toshiya; Nakao, Kazuhiko title: Endoplasmic Reticulum Stress Contributes to Helicobacter Pylori VacA-Induced Apoptosis date: 2013-12-13 journal: PLoS One DOI: 10.1371/journal.pone.0082322 sha: doc_id: 1145 cord_uid: hc9ssruz file: cache/cord-001126-uqr00nzd.json key: cord-001126-uqr00nzd authors: Zhang, Zhicheng; Dai, Wei; Dai, Dingzhen title: Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1 date: 2013-11-26 journal: PLoS One DOI: 10.1371/journal.pone.0081469 sha: doc_id: 1126 cord_uid: uqr00nzd file: cache/cord-001142-puj74k7y.json key: cord-001142-puj74k7y authors: Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; van der Werf, Sylvie title: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date: 2013-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0081550 sha: doc_id: 1142 cord_uid: puj74k7y file: cache/cord-001254-y2knt8g0.json key: cord-001254-y2knt8g0 authors: Parkhomenko, Taisiya A.; Doronin, Vasilii B.; Castellazzi, Massimiliano; Padroni, Marina; Pastore, Michela; Buneva, Valentina N.; Granieri, Enrico; Nevinsky, Georgy A. title: Comparison of DNA-Hydrolyzing Antibodies from the Cerebrospinal Fluid and Serum of Patients with Multiple Sclerosis date: 2014-04-15 journal: PLoS One DOI: 10.1371/journal.pone.0093001 sha: doc_id: 1254 cord_uid: y2knt8g0 file: cache/cord-001219-517gka4h.json key: cord-001219-517gka4h authors: Timpka, Toomas; Spreco, Armin; Gursky, Elin; Eriksson, Olle; Dahlström, Örjan; Strömgren, Magnus; Ekberg, Joakim; Pilemalm, Sofie; Karlsson, David; Hinkula, Jorma; Holm, Einar title: Intentions to Perform Non-Pharmaceutical Protective Behaviors during Influenza Outbreaks in Sweden: A Cross-Sectional Study following a Mass Vaccination Campaign date: 2014-03-07 journal: PLoS One DOI: 10.1371/journal.pone.0091060 sha: doc_id: 1219 cord_uid: 517gka4h file: cache/cord-001280-skavefji.json key: cord-001280-skavefji authors: Choi, Sang-Ho; Hong, Sang-Bum; Hong, Hyo-Lim; Kim, Sung-Han; Huh, Jin Won; Sung, Heungsup; Lee, Sang-Oh; Kim, Mi-Na; Jeong, Jin-Yong; Lim, Chae-Man; Kim, Yang Soo; Woo, Jun Hee; Koh, Younsuck title: Usefulness of Cellular Analysis of Bronchoalveolar Lavage Fluid for Predicting the Etiology of Pneumonia in Critically Ill Patients date: 2014-05-13 journal: PLoS One DOI: 10.1371/journal.pone.0097346 sha: doc_id: 1280 cord_uid: skavefji file: cache/cord-001359-c1uom5f7.json key: cord-001359-c1uom5f7 authors: Oslund, Karen L.; Zhou, Xu; Lee, Boram; Zhu, Lingxiang; Duong, Trang; Shih, Robert; Baumgarth, Nicole; Hung, Li-Yin; Wu, Reen; Chen, Yin title: Synergistic Up-Regulation of CXCL10 by Virus and IFN γ in Human Airway Epithelial Cells date: 2014-07-17 journal: PLoS One DOI: 10.1371/journal.pone.0100978 sha: doc_id: 1359 cord_uid: c1uom5f7 file: cache/cord-001249-awn9ayy6.json key: cord-001249-awn9ayy6 authors: Lasecka, Lidia; Baron, Michael D. title: The Nairovirus Nairobi Sheep Disease Virus/Ganjam Virus Induces the Translocation of Protein Disulphide Isomerase-Like Oxidoreductases from the Endoplasmic Reticulum to the Cell Surface and the Extracellular Space date: 2014-04-08 journal: PLoS One DOI: 10.1371/journal.pone.0094656 sha: doc_id: 1249 cord_uid: awn9ayy6 file: cache/cord-001275-a9o2dvke.json key: cord-001275-a9o2dvke authors: Chen, Xue; Liu, Hongyang; Zhang, Ting; Liu, Yanchun; Xie, Xixiu; Wang, Zhirong; Xu, Xuemei title: A Vaccine of L2 Epitope Repeats Fused with a Modified IgG1 Fc Induced Cross-Neutralizing Antibodies and Protective Immunity against Divergent Human Papillomavirus Types date: 2014-05-06 journal: PLoS One DOI: 10.1371/journal.pone.0095448 sha: doc_id: 1275 cord_uid: a9o2dvke file: cache/cord-001421-6t5puo6p.json key: cord-001421-6t5puo6p authors: Marfà, Santiago; Crespo, Gonzalo; Reichenbach, Vedrana; Forns, Xavier; Casals, Gregori; Morales-Ruiz, Manuel; Navasa, Miquel; Jiménez, Wladimiro title: Lack of a 5.9 kDa Peptide C-Terminal Fragment of Fibrinogen α Chain Precedes Fibrosis Progression in Patients with Liver Disease date: 2014-10-02 journal: PLoS One DOI: 10.1371/journal.pone.0109254 sha: doc_id: 1421 cord_uid: 6t5puo6p file: cache/cord-001432-d4zavkcn.json key: cord-001432-d4zavkcn authors: Nishida, Yoriko; Aida, Kaoru; Kihara, Makoto; Kobayashi, Tetsuro title: Antibody-Validated Proteins in Inflamed Islets of Fulminant Type 1 Diabetes Profiled by Laser-Capture Microdissection Followed by Mass Spectrometry date: 2014-10-16 journal: PLoS One DOI: 10.1371/journal.pone.0107664 sha: doc_id: 1432 cord_uid: d4zavkcn file: cache/cord-001435-ebl8yc92.json key: cord-001435-ebl8yc92 authors: Hoppe, Sebastian; Bier, Frank F.; von Nickisch-Rosenegk, Markus title: Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date: 2014-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0110703 sha: doc_id: 1435 cord_uid: ebl8yc92 file: cache/cord-001387-2g9dc5z4.json key: cord-001387-2g9dc5z4 authors: McIntyre, K. Marie; Setzkorn, Christian; Hepworth, Philip J.; Morand, Serge; Morse, Andrew P.; Baylis, Matthew title: A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe date: 2014-08-19 journal: PLoS One DOI: 10.1371/journal.pone.0103529 sha: doc_id: 1387 cord_uid: 2g9dc5z4 file: cache/cord-001537-i34vmfpp.json key: cord-001537-i34vmfpp authors: Lima, Francisco Esmaile de Sales; Cibulski, Samuel Paulo; dos Santos, Helton Fernandes; Teixeira, Thais Fumaco; Varela, Ana Paula Muterle; Roehe, Paulo Michel; Delwart, Eric; Franco, Ana Cláudia title: Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil date: 2015-02-17 journal: PLoS One DOI: 10.1371/journal.pone.0118070 sha: doc_id: 1537 cord_uid: i34vmfpp file: cache/cord-001420-b4zcvd04.json key: cord-001420-b4zcvd04 authors: Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; Frigard, Vianney; Poulain, Damien; van der Werf, Sylvie title: Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date: 2014-09-30 journal: PLoS One DOI: 10.1371/journal.pone.0109046 sha: doc_id: 1420 cord_uid: b4zcvd04 file: cache/cord-001455-n7quwr4s.json key: cord-001455-n7quwr4s authors: Rapin, Noreen; Johns, Kirk; Martin, Lauren; Warnecke, Lisa; Turner, James M.; Bollinger, Trent K.; Willis, Craig K. R.; Voyles, Jamie; Misra, Vikram title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date: 2014-11-12 journal: PLoS One DOI: 10.1371/journal.pone.0112285 sha: doc_id: 1455 cord_uid: n7quwr4s file: cache/cord-001599-pfdnmzx2.json key: cord-001599-pfdnmzx2 authors: Wee, Yin Shen; Weis, Janis J.; Gahring, Lorise C.; Rogers, Scott W.; Weis, John H. title: Age-Related Onset of Obesity Corresponds with Metabolic Dysregulation and Altered Microglia Morphology in Mice Deficient for Ifitm Proteins date: 2015-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0123218 sha: doc_id: 1599 cord_uid: pfdnmzx2 file: cache/cord-001263-hqxiyxfj.json key: cord-001263-hqxiyxfj authors: Kam, Yiu-Wing; Lee, Wendy W. L.; Simarmata, Diane; Le Grand, Roger; Tolou, Hugues; Merits, Andres; Roques, Pierre; Ng, Lisa F. P. title: Unique Epitopes Recognized by Antibodies Induced in Chikungunya Virus-Infected Non-Human Primates: Implications for the Study of Immunopathology and Vaccine Development date: 2014-04-22 journal: PLoS One DOI: 10.1371/journal.pone.0095647 sha: doc_id: 1263 cord_uid: hqxiyxfj file: cache/cord-001343-3euy4u9k.json key: cord-001343-3euy4u9k authors: Wang, Yadong; Li, Xiangrui; Yuan, Yiwen; Patel, Mahomed S. title: A Multi-Method Approach to Curriculum Development for In-Service Training in China’s Newly Established Health Emergency Response Offices date: 2014-06-27 journal: PLoS One DOI: 10.1371/journal.pone.0100892 sha: doc_id: 1343 cord_uid: 3euy4u9k file: cache/cord-001446-mpuovmeb.json key: cord-001446-mpuovmeb authors: Bratcher, Preston E.; Gaggar, Amit title: Factors Influencing the Measurement of Plasma/Serum Surfactant Protein D Levels by ELISA date: 2014-11-03 journal: PLoS One DOI: 10.1371/journal.pone.0111466 sha: doc_id: 1446 cord_uid: mpuovmeb file: cache/cord-001363-irysq6pf.json key: cord-001363-irysq6pf authors: Liu, Zhenjiang; Yuan, Zhengwei; Zhao, Qun title: SELDI-TOF-MS Proteomic Profiling of Serum, Urine, and Amniotic Fluid in Neural Tube Defects date: 2014-07-23 journal: PLoS One DOI: 10.1371/journal.pone.0103276 sha: doc_id: 1363 cord_uid: irysq6pf file: cache/cord-001571-drcfdv9z.json key: cord-001571-drcfdv9z authors: Alvarez, Julio; Sarradell, Javier; Morrison, Robert; Perez, Andres title: Impact of Porcine Epidemic Diarrhea on Performance of Growing Pigs date: 2015-03-13 journal: PLoS One DOI: 10.1371/journal.pone.0120532 sha: doc_id: 1571 cord_uid: drcfdv9z file: cache/cord-001447-oi7bkm4z.json key: cord-001447-oi7bkm4z authors: Dhanasekaran, Sakthivel; Biswas, Moanaro; Vignesh, Ambothi R.; Ramya, R.; Raj, Gopal Dhinakar; Tirumurugaan, Krishnaswamy G.; Raja, Angamuthu; Kataria, Ranjit S.; Parida, Satya; Subbiah, Elankumaran title: Toll-Like Receptor Responses to Peste des petits ruminants Virus in Goats and Water Buffalo date: 2014-11-04 journal: PLoS One DOI: 10.1371/journal.pone.0111609 sha: doc_id: 1447 cord_uid: oi7bkm4z file: cache/cord-001546-ndz3oarf.json key: cord-001546-ndz3oarf authors: Ayithan, Natarajan; Bradfute, Steven B.; Anthony, Scott M.; Stuthman, Kelly S.; Bavari, Sina; Bray, Mike; Ozato, Keiko title: Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date: 2015-02-26 journal: PLoS One DOI: 10.1371/journal.pone.0118345 sha: doc_id: 1546 cord_uid: ndz3oarf file: cache/cord-001605-8p06bpt1.json key: cord-001605-8p06bpt1 authors: Sapmak, Ariya; Boyce, Kylie J.; Andrianopoulos, Alex; Vanittanakom, Nongnuch title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date: 2015-04-13 journal: PLoS One DOI: 10.1371/journal.pone.0122728 sha: doc_id: 1605 cord_uid: 8p06bpt1 file: cache/cord-001734-bbeznd3r.json key: cord-001734-bbeznd3r authors: Gupta, Garvita; Lim, Liangzhong; Song, Jianxing title: NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date: 2015-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0134823 sha: doc_id: 1734 cord_uid: bbeznd3r file: cache/cord-001781-afg1nmib.json key: cord-001781-afg1nmib authors: Saksena, Sumeet; Fox, Jefferson; Epprecht, Michael; Tran, Chinh C.; Nong, Duong H.; Spencer, James H.; Nguyen, Lam; Finucane, Melissa L.; Tran, Vien D.; Wilcox, Bruce A. title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam date: 2015-09-23 journal: PLoS One DOI: 10.1371/journal.pone.0138138 sha: doc_id: 1781 cord_uid: afg1nmib file: cache/cord-001958-2gt3fwpy.json key: cord-001958-2gt3fwpy authors: Meseda, Clement A.; Atukorale, Vajini; Kuhn, Jordan; Schmeisser, Falko; Weir, Jerry P. title: Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date: 2016-02-19 journal: PLoS One DOI: 10.1371/journal.pone.0149364 sha: doc_id: 1958 cord_uid: 2gt3fwpy file: cache/cord-001620-yy5gq0ki.json key: cord-001620-yy5gq0ki authors: Woo, Hye-Min; Lee, Jin-Moo; Yim, Sanggyu; Jeong, Yong-Joo title: Isolation of Single-Stranded DNA Aptamers That Distinguish Influenza Virus Hemagglutinin Subtype H1 from H5 date: 2015-04-22 journal: PLoS One DOI: 10.1371/journal.pone.0125060 sha: doc_id: 1620 cord_uid: yy5gq0ki file: cache/cord-001748-7e8px4vx.json key: cord-001748-7e8px4vx authors: Nobach, Daniel; Bourg, Manon; Herzog, Sibylle; Lange-Herbst, Hildburg; Encarnação, Jorge A.; Eickmann, Markus; Herden, Christiane title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 journal: PLoS One DOI: 10.1371/journal.pone.0137018 sha: doc_id: 1748 cord_uid: 7e8px4vx file: cache/cord-001383-hww0watl.json key: cord-001383-hww0watl authors: Li, Wenchao; Jin, Hongyan; Sui, Xiukun; Zhao, Zhanzhong; Yang, Chenghuai; Wang, Wenquan; Li, Junping; Li, Gang title: Self-Assembly and Release of Peste des Petits Ruminants Virus-Like Particles in an Insect Cell-Baculovirus System and Their Immunogenicity in Mice and Goats date: 2014-08-12 journal: PLoS One DOI: 10.1371/journal.pone.0104791 sha: doc_id: 1383 cord_uid: hww0watl file: cache/cord-001601-tsuz3j40.json key: cord-001601-tsuz3j40 authors: Ngan, Luong Thi My; Jang, Myeong Jin; Kwon, Min Jung; Ahn, Young Joon title: Antiviral Activity and Possible Mechanism of Action of Constituents Identified in Paeonia lactiflora Root toward Human Rhinoviruses date: 2015-04-10 journal: PLoS One DOI: 10.1371/journal.pone.0121629 sha: doc_id: 1601 cord_uid: tsuz3j40 file: cache/cord-001603-vlv8x8l8.json key: cord-001603-vlv8x8l8 authors: Ul-Haq, Zaheer; Saeed, Maria; Halim, Sobia Ahsan; Khan, Waqasuddin title: 3D Structure Prediction of Human β1-Adrenergic Receptor via Threading-Based Homology Modeling for Implications in Structure-Based Drug Designing date: 2015-04-10 journal: PLoS One DOI: 10.1371/journal.pone.0122223 sha: doc_id: 1603 cord_uid: vlv8x8l8 file: cache/cord-001639-p9mbmfaq.json key: cord-001639-p9mbmfaq authors: Alfonso-Morales, Abdulahi; Rios, Liliam; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I.; Pérez, Lester J. title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent date: 2015-05-06 journal: PLoS One DOI: 10.1371/journal.pone.0125853 sha: doc_id: 1639 cord_uid: p9mbmfaq file: cache/cord-001716-lbtdex4p.json key: cord-001716-lbtdex4p authors: Gilca, Rodica; Skowronski, Danuta M.; Douville-Fradet, Monique; Amini, Rachid; Boulianne, Nicole; Rouleau, Isabelle; Martineau, Christine; Charest, Hugues; De Serres, Gaston title: Mid-Season Estimates of Influenza Vaccine Effectiveness against Influenza A(H3N2) Hospitalization in the Elderly in Quebec, Canada, January 2015 date: 2015-07-22 journal: PLoS One DOI: 10.1371/journal.pone.0132195 sha: doc_id: 1716 cord_uid: lbtdex4p file: cache/cord-001909-yy9xp5ms.json key: cord-001909-yy9xp5ms authors: Buß, O.; Jager, S.; Dold, S. -M.; Zimmermann, S.; Hamacher, K.; Schmitz, K.; Rudat, J. title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters date: 2016-01-05 journal: PLoS One DOI: 10.1371/journal.pone.0146104 sha: doc_id: 1909 cord_uid: yy9xp5ms file: cache/cord-001964-iy6qzq58.json key: cord-001964-iy6qzq58 authors: Muñoz-González, Sara; Pérez-Simó, Marta; Colom-Cadena, Andreu; Cabezón, Oscar; Bohórquez, José Alejandro; Rosell, Rosa; Pérez, Lester Josué; Marco, Ignasi; Lavín, Santiago; Domingo, Mariano; Ganges, Llilianne title: Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date: 2016-02-26 journal: PLoS One DOI: 10.1371/journal.pone.0149469 sha: doc_id: 1964 cord_uid: iy6qzq58 file: cache/cord-002044-9xgt3tf4.json key: cord-002044-9xgt3tf4 authors: Hendiger, Jacek; Chludzińska, Marta; Ziętek, Piotr title: Influence of the Pressure Difference and Door Swing on Heavy Contaminants Migration between Rooms date: 2016-05-12 journal: PLoS One DOI: 10.1371/journal.pone.0155159 sha: doc_id: 2044 cord_uid: 9xgt3tf4 file: cache/cord-002141-9mxi4dzi.json key: cord-002141-9mxi4dzi authors: Memczak, Henry; Lauster, Daniel; Kar, Parimal; Di Lella, Santiago; Volkmer, Rudolf; Knecht, Volker; Herrmann, Andreas; Ehrentreich-Förster, Eva; Bier, Frank F.; Stöcklein, Walter F. M. title: Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding date: 2016-07-14 journal: PLoS One DOI: 10.1371/journal.pone.0159074 sha: doc_id: 2141 cord_uid: 9mxi4dzi file: cache/cord-001460-eo2bxxbq.json key: cord-001460-eo2bxxbq authors: Padhi, Siladitya; Burri, Raghunadha Reddy; Jameel, Shahid; Priyakumar, U. Deva title: Atomistic Detailed Mechanism and Weak Cation-Conducting Activity of HIV-1 Vpu Revealed by Free Energy Calculations date: 2014-11-13 journal: PLoS One DOI: 10.1371/journal.pone.0112983 sha: doc_id: 1460 cord_uid: eo2bxxbq file: cache/cord-002043-z1b7pj3s.json key: cord-002043-z1b7pj3s authors: Wang, Xue-Yang; Yu, Hai-Zhong; Geng, Lei; Xu, Jia-Ping; Yu, Dong; Zhang, Shang-Zhi; Ma, Yan; Fei, Dong-Qiong title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains date: 2016-05-11 journal: PLoS One DOI: 10.1371/journal.pone.0155341 sha: doc_id: 2043 cord_uid: z1b7pj3s file: cache/cord-002094-7tewne3a.json key: cord-002094-7tewne3a authors: Tago, Damian; Hammitt, James K.; Thomas, Alban; Raboisson, Didier title: The Impact of Farmers’ Strategic Behavior on the Spread of Animal Infectious Diseases date: 2016-06-14 journal: PLoS One DOI: 10.1371/journal.pone.0157450 sha: doc_id: 2094 cord_uid: 7tewne3a file: cache/cord-001707-piyo00yg.json key: cord-001707-piyo00yg authors: Murray, Jillian; Cohen, Adam; Walaza, Sibongile; Groome, Michelle; Madhi, Shabir; Variava, Ebrahim; Kahn, Kathleen; Dawood, Halima; Tempia, Stefano; Tshangela, Akhona; Venter, Marietje; Feikin, Daniel; Cohen, Cheryl title: Determining the Provincial and National Burden of Influenza-Associated Severe Acute Respiratory Illness in South Africa Using a Rapid Assessment Methodology date: 2015-07-08 journal: PLoS One DOI: 10.1371/journal.pone.0132078 sha: doc_id: 1707 cord_uid: piyo00yg file: cache/cord-001982-arczqdza.json key: cord-001982-arczqdza authors: Khajah, Maitham A.; Fateel, Maryam M.; Ananthalakshmi, Kethireddy V.; Luqmani, Yunus A. title: Anti-Inflammatory Action of Angiotensin 1-7 in Experimental Colitis date: 2016-03-10 journal: PLoS One DOI: 10.1371/journal.pone.0150861 sha: doc_id: 1982 cord_uid: arczqdza file: cache/cord-001761-yvd1n42f.json key: cord-001761-yvd1n42f authors: Yoshimura, Takeo; Suzuki, Takamasa; Mineki, Shigeru; Ohuchi, Shokichi title: Controlled Microwave Heating Accelerates Rolling Circle Amplification date: 2015-09-08 journal: PLoS One DOI: 10.1371/journal.pone.0136532 sha: doc_id: 1761 cord_uid: yvd1n42f file: cache/cord-002023-7zd5zhbz.json key: cord-002023-7zd5zhbz authors: Hiremath, Jagadish; Kang, Kyung-il; Xia, Ming; Elaish, Mohamed; Binjawadagi, Basavaraj; Ouyang, Kang; Dhakal, Santosh; Arcos, Jesus; Torrelles, Jordi B.; Jiang, X.; Lee, Chang Won; Renukaradhya, Gourapura J. title: Entrapment of H1N1 Influenza Virus Derived Conserved Peptides in PLGA Nanoparticles Enhances T Cell Response and Vaccine Efficacy in Pigs date: 2016-04-19 journal: PLoS One DOI: 10.1371/journal.pone.0151922 sha: doc_id: 2023 cord_uid: 7zd5zhbz file: cache/cord-002834-2htnywef.json key: cord-002834-2htnywef authors: Tsuchiaka, Shinobu; Naoi, Yuki; Imai, Ryo; Masuda, Tsuneyuki; Ito, Mika; Akagami, Masataka; Ouchi, Yoshinao; Ishii, Kazuo; Sakaguchi, Shoichi; Omatsu, Tsutomu; Katayama, Yukie; Oba, Mami; Shirai, Junsuke; Satani, Yuki; Takashima, Yasuhiro; Taniguchi, Yuji; Takasu, Masaki; Madarame, Hiroo; Sunaga, Fujiko; Aoki, Hiroshi; Makino, Shinji; Mizutani, Tetsuya; Nagai, Makoto title: Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population date: 2018-01-11 journal: PLoS One DOI: 10.1371/journal.pone.0190819 sha: doc_id: 2834 cord_uid: 2htnywef file: cache/cord-001898-ntqyjqqk.json key: cord-001898-ntqyjqqk authors: Huang, Chih-Wei; Lin, Hui-Chen; Chou, Chi-Yuan; Kao, Wei-Chuo; Chou, Wei-Yuan; Lee, Hwei-Jen title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly date: 2016-01-05 journal: PLoS One DOI: 10.1371/journal.pone.0145957 sha: doc_id: 1898 cord_uid: ntqyjqqk file: cache/cord-001983-zo9yngfc.json key: cord-001983-zo9yngfc authors: Napp, S.; Allepuz, A.; Purse, B. V.; Casal, J.; García-Bocanegra, I.; Burgin, L. E.; Searle, K. R. title: Understanding Spatio-Temporal Variability in the Reproduction Ratio of the Bluetongue (BTV-1) Epidemic in Southern Spain (Andalusia) in 2007 Using Epidemic Trees date: 2016-03-10 journal: PLoS One DOI: 10.1371/journal.pone.0151151 sha: doc_id: 1983 cord_uid: zo9yngfc file: cache/cord-002222-rgqwm3vb.json key: cord-002222-rgqwm3vb authors: Olarte-Castillo, Ximena A.; Hofer, Heribert; Goller, Katja V.; Martella, Vito; Moehlman, Patricia D.; East, Marion L. title: Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date: 2016-09-23 journal: PLoS One DOI: 10.1371/journal.pone.0163548 sha: doc_id: 2222 cord_uid: rgqwm3vb file: cache/cord-001865-ji83zmy7.json key: cord-001865-ji83zmy7 authors: Kuroda, Kengo; Kiyono, Tohru; Isogai, Emiko; Masuda, Mizuki; Narita, Moe; Okuno, Katsuya; Koyanagi, Yukako; Fukuda, Tomokazu title: Immortalization of Fetal Bovine Colon Epithelial Cells by Expression of Human Cyclin D1, Mutant Cyclin Dependent Kinase 4, and Telomerase Reverse Transcriptase: An In Vitro Model for Bacterial Infection date: 2015-12-01 journal: PLoS One DOI: 10.1371/journal.pone.0143473 sha: doc_id: 1865 cord_uid: ji83zmy7 file: cache/cord-002473-2kpxhzbe.json key: cord-002473-2kpxhzbe authors: Das, Jayanta Kumar; Pal Choudhury, Pabitra title: Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach date: 2017-03-31 journal: PLoS One DOI: 10.1371/journal.pone.0175031 sha: doc_id: 2473 cord_uid: 2kpxhzbe file: cache/cord-002602-2qvyhjlp.json key: cord-002602-2qvyhjlp authors: Roy, Amrita; Lim, Liangzhong; Srivastava, Shagun; Lu, Yimei; Song, Jianxing title: Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants date: 2017-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0180632 sha: doc_id: 2602 cord_uid: 2qvyhjlp file: cache/cord-002100-dt5zvebj.json key: cord-002100-dt5zvebj authors: He, Yonghua; Schmidt, Monica A.; Erwin, Christopher; Guo, Jun; Sun, Raphael; Pendarvis, Ken; Warner, Brad W.; Herman, Eliot M. title: Transgenic Soybean Production of Bioactive Human Epidermal Growth Factor (EGF) date: 2016-06-17 journal: PLoS One DOI: 10.1371/journal.pone.0157034 sha: doc_id: 2100 cord_uid: dt5zvebj file: cache/cord-002305-qq73gr9y.json key: cord-002305-qq73gr9y authors: Anson, Marie; Amado, Inês; Mailhé, Marie-Pierre; Donnadieu, Emmanuel; Garcia, Sylvie; Huetz, François; Freitas, Antonio A. title: Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool date: 2016-11-23 journal: PLoS One DOI: 10.1371/journal.pone.0167003 sha: doc_id: 2305 cord_uid: qq73gr9y file: cache/cord-001843-ceatyj3o.json key: cord-001843-ceatyj3o authors: Huang, Yong; Xing, Na; Wang, Zengguo; Zhang, Xiujuan; Zhao, Xiaomin; Du, Qian; Chang, Lingling; Tong, Dewen title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 journal: PLoS One DOI: 10.1371/journal.pone.0141545 sha: doc_id: 1843 cord_uid: ceatyj3o file: cache/cord-002601-d8908t93.json key: cord-002601-d8908t93 authors: Arellano-Llamas, Rocío; Alfaro-Ruiz, Luis; Arriaga Canon, Cristian; Imaz Rosshandler, Ivan; Cruz-Lagunas, Alfredo; Zúñiga, Joaquín; Rebollar Vega, Rosa; Wong, Christopher W.; Maurer-Stroh, Sebastian; Romero Córdoba, Sandra; Liu, Edison T.; Hidalgo-Miranda, Alfredo; Vázquez-Pérez, Joel A. title: Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date: 2017-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0180419 sha: doc_id: 2601 cord_uid: d8908t93 file: cache/cord-002624-59nznqsd.json key: cord-002624-59nznqsd authors: Ti, Jinfeng; Li, Zhijie; Li, Xiuli; Lu, Yunjian; Diao, Youxiang; Li, Fang title: Identification of one B-cell epitope from NS1 protein of duck Tembusu virus with monoclonal antibodies date: 2017-07-26 journal: PLoS One DOI: 10.1371/journal.pone.0181177 sha: doc_id: 2624 cord_uid: 59nznqsd file: cache/cord-002811-5hrydciz.json key: cord-002811-5hrydciz authors: Hercik, Christine; Cosmas, Leonard; Mogeni, Ondari D.; Wamola, Newton; Kohi, Wanze; Omballa, Victor; Ochieng, Melvin; Lidechi, Shirley; Bonventure, Juma; Ochieng, Caroline; Onyango, Clayton; Fields, Barry S.; Mfinanga, Sayoki; Montgomery, Joel M. title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania date: 2017-12-29 journal: PLoS One DOI: 10.1371/journal.pone.0189712 sha: doc_id: 2811 cord_uid: 5hrydciz file: cache/cord-001910-6zfz2ns5.json key: cord-001910-6zfz2ns5 authors: Zhang, Xianming; Wu, Weiliang; Zhu, Yongcheng; Jiang, Ying; Du, Juan; Chen, Rongchang title: Abdominal Muscle Activity during Mechanical Ventilation Increases Lung Injury in Severe Acute Respiratory Distress Syndrome date: 2016-01-08 journal: PLoS One DOI: 10.1371/journal.pone.0145694 sha: doc_id: 1910 cord_uid: 6zfz2ns5 file: cache/cord-002705-ntokyoai.json key: cord-002705-ntokyoai authors: Nasir, Nazrila Hairin; Mohamad, Mohazmi; Lum, Lucy Chai See; Ng, Chirk Jenn title: Effectiveness of a fluid chart in outpatient management of suspected dengue fever: A pilot study date: 2017-10-04 journal: PLoS One DOI: 10.1371/journal.pone.0183544 sha: doc_id: 2705 cord_uid: ntokyoai file: cache/cord-002901-u4ybz8ds.json key: cord-002901-u4ybz8ds authors: Yu, Chanki; Yang, Sejung; Kim, Wonoh; Jung, Jinwoong; Chung, Kee-Yang; Lee, Sang Wook; Oh, Byungho title: Acral melanoma detection using a convolutional neural network for dermoscopy images date: 2018-03-07 journal: PLoS One DOI: 10.1371/journal.pone.0193321 sha: doc_id: 2901 cord_uid: u4ybz8ds file: cache/cord-003024-17f1evh3.json key: cord-003024-17f1evh3 authors: Nunes, Márcio Roberto Teixeira; de Souza, William Marciel; Acrani, Gustavo Olszanski; Cardoso, Jedson Ferreira; da Silva, Sandro Patroca; Badra, Soraya Jabur; Figueiredo, Luiz Tadeu Moraes; Vasconcelos, Pedro Fernando da Costa title: Revalidation and genetic characterization of new members of Group C (Orthobunyavirus genus, Peribunyaviridae family) isolated in the Americas date: 2018-05-24 journal: PLoS One DOI: 10.1371/journal.pone.0197294 sha: doc_id: 3024 cord_uid: 17f1evh3 file: cache/cord-002621-sq5iod1w.json key: cord-002621-sq5iod1w authors: Attia, Mohamed I.; Eldehna, Wagdy M.; Afifi, Samar A.; Keeton, Adam B.; Piazza, Gary A.; Abdel-Aziz, Hatem A. title: New hydrazonoindolin-2-ones: Synthesis, exploration of the possible anti-proliferative mechanism of action and encapsulation into PLGA microspheres date: 2017-07-25 journal: PLoS One DOI: 10.1371/journal.pone.0181241 sha: doc_id: 2621 cord_uid: sq5iod1w file: cache/cord-002398-0a3okta0.json key: cord-002398-0a3okta0 authors: Myllykoski, Matti; Kursula, Petri title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase date: 2017-01-31 journal: PLoS One DOI: 10.1371/journal.pone.0170355 sha: doc_id: 2398 cord_uid: 0a3okta0 file: cache/cord-003244-abs3tc3r.json key: cord-003244-abs3tc3r authors: Chong, Ka Chun; Hu, Pei; Lau, Steven; Jia, Katherine Min; Liang, Wenjia; Wang, Maggie Haitian; Zee, Benny Chung Ying; Sun, Riyang; Zheng, Huizhen title: Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China date: 2018-10-08 journal: PLoS One DOI: 10.1371/journal.pone.0205339 sha: doc_id: 3244 cord_uid: abs3tc3r file: cache/cord-003507-22ylifqo.json key: cord-003507-22ylifqo authors: Kelly, J. Daniel; Worden, Lee; Wannier, S. Rae; Hoff, Nicole A.; Mukadi, Patrick; Sinai, Cyrus; Ackley, Sarah; Chen, Xianyun; Gao, Daozhou; Selo, Bernice; Mossoko, Mathais; Okitolonda-Wemakoy, Emile; Richardson, Eugene T.; Rutherford, George W.; Lietman, Thomas M.; Muyembe-Tamfum, Jean Jacques; Rimoin, Anne W.; Porco, Travis C. title: Projections of Ebola outbreak size and duration with and without vaccine use in Équateur, Democratic Republic of Congo, as of May 27, 2018 date: 2019-03-07 journal: PLoS One DOI: 10.1371/journal.pone.0213190 sha: doc_id: 3507 cord_uid: 22ylifqo file: cache/cord-002848-w6q1x1zs.json key: cord-002848-w6q1x1zs authors: Zhang, Ailian; Yang, Xiumei; Li, Quanxiao; Yang, Yu; Zhao, Gan; Wang, Bin; Wu, Daocheng title: Immunostimulatory activity of water-extractable polysaccharides from Cistanche deserticola as a plant adjuvant in vitro and in vivo date: 2018-01-23 journal: PLoS One DOI: 10.1371/journal.pone.0191356 sha: doc_id: 2848 cord_uid: w6q1x1zs file: cache/cord-002890-g7aje88u.json key: cord-002890-g7aje88u authors: Wood, Paul L.; Steinman, Margaret; Erol, Erdal; Carter, Craig; Christmann, Undine; Verma, Ashutosh title: Lipidomic analysis of immune activation in equine leptospirosis and Leptospira-vaccinated horses date: 2018-02-23 journal: PLoS One DOI: 10.1371/journal.pone.0193424 sha: doc_id: 2890 cord_uid: g7aje88u file: cache/cord-002180-gsdk5x3e.json key: cord-002180-gsdk5x3e authors: Davies, Colin; Ward, Vernon K. title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date: 2016-08-24 journal: PLoS One DOI: 10.1371/journal.pone.0161582 sha: doc_id: 2180 cord_uid: gsdk5x3e file: cache/cord-002913-k5b6abyk.json key: cord-002913-k5b6abyk authors: Kim, Ha Kyun; Kim, Hyun Jung; Kim, Jae Hyung; Kim, Tae Hoon; Lee, Sang Hag title: Asymmetric expression level of clock genes in left vs. right nasal mucosa in humans with and without allergies and in rats: Circadian characteristics and possible contribution to nasal cycle date: 2018-03-13 journal: PLoS One DOI: 10.1371/journal.pone.0194018 sha: doc_id: 2913 cord_uid: k5b6abyk file: cache/cord-002935-jq1xumrh.json key: cord-002935-jq1xumrh authors: Postnikova, Elena; Cong, Yu; DeWald, Lisa Evans; Dyall, Julie; Yu, Shuiqing; Hart, Brit J.; Zhou, Huanying; Gross, Robin; Logue, James; Cai, Yingyun; Deiuliis, Nicole; Michelotti, Julia; Honko, Anna N.; Bennett, Richard S.; Holbrook, Michael R.; Olinger, Gene G.; Hensley, Lisa E.; Jahrling, Peter B. title: Testing therapeutics in cell-based assays: Factors that influence the apparent potency of drugs date: 2018-03-22 journal: PLoS One DOI: 10.1371/journal.pone.0194880 sha: doc_id: 2935 cord_uid: jq1xumrh file: cache/cord-002560-pue5q5wp.json key: cord-002560-pue5q5wp authors: Moreno, Paloma S.; Wagner, Josef; Mansfield, Caroline S.; Stevens, Matthew; Gilkerson, James R.; Kirkwood, Carl D. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 journal: PLoS One DOI: 10.1371/journal.pone.0178433 sha: doc_id: 2560 cord_uid: pue5q5wp file: cache/cord-002957-gw2cow0d.json key: cord-002957-gw2cow0d authors: Gray, Darren W.; Welsh, Michael D.; Mansoor, Fawad; Doherty, Simon; Chevallier, Olivier P.; Elliott, Christopher T.; Mooney, Mark H. title: DIVA metabolomics: Differentiating vaccination status following viral challenge using metabolomic profiles date: 2018-04-05 journal: PLoS One DOI: 10.1371/journal.pone.0194488 sha: doc_id: 2957 cord_uid: gw2cow0d file: cache/cord-003551-jzfl4xuk.json key: cord-003551-jzfl4xuk authors: Ciejka, Justyna; Botwina, Paweł; Nowakowska, Maria; Szczubiałka, Krzysztof; Pyrc, Krzysztof title: Synthetic sulfonated derivatives of poly(allylamine hydrochloride) as inhibitors of human metapneumovirus date: 2019-03-28 journal: PLoS One DOI: 10.1371/journal.pone.0214646 sha: doc_id: 3551 cord_uid: jzfl4xuk file: cache/cord-002426-5e1xn7kj.json key: cord-002426-5e1xn7kj authors: Falcón-Lezama, Jorge Abelardo; Santos-Luna, René; Román-Pérez, Susana; Martínez-Vega, Ruth Aralí; Herrera-Valdez, Marco Arieli; Kuri-Morales, Ángel Fernando; Adams, Ben; Kuri-Morales, Pablo Antonio; López-Cervantes, Malaquías; Ramos-Castañeda, José title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico date: 2017-02-22 journal: PLoS One DOI: 10.1371/journal.pone.0172313 sha: doc_id: 2426 cord_uid: 5e1xn7kj file: cache/cord-004017-gcmpatlb.json key: cord-004017-gcmpatlb authors: Errecaborde, Kaylee Myhre; Macy, Katelyn Wuebbolt; Pekol, Amy; Perez, Sol; O’Brien, Mary Katherine; Allen, Ian; Contadini, Francesca; Lee, Julia Yeri; Mumford, Elizabeth; Bender, Jeff B.; Pelican, Katharine title: Factors that enable effective One Health collaborations - A scoping review of the literature date: 2019-12-04 journal: PLoS One DOI: 10.1371/journal.pone.0224660 sha: doc_id: 4017 cord_uid: gcmpatlb file: cache/cord-003602-wtestt8i.json key: cord-003602-wtestt8i authors: Jung, Eunok; de los Reyes V, Aurelio A.; Pumares, Kurt Jan A.; Kim, Yangjin title: Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy date: 2019-04-22 journal: PLoS One DOI: 10.1371/journal.pone.0215547 sha: doc_id: 3602 cord_uid: wtestt8i file: cache/cord-003377-9vkhptas.json key: cord-003377-9vkhptas authors: Wu, Tong; Perrings, Charles title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia date: 2018-12-19 journal: PLoS One DOI: 10.1371/journal.pone.0208197 sha: doc_id: 3377 cord_uid: 9vkhptas file: cache/cord-003270-vu9b5a14.json key: cord-003270-vu9b5a14 authors: Panahi, Heidar Ali; Bolhassani, Azam; Javadi, Gholamreza; Noormohammadi, Zahra title: A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins date: 2018-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0205933 sha: doc_id: 3270 cord_uid: vu9b5a14 file: cache/cord-003548-zuwt7gk5.json key: cord-003548-zuwt7gk5 authors: Cai, Haiming; Deng, Jinbo; Li, Jiaoqing; Ma, Miaopeng; Huang, Chaoyuan; Zhao, Peijing; Ming, Feiping; Liang, Qianyi; Jia, Junhao; Zhang, Shuxia; Zeng, Min; Zhang, Linghua title: Modulating the 3’ end-DNA and the fermentation process for enhanced production and biological activity of porcine interferon-gamma date: 2019-03-26 journal: PLoS One DOI: 10.1371/journal.pone.0214319 sha: doc_id: 3548 cord_uid: zuwt7gk5 file: cache/cord-003841-7uaj9hmx.json key: cord-003841-7uaj9hmx authors: Desmonts de Lamache, D.; Moges, R.; Siddiq, A.; Allain, T.; Feener, T. D.; Muench, G. P.; McKenna, N.; Yates, R. M.; Buret, A. G. title: Immuno-modulating properties of Tulathromycin in porcine monocyte-derived macrophages infected with porcine reproductive and respiratory syndrome virus date: 2019-08-23 journal: PLoS One DOI: 10.1371/journal.pone.0221560 sha: doc_id: 3841 cord_uid: 7uaj9hmx file: cache/cord-003125-iptisi1m.json key: cord-003125-iptisi1m authors: Machablishvili, Ann; Chakhunashvili, Giorgi; Zakhashvili, Khatuna; Karseladze, Irakli; Tarkhan-Mouravi, Olgha; Gavashelidze, Mari; Jashiashvili, Tamar; Sabadze, Lela; Imnadze, Paata; Daniels, Rodney S.; Ermetal, Burcu; McCauley, John W. title: Overview of three influenza seasons in Georgia, 2014–2017 date: 2018-07-27 journal: PLoS One DOI: 10.1371/journal.pone.0201207 sha: doc_id: 3125 cord_uid: iptisi1m file: cache/cord-004091-gex0zvoa.json key: cord-004091-gex0zvoa authors: Abdulkareem, Shaheen A.; Augustijn, Ellen-Wien; Filatova, Tatiana; Musial, Katarzyna; Mustafa, Yaseen T. title: Risk perception and behavioral change during epidemics: Comparing models of individual and collective learning date: 2020-01-06 journal: PLoS One DOI: 10.1371/journal.pone.0226483 sha: doc_id: 4091 cord_uid: gex0zvoa file: cache/cord-003503-t6cnjwpd.json key: cord-003503-t6cnjwpd authors: Sung, Ming-Hua; Lin, Chao-Nan; Chiou, Ming-Tang; Cheng, I-Ju; Thanh, Quang-Hien; Chao, Day-Yu; Lan, Yu-Ching title: Phylogeographic investigation of 2014 porcine epidemic diarrhea virus (PEDV) transmission in Taiwan date: 2019-03-06 journal: PLoS One DOI: 10.1371/journal.pone.0213153 sha: doc_id: 3503 cord_uid: t6cnjwpd file: cache/cord-003712-mafz21no.json key: cord-003712-mafz21no authors: Perez Vidakovics, Maria Laura A.; Ure, Agustín E.; Arrías, Paula N.; Romanowski, Víctor; Gómez, Ricardo M. title: Junín virus induces autophagy in human A549 cells date: 2019-06-19 journal: PLoS One DOI: 10.1371/journal.pone.0218730 sha: doc_id: 3712 cord_uid: mafz21no file: cache/cord-010368-plpghewn.json key: cord-010368-plpghewn authors: Kenmoe, Sebastien; Kengne-Nde, Cyprien; Modiyinji, Abdou Fatawou; Bigna, Jean Joel; Njouom, Richard title: Association of early viral lower respiratory infections and subsequent development of atopy, a systematic review and meta-analysis of cohort studies date: 2020-04-24 journal: PLoS One DOI: 10.1371/journal.pone.0231816 sha: doc_id: 10368 cord_uid: plpghewn file: cache/cord-002889-fie121ns.json key: cord-002889-fie121ns authors: White, Michael; Freistaedter, Andrew; Jones, Gwendolyn J. B.; Zervos, Emmanuel; Roper, Rachel L. title: Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date: 2018-02-23 journal: PLoS One DOI: 10.1371/journal.pone.0193131 sha: doc_id: 2889 cord_uid: fie121ns file: cache/cord-003062-qm8kalyt.json key: cord-003062-qm8kalyt authors: Chowdhury, Fazle Rabbi; Ibrahim, Quazi Shihab Uddin; Bari, Md. Shafiqul; Alam, M. M. Jahangir; Dunachie, Susanna J.; Rodriguez-Morales, Alfonso J.; Patwary, Md. Ismail title: The association between temperature, rainfall and humidity with common climate-sensitive infectious diseases in Bangladesh date: 2018-06-21 journal: PLoS One DOI: 10.1371/journal.pone.0199579 sha: doc_id: 3062 cord_uid: qm8kalyt file: cache/cord-012387-1ogcxd7b.json key: cord-012387-1ogcxd7b authors: Kaufman, Aaron R.; Hersh, Eitan D. title: The political consequences of opioid overdoses date: 2020-08-04 journal: PLoS One DOI: 10.1371/journal.pone.0236815 sha: doc_id: 12387 cord_uid: 1ogcxd7b file: cache/cord-003484-ylpa702c.json key: cord-003484-ylpa702c authors: Blázquez, Elena; Rodríguez, Carmen; Ródenas, Jesús; Navarro, Núria; Riquelme, Cristina; Rosell, Rosa; Campbell, Joy; Crenshaw, Joe; Segalés, Joaquim; Pujols, Joan; Polo, Javier title: Evaluation of the effectiveness of the SurePure Turbulator ultraviolet-C irradiation equipment on inactivation of different enveloped and non-enveloped viruses inoculated in commercially collected liquid animal plasma date: 2019-02-21 journal: PLoS One DOI: 10.1371/journal.pone.0212332 sha: doc_id: 3484 cord_uid: ylpa702c file: cache/cord-004068-d66lwylf.json key: cord-004068-d66lwylf authors: Shimoda, Tomoko; Okubo, Torahiko; Enoeda, Yoshiki; Yano, Rika; Nakamura, Shinji; Thapa, Jeewan; Yamaguchi, Hiroyuki title: Effect of thermal control of dry fomites on regulating the survival of human pathogenic bacteria responsible for nosocomial infections date: 2019-12-27 journal: PLoS One DOI: 10.1371/journal.pone.0226952 sha: doc_id: 4068 cord_uid: d66lwylf file: cache/cord-012889-dtil5xeo.json key: cord-012889-dtil5xeo authors: Holzer, Joshua title: The effect of copartisan justice ministers on human rights in presidential democracies date: 2020-09-02 journal: PLoS One DOI: 10.1371/journal.pone.0234938 sha: doc_id: 12889 cord_uid: dtil5xeo file: cache/cord-010369-x9z8dg6a.json key: cord-010369-x9z8dg6a authors: Saito, Kyoko; Fukasawa, Masayoshi; Shirasago, Yoshitaka; Suzuki, Ryosuke; Osada, Naoki; Yamaji, Toshiyuki; Wakita, Takaji; Konishi, Eiji; Hanada, Kentaro title: Comparative characterization of flavivirus production in two cell lines: Human hepatoma-derived Huh7.5.1-8 and African green monkey kidney-derived Vero date: 2020-04-24 journal: PLoS One DOI: 10.1371/journal.pone.0232274 sha: doc_id: 10369 cord_uid: x9z8dg6a file: cache/cord-002973-bkr4ndl2.json key: cord-002973-bkr4ndl2 authors: Seifi, Morteza; Walter, Michael A. title: Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms date: 2018-04-17 journal: PLoS One DOI: 10.1371/journal.pone.0195971 sha: doc_id: 2973 cord_uid: bkr4ndl2 file: cache/cord-002939-6a3ga6v9.json key: cord-002939-6a3ga6v9 authors: Ribeiro, Ana Freitas; Pellini, Alessandra Cristina Guedes; Kitagawa, Beatriz Yuko; Marques, Daniel; Madalosso, Geraldine; Fred, Joao; Albernaz, Ricardo Kerti Mangabeira; Carvalhanas, Telma Regina Marques Pinto; Zanetta, Dirce Maria Trevisan title: Severe influenza A(H1N1)pdm09 in pregnant women and neonatal outcomes, State of Sao Paulo, Brazil, 2009 date: 2018-03-26 journal: PLoS One DOI: 10.1371/journal.pone.0194392 sha: doc_id: 2939 cord_uid: 6a3ga6v9 file: cache/cord-012461-v8d91fdo.json key: cord-012461-v8d91fdo authors: Marnissi, Boutheina; Kamali-Moghaddam, Masood; Ghram, Abdeljelil; Hmila, Issam title: Generation of ssDNA aptamers as diagnostic tool for Newcastle avian virus date: 2020-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0237253 sha: doc_id: 12461 cord_uid: v8d91fdo file: cache/cord-003404-eqgc8v7y.json key: cord-003404-eqgc8v7y authors: May, Win Lai; Kyaw, Myat Phone; Blacksell, Stuart D.; Pukrittayakamee, Sasithon; Chotivanich, Kesinee; Hanboonkunupakarn, Borimas; Thein, Khin Nyo; Lim, Chae Seung; Thaipadungpanit, Janjira; Althaus, Thomas; Jittamala, Podjanee title: Impact of glucose-6-phosphate dehydrogenase deficiency on dengue infection in Myanmar children date: 2019-01-02 journal: PLoS One DOI: 10.1371/journal.pone.0209204 sha: doc_id: 3404 cord_uid: eqgc8v7y file: cache/cord-011857-brbqgbpz.json key: cord-011857-brbqgbpz authors: Beasley, Steven A.; Kellum, Chloe E.; Orlomoski, Rachel J.; Idrizi, Feston; Spratt, Donald E. title: An Angelman syndrome substitution in the HECT E3 ubiquitin ligase C-terminal Lobe of E6AP affects protein stability and activity date: 2020-07-08 journal: PLoS One DOI: 10.1371/journal.pone.0235925 sha: doc_id: 11857 cord_uid: brbqgbpz file: cache/cord-002953-4rqoenhr.json key: cord-002953-4rqoenhr authors: Arruda, Andréia Gonçalves; Vilalta, Carles; Puig, Pere; Perez, Andres; Alba, Anna title: Time-series analysis for porcine reproductive and respiratory syndrome in the United States date: 2018-04-03 journal: PLoS One DOI: 10.1371/journal.pone.0195282 sha: doc_id: 2953 cord_uid: 4rqoenhr file: cache/cord-012891-heqsfzkm.json key: cord-012891-heqsfzkm authors: Blanco Vázquez, Cristina; Alonso-Hearn, Marta; Juste, Ramón A.; Canive, María; Iglesias, Tania; Iglesias, Natalia; Amado, Javier; Vicente, Fernando; Balseiro, Ana; Casais, Rosa title: Detection of latent forms of Mycobacterium avium subsp. paratuberculosis infection using host biomarker-based ELISAs greatly improves paratuberculosis diagnostic sensitivity date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0236336 sha: doc_id: 12891 cord_uid: heqsfzkm file: cache/cord-013333-7jx4t0ol.json key: cord-013333-7jx4t0ol authors: Palloni, Alberto; McEniry, Mary; Huangfu, Yiyue; Beltran-Sanchez, Hiram title: Impacts of the 1918 flu on survivors' nutritional status: A double quasi-natural experiment date: 2020-10-20 journal: PLoS One DOI: 10.1371/journal.pone.0232805 sha: doc_id: 13333 cord_uid: 7jx4t0ol file: cache/cord-048471-7jszm1nd.json key: cord-048471-7jszm1nd authors: Salim, Omar; Clarke, Ian N.; Lambden, Paul R. title: Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date: 2008-05-14 journal: PLoS One DOI: 10.1371/journal.pone.0002169 sha: doc_id: 48471 cord_uid: 7jszm1nd file: cache/cord-011496-r8e19t0c.json key: cord-011496-r8e19t0c authors: de Rooij, Doret; Rebel, Rebekka; Raab, Jörg; Hadjichristodoulou, Christos; Belfroid, Evelien; Timen, Aura title: Development of a competency profile for professionals involved in infectious disease preparedness and response in the air transport public health sector date: 2020-05-21 journal: PLoS One DOI: 10.1371/journal.pone.0233360 sha: doc_id: 11496 cord_uid: r8e19t0c file: cache/cord-011798-uss38ped.json key: cord-011798-uss38ped authors: Li, Guowei; Luo, Zhe; Anwar, Muhammad; Lu, Yuqiu; Wang, Xiantao; Liu, Xuening title: Intellectual capital and the efficiency of SMEs in the transition economy China; Do financial resources strengthen the routes? date: 2020-07-02 journal: PLoS One DOI: 10.1371/journal.pone.0235462 sha: doc_id: 11798 cord_uid: uss38ped file: cache/cord-012967-w1oc0wdd.json key: cord-012967-w1oc0wdd authors: Eberle, Jaelyn J.; von Koenigswald, Wighart; Eberth, David A. title: Using tooth enamel microstructure to identify mammalian fossils at an Eocene Arctic forest date: 2020-09-23 journal: PLoS One DOI: 10.1371/journal.pone.0239073 sha: doc_id: 12967 cord_uid: w1oc0wdd file: cache/cord-048358-z5klydpi.json key: cord-048358-z5klydpi authors: Catic, André; Fiebiger, Edda; Korbel, Gregory A.; Blom, Daniël; Galardy, Paul J.; Ploegh, Hidde L. title: Screen for ISG15-crossreactive Deubiquitinases date: 2007-07-25 journal: PLoS One DOI: 10.1371/journal.pone.0000679 sha: doc_id: 48358 cord_uid: z5klydpi file: cache/cord-003498-4ct0ywnw.json key: cord-003498-4ct0ywnw authors: Bdeir, Najat; Arora, Prerna; Gärtner, Sabine; Hoffmann, Markus; Reichl, Udo; Pöhlmann, Stefan; Winkler, Michael title: A system for production of defective interfering particles in the absence of infectious influenza A virus date: 2019-03-01 journal: PLoS One DOI: 10.1371/journal.pone.0212757 sha: doc_id: 3498 cord_uid: 4ct0ywnw file: cache/cord-048446-gaemgm0t.json key: cord-048446-gaemgm0t authors: White, Laura Forsberg; Pagano, Marcello title: Transmissibility of the Influenza Virus in the 1918 Pandemic date: 2008-01-30 journal: PLoS One DOI: 10.1371/journal.pone.0001498 sha: doc_id: 48446 cord_uid: gaemgm0t file: cache/cord-048353-hqc7u9w3.json key: cord-048353-hqc7u9w3 authors: Chis Ster, Irina; Ferguson, Neil M. title: Transmission Parameters of the 2001 Foot and Mouth Epidemic in Great Britain date: 2007-06-06 journal: PLoS One DOI: 10.1371/journal.pone.0000502 sha: doc_id: 48353 cord_uid: hqc7u9w3 file: cache/cord-013263-xw611i8k.json key: cord-013263-xw611i8k authors: Dederichs, Melina; Weber, Jeannette; Muth, Thomas; Angerer, Peter; Loerbroks, Adrian title: Students’ perspectives on interventions to reduce stress in medical school: A qualitative study date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240587 sha: doc_id: 13263 cord_uid: xw611i8k file: cache/cord-048364-yfn8sy1m.json key: cord-048364-yfn8sy1m authors: Fraser, Christophe title: Estimating Individual and Household Reproduction Numbers in an Emerging Epidemic date: 2007-08-22 journal: PLoS One DOI: 10.1371/journal.pone.0000758 sha: doc_id: 48364 cord_uid: yfn8sy1m file: cache/cord-252838-av7ducrk.json key: cord-252838-av7ducrk authors: Lucchi, Naomi W.; Demas, Allison; Narayanan, Jothikumar; Sumari, Deborah; Kabanywanyi, Abdunoor; Kachur, S. Patrick; Barnwell, John W.; Udhayakumar, Venkatachalam title: Real-Time Fluorescence Loop Mediated Isothermal Amplification for the Diagnosis of Malaria date: 2010-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0013733 sha: doc_id: 252838 cord_uid: av7ducrk file: cache/cord-252347-vnn4135b.json key: cord-252347-vnn4135b authors: Lee, Wai-Ming; Kiesner, Christin; Pappas, Tressa; Lee, Iris; Grindle, Kris; Jartti, Tuomas; Jakiela, Bogdan; Lemanske, Robert F.; Shult, Peter A.; Gern, James E. title: A Diverse Group of Previously Unrecognized Human Rhinoviruses Are Common Causes of Respiratory Illnesses in Infants date: 2007-10-03 journal: PLoS One DOI: 10.1371/journal.pone.0000966 sha: doc_id: 252347 cord_uid: vnn4135b file: cache/cord-013265-qrfi6e5c.json key: cord-013265-qrfi6e5c authors: Isono, Toshihito; Domon, Hisanori; Nagai, Kosuke; Maekawa, Tomoki; Tamura, Hikaru; Hiyoshi, Takumi; Yanagihara, Katsunori; Kunitomo, Eiji; Takenaka, Shoji; Noiri, Yuichiro; Terao, Yutaka title: Treatment of severe pneumonia by hinokitiol in a murine antimicrobial-resistant pneumococcal pneumonia model date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240329 sha: doc_id: 13265 cord_uid: qrfi6e5c file: cache/cord-048367-yya6w976.json key: cord-048367-yya6w976 authors: Jónsson, Stefán R.; LaRue, Rebecca S.; Stenglein, Mark D.; Fahrenkrug, Scott C.; Andrésdóttir, Valgerdur; Harris, Reuben S. title: The Restriction of Zoonotic PERV Transmission by Human APOBEC3G date: 2007-09-12 journal: PLoS One DOI: 10.1371/journal.pone.0000893 sha: doc_id: 48367 cord_uid: yya6w976 file: cache/cord-048492-4z38v9rg.json key: cord-048492-4z38v9rg authors: Tang, Julian W.; Ngai, Karry L. K.; Lam, Wai Y.; Chan, Paul K. S. title: Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006) date: 2008-07-23 journal: PLoS One DOI: 10.1371/journal.pone.0002768 sha: doc_id: 48492 cord_uid: 4z38v9rg file: cache/cord-251979-j3mme15e.json key: cord-251979-j3mme15e authors: Kandeel, Amr; Dawson, Patrick; Labib, Manal; Said, Mayar; El-Refai, Samir; El-Gohari, Amani; Talaat, Maha title: Morbidity, Mortality, and Seasonality of Influenza Hospitalizations in Egypt, November 2007-November 2014 date: 2016-09-08 journal: PLoS One DOI: 10.1371/journal.pone.0161301 sha: doc_id: 251979 cord_uid: j3mme15e file: cache/cord-048483-umvrwgaw.json key: cord-048483-umvrwgaw authors: van der Sande, Marianne; Teunis, Peter; Sabel, Rob title: Professional and Home-Made Face Masks Reduce Exposure to Respiratory Infections among the General Population date: 2008-07-09 journal: PLoS One DOI: 10.1371/journal.pone.0002618 sha: doc_id: 48483 cord_uid: umvrwgaw file: cache/cord-254025-j1l0mder.json key: cord-254025-j1l0mder authors: de Melo, Andreia C.; Thuler, Luiz C. S.; da Silva, Jesse L.; de Albuquerque, Lucas Z.; Pecego, Ana C.; Rodrigues, Luciana de O. R.; da Conceição, Magda S.; Garrido, Marianne M.; Quintella Mendes, Gelcio L.; Mendes Pereira, Ana Cristina P.; Soares, Marcelo A.; Viola, João P. B. title: Cancer inpatients with COVID-19: A report from the Brazilian National Cancer Institute date: 2020-10-26 journal: PLoS One DOI: 10.1371/journal.pone.0241261 sha: doc_id: 254025 cord_uid: j1l0mder file: cache/cord-252739-1manzf3l.json key: cord-252739-1manzf3l authors: Zheng, Yueming; Zhu, Xuejing; Zhou, Pingzheng; Lan, Xi; Xu, Haiyan; Li, Min; Gao, Zhaobing title: Hexachlorophene Is a Potent KCNQ1/KCNE1 Potassium Channel Activator Which Rescues LQTs Mutants date: 2012-12-12 journal: PLoS One DOI: 10.1371/journal.pone.0051820 sha: doc_id: 252739 cord_uid: 1manzf3l file: cache/cord-254117-2ttwaegh.json key: cord-254117-2ttwaegh authors: Priest, Patricia C.; Duncan, Alasdair R.; Jennings, Lance C.; Baker, Michael G. title: Thermal Image Scanning for Influenza Border Screening: Results of an Airport Screening Study date: 2011-01-05 journal: PLoS One DOI: 10.1371/journal.pone.0014490 sha: doc_id: 254117 cord_uid: 2ttwaegh file: cache/cord-013099-j816c3tw.json key: cord-013099-j816c3tw authors: Blease, Charlotte; Kharko, Anna; Locher, Cosima; DesRoches, Catherine M.; Mandl, Kenneth D. title: US primary care in 2029: A Delphi survey on the impact of machine learning date: 2020-10-08 journal: PLoS One DOI: 10.1371/journal.pone.0239947 sha: doc_id: 13099 cord_uid: j816c3tw file: cache/cord-013334-cptu0k7s.json key: cord-013334-cptu0k7s authors: Holst-Hansen, Joachim A.; Bergenholtz, Carsten title: Does the size of rewards influence performance in cognitively demanding tasks? date: 2020-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0240291 sha: doc_id: 13334 cord_uid: cptu0k7s file: cache/cord-048360-n9sih438.json key: cord-048360-n9sih438 authors: Villard, Viviane; Agak, George W.; Frank, Géraldine; Jafarshad, Ali; Servis, Catherine; Nébié, Issa; Sirima, Sodiomon B.; Felger, Ingrid; Arevalo-Herrera, Myriam; Herrera, Socrates; Heitz, Frederic; Bäcker, Volker; Druilhe, Pierre; Kajava, Andrey V.; Corradin, Giampietro title: Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date: 2007-07-25 journal: PLoS One DOI: 10.1371/journal.pone.0000645 sha: doc_id: 48360 cord_uid: n9sih438 file: cache/cord-259771-653opx0h.json key: cord-259771-653opx0h authors: Dwivedi, Varun; Manickam, Cordelia; Binjawadagi, Basavaraj; Joyappa, Dechamma; Renukaradhya, Gourapura J. title: Biodegradable Nanoparticle-Entrapped Vaccine Induces Cross-Protective Immune Response against a Virulent Heterologous Respiratory Viral Infection in Pigs date: 2012-12-11 journal: PLoS One DOI: 10.1371/journal.pone.0051794 sha: doc_id: 259771 cord_uid: 653opx0h file: cache/cord-254313-g2oc32dm.json key: cord-254313-g2oc32dm authors: Klink, Thomas; Rankin, Danielle A.; Piya, Bhinnata; Spieker, Andrew J.; Faouri, Samir; Shehabi, Asem; Williams, John V.; Khuri-Bulos, Najwa; Halasa, Natasha B. title: Evaluating the diagnostic accuracy of the WHO Severe Acute Respiratory Infection (SARI) criteria in Middle Eastern children under two years over three respiratory seasons date: 2020-04-30 journal: PLoS One DOI: 10.1371/journal.pone.0232188 sha: doc_id: 254313 cord_uid: g2oc32dm file: cache/cord-255013-njpuc475.json key: cord-255013-njpuc475 authors: He, Xiaocui; Korytář, Tomáš; Zhu, Yaqing; Pikula, Jiří; Bandouchova, Hana; Zukal, Jan; Köllner, Bernd title: Establishment of Myotis myotis Cell Lines - Model for Investigation of Host-Pathogen Interaction in a Natural Host for Emerging Viruses date: 2014-10-08 journal: PLoS One DOI: 10.1371/journal.pone.0109795 sha: doc_id: 255013 cord_uid: njpuc475 file: cache/cord-253056-765rs3e7.json key: cord-253056-765rs3e7 authors: Dionne, Audrey; Le, Cathie-Kim; Poupart, Steffany; Autmizguine, Julie; Meloche-Dumas, Léamarie; Turgeon, Jean; Fournier, Anne; Dahdah, Nagib title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date: 2018-10-17 journal: PLoS One DOI: 10.1371/journal.pone.0206001 sha: doc_id: 253056 cord_uid: 765rs3e7 file: cache/cord-254000-pbzcupjg.json key: cord-254000-pbzcupjg authors: Suvannachart, Pukkapol; Asawaphureekorn, Somkiat; Chansangpetch, Sunee; Inobhas, Abhibol; Pongpirul, Krit title: Repeatability, reproducibility, agreement, and safety of Tono-Pen tip cover for intraocular measurement using latex and polyethylene wrap date: 2020-09-28 journal: PLoS One DOI: 10.1371/journal.pone.0239875 sha: doc_id: 254000 cord_uid: pbzcupjg file: cache/cord-048339-nzh87aux.json key: cord-048339-nzh87aux authors: Caley, Peter; Becker, Niels G.; Philp, David J. title: The Waiting Time for Inter-Country Spread of Pandemic Influenza date: 2007-01-03 journal: PLoS One DOI: 10.1371/journal.pone.0000143 sha: doc_id: 48339 cord_uid: nzh87aux file: cache/cord-013356-y6vceq2x.json key: cord-013356-y6vceq2x authors: Peace, Angela; Pattemore, David; Broussard, Melissa; Fonseka, Dilini; Tomer, Nathan; Bosque-Pérez, Nilsa A.; Crowder, David; Shaw, Allison K.; Jesson, Linley; Howlett, Brad G.; Jochym, Mateusz; Li, Jing title: Orchard layout and plant traits influence fruit yield more strongly than pollinator behaviour and density in a dioecious crop date: 2020-10-23 journal: PLoS One DOI: 10.1371/journal.pone.0231120 sha: doc_id: 13356 cord_uid: y6vceq2x file: cache/cord-255576-738khdwv.json key: cord-255576-738khdwv authors: Van Duyne, Rachel; Guendel, Irene; Klase, Zachary; Narayanan, Aarthi; Coley, William; Jaworski, Elizabeth; Roman, Jessica; Popratiloff, Anastas; Mahieux, Renaud; Kehn-Hall, Kylene; Kashanchi, Fatah title: Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date: 2012-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0040662 sha: doc_id: 255576 cord_uid: 738khdwv file: cache/cord-260432-imslfm4l.json key: cord-260432-imslfm4l authors: Marshall, Jenika D.; Courage, Emily R.; Elliott, Ryan F.; Fitzpatrick, Madeline N.; Kim, Anne D.; Lopez-Clavijo, Andrea F.; Woolfrey, Bronwyn A.; Ouimet, Mireille; Wakelam, Michael J. O.; Brown, Robert J. title: THP-1 macrophage cholesterol efflux is impaired by palmitoleate through Akt activation date: 2020-05-21 journal: PLoS One DOI: 10.1371/journal.pone.0233180 sha: doc_id: 260432 cord_uid: imslfm4l file: cache/cord-254825-c5d0wul9.json key: cord-254825-c5d0wul9 authors: Kim, Sei Won; Jo, Sung Jin; Lee, Heayon; Oh, Jung Hwan; Lim, Jihyang; Lee, Sang Haak; Choi, Jung Hyun; Lee, Jehoon title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 journal: PLoS One DOI: 10.1371/journal.pone.0237692 sha: doc_id: 254825 cord_uid: c5d0wul9 file: cache/cord-260653-5qwtvm9x.json key: cord-260653-5qwtvm9x authors: Chikhlikar, Priya; de Arruda, Luciana Barros; Maciel, Milton; Silvera, Peter; Lewis, Mark G.; August, J. Thomas; Marques, Ernesto T.A. title: DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques date: 2006-12-27 journal: PLoS One DOI: 10.1371/journal.pone.0000135 sha: doc_id: 260653 cord_uid: 5qwtvm9x file: cache/cord-257603-ov0b8yub.json key: cord-257603-ov0b8yub authors: Azlan, Arina Anis; Hamzah, Mohammad Rezal; Sern, Tham Jen; Ayub, Suffian Hadi; Mohamad, Emma title: Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia date: 2020-05-21 journal: PLoS One DOI: 10.1371/journal.pone.0233668 sha: doc_id: 257603 cord_uid: ov0b8yub file: cache/cord-254340-e1x0z3rh.json key: cord-254340-e1x0z3rh authors: Cruz, Christian Joy Pattawi; Ganly, Rachel; Li, Zilin; Gietel-Basten, Stuart title: Exploring the young demographic profile of COVID-19 cases in Hong Kong: Evidence from migration and travel history data date: 2020-06-26 journal: PLoS One DOI: 10.1371/journal.pone.0235306 sha: doc_id: 254340 cord_uid: e1x0z3rh file: cache/cord-260572-vd65ygtm.json key: cord-260572-vd65ygtm authors: Kim, Curi; Ahmed, Jamal A.; Eidex, Rachel B.; Nyoka, Raymond; Waiboci, Lilian W.; Erdman, Dean; Tepo, Adan; Mahamud, Abdirahman S.; Kabura, Wamburu; Nguhi, Margaret; Muthoka, Philip; Burton, Wagacha; Breiman, Robert F.; Njenga, M. Kariuki; Katz, Mark A. title: Comparison of Nasopharyngeal and Oropharyngeal Swabs for the Diagnosis of Eight Respiratory Viruses by Real-Time Reverse Transcription-PCR Assays date: 2011-06-30 journal: PLoS One DOI: 10.1371/journal.pone.0021610 sha: doc_id: 260572 cord_uid: vd65ygtm file: cache/cord-252795-x66zqmgv.json key: cord-252795-x66zqmgv authors: Islam, Md. Akhtarul; Barna, Sutapa Dey; Raihan, Hasin; Khan, Md. Nafiul Alam; Hossain, Md. Tanvir title: Depression and anxiety among university students during the COVID-19 pandemic in Bangladesh: A web-based cross-sectional survey date: 2020-08-26 journal: PLoS One DOI: 10.1371/journal.pone.0238162 sha: doc_id: 252795 cord_uid: x66zqmgv file: cache/cord-256424-t3dtabi4.json key: cord-256424-t3dtabi4 authors: Bousbia, Sabri; Papazian, Laurent; Saux, Pierre; Forel, Jean Marie; Auffray, Jean-Pierre; Martin, Claude; Raoult, Didier; La Scola, Bernard title: Repertoire of Intensive Care Unit Pneumonia Microbiota date: 2012-02-28 journal: PLoS One DOI: 10.1371/journal.pone.0032486 sha: doc_id: 256424 cord_uid: t3dtabi4 file: cache/cord-262345-hti1jjpn.json key: cord-262345-hti1jjpn authors: Eddy, Lucy H.; Bingham, Daniel D.; Crossley, Kirsty L.; Shahid, Nishaat F.; Ellingham-Khan, Marsha; Otteslev, Ava; Figueredo, Natalie S.; Mon-Williams, Mark; Hill, Liam J. B. title: The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review date: 2020-08-25 journal: PLoS One DOI: 10.1371/journal.pone.0237919 sha: doc_id: 262345 cord_uid: hti1jjpn file: cache/cord-253436-dz84icdc.json key: cord-253436-dz84icdc authors: Wille, Michelle; Muradrasoli, Shaman; Nilsson, Anna; Järhult, Josef D. title: High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl date: 2016-03-03 journal: PLoS One DOI: 10.1371/journal.pone.0150198 sha: doc_id: 253436 cord_uid: dz84icdc file: cache/cord-258366-fu9b446y.json key: cord-258366-fu9b446y authors: Couto, Carla R.; Pannuti, Cláudio S.; Paz, José P.; Fink, Maria C. D.; Machado, Alessandra A.; de Marchi, Michela; Machado, Clarisse M. title: Fighting Misconceptions to Improve Compliance with Influenza Vaccination among Health Care Workers: An Educational Project date: 2012-02-06 journal: PLoS One DOI: 10.1371/journal.pone.0030670 sha: doc_id: 258366 cord_uid: fu9b446y file: cache/cord-258172-p54j4zzo.json key: cord-258172-p54j4zzo authors: Barker, Harlan; Parkkila, Seppo title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0240647 sha: doc_id: 258172 cord_uid: p54j4zzo file: cache/cord-258243-2utl2mfl.json key: cord-258243-2utl2mfl authors: Chen, Jeng-Wen; Liao, Po-Wu; Hsieh, Chi-Jeng; Chen, Chu-Chieh; Chiou, Shang-Jyh title: Factors associated with changing indications for adenotonsillectomy: A population-based longitudinal study date: 2018-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0193317 sha: doc_id: 258243 cord_uid: 2utl2mfl file: cache/cord-261908-olcuq6tm.json key: cord-261908-olcuq6tm authors: Lai, Ka-Man; Bottomley, Christian; McNerney, Ruth title: Propagation of Respiratory Aerosols by the Vuvuzela date: 2011-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0020086 sha: doc_id: 261908 cord_uid: olcuq6tm file: cache/cord-255351-vp19ydce.json key: cord-255351-vp19ydce authors: Lanata, Claudio F.; Fischer-Walker, Christa L.; Olascoaga, Ana C.; Torres, Carla X.; Aryee, Martin J.; Black, Robert E. title: Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review date: 2013-09-04 journal: PLoS One DOI: 10.1371/journal.pone.0072788 sha: doc_id: 255351 cord_uid: vp19ydce file: cache/cord-255588-nh34lgdh.json key: cord-255588-nh34lgdh authors: Guo, Fang; Mead, Jennifer; Aliya, Nishat; Wang, Lijuan; Cuconati, Andrea; Wei, Lai; Li, Kui; Block, Timothy M.; Guo, Ju-Tao; Chang, Jinhong title: RO 90-7501 Enhances TLR3 and RLR Agonist Induced Antiviral Response date: 2012-10-03 journal: PLoS One DOI: 10.1371/journal.pone.0042583 sha: doc_id: 255588 cord_uid: nh34lgdh file: cache/cord-048477-ze511t38.json key: cord-048477-ze511t38 authors: Patel, Mahomed S.; Phillips, Christine B.; Pearce, Christopher; Kljakovic, Marjan; Dugdale, Paul; Glasgow, Nicholas title: General Practice and Pandemic Influenza: A Framework for Planning and Comparison of Plans in Five Countries date: 2008-05-28 journal: PLoS One DOI: 10.1371/journal.pone.0002269 sha: doc_id: 48477 cord_uid: ze511t38 file: cache/cord-261410-kb91eagd.json key: cord-261410-kb91eagd authors: Park, Ji Young; Kim, Bong-Joon; Lee, Eun Jung; Park, Kwi Sung; Park, Hee Sun; Jung, Sung Soo; Kim, Ju Ock title: Clinical Features and Courses of Adenovirus Pneumonia in Healthy Young Adults during an Outbreak among Korean Military Personnel date: 2017-01-23 journal: PLoS One DOI: 10.1371/journal.pone.0170592 sha: doc_id: 261410 cord_uid: kb91eagd file: cache/cord-260843-c97kctjz.json key: cord-260843-c97kctjz authors: Dai, Lei; Hu, Wei Wei; Xia, Lu; Xia, Mi; Yang, Qian title: Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake date: 2016-11-16 journal: PLoS One DOI: 10.1371/journal.pone.0165585 sha: doc_id: 260843 cord_uid: c97kctjz file: cache/cord-262759-ec2c25q3.json key: cord-262759-ec2c25q3 authors: Hsieh, Yi-Ting; Lin, Mei-Hui; Ho, Hung-Yao; Chen, Lei-Chin; Chen, Chien-Cheng; Shu, Jwu-Ching title: Glucose-6-Phosphate Dehydrogenase (G6PD)-Deficient Epithelial Cells Are Less Tolerant to Infection by Staphylococcus aureus date: 2013-11-04 journal: PLoS One DOI: 10.1371/journal.pone.0079566 sha: doc_id: 262759 cord_uid: ec2c25q3 file: cache/cord-260728-4w23kwzu.json key: cord-260728-4w23kwzu authors: Timmermans, Ans; Melendrez, Melanie C.; Se, Youry; Chuang, Ilin; Samon, Nou; Uthaimongkol, Nichapat; Klungthong, Chonticha; Manasatienkij, Wudtichai; Thaisomboonsuk, Butsaya; Tyner, Stuart D.; Rith, Sareth; Horm, Viseth Srey; Jarman, Richard G.; Bethell, Delia; Chanarat, Nitima; Pavlin, Julie; Wongstitwilairoong, Tippa; Saingam, Piyaporn; El, But Sam; Fukuda, Mark M.; Touch, Sok; Sovann, Ly; Fernandez, Stefan; Buchy, Philippe; Chanthap, Lon; Saunders, David title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 journal: PLoS One DOI: 10.1371/journal.pone.0152529 sha: doc_id: 260728 cord_uid: 4w23kwzu file: cache/cord-260647-7bjhobg7.json key: cord-260647-7bjhobg7 authors: Coudray-Meunier, Coralie; Fraisse, Audrey; Martin-Latil, Sandra; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 journal: PLoS One DOI: 10.1371/journal.pone.0147832 sha: doc_id: 260647 cord_uid: 7bjhobg7 file: cache/cord-256326-3ebcuzd6.json key: cord-256326-3ebcuzd6 authors: Liotta, Giuseppe; Marazzi, Maria Cristina; Orlando, Stefano; Palombi, Leonardo title: Is social connectedness a risk factor for the spreading of COVID-19 among older adults? The Italian paradox date: 2020-05-21 journal: PLoS One DOI: 10.1371/journal.pone.0233329 sha: doc_id: 256326 cord_uid: 3ebcuzd6 file: cache/cord-262846-1mhimfsf.json key: cord-262846-1mhimfsf authors: Gray, Nicholas; Calleja, Dominic; Wimbush, Alexander; Miralles-Dolz, Enrique; Gray, Ander; De Angelis, Marco; Derrer-Merk, Elfriede; Oparaji, Bright Uchenna; Stepanov, Vladimir; Clearkin, Louis; Ferson, Scott title: Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date: 2020-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0240775 sha: doc_id: 262846 cord_uid: 1mhimfsf file: cache/cord-256837-100ir651.json key: cord-256837-100ir651 authors: Smith, Steven B.; Dampier, William; Tozeren, Aydin; Brown, James R.; Magid-Slav, Michal title: Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date: 2012-03-14 journal: PLoS One DOI: 10.1371/journal.pone.0033174 sha: doc_id: 256837 cord_uid: 100ir651 file: cache/cord-263276-keyu60in.json key: cord-263276-keyu60in authors: Zhou, Weimin; Lin, Feng; Teng, Lingfang; Li, Hua; Hou, Jianyi; Tong, Rui; Zheng, Changhua; Lou, Yongliang; Tan, Wenjie title: Prevalence of Herpes and Respiratory Viruses in Induced Sputum among Hospitalized Children with Non Typical Bacterial Community-Acquired Pneumonia date: 2013-11-18 journal: PLoS One DOI: 10.1371/journal.pone.0079477 sha: doc_id: 263276 cord_uid: keyu60in file: cache/cord-257077-cdnkk6ou.json key: cord-257077-cdnkk6ou authors: Gabor, Kristin A.; Stevens, Chad R.; Pietraszewski, Matthew J.; Gould, Travis J.; Shim, Juyoung; Yoder, Jeffrey A.; Lam, Siew Hong; Gong, Zhiyuan; Hess, Samuel T.; Kim, Carol H. title: Super Resolution Microscopy Reveals that Caveolin-1 Is Required for Spatial Organization of CRFB1 and Subsequent Antiviral Signaling in Zebrafish date: 2013-07-09 journal: PLoS One DOI: 10.1371/journal.pone.0068759 sha: doc_id: 257077 cord_uid: cdnkk6ou file: cache/cord-263453-7v4y02j6.json key: cord-263453-7v4y02j6 authors: Nishiura, Hiroshi; Klinkenberg, Don; Roberts, Mick; Heesterbeek, Johan A. P. title: Early Epidemiological Assessment of the Virulence of Emerging Infectious Diseases: A Case Study of an Influenza Pandemic date: 2009-08-31 journal: PLoS One DOI: 10.1371/journal.pone.0006852 sha: doc_id: 263453 cord_uid: 7v4y02j6 file: cache/cord-262876-civfvk45.json key: cord-262876-civfvk45 authors: Su, Tong; Han, Xue; Chen, Fei; Du, Yan; Zhang, Hongwei; Yin, Jianhua; Tan, Xiaojie; Chang, Wenjun; Ding, Yibo; Han, Yifang; Cao, Guangwen title: Knowledge Levels and Training Needs of Disaster Medicine among Health Professionals, Medical Students, and Local Residents in Shanghai, China date: 2013-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0067041 sha: doc_id: 262876 cord_uid: civfvk45 file: cache/cord-263978-jk82bk1a.json key: cord-263978-jk82bk1a authors: Karaivanov, Alexander title: A social network model of COVID-19 date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0240878 sha: doc_id: 263978 cord_uid: jk82bk1a file: cache/cord-265138-i5m3ax7g.json key: cord-265138-i5m3ax7g authors: Wang, Xi-Ling; Yang, Lin; Chan, King-Pan; Chiu, Susan S.; Chan, Kwok-Hung; Peiris, J. S. Malik; Wong, Chit-Ming title: Model Selection in Time Series Studies of Influenza-Associated Mortality date: 2012-06-20 journal: PLoS One DOI: 10.1371/journal.pone.0039423 sha: doc_id: 265138 cord_uid: i5m3ax7g file: cache/cord-255384-tljyx6ua.json key: cord-255384-tljyx6ua authors: Decaro, Nicola; Pinto, Pierfrancesco; Mari, Viviana; Elia, Gabriella; Larocca, Vittorio; Camero, Michele; Terio, Valentina; Losurdo, Michele; Martella, Vito; Buonavoglia, Canio title: Full-Genome Analysis of a Canine Pneumovirus Causing Acute Respiratory Disease in Dogs, Italy date: 2014-01-06 journal: PLoS One DOI: 10.1371/journal.pone.0085220 sha: doc_id: 255384 cord_uid: tljyx6ua file: cache/cord-266797-uglsx7se.json key: cord-266797-uglsx7se authors: Anastassopoulou, Cleo; Russo, Lucia; Tsakris, Athanasios; Siettos, Constantinos title: Data-based analysis, modelling and forecasting of the COVID-19 outbreak date: 2020-03-31 journal: PLoS One DOI: 10.1371/journal.pone.0230405 sha: doc_id: 266797 cord_uid: uglsx7se file: cache/cord-257217-f9sdt7ax.json key: cord-257217-f9sdt7ax authors: Nunes, Marta C.; Kuschner, Zachary; Rabede, Zelda; Madimabe, Richard; Van Niekerk, Nadia; Moloi, Jackie; Kuwanda, Locadiah; Rossen, John W.; Klugman, Keith P.; Adrian, Peter V.; Madhi, Shabir A. title: Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date: 2014-02-03 journal: PLoS One DOI: 10.1371/journal.pone.0086448 sha: doc_id: 257217 cord_uid: f9sdt7ax file: cache/cord-262748-v4xue7ha.json key: cord-262748-v4xue7ha authors: Xu, Yongtao; Yu, Shui; Zou, Jian-Wei; Hu, Guixiang; Rahman, Noorsaadah A. B. D.; Othman, Rozana Binti; Tao, Xia; Huang, Meilan title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date: 2015-12-04 journal: PLoS One DOI: 10.1371/journal.pone.0144171 sha: doc_id: 262748 cord_uid: v4xue7ha file: cache/cord-263464-fdosch11.json key: cord-263464-fdosch11 authors: Nuvey, Francis Sena; Edu-Quansah, Elijah Paa; Kuma, George Khumalo; Eleeza, John; Kenu, Ernest; Sackey, Samuel; Ameme, Donne; Abakar, Mahamat Fayiz; Kreppel, Katharina; Ngandolo, Richard Bongo; Afari, Edwin; Bonfoh, Bassirou title: Evaluation of the sentinel surveillance system for influenza-like illnesses in the Greater Accra region, Ghana, 2018 date: 2019-03-14 journal: PLoS One DOI: 10.1371/journal.pone.0213627 sha: doc_id: 263464 cord_uid: fdosch11 file: cache/cord-265812-1hcp36cw.json key: cord-265812-1hcp36cw authors: De Jong, Cornelis N.; Saes, Lotte; Klerk, Clara P. W.; Van der Klift, Marjolein; Cornelissen, Jan J.; Broers, Annoek E. C. title: Etanercept for steroid-refractory acute graft-versus-host disease: A single center experience date: 2017-10-26 journal: PLoS One DOI: 10.1371/journal.pone.0187184 sha: doc_id: 265812 cord_uid: 1hcp36cw file: cache/cord-267189-xq70rn1j.json key: cord-267189-xq70rn1j authors: Wang, Xinyu; Li, Chunqiu; Guo, Donghua; Wang, Xinyu; Wei, Shan; Geng, Yufei; Wang, Enyu; Wang, Zhihui; Zhao, Xiwen; Su, Mingjun; Liu, Qiujin; Zhang, Siyao; Feng, Li; Sun, Dongbo title: Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China date: 2016-01-15 journal: PLoS One DOI: 10.1371/journal.pone.0146975 sha: doc_id: 267189 cord_uid: xq70rn1j file: cache/cord-263684-3535k3op.json key: cord-263684-3535k3op authors: Tang, Julian W.; Nicolle, Andre; Pantelic, Jovan; Klettner, Christian A.; Su, Ruikun; Kalliomaki, Petri; Saarinen, Pekka; Koskela, Hannu; Reijula, Kari; Mustakallio, Panu; Cheong, David K. W.; Sekhar, Chandra; Tham, Kwok Wai title: Different Types of Door-Opening Motions as Contributing Factors to Containment Failures in Hospital Isolation Rooms date: 2013-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0066663 sha: doc_id: 263684 cord_uid: 3535k3op file: cache/cord-262832-5iejckwx.json key: cord-262832-5iejckwx authors: Yen, Muh-Yong; Wu, Tsung-Shu Joseph; Chiu, Allen Wen-Hsiang; Wong, Wing-Wai; Wang, Po-En; Chan, Ta-Chien; King, Chwan-Chuen title: Taipei's Use of a Multi-Channel Mass Risk Communication Program to Rapidly Reverse an Epidemic of Highly Communicable Disease date: 2009-11-23 journal: PLoS One DOI: 10.1371/journal.pone.0007962 sha: doc_id: 262832 cord_uid: 5iejckwx file: cache/cord-267519-a0bcmjkn.json key: cord-267519-a0bcmjkn authors: Bravi, Francesca; Flacco, Maria Elena; Carradori, Tiziano; Volta, Carlo Alberto; Cosenza, Giuseppe; De Togni, Aldo; Acuti Martellucci, Cecilia; Parruti, Giustino; Mantovani, Lorenzo; Manzoli, Lamberto title: Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens date: 2020-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0235248 sha: doc_id: 267519 cord_uid: a0bcmjkn file: cache/cord-267307-kyh0xsrp.json key: cord-267307-kyh0xsrp authors: Kasting, Monica L.; Head, Katharine J.; Hartsock, Jane A.; Sturm, Lynne; Zimet, Gregory D. title: Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date: 2020-11-04 journal: PLoS One DOI: 10.1371/journal.pone.0241662 sha: doc_id: 267307 cord_uid: kyh0xsrp file: cache/cord-267644-guzn0peq.json key: cord-267644-guzn0peq authors: Livadiotis, George title: Statistical analysis of the impact of environmental temperature on the exponential growth rate of cases infected by COVID-19 date: 2020-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0233875 sha: doc_id: 267644 cord_uid: guzn0peq file: cache/cord-267973-uvz7kavu.json key: cord-267973-uvz7kavu authors: Do, Lien Anh Ha; Bryant, Juliet E.; Tran, Anh Tuan; Nguyen, Bach Hue; Tran, Thi Thu Loan; Tran, Quynh Huong; Vo, Quoc Bao; Tran Dac, Nguyen Anh; Trinh, Hong Nhien; Nguyen, Thi Thanh Hai; Le Binh, Bao Tinh; Le, Khanh; Nguyen, Minh Tien; Thai, Quang Tung; Vo, Thanh Vu; Ngo, Ngoc Quang Minh; Dang, Thi Kim Huyen; Cao, Ngoc Huong; Tran, Thu Van; Ho, Lu Viet; Farrar, Jeremy; de Jong, Menno; van Doorn, H. Rogier title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity date: 2016-08-08 journal: PLoS One DOI: 10.1371/journal.pone.0160606 sha: doc_id: 267973 cord_uid: uvz7kavu file: cache/cord-266799-t7lqlv41.json key: cord-266799-t7lqlv41 authors: Rotejanaprasert, Chawarat; Lawpoolsri, Saranath; Pan-ngum, Wirichada; Maude, Richard J. title: Preliminary estimation of temporal and spatiotemporal dynamic measures of COVID-19 transmission in Thailand date: 2020-09-24 journal: PLoS One DOI: 10.1371/journal.pone.0239645 sha: doc_id: 266799 cord_uid: t7lqlv41 file: cache/cord-267566-gdjl0qmu.json key: cord-267566-gdjl0qmu authors: Kweon, Oh Joo; Lim, Yong Kwan; Kim, Hye Ryoun; Kim, Min-Chul; Choi, Seong-Ho; Chung, Jin-Won; Lee, Mi-Kyung title: Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date: 2020-10-22 journal: PLoS One DOI: 10.1371/journal.pone.0240395 sha: doc_id: 267566 cord_uid: gdjl0qmu file: cache/cord-267605-efb10j3u.json key: cord-267605-efb10j3u authors: Zheng, Li-Zhen; Liu, Zhong; Lei, Ming; Peng, Jiang; He, Yi-Xin; Xie, Xin-Hui; Man, Chi-Wai; Huang, Le; Wang, Xin-Luan; Fong, Daniel Tik-Pui; Xiao, De-Ming; Wang, Da-Ping; Chen, Yang; Feng, Jian Q.; Liu, Ying; Zhang, Ge; Qin, Ling title: Steroid-Associated Hip Joint Collapse in Bipedal Emus date: 2013-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0076797 sha: doc_id: 267605 cord_uid: efb10j3u file: cache/cord-268816-nth3o6ot.json key: cord-268816-nth3o6ot authors: Roy, Satyaki; Ghosh, Preetam title: Factors affecting COVID-19 infected and death rates inform lockdown-related policymaking date: 2020-10-23 journal: PLoS One DOI: 10.1371/journal.pone.0241165 sha: doc_id: 268816 cord_uid: nth3o6ot file: cache/cord-268977-hcg2rrhl.json key: cord-268977-hcg2rrhl authors: Feikin, Daniel R.; Njenga, M. Kariuki; Bigogo, Godfrey; Aura, Barrack; Aol, George; Audi, Allan; Jagero, Geoffrey; Muluare, Peter Ochieng; Gikunju, Stella; Nderitu, Leonard; Balish, Amanda; Winchell, Jonas; Schneider, Eileen; Erdman, Dean; Oberste, M. Steven; Katz, Mark A.; Breiman, Robert F. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 journal: PLoS One DOI: 10.1371/journal.pone.0043656 sha: doc_id: 268977 cord_uid: hcg2rrhl file: cache/cord-272655-qeojdpez.json key: cord-272655-qeojdpez authors: Remolina, Yuly Andrea; Ulloa, María Mercedes; Vargas, Hernán; Díaz, Liliana; Gómez, Sandra Liliana; Saavedra, Alfredo; Sánchez, Edgar; Cortés, Jorge Alberto title: Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia date: 2015-11-17 journal: PLoS One DOI: 10.1371/journal.pone.0143152 sha: doc_id: 272655 cord_uid: qeojdpez file: cache/cord-272445-0xauff51.json key: cord-272445-0xauff51 authors: Naaber, Paul; Hunt, Kaidi; Pesukova, Jaana; Haljasmägi, Liis; Rumm, Pauliina; Peterson, Pärt; Hololejenko, Jelena; Eero, Irina; Jõgi, Piia; Toompere, Karolin; Sepp, Epp title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date: 2020-10-27 journal: PLoS One DOI: 10.1371/journal.pone.0237548 sha: doc_id: 272445 cord_uid: 0xauff51 file: cache/cord-264880-0tmd9knh.json key: cord-264880-0tmd9knh authors: Li, Zhao; Liu, Yong; Wei, Qingquan; Liu, Yuanjie; Liu, Wenwen; Zhang, Xuelian; Yu, Yude title: Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date: 2016-04-13 journal: PLoS One DOI: 10.1371/journal.pone.0153359 sha: doc_id: 264880 cord_uid: 0tmd9knh file: cache/cord-273343-als886fe.json key: cord-273343-als886fe authors: McClenahan, Shasta D.; Scherba, Gail; Borst, Luke; Fredrickson, Richard L.; Krause, Philip R.; Uhlenhaut, Christine title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 journal: PLoS One DOI: 10.1371/journal.pone.0068777 sha: doc_id: 273343 cord_uid: als886fe file: cache/cord-268429-drejl99k.json key: cord-268429-drejl99k authors: Almberg, Emily S.; Mech, L. David; Smith, Douglas W.; Sheldon, Jennifer W.; Crabtree, Robert L. title: A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community date: 2009-09-16 journal: PLoS One DOI: 10.1371/journal.pone.0007042 sha: doc_id: 268429 cord_uid: drejl99k file: cache/cord-269453-30l6rzgo.json key: cord-269453-30l6rzgo authors: Yang, Po; Qi, Jun; Zhang, Shuhao; Wang, Xulong; Bi, Gaoshan; Yang, Yun; Sheng, Bin; Yang, Geng title: Feasibility study of mitigation and suppression strategies for controlling COVID-19 outbreaks in London and Wuhan date: 2020-08-06 journal: PLoS One DOI: 10.1371/journal.pone.0236857 sha: doc_id: 269453 cord_uid: 30l6rzgo file: cache/cord-276763-x3dqi0ym.json key: cord-276763-x3dqi0ym authors: Lowery-North, Douglas W.; Hertzberg, Vicki Stover; Elon, Lisa; Cotsonis, George; Hilton, Sarah A.; Vaughns, Christopher F.; Hill, Eric; Shrestha, Alok; Jo, Alexandria; Adams, Nathan title: Measuring Social Contacts in the Emergency Department date: 2013-08-21 journal: PLoS One DOI: 10.1371/journal.pone.0070854 sha: doc_id: 276763 cord_uid: x3dqi0ym file: cache/cord-276577-06boh550.json key: cord-276577-06boh550 authors: Schanzer, Dena L.; Garner, Michael J.; Hatchette, Todd F.; Langley, Joanne M.; Aziz, Samina; Tam, Theresa W. S. title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling date: 2009-08-18 journal: PLoS One DOI: 10.1371/journal.pone.0006681 sha: doc_id: 276577 cord_uid: 06boh550 file: cache/cord-278087-0nicp0eq.json key: cord-278087-0nicp0eq authors: García-García, María Luz; Calvo, Cristina; Rey, Cristina; Díaz, Beatriz; Molinero, Maria del Mar; Pozo, Francisco; Casas, Inmaculada title: Human metapnuemovirus infections in hospitalized children and comparison with other respiratory viruses. 2005-2014 prospective study date: 2017-03-16 journal: PLoS One DOI: 10.1371/journal.pone.0173504 sha: doc_id: 278087 cord_uid: 0nicp0eq file: cache/cord-267042-nvwnbp2j.json key: cord-267042-nvwnbp2j authors: Gaspard, Philippe; Mosnier, Anne; Simon, Loic; Ali-Brandmeyer, Olivia; Rabaud, Christian; Larocca, Sabrina; Heck, Béatrice; Aho-Glélé, Serge; Pothier, Pierre; Ambert-Balay, Katia title: Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents date: 2019-09-24 journal: PLoS One DOI: 10.1371/journal.pone.0222321 sha: doc_id: 267042 cord_uid: nvwnbp2j file: cache/cord-271660-5sfkhg19.json key: cord-271660-5sfkhg19 authors: Sun, Hsin-Yun; Wang, Jann-Yuan; Chen, Yee-Chun; Hsueh, Po-Ren; Chen, Yi-Hsuan; Chuang, Yu-Chung; Fang, Chi-Tai; Chang, Shan-Chwen; Wang, Jung-Der title: Impact of introducing fluorescent microscopy on hospital tuberculosis control: A before-after study at a high caseload medical center in Taiwan date: 2020-04-03 journal: PLoS One DOI: 10.1371/journal.pone.0230067 sha: doc_id: 271660 cord_uid: 5sfkhg19 file: cache/cord-272878-6f0q661e.json key: cord-272878-6f0q661e authors: Schnepf, Nathalie; Resche-Rigon, Matthieu; Chaillon, Antoine; Scemla, Anne; Gras, Guillaume; Semoun, Oren; Taboulet, Pierre; Molina, Jean-Michel; Simon, François; Goudeau, Alain; LeGoff, Jérôme title: High Burden of Non-Influenza Viruses in Influenza-Like Illness in the Early Weeks of H1N1v Epidemic in France date: 2011-08-17 journal: PLoS One DOI: 10.1371/journal.pone.0023514 sha: doc_id: 272878 cord_uid: 6f0q661e file: cache/cord-273175-bao8xxe2.json key: cord-273175-bao8xxe2 authors: Tran, Viet-Thi; Ravaud, Philippe title: COVID-19–related perceptions, context and attitudes of adults with chronic conditions: Results from a cross-sectional survey nested in the ComPaRe e-cohort date: 2020-08-06 journal: PLoS One DOI: 10.1371/journal.pone.0237296 sha: doc_id: 273175 cord_uid: bao8xxe2 file: cache/cord-273764-itu39mln.json key: cord-273764-itu39mln authors: Li, Taisheng; Xie, Jing; He, Yuxian; Fan, Hongwei; Baril, Laurence; Qiu, Zhifeng; Han, Yang; Xu, Wenbing; Zhang, Weihong; You, Hui; Zuo, Yanling; Fang, Qing; Yu, Jian; Chen, Zhiwei; Zhang, Linqi title: Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date: 2006-12-20 journal: PLoS One DOI: 10.1371/journal.pone.0000024 sha: doc_id: 273764 cord_uid: itu39mln file: cache/cord-268524-lr51ubz5.json key: cord-268524-lr51ubz5 authors: Droit-Volet, Sylvie; Gil, Sandrine; Martinelli, Natalia; Andant, Nicolas; Clinchamps, Maélys; Parreira, Lénise; Rouffiac, Karine; Dambrun, Michael; Huguet, Pascal; Dubuis, Benoît; Pereira, Bruno; Bouillon, Jean-Baptiste; Dutheil, Frédéric title: Time and Covid-19 stress in the lockdown situation: Time free, «Dying» of boredom and sadness date: 2020-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0236465 sha: doc_id: 268524 cord_uid: lr51ubz5 file: cache/cord-270683-982eqtog.json key: cord-270683-982eqtog authors: Pavel, Shaikh Terkis Islam; Yetiskin, Hazel; Aydin, Gunsu; Holyavkin, Can; Uygut, Muhammet Ali; Dursun, Zehra Bestepe; Celik, İlhami; Cevik, Ceren; Ozdarendeli, Aykut title: Isolation and characterization of severe acute respiratory syndrome coronavirus 2 in Turkey date: 2020-09-16 journal: PLoS One DOI: 10.1371/journal.pone.0238614 sha: doc_id: 270683 cord_uid: 982eqtog file: cache/cord-272971-9luzvzsu.json key: cord-272971-9luzvzsu authors: Guo, Hainan; Zhao, Yang; Niu, Tie; Tsui, Kwok-Leung title: Hong Kong Hospital Authority resource efficiency evaluation: Via a novel DEA-Malmquist model and Tobit regression model date: 2017-09-08 journal: PLoS One DOI: 10.1371/journal.pone.0184211 sha: doc_id: 272971 cord_uid: 9luzvzsu file: cache/cord-273594-vmbhok1u.json key: cord-273594-vmbhok1u authors: Sichelstiel, Anke; Yadava, Koshika; Trompette, Aurélien; Salami, Olawale; Iwakura, Yoichiro; Nicod, Laurent P.; Marsland, Benjamin J. title: Targeting IL-1β and IL-17A Driven Inflammation during Influenza-Induced Exacerbations of Chronic Lung Inflammation date: 2014-06-11 journal: PLoS One DOI: 10.1371/journal.pone.0098440 sha: doc_id: 273594 cord_uid: vmbhok1u file: cache/cord-269690-6r2bfydw.json key: cord-269690-6r2bfydw authors: De Lorenzo, Rebecca; Conte, Caterina; Lanzani, Chiara; Benedetti, Francesco; Roveri, Luisa; Mazza, Mario G.; Brioni, Elena; Giacalone, Giacomo; Canti, Valentina; Sofia, Valentina; D’Amico, Marta; Di Napoli, Davide; Ambrosio, Alberto; Scarpellini, Paolo; Castagna, Antonella; Landoni, Giovanni; Zangrillo, Alberto; Bosi, Emanuele; Tresoldi, Moreno; Ciceri, Fabio; Rovere-Querini, Patrizia title: Residual clinical damage after COVID-19: A retrospective and prospective observational cohort study date: 2020-10-14 journal: PLoS One DOI: 10.1371/journal.pone.0239570 sha: doc_id: 269690 cord_uid: 6r2bfydw file: cache/cord-270681-6ayciihs.json key: cord-270681-6ayciihs authors: Bálint, Ádám; Farsang, Attila; Zádori, Zoltán; Belák, Sándor title: Comparative In Vivo Analysis of Recombinant Type II Feline Coronaviruses with Truncated and Completed ORF3 Region date: 2014-02-20 journal: PLoS One DOI: 10.1371/journal.pone.0088758 sha: doc_id: 270681 cord_uid: 6ayciihs file: cache/cord-277409-q5wx313k.json key: cord-277409-q5wx313k authors: Resende, Lucilene Aparecida; Aguiar-Soares, Rodrigo Dian de Oliveira; Gama-Ker, Henrique; Roatt, Bruno Mendes; de Mendonça, Ludmila Zanandreis; Alves, Marina Luiza Rodrigues; da Silveira-Lemos, Denise; Corrêa-Oliveira, Rodrigo; Martins-Filho, Olindo Assis; Araújo, Márcio Sobreira Silva; Fujiwara, Ricardo Toshio; Gontijo, Nelder Figueiredo; Reis, Alexandre Barbosa; Giunchetti, Rodolfo Cordeiro title: Impact of LbSapSal Vaccine in Canine Immunological and Parasitological Features before and after Leishmania chagasi-Challenge date: 2016-08-24 journal: PLoS One DOI: 10.1371/journal.pone.0161169 sha: doc_id: 277409 cord_uid: q5wx313k file: cache/cord-275058-61eof7y8.json key: cord-275058-61eof7y8 authors: Inoue, Hiroyasu; Todo, Yasuyuki title: The propagation of economic impacts through supply chains: The case of a mega-city lockdown to prevent the spread of COVID-19 date: 2020-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0239251 sha: doc_id: 275058 cord_uid: 61eof7y8 file: cache/cord-277306-r8jki3x4.json key: cord-277306-r8jki3x4 authors: Osborne, Christina; Cryan, Paul M.; O'Shea, Thomas J.; Oko, Lauren M.; Ndaluka, Christina; Calisher, Charles H.; Berglund, Andrew D.; Klavetter, Mead L.; Bowen, Richard A.; Holmes, Kathryn V.; Dominguez, Samuel R. title: Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans date: 2011-05-12 journal: PLoS One DOI: 10.1371/journal.pone.0019156 sha: doc_id: 277306 cord_uid: r8jki3x4 file: cache/cord-278224-sq7tokbx.json key: cord-278224-sq7tokbx authors: Protopopova, Alexandra; Hall, Nathaniel J.; Brown, Kelsea M.; Andrukonis, Allison S.; Hekman, Jessica P. title: Behavioral predictors of subsequent respiratory illness signs in dogs admitted to an animal shelter date: 2019-10-23 journal: PLoS One DOI: 10.1371/journal.pone.0224252 sha: doc_id: 278224 cord_uid: sq7tokbx file: cache/cord-275395-w2u7fq1g.json key: cord-275395-w2u7fq1g authors: Romero-Severson, Ethan Obie; Hengartner, Nick; Meadors, Grant; Ke, Ruian title: Change in global transmission rates of COVID-19 through May 6 2020 date: 2020-08-06 journal: PLoS One DOI: 10.1371/journal.pone.0236776 sha: doc_id: 275395 cord_uid: w2u7fq1g file: cache/cord-279259-eu80ccm6.json key: cord-279259-eu80ccm6 authors: Pandey, Aseem; Singh, Neetu; Vemula, Sai V.; Couëtil, Laurent; Katz, Jacqueline M.; Donis, Ruben; Sambhara, Suryaprakash; Mittal, Suresh K. title: Impact of Preexisting Adenovirus Vector Immunity on Immunogenicity and Protection Conferred with an Adenovirus-Based H5N1 Influenza Vaccine date: 2012-03-14 journal: PLoS One DOI: 10.1371/journal.pone.0033428 sha: doc_id: 279259 cord_uid: eu80ccm6 file: cache/cord-277548-hgmmtew3.json key: cord-277548-hgmmtew3 authors: Lou, Emil; Teoh, Deanna; Brown, Katherine; Blaes, Anne; Holtan, Shernan G.; Jewett, Patricia; Parsons, Helen; Mburu, E. Waruiru; Thomaier, Lauren; Hui, Jane Yuet Ching; Nelson, Heather H.; Vogel, Rachel I. title: Perspectives of cancer patients and their health during the COVID-19 pandemic date: 2020-10-30 journal: PLoS One DOI: 10.1371/journal.pone.0241741 sha: doc_id: 277548 cord_uid: hgmmtew3 file: cache/cord-280482-o887a7q9.json key: cord-280482-o887a7q9 authors: Xu, Suming; Wang, Xu; Wang, Yaoqin; Lutgendorf, Susan; Bradley, Catherine; Schrepf, Andrew; Kreder, Karl; O'Donnell, Michael; Luo, Yi title: Transgenic Mice Expressing MCP-1 by the Urothelium Demonstrate Bladder Hypersensitivity, Pelvic Pain and Voiding Dysfunction: A Multidisciplinary Approach to the Study of Chronic Pelvic Pain Research Network Animal Model Study date: 2016-09-29 journal: PLoS One DOI: 10.1371/journal.pone.0163829 sha: doc_id: 280482 cord_uid: o887a7q9 file: cache/cord-274268-0ucqp3uz.json key: cord-274268-0ucqp3uz authors: Chorus, Caspar; Sandorf, Erlend Dancke; Mouter, Niek title: Diabolical dilemmas of COVID-19: An empirical study into Dutch society’s trade-offs between health impacts and other effects of the lockdown date: 2020-09-16 journal: PLoS One DOI: 10.1371/journal.pone.0238683 sha: doc_id: 274268 cord_uid: 0ucqp3uz file: cache/cord-276898-ia80cy8j.json key: cord-276898-ia80cy8j authors: Yamanaka, Atsushi; Iwakiri, Akira; Yoshikawa, Tomoki; Sakai, Kouji; Singh, Harpal; Himeji, Daisuke; Kikuchi, Ikuo; Ueda, Akira; Yamamoto, Seigo; Miura, Miho; Shioyama, Yoko; Kawano, Kimiko; Nagaishi, Tokiko; Saito, Minako; Minomo, Masumi; Iwamoto, Naoyasu; Hidaka, Yoshio; Sohma, Hirotoshi; Kobayashi, Takeshi; Kanai, Yuta; Kawagishi, Takehiro; Nagata, Noriyo; Fukushi, Shuetsu; Mizutani, Tetsuya; Tani, Hideki; Taniguchi, Satoshi; Fukuma, Aiko; Shimojima, Masayuki; Kurane, Ichiro; Kageyama, Tsutomu; Odagiri, Takato; Saijo, Masayuki; Morikawa, Shigeru title: Imported Case of Acute Respiratory Tract Infection Associated with a Member of Species Nelson Bay Orthoreovirus date: 2014-03-25 journal: PLoS One DOI: 10.1371/journal.pone.0092777 sha: doc_id: 276898 cord_uid: ia80cy8j file: cache/cord-280846-bbv6f5gf.json key: cord-280846-bbv6f5gf authors: Greninger, Alexander L.; Chen, Eunice C.; Sittler, Taylor; Scheinerman, Alex; Roubinian, Nareg; Yu, Guixia; Kim, Edward; Pillai, Dylan R.; Guyard, Cyril; Mazzulli, Tony; Isa, Pavel; Arias, Carlos F.; Hackett, John; Schochetman, Gerald; Miller, Steve; Tang, Patrick; Chiu, Charles Y. title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date: 2010-10-18 journal: PLoS One DOI: 10.1371/journal.pone.0013381 sha: doc_id: 280846 cord_uid: bbv6f5gf file: cache/cord-278123-mq56em3z.json key: cord-278123-mq56em3z authors: Hasan, Mohammad Rubayet; Mirza, Faheem; Al-Hail, Hamad; Sundararaju, Sathyavathi; Xaba, Thabisile; Iqbal, Muhammad; Alhussain, Hashim; Yassine, Hadi Mohamad; Perez-Lopez, Andres; Tang, Patrick title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0236564 sha: doc_id: 278123 cord_uid: mq56em3z file: cache/cord-270647-vn4kirrx.json key: cord-270647-vn4kirrx authors: Romero-Espinoza, Jose A.; Moreno-Valencia, Yazmin; Coronel-Tellez, Rodrigo H.; Castillejos-Lopez, Manuel; Hernandez, Andres; Dominguez, Aaron; Miliar-Garcia, Angel; Barbachano-Guerrero, Arturo; Perez-Padilla, Rogelio; Alejandre-Garcia, Alejandro; Vazquez-Perez, Joel A. title: Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date: 2018-02-15 journal: PLoS One DOI: 10.1371/journal.pone.0192878 sha: doc_id: 270647 cord_uid: vn4kirrx file: cache/cord-280386-a8qr7nl6.json key: cord-280386-a8qr7nl6 authors: Pires, Sara M.; Fischer-Walker, Christa L.; Lanata, Claudio F.; Devleesschauwer, Brecht; Hall, Aron J.; Kirk, Martyn D.; Duarte, Ana S. R.; Black, Robert E.; Angulo, Frederick J. title: Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date: 2015-12-03 journal: PLoS One DOI: 10.1371/journal.pone.0142927 sha: doc_id: 280386 cord_uid: a8qr7nl6 file: cache/cord-270408-4qqyb8sd.json key: cord-270408-4qqyb8sd authors: Pane, Masdalina; Imari, Sholah; Alwi, Qomariah; Nyoman Kandun, I; Cook, Alex R.; Samaan, Gina title: Causes of Mortality for Indonesian Hajj Pilgrims: Comparison between Routine Death Certificate and Verbal Autopsy Findings date: 2013-08-21 journal: PLoS One DOI: 10.1371/journal.pone.0073243 sha: doc_id: 270408 cord_uid: 4qqyb8sd file: cache/cord-277357-lpurk7pe.json key: cord-277357-lpurk7pe authors: González-González, Everardo; Trujillo-de Santiago, Grissel; Lara-Mayorga, Itzel Montserrat; Martínez-Chapa, Sergio Omar; Alvarez, Mario Moisés title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0237418 sha: doc_id: 277357 cord_uid: lpurk7pe file: cache/cord-278099-ypov9ha3.json key: cord-278099-ypov9ha3 authors: Kumar, Surender; Subbarao, Burra L.; Kumari, Reenu; Hallan, Vipin title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 journal: PLoS One DOI: 10.1371/journal.pone.0181829 sha: doc_id: 278099 cord_uid: ypov9ha3 file: cache/cord-280471-cqypwi5d.json key: cord-280471-cqypwi5d authors: Sun, Hua-Bao; Zhang, Yi-Ming; Huang, Li-Gui; Lai, Qi-Nan; Mo, Qun; Ye, Xin-Zhou; Wang, Tao; Zhu, Zhong-Zhen; Lv, Xiao-Lin; Luo, Yan-Ji; Gao, Shi-Ding; Xu, Jin-Song; Zhu, Hao-Hao; Li, Ting; Wang, Zhan-Ke title: The changes of the peripheral CD4+ lymphocytes and inflammatory cytokines in Patients with COVID-19 date: 2020-09-25 journal: PLoS One DOI: 10.1371/journal.pone.0239532 sha: doc_id: 280471 cord_uid: cqypwi5d file: cache/cord-278018-3qemb0x3.json key: cord-278018-3qemb0x3 authors: Li, Li; Qiao, Dan; Fu, Xiaoying; Lao, Suihua; Zhang, Xianlan; Wu, Changyou title: Identification of M.tuberculosis-Specific Th1 Cells Expressing CD69 Generated in vivo in Pleural Fluid Cells from Patients with Tuberculous Pleurisy date: 2011-08-22 journal: PLoS One DOI: 10.1371/journal.pone.0023700 sha: doc_id: 278018 cord_uid: 3qemb0x3 file: cache/cord-274241-biqbsggu.json key: cord-274241-biqbsggu authors: Shaw, Timothy I.; Srivastava, Anuj; Chou, Wen-Chi; Liu, Liang; Hawkinson, Ann; Glenn, Travis C.; Adams, Rick; Schountz, Tony title: Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis) date: 2012-11-15 journal: PLoS One DOI: 10.1371/journal.pone.0048472 sha: doc_id: 274241 cord_uid: biqbsggu file: cache/cord-281815-zvs5qe8x.json key: cord-281815-zvs5qe8x authors: Subramanian, Shoba; Hardt, Markus; Choe, Youngchool; Niles, Richard K.; Johansen, Eric B.; Legac, Jennifer; Gut, Jiri; Kerr, Iain D.; Craik, Charles S.; Rosenthal, Philip J. title: Hemoglobin Cleavage Site-Specificity of the Plasmodium falciparum Cysteine Proteases Falcipain-2 and Falcipain-3 date: 2009-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0005156 sha: doc_id: 281815 cord_uid: zvs5qe8x file: cache/cord-282303-idh7io9v.json key: cord-282303-idh7io9v authors: Hassan, Md. Zakiul; Sturm-Ramirez, Katharine; Rahman, Mohammad Ziaur; Hossain, Kamal; Aleem, Mohammad Abdul; Bhuiyan, Mejbah Uddin; Islam, Md. Muzahidul; Rahman, Mahmudur; Gurley, Emily S. title: Contamination of hospital surfaces with respiratory pathogens in Bangladesh date: 2019-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0224065 sha: doc_id: 282303 cord_uid: idh7io9v file: cache/cord-276372-q1fzxt3r.json key: cord-276372-q1fzxt3r authors: Conde, Dalia A.; Colchero, Fernando; Gusset, Markus; Pearce-Kelly, Paul; Byers, Onnie; Flesness, Nate; Browne, Robert K.; Jones, Owen R. title: Zoos through the Lens of the IUCN Red List: A Global Metapopulation Approach to Support Conservation Breeding Programs date: 2013-12-11 journal: PLoS One DOI: 10.1371/journal.pone.0080311 sha: doc_id: 276372 cord_uid: q1fzxt3r file: cache/cord-281161-u896icp9.json key: cord-281161-u896icp9 authors: Wang, Jing; Tricoche, Nancy; Du, Lanying; Hunter, Meredith; Zhan, Bin; Goud, Gaddam; Didier, Elizabeth S.; Liu, Jing; Lu, Lu; Marx, Preston A.; Jiang, Shibo; Lustigman, Sara title: The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date: 2012-05-17 journal: PLoS One DOI: 10.1371/journal.pone.0037019 sha: doc_id: 281161 cord_uid: u896icp9 file: cache/cord-286708-igu984oc.json key: cord-286708-igu984oc authors: Chua, Kaw Bing; Voon, Kenny; Crameri, Gary; Tan, Hui Siu; Rosli, Juliana; McEachern, Jennifer A.; Suluraju, Sivagami; Yu, Meng; Wang, Lin-Fa title: Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date: 2008-11-25 journal: PLoS One DOI: 10.1371/journal.pone.0003803 sha: doc_id: 286708 cord_uid: igu984oc file: cache/cord-281124-4nhy35xn.json key: cord-281124-4nhy35xn authors: Soowannayan, Chumporn; Cowley, Jeff A.; Michalski, Wojtek P.; Walker, Peter J. title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date: 2011-08-03 journal: PLoS One DOI: 10.1371/journal.pone.0022156 sha: doc_id: 281124 cord_uid: 4nhy35xn file: cache/cord-286065-x0g67pnb.json key: cord-286065-x0g67pnb authors: Metzgar, David; Frinder, Mark W.; Rothman, Richard E.; Peterson, Stephen; Carroll, Karen C.; Zhang, Sean X.; Avornu, Gideon D.; Rounds, Megan A.; Carolan, Heather E.; Toleno, Donna M.; Moore, David; Hall, Thomas A.; Massire, Christian; Richmond, Gregory S.; Gutierrez, Jose R.; Sampath, Rangarajan; Ecker, David J.; Blyn, Lawrence B. title: The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date: 2016-07-06 journal: PLoS One DOI: 10.1371/journal.pone.0158186 sha: doc_id: 286065 cord_uid: x0g67pnb file: cache/cord-282202-q2q4vies.json key: cord-282202-q2q4vies authors: Banerjee, Amitava; Katsoulis, Michail; Lai, Alvina G.; Pasea, Laura; Treibel, Thomas A.; Manisty, Charlotte; Denaxas, Spiros; Quarta, Giovanni; Hemingway, Harry; Cavalcante, João L.; Noursadeghi, Mahdad; Moon, James C. title: Clinical academic research in the time of Corona: A simulation study in England and a call for action date: 2020-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0237298 sha: doc_id: 282202 cord_uid: q2q4vies file: cache/cord-284275-bqo203pf.json key: cord-284275-bqo203pf authors: Lu, Roujian; Yu, Xiaoyan; Wang, Wen; Duan, Xijie; Zhang, Linglin; Zhou, Weimin; Xu, Jin; Xu, Lingjie; Hu, Qin; Lu, Jianxin; Ruan, Li; Wang, Zhong; Tan, Wenjie title: Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays date: 2012-06-15 journal: PLoS One DOI: 10.1371/journal.pone.0038638 sha: doc_id: 284275 cord_uid: bqo203pf file: cache/cord-283976-jgae7r2q.json key: cord-283976-jgae7r2q authors: Armstrong, Melissa J.; Gamez, Noheli; Alliance, Slande; Majid, Tabassum; Taylor, Angela; Kurasz, Andrea M.; Patel, Bhavana; Smith, Glenn title: Research priorities of caregivers and individuals with dementia with Lewy bodies: An interview study date: 2020-10-07 journal: PLoS One DOI: 10.1371/journal.pone.0239279 sha: doc_id: 283976 cord_uid: jgae7r2q file: cache/cord-285546-5tjhdczt.json key: cord-285546-5tjhdczt authors: Green, Manfred S.; Peer, Victoria; Schwartz, Naama; Nitzan, Dorit title: The confounded crude case-fatality rates (CFR) for COVID-19 hide more than they reveal—a comparison of age-specific and age-adjusted CFRs between seven countries date: 2020-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0241031 sha: doc_id: 285546 cord_uid: 5tjhdczt file: cache/cord-279421-rxocrgfu.json key: cord-279421-rxocrgfu authors: Zhang, Dan; Feng, Zhishan; Zhao, Mengchuan; Wang, Hao; Wang, Le; Yang, Shuo; Li, Guixia; Lu, Li; Ma, Xuejun title: Clinical Evaluation of a Single-Tube Multiple RT-PCR Assay for the Detection of 13 Common Virus Types/Subtypes Associated with Acute Respiratory Infection date: 2016-04-04 journal: PLoS One DOI: 10.1371/journal.pone.0152702 sha: doc_id: 279421 cord_uid: rxocrgfu file: cache/cord-287739-58fth3xl.json key: cord-287739-58fth3xl authors: Huang, Yhu-Chering; Lien, Rey-In; Su, Lin-Hui; Chou, Yi-Hong; Lin, Tzou-Yien title: Successful Control of Methicillin-Resistant Staphylococcus aureus in Endemic Neonatal Intensive Care Units—A 7-Year Campaign date: 2011-08-12 journal: PLoS One DOI: 10.1371/journal.pone.0023001 sha: doc_id: 287739 cord_uid: 58fth3xl file: cache/cord-281364-syg0wo77.json key: cord-281364-syg0wo77 authors: Caì, Yíngyún; Yú, Shuǐqìng; Postnikova, Elena N.; Mazur, Steven; Bernbaum, John G.; Burk, Robin; Zhāng, Téngfēi; Radoshitzky, Sheli R.; Müller, Marcel A.; Jordan, Ingo; Bollinger, Laura; Hensley, Lisa E.; Jahrling, Peter B.; Kuhn, Jens H. title: CD26/DPP4 Cell-Surface Expression in Bat Cells Correlates with Bat Cell Susceptibility to Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection and Evolution of Persistent Infection date: 2014-11-19 journal: PLoS One DOI: 10.1371/journal.pone.0112060 sha: doc_id: 281364 cord_uid: syg0wo77 file: cache/cord-282668-bs634hti.json key: cord-282668-bs634hti authors: Niang, Mbayame Ndiaye; Diop, Ndeye Sokhna; Fall, Amary; Kiori, Davy E.; Sarr, Fatoumata Diene; Sy, Sara; Goudiaby, Déborah; Barry, Mamadou Aliou; Fall, Malick; Dia, Ndongo title: Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date: 2017-03-22 journal: PLoS One DOI: 10.1371/journal.pone.0174287 sha: doc_id: 282668 cord_uid: bs634hti file: cache/cord-284501-5i0w74q4.json key: cord-284501-5i0w74q4 authors: Armesto, Maria; Cavanagh, Dave; Britton, Paul title: The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date: 2009-10-09 journal: PLoS One DOI: 10.1371/journal.pone.0007384 sha: doc_id: 284501 cord_uid: 5i0w74q4 file: cache/cord-281665-6n7aq4k9.json key: cord-281665-6n7aq4k9 authors: Qiu, Sangsang; Pan, Hongqiu; Zhang, Simin; Peng, Xianzhen; Zheng, Xianzhi; Xu, Guisheng; Wang, Min; Wang, Jianming; Lu, Hui title: Is Tuberculosis Treatment Really Free in China? A Study Comparing Two Areas with Different Management Models date: 2015-05-20 journal: PLoS One DOI: 10.1371/journal.pone.0126770 sha: doc_id: 281665 cord_uid: 6n7aq4k9 file: cache/cord-284016-zb6cv8ik.json key: cord-284016-zb6cv8ik authors: Li, Wei; Liu, Yan; Mukhtar, Muhammad Mahmood; Gong, Rui; Pan, Ying; Rasool, Sahibzada T.; Gao, Yecheng; Kang, Lei; Hao, Qian; Peng, Guiqing; Chen, Yanni; Chen, Xin; Wu, Jianguo; Zhu, Ying title: Activation of Interleukin-32 Pro-Inflammatory Pathway in Response to Influenza A Virus Infection date: 2008-04-16 journal: PLoS One DOI: 10.1371/journal.pone.0001985 sha: doc_id: 284016 cord_uid: zb6cv8ik file: cache/cord-286837-j2sqs20q.json key: cord-286837-j2sqs20q authors: Koetsier, Antonie; van Asten, Liselotte; Dijkstra, Frederika; van der Hoek, Wim; Snijders, Bianca E.; van den Wijngaard, Cees C.; Boshuizen, Hendriek C.; Donker, Gé A.; de Lange, Dylan W.; de Keizer, Nicolette F.; Peek, Niels title: Do Intensive Care Data on Respiratory Infections Reflect Influenza Epidemics? date: 2013-12-31 journal: PLoS One DOI: 10.1371/journal.pone.0083854 sha: doc_id: 286837 cord_uid: j2sqs20q file: cache/cord-287784-f7usy52w.json key: cord-287784-f7usy52w authors: Maestre, Ana M.; Garzón, Ana; Rodríguez, Dolores title: Equine Torovirus (BEV) Induces Caspase-Mediated Apoptosis in Infected Cells date: 2011-06-15 journal: PLoS One DOI: 10.1371/journal.pone.0020972 sha: doc_id: 287784 cord_uid: f7usy52w file: cache/cord-289305-mfjyjjer.json key: cord-289305-mfjyjjer authors: Lee, Min Hye; Lee, Gyeoung Ah; Lee, Seong Hyeon; Park, Yeon-Hwan title: A systematic review on the causes of the transmission and control measures of outbreaks in long-term care facilities: Back to basics of infection control date: 2020-03-10 journal: PLoS One DOI: 10.1371/journal.pone.0229911 sha: doc_id: 289305 cord_uid: mfjyjjer file: cache/cord-287761-73qgx58i.json key: cord-287761-73qgx58i authors: Aly, Mahmoud; Elrobh, Mohamed; Alzayer, Maha; Aljuhani, Sameera; Balkhy, Hanan title: Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update date: 2017-10-13 journal: PLoS One DOI: 10.1371/journal.pone.0183850 sha: doc_id: 287761 cord_uid: 73qgx58i file: cache/cord-285433-ehnu83qe.json key: cord-285433-ehnu83qe authors: Sun, Hongliu; Qi, Cai; Niu, Yu; Kang, Tengfei; Wei, Yongxin; Jin, Gang; Dong, Xianzhi; Wang, Chunhua; Zhu, Wei title: Detection of Cytomegalovirus Antibodies Using a Biosensor Based on Imaging Ellipsometry date: 2015-08-21 journal: PLoS One DOI: 10.1371/journal.pone.0136253 sha: doc_id: 285433 cord_uid: ehnu83qe file: cache/cord-283604-fqc9jp0l.json key: cord-283604-fqc9jp0l authors: Chen, Meng; Zhu, Zhen; Huang, Fang; Liu, Donglei; Zhang, Tiegang; Ying, Deng; Wu, Jiang; Xu, Wenbo title: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date: 2015-03-27 journal: PLoS One DOI: 10.1371/journal.pone.0121375 sha: doc_id: 283604 cord_uid: fqc9jp0l file: cache/cord-286613-cmtsu73g.json key: cord-286613-cmtsu73g authors: Lee, Sung Woo; Yu, Mi-yeon; Lee, Hajeong; Ahn, Shin Young; Kim, Sejoong; Chin, Ho Jun; Na, Ki Young title: Risk Factors for Acute Kidney Injury and In-Hospital Mortality in Patients Receiving Extracorporeal Membrane Oxygenation date: 2015-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0140674 sha: doc_id: 286613 cord_uid: cmtsu73g file: cache/cord-289555-1z4vbldd.json key: cord-289555-1z4vbldd authors: Mühldorfer, Kristin; Speck, Stephanie; Kurth, Andreas; Lesnik, René; Freuling, Conrad; Müller, Thomas; Kramer-Schadt, Stephanie; Wibbelt, Gudrun title: Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates date: 2011-12-28 journal: PLoS One DOI: 10.1371/journal.pone.0029773 sha: doc_id: 289555 cord_uid: 1z4vbldd file: cache/cord-286404-eggkqq3b.json key: cord-286404-eggkqq3b authors: Strayer, David R.; Young, Diane; Mitchell, William M. title: Effect of disease duration in a randomized Phase III trial of rintatolimod, an immune modulator for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0240403 sha: doc_id: 286404 cord_uid: eggkqq3b file: cache/cord-288440-w7g2agaf.json key: cord-288440-w7g2agaf authors: Jia, Rui; Ding, Shilei; Pan, Qinghua; Liu, Shan-Lu; Qiao, Wentao; Liang, Chen title: The C-Terminal Sequence of IFITM1 Regulates Its Anti-HIV-1 Activity date: 2015-03-04 journal: PLoS One DOI: 10.1371/journal.pone.0118794 sha: doc_id: 288440 cord_uid: w7g2agaf file: cache/cord-289285-aof7xy13.json key: cord-289285-aof7xy13 authors: Michaelis, Martin; Geiler, Janina; Naczk, Patrizia; Sithisarn, Patchima; Leutz, Anke; Doerr, Hans Wilhelm; Cinatl, Jindrich title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression date: 2011-05-17 journal: PLoS One DOI: 10.1371/journal.pone.0019705 sha: doc_id: 289285 cord_uid: aof7xy13 file: cache/cord-290773-kgb8r561.json key: cord-290773-kgb8r561 authors: Ahn, Jong Gyun; Kim, Dong Soo; Kim, Ki Hwan title: Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus date: 2018-07-03 journal: PLoS One DOI: 10.1371/journal.pone.0198624 sha: doc_id: 290773 cord_uid: kgb8r561 file: cache/cord-289093-si8btsab.json key: cord-289093-si8btsab authors: Beard, Philippa M.; Griffiths, Samantha J.; Gonzalez, Orland; Haga, Ismar R.; Pechenick Jowers, Tali; Reynolds, Danielle K.; Wildenhain, Jan; Tekotte, Hille; Auer, Manfred; Tyers, Mike; Ghazal, Peter; Zimmer, Ralf; Haas, Jürgen title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 journal: PLoS One DOI: 10.1371/journal.pone.0098431 sha: doc_id: 289093 cord_uid: si8btsab file: cache/cord-289873-6hivjqof.json key: cord-289873-6hivjqof authors: Lu, Rui; Huang, Tianhui; Hu, Haiqing; Liu, Xiao-Ping title: Patients with mild and general COVID-19 should be negative for at least 3 consecutive nucleic acid tests before discharged date: 2020-10-02 journal: PLoS One DOI: 10.1371/journal.pone.0240081 sha: doc_id: 289873 cord_uid: 6hivjqof file: cache/cord-290446-43h1r4pm.json key: cord-290446-43h1r4pm authors: Vazquez, Leonardo; e Lima, Luis Mauricio Trambaioli da Rocha; Almeida, Marcius da Silva title: Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus date: 2017-07-27 journal: PLoS One DOI: 10.1371/journal.pone.0182132 sha: doc_id: 290446 cord_uid: 43h1r4pm file: cache/cord-289017-vwye3pk9.json key: cord-289017-vwye3pk9 authors: Comach, Guillermo; Teneza-Mora, Nimfa; Kochel, Tadeusz J.; Espino, Carlos; Sierra, Gloria; Camacho, Daria E.; Laguna-Torres, V. Alberto; Garcia, Josefina; Chauca, Gloria; Gamero, Maria E.; Sovero, Merly; Bordones, Slave; Villalobos, Iris; Melchor, Angel; Halsey, Eric S. title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0044511 sha: doc_id: 289017 cord_uid: vwye3pk9 file: cache/cord-288502-qqg41daz.json key: cord-288502-qqg41daz authors: Martini, Katharina; Blüthgen, Christian; Walter, Joan Elias; Nguyen-Kim, Thi Dan Linh; Thienemann, Friedrich; Frauenfelder, Thomas title: Patterns of organizing pneumonia and microinfarcts as surrogate for endothelial disruption and microangiopathic thromboembolic events in patients with coronavirus disease 2019 date: 2020-10-05 journal: PLoS One DOI: 10.1371/journal.pone.0240078 sha: doc_id: 288502 cord_uid: qqg41daz file: cache/cord-291756-ejh1r8h4.json key: cord-291756-ejh1r8h4 authors: Pérez-Fuentes, María del Carmen; Molero Jurado, María del Mar; Martos Martínez, África; Gázquez Linares, Jose Jesús title: Threat of COVID-19 and emotional state during quarantine: Positive and negative affect as mediators in a cross-sectional study of the Spanish population date: 2020-06-25 journal: PLoS One DOI: 10.1371/journal.pone.0235305 sha: doc_id: 291756 cord_uid: ejh1r8h4 file: cache/cord-282194-0sjmf1yn.json key: cord-282194-0sjmf1yn authors: Cherak, Stephana J.; Rosgen, Brianna K.; Amarbayan, Mungunzul; Plotnikoff, Kara; Wollny, Krista; Stelfox, Henry T.; Fiest, Kirsten M. title: Impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit: A scoping review date: 2020-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0238803 sha: doc_id: 282194 cord_uid: 0sjmf1yn file: cache/cord-285749-0ejhd9nw.json key: cord-285749-0ejhd9nw authors: Hoffmann, Markus; Krüger, Nadine; Zmora, Pawel; Wrensch, Florian; Herrler, Georg; Pöhlmann, Stefan title: The Hemagglutinin of Bat-Associated Influenza Viruses Is Activated by TMPRSS2 for pH-Dependent Entry into Bat but Not Human Cells date: 2016-03-30 journal: PLoS One DOI: 10.1371/journal.pone.0152134 sha: doc_id: 285749 cord_uid: 0ejhd9nw file: cache/cord-289510-spmknns5.json key: cord-289510-spmknns5 authors: Curado, Evaldo M. F.; Curado, Marco R. title: A discrete-time-evolution model to forecast progress of Covid-19 outbreak date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0241472 sha: doc_id: 289510 cord_uid: spmknns5 file: cache/cord-289892-yh1lioyz.json key: cord-289892-yh1lioyz authors: Bai, Bingke; Hu, Qinxue; Hu, Hui; Zhou, Peng; Shi, Zhengli; Meng, Jin; Lu, Baojing; Huang, Yi; Mao, Panyong; Wang, Hanzhong title: Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date: 2008-07-16 journal: PLoS One DOI: 10.1371/journal.pone.0002685 sha: doc_id: 289892 cord_uid: yh1lioyz file: cache/cord-290120-fd26t8ja.json key: cord-290120-fd26t8ja authors: Tan, Chew Yee; Opaskornkul, Keerati; Thanawongnuwech, Roongroje; Arshad, Siti Suri; Hassan, Latiffah; Ooi, Peck Toung title: First molecular detection and complete sequence analysis of porcine circovirus type 3 (PCV3) in Peninsular Malaysia date: 2020-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0235832 sha: doc_id: 290120 cord_uid: fd26t8ja file: cache/cord-290833-m0wodqr3.json key: cord-290833-m0wodqr3 authors: Yuan, Lvfeng; Zhang, Shuai; Peng, Jie; Li, Yuchen; Yang, Qian title: Synthetic surfactin analogues have improved anti-PEDV properties date: 2019-04-11 journal: PLoS One DOI: 10.1371/journal.pone.0215227 sha: doc_id: 290833 cord_uid: m0wodqr3 file: cache/cord-290034-4b0mshqa.json key: cord-290034-4b0mshqa authors: Le, Yen H.; Nguyen, Khanh C.; Coleman, Kristen K.; Nguyen, Tham T.; Than, Son T.; Phan, Hai H.; Nguyen, Manh D.; Ngu, Nghia D.; Phan, Dan T.; Hoang, Phuong V. M.; Trieu, Long P.; Bailey, Emily S.; Warkentien, Tyler E.; Gray, Gregory C. title: Virus detections among patients with severe acute respiratory illness, Northern Vietnam date: 2020-05-12 journal: PLoS One DOI: 10.1371/journal.pone.0233117 sha: doc_id: 290034 cord_uid: 4b0mshqa file: cache/cord-290539-8ak2tths.json key: cord-290539-8ak2tths authors: Cagno, Valeria; Tintori, Cristina; Civra, Andrea; Cavalli, Roberta; Tiberi, Marika; Botta, Lorenzo; Brai, Annalaura; Poli, Giulio; Tapparel, Caroline; Lembo, David; Botta, Maurizio title: Novel broad spectrum virucidal molecules against enveloped viruses date: 2018-12-07 journal: PLoS One DOI: 10.1371/journal.pone.0208333 sha: doc_id: 290539 cord_uid: 8ak2tths file: cache/cord-292237-45hi4iz2.json key: cord-292237-45hi4iz2 authors: Calvo-Pinilla, Eva; Rodríguez-Calvo, Teresa; Anguita, Juan; Sevilla, Noemí; Ortego, Javier title: Establishment of a Bluetongue Virus Infection Model in Mice that Are Deficient in the Alpha/Beta Interferon Receptor date: 2009-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0005171 sha: doc_id: 292237 cord_uid: 45hi4iz2 file: cache/cord-291417-p49ukyhx.json key: cord-291417-p49ukyhx authors: Mikulska, Malgorzata; Nicolini, Laura Ambra; Signori, Alessio; Di Biagio, Antonio; Sepulcri, Chiara; Russo, Chiara; Dettori, Silvia; Berruti, Marco; Sormani, Maria Pia; Giacobbe, Daniele Roberto; Vena, Antonio; De Maria, Andrea; Dentone, Chiara; Taramasso, Lucia; Mirabella, Michele; Magnasco, Laura; Mora, Sara; Delfino, Emanuele; Toscanini, Federica; Balletto, Elisa; Alessandrini, Anna Ida; Baldi, Federico; Briano, Federica; Camera, Marco; Dodi, Ferdinando; Ferrazin, Antonio; Labate, Laura; Mazzarello, Giovanni; Pincino, Rachele; Portunato, Federica; Tutino, Stefania; Barisione, Emanuela; Bruzzone, Bianca; Orsi, Andrea; Schenone, Eva; Rosseti, Nirmala; Sasso, Elisabetta; Da Rin, Giorgio; Pelosi, Paolo; Beltramini, Sabrina; Giacomini, Mauro; Icardi, Giancarlo; Gratarola, Angelo; Bassetti, Matteo title: Tocilizumab and steroid treatment in patients with COVID-19 pneumonia date: 2020-08-20 journal: PLoS One DOI: 10.1371/journal.pone.0237831 sha: doc_id: 291417 cord_uid: p49ukyhx file: cache/cord-293794-vudufao5.json key: cord-293794-vudufao5 authors: Cuthbertson, Leah; Oo, Stephen W. C.; Cox, Michael J.; Khoo, Siew-Kim; Cox, Des W.; Chidlow, Glenys; Franks, Kimberley; Prastanti, Franciska; Borland, Meredith L.; Gern, James E.; Smith, David W.; Bizzintino, Joelene A.; Laing, Ingrid A.; Le Souëf, Peter N.; Moffatt, Miriam F.; Cookson, William O. C. title: Viral respiratory infections and the oropharyngeal bacterial microbiota in acutely wheezing children date: 2019-10-17 journal: PLoS One DOI: 10.1371/journal.pone.0223990 sha: doc_id: 293794 cord_uid: vudufao5 file: cache/cord-293072-giakcaki.json key: cord-293072-giakcaki authors: Xu, Wan-Xiang; Wang, Jian; Tang, Hai-Ping; Chen, Ling-Han; Lian, Wen-Bo; Zhan, Jian-Min; Gupta, Satish K.; Ji, Chao-Neng; Gu, Shao-Hua; Xie, Yi title: A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping date: 2017-10-12 journal: PLoS One DOI: 10.1371/journal.pone.0186097 sha: doc_id: 293072 cord_uid: giakcaki file: cache/cord-291360-z19ri377.json key: cord-291360-z19ri377 authors: Lan, Fan-Yun; Filler, Robert; Mathew, Soni; Buley, Jane; Iliaki, Eirini; Bruno-Murtha, Lou Ann; Osgood, Rebecca; Christophi, Costas A.; Fernandez-Montero, Alejandro; Kales, Stefanos N. title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 journal: PLoS One DOI: 10.1371/journal.pone.0235460 sha: doc_id: 291360 cord_uid: z19ri377 file: cache/cord-291176-evb6yt0r.json key: cord-291176-evb6yt0r authors: Giorgi Rossi, Paolo; Marino, Massimiliano; Formisano, Debora; Venturelli, Francesco; Vicentini, Massimo; Grilli, Roberto title: Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date: 2020-08-27 journal: PLoS One DOI: 10.1371/journal.pone.0238281 sha: doc_id: 291176 cord_uid: evb6yt0r file: cache/cord-292396-8w06oc5i.json key: cord-292396-8w06oc5i authors: Leger, Thomas; Jacquier, Alexis; Barral, Pierre-Antoine; Castelli, Maxime; Finance, Julie; Lagier, Jean-Christophe; Million, Matthieu; Parola, Philippe; Brouqui, Philippe; Raoult, Didier; Bartoli, Axel; Gaubert, Jean-Yves; Habert, Paul title: Low-dose chest CT for diagnosing and assessing the extent of lung involvement of SARS-CoV-2 pneumonia using a semi quantitative score date: 2020-11-03 journal: PLoS One DOI: 10.1371/journal.pone.0241407 sha: doc_id: 292396 cord_uid: 8w06oc5i file: cache/cord-292475-jrl1fowa.json key: cord-292475-jrl1fowa authors: Abry, Patrice; Pustelnik, Nelly; Roux, Stéphane; Jensen, Pablo; Flandrin, Patrick; Gribonval, Rémi; Lucas, Charles-Gérard; Guichard, Éric; Borgnat, Pierre; Garnier, Nicolas title: Spatial and temporal regularization to estimate COVID-19 reproduction number R(t): Promoting piecewise smoothness via convex optimization date: 2020-08-20 journal: PLoS One DOI: 10.1371/journal.pone.0237901 sha: doc_id: 292475 cord_uid: jrl1fowa file: cache/cord-292537-9ra4r6v6.json key: cord-292537-9ra4r6v6 authors: Liu, Fenglin; Wang, Jie; Liu, Jiawen; Li, Yue; Liu, Dagong; Tong, Junliang; Li, Zhuoqun; Yu, Dan; Fan, Yifan; Bi, Xiaohui; Zhang, Xueting; Mo, Steven title: Predicting and analyzing the COVID-19 epidemic in China: Based on SEIRD, LSTM and GWR models date: 2020-08-27 journal: PLoS One DOI: 10.1371/journal.pone.0238280 sha: doc_id: 292537 cord_uid: 9ra4r6v6 file: cache/cord-293393-kbndie8e.json key: cord-293393-kbndie8e authors: Braesch-Andersen, Sten; Beckman, Lena; Paulie, Staffan; Kumagai-Braesch, Makiko title: ApoD Mediates Binding of HDL to LDL and to Growing T24 Carcinoma date: 2014-12-16 journal: PLoS One DOI: 10.1371/journal.pone.0115180 sha: doc_id: 293393 cord_uid: kbndie8e file: cache/cord-294568-12eyo13f.json key: cord-294568-12eyo13f authors: Fernandes-Matano, Larissa; Monroy-Muñoz, Irma Eloísa; Angeles-Martínez, Javier; Sarquiz-Martinez, Brenda; Palomec-Nava, Iliana Donají; Pardavé-Alejandre, Hector Daniel; Santos Coy-Arechavaleta, Andrea; Santacruz-Tinoco, Clara Esperanza; González-Ibarra, Joaquín; González-Bonilla, Cesar Raúl; Muñoz-Medina, José Esteban title: Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date: 2017-05-03 journal: PLoS One DOI: 10.1371/journal.pone.0176298 sha: doc_id: 294568 cord_uid: 12eyo13f file: cache/cord-294768-bs6thjw2.json key: cord-294768-bs6thjw2 authors: Alonso-Fernández, Alberto; Toledo-Pons, Nuria; Cosío, Borja G.; Millán, Aina; Calvo, Néstor; Ramón, Luisa; de Mendoza, Sara Hermoso; Morell-García, Daniel; Bauça-Rossello, Josep Miquel; Núñez, Belén; Pons, Jaume; Palmer, Juan A.; Martín, Luisa; Peñaranda, María; Pou, Joan A.; Sauleda, Jaume; Sala-Llinas, Ernest title: Prevalence of pulmonary embolism in patients with COVID-19 pneumonia and high D-dimer values: A prospective study date: 2020-08-25 journal: PLoS One DOI: 10.1371/journal.pone.0238216 sha: doc_id: 294768 cord_uid: bs6thjw2 file: cache/cord-293946-4bquxdqa.json key: cord-293946-4bquxdqa authors: Huong, Nguyen Quynh; Nga, Nguyen Thi Thanh; Long, Nguyen Van; Luu, Bach Duc; Latinne, Alice; Pruvot, Mathieu; Phuong, Nguyen Thanh; Quang, Le Tin Vinh; Hung, Vo Van; Lan, Nguyen Thi; Hoa, Nguyen Thi; Minh, Phan Quang; Diep, Nguyen Thi; Tung, Nguyen; Ky, Van Dang; Roberton, Scott I.; Thuy, Hoang Bich; Long, Nguyen Van; Gilbert, Martin; Wicker, Leanne; Mazet, Jonna A. K.; Johnson, Christine Kreuder; Goldstein, Tracey; Tremeau-Bravard, Alex; Ontiveros, Victoria; Joly, Damien O.; Walzer, Chris; Fine, Amanda E.; Olson, Sarah H. title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date: 2020-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0237129 sha: doc_id: 293946 cord_uid: 4bquxdqa file: cache/cord-294645-yzh8h7zo.json key: cord-294645-yzh8h7zo authors: Freeman, David W.; Noren Hooten, Nicole; Kim, Yoonseo; Mode, Nicolle A.; Ejiogu, Ngozi; Zonderman, Alan B.; Evans, Michele K. title: Association between GDF15, poverty and mortality in urban middle-aged African American and white adults date: 2020-08-07 journal: PLoS One DOI: 10.1371/journal.pone.0237059 sha: doc_id: 294645 cord_uid: yzh8h7zo file: cache/cord-291104-6chpmgry.json key: cord-291104-6chpmgry authors: Leung, Danny T. M.; Lim, Pak-Leong; Cheung, Tak-Hong; Wong, Raymond R. Y.; Yim, So-Fan; Ng, Margaret H. L.; Tam, Frankie C. H.; Chung, Tony K. H.; Wong, Yick-Fu title: Osteopontin Fragments with Intact Thrombin-Sensitive Site Circulate in Cervical Cancer Patients date: 2016-08-05 journal: PLoS One DOI: 10.1371/journal.pone.0160412 sha: doc_id: 291104 cord_uid: 6chpmgry file: cache/cord-292777-oztmw8jo.json key: cord-292777-oztmw8jo authors: Wong, Michelle; Barqasho, Babilonia; Öhrmalm, Lars; Tolfvenstam, Thomas; Nowak, Piotr title: Microbial Translocation Contribute to Febrile Episodes in Adults with Chemotherapy-Induced Neutropenia date: 2013-07-16 journal: PLoS One DOI: 10.1371/journal.pone.0068056 sha: doc_id: 292777 cord_uid: oztmw8jo file: cache/cord-294023-knaxr7t0.json key: cord-294023-knaxr7t0 authors: Murri, Rita; Segala, Francesco Vladimiro; Del Vecchio, Pierluigi; Cingolani, Antonella; Taddei, Eleonora; Micheli, Giulia; Fantoni, Massimo title: Social media as a tool for scientific updating at the time of COVID pandemic: Results from a national survey in Italy date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0238414 sha: doc_id: 294023 cord_uid: knaxr7t0 file: cache/cord-295339-nzc47itk.json key: cord-295339-nzc47itk authors: Baker, Marissa G.; Peckham, Trevor K.; Seixas, Noah S. title: Estimating the burden of United States workers exposed to infection or disease: A key factor in containing risk of COVID-19 infection date: 2020-04-28 journal: PLoS One DOI: 10.1371/journal.pone.0232452 sha: doc_id: 295339 cord_uid: nzc47itk file: cache/cord-295352-b8kztgt8.json key: cord-295352-b8kztgt8 authors: Maksimowski, Nicholas; Williams, Vanessa R.; Scholey, James W. title: Kidney ACE2 expression: Implications for chronic kidney disease date: 2020-10-30 journal: PLoS One DOI: 10.1371/journal.pone.0241534 sha: doc_id: 295352 cord_uid: b8kztgt8 file: cache/cord-294372-pec1886j.json key: cord-294372-pec1886j authors: Greene, Dina N.; Jackson, Michael L.; Hillyard, David R.; Delgado, Julio C.; Schmidt, Robert L. title: Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240783 sha: doc_id: 294372 cord_uid: pec1886j file: cache/cord-295781-b831y105.json key: cord-295781-b831y105 authors: VanLeuven, James T.; Ridenhour, Benjamin J.; Gonzalez, Andres J.; Miller, Craig R.; Miura, Tanya A. title: Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses date: 2017-06-02 journal: PLoS One DOI: 10.1371/journal.pone.0178408 sha: doc_id: 295781 cord_uid: b831y105 file: cache/cord-294591-793ywpcd.json key: cord-294591-793ywpcd authors: Hu, Xiaoyun; Zhang, Zhidan; Li, Na; Liu, Dexin; Zhang, Li; He, Wei; Zhang, Wei; Li, Yuexia; Zhu, Cheng; Zhu, Guijun; Zhang, Lipeng; Xu, Fang; Wang, Shouhong; Cao, Xiangyuan; Zhao, Huiying; Li, Qian; Zhang, Xijing; Lin, Jiandong; Zhao, Shuangping; Li, Chen; Du, Bin title: Self-Reported Use of Personal Protective Equipment among Chinese Critical Care Clinicians during 2009 H1N1 Influenza Pandemic date: 2012-09-05 journal: PLoS One DOI: 10.1371/journal.pone.0044723 sha: doc_id: 294591 cord_uid: 793ywpcd file: cache/cord-294592-zwvr57a0.json key: cord-294592-zwvr57a0 authors: Mukherjee, Moumita; Goswami, Srikanta title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 journal: PLoS One DOI: 10.1371/journal.pone.0237559 sha: doc_id: 294592 cord_uid: zwvr57a0 file: cache/cord-296399-vvbjulm9.json key: cord-296399-vvbjulm9 authors: Brinkmann, Constantin; Hoffmann, Markus; Lübke, Anastasia; Nehlmeier, Inga; Krämer-Kühl, Annika; Winkler, Michael; Pöhlmann, Stefan title: The glycoprotein of vesicular stomatitis virus promotes release of virus-like particles from tetherin-positive cells date: 2017-12-07 journal: PLoS One DOI: 10.1371/journal.pone.0189073 sha: doc_id: 296399 cord_uid: vvbjulm9 file: cache/cord-295201-u2dola34.json key: cord-295201-u2dola34 authors: Morimoto, Konosuke; Suzuki, Motoi; Ishifuji, Tomoko; Yaegashi, Makito; Asoh, Norichika; Hamashige, Naohisa; Abe, Masahiko; Aoshima, Masahiro; Ariyoshi, Koya title: The Burden and Etiology of Community-Onset Pneumonia in the Aging Japanese Population: A Multicenter Prospective Study date: 2015-03-30 journal: PLoS One DOI: 10.1371/journal.pone.0122247 sha: doc_id: 295201 cord_uid: u2dola34 file: cache/cord-295536-dbpt4dhr.json key: cord-295536-dbpt4dhr authors: Shook, Natalie J.; Sevi, Barış; Lee, Jerin; Oosterhoff, Benjamin; Fitzgerald, Holly N. title: Disease avoidance in the time of COVID-19: The behavioral immune system is associated with concern and preventative health behaviors date: 2020-08-20 journal: PLoS One DOI: 10.1371/journal.pone.0238015 sha: doc_id: 295536 cord_uid: dbpt4dhr file: cache/cord-296487-m4xba78g.json key: cord-296487-m4xba78g authors: MacIntyre, Chandini Raina; Costantino, Valentina; Kunasekaran, Mohana Priya title: Health system capacity in Sydney, Australia in the event of a biological attack with smallpox date: 2019-06-14 journal: PLoS One DOI: 10.1371/journal.pone.0217704 sha: doc_id: 296487 cord_uid: m4xba78g file: cache/cord-296435-6dergkha.json key: cord-296435-6dergkha authors: Wang, Tiehua; Liu, Zhuang; Wang, Zhaoxi; Duan, Meili; Li, Gang; Wang, Shupeng; Li, Wenxiong; Zhu, Zhaozhong; Wei, Yongyue; Christiani, David C.; Li, Ang; Zhu, Xi title: Thrombocytopenia Is Associated with Acute Respiratory Distress Syndrome Mortality: An International Study date: 2014-04-14 journal: PLoS One DOI: 10.1371/journal.pone.0094124 sha: doc_id: 296435 cord_uid: 6dergkha file: cache/cord-299509-7xjdryoq.json key: cord-299509-7xjdryoq authors: Scholte, Florine E. M.; Tas, Ali; Martina, Byron E. E.; Cordioli, Paolo; Narayanan, Krishna; Makino, Shinji; Snijder, Eric J.; van Hemert, Martijn J. title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date: 2013-08-01 journal: PLoS One DOI: 10.1371/journal.pone.0071047 sha: doc_id: 299509 cord_uid: 7xjdryoq file: cache/cord-297835-ukrz8tlv.json key: cord-297835-ukrz8tlv authors: Leith, Douglas J.; Farrell, Stephen title: Measurement-based evaluation of Google/Apple Exposure Notification API for proximity detection in a light-rail tram date: 2020-09-30 journal: PLoS One DOI: 10.1371/journal.pone.0239943 sha: doc_id: 297835 cord_uid: ukrz8tlv file: cache/cord-294912-xl0wzi16.json key: cord-294912-xl0wzi16 authors: Alteri, Claudia; Cento, Valeria; Antonello, Maria; Colagrossi, Luna; Merli, Marco; Ughi, Nicola; Renica, Silvia; Matarazzo, Elisa; Di Ruscio, Federica; Tartaglione, Livia; Colombo, Jacopo; Grimaldi, Chiara; Carta, Stefania; Nava, Alice; Costabile, Valentino; Baiguera, Chiara; Campisi, Daniela; Fanti, Diana; Vismara, Chiara; Fumagalli, Roberto; Scaglione, Francesco; Epis, Oscar Massimiliano; Puoti, Massimo; Perno, Carlo Federico title: Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date: 2020-09-08 journal: PLoS One DOI: 10.1371/journal.pone.0236311 sha: doc_id: 294912 cord_uid: xl0wzi16 file: cache/cord-295293-ickp2n47.json key: cord-295293-ickp2n47 authors: Latsuzbaia, Ardashel; Herold, Malte; Bertemes, Jean-Paul; Mossong, Joël title: Evolving social contact patterns during the COVID-19 crisis in Luxembourg date: 2020-08-06 journal: PLoS One DOI: 10.1371/journal.pone.0237128 sha: doc_id: 295293 cord_uid: ickp2n47 file: cache/cord-298679-w0yp4u19.json key: cord-298679-w0yp4u19 authors: Iftimie, Simona; López-Azcona, Ana F.; Vicente-Miralles, Manuel; Descarrega-Reina, Ramon; Hernández-Aguilera, Anna; Riu, Francesc; Simó, Josep M.; Garrido, Pedro; Joven, Jorge; Camps, Jordi; Castro, Antoni title: Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0234452 sha: doc_id: 298679 cord_uid: w0yp4u19 file: cache/cord-299852-t0mqe7yy.json key: cord-299852-t0mqe7yy authors: Janssen, Loes H. C.; Kullberg, Marie-Louise J.; Verkuil, Bart; van Zwieten, Noa; Wever, Mirjam C. M.; van Houtum, Lisanne A. E. M.; Wentholt, Wilma G. M.; Elzinga, Bernet M. title: Does the COVID-19 pandemic impact parents’ and adolescents’ well-being? An EMA-study on daily affect and parenting date: 2020-10-16 journal: PLoS One DOI: 10.1371/journal.pone.0240962 sha: doc_id: 299852 cord_uid: t0mqe7yy file: cache/cord-296550-wkmnfph3.json key: cord-296550-wkmnfph3 authors: Hossain, Mohammad Anwar; Jahid, Md. Iqbal Kabir; Hossain, K. M Amran; Walton, Lori Maria; Uddin, Zakir; Haque, Md. Obaidul; Kabir, Md. Feroz; Arafat, S. M. Yasir; Sakel, Mohamed; Faruqui, Rafey; Hossain, Zahid title: Knowledge, attitudes, and fear of COVID-19 during the Rapid Rise Period in Bangladesh date: 2020-09-24 journal: PLoS One DOI: 10.1371/journal.pone.0239646 sha: doc_id: 296550 cord_uid: wkmnfph3 file: cache/cord-296635-8r3tm966.json key: cord-296635-8r3tm966 authors: Breed, Andrew C.; Breed, Martin F.; Meers, Joanne; Field, Hume E. title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date: 2011-12-14 journal: PLoS One DOI: 10.1371/journal.pone.0028816 sha: doc_id: 296635 cord_uid: 8r3tm966 file: cache/cord-299491-8rfm0jxh.json key: cord-299491-8rfm0jxh authors: Xiao, Shenglan; Li, Yuguo; Wong, Tze-wai; Hui, David S. C. title: Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date: 2017-07-20 journal: PLoS One DOI: 10.1371/journal.pone.0181558 sha: doc_id: 299491 cord_uid: 8rfm0jxh file: cache/cord-302200-9gekjgr0.json key: cord-302200-9gekjgr0 authors: Kilich, Eliz; Dada, Sara; Francis, Mark R.; Tazare, John; Chico, R. Matthew; Paterson, Pauline; Larson, Heidi J. title: Factors that influence vaccination decision-making among pregnant women: A systematic review and meta-analysis date: 2020-07-09 journal: PLoS One DOI: 10.1371/journal.pone.0234827 sha: doc_id: 302200 cord_uid: 9gekjgr0 file: cache/cord-295559-yc8q62z8.json key: cord-295559-yc8q62z8 authors: Qian, Zhaohui; Dominguez, Samuel R.; Holmes, Kathryn V. title: Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date: 2013-10-03 journal: PLoS One DOI: 10.1371/journal.pone.0076469 sha: doc_id: 295559 cord_uid: yc8q62z8 file: cache/cord-296691-cg463fbn.json key: cord-296691-cg463fbn authors: Wang, Ren; Xu, Sheng; Jiang, Yumei; Jiang, Jingwei; Li, Xiaodan; Liang, Lijian; He, Jia; Peng, Feng; Xia, Bing title: De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing date: 2013-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0060449 sha: doc_id: 296691 cord_uid: cg463fbn file: cache/cord-299953-sasfvcun.json key: cord-299953-sasfvcun authors: Whitehead, Ashley B. R.; Butcher, Gary D.; Walden, Heather S.; Duque, Viviana; Cruz, Marilyn; Hernandez, Jorge A. title: Burden of exposure to infectious bursal disease virus, infectious bronchitis virus, Newcastle disease virus, Mycoplasma gallisepticum, and intestinal parasites in introduced broiler chickens on the Galapagos date: 2018-09-24 journal: PLoS One DOI: 10.1371/journal.pone.0203658 sha: doc_id: 299953 cord_uid: sasfvcun file: cache/cord-302355-3se1wp8o.json key: cord-302355-3se1wp8o authors: Chen, Yi-Shiuan; Fan, Yi-Hsin; Tien, Chih-Feng; Yueh, Andrew; Chang, Ruey-Yi title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 journal: PLoS One DOI: 10.1371/journal.pone.0201250 sha: doc_id: 302355 cord_uid: 3se1wp8o file: cache/cord-301180-ndiwmnv0.json key: cord-301180-ndiwmnv0 authors: Lin, Min-Hsuan; Sivakumaran, Haran; Apolloni, Ann; Wei, Ting; Jans, David A.; Harrich, David title: Nullbasic, a Potent Anti-HIV Tat Mutant, Induces CRM1-Dependent Disruption of HIV Rev Trafficking date: 2012-12-10 journal: PLoS One DOI: 10.1371/journal.pone.0051466 sha: doc_id: 301180 cord_uid: ndiwmnv0 file: cache/cord-300859-nqklx0vn.json key: cord-300859-nqklx0vn authors: Henderson, Kelley C.; Benitez, Alvaro J.; Ratliff, Amy E.; Crabb, Donna M.; Sheppard, Edward S.; Winchell, Jonas M.; Dluhy, Richard A.; Waites, Ken B.; Atkinson, T. Prescott; Krause, Duncan C. title: Specificity and Strain-Typing Capabilities of Nanorod Array-Surface Enhanced Raman Spectroscopy for Mycoplasma pneumoniae Detection date: 2015-06-29 journal: PLoS One DOI: 10.1371/journal.pone.0131831 sha: doc_id: 300859 cord_uid: nqklx0vn file: cache/cord-304993-t4rua95e.json key: cord-304993-t4rua95e authors: Jung, Kwonil; Wang, Qiuhong; Kim, Yunjeong; Scheuer, Kelly; Zhang, Zhenwen; Shen, Quan; Chang, Kyeong-Ok; Saif, Linda J. title: The Effects of Simvastatin or Interferon-α on Infectivity of Human Norovirus Using a Gnotobiotic Pig Model for the Study of Antivirals date: 2012-07-23 journal: PLoS One DOI: 10.1371/journal.pone.0041619 sha: doc_id: 304993 cord_uid: t4rua95e file: cache/cord-298078-uqrwq5qk.json key: cord-298078-uqrwq5qk authors: Kwak, Hoyun; Park, Min Woo; Jeong, Sunjoo title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date: 2011-08-30 journal: PLoS One DOI: 10.1371/journal.pone.0024067 sha: doc_id: 298078 cord_uid: uqrwq5qk file: cache/cord-305303-82n96ukr.json key: cord-305303-82n96ukr authors: Shapira, Assaf; Shapira, Shiran; Gal-Tanamy, Meital; Zemel, Romy; Tur-Kaspa, Ran; Benhar, Itai title: Removal of Hepatitis C Virus-Infected Cells by a Zymogenized Bacterial Toxin date: 2012-02-16 journal: PLoS One DOI: 10.1371/journal.pone.0032320 sha: doc_id: 305303 cord_uid: 82n96ukr file: cache/cord-306466-y4yg42p8.json key: cord-306466-y4yg42p8 authors: Nofal, Ahmed Maged; Cacciotti, Gabriella; Lee, Nick title: Who complies with COVID-19 transmission mitigation behavioral guidelines? date: 2020-10-08 journal: PLoS One DOI: 10.1371/journal.pone.0240396 sha: doc_id: 306466 cord_uid: y4yg42p8 file: cache/cord-297287-0i4nc353.json key: cord-297287-0i4nc353 authors: Braun, Benjamin; Taraktaş, Başak; Beckage, Brian; Molofsky, Jane title: Simulating phase transitions and control measures for network epidemics caused by infections with presymptomatic, asymptomatic, and symptomatic stages date: 2020-09-10 journal: PLoS One DOI: 10.1371/journal.pone.0238412 sha: doc_id: 297287 cord_uid: 0i4nc353 file: cache/cord-301811-ykpiorgo.json key: cord-301811-ykpiorgo authors: Tanaka, Takuma; Yamaguchi, Takayuki; Sakamoto, Yohei title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0241170 sha: doc_id: 301811 cord_uid: ykpiorgo file: cache/cord-302529-43pd2qsp.json key: cord-302529-43pd2qsp authors: El Moussi, Awatef; Pozo, Francisco; Ben Hadj Kacem, Mohamed Ali; Ledesma, Juan; Cuevas, Maria Teresa; Casas, Inmaculada; Slim, Amine title: Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date: 2013-09-19 journal: PLoS One DOI: 10.1371/journal.pone.0074064 sha: doc_id: 302529 cord_uid: 43pd2qsp file: cache/cord-305547-e66o5j85.json key: cord-305547-e66o5j85 authors: Bénet, Thomas; Sylla, Mariam; Messaoudi, Mélina; Sánchez Picot, Valentina; Telles, Jean-Noël; Diakite, Abdoul-Aziz; Komurian-Pradel, Florence; Endtz, Hubert; Diallo, Souleymane; Paranhos-Baccalà, Gláucia; Vanhems, Philippe title: Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study date: 2015-12-22 journal: PLoS One DOI: 10.1371/journal.pone.0145447 sha: doc_id: 305547 cord_uid: e66o5j85 file: cache/cord-298131-zolwjl9u.json key: cord-298131-zolwjl9u authors: Xiao, Shuqi; Jia, Jianyu; Mo, Delin; Wang, Qiwei; Qin, Limei; He, Zuyong; Zhao, Xiao; Huang, Yuankai; Li, Anning; Yu, Jingwei; Niu, Yuna; Liu, Xiaohong; Chen, Yaosheng title: Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing date: 2010-06-29 journal: PLoS One DOI: 10.1371/journal.pone.0011377 sha: doc_id: 298131 cord_uid: zolwjl9u file: cache/cord-303187-ny4qr2a2.json key: cord-303187-ny4qr2a2 authors: Belo, Vinícius Silva; Struchiner, Claudio José; Werneck, Guilherme Loureiro; Teixeira Neto, Rafael Gonçalves; Tonelli, Gabriel Barbosa; de Carvalho Júnior, Clóvis Gomes; Ribeiro, Renata Aparecida Nascimento; da Silva, Eduardo Sérgio title: Abundance, survival, recruitment and effectiveness of sterilization of free-roaming dogs: A capture and recapture study in Brazil date: 2017-11-01 journal: PLoS One DOI: 10.1371/journal.pone.0187233 sha: doc_id: 303187 cord_uid: ny4qr2a2 file: cache/cord-303331-xolksoy3.json key: cord-303331-xolksoy3 authors: Pourghasemi, Hamid Reza; Pouyan, Soheila; Farajzadeh, Zakariya; Sadhasivam, Nitheshnirmal; Heidari, Bahram; Babaei, Sedigheh; Tiefenbacher, John P. title: Assessment of the outbreak risk, mapping and infection behavior of COVID-19: Application of the autoregressive integrated-moving average (ARIMA) and polynomial models date: 2020-07-28 journal: PLoS One DOI: 10.1371/journal.pone.0236238 sha: doc_id: 303331 cord_uid: xolksoy3 file: cache/cord-302962-qw6s1t7j.json key: cord-302962-qw6s1t7j authors: Hause, Ben M.; Collin, Emily A.; Anderson, Joe; Hesse, Richard A.; Anderson, Gary title: Bovine Rhinitis Viruses Are Common in U.S. Cattle with Bovine Respiratory Disease date: 2015-03-19 journal: PLoS One DOI: 10.1371/journal.pone.0121998 sha: doc_id: 302962 cord_uid: qw6s1t7j file: cache/cord-303490-rixuuytu.json key: cord-303490-rixuuytu authors: Pazos, Michael A.; Kraus, Thomas A.; Muñoz-Fontela, César; Moran, Thomas M. title: Estrogen Mediates Innate and Adaptive Immune Alterations to Influenza Infection in Pregnant Mice date: 2012-07-05 journal: PLoS One DOI: 10.1371/journal.pone.0040502 sha: doc_id: 303490 cord_uid: rixuuytu file: cache/cord-306278-c4q4la5c.json key: cord-306278-c4q4la5c authors: Esposito, Susanna; Zampiero, Alberto; Bianchini, Sonia; Mori, Alessandro; Scala, Alessia; Tagliabue, Claudia; Sciarrabba, Calogero Sathya; Fossali, Emilio; Piralla, Antonio; Principi, Nicola title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 journal: PLoS One DOI: 10.1371/journal.pone.0152375 sha: doc_id: 306278 cord_uid: c4q4la5c file: cache/cord-307934-84zfabti.json key: cord-307934-84zfabti authors: Lai, Chao-Kuen; Saxena, Vikas; Tseng, Chung-Hsin; Jeng, King-Song; Kohara, Michinori; Lai, Michael M. C. title: Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date: 2014-06-06 journal: PLoS One DOI: 10.1371/journal.pone.0099022 sha: doc_id: 307934 cord_uid: 84zfabti file: cache/cord-302189-3xab3yxc.json key: cord-302189-3xab3yxc authors: Tillmann, Ramona Liza; Simon, Arne; Müller, Andreas; Schildgen, Oliver title: Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date: 2007-12-26 journal: PLoS One DOI: 10.1371/journal.pone.0001357 sha: doc_id: 302189 cord_uid: 3xab3yxc file: cache/cord-306958-8bx8kxxh.json key: cord-306958-8bx8kxxh authors: Christensen, Sarah R.; Pilling, Emily B.; Eyring, J. B.; Dickerson, Grace; Sloan, Chantel D.; Magnusson, Brianna M. title: Political and personal reactions to COVID-19 during initial weeks of social distancing in the United States date: 2020-09-24 journal: PLoS One DOI: 10.1371/journal.pone.0239693 sha: doc_id: 306958 cord_uid: 8bx8kxxh file: cache/cord-305274-mcsdem7y.json key: cord-305274-mcsdem7y authors: Beniac, Daniel R.; deVarennes, Shauna L.; Andonov, Anton; He, Runtao; Booth, Tim F. title: Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date: 2007-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0001082 sha: doc_id: 305274 cord_uid: mcsdem7y file: cache/cord-305071-4ck8nd24.json key: cord-305071-4ck8nd24 authors: Calvo, Cristina; García-García, María Luz; Sanchez-Dehesa, Rosa; Román, Cristina; Tabares, Ana; Pozo, Francisco; Casas, Inmaculada title: Eight Year Prospective Study of Adenoviruses Infections in Hospitalized Children. Comparison with Other Respiratory Viruses date: 2015-07-06 journal: PLoS One DOI: 10.1371/journal.pone.0132162 sha: doc_id: 305071 cord_uid: 4ck8nd24 file: cache/cord-305900-ht7hb2rc.json key: cord-305900-ht7hb2rc authors: van den Brand, Judith M. A.; Stittelaar, Koert J.; van Amerongen, Geert; Reperant, Leslie; de Waal, Leon; Osterhaus, Albert D. M. E.; Kuiken, Thijs title: Comparison of Temporal and Spatial Dynamics of Seasonal H3N2, Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Virus Infections in Ferrets date: 2012-08-08 journal: PLoS One DOI: 10.1371/journal.pone.0042343 sha: doc_id: 305900 cord_uid: ht7hb2rc file: cache/cord-306135-pt4jsr6d.json key: cord-306135-pt4jsr6d authors: Chan, Kamfai; Wong, Pui-Yan; Yu, Peter; Hardick, Justin; Wong, Kah-Yat; Wilson, Scott A.; Wu, Tiffany; Hui, Zoe; Gaydos, Charlotte; Wong, Season S. title: A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date: 2016-02-12 journal: PLoS One DOI: 10.1371/journal.pone.0149150 sha: doc_id: 306135 cord_uid: pt4jsr6d file: cache/cord-309621-6jj19xpr.json key: cord-309621-6jj19xpr authors: Yu, Pin; Xu, Yanfeng; Deng, Wei; Bao, Linlin; Huang, Lan; Xu, Yuhuan; Yao, Yanfeng; Qin, Chuan title: Comparative pathology of rhesus macaque and common marmoset animal models with Middle East respiratory syndrome coronavirus date: 2017-02-24 journal: PLoS One DOI: 10.1371/journal.pone.0172093 sha: doc_id: 309621 cord_uid: 6jj19xpr file: cache/cord-303845-y6ws3u6x.json key: cord-303845-y6ws3u6x authors: DeLisle, Sylvain; South, Brett; Anthony, Jill A.; Kalp, Ericka; Gundlapallli, Adi; Curriero, Frank C.; Glass, Greg E.; Samore, Matthew; Perl, Trish M. title: Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections date: 2010-10-14 journal: PLoS One DOI: 10.1371/journal.pone.0013377 sha: doc_id: 303845 cord_uid: y6ws3u6x file: cache/cord-305811-987dhnf7.json key: cord-305811-987dhnf7 authors: Cho, Che-Pei; Lin, Szu-Chieh; Chou, Ming-Yuan; Hsu, Hsiu-Ting; Chang, Kung-Yao title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date: 2013-04-29 journal: PLoS One DOI: 10.1371/journal.pone.0062283 sha: doc_id: 305811 cord_uid: 987dhnf7 file: cache/cord-308344-ao9z00t7.json key: cord-308344-ao9z00t7 authors: Diep, Nguyen Van; Norimine, Junzo; Sueyoshi, Masuo; Lan, Nguyen Thi; Yamaguchi, Ryoji title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date: 2017-01-17 journal: PLoS One DOI: 10.1371/journal.pone.0170126 sha: doc_id: 308344 cord_uid: ao9z00t7 file: cache/cord-305393-96mrxt8a.json key: cord-305393-96mrxt8a authors: Lai, Yvonne; Yi, Guanghui; Chen, Alice; Bhardwaj, Kanchan; Tragesser, Brady J.; Rodrigo A. Valverde,; Zlotnick, Adam; Mukhopadhyay, Suchetana; Ranjith-Kumar, C. T.; Kao, C. Cheng title: Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date: 2011-10-10 journal: PLoS One DOI: 10.1371/journal.pone.0025837 sha: doc_id: 305393 cord_uid: 96mrxt8a file: cache/cord-309194-jtouafgd.json key: cord-309194-jtouafgd authors: Lu, Xiao; Zhang, Mao; Qian, Anyu; Tang, Luping; Xu, Shanxiang title: Lung ultrasound score in establishing the timing of intubation in COVID-19 interstitial pneumonia: A preliminary retrospective observational study date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0238679 sha: doc_id: 309194 cord_uid: jtouafgd file: cache/cord-310438-744r7gc3.json key: cord-310438-744r7gc3 authors: Chan, Ta-Chien; Hsiao, Chuhsing Kate; Lee, Chang-Chun; Chiang, Po-Huang; Kao, Chuan-Liang; Liu, Chung-Ming; King, Chwan-Chuen title: The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date: 2010-06-25 journal: PLoS One DOI: 10.1371/journal.pone.0011317 sha: doc_id: 310438 cord_uid: 744r7gc3 file: cache/cord-311074-j3fw4dfc.json key: cord-311074-j3fw4dfc authors: Alviset, Sophie; Riller, Quentin; Aboab, Jérôme; Dilworth, Kelly; Billy, Pierre-Antoine; Lombardi, Yannis; Azzi, Mathilde; Ferreira Vargas, Luis; Laine, Laurent; Lermuzeaux, Mathilde; Mémain, Nathalie; Silva, Daniel; Tchoubou, Tona; Ushmorova, Daria; Dabbagh, Hanane; Escoda, Simon; Lefrançois, Rémi; Nardi, Annelyse; Ngima, Armand; Ioos, Vincent title: Continuous Positive Airway Pressure (CPAP) face-mask ventilation is an easy and cheap option to manage a massive influx of patients presenting acute respiratory failure during the SARS-CoV-2 outbreak: A retrospective cohort study date: 2020-10-14 journal: PLoS One DOI: 10.1371/journal.pone.0240645 sha: doc_id: 311074 cord_uid: j3fw4dfc file: cache/cord-307036-n44yml79.json key: cord-307036-n44yml79 authors: Ng, Oi-Wing; Keng, Choong-Tat; Leung, Cynthia Sau-Wai; Peiris, J. S. Malik; Poon, Leo Lit Man; Tan, Yee-Joo title: Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date: 2014-07-14 journal: PLoS One DOI: 10.1371/journal.pone.0102415 sha: doc_id: 307036 cord_uid: n44yml79 file: cache/cord-310678-33c3mp1o.json key: cord-310678-33c3mp1o authors: Morgantini, Luca A.; Naha, Ushasi; Wang, Heng; Francavilla, Simone; Acar, Ömer; Flores, Jose M.; Crivellaro, Simone; Moreira, Daniel; Abern, Michael; Eklund, Martin; Vigneswaran, Hari T.; Weine, Stevan M. title: Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0238217 sha: doc_id: 310678 cord_uid: 33c3mp1o file: cache/cord-304616-k92fa15l.json key: cord-304616-k92fa15l authors: Izes, Aaron M.; Kimble, Benjamin; Norris, Jacqueline M.; Govendir, Merran title: Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats date: 2020-08-05 journal: PLoS One DOI: 10.1371/journal.pone.0236754 sha: doc_id: 304616 cord_uid: k92fa15l file: cache/cord-308249-es948mux.json key: cord-308249-es948mux authors: Dokuka, Sofia; Valeeva, Diliara; Yudkevich, Maria title: How academic achievement spreads: The role of distinct social networks in academic performance diffusion date: 2020-07-27 journal: PLoS One DOI: 10.1371/journal.pone.0236737 sha: doc_id: 308249 cord_uid: es948mux file: cache/cord-308261-hxlebas8.json key: cord-308261-hxlebas8 authors: Broekhuis, Femke; Madsen, Emily K.; Keiwua, Kosiom; Macdonald, David W. title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date: 2019-04-03 journal: PLoS One DOI: 10.1371/journal.pone.0213910 sha: doc_id: 308261 cord_uid: hxlebas8 file: cache/cord-309010-tmfm5u5h.json key: cord-309010-tmfm5u5h authors: Dietert, Kristina; Gutbier, Birgitt; Wienhold, Sandra M.; Reppe, Katrin; Jiang, Xiaohui; Yao, Ling; Chaput, Catherine; Naujoks, Jan; Brack, Markus; Kupke, Alexandra; Peteranderl, Christin; Becker, Stephan; von Lachner, Carolin; Baal, Nelli; Slevogt, Hortense; Hocke, Andreas C.; Witzenrath, Martin; Opitz, Bastian; Herold, Susanne; Hackstein, Holger; Sander, Leif E.; Suttorp, Norbert; Gruber, Achim D. title: Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia date: 2017-11-20 journal: PLoS One DOI: 10.1371/journal.pone.0188251 sha: doc_id: 309010 cord_uid: tmfm5u5h file: cache/cord-309981-4p3ybrn1.json key: cord-309981-4p3ybrn1 authors: Dai, Ling-Ling; Wang, Xi; Jiang, Tian-Ci; Li, Peng-Fei; Wang, Yu; Wu, Shu-Jun; Jia, Liu-Qun; Liu, Meng; An, Lin; Cheng, Zhe title: Anxiety and depressive symptoms among COVID-19 patients in Jianghan Fangcang Shelter Hospital in Wuhan, China date: 2020-08-28 journal: PLoS One DOI: 10.1371/journal.pone.0238416 sha: doc_id: 309981 cord_uid: 4p3ybrn1 file: cache/cord-310061-nro623aa.json key: cord-310061-nro623aa authors: Valitutto, Marc T.; Aung, Ohnmar; Tun, Kyaw Yan Naing; Vodzak, Megan E.; Zimmerman, Dawn; Yu, Jennifer H.; Win, Ye Tun; Maw, Min Thein; Thein, Wai Zin; Win, Htay Htay; Dhanota, Jasjeet; Ontiveros, Victoria; Smith, Brett; Tremeau-Brevard, Alexandre; Goldstein, Tracey; Johnson, Christine K.; Murray, Suzan; Mazet, Jonna title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0230802 sha: doc_id: 310061 cord_uid: nro623aa file: cache/cord-310466-0lbbiq7u.json key: cord-310466-0lbbiq7u authors: Fu, Yang-chih; Wang, Da-Wei; Chuang, Jen-Hsiang title: Representative Contact Diaries for Modeling the Spread of Infectious Diseases in Taiwan date: 2012-10-03 journal: PLoS One DOI: 10.1371/journal.pone.0045113 sha: doc_id: 310466 cord_uid: 0lbbiq7u file: cache/cord-311065-ie3gty6e.json key: cord-311065-ie3gty6e authors: Gaddi, Pamela J.; Crane, Meredith J.; Kamanaka, Masahito; Flavell, Richard A.; Yap, George S.; Salazar-Mather, Thais P. title: IL-10 Mediated Regulation of Liver Inflammation during Acute Murine Cytomegalovirus Infection date: 2012-08-03 journal: PLoS One DOI: 10.1371/journal.pone.0042850 sha: doc_id: 311065 cord_uid: ie3gty6e file: cache/cord-312493-wbhji81g.json key: cord-312493-wbhji81g authors: Tay, Ee Laine; Grant, Kristina; Kirk, Martyn; Mounts, Anthony; Kelly, Heath title: Exploring a Proposed WHO Method to Determine Thresholds for Seasonal Influenza Surveillance date: 2013-10-11 journal: PLoS One DOI: 10.1371/journal.pone.0077244 sha: doc_id: 312493 cord_uid: wbhji81g file: cache/cord-310790-3ikgmiof.json key: cord-310790-3ikgmiof authors: Cherrak, Sabri Ahmed; Merzouk, Hafida; Mokhtari-Soulimane, Nassima title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240653 sha: doc_id: 310790 cord_uid: 3ikgmiof file: cache/cord-310396-jitao9k0.json key: cord-310396-jitao9k0 authors: Lei, Yu; Moore, Chris B.; Liesman, Rachael M.; O'Connor, Brian P.; Bergstralh, Daniel T.; Chen, Zhijian J.; Pickles, Raymond J.; Ting, Jenny P.-Y. title: MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date: 2009-03-07 journal: PLoS One DOI: 10.1371/journal.pone.0005466 sha: doc_id: 310396 cord_uid: jitao9k0 file: cache/cord-303034-w72oeoxq.json key: cord-303034-w72oeoxq authors: Haischer, Michael H.; Beilfuss, Rachel; Hart, Meggie Rose; Opielinski, Lauren; Wrucke, David; Zirgaitis, Gretchen; Uhrich, Toni D.; Hunter, Sandra K. title: Who is wearing a mask? Gender-, age-, and location-related differences during the COVID-19 pandemic date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240785 sha: doc_id: 303034 cord_uid: w72oeoxq file: cache/cord-307540-dr5m9pfk.json key: cord-307540-dr5m9pfk authors: Coelho, Flávio C.; Lana, Raquel M.; Cruz, Oswaldo G.; Villela, Daniel A. M.; Bastos, Leonardo S.; Pastore y Piontti, Ana; Davis, Jessica T.; Vespignani, Alessandro; Codeço, Claudia T.; Gomes, Marcelo F. C. title: Assessing the spread of COVID-19 in Brazil: Mobility, morbidity and social vulnerability date: 2020-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0238214 sha: doc_id: 307540 cord_uid: dr5m9pfk file: cache/cord-308480-t2vukbwp.json key: cord-308480-t2vukbwp authors: Liang, Zhongjie; Li, Lianchun; Wang, Yuanyuan; Chen, Limin; Kong, Xiangqian; Hong, Yao; Lan, Lefu; Zheng, Mingyue; Guang-Yang, Cai; Liu, Hong; Shen, Xu; Luo, Cheng; Li, Keqin Kathy; Chen, Kaixian; Jiang, Hualiang title: Molecular Basis of NDM-1, a New Antibiotic Resistance Determinant date: 2011-08-24 journal: PLoS One DOI: 10.1371/journal.pone.0023606 sha: doc_id: 308480 cord_uid: t2vukbwp file: cache/cord-312033-iarl77n0.json key: cord-312033-iarl77n0 authors: López Barreda, Rodrigo; Guerrero, Alonso; de la Cuadra, Juan Cristóbal; Scotoni, Manuela; Salas, Wilbaldo; Baraona, Fernando; Arancibia, Francisca; Uriarte, Polentzi title: Poverty, quality of life and psychological wellbeing in adults with congenital heart disease in Chile date: 2020-10-08 journal: PLoS One DOI: 10.1371/journal.pone.0240383 sha: doc_id: 312033 cord_uid: iarl77n0 file: cache/cord-312367-24huwt3y.json key: cord-312367-24huwt3y authors: Coelho, Camila; Gallo, Gloria; Campos, Claudia B.; Hardy, Leon; Würtele, Martin title: Biochemical screening for SARS-CoV-2 main protease inhibitors date: 2020-10-06 journal: PLoS One DOI: 10.1371/journal.pone.0240079 sha: doc_id: 312367 cord_uid: 24huwt3y file: cache/cord-308764-9z4qcoqz.json key: cord-308764-9z4qcoqz authors: Wei, Lin; Li, Shenghua; Liu, Shenggui; He, Anna; Wang, Dan; Wang, Jie; Tang, Yulian; Wu, Xianjin title: Transcriptome Analysis of Houttuynia cordata Thunb. by Illumina Paired-End RNA Sequencing and SSR Marker Discovery date: 2014-01-02 journal: PLoS One DOI: 10.1371/journal.pone.0084105 sha: doc_id: 308764 cord_uid: 9z4qcoqz file: cache/cord-312002-4qhvljpv.json key: cord-312002-4qhvljpv authors: Pacheco-Barrios, Kevin; Cardenas-Rojas, Alejandra; Giannoni-Luza, Stefano; Fregni, Felipe title: COVID-19 pandemic and Farr’s law: A global comparison and prediction of outbreak acceleration and deceleration rates date: 2020-09-17 journal: PLoS One DOI: 10.1371/journal.pone.0239175 sha: doc_id: 312002 cord_uid: 4qhvljpv file: cache/cord-311531-wezrs7gc.json key: cord-311531-wezrs7gc authors: Parčina, Marijo; Schneider, Uffe Vest; Visseaux, Benoit; Jozić, Robert; Hannet, Irene; Lisby, Jan Gorm title: Multicenter evaluation of the QIAstat Respiratory Panel—A new rapid highly multiplexed PCR based assay for diagnosis of acute respiratory tract infections date: 2020-03-12 journal: PLoS One DOI: 10.1371/journal.pone.0230183 sha: doc_id: 311531 cord_uid: wezrs7gc file: cache/cord-309471-lr68epyb.json key: cord-309471-lr68epyb authors: Xia, Jingya; Veselenak, Ronald L.; Gorder, Summer R.; Bourne, Nigel; Milligan, Gregg N. title: Virus-Specific Immune Memory at Peripheral Sites of Herpes Simplex Virus Type 2 (HSV-2) Infection in Guinea Pigs date: 2014-12-08 journal: PLoS One DOI: 10.1371/journal.pone.0114652 sha: doc_id: 309471 cord_uid: lr68epyb file: cache/cord-310947-aqau2n7q.json key: cord-310947-aqau2n7q authors: Pan, Ji'An; Peng, Xiaoxue; Gao, Yajing; Li, Zhilin; Lu, Xiaolu; Chen, Yingzhao; Ishaq, Musarat; Liu, Dan; DeDiego, Marta L.; Enjuanes, Luis; Guo, Deyin title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 journal: PLoS One DOI: 10.1371/journal.pone.0003299 sha: doc_id: 310947 cord_uid: aqau2n7q file: cache/cord-311941-0dpm35dd.json key: cord-311941-0dpm35dd authors: Jones, Bryony A.; Sauter-Louis, Carola; Henning, Joerg; Stoll, Alexander; Nielen, Mirjam; Van Schaik, Gerdien; Smolenaars, Anja; Schouten, Matthijs; den Uijl, Ingrid; Fourichon, Christine; Guatteo, Raphael; Madouasse, Aurélien; Nusinovici, Simon; Deprez, Piet; De Vliegher, Sarne; Laureyns, Jozef; Booth, Richard; Cardwell, Jackie M.; Pfeiffer, Dirk U. title: Calf-Level Factors Associated with Bovine Neonatal Pancytopenia – A Multi-Country Case-Control Study date: 2013-12-02 journal: PLoS One DOI: 10.1371/journal.pone.0080619 sha: doc_id: 311941 cord_uid: 0dpm35dd file: cache/cord-311288-6ttux2uu.json key: cord-311288-6ttux2uu authors: Luo, Chen; Li, Yuru; Chen, Anfan; Tang, Yulong title: What triggers online help-seeking retransmission during the COVID-19 period? Empirical evidence from Chinese social media date: 2020-11-03 journal: PLoS One DOI: 10.1371/journal.pone.0241465 sha: doc_id: 311288 cord_uid: 6ttux2uu file: cache/cord-312678-81gnmxbk.json key: cord-312678-81gnmxbk authors: Elayeh, Eman; Aleidi, Shereen M.; Ya’acoub, Rawan; Haddadin, Randa N. title: Before and after case reporting: A comparison of the knowledge, attitude and practices of the Jordanian population towards COVID-19 date: 2020-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0240780 sha: doc_id: 312678 cord_uid: 81gnmxbk file: cache/cord-313107-6cfenpxm.json key: cord-313107-6cfenpxm authors: Singh, Anirudh K.; Nema, Ram Kumar; Joshi, Ankur; Shankar, Prem; Nema, Shashwati; Raghuwanshi, Arun; Patankar, Chitra; Mathew, Bijina J.; Shrivas, Arti; Pandey, Ritu; Tripathi, Ranu; Biswas, Debasis; Singh, Sarman title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 journal: PLoS One DOI: 10.1371/journal.pone.0239492 sha: doc_id: 313107 cord_uid: 6cfenpxm file: cache/cord-314651-e4uaw5fy.json key: cord-314651-e4uaw5fy authors: Zhao, Guangyu; Jiang, Yuting; Qiu, Hongjie; Gao, Tongtong; Zeng, Yang; Guo, Yan; Yu, Hong; Li, Junfeng; Kou, Zhihua; Du, Lanying; Tan, Wenjie; Jiang, Shibo; Sun, Shihui; Zhou, Yusen title: Multi-Organ Damage in Human Dipeptidyl Peptidase 4 Transgenic Mice Infected with Middle East Respiratory Syndrome-Coronavirus date: 2015-12-23 journal: PLoS One DOI: 10.1371/journal.pone.0145561 sha: doc_id: 314651 cord_uid: e4uaw5fy file: cache/cord-315531-2gc2dc46.json key: cord-315531-2gc2dc46 authors: McGarvey, Peter B.; Huang, Hongzhan; Mazumder, Raja; Zhang, Jian; Chen, Yongxing; Zhang, Chengdong; Cammer, Stephen; Will, Rebecca; Odle, Margie; Sobral, Bruno; Moore, Margaret; Wu, Cathy H. title: Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets date: 2009-09-25 journal: PLoS One DOI: 10.1371/journal.pone.0007162 sha: doc_id: 315531 cord_uid: 2gc2dc46 file: cache/cord-309043-dlmx12vt.json key: cord-309043-dlmx12vt authors: von Brunn, Albrecht; Teepe, Carola; Simpson, Jeremy C.; Pepperkok, Rainer; Friedel, Caroline C.; Zimmer, Ralf; Roberts, Rhonda; Baric, Ralph; Haas, Jürgen title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0000459 sha: doc_id: 309043 cord_uid: dlmx12vt file: cache/cord-313506-6bb4q7nv.json key: cord-313506-6bb4q7nv authors: Sano, Akiko; Matsushita, Hiroaki; Wu, Hua; Jiao, Jin-An; Kasinathan, Poothappillai; Sullivan, Eddie J.; Wang, Zhongde; Kuroiwa, Yoshimi title: Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date: 2013-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0078119 sha: doc_id: 313506 cord_uid: 6bb4q7nv file: cache/cord-314908-kp2jznwb.json key: cord-314908-kp2jznwb authors: Roczniewska, Marta; Rogala, Anna; Puchalska-Kaminska, Malwina; Cieślak, Roman; Retowski, Sylwiusz title: I believe I can craft! introducing Job Crafting Self-Efficacy Scale (JCSES) date: 2020-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0237250 sha: doc_id: 314908 cord_uid: kp2jznwb file: cache/cord-315343-ywgoqlxj.json key: cord-315343-ywgoqlxj authors: Ribeiro, Haroldo V.; Sunahara, Andre S.; Sutton, Jack; Perc, Matjaž; Hanley, Quentin S. title: City size and the spreading of COVID-19 in Brazil date: 2020-09-23 journal: PLoS One DOI: 10.1371/journal.pone.0239699 sha: doc_id: 315343 cord_uid: ywgoqlxj file: cache/cord-312817-gskbu0oh.json key: cord-312817-gskbu0oh authors: Witte, Carmel; Hungerford, Laura L.; Rideout, Bruce A.; Papendick, Rebecca; Fowler, James H. title: Spatiotemporal network structure among “friends of friends” reveals contagious disease process date: 2020-08-06 journal: PLoS One DOI: 10.1371/journal.pone.0237168 sha: doc_id: 312817 cord_uid: gskbu0oh file: cache/cord-317244-4su5on6s.json key: cord-317244-4su5on6s authors: Maganga, Gael D.; Bourgarel, Mathieu; Obame Nkoghe, Judicael; N'Dilimabaka, Nadine; Drosten, Christian; Paupy, Christophe; Morand, Serge; Drexler, Jan Felix; Leroy, Eric M. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 journal: PLoS One DOI: 10.1371/journal.pone.0115588 sha: doc_id: 317244 cord_uid: 4su5on6s file: cache/cord-316319-m6uha1qn.json key: cord-316319-m6uha1qn authors: Daleno, Cristina; Piralla, Antonio; Scala, Alessia; Senatore, Laura; Principi, Nicola; Esposito, Susanna title: Phylogenetic Analysis of Human Rhinovirus Isolates Collected from Otherwise Healthy Children with Community-Acquired Pneumonia during Five Successive Years date: 2013-11-19 journal: PLoS One DOI: 10.1371/journal.pone.0080614 sha: doc_id: 316319 cord_uid: m6uha1qn file: cache/cord-318696-jheb2fnn.json key: cord-318696-jheb2fnn authors: Kesic, Matthew J.; Meyer, Megan; Bauer, Rebecca; Jaspers, Ilona title: Exposure to Ozone Modulates Human Airway Protease/Antiprotease Balance Contributing to Increased Influenza A Infection date: 2012-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0035108 sha: doc_id: 318696 cord_uid: jheb2fnn file: cache/cord-316703-8kxx3034.json key: cord-316703-8kxx3034 authors: Parera, Mariona; Martrus, Gloria; Franco, Sandra; Clotet, Bonaventura; Martinez, Miguel Angel title: Canine Hepacivirus NS3 Serine Protease Can Cleave the Human Adaptor Proteins MAVS and TRIF date: 2012-08-01 journal: PLoS One DOI: 10.1371/journal.pone.0042481 sha: doc_id: 316703 cord_uid: 8kxx3034 file: cache/cord-316047-d9cpe9yl.json key: cord-316047-d9cpe9yl authors: Gonzalez, T.; de la Rubia, M. A.; Hincz, K. P.; Comas-Lopez, M.; Subirats, Laia; Fort, Santi; Sacha, G. M. title: Influence of COVID-19 confinement on students’ performance in higher education date: 2020-10-09 journal: PLoS One DOI: 10.1371/journal.pone.0239490 sha: doc_id: 316047 cord_uid: d9cpe9yl file: cache/cord-316853-vaea6siv.json key: cord-316853-vaea6siv authors: Xie, Nanzhen; Qin, Yan; Wang, Taiwu; Zeng, Ying; Deng, Xia; Guan, Li title: Prevalence of depressive symptoms among nurses in China: A systematic review and meta-analysis date: 2020-07-07 journal: PLoS One DOI: 10.1371/journal.pone.0235448 sha: doc_id: 316853 cord_uid: vaea6siv file: cache/cord-318614-518giv0m.json key: cord-318614-518giv0m authors: Tsai, Jih-Jin; Liu, Wei-Liang; Lin, Ping-Chang; Huang, Bo-Yi; Tsai, Ching-Yi; Lee, Pei-Yu Alison; Tsai, Yun-Long; Chou, Pin-Hsing; Chung, Simon; Liu, Li-Teh; Chen, Chun-Hong title: A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos date: 2019-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0218139 sha: doc_id: 318614 cord_uid: 518giv0m file: cache/cord-317912-v2wovcqd.json key: cord-317912-v2wovcqd authors: Akmatov, Manas K.; Gatzemeier, Anja; Schughart, Klaus; Pessler, Frank title: Equivalence of Self- and Staff-Collected Nasal Swabs for the Detection of Viral Respiratory Pathogens date: 2012-11-14 journal: PLoS One DOI: 10.1371/journal.pone.0048508 sha: doc_id: 317912 cord_uid: v2wovcqd file: cache/cord-318008-4s9eoae3.json key: cord-318008-4s9eoae3 authors: Parsons Leigh, Jeanna; Fiest, Kirsten; Brundin-Mather, Rebecca; Plotnikoff, Kara; Soo, Andrea; Sypes, Emma E.; Whalen-Browne, Liam; Ahmed, Sofia B.; Burns, Karen E. A.; Fox-Robichaud, Alison; Kupsch, Shelly; Longmore, Shelly; Murthy, Srinivas; Niven, Daniel J.; Rochwerg, Bram; Stelfox, Henry T. title: A national cross-sectional survey of public perceptions of the COVID-19 pandemic: Self-reported beliefs, knowledge, and behaviors date: 2020-10-23 journal: PLoS One DOI: 10.1371/journal.pone.0241259 sha: doc_id: 318008 cord_uid: 4s9eoae3 file: cache/cord-319706-2e9jrv0s.json key: cord-319706-2e9jrv0s authors: Ebinger, Joseph E.; Achamallah, Natalie; Ji, Hongwei; Claggett, Brian L.; Sun, Nancy; Botting, Patrick; Nguyen, Trevor-Trung; Luong, Eric; Kim, Elizabeth H.; Park, Eunice; Liu, Yunxian; Rosenberry, Ryan; Matusov, Yuri; Zhao, Steven; Pedraza, Isabel; Zaman, Tanzira; Thompson, Michael; Raedschelders, Koen; Berg, Anders H.; Grein, Jonathan D.; Noble, Paul W.; Chugh, Sumeet S.; Bairey Merz, C. Noel; Marbán, Eduardo; Van Eyk, Jennifer E.; Solomon, Scott D.; Albert, Christine M.; Chen, Peter; Cheng, Susan title: Pre-existing traits associated with Covid-19 illness severity date: 2020-07-23 journal: PLoS One DOI: 10.1371/journal.pone.0236240 sha: doc_id: 319706 cord_uid: 2e9jrv0s file: cache/cord-319538-bawzonq1.json key: cord-319538-bawzonq1 authors: Krause, Martin; Douin, David J.; Tran, Timothy T.; Fernandez-Bustamante, Ana; Aftab, Muhammad; Bartels, Karsten title: Association between procalcitonin levels and duration of mechanical ventilation in COVID-19 patients date: 2020-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0239174 sha: doc_id: 319538 cord_uid: bawzonq1 file: cache/cord-317058-anvmj4li.json key: cord-317058-anvmj4li authors: Liu, Xinkui; Yue, Xinpei; Liu, Furong; Wei, Le; Chu, Yuntian; Bao, Honghong; Dong, Yichao; Cheng, Wenjie; Yang, Linpeng title: Analysis of clinical features and early warning signs in patients with severe COVID-19: A retrospective cohort study date: 2020-06-26 journal: PLoS One DOI: 10.1371/journal.pone.0235459 sha: doc_id: 317058 cord_uid: anvmj4li file: cache/cord-319845-oob2ktnz.json key: cord-319845-oob2ktnz authors: Proença-Modena, José Luiz; Gagliardi, Talita Bianca; Escremim de Paula, Flávia; Iwamoto, Marisa Akiko; Criado, Miriã Ferreira; Camara, Ataíde A.; Acrani, Gustavo Olszanski; Cintra, Otávio Augusto Leite; Cervi, Maria Célia; de Paula Arruda, Luisa Karla; Arruda, Eurico title: Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date: 2011-06-20 journal: PLoS One DOI: 10.1371/journal.pone.0021083 sha: doc_id: 319845 cord_uid: oob2ktnz file: cache/cord-321705-6a7avlro.json key: cord-321705-6a7avlro authors: Hou, Tianya; Zhang, Taiquan; Cai, Wenpeng; Song, Xiangrui; Chen, Aibin; Deng, Guanghui; Ni, Chunyan title: Social support and mental health among health care workers during Coronavirus Disease 2019 outbreak: A moderated mediation model date: 2020-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0233831 sha: doc_id: 321705 cord_uid: 6a7avlro file: cache/cord-317779-j67vb7f3.json key: cord-317779-j67vb7f3 authors: Irizarry, Kristopher J. L.; Downs, Eileen; Bryden, Randall; Clark, Jory; Griggs, Lisa; Kopulos, Renee; Boettger, Cynthia M.; Carr, Thomas J.; Keeler, Calvin L.; Collisson, Ellen; Drechsler, Yvonne title: RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes date: 2017-08-28 journal: PLoS One DOI: 10.1371/journal.pone.0179391 sha: doc_id: 317779 cord_uid: j67vb7f3 file: cache/cord-319256-7pyinx1a.json key: cord-319256-7pyinx1a authors: Jin, Xin; Duan, Yongwei; Bao, Tengfei; Gu, Junjuan; Chen, Yawen; Li, Yuanyuan; Mao, Shi; Chen, Yongfeng; Xie, Wen title: The values of coagulation function in COVID-19 patients date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0241329 sha: doc_id: 319256 cord_uid: 7pyinx1a file: cache/cord-319921-uxtydu60.json key: cord-319921-uxtydu60 authors: Meli, Marina L.; Cattori, Valentino; Martínez, Fernando; López, Guillermo; Vargas, Astrid; Simón, Miguel A.; Zorrilla, Irene; Muñoz, Alvaro; Palomares, Francisco; López-Bao, Jose V.; Pastor, Josep; Tandon, Ravi; Willi, Barbara; Hofmann-Lehmann, Regina; Lutz, Hans title: Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date: 2009-03-09 journal: PLoS One DOI: 10.1371/journal.pone.0004744 sha: doc_id: 319921 cord_uid: uxtydu60 file: cache/cord-320466-l7017jis.json key: cord-320466-l7017jis authors: Akgun, Emel; Tuzuner, Mete Bora; Sahin, Betul; Kilercik, Meltem; Kulah, Canan; Cakiroglu, Hacer Nur; Serteser, Mustafa; Unsal, Ibrahim; Baykal, Ahmet Tarik title: Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date: 2020-10-20 journal: PLoS One DOI: 10.1371/journal.pone.0240012 sha: doc_id: 320466 cord_uid: l7017jis file: cache/cord-320938-f526k9q1.json key: cord-320938-f526k9q1 authors: Chen, Hongjun; Ye, Jianqiang; Xu, Kemin; Angel, Matthew; Shao, Hongxia; Ferrero, Andrea; Sutton, Troy; Perez, Daniel R. title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 journal: PLoS One DOI: 10.1371/journal.pone.0046378 sha: doc_id: 320938 cord_uid: f526k9q1 file: cache/cord-321855-7b1c2xdh.json key: cord-321855-7b1c2xdh authors: Alshami, Alanoud; Alattas, Rabab; Anan, Hadeel; Alhalimi, Abdulbary; Alfaraj, Ahmed; Al Qahtani, Hadi title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 journal: PLoS One DOI: 10.1371/journal.pone.0241258 sha: doc_id: 321855 cord_uid: 7b1c2xdh file: cache/cord-321438-llnqzkqt.json key: cord-321438-llnqzkqt authors: Ma, Ruili; Zhang, Yanming; Liu, Haiquan; Ning, Pengbo title: Proteome Profile of Swine Testicular Cells Infected with Porcine Transmissible Gastroenteritis Coronavirus date: 2014-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0110647 sha: doc_id: 321438 cord_uid: llnqzkqt file: cache/cord-319190-esjfhztp.json key: cord-319190-esjfhztp authors: Lu, Xi; Yang, Xinyi; Li, Xue; Lu, Yun; Ren, Zhitao; Zhao, Longyin; Hu, Xinxin; Jiang, Jiandong; You, Xuefu title: In Vitro Activity of Sodium New Houttuyfonate Alone and in Combination with Oxacillin or Netilmicin against Methicillin-Resistant Staphylococcus aureus date: 2013-07-02 journal: PLoS One DOI: 10.1371/journal.pone.0068053 sha: doc_id: 319190 cord_uid: esjfhztp file: cache/cord-319675-mwy3t1ny.json key: cord-319675-mwy3t1ny authors: Gu, Li; Qu, Jiuxin; Sun, Bing; Yu, Xiaomin; Li, Hui; Cao, Bin title: Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date: 2016-08-17 journal: PLoS One DOI: 10.1371/journal.pone.0160777 sha: doc_id: 319675 cord_uid: mwy3t1ny file: cache/cord-320091-2lrqubdl.json key: cord-320091-2lrqubdl authors: Badawi, Alaa; Velummailum, Russanthy; Ryoo, Seung Gwan; Senthinathan, Arrani; Yaghoubi, Sahar; Vasileva, Denitsa; Ostermeier, Emma; Plishka, Mikayla; Soosaipillai, Marcel; Arora, Paul title: Prevalence of chronic comorbidities in dengue fever and West Nile virus: A systematic review and meta-analysis date: 2018-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0200200 sha: doc_id: 320091 cord_uid: 2lrqubdl file: cache/cord-321834-n5w88l23.json key: cord-321834-n5w88l23 authors: Huang, Cheng-Yang title: Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases date: 2015-05-19 journal: PLoS One DOI: 10.1371/journal.pone.0127634 sha: doc_id: 321834 cord_uid: n5w88l23 file: cache/cord-318845-w7q5o8wc.json key: cord-318845-w7q5o8wc authors: Pendell, Dustin L.; Marsh, Thomas L.; Coble, Keith H.; Lusk, Jayson L.; Szmania, Sara C. title: Economic Assessment of FMDv Releases from the National Bio and Agro Defense Facility date: 2015-06-26 journal: PLoS One DOI: 10.1371/journal.pone.0129134 sha: doc_id: 318845 cord_uid: w7q5o8wc file: cache/cord-322414-dpx191xh.json key: cord-322414-dpx191xh authors: Harke, Nina N.; Radtke, Jan P.; Hadaschik, Boris A.; Bach, Christian; Berger, Frank P.; Blana, Andreas; Borgmann, Hendrik; Distler, Florian A.; Edeling, Sebastian; Egner, Tobias; Engels, Christina L.; Farzat, Mahmoud; Haese, Alexander; Hein, Rainer; Kuczyk, Markus A.; Manseck, Andreas; Moritz, Rudolf; Musch, Michael; Peters, Inga; Pokupic, Sasa; Rocco, Bernardo; Schneider, Andreas; Schumann, André; Schwentner, Christian; Sighinolfi, Chiara M.; Buse, Stephan; Stolzenburg, Jens-Uwe; Truß, Michael C.; Waldner, Michael; Wülfing, Christian; Zimmermanns, Volker; Witt, Jörn H.; Wagner, Christian title: To defer or not to defer? A German longitudinal multicentric assessment of clinical practice in urology during the COVID-19 pandemic date: 2020-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0239027 sha: doc_id: 322414 cord_uid: dpx191xh file: cache/cord-323433-9km824uh.json key: cord-323433-9km824uh authors: van den Wijngaard, Cees C.; van Asten, Liselotte; van Pelt, Wilfrid; Doornbos, Gerda; Nagelkerke, Nico J. D.; Donker, Gé A.; van der Hoek, Wim; Koopmans, Marion P. G. title: Syndromic Surveillance for Local Outbreaks of Lower-Respiratory Infections: Would It Work? date: 2010-04-29 journal: PLoS One DOI: 10.1371/journal.pone.0010406 sha: doc_id: 323433 cord_uid: 9km824uh file: cache/cord-322827-h33su548.json key: cord-322827-h33su548 authors: Guan, Lili; Liu, Jin; Wu, Xia Min; Chen, Dafang; Wang, Xun; Ma, Ning; Wang, Yan; Good, Byron; Ma, Hong; Yu, Xin; Good, Mary-Jo title: Unlocking Patients with Mental Disorders Who Were in Restraints at Home: A National Follow-Up Study of China’s New Public Mental Health Initiatives date: 2015-04-07 journal: PLoS One DOI: 10.1371/journal.pone.0121425 sha: doc_id: 322827 cord_uid: h33su548 file: cache/cord-324405-6uanhe2p.json key: cord-324405-6uanhe2p authors: Burke, Rachel M.; Balter, Sharon; Barnes, Emily; Barry, Vaughn; Bartlett, Karri; Beer, Karlyn D.; Benowitz, Isaac; Biggs, Holly M.; Bruce, Hollianne; Bryant-Genevier, Jonathan; Cates, Jordan; Chatham-Stephens, Kevin; Chea, Nora; Chiou, Howard; Christiansen, Demian; Chu, Victoria T.; Clark, Shauna; Cody, Sara H.; Cohen, Max; Conners, Erin E.; Dasari, Vishal; Dawson, Patrick; DeSalvo, Traci; Donahue, Matthew; Dratch, Alissa; Duca, Lindsey; Duchin, Jeffrey; Dyal, Jonathan W.; Feldstein, Leora R.; Fenstersheib, Marty; Fischer, Marc; Fisher, Rebecca; Foo, Chelsea; Freeman-Ponder, Brandi; Fry, Alicia M.; Gant, Jessica; Gautom, Romesh; Ghinai, Isaac; Gounder, Prabhu; Grigg, Cheri T.; Gunzenhauser, Jeffrey; Hall, Aron J.; Han, George S.; Haupt, Thomas; Holshue, Michelle; Hunter, Jennifer; Ibrahim, Mireille B.; Jacobs, Max W.; Jarashow, M. Claire; Joshi, Kiran; Kamali, Talar; Kawakami, Vance; Kim, Moon; Kirking, Hannah L.; Kita-Yarbro, Amanda; Klos, Rachel; Kobayashi, Miwako; Kocharian, Anna; Lang, Misty; Layden, Jennifer; Leidman, Eva; Lindquist, Scott; Lindstrom, Stephen; Link-Gelles, Ruth; Marlow, Mariel; Mattison, Claire P.; McClung, Nancy; McPherson, Tristan D.; Mello, Lynn; Midgley, Claire M.; Novosad, Shannon; Patel, Megan T.; Pettrone, Kristen; Pillai, Satish K.; Pray, Ian W.; Reese, Heather E.; Rhodes, Heather; Robinson, Susan; Rolfes, Melissa; Routh, Janell; Rubin, Rachel; Rudman, Sarah L.; Russell, Denny; Scott, Sarah; Shetty, Varun; Smith-Jeffcoat, Sarah E.; Soda, Elizabeth A.; Spitters, Christopher; Stierman, Bryan; Sunenshine, Rebecca; Terashita, Dawn; Traub, Elizabeth; Vahey, Grace M.; Verani, Jennifer R.; Wallace, Megan; Westercamp, Matthew; Wortham, Jonathan; Xie, Amy; Yousaf, Anna; Zahn, Matthew title: Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date: 2020-09-02 journal: PLoS One DOI: 10.1371/journal.pone.0238342 sha: doc_id: 324405 cord_uid: 6uanhe2p file: cache/cord-322446-ddv86eoy.json key: cord-322446-ddv86eoy authors: Sharma, Kulbhushan; Åkerström, Sara; Sharma, Anuj Kumar; Chow, Vincent T. K.; Teow, Shumein; Abrenica, Bernard; Booth, Stephanie A.; Booth, Timothy F.; Mirazimi, Ali; Lal, Sunil K. title: SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date: 2011-05-27 journal: PLoS One DOI: 10.1371/journal.pone.0019436 sha: doc_id: 322446 cord_uid: ddv86eoy file: cache/cord-322533-adqqm0n9.json key: cord-322533-adqqm0n9 authors: Sha, Dexuan; Miao, Xin; Lan, Hai; Stewart, Kathleen; Ruan, Shiyang; Tian, Yifei; Tian, Yuyang; Yang, Chaowei title: Spatiotemporal analysis of medical resource deficiencies in the U.S. under COVID-19 pandemic date: 2020-10-14 journal: PLoS One DOI: 10.1371/journal.pone.0240348 sha: doc_id: 322533 cord_uid: adqqm0n9 file: cache/cord-323330-ghwhgkdm.json key: cord-323330-ghwhgkdm authors: Ekundayo, Temitope Cyrus; Okoh, Anthony I. title: A global bibliometric analysis of Plesiomonas-related research (1990 – 2017) date: 2018-11-29 journal: PLoS One DOI: 10.1371/journal.pone.0207655 sha: doc_id: 323330 cord_uid: ghwhgkdm file: cache/cord-324410-be2ith3z.json key: cord-324410-be2ith3z authors: Wang, Qi; Pang, Yuan-Ping title: Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry date: 2007-06-13 journal: PLoS One DOI: 10.1371/journal.pone.0000531 sha: doc_id: 324410 cord_uid: be2ith3z file: cache/cord-327199-ggomuomb.json key: cord-327199-ggomuomb authors: Moerdyk-Schauwecker, Megan; Hwang, Sun-Il; Grdzelishvili, Valery Z. title: Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date: 2014-08-08 journal: PLoS One DOI: 10.1371/journal.pone.0104688 sha: doc_id: 327199 cord_uid: ggomuomb file: cache/cord-321624-z2mntwef.json key: cord-321624-z2mntwef authors: Kowitdamrong, Ekasit; Puthanakit, Thanyawee; Jantarabenjakul, Watsamon; Prompetchara, Eakachai; Suchartlikitwong, Pintip; Putcharoen, Opass; Hirankarn, Nattiya title: Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date: 2020-10-09 journal: PLoS One DOI: 10.1371/journal.pone.0240502 sha: doc_id: 321624 cord_uid: z2mntwef file: cache/cord-325113-sou8xyld.json key: cord-325113-sou8xyld authors: Kuiper, Johannes W. P.; Baade, Timo; Kremer, Marcel; Kranaster, Ramon; Irmisch, Linda; Schuchmann, Marcus; Zander, Johannes; Marx, Andreas; Hauck, Christof R. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 journal: PLoS One DOI: 10.1371/journal.pone.0241740 sha: doc_id: 325113 cord_uid: sou8xyld file: cache/cord-326011-5rmhjbri.json key: cord-326011-5rmhjbri authors: Cui, Dawei; Feng, Luzhao; Chen, Yu; Lai, Shengjie; Zhang, Zike; Yu, Fei; Zheng, Shufa; Li, Zhongjie; Yu, Hongjie title: Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study date: 2016-11-01 journal: PLoS One DOI: 10.1371/journal.pone.0165437 sha: doc_id: 326011 cord_uid: 5rmhjbri file: cache/cord-324091-nljd2ok1.json key: cord-324091-nljd2ok1 authors: Gordon, Jennifer L.; Balsom, Ashley A. title: The psychological impact of fertility treatment suspensions during the COVID-19 pandemic date: 2020-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0239253 sha: doc_id: 324091 cord_uid: nljd2ok1 file: cache/cord-327257-doygrgrc.json key: cord-327257-doygrgrc authors: Zhu, Jocelyn; Shen, Beiyi; Abbasi, Almas; Hoshmand-Kochi, Mahsa; Li, Haifang; Duong, Tim Q. title: Deep transfer learning artificial intelligence accurately stages COVID-19 lung disease severity on portable chest radiographs date: 2020-07-28 journal: PLoS One DOI: 10.1371/journal.pone.0236621 sha: doc_id: 327257 cord_uid: doygrgrc file: cache/cord-327534-f2wvh6la.json key: cord-327534-f2wvh6la authors: Zhou, Peng; Cowled, Chris; Mansell, Ashley; Monaghan, Paul; Green, Diane; Wu, Lijun; Shi, Zhengli; Wang, Lin-Fa; Baker, Michelle L. title: IRF7 in the Australian Black Flying Fox, Pteropus alecto: Evidence for a Unique Expression Pattern and Functional Conservation date: 2014-08-06 journal: PLoS One DOI: 10.1371/journal.pone.0103875 sha: doc_id: 327534 cord_uid: f2wvh6la file: cache/cord-323185-n0rubc72.json key: cord-323185-n0rubc72 authors: Varshney, Bhavna; Agnihotram, Sudhakar; Tan, Yee-Joo; Baric, Ralph; Lal, Sunil K. title: SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date: 2012-01-12 journal: PLoS One DOI: 10.1371/journal.pone.0029542 sha: doc_id: 323185 cord_uid: n0rubc72 file: cache/cord-324359-88vy3dre.json key: cord-324359-88vy3dre authors: Kamara, Foday Mamoud; Mokuwa, Esther Yei; Richards, Paul title: How villagers in central Sierra Leone understand infection risks under threat of Covid-19 date: 2020-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0235108 sha: doc_id: 324359 cord_uid: 88vy3dre file: cache/cord-328627-cf8f71dr.json key: cord-328627-cf8f71dr authors: Jando, Julia; Camargo, Simone M. R.; Herzog, Brigitte; Verrey, François title: Expression and regulation of the neutral amino acid transporter B(0)AT1 in rat small intestine date: 2017-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0184845 sha: doc_id: 328627 cord_uid: cf8f71dr file: cache/cord-326568-twv2i3fb.json key: cord-326568-twv2i3fb authors: Bruminhent, Jackrapong; Ruangsubvilai, Nattanon; Nabhindhakara, Jeff; Ingsathit, Atiporn; Kiertiburanakul, Sasisopin title: Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date: 2020-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0239250 sha: doc_id: 326568 cord_uid: twv2i3fb file: cache/cord-331885-8zmuhebu.json key: cord-331885-8zmuhebu authors: Xu, Xiuyan title: Risk factor analysis combined with deep learning in the risk assessment of overseas investment of enterprises date: 2020-10-02 journal: PLoS One DOI: 10.1371/journal.pone.0239635 sha: doc_id: 331885 cord_uid: 8zmuhebu file: cache/cord-329223-f84gjxm1.json key: cord-329223-f84gjxm1 authors: Kouokam, Joseph Calvin; Huskens, Dana; Schols, Dominique; Johannemann, Andrew; Riedell, Shonna K.; Walter, Wendye; Walker, Janice M.; Matoba, Nobuyuki; O'Keefe, Barry R.; Palmer, Kenneth E. title: Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date: 2011-08-02 journal: PLoS One DOI: 10.1371/journal.pone.0022635 sha: doc_id: 329223 cord_uid: f84gjxm1 file: cache/cord-328633-c31xsyeo.json key: cord-328633-c31xsyeo authors: Moser, Michael J.; DiFrancesco, Robert A.; Gowda, Krishne; Klingele, Audrey J.; Sugar, Darby R.; Stocki, Stacy; Mead, David A.; Schoenfeld, Thomas W. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 journal: PLoS One DOI: 10.1371/journal.pone.0038371 sha: doc_id: 328633 cord_uid: c31xsyeo file: cache/cord-333208-tibtngy8.json key: cord-333208-tibtngy8 authors: Muñoz-Moreno, Raquel; Cuesta-Geijo, Miguel Ángel; Martínez-Romero, Carles; Barrado-Gil, Lucía; Galindo, Inmaculada; García-Sastre, Adolfo; Alonso, Covadonga title: Antiviral Role of IFITM Proteins in African Swine Fever Virus Infection date: 2016-04-26 journal: PLoS One DOI: 10.1371/journal.pone.0154366 sha: doc_id: 333208 cord_uid: tibtngy8 file: cache/cord-316287-4i1grvlr.json key: cord-316287-4i1grvlr authors: Yim, Sung Sun; Bang, Hyun Bae; Kim, Young Hwan; Lee, Yong Jae; Jeong, Gu Min; Jeong, Ki Jun title: Rapid Isolation of Antibody from a Synthetic Human Antibody Library by Repeated Fluorescence-Activated Cell Sorting (FACS) date: 2014-10-10 journal: PLoS One DOI: 10.1371/journal.pone.0108225 sha: doc_id: 316287 cord_uid: 4i1grvlr file: cache/cord-328206-iylw1bvw.json key: cord-328206-iylw1bvw authors: Yu, Daojun; Chen, Yu; Wu, Shenghai; Wang, Baohong; Tang, Yi-Wei; Li, Lanjuan title: Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date: 2012-11-09 journal: PLoS One DOI: 10.1371/journal.pone.0048972 sha: doc_id: 328206 cord_uid: iylw1bvw file: cache/cord-323133-gdg50omp.json key: cord-323133-gdg50omp authors: Buzatto, G. P.; Tamashiro, E.; Proenca-Modena, J. L.; Saturno, T. H.; Prates, M. C.; Gagliardi, T. B.; Carenzi, L. R.; Massuda, E. T.; Hyppolito, M. A.; Valera, F. C. P.; Arruda, E.; Anselmo-Lima, W. T. title: The pathogens profile in children with otitis media with effusion and adenoid hypertrophy date: 2017-02-23 journal: PLoS One DOI: 10.1371/journal.pone.0171049 sha: doc_id: 323133 cord_uid: gdg50omp file: cache/cord-330110-pamxy4av.json key: cord-330110-pamxy4av authors: Teissier, Elodie; Zandomeneghi, Giorgia; Loquet, Antoine; Lavillette, Dimitri; Lavergne, Jean-Pierre; Montserret, Roland; Cosset, François-Loïc; Böckmann, Anja; Meier, Beat H.; Penin, François; Pécheur, Eve-Isabelle title: Mechanism of Inhibition of Enveloped Virus Membrane Fusion by the Antiviral Drug Arbidol date: 2011-01-25 journal: PLoS One DOI: 10.1371/journal.pone.0015874 sha: doc_id: 330110 cord_uid: pamxy4av file: cache/cord-330749-xt4aa2ur.json key: cord-330749-xt4aa2ur authors: Schilling, Stefan; Fusco, Francesco Maria; De Iaco, Giuseppina; Bannister, Barbara; Maltezou, Helena C.; Carson, Gail; Gottschalk, Rene; Brodt, Hans-Reinhard; Brouqui, Philippe; Puro, Vincenzo; Ippolito, Giuseppe title: Isolation Facilities for Highly Infectious Diseases in Europe – A Cross-Sectional Analysis in 16 Countries date: 2014-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0100401 sha: doc_id: 330749 cord_uid: xt4aa2ur file: cache/cord-333522-zsdymkjd.json key: cord-333522-zsdymkjd authors: Gruse, Jeannine; Kanitz, Ellen; Weitzel, Joachim M.; Tuchscherer, Armin; Stefaniak, Tadeusz; Jawor, Paulina; Wolffram, Siegfried; Hammon, Harald M. title: Quercetin Feeding in Newborn Dairy Calves Cannot Compensate Colostrum Deprivation: Study on Metabolic, Antioxidative and Inflammatory Traits date: 2016-01-11 journal: PLoS One DOI: 10.1371/journal.pone.0146932 sha: doc_id: 333522 cord_uid: zsdymkjd file: cache/cord-329468-vjsurl60.json key: cord-329468-vjsurl60 authors: Okino, Cintia Hiromi; Mores, Marcos Antônio Zanella; Trevisol, Iara Maria; Coldebella, Arlei; Montassier, Hélio José; Brentano, Liana title: Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles date: 2017-02-15 journal: PLoS One DOI: 10.1371/journal.pone.0172275 sha: doc_id: 329468 cord_uid: vjsurl60 file: cache/cord-329727-h47q76y8.json key: cord-329727-h47q76y8 authors: Sisó-Almirall, Antoni; Kostov, Belchin; Mas-Heredia, Minerva; Vilanova-Rotllan, Sergi; Sequeira-Aymar, Ethel; Sans-Corrales, Mireia; Sant-Arderiu, Elisenda; Cayuelas-Redondo, Laia; Martínez-Pérez, Angela; García-Plana, Noemí; Anguita-Guimet, August; Benavent-Àreu, Jaume title: Prognostic factors in Spanish COVID-19 patients: A case series from Barcelona date: 2020-08-21 journal: PLoS One DOI: 10.1371/journal.pone.0237960 sha: doc_id: 329727 cord_uid: h47q76y8 file: cache/cord-333853-p2kbjwpy.json key: cord-333853-p2kbjwpy authors: Smee, Donald F.; Wong, Min-Hui; Russell, Andrew; Ennis, Jane; Turner, Jeffrey D. title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date: 2011-10-13 journal: PLoS One DOI: 10.1371/journal.pone.0026330 sha: doc_id: 333853 cord_uid: p2kbjwpy file: cache/cord-333955-bnzbppof.json key: cord-333955-bnzbppof authors: Biesold, Susanne E.; Ritz, Daniel; Gloza-Rausch, Florian; Wollny, Robert; Drexler, Jan Felix; Corman, Victor M.; Kalko, Elisabeth K. V.; Oppong, Samuel; Drosten, Christian; Müller, Marcel A. title: Type I Interferon Reaction to Viral Infection in Interferon-Competent, Immortalized Cell Lines from the African Fruit Bat Eidolon helvum date: 2011-11-30 journal: PLoS One DOI: 10.1371/journal.pone.0028131 sha: doc_id: 333955 cord_uid: bnzbppof file: cache/cord-334218-bkjfy66e.json key: cord-334218-bkjfy66e authors: Lin, Jung-Da; Lin, Chuen-Fu; Chung, Wen-Bin; Chiou, Ming-Tang; Lin, Chao-Nan title: Impact of Mated Female Nonproductive Days in Breeding Herd after Porcine Epidemic Diarrhea Virus Outbreak date: 2016-01-15 journal: PLoS One DOI: 10.1371/journal.pone.0147316 sha: doc_id: 334218 cord_uid: bkjfy66e file: cache/cord-334955-gnu92up6.json key: cord-334955-gnu92up6 authors: Sutton, Jeannette; Renshaw, Scott L.; Butts, Carter T. title: COVID-19: Retransmission of official communications in an emerging pandemic date: 2020-09-16 journal: PLoS One DOI: 10.1371/journal.pone.0238491 sha: doc_id: 334955 cord_uid: gnu92up6 file: cache/cord-335272-jypxi99z.json key: cord-335272-jypxi99z authors: Sharma, Anupam Joya; Subramanyam, Malavika A. title: A cross-sectional study of psychological wellbeing of Indian adults during the Covid-19 lockdown: Different strokes for different folks date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0238761 sha: doc_id: 335272 cord_uid: jypxi99z file: cache/cord-329999-flzqm3wh.json key: cord-329999-flzqm3wh authors: Buchanan, Tom title: Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date: 2020-10-07 journal: PLoS One DOI: 10.1371/journal.pone.0239666 sha: doc_id: 329999 cord_uid: flzqm3wh file: cache/cord-331652-oc5s1if2.json key: cord-331652-oc5s1if2 authors: Trudeau, Michaela P.; Verma, Harsha; Sampedro, Fernando; Urriola, Pedro E.; Shurson, Gerald C.; McKelvey, Jessica; Pillai, Suresh D.; Goyal, Sagar M. title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date: 2016-06-24 journal: PLoS One DOI: 10.1371/journal.pone.0158128 sha: doc_id: 331652 cord_uid: oc5s1if2 file: cache/cord-333413-8buawes0.json key: cord-333413-8buawes0 authors: Liebing, J.; Völker, I.; Curland, N.; Wohlsein, P.; Baumgärtner, W.; Braune, S.; Runge, M.; Moss, A.; Rautenschlein, S.; Jung, A.; Ryll, M.; Raue, K.; Strube, C.; Schulz, J.; Heffels-Redmann, U.; Fischer, L.; Gethöffer, F.; Voigt, U.; Lierz, M.; Siebert, U. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 journal: PLoS One DOI: 10.1371/journal.pone.0234044 sha: doc_id: 333413 cord_uid: 8buawes0 file: cache/cord-330537-xz0wt1sz.json key: cord-330537-xz0wt1sz authors: Biermann, Olivia; Tran, Phuong Bich; Viney, Kerri; Caws, Maxine; Lönnroth, Knut; Sidney Annerstedt, Kristi title: Active case-finding policy development, implementation and scale-up in high-burden countries: A mixed-methods survey with National Tuberculosis Programme managers and document review date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0240696 sha: doc_id: 330537 cord_uid: xz0wt1sz file: cache/cord-336364-2ust3qoq.json key: cord-336364-2ust3qoq authors: Artigas, Laura; Coma, Mireia; Matos-Filipe, Pedro; Aguirre-Plans, Joaquim; Farrés, Judith; Valls, Raquel; Fernandez-Fuentes, Narcis; de la Haba-Rodriguez, Juan; Olvera, Alex; Barbera, Jose; Morales, Rafael; Oliva, Baldo; Mas, Jose Manuel title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 journal: PLoS One DOI: 10.1371/journal.pone.0240149 sha: doc_id: 336364 cord_uid: 2ust3qoq file: cache/cord-336615-jfnj6l41.json key: cord-336615-jfnj6l41 authors: Wong, Sarah Sze Wah; Kao, Richard Yi Tsun; Yuen, Kwok Yong; Wang, Yu; Yang, Dan; Samaranayake, Lakshman Perera; Seneviratne, Chaminda Jayampath title: In Vitro and In Vivo Activity of a Novel Antifungal Small Molecule against Candida Infections date: 2014-01-22 journal: PLoS One DOI: 10.1371/journal.pone.0085836 sha: doc_id: 336615 cord_uid: jfnj6l41 file: cache/cord-335859-k37jivp6.json key: cord-335859-k37jivp6 authors: Wu, Daphne C.; Jha, Prabhat; Lam, Teresa; Brown, Patrick; Gelband, Hellen; Nagelkerke, Nico; Birnboim, H. Chaim; Reid, Angus title: Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date: 2020-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0240778 sha: doc_id: 335859 cord_uid: k37jivp6 file: cache/cord-336420-1a2u9p4t.json key: cord-336420-1a2u9p4t authors: Söderman, Martina; Rhedin, Samuel; Tolfvenstam, Thomas; Rotzén-Östlund, Maria; Albert, Jan; Broliden, Kristina; Lindblom, Anna title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date: 2016-06-16 journal: PLoS One DOI: 10.1371/journal.pone.0157398 sha: doc_id: 336420 cord_uid: 1a2u9p4t file: cache/cord-335441-bj3me7p8.json key: cord-335441-bj3me7p8 authors: Jourdain, Elsa; Gunnarsson, Gunnar; Wahlgren, John; Latorre-Margalef, Neus; Bröjer, Caroline; Sahlin, Sofie; Svensson, Lovisa; Waldenström, Jonas; Lundkvist, Åke; Olsen, Björn title: Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date: 2010-01-28 journal: PLoS One DOI: 10.1371/journal.pone.0008935 sha: doc_id: 335441 cord_uid: bj3me7p8 file: cache/cord-337795-khqx4t4q.json key: cord-337795-khqx4t4q authors: Pellecchia, Umberto; Crestani, Rosa; Decroo, Tom; Van den Bergh, Rafael; Al-Kourdi, Yasmine title: Social Consequences of Ebola Containment Measures in Liberia date: 2015-12-09 journal: PLoS One DOI: 10.1371/journal.pone.0143036 sha: doc_id: 337795 cord_uid: khqx4t4q file: cache/cord-330079-pdaowkop.json key: cord-330079-pdaowkop authors: Xu, Lin; He, Xia; Zhang, Ding-mei; Feng, Fa-shen; Wang, Zhu; Guan, Lin-lin; Wu, Jue-heng; Zhou, Rong; Zheng, Bo-jian; Yuen, Kwok-yung; Li, Meng-feng; Cao, Kai-yuan title: Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date: 2012-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0044876 sha: doc_id: 330079 cord_uid: pdaowkop file: cache/cord-335880-m8gecsf0.json key: cord-335880-m8gecsf0 authors: Peci, Adriana; Winter, Anne-Luise; Warshawsky, Bryna; Booth, Tim F.; Eshaghi, AliReza; Li, Aimin; Perusini, Stephen; Olsha, Romy; Marchand-Austin, Alex; Kristjanson, Erik; Gubbay, Jonathan B. title: Epidemiology of Enterovirus D68 in Ontario date: 2015-11-23 journal: PLoS One DOI: 10.1371/journal.pone.0142841 sha: doc_id: 335880 cord_uid: m8gecsf0 file: cache/cord-336441-m6pur6td.json key: cord-336441-m6pur6td authors: Wang, Changjian; Wu, Kangmin; Zhang, Xinlin; Wang, Fei; Zhang, Hongou; Ye, Yuyao; Wu, Qitao; Huang, Gengzhi; Wang, Yang; Wen, Bin title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date: 2019-02-11 journal: PLoS One DOI: 10.1371/journal.pone.0210430 sha: doc_id: 336441 cord_uid: m6pur6td file: cache/cord-332922-2qjae0x7.json key: cord-332922-2qjae0x7 authors: Mbuvha, Rendani; Marwala, Tshilidzi title: Bayesian inference of COVID-19 spreading rates in South Africa date: 2020-08-05 journal: PLoS One DOI: 10.1371/journal.pone.0237126 sha: doc_id: 332922 cord_uid: 2qjae0x7 file: cache/cord-335505-s013j5ex.json key: cord-335505-s013j5ex authors: Zhang, Chen; Zhu, Na; Xie, Zhengde; Lu, Roujian; He, Bin; Liu, Chunyan; Ma, Xuejun; Tan, Wenjie title: Viral Etiology and Clinical Profiles of Children with Severe Acute Respiratory Infections in China date: 2013-08-22 journal: PLoS One DOI: 10.1371/journal.pone.0072606 sha: doc_id: 335505 cord_uid: s013j5ex file: cache/cord-335404-s48psqth.json key: cord-335404-s48psqth authors: Mukandavire, Zindoga; Nyabadza, Farai; Malunguza, Noble J.; Cuadros, Diego F.; Shiri, Tinevimbo; Musuka, Godfrey title: Quantifying early COVID-19 outbreak transmission in South Africa and exploring vaccine efficacy scenarios date: 2020-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0236003 sha: doc_id: 335404 cord_uid: s48psqth file: cache/cord-333248-5342lyeu.json key: cord-333248-5342lyeu authors: Elenius, Varpu; Palomares, Oscar; Waris, Matti; Turunen, Riitta; Puhakka, Tuomo; Rückert, Beate; Vuorinen, Tytti; Allander, Tobias; Vahlberg, Tero; Akdis, Mübeccel; Camargo, Carlos A.; Akdis, Cezmi A.; Jartti, Tuomas title: The relationship of serum vitamins A, D, E and LL-37 levels with allergic status, tonsillar virus detection and immune response date: 2017-02-24 journal: PLoS One DOI: 10.1371/journal.pone.0172350 sha: doc_id: 333248 cord_uid: 5342lyeu file: cache/cord-333650-4towah1t.json key: cord-333650-4towah1t authors: Malmo, Jostein; Moe, Nina; Krokstad, Sidsel; Ryan, Liv; Loevenich, Simon; Johnsen, Ingvild B.; Espevik, Terje; Nordbø, Svein Arne; Døllner, Henrik; Anthonsen, Marit W. title: Cytokine Profiles in Human Metapneumovirus Infected Children: Identification of Genes Involved in the Antiviral Response and Pathogenesis date: 2016-05-12 journal: PLoS One DOI: 10.1371/journal.pone.0155484 sha: doc_id: 333650 cord_uid: 4towah1t file: cache/cord-338067-vjyad10p.json key: cord-338067-vjyad10p authors: Hao, Yan; Xu, Ting; Hu, Hongping; Wang, Peng; Bai, Yanping title: Prediction and analysis of Corona Virus Disease 2019 date: 2020-10-05 journal: PLoS One DOI: 10.1371/journal.pone.0239960 sha: doc_id: 338067 cord_uid: vjyad10p file: cache/cord-339026-eu11larc.json key: cord-339026-eu11larc authors: Ryals, Renee C.; Patel, Siddharth; Acosta, Chris; McKinney, Madison; Pennesi, Mark E.; Sahay, Gaurav title: The effects of PEGylation on LNP based mRNA delivery to the eye date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0241006 sha: doc_id: 339026 cord_uid: eu11larc file: cache/cord-339789-151d1j4n.json key: cord-339789-151d1j4n authors: Hong, Hyokyoung G.; Li, Yi title: Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic date: 2020-07-21 journal: PLoS One DOI: 10.1371/journal.pone.0236464 sha: doc_id: 339789 cord_uid: 151d1j4n file: cache/cord-336843-c0sr3six.json key: cord-336843-c0sr3six authors: Gerritsen, M. G.; Willemink, M. J.; Pompe, E.; van der Bruggen, T.; van Rhenen, A.; Lammers, J. W. J.; Wessels, F.; Sprengers, R. W.; de Jong, P. A.; Minnema, M. C. title: Improving early diagnosis of pulmonary infections in patients with febrile neutropenia using low-dose chest computed tomography date: 2017-02-24 journal: PLoS One DOI: 10.1371/journal.pone.0172256 sha: doc_id: 336843 cord_uid: c0sr3six file: cache/cord-339578-eg19rfvi.json key: cord-339578-eg19rfvi authors: Garcia-Garcia, Maria Luz; Calvo, Cristina; Ruiz, Sara; Pozo, Francisco; del Pozo, Victoria; Remedios, Laura; Exposito, Nadia; Tellez, Ana; Casas, Inmaculada title: Role of viral coinfections in asthma development date: 2017-12-05 journal: PLoS One DOI: 10.1371/journal.pone.0189083 sha: doc_id: 339578 cord_uid: eg19rfvi file: cache/cord-337585-kpghvb6u.json key: cord-337585-kpghvb6u authors: Moustaqim-Barrette, Amina; Papamihali, Kristi; Mamdani, Zahra; Williams, Sierra; Buxton, Jane A. title: Accessing Take-Home Naloxone in British Columbia and the role of community pharmacies: Results from the analysis of administrative data date: 2020-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0238618 sha: doc_id: 337585 cord_uid: kpghvb6u file: cache/cord-339157-wj47xeqj.json key: cord-339157-wj47xeqj authors: Zhang, Chao; Chen, Shuaiyin; Zhou, Guangyuan; Jin, Yuefei; Zhang, Rongguang; Yang, Haiyan; Xi, Yuanlin; Ren, Jingchao; Duan, Guangcai title: Involvement of the renin-angiotensin system in the progression of severe hand-foot-and-mouth disease date: 2018-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0197861 sha: doc_id: 339157 cord_uid: wj47xeqj file: cache/cord-338594-wft7yy6j.json key: cord-338594-wft7yy6j authors: Winkler, Michael; Gärtner, Sabine; Wrensch, Florian; Krawczak, Michael; Sauermann, Ulrike; Pöhlmann, Stefan title: Rhesus macaque IFITM3 gene polymorphisms and SIV infection date: 2017-03-03 journal: PLoS One DOI: 10.1371/journal.pone.0172847 sha: doc_id: 338594 cord_uid: wft7yy6j file: cache/cord-334695-cjxlw1tu.json key: cord-334695-cjxlw1tu authors: Kam, Yiu-Wing; Okumura, Yuushi; Kido, Hiroshi; Ng, Lisa F. P.; Bruzzone, Roberto; Altmeyer, Ralf title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date: 2009-11-17 journal: PLoS One DOI: 10.1371/journal.pone.0007870 sha: doc_id: 334695 cord_uid: cjxlw1tu file: cache/cord-335245-1eksm537.json key: cord-335245-1eksm537 authors: Pattyn, Els; Verhee, Annick; Uyttendaele, Isabel; Piessevaux, Julie; Timmerman, Evy; Gevaert, Kris; Vandekerckhove, Joël; Peelman, Frank; Tavernier, Jan title: HyperISGylation of Old World Monkey ISG15 in Human Cells date: 2008-06-18 journal: PLoS One DOI: 10.1371/journal.pone.0002427 sha: doc_id: 335245 cord_uid: 1eksm537 file: cache/cord-337067-j8ebslif.json key: cord-337067-j8ebslif authors: Mades, Andreas; Gotthardt, Katherina; Awe, Karin; Stieler, Jens; Döring, Tatjana; Füser, Sabine; Prange, Reinhild title: Role of Human Sec63 in Modulating the Steady-State Levels of Multi-Spanning Membrane Proteins date: 2012-11-15 journal: PLoS One DOI: 10.1371/journal.pone.0049243 sha: doc_id: 337067 cord_uid: j8ebslif file: cache/cord-339327-4422s317.json key: cord-339327-4422s317 authors: Norris, Susan L.; Sawin, Veronica Ivey; Ferri, Mauricio; Raques Sastre, Laura; Porgo, Teegwendé V. title: An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date: 2018-05-30 journal: PLoS One DOI: 10.1371/journal.pone.0198125 sha: doc_id: 339327 cord_uid: 4422s317 file: cache/cord-340027-6l55rcfm.json key: cord-340027-6l55rcfm authors: Mamode Khan, Naushad; Soobhug, Ashwinee Devi; Heenaye-Mamode Khan, Maleika title: Studying the trend of the novel coronavirus series in Mauritius and its implications date: 2020-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0235730 sha: doc_id: 340027 cord_uid: 6l55rcfm file: cache/cord-339724-roj8ksvc.json key: cord-339724-roj8ksvc authors: Lan, Jiaming; Deng, Yao; Chen, Hong; Lu, Guangwen; Wang, Wen; Guo, Xiaojuan; Lu, Zhuozhuang; Gao, George F.; Tan, Wenjie title: Tailoring Subunit Vaccine Immunity with Adjuvant Combinations and Delivery Routes Using the Middle East Respiratory Coronavirus (MERS-CoV) Receptor-Binding Domain as an Antigen date: 2014-11-18 journal: PLoS One DOI: 10.1371/journal.pone.0112602 sha: doc_id: 339724 cord_uid: roj8ksvc file: cache/cord-340763-cxnu9g8y.json key: cord-340763-cxnu9g8y authors: Grimm, Sebastian K.; Battles, Michael B.; Ackerman, Margaret E. title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date: 2015-02-17 journal: PLoS One DOI: 10.1371/journal.pone.0117227 sha: doc_id: 340763 cord_uid: cxnu9g8y file: cache/cord-337913-eu2gn4bl.json key: cord-337913-eu2gn4bl authors: Stojanov, Ana; Bering, Jesse M.; Halberstadt, Jamin title: Does Perceived Lack of Control Lead to Conspiracy Theory Beliefs? Findings from an online MTurk sample date: 2020-08-17 journal: PLoS One DOI: 10.1371/journal.pone.0237771 sha: doc_id: 337913 cord_uid: eu2gn4bl file: cache/cord-337879-liqhbqxl.json key: cord-337879-liqhbqxl authors: Kriesel, John D.; Hobbs, Maurine R.; Jones, Brandt B.; Milash, Brett; Nagra, Rashed M.; Fischer, Kael F. title: Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date: 2012-03-08 journal: PLoS One DOI: 10.1371/journal.pone.0031886 sha: doc_id: 337879 cord_uid: liqhbqxl file: cache/cord-340195-425rd7ul.json key: cord-340195-425rd7ul authors: Smith, Kristine M.; Anthony, Simon J.; Switzer, William M.; Epstein, Jonathan H.; Seimon, Tracie; Jia, Hongwei; Sanchez, Maria D.; Huynh, Thanh Thao; Galland, G. Gale; Shapiro, Sheryl E.; Sleeman, Jonathan M.; McAloose, Denise; Stuchin, Margot; Amato, George; Kolokotronis, Sergios-Orestis; Lipkin, W. Ian; Karesh, William B.; Daszak, Peter; Marano, Nina title: Zoonotic Viruses Associated with Illegally Imported Wildlife Products date: 2012-01-10 journal: PLoS One DOI: 10.1371/journal.pone.0029505 sha: doc_id: 340195 cord_uid: 425rd7ul file: cache/cord-339920-dr5bvpm0.json key: cord-339920-dr5bvpm0 authors: Soberman, Roy J.; MacKay, Christopher R.; Vaine, Christine A.; Ryan, Glennice Bowen; Cerny, Anna M.; Thompson, Mikayla R.; Nikolic, Boris; Primo, Valeria; Christmas, Peter; Sheiffele, Paul; Aronov, Lisa; Knipe, David M.; Kurt-Jones, Evelyn A. title: CD200R1 Supports HSV-1 Viral Replication and Licenses Pro-Inflammatory Signaling Functions of TLR2 date: 2012-10-17 journal: PLoS One DOI: 10.1371/journal.pone.0047740 sha: doc_id: 339920 cord_uid: dr5bvpm0 file: cache/cord-339392-2ocz784l.json key: cord-339392-2ocz784l authors: Sharma, Kulbhushan; Tripathi, Shashank; Ranjan, Priya; Kumar, Purnima; Garten, Rebecca; Deyde, Varough; Katz, Jacqueline M.; Cox, Nancy J.; Lal, Renu B.; Sambhara, Suryaprakash; Lal, Sunil K. title: Influenza A Virus Nucleoprotein Exploits Hsp40 to Inhibit PKR Activation date: 2011-06-15 journal: PLoS One DOI: 10.1371/journal.pone.0020215 sha: doc_id: 339392 cord_uid: 2ocz784l file: cache/cord-337630-ojhk5opy.json key: cord-337630-ojhk5opy authors: Tasic, Velibor; Hynes, Ann Marie; Kitamura, Kenichiro; Cheong, Hae Il; Lozanovski, Vladimir J.; Gucev, Zoran; Jutabha, Promsuk; Anzai, Naohiko; Sayer, John A. title: Clinical and Functional Characterization of URAT1 Variants date: 2011-12-16 journal: PLoS One DOI: 10.1371/journal.pone.0028641 sha: doc_id: 337630 cord_uid: ojhk5opy file: cache/cord-341914-l2bomgji.json key: cord-341914-l2bomgji authors: Flies, Andrew S.; Mansfield, Linda S.; Grant, Chris K.; Weldele, Mary L.; Holekamp, Kay E. title: Markedly Elevated Antibody Responses in Wild versus Captive Spotted Hyenas Show that Environmental and Ecological Factors Are Important Modulators of Immunity date: 2015-10-07 journal: PLoS One DOI: 10.1371/journal.pone.0137679 sha: doc_id: 341914 cord_uid: l2bomgji file: cache/cord-339796-gccnvh0z.json key: cord-339796-gccnvh0z authors: Zhang, Si Min; Jejcic, Alenka; Tam, James P.; Vahlne, Anders title: Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date: 2015-07-31 journal: PLoS One DOI: 10.1371/journal.pone.0134851 sha: doc_id: 339796 cord_uid: gccnvh0z file: cache/cord-340718-amfs4zay.json key: cord-340718-amfs4zay authors: Zhu, Gengping; Peterson, A. Townsend title: Potential Geographic Distribution of the Novel Avian-Origin Influenza A (H7N9) Virus date: 2014-04-01 journal: PLoS One DOI: 10.1371/journal.pone.0093390 sha: doc_id: 340718 cord_uid: amfs4zay file: cache/cord-340703-vtuy806l.json key: cord-340703-vtuy806l authors: Cascio, Antonio; Colomba, Claudia; Di Carlo, Paola; Serra, Nicola; Lo Re, Giuseppe; Gambino, Angelo; Lo Casto, Antonio; Guglielmi, Giuseppe; Veronese, Nicola; Lagalla, Roberto; Sergi, Consolato title: Low bone mineral density in HIV-positive young Italians and migrants date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0237984 sha: doc_id: 340703 cord_uid: vtuy806l file: cache/cord-340713-v5sdowb7.json key: cord-340713-v5sdowb7 authors: Bird, Jordan J.; Barnes, Chloe M.; Premebida, Cristiano; Ekárt, Anikó; Faria, Diego R. title: Country-level pandemic risk and preparedness classification based on COVID-19 data: A machine learning approach date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0241332 sha: doc_id: 340713 cord_uid: v5sdowb7 file: cache/cord-340656-ltd6ueoi.json key: cord-340656-ltd6ueoi authors: Grant, Michael C.; Geoghegan, Luke; Arbyn, Marc; Mohammed, Zakaria; McGuinness, Luke; Clarke, Emily L.; Wade, Ryckie G. title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date: 2020-06-23 journal: PLoS One DOI: 10.1371/journal.pone.0234765 sha: doc_id: 340656 cord_uid: ltd6ueoi file: cache/cord-340627-xyvzgkxl.json key: cord-340627-xyvzgkxl authors: Ornaghi, Sara; Callegari, Clelia; Milazzo, Roberta; La Milia, Laura; Brunetti, Federica; Lubrano, Chiara; Tasca, Chiara; Livio, Stefania; Savasi, Valeria Maria; Cetin, Irene; Vergani, Patrizia title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 journal: PLoS One DOI: 10.1371/journal.pone.0239173 sha: doc_id: 340627 cord_uid: xyvzgkxl file: cache/cord-340937-6mpob1nx.json key: cord-340937-6mpob1nx authors: Varshney, Mohit; Parel, Jithin Thomas; Raizada, Neeraj; Sarin, Shiv Kumar title: Initial psychological impact of COVID-19 and its correlates in Indian Community: An online (FEEL-COVID) survey date: 2020-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0233874 sha: doc_id: 340937 cord_uid: 6mpob1nx file: cache/cord-339869-euikj8fv.json key: cord-339869-euikj8fv authors: Cebey-López, Miriam; Herberg, Jethro; Pardo-Seco, Jacobo; Gómez-Carballa, Alberto; Martinón-Torres, Nazareth; Salas, Antonio; Martinón-Sánchez, José María; Justicia, Antonio; Rivero-Calle, Irene; Sumner, Edward; Fink, Colin; Martinón-Torres, Federico title: Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date: 2016-04-20 journal: PLoS One DOI: 10.1371/journal.pone.0152481 sha: doc_id: 339869 cord_uid: euikj8fv file: cache/cord-340766-aic570x8.json key: cord-340766-aic570x8 authors: Kim, Se Jin; Kim, Kang; Park, Sung Bum; Hong, Duck Jin; Jhun, Byung Woo title: Outcomes of Early Administration of Cidofovir in Non-Immunocompromised Patients with Severe Adenovirus Pneumonia date: 2015-04-15 journal: PLoS One DOI: 10.1371/journal.pone.0122642 sha: doc_id: 340766 cord_uid: aic570x8 file: cache/cord-340387-ohkjheat.json key: cord-340387-ohkjheat authors: Wynne, James W.; Di Rubbo, Antonio; Shiell, Brian J.; Beddome, Gary; Cowled, Christopher; Peck, Grantley R.; Huang, Jing; Grimley, Samantha L.; Baker, Michelle L.; Michalski, Wojtek P. title: Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA date: 2013-01-07 journal: PLoS One DOI: 10.1371/journal.pone.0052930 sha: doc_id: 340387 cord_uid: ohkjheat file: cache/cord-342476-0rupk21u.json key: cord-342476-0rupk21u authors: van Rijn, Anneloes L.; van Boheemen, Sander; Sidorov, Igor; Carbo, Ellen C.; Pappas, Nikos; Mei, Hailiang; Feltkamp, Mariet; Aanerud, Marianne; Bakke, Per; Claas, Eric C. J.; Eagan, Tomas M.; Hiemstra, Pieter S.; Kroes, Aloys C. M.; de Vries, Jutte J. C. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0223952 sha: doc_id: 342476 cord_uid: 0rupk21u file: cache/cord-341880-wxliz485.json key: cord-341880-wxliz485 authors: Mottaleb, Khondoker Abdul; Mainuddin, Mohammed; Sonobe, Tetsushi title: COVID-19 induced economic loss and ensuring food security for vulnerable groups: Policy implications from Bangladesh date: 2020-10-16 journal: PLoS One DOI: 10.1371/journal.pone.0240709 sha: doc_id: 341880 cord_uid: wxliz485 file: cache/cord-343135-m0pdixw5.json key: cord-343135-m0pdixw5 authors: Marguet, Christophe; Lubrano, Marc; Gueudin, Marie; Le Roux, Pascal; Deschildre, Antoine; Forget, Chantal; Couderc, Laure; Siret, Daniel; Donnou, Marie-Dominique; Bubenheim, Michael; Vabret, Astrid; Freymuth, François title: In Very Young Infants Severity of Acute Bronchiolitis Depends On Carried Viruses date: 2009-02-25 journal: PLoS One DOI: 10.1371/journal.pone.0004596 sha: doc_id: 343135 cord_uid: m0pdixw5 file: cache/cord-342133-khrljehj.json key: cord-342133-khrljehj authors: Principi, Nicola; Piralla, Antonio; Zampiero, Alberto; Bianchini, Sonia; Umbrello, Giulia; Scala, Alessia; Bosis, Samantha; Fossali, Emilio; Baldanti, Fausto; Esposito, Susanna title: Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date: 2015-08-12 journal: PLoS One DOI: 10.1371/journal.pone.0135640 sha: doc_id: 342133 cord_uid: khrljehj file: cache/cord-341097-c96hm610.json key: cord-341097-c96hm610 authors: Mayer, Craig S.; Williams, Nick; Huser, Vojtech title: Analysis of data dictionary formats of HIV clinical trials date: 2020-10-05 journal: PLoS One DOI: 10.1371/journal.pone.0240047 sha: doc_id: 341097 cord_uid: c96hm610 file: cache/cord-342519-tjr6dvtt.json key: cord-342519-tjr6dvtt authors: Souza, Thiago Moreno L.; Salluh, Jorge I. F.; Bozza, Fernando A.; Mesquita, Milene; Soares, Márcio; Motta, Fernando C.; Pitrowsky, Melissa Tassano; de Lourdes Oliveira, Maria; Mishin, Vasiliy P.; Gubareva, Larissa V.; Whitney, Anne; Rocco, Sandra Amaral; Gonçalves, Vânia Maria C.; Marques, Venceslaine Prado; Velasco, Eduardo; Siqueira, Marilda M. title: H1N1pdm Influenza Infection in Hospitalized Cancer Patients: Clinical Evolution and Viral Analysis date: 2010-11-30 journal: PLoS One DOI: 10.1371/journal.pone.0014158 sha: doc_id: 342519 cord_uid: tjr6dvtt file: cache/cord-344782-ond1ziu5.json key: cord-344782-ond1ziu5 authors: Zhang, Jing; Finlaison, Deborah S.; Frost, Melinda J.; Gestier, Sarah; Gu, Xingnian; Hall, Jane; Jenkins, Cheryl; Parrish, Kate; Read, Andrew J.; Srivastava, Mukesh; Rose, Karrie; Kirkland, Peter D. title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0205209 sha: doc_id: 344782 cord_uid: ond1ziu5 file: cache/cord-343973-n5ogyxz7.json key: cord-343973-n5ogyxz7 authors: Ip, Andrew; Berry, Donald A.; Hansen, Eric; Goy, Andre H.; Pecora, Andrew L.; Sinclaire, Brittany A.; Bednarz, Urszula; Marafelias, Michael; Berry, Scott M.; Berry, Nicholas S.; Mathura, Shivam; Sawczuk, Ihor S.; Biran, Noa; Go, Ronaldo C.; Sperber, Steven; Piwoz, Julia A.; Balani, Bindu; Cicogna, Cristina; Sebti, Rani; Zuckerman, Jerry; Rose, Keith M.; Tank, Lisa; Jacobs, Laurie G.; Korcak, Jason; Timmapuri, Sarah L.; Underwood, Joseph P.; Sugalski, Gregory; Barsky, Carol; Varga, Daniel W.; Asif, Arif; Landolfi, Joseph C.; Goldberg, Stuart L. title: Hydroxychloroquine and tocilizumab therapy in COVID-19 patients—An observational study date: 2020-08-13 journal: PLoS One DOI: 10.1371/journal.pone.0237693 sha: doc_id: 343973 cord_uid: n5ogyxz7 file: cache/cord-344357-ocyaqs1y.json key: cord-344357-ocyaqs1y authors: Fu, Yue-Qiang; Sun, Yue-Lin; Lu, Si-Wei; Yang, Yang; Wang, Yi; Xu, Feng title: Effect of blood analysis and immune function on the prognosis of patients with COVID-19 date: 2020-10-30 journal: PLoS One DOI: 10.1371/journal.pone.0240751 sha: doc_id: 344357 cord_uid: ocyaqs1y file: cache/cord-344839-r05p9h0e.json key: cord-344839-r05p9h0e authors: Majmundar, Monil; Kansara, Tikal; Lenik, Joanna Marta; Park, Hansang; Ghosh, Kuldeep; Doshi, Rajkumar; Shah, Palak; Kumar, Ashish; Amin, Hossam; Chaudhari, Shobhana; Habtes, Imnett title: Efficacy of corticosteroids in non-intensive care unit patients with COVID-19 pneumonia from the New York Metropolitan region date: 2020-09-09 journal: PLoS One DOI: 10.1371/journal.pone.0238827 sha: doc_id: 344839 cord_uid: r05p9h0e file: cache/cord-344870-tbgqulpu.json key: cord-344870-tbgqulpu authors: Lloyd-Smith, James O. title: Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases date: 2007-02-14 journal: PLoS One DOI: 10.1371/journal.pone.0000180 sha: doc_id: 344870 cord_uid: tbgqulpu file: cache/cord-342730-b7y8mybg.json key: cord-342730-b7y8mybg authors: Dellagi, Koussay; Rollot, Olivier; Temmam, Sarah; Salez, Nicolas; Guernier, Vanina; Pascalis, Hervé; Gérardin, Patrick; Fianu, Adrian; Lapidus, Nathanael; Naty, Nadège; Tortosa, Pablo; Boussaïd, Karim; Jaffar-Banjee, Marie-Christine; Filleul, Laurent; Flahault, Antoine; Carrat, Fabrice; Favier, Francois; de Lamballerie, Xavier title: Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009 date: 2011-09-29 journal: PLoS One DOI: 10.1371/journal.pone.0025738 sha: doc_id: 342730 cord_uid: b7y8mybg file: cache/cord-342639-vf9n2vf9.json key: cord-342639-vf9n2vf9 authors: Chang, Chung-ke; Chen, Chia-Min Michael; Chiang, Ming-hui; Hsu, Yen-lan; Huang, Tai-huang title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0065045 sha: doc_id: 342639 cord_uid: vf9n2vf9 file: cache/cord-345695-5vi9wibk.json key: cord-345695-5vi9wibk authors: Hicks, Lorin L.; Schwab, Nathan A.; Homyack, Jessica A.; Jones, Jay E.; Maxell, Bryce A.; Burkholder, Braden O. title: A statistical approach to white-nose syndrome surveillance monitoring using acoustic data date: 2020-10-22 journal: PLoS One DOI: 10.1371/journal.pone.0241052 sha: doc_id: 345695 cord_uid: 5vi9wibk file: cache/cord-345717-ktajrf7d.json key: cord-345717-ktajrf7d authors: Monagin, Corina; Paccha, Blanca; Liang, Ning; Trufan, Sally; Zhou, Huiqiong; Wu, De; Schneider, Bradley S.; Chmura, Aleksei; Epstein, Jonathan; Daszak, Peter; Ke, Changwen; Rabinowitz, Peter M. title: Serologic and behavioral risk survey of workers with wildlife contact in China date: 2018-04-03 journal: PLoS One DOI: 10.1371/journal.pone.0194647 sha: doc_id: 345717 cord_uid: ktajrf7d file: cache/cord-346586-fxxceffl.json key: cord-346586-fxxceffl authors: Razanajatovo, Norosoa Harline; Guillebaud, Julia; Harimanana, Aina; Rajatonirina, Soatiana; Ratsima, Elisoa Hariniaina; Andrianirina, Zo Zafitsara; Rakotoariniaina, Hervé; Andriatahina, Todisoa; Orelle, Arnaud; Ratovoson, Rila; Irinantenaina, Judickaelle; Rakotonanahary, Dina Arinalina; Ramparany, Lovasoa; Randrianirina, Frédérique; Richard, Vincent; Heraud, Jean-Michel title: Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date: 2018-11-21 journal: PLoS One DOI: 10.1371/journal.pone.0205124 sha: doc_id: 346586 cord_uid: fxxceffl file: cache/cord-345019-i7zm9bt1.json key: cord-345019-i7zm9bt1 authors: Al-Waleedi, Ali Ahmed; Naiene, Jeremias D.; Thabet, Ahmed A. K.; Dandarawe, Adham; Salem, Hanan; Mohammed, Nagat; Al Noban, Maysa; Bin-Azoon, Nasreen Salem; Shawqi, Ammar; Rajamanar, Mohammed; Al-Jariri, Riyadh; Al Hyubaishi, Mansoor; Khanbari, Lina; Thabit, Najib; Obaid, Basel; Baaees, Manal; Assaf, Denise; Senga, Mikiko; Bashir, Ismail Mahat; Mahmoud, Nuha; Cosico, Roy; Smith, Philip; Musani, Altaf title: The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0241260 sha: doc_id: 345019 cord_uid: i7zm9bt1 file: cache/cord-344152-pb1e2w7s.json key: cord-344152-pb1e2w7s authors: Kolatkar, Anand; Kennedy, Kevin; Halabuk, Dan; Kunken, Josh; Marrinucci, Dena; Bethel, Kelly; Guzman, Rodney; Huckaby, Tim; Kuhn, Peter title: C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training date: 2008-02-20 journal: PLoS One DOI: 10.1371/journal.pone.0001621 sha: doc_id: 344152 cord_uid: pb1e2w7s file: cache/cord-347465-yu6oj30v.json key: cord-347465-yu6oj30v authors: Kurskaya, Olga; Ryabichenko, Tatyana; Leonova, Natalya; Shi, Weifeng; Bi, Hongtao; Sharshov, Kirill; Kazachkova, Eugenia; Sobolev, Ivan; Prokopyeva, Elena; Kartseva, Tatiana; Alekseev, Alexander; Shestopalov, Alexander title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0200117 sha: doc_id: 347465 cord_uid: yu6oj30v file: cache/cord-348055-azlb1zy1.json key: cord-348055-azlb1zy1 authors: Patel, Mira C.; Wang, Wei; Pletneva, Lioubov M.; Rajagopala, Seesandra V.; Tan, Yi; Hartert, Tina V.; Boukhvalova, Marina S.; Vogel, Stefanie N.; Das, Suman R.; Blanco, Jorge C. G. title: Enterovirus D-68 Infection, Prophylaxis, and Vaccination in a Novel Permissive Animal Model, the Cotton Rat (Sigmodon hispidus) date: 2016-11-04 journal: PLoS One DOI: 10.1371/journal.pone.0166336 sha: doc_id: 348055 cord_uid: azlb1zy1 file: cache/cord-346089-u31n0qxa.json key: cord-346089-u31n0qxa authors: McDade, Thomas W.; McNally, Elizabeth M.; Zelikovich, Aaron S.; D’Aquila, Richard; Mustanski, Brian; Miller, Aaron; Vaught, Lauren A.; Reiser, Nina L.; Bogdanovic, Elena; Fallon, Katherine S.; Demonbreun, Alexis R. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-08-14 journal: PLoS One DOI: 10.1371/journal.pone.0237833 sha: doc_id: 346089 cord_uid: u31n0qxa file: cache/cord-346067-zly8p0y7.json key: cord-346067-zly8p0y7 authors: Ruiz-Irastorza, Guillermo; Pijoan, Jose-Ignacio; Bereciartua, Elena; Dunder, Susanna; Dominguez, Jokin; Garcia-Escudero, Paula; Rodrigo, Alejandro; Gomez-Carballo, Carlota; Varona, Jimena; Guio, Laura; Ibarrola, Marta; Ugarte, Amaia; Martinez-Berriotxoa, Agustin title: Second week methyl-prednisolone pulses improve prognosis in patients with severe coronavirus disease 2019 pneumonia: An observational comparative study using routine care data date: 2020-09-22 journal: PLoS One DOI: 10.1371/journal.pone.0239401 sha: doc_id: 346067 cord_uid: zly8p0y7 file: cache/cord-346347-r4ork18p.json key: cord-346347-r4ork18p authors: Borrion, Hervé; Kurland, Justin; Tilley, Nick; Chen, Peng title: Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China date: 2020-10-14 journal: PLoS One DOI: 10.1371/journal.pone.0240077 sha: doc_id: 346347 cord_uid: r4ork18p file: cache/cord-346819-11fkgzaa.json key: cord-346819-11fkgzaa authors: Khan, Mohd Imran; Khan, Zainul A.; Baig, Mohammad Hassan; Ahmad, Irfan; Farouk, Abd-ElAziem; Song, Young Goo; Dong, Jae-Jun title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0238344 sha: doc_id: 346819 cord_uid: 11fkgzaa file: cache/cord-348807-9xxc5hyl.json key: cord-348807-9xxc5hyl authors: Cuomo, Raphael E.; Purushothaman, Vidya; Li, Jiawei; Cai, Mingxiang; Mackey, Timothy K. title: Sub-national longitudinal and geospatial analysis of COVID-19 tweets date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0241330 sha: doc_id: 348807 cord_uid: 9xxc5hyl file: cache/cord-346314-o9fjpqaj.json key: cord-346314-o9fjpqaj authors: Jarboui, Mohamed Ali; Bidoia, Carlo; Woods, Elena; Roe, Barbara; Wynne, Kieran; Elia, Giuliano; Hall, William W.; Gautier, Virginie W. title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 journal: PLoS One DOI: 10.1371/journal.pone.0048702 sha: doc_id: 346314 cord_uid: o9fjpqaj file: cache/cord-347014-88zmtky7.json key: cord-347014-88zmtky7 authors: Esposito, Susanna; Di Gangi, Maria; Cardinale, Fabio; Baraldi, Eugenio; Corsini, Ilaria; Da Dalt, Liviana; Tovo, Pier Angelo; Correra, Antonio; Villani, Alberto; Sacco, Oliviero; Tenero, Laura; Dones, Piera; Gambino, Monia; Zampiero, Alberto; Principi, Nicola title: Sensitivity and Specificity of Soluble Triggering Receptor Expressed on Myeloid Cells-1, Midregional Proatrial Natriuretic Peptide and Midregional Proadrenomedullin for Distinguishing Etiology and to Assess Severity in Community-Acquired Pneumonia date: 2016-11-15 journal: PLoS One DOI: 10.1371/journal.pone.0163262 sha: doc_id: 347014 cord_uid: 88zmtky7 file: cache/cord-348243-e5tdb08v.json key: cord-348243-e5tdb08v authors: Schermer, Bernhard; Fabretti, Francesca; Damagnez, Maximilian; Di Cristanziano, Veronica; Heger, Eva; Arjune, Sita; Tanner, Nathan A.; Imhof, Thomas; Koch, Manuel; Ladha, Alim; Joung, Julia; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Burst, Volker; Zhang, Feng; Klein, Florian; Benzing, Thomas; Müller, Roman-Ulrich title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 journal: PLoS One DOI: 10.1371/journal.pone.0238612 sha: doc_id: 348243 cord_uid: e5tdb08v file: cache/cord-346858-18q8rxzg.json key: cord-346858-18q8rxzg authors: Hossain, Md. Tanvir; Ahammed, Benojir; Chanda, Sanjoy Kumar; Jahan, Nusrat; Ela, Mahfuza Zaman; Islam, Md. Nazrul title: Social and electronic media exposure and generalized anxiety disorder among people during COVID-19 outbreak in Bangladesh: A preliminary observation date: 2020-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0238974 sha: doc_id: 346858 cord_uid: 18q8rxzg file: cache/cord-347317-qcghtkk0.json key: cord-347317-qcghtkk0 authors: Russo, Lucia; Anastassopoulou, Cleo; Tsakris, Athanasios; Bifulco, Gennaro Nicola; Campana, Emilio Fortunato; Toraldo, Gerardo; Siettos, Constantinos title: Tracing day-zero and forecasting the COVID-19 outbreak in Lombardy, Italy: A compartmental modelling and numerical optimization approach date: 2020-10-30 journal: PLoS One DOI: 10.1371/journal.pone.0240649 sha: doc_id: 347317 cord_uid: qcghtkk0 file: cache/cord-348499-7ll7sd3o.json key: cord-348499-7ll7sd3o authors: Manderstedt, Eric; Lind-Halldén, Christina; Lethagen, Stefan; Halldén, Christer title: Genetic variation in the C-type lectin receptor CLEC4M in type 1 von Willebrand Disease patients date: 2018-02-01 journal: PLoS One DOI: 10.1371/journal.pone.0192024 sha: doc_id: 348499 cord_uid: 7ll7sd3o file: cache/cord-349029-zyfop43z.json key: cord-349029-zyfop43z authors: Dobrovolny, Hana M. title: Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date: 2020-08-10 journal: PLoS One DOI: 10.1371/journal.pone.0236976 sha: doc_id: 349029 cord_uid: zyfop43z file: cache/cord-349217-vpih1wvs.json key: cord-349217-vpih1wvs authors: Petropoulos, Fotios; Makridakis, Spyros title: Forecasting the novel coronavirus COVID-19 date: 2020-03-31 journal: PLoS One DOI: 10.1371/journal.pone.0231236 sha: doc_id: 349217 cord_uid: vpih1wvs file: cache/cord-350842-4m82l5t8.json key: cord-350842-4m82l5t8 authors: Xing, Jun; Sun, Ning; Xu, Jun; Geng, Shuling; Li, Yuqian title: Study of the mental health status of medical personnel dealing with new coronavirus pneumonia date: 2020-05-19 journal: PLoS One DOI: 10.1371/journal.pone.0233145 sha: doc_id: 350842 cord_uid: 4m82l5t8 file: cache/cord-349476-iac9fak3.json key: cord-349476-iac9fak3 authors: Mao, Liang title: Evaluating the Combined Effectiveness of Influenza Control Strategies and Human Preventive Behavior date: 2011-10-17 journal: PLoS One DOI: 10.1371/journal.pone.0024706 sha: doc_id: 349476 cord_uid: iac9fak3 file: cache/cord-349781-l93978vq.json key: cord-349781-l93978vq authors: Cong, Yu; Hart, Brit J.; Gross, Robin; Zhou, Huanying; Frieman, Matthew; Bollinger, Laura; Wada, Jiro; Hensley, Lisa E.; Jahrling, Peter B.; Dyall, Julie; Holbrook, Michael R. title: MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells date: 2018-03-22 journal: PLoS One DOI: 10.1371/journal.pone.0194868 sha: doc_id: 349781 cord_uid: l93978vq file: cache/cord-350443-ca5avyjf.json key: cord-350443-ca5avyjf authors: Zhang, Lei; Wilson, David P. title: Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date: 2012-02-16 journal: PLoS One DOI: 10.1371/journal.pone.0031076 sha: doc_id: 350443 cord_uid: ca5avyjf file: cache/cord-351868-w4d45fue.json key: cord-351868-w4d45fue authors: Zuwała, Kaja; Golda, Anna; Kabala, Wojciech; Burmistrz, Michał; Zdzalik, Michal; Nowak, Paulina; Kedracka-Krok, Sylwia; Zarebski, Mirosław; Dobrucki, Jerzy; Florek, Dominik; Zeglen, Sławomir; Wojarski, Jacek; Potempa, Jan; Dubin, Grzegorz; Pyrc, Krzysztof title: The Nucleocapsid Protein of Human Coronavirus NL63 date: 2015-02-20 journal: PLoS One DOI: 10.1371/journal.pone.0117833 sha: doc_id: 351868 cord_uid: w4d45fue file: cache/cord-349911-dx8wvqkm.json key: cord-349911-dx8wvqkm authors: Dahl, Viktor; Tegnell, Anders; Wallensten, Anders title: Communicable Diseases Prioritized According to Their Public Health Relevance, Sweden, 2013 date: 2015-09-23 journal: PLoS One DOI: 10.1371/journal.pone.0136353 sha: doc_id: 349911 cord_uid: dx8wvqkm file: cache/cord-351142-g20f6bxc.json key: cord-351142-g20f6bxc authors: Kiaghadi, Amin; Rifai, Hanadi S.; Liaw, Winston title: Assessing COVID-19 risk, vulnerability and infection prevalence in communities date: 2020-10-29 journal: PLoS One DOI: 10.1371/journal.pone.0241166 sha: doc_id: 351142 cord_uid: g20f6bxc file: cache/cord-352200-i05h8csb.json key: cord-352200-i05h8csb authors: Xu, Yi; Zhou, Wenwu; Zhou, Yijun; Wu, Jianxiang; Zhou, Xueping title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 journal: PLoS One DOI: 10.1371/journal.pone.0036238 sha: doc_id: 352200 cord_uid: i05h8csb file: cache/cord-351387-i0zamkpd.json key: cord-351387-i0zamkpd authors: Witte, Katrin; Koch, Egon; Volk, Hans-Dieter; Wolk, Kerstin; Sabat, Robert title: The Pelargonium sidoides Extract EPs 7630 Drives the Innate Immune Defense by Activating Selected MAP Kinase Pathways in Human Monocytes date: 2015-09-25 journal: PLoS One DOI: 10.1371/journal.pone.0138075 sha: doc_id: 351387 cord_uid: i0zamkpd file: cache/cord-351185-3y3gou6v.json key: cord-351185-3y3gou6v authors: Buckles, Thomas C.; Ziemba, Brian P.; Djukovic, Danijel; Falke, Joseph J. title: Rapid exposure of macrophages to drugs resolves four classes of effects on the leading edge sensory pseudopod: Non-perturbing, adaptive, disruptive, and activating date: 2020-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0233012 sha: doc_id: 351185 cord_uid: 3y3gou6v file: cache/cord-352222-zq9o66i4.json key: cord-352222-zq9o66i4 authors: Rajatonirina, Soatiana; Razanajatovo, Norosoa Harline; Ratsima, Elisoa Hariniana; Orelle, Arnaud; Ratovoson, Rila; Andrianirina, Zo Zafitsara; Andriatahina, Todisoa; Ramparany, Lovasoa; Herindrainy, Perlinot; Randrianirina, Frédérique; Heraud, Jean-Michel; Richard, Vincent title: Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date: 2013-09-12 journal: PLoS One DOI: 10.1371/journal.pone.0072839 sha: doc_id: 352222 cord_uid: zq9o66i4 file: cache/cord-352403-4591ewsa.json key: cord-352403-4591ewsa authors: Hartwig, Stacey M.; Holman, Kaitlyn M.; Varga, Steven M. title: Depletion of Alveolar Macrophages Ameliorates Virus-Induced Disease following a Pulmonary Coronavirus Infection date: 2014-03-07 journal: PLoS One DOI: 10.1371/journal.pone.0090720 sha: doc_id: 352403 cord_uid: 4591ewsa file: cache/cord-351990-aham72b9.json key: cord-351990-aham72b9 authors: Radin, Jennifer M.; Hawksworth, Anthony W.; Kammerer, Peter E.; Balansay, Melinda; Raman, Rema; Lindsay, Suzanne P.; Brice, Gary T. title: Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date: 2014-12-30 journal: PLoS One DOI: 10.1371/journal.pone.0114871 sha: doc_id: 351990 cord_uid: aham72b9 file: cache/cord-351918-pu7i1jfe.json key: cord-351918-pu7i1jfe authors: Baek, Yae Jee; Lee, Taeyong; Cho, Yunsuk; Hyun, Jong Hoon; Kim, Moo Hyun; Sohn, Yujin; Kim, Jung Ho; Ahn, Jin Young; Jeong, Su Jin; Ku, Nam Su; Yeom, Joon-Sup; Lee, Jeehyun; Choi, Jun Yong title: A mathematical model of COVID-19 transmission in a tertiary hospital and assessment of the effects of different intervention strategies date: 2020-10-26 journal: PLoS One DOI: 10.1371/journal.pone.0241169 sha: doc_id: 351918 cord_uid: pu7i1jfe file: cache/cord-351098-x729wpp7.json key: cord-351098-x729wpp7 authors: Long, Rachel B.; Krumlauf, Kristi; Young, Anna M. title: Characterizing trends in human-wildlife conflicts in the American Midwest using wildlife rehabilitation records date: 2020-09-11 journal: PLoS One DOI: 10.1371/journal.pone.0238805 sha: doc_id: 351098 cord_uid: x729wpp7 file: cache/cord-352564-2j4pjjwk.json key: cord-352564-2j4pjjwk authors: Dominguez, Samuel R.; Travanty, Emily A.; Qian, Zhaohui; Mason, Robert J. title: Human Coronavirus HKU1 Infection of Primary Human Type II Alveolar Epithelial Cells: Cytopathic Effects and Innate Immune Response date: 2013-07-24 journal: PLoS One DOI: 10.1371/journal.pone.0070129 sha: doc_id: 352564 cord_uid: 2j4pjjwk file: cache/cord-353200-5csewb1k.json key: cord-353200-5csewb1k authors: Jehi, Lara; Ji, Xinge; Milinovich, Alex; Erzurum, Serpil; Merlino, Amy; Gordon, Steve; Young, James B.; Kattan, Michael W. title: Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date: 2020-08-11 journal: PLoS One DOI: 10.1371/journal.pone.0237419 sha: doc_id: 353200 cord_uid: 5csewb1k file: cache/cord-350398-w75flrwv.json key: cord-350398-w75flrwv authors: Sampath, Rangarajan; Mulholland, Niveen; Blyn, Lawrence B.; Massire, Christian; Whitehouse, Chris A.; Waybright, Nicole; Harter, Courtney; Bogan, Joseph; Miranda, Mary Sue; Smith, David; Baldwin, Carson; Wolcott, Mark; Norwood, David; Kreft, Rachael; Frinder, Mark; Lovari, Robert; Yasuda, Irene; Matthews, Heather; Toleno, Donna; Housley, Roberta; Duncan, David; Li, Feng; Warren, Robin; Eshoo, Mark W.; Hall, Thomas A.; Hofstadler, Steven A.; Ecker, David J. title: Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date: 2012-06-29 journal: PLoS One DOI: 10.1371/journal.pone.0036528 sha: doc_id: 350398 cord_uid: w75flrwv file: cache/cord-352511-gkm7i62s.json key: cord-352511-gkm7i62s authors: Yamada, Yoshiyuki; Liu, Xiao Bo; Fang, Shou Guo; Tay, Felicia P. L.; Liu, Ding Xiang title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date: 2009-07-02 journal: PLoS One DOI: 10.1371/journal.pone.0006130 sha: doc_id: 352511 cord_uid: gkm7i62s file: cache/cord-353866-0r1b44id.json key: cord-353866-0r1b44id authors: Sun, Hongpeng; Zhang, Qiuju; Luo, Xiao; Quan, Hude; Zhang, Feng; Liu, Chang; Liu, Meina title: Changes of Adult Population Health Status in China from 2003 to 2008 date: 2011-12-02 journal: PLoS One DOI: 10.1371/journal.pone.0028411 sha: doc_id: 353866 cord_uid: 0r1b44id file: cache/cord-352219-z245sb3s.json key: cord-352219-z245sb3s authors: Tallam, Aravind; Perumal, Thaneer M.; Antony, Paul M.; Jäger, Christian; Fritz, Joëlle V.; Vallar, Laurent; Balling, Rudi; del Sol, Antonio; Michelucci, Alessandro title: Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages date: 2016-02-12 journal: PLoS One DOI: 10.1371/journal.pone.0149050 sha: doc_id: 352219 cord_uid: z245sb3s file: cache/cord-352522-qnvgg2e9.json key: cord-352522-qnvgg2e9 authors: Langille, Morgan G. I.; Eisen, Jonathan A. title: BioTorrents: A File Sharing Service for Scientific Data date: 2010-04-14 journal: PLoS One DOI: 10.1371/journal.pone.0010071 sha: doc_id: 352522 cord_uid: qnvgg2e9 file: cache/cord-352720-z1cvjc2y.json key: cord-352720-z1cvjc2y authors: Díaz-Corvillón, Pilar; Mönckeberg, Max; Barros, Antonia; Illanes, Sebastián E.; Soldati, Arturo; Nien, Jyh-Kae; Schepeler, Manuel; Caradeux, Javier title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 journal: PLoS One DOI: 10.1371/journal.pone.0239887 sha: doc_id: 352720 cord_uid: z1cvjc2y file: cache/cord-353245-es7b1rs0.json key: cord-353245-es7b1rs0 authors: Song, Deping; Huang, Dongyan; Peng, Qi; Huang, Tao; Chen, Yanjun; Zhang, Tiansheng; Nie, Xiaowei; He, Houjun; Wang, Ping; Liu, Qinglan; Tang, Yuxin title: Molecular Characterization and Phylogenetic Analysis of Porcine Epidemic Diarrhea Viruses Associated with Outbreaks of Severe Diarrhea in Piglets in Jiangxi, China 2013 date: 2015-03-19 journal: PLoS One DOI: 10.1371/journal.pone.0120310 sha: doc_id: 353245 cord_uid: es7b1rs0 file: cache/cord-352447-bc1pf272.json key: cord-352447-bc1pf272 authors: Nishida, Yu; Hosomi, Shuhei; Yamagami, Hirokazu; Fujimoto, Koji; Nakata, Rieko; Itani, Shigehiro; Nadatani, Yuji; Fukunaga, Shusei; Otani, Koji; Tanaka, Fumio; Nagami, Yasuaki; Taira, Koichi; Kamata, Noriko; Watanabe, Toshio; Iseki, Yasuhito; Fukuoka, Tatsunari; Shibutani, Masatsune; Nagahara, Hisashi; Ohfuji, Satoko; Fujiwara, Yasuhiro title: Novel prognostic biomarkers of pouchitis after ileal pouch-anal anastomosis for ulcerative colitis: Neutrophil-to-lymphocyte ratio date: 2020-10-26 journal: PLoS One DOI: 10.1371/journal.pone.0241322 sha: doc_id: 352447 cord_uid: bc1pf272 file: cache/cord-353869-l53ms3q8.json key: cord-353869-l53ms3q8 authors: Friesen, Robert H. E.; Koudstaal, Wouter; Koldijk, Martin H.; Weverling, Gerrit Jan; Brakenhoff, Just P. J.; Lenting, Peter J.; Stittelaar, Koert J.; Osterhaus, Albert D. M. E.; Kompier, Ronald; Goudsmit, Jaap title: New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date: 2010-02-08 journal: PLoS One DOI: 10.1371/journal.pone.0009106 sha: doc_id: 353869 cord_uid: l53ms3q8 file: cache/cord-356132-1nisyl5r.json key: cord-356132-1nisyl5r authors: Wang, Huiyao; Xia, Qian; Xiong, Zhenzhen; Li, Zhixiong; Xiang, Weiyi; Yuan, Yiwen; Liu, Yaya; Li, Zhe title: The psychological distress and coping styles in the early stages of the 2019 coronavirus disease (COVID-19) epidemic in the general mainland Chinese population: A web-based survey date: 2020-05-14 journal: PLoS One DOI: 10.1371/journal.pone.0233410 sha: doc_id: 356132 cord_uid: 1nisyl5r file: cache/cord-353253-kk2q71vg.json key: cord-353253-kk2q71vg authors: Itokawa, Kentaro; Sekizuka, Tsuyoshi; Hashino, Masanori; Tanaka, Rina; Kuroda, Makoto title: Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date: 2020-09-18 journal: PLoS One DOI: 10.1371/journal.pone.0239403 sha: doc_id: 353253 cord_uid: kk2q71vg file: cache/cord-355874-nz6eqcdb.json key: cord-355874-nz6eqcdb authors: Wang, Le; Zhao, Mengchuan; Shi, Zhongren; Feng, Zhishan; Guo, Weiwei; Yang, Shuo; Liu, Lanping; Li, Guixia title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date: 2016-09-14 journal: PLoS One DOI: 10.1371/journal.pone.0162411 sha: doc_id: 355874 cord_uid: nz6eqcdb file: cache/cord-353410-tbmtg88k.json key: cord-353410-tbmtg88k authors: Sharma, Shreela V.; Haidar, Amier; Noyola, Jacqueline; Tien, Jacqueline; Rushing, Melinda; Naylor, Brittni M.; Chuang, Ru-Jye; Markham, Christine title: Using a rapid assessment methodology to identify and address immediate needs among low-income households with children during COVID-19 date: 2020-10-01 journal: PLoS One DOI: 10.1371/journal.pone.0240009 sha: doc_id: 353410 cord_uid: tbmtg88k file: cache/cord-354000-jxqskt4k.json key: cord-354000-jxqskt4k authors: Warren, Cody J.; Griffin, Laura M.; Little, Alexander S.; Huang, I-Chueh; Farzan, Michael; Pyeon, Dohun title: The Antiviral Restriction Factors IFITM1, 2 and 3 Do Not Inhibit Infection of Human Papillomavirus, Cytomegalovirus and Adenovirus date: 2014-05-14 journal: PLoS One DOI: 10.1371/journal.pone.0096579 sha: doc_id: 354000 cord_uid: jxqskt4k file: cache/cord-356364-ipi81ce3.json key: cord-356364-ipi81ce3 authors: Ho, Bo-Lin; Cheng, Shu-Chun; Shi, Lin; Wang, Ting-Yun; Ho, Kuan-I; Chou, Chi-Yuan title: Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date: 2015-12-14 journal: PLoS One DOI: 10.1371/journal.pone.0144865 sha: doc_id: 356364 cord_uid: ipi81ce3 file: cache/cord-354052-x4ckzw64.json key: cord-354052-x4ckzw64 authors: Li, Chunhua; Li, Zhen; Zou, Yong; Wicht, Oliver; van Kuppeveld, Frank J. M.; Rottier, Peter J. M.; Bosch, Berend Jan title: Manipulation of the Porcine Epidemic Diarrhea Virus Genome Using Targeted RNA Recombination date: 2013-08-02 journal: PLoS One DOI: 10.1371/journal.pone.0069997 sha: doc_id: 354052 cord_uid: x4ckzw64 file: cache/cord-354763-odzrco6q.json key: cord-354763-odzrco6q authors: Drake, John M.; Chew, Suok Kai; Ma, Stefan title: Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date: 2006-12-20 journal: PLoS One DOI: 10.1371/journal.pone.0000020 sha: doc_id: 354763 cord_uid: odzrco6q file: cache/cord-355259-779czzzx.json key: cord-355259-779czzzx authors: Yang, Xiaoyun; Steukers, Lennert; Forier, Katrien; Xiong, Ranhua; Braeckmans, Kevin; Van Reeth, Kristien; Nauwynck, Hans title: A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date: 2014-10-15 journal: PLoS One DOI: 10.1371/journal.pone.0110026 sha: doc_id: 355259 cord_uid: 779czzzx file: cache/cord-353596-8iqjugcx.json key: cord-353596-8iqjugcx authors: Bédubourg, Gabriel; Le Strat, Yann title: Evaluation and comparison of statistical methods for early temporal detection of outbreaks: A simulation-based study date: 2017-07-17 journal: PLoS One DOI: 10.1371/journal.pone.0181227 sha: doc_id: 353596 cord_uid: 8iqjugcx file: cache/cord-354547-eomm1sl5.json key: cord-354547-eomm1sl5 authors: Wang, Jibin; Fang, Shouguo; Xiao, Han; Chen, Bo; Tam, James P.; Liu, Ding Xiang title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date: 2009-03-16 journal: PLoS One DOI: 10.1371/journal.pone.0004908 sha: doc_id: 354547 cord_uid: eomm1sl5 file: cache/cord-353730-owcapg8h.json key: cord-353730-owcapg8h authors: Dietrich, Jes; Andreasen, Lars Vibe; Andersen, Peter; Agger, Else Marie title: Inducing Dose Sparing with Inactivated Polio Virus Formulated in Adjuvant CAF01 date: 2014-06-23 journal: PLoS One DOI: 10.1371/journal.pone.0100879 sha: doc_id: 353730 cord_uid: owcapg8h Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named journal-plosOne-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25772 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25605 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25804 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25274 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 24578 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23754 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25658 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25880 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26668 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25997 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26658 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26755 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 25708 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26758 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26783 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26776 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26779 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26579 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26750 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26660 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26728 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26927 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26859 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26258 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33178 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33158 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33350 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26821 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-000877-usz7pnvu author: Abdel-Moneim, Ahmed S. title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date: 2013-01-30 pages: extension: .txt txt: ./txt/cord-000877-usz7pnvu.txt cache: ./cache/cord-000877-usz7pnvu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000877-usz7pnvu.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33416 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33785 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33863 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-000366-u4649rtx author: Shan, Tongling title: Genomic Characterization and High Prevalence of Bocaviruses in Swine date: 2011-04-15 pages: extension: .txt txt: ./txt/cord-000366-u4649rtx.txt cache: ./cache/cord-000366-u4649rtx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000366-u4649rtx.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33822 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 34069 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-000063-tex6bgab author: Sui, Hong-Yan title: Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication date: 2009-05-22 pages: extension: .txt txt: ./txt/cord-000063-tex6bgab.txt cache: ./cache/cord-000063-tex6bgab.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000063-tex6bgab.txt' === file2bib.sh === id: cord-000721-leedutqo author: Nawaz, Sameena title: Human Bocaviruses Are Not Significantly Associated with Gastroenteritis: Results of Retesting Archive DNA from a Case Control Study in the UK date: 2012-07-24 pages: extension: .txt txt: ./txt/cord-000721-leedutqo.txt cache: ./cache/cord-000721-leedutqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000721-leedutqo.txt' === file2bib.sh === id: cord-000720-5b936n3g author: Nannyonga, Betty title: The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks date: 2012-07-24 pages: extension: .txt txt: ./txt/cord-000720-5b936n3g.txt cache: ./cache/cord-000720-5b936n3g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000720-5b936n3g.txt' === file2bib.sh === id: cord-000609-dpcgl6ig author: Raju, Sammeta V. title: Suppression of Adenosine-Activated Chloride Transport by Ethanol in Airway Epithelia date: 2012-03-19 pages: extension: .txt txt: ./txt/cord-000609-dpcgl6ig.txt cache: ./cache/cord-000609-dpcgl6ig.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000609-dpcgl6ig.txt' === file2bib.sh === id: cord-000478-88wo4xen author: Gowen, Brian B. title: Use of Recombinant Adenovirus Vectored Consensus IFN-α to Avert Severe Arenavirus Infection date: 2011-10-24 pages: extension: .txt txt: ./txt/cord-000478-88wo4xen.txt cache: ./cache/cord-000478-88wo4xen.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000478-88wo4xen.txt' === file2bib.sh === id: cord-000809-9voqa1oy author: Archer, Brett N. title: Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa date: 2012-11-16 pages: extension: .txt txt: ./txt/cord-000809-9voqa1oy.txt cache: ./cache/cord-000809-9voqa1oy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000809-9voqa1oy.txt' === file2bib.sh === id: cord-000574-7eflwyxk author: Liu, Yanli title: Effects of a Non-Conservative Sequence on the Properties of β-glucuronidase from Aspergillus terreus Li-20 date: 2012-02-07 pages: extension: .txt txt: ./txt/cord-000574-7eflwyxk.txt cache: ./cache/cord-000574-7eflwyxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000574-7eflwyxk.txt' === file2bib.sh === id: cord-000255-73nlxqgk author: Hosseini, Parviez title: Predictive Power of Air Travel and Socio-Economic Data for Early Pandemic Spread date: 2010-09-15 pages: extension: .txt txt: ./txt/cord-000255-73nlxqgk.txt cache: ./cache/cord-000255-73nlxqgk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000255-73nlxqgk.txt' === file2bib.sh === id: cord-000556-uu1oz2ei author: Kumar, Ranjit title: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” date: 2012-01-20 pages: extension: .txt txt: ./txt/cord-000556-uu1oz2ei.txt cache: ./cache/cord-000556-uu1oz2ei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000556-uu1oz2ei.txt' === file2bib.sh === id: cord-000715-zl1s82yi author: Shulman, Lester M. title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 pages: extension: .txt txt: ./txt/cord-000715-zl1s82yi.txt cache: ./cache/cord-000715-zl1s82yi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000715-zl1s82yi.txt' === file2bib.sh === id: cord-001014-8yrpcl94 author: Kitagawa, Hiroshi title: Intranasally Administered Antigen 85B Gene Vaccine in Non-Replicating Human Parainfluenza Type 2 Virus Vector Ameliorates Mouse Atopic Dermatitis date: 2013-07-03 pages: extension: .txt txt: ./txt/cord-001014-8yrpcl94.txt cache: ./cache/cord-001014-8yrpcl94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001014-8yrpcl94.txt' === file2bib.sh === id: cord-001007-645zegcv author: Kim, Hak title: Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections date: 2013-06-27 pages: extension: .txt txt: ./txt/cord-001007-645zegcv.txt cache: ./cache/cord-001007-645zegcv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001007-645zegcv.txt' === file2bib.sh === id: cord-000131-ugbwvy6j author: Jones, James Holland title: Early Assessment of Anxiety and Behavioral Response to Novel Swine-Origin Influenza A(H1N1) date: 2009-12-03 pages: extension: .txt txt: ./txt/cord-000131-ugbwvy6j.txt cache: ./cache/cord-000131-ugbwvy6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000131-ugbwvy6j.txt' === file2bib.sh === id: cord-000375-fvfl0bn1 author: Shen, Ching-I title: The Infection of Chicken Tracheal Epithelial Cells with a H6N1 Avian Influenza Virus date: 2011-05-06 pages: extension: .txt txt: ./txt/cord-000375-fvfl0bn1.txt cache: ./cache/cord-000375-fvfl0bn1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000375-fvfl0bn1.txt' === file2bib.sh === id: cord-000851-uylgyhs8 author: Wang, Zhenya title: Inhibitory Influence of Enterococcus faecium on the Propagation of Swine Influenza A Virus In Vitro date: 2013-01-07 pages: extension: .txt txt: ./txt/cord-000851-uylgyhs8.txt cache: ./cache/cord-000851-uylgyhs8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000851-uylgyhs8.txt' === file2bib.sh === id: cord-000374-gt2pwc9b author: Yang, Albert C. title: Clustering Heart Rate Dynamics Is Associated with β-Adrenergic Receptor Polymorphisms: Analysis by Information-Based Similarity Index date: 2011-05-04 pages: extension: .txt txt: ./txt/cord-000374-gt2pwc9b.txt cache: ./cache/cord-000374-gt2pwc9b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000374-gt2pwc9b.txt' === file2bib.sh === id: cord-000765-r7y1cqou author: Chang, Yu-Ming title: Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis date: 2012-09-21 pages: extension: .txt txt: ./txt/cord-000765-r7y1cqou.txt cache: ./cache/cord-000765-r7y1cqou.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000765-r7y1cqou.txt' === file2bib.sh === id: cord-000588-3wok0n21 author: Sainz, Juan title: Dectin-1 and DC-SIGN Polymorphisms Associated with Invasive Pulmonary Aspergillosis Infection date: 2012-02-27 pages: extension: .txt txt: ./txt/cord-000588-3wok0n21.txt cache: ./cache/cord-000588-3wok0n21.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000588-3wok0n21.txt' === file2bib.sh === id: cord-000077-d441jam3 author: Zhang, Hao-Jie title: The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date: 2009-07-03 pages: extension: .txt txt: ./txt/cord-000077-d441jam3.txt cache: ./cache/cord-000077-d441jam3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000077-d441jam3.txt' === file2bib.sh === id: cord-000460-h3owwjao author: Xiong, Jing title: Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide date: 2011-09-26 pages: extension: .txt txt: ./txt/cord-000460-h3owwjao.txt cache: ./cache/cord-000460-h3owwjao.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000460-h3owwjao.txt' === file2bib.sh === id: cord-000326-a18rch1f author: Zhou, Jun-Wei title: Apolipoprotein M Gene (APOM) Polymorphism Modifies Metabolic and Disease Traits in Type 2 Diabetes date: 2011-02-24 pages: extension: .txt txt: ./txt/cord-000326-a18rch1f.txt cache: ./cache/cord-000326-a18rch1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000326-a18rch1f.txt' === file2bib.sh === id: cord-000006-104sqoxz author: Bray, Daniel P. title: Composition and Function of Haemolymphatic Tissues in the European Common Shrew date: 2008-10-15 pages: extension: .txt txt: ./txt/cord-000006-104sqoxz.txt cache: ./cache/cord-000006-104sqoxz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000006-104sqoxz.txt' === file2bib.sh === id: cord-001045-jm60nxc2 author: DeLisle, Sylvain title: Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy date: 2013-08-13 pages: extension: .txt txt: ./txt/cord-001045-jm60nxc2.txt cache: ./cache/cord-001045-jm60nxc2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001045-jm60nxc2.txt' === file2bib.sh === id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 pages: extension: .txt txt: ./txt/cord-000265-llilwq1u.txt cache: ./cache/cord-000265-llilwq1u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000265-llilwq1u.txt' === file2bib.sh === id: cord-000539-uh3q65we author: Zhang, Yi title: Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date: 2012-01-03 pages: extension: .txt txt: ./txt/cord-000539-uh3q65we.txt cache: ./cache/cord-000539-uh3q65we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000539-uh3q65we.txt' === file2bib.sh === id: cord-000050-tfcerilc author: Rao, Srinivas title: Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date: 2008-06-18 pages: extension: .txt txt: ./txt/cord-000050-tfcerilc.txt cache: ./cache/cord-000050-tfcerilc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000050-tfcerilc.txt' === file2bib.sh === id: cord-000501-qz68gtd4 author: Greatorex, Jane S. title: Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date: 2011-11-22 pages: extension: .txt txt: ./txt/cord-000501-qz68gtd4.txt cache: ./cache/cord-000501-qz68gtd4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000501-qz68gtd4.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-000638-ss1435el author: Beq, Stephanie title: Altered Thymic Function during Interferon Therapy in HCV-Infected Patients date: 2012-04-16 pages: extension: .txt txt: ./txt/cord-000638-ss1435el.txt cache: ./cache/cord-000638-ss1435el.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000638-ss1435el.txt' === file2bib.sh === id: cord-000581-ewx5xhrb author: Rudge, James W. title: Health System Resource Gaps and Associated Mortality from Pandemic Influenza across Six Asian Territories date: 2012-02-21 pages: extension: .txt txt: ./txt/cord-000581-ewx5xhrb.txt cache: ./cache/cord-000581-ewx5xhrb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000581-ewx5xhrb.txt' === file2bib.sh === id: cord-000079-533xlisc author: Huszthy, Peter C. title: Remission of Invasive, Cancer Stem-Like Glioblastoma Xenografts Using Lentiviral Vector-Mediated Suicide Gene Therapy date: 2009-07-20 pages: extension: .txt txt: ./txt/cord-000079-533xlisc.txt cache: ./cache/cord-000079-533xlisc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000079-533xlisc.txt' === file2bib.sh === id: cord-000082-jy7j8sh0 author: Huang, Ting title: Evidence of Recombination and Genetic Diversity in Human Rhinoviruses in Children with Acute Respiratory Infection date: 2009-07-27 pages: extension: .txt txt: ./txt/cord-000082-jy7j8sh0.txt cache: ./cache/cord-000082-jy7j8sh0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000082-jy7j8sh0.txt' === file2bib.sh === id: cord-000408-pt3b4yc7 author: Lu, Sydney X. title: Ceacam1 Separates Graft-versus-Host-Disease from Graft-versus-Tumor Activity after Experimental Allogeneic Bone Marrow Transplantation date: 2011-07-06 pages: extension: .txt txt: ./txt/cord-000408-pt3b4yc7.txt cache: ./cache/cord-000408-pt3b4yc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000408-pt3b4yc7.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-000237-mticfoic author: Guan, Xuhua title: Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008 date: 2010-07-23 pages: extension: .txt txt: ./txt/cord-000237-mticfoic.txt cache: ./cache/cord-000237-mticfoic.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000237-mticfoic.txt' === file2bib.sh === id: cord-000434-ff2zadol author: Zhao, Rongmao title: Identification of a Highly Conserved H1 Subtype-Specific Epitope with Diagnostic Potential in the Hemagglutinin Protein of Influenza A Virus date: 2011-08-19 pages: extension: .txt txt: ./txt/cord-000434-ff2zadol.txt cache: ./cache/cord-000434-ff2zadol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000434-ff2zadol.txt' === file2bib.sh === id: cord-000580-dcid9emx author: Sällman Almén, Markus title: The Dispanins: A Novel Gene Family of Ancient Origin That Contains 14 Human Members date: 2012-02-20 pages: extension: .txt txt: ./txt/cord-000580-dcid9emx.txt cache: ./cache/cord-000580-dcid9emx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000580-dcid9emx.txt' === file2bib.sh === id: cord-000554-p4ufea6x author: Gao, Wei title: Distinct Regulation of Host Responses by ERK and JNK MAP Kinases in Swine Macrophages Infected with Pandemic (H1N1) 2009 Influenza Virus date: 2012-01-18 pages: extension: .txt txt: ./txt/cord-000554-p4ufea6x.txt cache: ./cache/cord-000554-p4ufea6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000554-p4ufea6x.txt' === file2bib.sh === id: cord-000413-h2e6h076 author: Zhang, Jingyu title: A Conformation-Sensitive Monoclonal Antibody against the A2 Domain of von Willebrand Factor Reduces Its Proteolysis by ADAMTS13 date: 2011-07-11 pages: extension: .txt txt: ./txt/cord-000413-h2e6h076.txt cache: ./cache/cord-000413-h2e6h076.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-000413-h2e6h076.txt' === file2bib.sh === id: cord-000959-nk2thkme author: Downer, Eric J. title: Identifying Early Inflammatory Changes in Monocyte-Derived Macrophages from a Population with IQ-Discrepant Episodic Memory date: 2013-05-06 pages: extension: .txt txt: ./txt/cord-000959-nk2thkme.txt cache: ./cache/cord-000959-nk2thkme.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000959-nk2thkme.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-000742-0r4z1zea author: Vittecoq, Marion title: High Influenza A Virus Infection Rates in Mallards Bred for Hunting in the Camargue, South of France date: 2012-08-27 pages: extension: .txt txt: ./txt/cord-000742-0r4z1zea.txt cache: ./cache/cord-000742-0r4z1zea.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000742-0r4z1zea.txt' === file2bib.sh === id: cord-000536-0mn1gbll author: Hu, Le-Le title: Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions date: 2011-12-29 pages: extension: .txt txt: ./txt/cord-000536-0mn1gbll.txt cache: ./cache/cord-000536-0mn1gbll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000536-0mn1gbll.txt' === file2bib.sh === id: cord-000180-howix091 author: MacLeod, Iain J. title: Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date: 2010-03-05 pages: extension: .txt txt: ./txt/cord-000180-howix091.txt cache: ./cache/cord-000180-howix091.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000180-howix091.txt' === file2bib.sh === id: cord-000726-tonaaft2 author: Chang, Binggong title: Influence of Mabs on PrP(Sc) Formation Using In Vitro and Cell-Free Systems date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-000726-tonaaft2.txt cache: ./cache/cord-000726-tonaaft2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000726-tonaaft2.txt' === file2bib.sh === id: cord-000261-ip32y0j5 author: Becker, Pablo D. title: Generation of Human Antigen-Specific Monoclonal IgM Antibodies Using Vaccinated “Human Immune System” Mice date: 2010-10-04 pages: extension: .txt txt: ./txt/cord-000261-ip32y0j5.txt cache: ./cache/cord-000261-ip32y0j5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000261-ip32y0j5.txt' === file2bib.sh === id: cord-000833-m6abyuvx author: Sekiguchi, Satoshi title: Immunization with a Recombinant Vaccinia Virus That Encodes Nonstructural Proteins of the Hepatitis C Virus Suppresses Viral Protein Levels in Mouse Liver date: 2012-12-17 pages: extension: .txt txt: ./txt/cord-000833-m6abyuvx.txt cache: ./cache/cord-000833-m6abyuvx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000833-m6abyuvx.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-000008-3dgjv0x1 author: Vali, Bahareh title: HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date: 2008-10-20 pages: extension: .txt txt: ./txt/cord-000008-3dgjv0x1.txt cache: ./cache/cord-000008-3dgjv0x1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000008-3dgjv0x1.txt' === file2bib.sh === id: cord-000269-v4jochbe author: Wittekindt, Nicola E. title: Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics date: 2010-10-18 pages: extension: .txt txt: ./txt/cord-000269-v4jochbe.txt cache: ./cache/cord-000269-v4jochbe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000269-v4jochbe.txt' === file2bib.sh === id: cord-000224-2lz03oqb author: Porter, Kristen A. title: Class II Transactivator (CIITA) Enhances Cytoplasmic Processing of HIV-1 Pr55Gag date: 2010-06-24 pages: extension: .txt txt: ./txt/cord-000224-2lz03oqb.txt cache: ./cache/cord-000224-2lz03oqb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000224-2lz03oqb.txt' === file2bib.sh === id: cord-000666-je9t4i6q author: Verbist, Katherine C. title: IL-15 Participates in the Respiratory Innate Immune Response to Influenza Virus Infection date: 2012-05-18 pages: extension: .txt txt: ./txt/cord-000666-je9t4i6q.txt cache: ./cache/cord-000666-je9t4i6q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000666-je9t4i6q.txt' === file2bib.sh === id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 pages: extension: .txt txt: ./txt/cord-000736-6f8vyziv.txt cache: ./cache/cord-000736-6f8vyziv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000736-6f8vyziv.txt' === file2bib.sh === id: cord-000208-th0wddvc author: Cornelissen, Lisette A. H. M. title: A Single Immunization with Soluble Recombinant Trimeric Hemagglutinin Protects Chickens against Highly Pathogenic Avian Influenza Virus H5N1 date: 2010-05-14 pages: extension: .txt txt: ./txt/cord-000208-th0wddvc.txt cache: ./cache/cord-000208-th0wddvc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000208-th0wddvc.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-000182-ni6iyzdn author: He, Zhisong title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features date: 2010-03-11 pages: extension: .txt txt: ./txt/cord-000182-ni6iyzdn.txt cache: ./cache/cord-000182-ni6iyzdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000182-ni6iyzdn.txt' === file2bib.sh === id: cord-000140-5kapn32k author: Wang, Pei-Gang title: Efficient Assembly and Secretion of Recombinant Subviral Particles of the Four Dengue Serotypes Using Native prM and E Proteins date: 2009-12-15 pages: extension: .txt txt: ./txt/cord-000140-5kapn32k.txt cache: ./cache/cord-000140-5kapn32k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000140-5kapn32k.txt' === file2bib.sh === id: cord-000336-57es391o author: Liao, Qiuyan title: Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study date: 2011-03-11 pages: extension: .txt txt: ./txt/cord-000336-57es391o.txt cache: ./cache/cord-000336-57es391o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000336-57es391o.txt' === file2bib.sh === id: cord-000266-xwfptmmv author: Liao, Qiuyan title: Situational Awareness and Health Protective Responses to Pandemic Influenza A (H1N1) in Hong Kong: A Cross-Sectional Study date: 2010-10-12 pages: extension: .txt txt: ./txt/cord-000266-xwfptmmv.txt cache: ./cache/cord-000266-xwfptmmv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000266-xwfptmmv.txt' === file2bib.sh === id: cord-000540-bbjmcdo5 author: Hellard, Eléonore title: True versus False Parasite Interactions: A Robust Method to Take Risk Factors into Account and Its Application to Feline Viruses date: 2012-01-03 pages: extension: .txt txt: ./txt/cord-000540-bbjmcdo5.txt cache: ./cache/cord-000540-bbjmcdo5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000540-bbjmcdo5.txt' === file2bib.sh === id: cord-000176-z76vjkxg author: Nguyen, Jack T. title: Triple Combination of Amantadine, Ribavirin, and Oseltamivir Is Highly Active and Synergistic against Drug Resistant Influenza Virus Strains In Vitro date: 2010-02-22 pages: extension: .txt txt: ./txt/cord-000176-z76vjkxg.txt cache: ./cache/cord-000176-z76vjkxg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000176-z76vjkxg.txt' === file2bib.sh === id: cord-000947-psguw47w author: Feng, Jianyu title: A Study of the Mechanism of the Chaperone-like Function of an scFv of Human Creatine Kinase by Computer Simulation date: 2013-04-24 pages: extension: .txt txt: ./txt/cord-000947-psguw47w.txt cache: ./cache/cord-000947-psguw47w.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000947-psguw47w.txt' === file2bib.sh === id: cord-000166-36bfeoqv author: Tracht, Samantha M. title: Mathematical Modeling of the Effectiveness of Facemasks in Reducing the Spread of Novel Influenza A (H1N1) date: 2010-02-10 pages: extension: .txt txt: ./txt/cord-000166-36bfeoqv.txt cache: ./cache/cord-000166-36bfeoqv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000166-36bfeoqv.txt' === file2bib.sh === id: cord-000321-ee7q7jhv author: Powell, Michael L. title: Further Characterisation of the Translational Termination-Reinitiation Signal of the Influenza B Virus Segment 7 RNA date: 2011-02-08 pages: extension: .txt txt: ./txt/cord-000321-ee7q7jhv.txt cache: ./cache/cord-000321-ee7q7jhv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000321-ee7q7jhv.txt' === file2bib.sh === id: cord-000346-9b6yz3f4 author: Holder, Benjamin P. title: Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model date: 2011-03-24 pages: extension: .txt txt: ./txt/cord-000346-9b6yz3f4.txt cache: ./cache/cord-000346-9b6yz3f4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000346-9b6yz3f4.txt' === file2bib.sh === id: cord-000143-2xvd5ogf author: Napthine, Sawsan title: Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy date: 2009-12-22 pages: extension: .txt txt: ./txt/cord-000143-2xvd5ogf.txt cache: ./cache/cord-000143-2xvd5ogf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000143-2xvd5ogf.txt' === file2bib.sh === id: cord-000725-rafwlw0t author: Hindinger, Claudia title: IFN-γ Signaling to Astrocytes Protects from Autoimmune Mediated Neurological Disability date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-000725-rafwlw0t.txt cache: ./cache/cord-000725-rafwlw0t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000725-rafwlw0t.txt' === file2bib.sh === id: cord-000837-rdpsxb4n author: Perez-Pepe, Marcelo title: BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis date: 2012-12-20 pages: extension: .txt txt: ./txt/cord-000837-rdpsxb4n.txt cache: ./cache/cord-000837-rdpsxb4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000837-rdpsxb4n.txt' === file2bib.sh === id: cord-000642-mkwpuav6 author: Moreira, Rebeca title: Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing date: 2012-04-19 pages: extension: .txt txt: ./txt/cord-000642-mkwpuav6.txt cache: ./cache/cord-000642-mkwpuav6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000642-mkwpuav6.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-000158-d08buwtu author: Corti, Davide title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals date: 2010-01-20 pages: extension: .txt txt: ./txt/cord-000158-d08buwtu.txt cache: ./cache/cord-000158-d08buwtu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000158-d08buwtu.txt' === file2bib.sh === id: cord-000013-pr9i9swk author: Croyle, Maria A. title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice date: 2008-10-29 pages: extension: .txt txt: ./txt/cord-000013-pr9i9swk.txt cache: ./cache/cord-000013-pr9i9swk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000013-pr9i9swk.txt' === file2bib.sh === id: cord-000425-isw6jeir author: Flori, Laurence title: Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation date: 2011-07-29 pages: extension: .txt txt: ./txt/cord-000425-isw6jeir.txt cache: ./cache/cord-000425-isw6jeir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000425-isw6jeir.txt' === file2bib.sh === id: cord-000547-adfigzc1 author: Beniac, Daniel R. title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date: 2012-01-11 pages: extension: .txt txt: ./txt/cord-000547-adfigzc1.txt cache: ./cache/cord-000547-adfigzc1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000547-adfigzc1.txt' === file2bib.sh === id: cord-001078-5m29nugu author: Chen, Xiaorong title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study date: 2013-09-17 pages: extension: .txt txt: ./txt/cord-001078-5m29nugu.txt cache: ./cache/cord-001078-5m29nugu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001078-5m29nugu.txt' === file2bib.sh === id: cord-001120-fxd533b4 author: Everitt, Aaron R. title: Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date: 2013-11-21 pages: extension: .txt txt: ./txt/cord-001120-fxd533b4.txt cache: ./cache/cord-001120-fxd533b4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001120-fxd533b4.txt' === file2bib.sh === id: cord-001142-puj74k7y author: Crescenzo-Chaigne, Bernadette title: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date: 2013-11-21 pages: extension: .txt txt: ./txt/cord-001142-puj74k7y.txt cache: ./cache/cord-001142-puj74k7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001142-puj74k7y.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-001162-z8cbbit3 author: Yun, Heather C. title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection date: 2014-01-08 pages: extension: .txt txt: ./txt/cord-001162-z8cbbit3.txt cache: ./cache/cord-001162-z8cbbit3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001162-z8cbbit3.txt' === file2bib.sh === id: cord-001199-9khx93c0 author: Liu, Fengchen title: Effect of the One-Child Policy on Influenza Transmission in China: A Stochastic Transmission Model date: 2014-02-06 pages: extension: .txt txt: ./txt/cord-001199-9khx93c0.txt cache: ./cache/cord-001199-9khx93c0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-001199-9khx93c0.txt' === file2bib.sh === id: cord-001117-llb4f74a author: Ji, Wen-Jie title: Spironolactone Attenuates Bleomycin-Induced Pulmonary Injury Partially via Modulating Mononuclear Phagocyte Phenotype Switching in Circulating and Alveolar Compartments date: 2013-11-19 pages: extension: .txt txt: ./txt/cord-001117-llb4f74a.txt cache: ./cache/cord-001117-llb4f74a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001117-llb4f74a.txt' === file2bib.sh === id: cord-001368-ymp1pj3r author: Zhang, Chao title: Recombinant Scorpine Produced Using SUMO Fusion Partner in Escherichia coli Has the Activities against Clinically Isolated Bacteria and Inhibits the Plasmodium falciparum Parasitemia In Vitro date: 2014-07-28 pages: extension: .txt txt: ./txt/cord-001368-ymp1pj3r.txt cache: ./cache/cord-001368-ymp1pj3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-001368-ymp1pj3r.txt' === file2bib.sh === id: cord-001213-gxqufddb author: Butt, Azeem Mehmood title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses date: 2014-03-04 pages: extension: .txt txt: ./txt/cord-001213-gxqufddb.txt cache: ./cache/cord-001213-gxqufddb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001213-gxqufddb.txt' === file2bib.sh === id: cord-001099-jirkkkvy author: Yousuf, Mohammad A. title: Caveolin-1 Associated Adenovirus Entry into Human Corneal Cells date: 2013-10-11 pages: extension: .txt txt: ./txt/cord-001099-jirkkkvy.txt cache: ./cache/cord-001099-jirkkkvy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001099-jirkkkvy.txt' === file2bib.sh === id: cord-001207-yjaiybwf author: Sachsenröder, Jana title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 pages: extension: .txt txt: ./txt/cord-001207-yjaiybwf.txt cache: ./cache/cord-001207-yjaiybwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001207-yjaiybwf.txt' === file2bib.sh === id: cord-001129-gi2kswai author: Lemos de Matos, Ana title: Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals date: 2013-11-27 pages: extension: .txt txt: ./txt/cord-001129-gi2kswai.txt cache: ./cache/cord-001129-gi2kswai.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001129-gi2kswai.txt' === file2bib.sh === id: cord-001126-uqr00nzd author: Zhang, Zhicheng title: Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1 date: 2013-11-26 pages: extension: .txt txt: ./txt/cord-001126-uqr00nzd.txt cache: ./cache/cord-001126-uqr00nzd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001126-uqr00nzd.txt' === file2bib.sh === id: cord-001251-forh7lw4 author: Jank, Johanna M. title: The Domain-Specific and Temperature-Dependent Protein Misfolding Phenotype of Variant Medium-Chain acyl-CoA Dehydrogenase date: 2014-04-09 pages: extension: .txt txt: ./txt/cord-001251-forh7lw4.txt cache: ./cache/cord-001251-forh7lw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001251-forh7lw4.txt' === file2bib.sh === id: cord-001145-hc9ssruz author: Akazawa, Yuko title: Endoplasmic Reticulum Stress Contributes to Helicobacter Pylori VacA-Induced Apoptosis date: 2013-12-13 pages: extension: .txt txt: ./txt/cord-001145-hc9ssruz.txt cache: ./cache/cord-001145-hc9ssruz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001145-hc9ssruz.txt' === file2bib.sh === id: cord-001186-jkg7qkj6 author: Skowronski, Danuta M. title: Randomized Controlled Ferret Study to Assess the Direct Impact of 2008–09 Trivalent Inactivated Influenza Vaccine on A(H1N1)pdm09 Disease Risk date: 2014-01-27 pages: extension: .txt txt: ./txt/cord-001186-jkg7qkj6.txt cache: ./cache/cord-001186-jkg7qkj6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001186-jkg7qkj6.txt' === file2bib.sh === id: cord-001254-y2knt8g0 author: Parkhomenko, Taisiya A. title: Comparison of DNA-Hydrolyzing Antibodies from the Cerebrospinal Fluid and Serum of Patients with Multiple Sclerosis date: 2014-04-15 pages: extension: .txt txt: ./txt/cord-001254-y2knt8g0.txt cache: ./cache/cord-001254-y2knt8g0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001254-y2knt8g0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38865 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39512 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38117 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38379 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38576 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38511 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38773 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39019 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39400 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39541 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39441 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39482 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40096 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 40822 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39606 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38450 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39173 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39462 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39473 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41010 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 41232 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42454 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43600 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 44338 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45785 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45929 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45936 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45985 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49109 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49353 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49356 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49706 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49833 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49815 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49983 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49986 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49399 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50130 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50089 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-002890-g7aje88u author: Wood, Paul L. title: Lipidomic analysis of immune activation in equine leptospirosis and Leptospira-vaccinated horses date: 2018-02-23 pages: extension: .txt txt: ./txt/cord-002890-g7aje88u.txt cache: ./cache/cord-002890-g7aje88u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002890-g7aje88u.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49397 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50053 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50451 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50262 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50342 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50421 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-001571-drcfdv9z author: Alvarez, Julio title: Impact of Porcine Epidemic Diarrhea on Performance of Growing Pigs date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-001571-drcfdv9z.txt cache: ./cache/cord-001571-drcfdv9z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001571-drcfdv9z.txt' === file2bib.sh === id: cord-003125-iptisi1m author: Machablishvili, Ann title: Overview of three influenza seasons in Georgia, 2014–2017 date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-003125-iptisi1m.txt cache: ./cache/cord-003125-iptisi1m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003125-iptisi1m.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-001620-yy5gq0ki author: Woo, Hye-Min title: Isolation of Single-Stranded DNA Aptamers That Distinguish Influenza Virus Hemagglutinin Subtype H1 from H5 date: 2015-04-22 pages: extension: .txt txt: ./txt/cord-001620-yy5gq0ki.txt cache: ./cache/cord-001620-yy5gq0ki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001620-yy5gq0ki.txt' === file2bib.sh === id: cord-002834-2htnywef author: Tsuchiaka, Shinobu title: Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population date: 2018-01-11 pages: extension: .txt txt: ./txt/cord-002834-2htnywef.txt cache: ./cache/cord-002834-2htnywef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002834-2htnywef.txt' === file2bib.sh === id: cord-002901-u4ybz8ds author: Yu, Chanki title: Acral melanoma detection using a convolutional neural network for dermoscopy images date: 2018-03-07 pages: extension: .txt txt: ./txt/cord-002901-u4ybz8ds.txt cache: ./cache/cord-002901-u4ybz8ds.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002901-u4ybz8ds.txt' /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-001455-n7quwr4s author: Rapin, Noreen title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date: 2014-11-12 pages: extension: .txt txt: ./txt/cord-001455-n7quwr4s.txt cache: ./cache/cord-001455-n7quwr4s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001455-n7quwr4s.txt' === file2bib.sh === id: cord-001716-lbtdex4p author: Gilca, Rodica title: Mid-Season Estimates of Influenza Vaccine Effectiveness against Influenza A(H3N2) Hospitalization in the Elderly in Quebec, Canada, January 2015 date: 2015-07-22 pages: extension: .txt txt: ./txt/cord-001716-lbtdex4p.txt cache: ./cache/cord-001716-lbtdex4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001716-lbtdex4p.txt' === file2bib.sh === id: cord-001910-6zfz2ns5 author: Zhang, Xianming title: Abdominal Muscle Activity during Mechanical Ventilation Increases Lung Injury in Severe Acute Respiratory Distress Syndrome date: 2016-01-08 pages: extension: .txt txt: ./txt/cord-001910-6zfz2ns5.txt cache: ./cache/cord-001910-6zfz2ns5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001910-6zfz2ns5.txt' === file2bib.sh === id: cord-002180-gsdk5x3e author: Davies, Colin title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date: 2016-08-24 pages: extension: .txt txt: ./txt/cord-002180-gsdk5x3e.txt cache: ./cache/cord-002180-gsdk5x3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002180-gsdk5x3e.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-003507-22ylifqo author: Kelly, J. Daniel title: Projections of Ebola outbreak size and duration with and without vaccine use in Équateur, Democratic Republic of Congo, as of May 27, 2018 date: 2019-03-07 pages: extension: .txt txt: ./txt/cord-003507-22ylifqo.txt cache: ./cache/cord-003507-22ylifqo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003507-22ylifqo.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-001363-irysq6pf author: Liu, Zhenjiang title: SELDI-TOF-MS Proteomic Profiling of Serum, Urine, and Amniotic Fluid in Neural Tube Defects date: 2014-07-23 pages: extension: .txt txt: ./txt/cord-001363-irysq6pf.txt cache: ./cache/cord-001363-irysq6pf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001363-irysq6pf.txt' === file2bib.sh === id: cord-002705-ntokyoai author: Nasir, Nazrila Hairin title: Effectiveness of a fluid chart in outpatient management of suspected dengue fever: A pilot study date: 2017-10-04 pages: extension: .txt txt: ./txt/cord-002705-ntokyoai.txt cache: ./cache/cord-002705-ntokyoai.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002705-ntokyoai.txt' === file2bib.sh === id: cord-001748-7e8px4vx author: Nobach, Daniel title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 pages: extension: .txt txt: ./txt/cord-001748-7e8px4vx.txt cache: ./cache/cord-001748-7e8px4vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001748-7e8px4vx.txt' === file2bib.sh === id: cord-001280-skavefji author: Choi, Sang-Ho title: Usefulness of Cellular Analysis of Bronchoalveolar Lavage Fluid for Predicting the Etiology of Pneumonia in Critically Ill Patients date: 2014-05-13 pages: extension: .txt txt: ./txt/cord-001280-skavefji.txt cache: ./cache/cord-001280-skavefji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001280-skavefji.txt' === file2bib.sh === id: cord-002624-59nznqsd author: Ti, Jinfeng title: Identification of one B-cell epitope from NS1 protein of duck Tembusu virus with monoclonal antibodies date: 2017-07-26 pages: extension: .txt txt: ./txt/cord-002624-59nznqsd.txt cache: ./cache/cord-002624-59nznqsd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002624-59nznqsd.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-002889-fie121ns author: White, Michael title: Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date: 2018-02-23 pages: extension: .txt txt: ./txt/cord-002889-fie121ns.txt cache: ./cache/cord-002889-fie121ns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002889-fie121ns.txt' === file2bib.sh === id: cord-003062-qm8kalyt author: Chowdhury, Fazle Rabbi title: The association between temperature, rainfall and humidity with common climate-sensitive infectious diseases in Bangladesh date: 2018-06-21 pages: extension: .txt txt: ./txt/cord-003062-qm8kalyt.txt cache: ./cache/cord-003062-qm8kalyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003062-qm8kalyt.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-001343-3euy4u9k author: Wang, Yadong title: A Multi-Method Approach to Curriculum Development for In-Service Training in China’s Newly Established Health Emergency Response Offices date: 2014-06-27 pages: extension: .txt txt: ./txt/cord-001343-3euy4u9k.txt cache: ./cache/cord-001343-3euy4u9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001343-3euy4u9k.txt' === file2bib.sh === id: cord-001546-ndz3oarf author: Ayithan, Natarajan title: Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date: 2015-02-26 pages: extension: .txt txt: ./txt/cord-001546-ndz3oarf.txt cache: ./cache/cord-001546-ndz3oarf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001546-ndz3oarf.txt' === file2bib.sh === id: cord-002044-9xgt3tf4 author: Hendiger, Jacek title: Influence of the Pressure Difference and Door Swing on Heavy Contaminants Migration between Rooms date: 2016-05-12 pages: extension: .txt txt: ./txt/cord-002044-9xgt3tf4.txt cache: ./cache/cord-002044-9xgt3tf4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002044-9xgt3tf4.txt' === file2bib.sh === id: cord-001761-yvd1n42f author: Yoshimura, Takeo title: Controlled Microwave Heating Accelerates Rolling Circle Amplification date: 2015-09-08 pages: extension: .txt txt: ./txt/cord-001761-yvd1n42f.txt cache: ./cache/cord-001761-yvd1n42f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-001761-yvd1n42f.txt' === file2bib.sh === id: cord-001359-c1uom5f7 author: Oslund, Karen L. title: Synergistic Up-Regulation of CXCL10 by Virus and IFN γ in Human Airway Epithelial Cells date: 2014-07-17 pages: extension: .txt txt: ./txt/cord-001359-c1uom5f7.txt cache: ./cache/cord-001359-c1uom5f7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001359-c1uom5f7.txt' === file2bib.sh === id: cord-001537-i34vmfpp author: Lima, Francisco Esmaile de Sales title: Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil date: 2015-02-17 pages: extension: .txt txt: ./txt/cord-001537-i34vmfpp.txt cache: ./cache/cord-001537-i34vmfpp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001537-i34vmfpp.txt' === file2bib.sh === id: cord-003377-9vkhptas author: Wu, Tong title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia date: 2018-12-19 pages: extension: .txt txt: ./txt/cord-003377-9vkhptas.txt cache: ./cache/cord-003377-9vkhptas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 210 resourceName b'cord-003377-9vkhptas.txt' === file2bib.sh === id: cord-004068-d66lwylf author: Shimoda, Tomoko title: Effect of thermal control of dry fomites on regulating the survival of human pathogenic bacteria responsible for nosocomial infections date: 2019-12-27 pages: extension: .txt txt: ./txt/cord-004068-d66lwylf.txt cache: ./cache/cord-004068-d66lwylf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004068-d66lwylf.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-001446-mpuovmeb author: Bratcher, Preston E. title: Factors Influencing the Measurement of Plasma/Serum Surfactant Protein D Levels by ELISA date: 2014-11-03 pages: extension: .txt txt: ./txt/cord-001446-mpuovmeb.txt cache: ./cache/cord-001446-mpuovmeb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001446-mpuovmeb.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-001843-ceatyj3o author: Huang, Yong title: Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date: 2015-11-06 pages: extension: .txt txt: ./txt/cord-001843-ceatyj3o.txt cache: ./cache/cord-001843-ceatyj3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001843-ceatyj3o.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-001420-b4zcvd04 author: Crescenzo-Chaigne, Bernadette title: Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date: 2014-09-30 pages: extension: .txt txt: ./txt/cord-001420-b4zcvd04.txt cache: ./cache/cord-001420-b4zcvd04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001420-b4zcvd04.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-001421-6t5puo6p author: Marfà, Santiago title: Lack of a 5.9 kDa Peptide C-Terminal Fragment of Fibrinogen α Chain Precedes Fibrosis Progression in Patients with Liver Disease date: 2014-10-02 pages: extension: .txt txt: ./txt/cord-001421-6t5puo6p.txt cache: ./cache/cord-001421-6t5puo6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001421-6t5puo6p.txt' === file2bib.sh === id: cord-001387-2g9dc5z4 author: McIntyre, K. Marie title: A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe date: 2014-08-19 pages: extension: .txt txt: ./txt/cord-001387-2g9dc5z4.txt cache: ./cache/cord-001387-2g9dc5z4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001387-2g9dc5z4.txt' === file2bib.sh === id: cord-001605-8p06bpt1 author: Sapmak, Ariya title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date: 2015-04-13 pages: extension: .txt txt: ./txt/cord-001605-8p06bpt1.txt cache: ./cache/cord-001605-8p06bpt1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001605-8p06bpt1.txt' === file2bib.sh === id: cord-002560-pue5q5wp author: Moreno, Paloma S. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 pages: extension: .txt txt: ./txt/cord-002560-pue5q5wp.txt cache: ./cache/cord-002560-pue5q5wp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002560-pue5q5wp.txt' === file2bib.sh === id: cord-002426-5e1xn7kj author: Falcón-Lezama, Jorge Abelardo title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico date: 2017-02-22 pages: extension: .txt txt: ./txt/cord-002426-5e1xn7kj.txt cache: ./cache/cord-002426-5e1xn7kj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002426-5e1xn7kj.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-003712-mafz21no author: Perez Vidakovics, Maria Laura A. title: Junín virus induces autophagy in human A549 cells date: 2019-06-19 pages: extension: .txt txt: ./txt/cord-003712-mafz21no.txt cache: ./cache/cord-003712-mafz21no.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003712-mafz21no.txt' === file2bib.sh === id: cord-001601-tsuz3j40 author: Ngan, Luong Thi My title: Antiviral Activity and Possible Mechanism of Action of Constituents Identified in Paeonia lactiflora Root toward Human Rhinoviruses date: 2015-04-10 pages: extension: .txt txt: ./txt/cord-001601-tsuz3j40.txt cache: ./cache/cord-001601-tsuz3j40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001601-tsuz3j40.txt' === file2bib.sh === id: cord-001275-a9o2dvke author: Chen, Xue title: A Vaccine of L2 Epitope Repeats Fused with a Modified IgG1 Fc Induced Cross-Neutralizing Antibodies and Protective Immunity against Divergent Human Papillomavirus Types date: 2014-05-06 pages: extension: .txt txt: ./txt/cord-001275-a9o2dvke.txt cache: ./cache/cord-001275-a9o2dvke.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001275-a9o2dvke.txt' === file2bib.sh === id: cord-001263-hqxiyxfj author: Kam, Yiu-Wing title: Unique Epitopes Recognized by Antibodies Induced in Chikungunya Virus-Infected Non-Human Primates: Implications for the Study of Immunopathology and Vaccine Development date: 2014-04-22 pages: extension: .txt txt: ./txt/cord-001263-hqxiyxfj.txt cache: ./cache/cord-001263-hqxiyxfj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001263-hqxiyxfj.txt' === file2bib.sh === id: cord-001447-oi7bkm4z author: Dhanasekaran, Sakthivel title: Toll-Like Receptor Responses to Peste des petits ruminants Virus in Goats and Water Buffalo date: 2014-11-04 pages: extension: .txt txt: ./txt/cord-001447-oi7bkm4z.txt cache: ./cache/cord-001447-oi7bkm4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001447-oi7bkm4z.txt' === file2bib.sh === id: cord-002043-z1b7pj3s author: Wang, Xue-Yang title: Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains date: 2016-05-11 pages: extension: .txt txt: ./txt/cord-002043-z1b7pj3s.txt cache: ./cache/cord-002043-z1b7pj3s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002043-z1b7pj3s.txt' === file2bib.sh === id: cord-002305-qq73gr9y author: Anson, Marie title: Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool date: 2016-11-23 pages: extension: .txt txt: ./txt/cord-002305-qq73gr9y.txt cache: ./cache/cord-002305-qq73gr9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002305-qq73gr9y.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-002473-2kpxhzbe author: Das, Jayanta Kumar title: Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach date: 2017-03-31 pages: extension: .txt txt: ./txt/cord-002473-2kpxhzbe.txt cache: ./cache/cord-002473-2kpxhzbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002473-2kpxhzbe.txt' === file2bib.sh === id: cord-002621-sq5iod1w author: Attia, Mohamed I. title: New hydrazonoindolin-2-ones: Synthesis, exploration of the possible anti-proliferative mechanism of action and encapsulation into PLGA microspheres date: 2017-07-25 pages: extension: .txt txt: ./txt/cord-002621-sq5iod1w.txt cache: ./cache/cord-002621-sq5iod1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002621-sq5iod1w.txt' === file2bib.sh === id: cord-001432-d4zavkcn author: Nishida, Yoriko title: Antibody-Validated Proteins in Inflamed Islets of Fulminant Type 1 Diabetes Profiled by Laser-Capture Microdissection Followed by Mass Spectrometry date: 2014-10-16 pages: extension: .txt txt: ./txt/cord-001432-d4zavkcn.txt cache: ./cache/cord-001432-d4zavkcn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001432-d4zavkcn.txt' === file2bib.sh === id: cord-001982-arczqdza author: Khajah, Maitham A. title: Anti-Inflammatory Action of Angiotensin 1-7 in Experimental Colitis date: 2016-03-10 pages: extension: .txt txt: ./txt/cord-001982-arczqdza.txt cache: ./cache/cord-001982-arczqdza.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001982-arczqdza.txt' === file2bib.sh === id: cord-001898-ntqyjqqk author: Huang, Chih-Wei title: Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly date: 2016-01-05 pages: extension: .txt txt: ./txt/cord-001898-ntqyjqqk.txt cache: ./cache/cord-001898-ntqyjqqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001898-ntqyjqqk.txt' === file2bib.sh === id: cord-002811-5hrydciz author: Hercik, Christine title: A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania date: 2017-12-29 pages: extension: .txt txt: ./txt/cord-002811-5hrydciz.txt cache: ./cache/cord-002811-5hrydciz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002811-5hrydciz.txt' === file2bib.sh === id: cord-001219-517gka4h author: Timpka, Toomas title: Intentions to Perform Non-Pharmaceutical Protective Behaviors during Influenza Outbreaks in Sweden: A Cross-Sectional Study following a Mass Vaccination Campaign date: 2014-03-07 pages: extension: .txt txt: ./txt/cord-001219-517gka4h.txt cache: ./cache/cord-001219-517gka4h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001219-517gka4h.txt' === file2bib.sh === id: cord-001909-yy9xp5ms author: Buß, O. title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters date: 2016-01-05 pages: extension: .txt txt: ./txt/cord-001909-yy9xp5ms.txt cache: ./cache/cord-001909-yy9xp5ms.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001909-yy9xp5ms.txt' === file2bib.sh === id: cord-002094-7tewne3a author: Tago, Damian title: The Impact of Farmers’ Strategic Behavior on the Spread of Animal Infectious Diseases date: 2016-06-14 pages: extension: .txt txt: ./txt/cord-002094-7tewne3a.txt cache: ./cache/cord-002094-7tewne3a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002094-7tewne3a.txt' === file2bib.sh === id: cord-003270-vu9b5a14 author: Panahi, Heidar Ali title: A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-003270-vu9b5a14.txt cache: ./cache/cord-003270-vu9b5a14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003270-vu9b5a14.txt' === file2bib.sh === id: cord-001599-pfdnmzx2 author: Wee, Yin Shen title: Age-Related Onset of Obesity Corresponds with Metabolic Dysregulation and Altered Microglia Morphology in Mice Deficient for Ifitm Proteins date: 2015-04-09 pages: extension: .txt txt: ./txt/cord-001599-pfdnmzx2.txt cache: ./cache/cord-001599-pfdnmzx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001599-pfdnmzx2.txt' === file2bib.sh === id: cord-003484-ylpa702c author: Blázquez, Elena title: Evaluation of the effectiveness of the SurePure Turbulator ultraviolet-C irradiation equipment on inactivation of different enveloped and non-enveloped viruses inoculated in commercially collected liquid animal plasma date: 2019-02-21 pages: extension: .txt txt: ./txt/cord-003484-ylpa702c.txt cache: ./cache/cord-003484-ylpa702c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003484-ylpa702c.txt' === file2bib.sh === id: cord-001958-2gt3fwpy author: Meseda, Clement A. title: Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date: 2016-02-19 pages: extension: .txt txt: ./txt/cord-001958-2gt3fwpy.txt cache: ./cache/cord-001958-2gt3fwpy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001958-2gt3fwpy.txt' === file2bib.sh === id: cord-001964-iy6qzq58 author: Muñoz-González, Sara title: Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date: 2016-02-26 pages: extension: .txt txt: ./txt/cord-001964-iy6qzq58.txt cache: ./cache/cord-001964-iy6qzq58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001964-iy6qzq58.txt' === file2bib.sh === id: cord-002222-rgqwm3vb author: Olarte-Castillo, Ximena A. title: Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date: 2016-09-23 pages: extension: .txt txt: ./txt/cord-002222-rgqwm3vb.txt cache: ./cache/cord-002222-rgqwm3vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002222-rgqwm3vb.txt' === file2bib.sh === id: cord-004091-gex0zvoa author: Abdulkareem, Shaheen A. title: Risk perception and behavioral change during epidemics: Comparing models of individual and collective learning date: 2020-01-06 pages: extension: .txt txt: ./txt/cord-004091-gex0zvoa.txt cache: ./cache/cord-004091-gex0zvoa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004091-gex0zvoa.txt' === file2bib.sh === id: cord-001383-hww0watl author: Li, Wenchao title: Self-Assembly and Release of Peste des Petits Ruminants Virus-Like Particles in an Insect Cell-Baculovirus System and Their Immunogenicity in Mice and Goats date: 2014-08-12 pages: extension: .txt txt: ./txt/cord-001383-hww0watl.txt cache: ./cache/cord-001383-hww0watl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001383-hww0watl.txt' === file2bib.sh === id: cord-002141-9mxi4dzi author: Memczak, Henry title: Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding date: 2016-07-14 pages: extension: .txt txt: ./txt/cord-002141-9mxi4dzi.txt cache: ./cache/cord-002141-9mxi4dzi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002141-9mxi4dzi.txt' === file2bib.sh === id: cord-001781-afg1nmib author: Saksena, Sumeet title: Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam date: 2015-09-23 pages: extension: .txt txt: ./txt/cord-001781-afg1nmib.txt cache: ./cache/cord-001781-afg1nmib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001781-afg1nmib.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-002100-dt5zvebj author: He, Yonghua title: Transgenic Soybean Production of Bioactive Human Epidermal Growth Factor (EGF) date: 2016-06-17 pages: extension: .txt txt: ./txt/cord-002100-dt5zvebj.txt cache: ./cache/cord-002100-dt5zvebj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002100-dt5zvebj.txt' === file2bib.sh === id: cord-001435-ebl8yc92 author: Hoppe, Sebastian title: Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date: 2014-10-21 pages: extension: .txt txt: ./txt/cord-001435-ebl8yc92.txt cache: ./cache/cord-001435-ebl8yc92.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001435-ebl8yc92.txt' === file2bib.sh === id: cord-002602-2qvyhjlp author: Roy, Amrita title: Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants date: 2017-07-10 pages: extension: .txt txt: ./txt/cord-002602-2qvyhjlp.txt cache: ./cache/cord-002602-2qvyhjlp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002602-2qvyhjlp.txt' === file2bib.sh === id: cord-004017-gcmpatlb author: Errecaborde, Kaylee Myhre title: Factors that enable effective One Health collaborations - A scoping review of the literature date: 2019-12-04 pages: extension: .txt txt: ./txt/cord-004017-gcmpatlb.txt cache: ./cache/cord-004017-gcmpatlb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004017-gcmpatlb.txt' === file2bib.sh === id: cord-001249-awn9ayy6 author: Lasecka, Lidia title: The Nairovirus Nairobi Sheep Disease Virus/Ganjam Virus Induces the Translocation of Protein Disulphide Isomerase-Like Oxidoreductases from the Endoplasmic Reticulum to the Cell Surface and the Extracellular Space date: 2014-04-08 pages: extension: .txt txt: ./txt/cord-001249-awn9ayy6.txt cache: ./cache/cord-001249-awn9ayy6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001249-awn9ayy6.txt' === file2bib.sh === id: cord-003548-zuwt7gk5 author: Cai, Haiming title: Modulating the 3’ end-DNA and the fermentation process for enhanced production and biological activity of porcine interferon-gamma date: 2019-03-26 pages: extension: .txt txt: ./txt/cord-003548-zuwt7gk5.txt cache: ./cache/cord-003548-zuwt7gk5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003548-zuwt7gk5.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-251979-j3mme15e author: Kandeel, Amr title: Morbidity, Mortality, and Seasonality of Influenza Hospitalizations in Egypt, November 2007-November 2014 date: 2016-09-08 pages: extension: .txt txt: ./txt/cord-251979-j3mme15e.txt cache: ./cache/cord-251979-j3mme15e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-251979-j3mme15e.txt' === file2bib.sh === id: cord-001734-bbeznd3r author: Gupta, Garvita title: NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date: 2015-08-10 pages: extension: .txt txt: ./txt/cord-001734-bbeznd3r.txt cache: ./cache/cord-001734-bbeznd3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001734-bbeznd3r.txt' === file2bib.sh === id: cord-048492-4z38v9rg author: Tang, Julian W. title: Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006) date: 2008-07-23 pages: extension: .txt txt: ./txt/cord-048492-4z38v9rg.txt cache: ./cache/cord-048492-4z38v9rg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-048492-4z38v9rg.txt' === file2bib.sh === id: cord-011798-uss38ped author: Li, Guowei title: Intellectual capital and the efficiency of SMEs in the transition economy China; Do financial resources strengthen the routes? date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-011798-uss38ped.txt cache: ./cache/cord-011798-uss38ped.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011798-uss38ped.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 53604 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55323 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 54889 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 54882 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55279 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55182 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55208 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55089 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55617 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55408 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55447 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55334 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55300 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55274 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 56047 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 56041 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55624 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55625 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57185 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-253436-dz84icdc author: Wille, Michelle title: High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl date: 2016-03-03 pages: extension: .txt txt: ./txt/cord-253436-dz84icdc.txt cache: ./cache/cord-253436-dz84icdc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-253436-dz84icdc.txt' === file2bib.sh === id: cord-256326-3ebcuzd6 author: Liotta, Giuseppe title: Is social connectedness a risk factor for the spreading of COVID-19 among older adults? The Italian paradox date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-256326-3ebcuzd6.txt cache: ./cache/cord-256326-3ebcuzd6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256326-3ebcuzd6.txt' === file2bib.sh === id: cord-267189-xq70rn1j author: Wang, Xinyu title: Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-267189-xq70rn1j.txt cache: ./cache/cord-267189-xq70rn1j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267189-xq70rn1j.txt' === file2bib.sh === id: cord-258366-fu9b446y author: Couto, Carla R. title: Fighting Misconceptions to Improve Compliance with Influenza Vaccination among Health Care Workers: An Educational Project date: 2012-02-06 pages: extension: .txt txt: ./txt/cord-258366-fu9b446y.txt cache: ./cache/cord-258366-fu9b446y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258366-fu9b446y.txt' === file2bib.sh === id: cord-254000-pbzcupjg author: Suvannachart, Pukkapol title: Repeatability, reproducibility, agreement, and safety of Tono-Pen tip cover for intraocular measurement using latex and polyethylene wrap date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-254000-pbzcupjg.txt cache: ./cache/cord-254000-pbzcupjg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254000-pbzcupjg.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-254025-j1l0mder author: de Melo, Andreia C. title: Cancer inpatients with COVID-19: A report from the Brazilian National Cancer Institute date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-254025-j1l0mder.txt cache: ./cache/cord-254025-j1l0mder.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254025-j1l0mder.txt' === file2bib.sh === id: cord-272445-0xauff51 author: Naaber, Paul title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-272445-0xauff51.txt cache: ./cache/cord-272445-0xauff51.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272445-0xauff51.txt' === file2bib.sh === id: cord-252795-x66zqmgv author: Islam, Md. Akhtarul title: Depression and anxiety among university students during the COVID-19 pandemic in Bangladesh: A web-based cross-sectional survey date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-252795-x66zqmgv.txt cache: ./cache/cord-252795-x66zqmgv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252795-x66zqmgv.txt' === file2bib.sh === id: cord-260572-vd65ygtm author: Kim, Curi title: Comparison of Nasopharyngeal and Oropharyngeal Swabs for the Diagnosis of Eight Respiratory Viruses by Real-Time Reverse Transcription-PCR Assays date: 2011-06-30 pages: extension: .txt txt: ./txt/cord-260572-vd65ygtm.txt cache: ./cache/cord-260572-vd65ygtm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260572-vd65ygtm.txt' === file2bib.sh === id: cord-258243-2utl2mfl author: Chen, Jeng-Wen title: Factors associated with changing indications for adenotonsillectomy: A population-based longitudinal study date: 2018-05-29 pages: extension: .txt txt: ./txt/cord-258243-2utl2mfl.txt cache: ./cache/cord-258243-2utl2mfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258243-2utl2mfl.txt' === file2bib.sh === id: cord-254117-2ttwaegh author: Priest, Patricia C. title: Thermal Image Scanning for Influenza Border Screening: Results of an Airport Screening Study date: 2011-01-05 pages: extension: .txt txt: ./txt/cord-254117-2ttwaegh.txt cache: ./cache/cord-254117-2ttwaegh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254117-2ttwaegh.txt' === file2bib.sh === id: cord-253056-765rs3e7 author: Dionne, Audrey title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date: 2018-10-17 pages: extension: .txt txt: ./txt/cord-253056-765rs3e7.txt cache: ./cache/cord-253056-765rs3e7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253056-765rs3e7.txt' === file2bib.sh === id: cord-252739-1manzf3l author: Zheng, Yueming title: Hexachlorophene Is a Potent KCNQ1/KCNE1 Potassium Channel Activator Which Rescues LQTs Mutants date: 2012-12-12 pages: extension: .txt txt: ./txt/cord-252739-1manzf3l.txt cache: ./cache/cord-252739-1manzf3l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252739-1manzf3l.txt' === file2bib.sh === id: cord-263276-keyu60in author: Zhou, Weimin title: Prevalence of Herpes and Respiratory Viruses in Induced Sputum among Hospitalized Children with Non Typical Bacterial Community-Acquired Pneumonia date: 2013-11-18 pages: extension: .txt txt: ./txt/cord-263276-keyu60in.txt cache: ./cache/cord-263276-keyu60in.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263276-keyu60in.txt' === file2bib.sh === id: cord-265812-1hcp36cw author: De Jong, Cornelis N. title: Etanercept for steroid-refractory acute graft-versus-host disease: A single center experience date: 2017-10-26 pages: extension: .txt txt: ./txt/cord-265812-1hcp36cw.txt cache: ./cache/cord-265812-1hcp36cw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265812-1hcp36cw.txt' === file2bib.sh === id: cord-267519-a0bcmjkn author: Bravi, Francesca title: Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-267519-a0bcmjkn.txt cache: ./cache/cord-267519-a0bcmjkn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267519-a0bcmjkn.txt' === file2bib.sh === id: cord-267566-gdjl0qmu author: Kweon, Oh Joo title: Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-267566-gdjl0qmu.txt cache: ./cache/cord-267566-gdjl0qmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267566-gdjl0qmu.txt' === file2bib.sh === id: cord-254825-c5d0wul9 author: Kim, Sei Won title: Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-254825-c5d0wul9.txt cache: ./cache/cord-254825-c5d0wul9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254825-c5d0wul9.txt' === file2bib.sh === id: cord-261908-olcuq6tm author: Lai, Ka-Man title: Propagation of Respiratory Aerosols by the Vuvuzela date: 2011-05-23 pages: extension: .txt txt: ./txt/cord-261908-olcuq6tm.txt cache: ./cache/cord-261908-olcuq6tm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-261908-olcuq6tm.txt' === file2bib.sh === id: cord-273764-itu39mln author: Li, Taisheng title: Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date: 2006-12-20 pages: extension: .txt txt: ./txt/cord-273764-itu39mln.txt cache: ./cache/cord-273764-itu39mln.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273764-itu39mln.txt' === file2bib.sh === id: cord-048360-n9sih438 author: Villard, Viviane title: Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date: 2007-07-25 pages: extension: .txt txt: ./txt/cord-048360-n9sih438.txt cache: ./cache/cord-048360-n9sih438.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048360-n9sih438.txt' === file2bib.sh === id: cord-266799-t7lqlv41 author: Rotejanaprasert, Chawarat title: Preliminary estimation of temporal and spatiotemporal dynamic measures of COVID-19 transmission in Thailand date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-266799-t7lqlv41.txt cache: ./cache/cord-266799-t7lqlv41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266799-t7lqlv41.txt' === file2bib.sh === id: cord-254313-g2oc32dm author: Klink, Thomas title: Evaluating the diagnostic accuracy of the WHO Severe Acute Respiratory Infection (SARI) criteria in Middle Eastern children under two years over three respiratory seasons date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-254313-g2oc32dm.txt cache: ./cache/cord-254313-g2oc32dm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254313-g2oc32dm.txt' === file2bib.sh === id: cord-013356-y6vceq2x author: Peace, Angela title: Orchard layout and plant traits influence fruit yield more strongly than pollinator behaviour and density in a dioecious crop date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-013356-y6vceq2x.txt cache: ./cache/cord-013356-y6vceq2x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013356-y6vceq2x.txt' === file2bib.sh === id: cord-257603-ov0b8yub author: Azlan, Arina Anis title: Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-257603-ov0b8yub.txt cache: ./cache/cord-257603-ov0b8yub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257603-ov0b8yub.txt' === file2bib.sh === id: cord-272655-qeojdpez author: Remolina, Yuly Andrea title: Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia date: 2015-11-17 pages: extension: .txt txt: ./txt/cord-272655-qeojdpez.txt cache: ./cache/cord-272655-qeojdpez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272655-qeojdpez.txt' === file2bib.sh === id: cord-257217-f9sdt7ax author: Nunes, Marta C. title: Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date: 2014-02-03 pages: extension: .txt txt: ./txt/cord-257217-f9sdt7ax.txt cache: ./cache/cord-257217-f9sdt7ax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257217-f9sdt7ax.txt' === file2bib.sh === id: cord-255588-nh34lgdh author: Guo, Fang title: RO 90-7501 Enhances TLR3 and RLR Agonist Induced Antiviral Response date: 2012-10-03 pages: extension: .txt txt: ./txt/cord-255588-nh34lgdh.txt cache: ./cache/cord-255588-nh34lgdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255588-nh34lgdh.txt' === file2bib.sh === id: cord-263464-fdosch11 author: Nuvey, Francis Sena title: Evaluation of the sentinel surveillance system for influenza-like illnesses in the Greater Accra region, Ghana, 2018 date: 2019-03-14 pages: extension: .txt txt: ./txt/cord-263464-fdosch11.txt cache: ./cache/cord-263464-fdosch11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-263464-fdosch11.txt' === file2bib.sh === id: cord-254340-e1x0z3rh author: Cruz, Christian Joy Pattawi title: Exploring the young demographic profile of COVID-19 cases in Hong Kong: Evidence from migration and travel history data date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-254340-e1x0z3rh.txt cache: ./cache/cord-254340-e1x0z3rh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254340-e1x0z3rh.txt' === file2bib.sh === id: cord-265138-i5m3ax7g author: Wang, Xi-Ling title: Model Selection in Time Series Studies of Influenza-Associated Mortality date: 2012-06-20 pages: extension: .txt txt: ./txt/cord-265138-i5m3ax7g.txt cache: ./cache/cord-265138-i5m3ax7g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265138-i5m3ax7g.txt' === file2bib.sh === id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 pages: extension: .txt txt: ./txt/cord-260647-7bjhobg7.txt cache: ./cache/cord-260647-7bjhobg7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260647-7bjhobg7.txt' === file2bib.sh === id: cord-255384-tljyx6ua author: Decaro, Nicola title: Full-Genome Analysis of a Canine Pneumovirus Causing Acute Respiratory Disease in Dogs, Italy date: 2014-01-06 pages: extension: .txt txt: ./txt/cord-255384-tljyx6ua.txt cache: ./cache/cord-255384-tljyx6ua.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255384-tljyx6ua.txt' === file2bib.sh === id: cord-255013-njpuc475 author: He, Xiaocui title: Establishment of Myotis myotis Cell Lines - Model for Investigation of Host-Pathogen Interaction in a Natural Host for Emerging Viruses date: 2014-10-08 pages: extension: .txt txt: ./txt/cord-255013-njpuc475.txt cache: ./cache/cord-255013-njpuc475.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255013-njpuc475.txt' === file2bib.sh === id: cord-261410-kb91eagd author: Park, Ji Young title: Clinical Features and Courses of Adenovirus Pneumonia in Healthy Young Adults during an Outbreak among Korean Military Personnel date: 2017-01-23 pages: extension: .txt txt: ./txt/cord-261410-kb91eagd.txt cache: ./cache/cord-261410-kb91eagd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261410-kb91eagd.txt' === file2bib.sh === id: cord-013099-j816c3tw author: Blease, Charlotte title: US primary care in 2029: A Delphi survey on the impact of machine learning date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-013099-j816c3tw.txt cache: ./cache/cord-013099-j816c3tw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013099-j816c3tw.txt' === file2bib.sh === id: cord-273343-als886fe author: McClenahan, Shasta D. title: Discovery of a Bovine Enterovirus in Alpaca date: 2013-08-12 pages: extension: .txt txt: ./txt/cord-273343-als886fe.txt cache: ./cache/cord-273343-als886fe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273343-als886fe.txt' === file2bib.sh === id: cord-267307-kyh0xsrp author: Kasting, Monica L. title: Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date: 2020-11-04 pages: extension: .txt txt: ./txt/cord-267307-kyh0xsrp.txt cache: ./cache/cord-267307-kyh0xsrp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267307-kyh0xsrp.txt' === file2bib.sh === id: cord-262759-ec2c25q3 author: Hsieh, Yi-Ting title: Glucose-6-Phosphate Dehydrogenase (G6PD)-Deficient Epithelial Cells Are Less Tolerant to Infection by Staphylococcus aureus date: 2013-11-04 pages: extension: .txt txt: ./txt/cord-262759-ec2c25q3.txt cache: ./cache/cord-262759-ec2c25q3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262759-ec2c25q3.txt' === file2bib.sh === id: cord-263453-7v4y02j6 author: Nishiura, Hiroshi title: Early Epidemiological Assessment of the Virulence of Emerging Infectious Diseases: A Case Study of an Influenza Pandemic date: 2009-08-31 pages: extension: .txt txt: ./txt/cord-263453-7v4y02j6.txt cache: ./cache/cord-263453-7v4y02j6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263453-7v4y02j6.txt' === file2bib.sh === id: cord-262876-civfvk45 author: Su, Tong title: Knowledge Levels and Training Needs of Disaster Medicine among Health Professionals, Medical Students, and Local Residents in Shanghai, China date: 2013-06-24 pages: extension: .txt txt: ./txt/cord-262876-civfvk45.txt cache: ./cache/cord-262876-civfvk45.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262876-civfvk45.txt' === file2bib.sh === id: cord-013334-cptu0k7s author: Holst-Hansen, Joachim A. title: Does the size of rewards influence performance in cognitively demanding tasks? date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-013334-cptu0k7s.txt cache: ./cache/cord-013334-cptu0k7s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013334-cptu0k7s.txt' === file2bib.sh === id: cord-266797-uglsx7se author: Anastassopoulou, Cleo title: Data-based analysis, modelling and forecasting of the COVID-19 outbreak date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-266797-uglsx7se.txt cache: ./cache/cord-266797-uglsx7se.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-266797-uglsx7se.txt' === file2bib.sh === id: cord-256424-t3dtabi4 author: Bousbia, Sabri title: Repertoire of Intensive Care Unit Pneumonia Microbiota date: 2012-02-28 pages: extension: .txt txt: ./txt/cord-256424-t3dtabi4.txt cache: ./cache/cord-256424-t3dtabi4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256424-t3dtabi4.txt' === file2bib.sh === id: cord-267605-efb10j3u author: Zheng, Li-Zhen title: Steroid-Associated Hip Joint Collapse in Bipedal Emus date: 2013-10-21 pages: extension: .txt txt: ./txt/cord-267605-efb10j3u.txt cache: ./cache/cord-267605-efb10j3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267605-efb10j3u.txt' === file2bib.sh === id: cord-262748-v4xue7ha author: Xu, Yongtao title: Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date: 2015-12-04 pages: extension: .txt txt: ./txt/cord-262748-v4xue7ha.txt cache: ./cache/cord-262748-v4xue7ha.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262748-v4xue7ha.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-259771-653opx0h author: Dwivedi, Varun title: Biodegradable Nanoparticle-Entrapped Vaccine Induces Cross-Protective Immune Response against a Virulent Heterologous Respiratory Viral Infection in Pigs date: 2012-12-11 pages: extension: .txt txt: ./txt/cord-259771-653opx0h.txt cache: ./cache/cord-259771-653opx0h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259771-653opx0h.txt' === file2bib.sh === id: cord-268524-lr51ubz5 author: Droit-Volet, Sylvie title: Time and Covid-19 stress in the lockdown situation: Time free, «Dying» of boredom and sadness date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-268524-lr51ubz5.txt cache: ./cache/cord-268524-lr51ubz5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268524-lr51ubz5.txt' === file2bib.sh === id: cord-255351-vp19ydce author: Lanata, Claudio F. title: Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review date: 2013-09-04 pages: extension: .txt txt: ./txt/cord-255351-vp19ydce.txt cache: ./cache/cord-255351-vp19ydce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255351-vp19ydce.txt' === file2bib.sh === id: cord-260653-5qwtvm9x author: Chikhlikar, Priya title: DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques date: 2006-12-27 pages: extension: .txt txt: ./txt/cord-260653-5qwtvm9x.txt cache: ./cache/cord-260653-5qwtvm9x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260653-5qwtvm9x.txt' === file2bib.sh === id: cord-271660-5sfkhg19 author: Sun, Hsin-Yun title: Impact of introducing fluorescent microscopy on hospital tuberculosis control: A before-after study at a high caseload medical center in Taiwan date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-271660-5sfkhg19.txt cache: ./cache/cord-271660-5sfkhg19.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271660-5sfkhg19.txt' === file2bib.sh === id: cord-048339-nzh87aux author: Caley, Peter title: The Waiting Time for Inter-Country Spread of Pandemic Influenza date: 2007-01-03 pages: extension: .txt txt: ./txt/cord-048339-nzh87aux.txt cache: ./cache/cord-048339-nzh87aux.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048339-nzh87aux.txt' === file2bib.sh === id: cord-263684-3535k3op author: Tang, Julian W. title: Different Types of Door-Opening Motions as Contributing Factors to Containment Failures in Hospital Isolation Rooms date: 2013-06-24 pages: extension: .txt txt: ./txt/cord-263684-3535k3op.txt cache: ./cache/cord-263684-3535k3op.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-263684-3535k3op.txt' === file2bib.sh === id: cord-260843-c97kctjz author: Dai, Lei title: Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake date: 2016-11-16 pages: extension: .txt txt: ./txt/cord-260843-c97kctjz.txt cache: ./cache/cord-260843-c97kctjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260843-c97kctjz.txt' === file2bib.sh === id: cord-260432-imslfm4l author: Marshall, Jenika D. title: THP-1 macrophage cholesterol efflux is impaired by palmitoleate through Akt activation date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-260432-imslfm4l.txt cache: ./cache/cord-260432-imslfm4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260432-imslfm4l.txt' === file2bib.sh === id: cord-267973-uvz7kavu author: Do, Lien Anh Ha title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity date: 2016-08-08 pages: extension: .txt txt: ./txt/cord-267973-uvz7kavu.txt cache: ./cache/cord-267973-uvz7kavu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267973-uvz7kavu.txt' === file2bib.sh === id: cord-262832-5iejckwx author: Yen, Muh-Yong title: Taipei's Use of a Multi-Channel Mass Risk Communication Program to Rapidly Reverse an Epidemic of Highly Communicable Disease date: 2009-11-23 pages: extension: .txt txt: ./txt/cord-262832-5iejckwx.txt cache: ./cache/cord-262832-5iejckwx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262832-5iejckwx.txt' === file2bib.sh === id: cord-268977-hcg2rrhl author: Feikin, Daniel R. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 pages: extension: .txt txt: ./txt/cord-268977-hcg2rrhl.txt cache: ./cache/cord-268977-hcg2rrhl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268977-hcg2rrhl.txt' === file2bib.sh === id: cord-268816-nth3o6ot author: Roy, Satyaki title: Factors affecting COVID-19 infected and death rates inform lockdown-related policymaking date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-268816-nth3o6ot.txt cache: ./cache/cord-268816-nth3o6ot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268816-nth3o6ot.txt' === file2bib.sh === id: cord-267042-nvwnbp2j author: Gaspard, Philippe title: Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents date: 2019-09-24 pages: extension: .txt txt: ./txt/cord-267042-nvwnbp2j.txt cache: ./cache/cord-267042-nvwnbp2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267042-nvwnbp2j.txt' === file2bib.sh === id: cord-270681-6ayciihs author: Bálint, Ádám title: Comparative In Vivo Analysis of Recombinant Type II Feline Coronaviruses with Truncated and Completed ORF3 Region date: 2014-02-20 pages: extension: .txt txt: ./txt/cord-270681-6ayciihs.txt cache: ./cache/cord-270681-6ayciihs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270681-6ayciihs.txt' === file2bib.sh === id: cord-267644-guzn0peq author: Livadiotis, George title: Statistical analysis of the impact of environmental temperature on the exponential growth rate of cases infected by COVID-19 date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-267644-guzn0peq.txt cache: ./cache/cord-267644-guzn0peq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267644-guzn0peq.txt' === file2bib.sh === id: cord-279259-eu80ccm6 author: Pandey, Aseem title: Impact of Preexisting Adenovirus Vector Immunity on Immunogenicity and Protection Conferred with an Adenovirus-Based H5N1 Influenza Vaccine date: 2012-03-14 pages: extension: .txt txt: ./txt/cord-279259-eu80ccm6.txt cache: ./cache/cord-279259-eu80ccm6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279259-eu80ccm6.txt' === file2bib.sh === id: cord-268429-drejl99k author: Almberg, Emily S. title: A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community date: 2009-09-16 pages: extension: .txt txt: ./txt/cord-268429-drejl99k.txt cache: ./cache/cord-268429-drejl99k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268429-drejl99k.txt' === file2bib.sh === id: cord-048477-ze511t38 author: Patel, Mahomed S. title: General Practice and Pandemic Influenza: A Framework for Planning and Comparison of Plans in Five Countries date: 2008-05-28 pages: extension: .txt txt: ./txt/cord-048477-ze511t38.txt cache: ./cache/cord-048477-ze511t38.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-048477-ze511t38.txt' === file2bib.sh === id: cord-258172-p54j4zzo author: Barker, Harlan title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-258172-p54j4zzo.txt cache: ./cache/cord-258172-p54j4zzo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258172-p54j4zzo.txt' === file2bib.sh === id: cord-260728-4w23kwzu author: Timmermans, Ans title: Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date: 2016-03-30 pages: extension: .txt txt: ./txt/cord-260728-4w23kwzu.txt cache: ./cache/cord-260728-4w23kwzu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260728-4w23kwzu.txt' === file2bib.sh === id: cord-262846-1mhimfsf author: Gray, Nicholas title: Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-262846-1mhimfsf.txt cache: ./cache/cord-262846-1mhimfsf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262846-1mhimfsf.txt' === file2bib.sh === id: cord-262345-hti1jjpn author: Eddy, Lucy H. title: The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-262345-hti1jjpn.txt cache: ./cache/cord-262345-hti1jjpn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262345-hti1jjpn.txt' === file2bib.sh === id: cord-264880-0tmd9knh author: Li, Zhao title: Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date: 2016-04-13 pages: extension: .txt txt: ./txt/cord-264880-0tmd9knh.txt cache: ./cache/cord-264880-0tmd9knh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-264880-0tmd9knh.txt' === file2bib.sh === id: cord-255576-738khdwv author: Van Duyne, Rachel title: Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date: 2012-07-10 pages: extension: .txt txt: ./txt/cord-255576-738khdwv.txt cache: ./cache/cord-255576-738khdwv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255576-738khdwv.txt' === file2bib.sh === id: cord-256837-100ir651 author: Smith, Steven B. title: Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date: 2012-03-14 pages: extension: .txt txt: ./txt/cord-256837-100ir651.txt cache: ./cache/cord-256837-100ir651.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256837-100ir651.txt' === file2bib.sh === id: cord-270408-4qqyb8sd author: Pane, Masdalina title: Causes of Mortality for Indonesian Hajj Pilgrims: Comparison between Routine Death Certificate and Verbal Autopsy Findings date: 2013-08-21 pages: extension: .txt txt: ./txt/cord-270408-4qqyb8sd.txt cache: ./cache/cord-270408-4qqyb8sd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270408-4qqyb8sd.txt' === file2bib.sh === id: cord-270647-vn4kirrx author: Romero-Espinoza, Jose A. title: Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-270647-vn4kirrx.txt cache: ./cache/cord-270647-vn4kirrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270647-vn4kirrx.txt' === file2bib.sh === id: cord-276898-ia80cy8j author: Yamanaka, Atsushi title: Imported Case of Acute Respiratory Tract Infection Associated with a Member of Species Nelson Bay Orthoreovirus date: 2014-03-25 pages: extension: .txt txt: ./txt/cord-276898-ia80cy8j.txt cache: ./cache/cord-276898-ia80cy8j.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276898-ia80cy8j.txt' === file2bib.sh === id: cord-278123-mq56em3z author: Hasan, Mohammad Rubayet title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-278123-mq56em3z.txt cache: ./cache/cord-278123-mq56em3z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278123-mq56em3z.txt' === file2bib.sh === id: cord-277357-lpurk7pe author: González-González, Everardo title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-277357-lpurk7pe.txt cache: ./cache/cord-277357-lpurk7pe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277357-lpurk7pe.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61947 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-280471-cqypwi5d author: Sun, Hua-Bao title: The changes of the peripheral CD4+ lymphocytes and inflammatory cytokines in Patients with COVID-19 date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-280471-cqypwi5d.txt cache: ./cache/cord-280471-cqypwi5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280471-cqypwi5d.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61951 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62141 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61957 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61989 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61963 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 61960 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62020 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-276372-q1fzxt3r author: Conde, Dalia A. title: Zoos through the Lens of the IUCN Red List: A Global Metapopulation Approach to Support Conservation Breeding Programs date: 2013-12-11 pages: extension: .txt txt: ./txt/cord-276372-q1fzxt3r.txt cache: ./cache/cord-276372-q1fzxt3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276372-q1fzxt3r.txt' === file2bib.sh === id: cord-278018-3qemb0x3 author: Li, Li title: Identification of M.tuberculosis-Specific Th1 Cells Expressing CD69 Generated in vivo in Pleural Fluid Cells from Patients with Tuberculous Pleurisy date: 2011-08-22 pages: extension: .txt txt: ./txt/cord-278018-3qemb0x3.txt cache: ./cache/cord-278018-3qemb0x3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278018-3qemb0x3.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62045 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62109 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-281815-zvs5qe8x author: Subramanian, Shoba title: Hemoglobin Cleavage Site-Specificity of the Plasmodium falciparum Cysteine Proteases Falcipain-2 and Falcipain-3 date: 2009-04-09 pages: extension: .txt txt: ./txt/cord-281815-zvs5qe8x.txt cache: ./cache/cord-281815-zvs5qe8x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281815-zvs5qe8x.txt' === file2bib.sh === id: cord-282303-idh7io9v author: Hassan, Md. Zakiul title: Contamination of hospital surfaces with respiratory pathogens in Bangladesh date: 2019-10-28 pages: extension: .txt txt: ./txt/cord-282303-idh7io9v.txt cache: ./cache/cord-282303-idh7io9v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282303-idh7io9v.txt' === file2bib.sh === id: cord-263978-jk82bk1a author: Karaivanov, Alexander title: A social network model of COVID-19 date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-263978-jk82bk1a.txt cache: ./cache/cord-263978-jk82bk1a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263978-jk82bk1a.txt' === file2bib.sh === id: cord-282202-q2q4vies author: Banerjee, Amitava title: Clinical academic research in the time of Corona: A simulation study in England and a call for action date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-282202-q2q4vies.txt cache: ./cache/cord-282202-q2q4vies.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282202-q2q4vies.txt' === file2bib.sh === id: cord-286065-x0g67pnb author: Metzgar, David title: The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date: 2016-07-06 pages: extension: .txt txt: ./txt/cord-286065-x0g67pnb.txt cache: ./cache/cord-286065-x0g67pnb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286065-x0g67pnb.txt' === file2bib.sh === id: cord-285546-5tjhdczt author: Green, Manfred S. title: The confounded crude case-fatality rates (CFR) for COVID-19 hide more than they reveal—a comparison of age-specific and age-adjusted CFRs between seven countries date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-285546-5tjhdczt.txt cache: ./cache/cord-285546-5tjhdczt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285546-5tjhdczt.txt' === file2bib.sh === id: cord-284275-bqo203pf author: Lu, Roujian title: Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays date: 2012-06-15 pages: extension: .txt txt: ./txt/cord-284275-bqo203pf.txt cache: ./cache/cord-284275-bqo203pf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284275-bqo203pf.txt' === file2bib.sh === id: cord-279421-rxocrgfu author: Zhang, Dan title: Clinical Evaluation of a Single-Tube Multiple RT-PCR Assay for the Detection of 13 Common Virus Types/Subtypes Associated with Acute Respiratory Infection date: 2016-04-04 pages: extension: .txt txt: ./txt/cord-279421-rxocrgfu.txt cache: ./cache/cord-279421-rxocrgfu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279421-rxocrgfu.txt' === file2bib.sh === id: cord-281161-u896icp9 author: Wang, Jing title: The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date: 2012-05-17 pages: extension: .txt txt: ./txt/cord-281161-u896icp9.txt cache: ./cache/cord-281161-u896icp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281161-u896icp9.txt' === file2bib.sh === id: cord-280386-a8qr7nl6 author: Pires, Sara M. title: Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date: 2015-12-03 pages: extension: .txt txt: ./txt/cord-280386-a8qr7nl6.txt cache: ./cache/cord-280386-a8qr7nl6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280386-a8qr7nl6.txt' === file2bib.sh === id: cord-281124-4nhy35xn author: Soowannayan, Chumporn title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date: 2011-08-03 pages: extension: .txt txt: ./txt/cord-281124-4nhy35xn.txt cache: ./cache/cord-281124-4nhy35xn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281124-4nhy35xn.txt' === file2bib.sh === id: cord-289873-6hivjqof author: Lu, Rui title: Patients with mild and general COVID-19 should be negative for at least 3 consecutive nucleic acid tests before discharged date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-289873-6hivjqof.txt cache: ./cache/cord-289873-6hivjqof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289873-6hivjqof.txt' === file2bib.sh === id: cord-274241-biqbsggu author: Shaw, Timothy I. title: Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis) date: 2012-11-15 pages: extension: .txt txt: ./txt/cord-274241-biqbsggu.txt cache: ./cache/cord-274241-biqbsggu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274241-biqbsggu.txt' === file2bib.sh === id: cord-283604-fqc9jp0l author: Chen, Meng title: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date: 2015-03-27 pages: extension: .txt txt: ./txt/cord-283604-fqc9jp0l.txt cache: ./cache/cord-283604-fqc9jp0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-283604-fqc9jp0l.txt' === file2bib.sh === id: cord-290773-kgb8r561 author: Ahn, Jong Gyun title: Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus date: 2018-07-03 pages: extension: .txt txt: ./txt/cord-290773-kgb8r561.txt cache: ./cache/cord-290773-kgb8r561.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290773-kgb8r561.txt' === file2bib.sh === id: cord-287739-58fth3xl author: Huang, Yhu-Chering title: Successful Control of Methicillin-Resistant Staphylococcus aureus in Endemic Neonatal Intensive Care Units—A 7-Year Campaign date: 2011-08-12 pages: extension: .txt txt: ./txt/cord-287739-58fth3xl.txt cache: ./cache/cord-287739-58fth3xl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287739-58fth3xl.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-286708-igu984oc author: Chua, Kaw Bing title: Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date: 2008-11-25 pages: extension: .txt txt: ./txt/cord-286708-igu984oc.txt cache: ./cache/cord-286708-igu984oc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286708-igu984oc.txt' === file2bib.sh === id: cord-285433-ehnu83qe author: Sun, Hongliu title: Detection of Cytomegalovirus Antibodies Using a Biosensor Based on Imaging Ellipsometry date: 2015-08-21 pages: extension: .txt txt: ./txt/cord-285433-ehnu83qe.txt cache: ./cache/cord-285433-ehnu83qe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285433-ehnu83qe.txt' === file2bib.sh === id: cord-280846-bbv6f5gf author: Greninger, Alexander L. title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date: 2010-10-18 pages: extension: .txt txt: ./txt/cord-280846-bbv6f5gf.txt cache: ./cache/cord-280846-bbv6f5gf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280846-bbv6f5gf.txt' === file2bib.sh === id: cord-281364-syg0wo77 author: Caì, Yíngyún title: CD26/DPP4 Cell-Surface Expression in Bat Cells Correlates with Bat Cell Susceptibility to Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection and Evolution of Persistent Infection date: 2014-11-19 pages: extension: .txt txt: ./txt/cord-281364-syg0wo77.txt cache: ./cache/cord-281364-syg0wo77.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281364-syg0wo77.txt' === file2bib.sh === id: cord-283976-jgae7r2q author: Armstrong, Melissa J. title: Research priorities of caregivers and individuals with dementia with Lewy bodies: An interview study date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-283976-jgae7r2q.txt cache: ./cache/cord-283976-jgae7r2q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283976-jgae7r2q.txt' === file2bib.sh === id: cord-286613-cmtsu73g author: Lee, Sung Woo title: Risk Factors for Acute Kidney Injury and In-Hospital Mortality in Patients Receiving Extracorporeal Membrane Oxygenation date: 2015-10-15 pages: extension: .txt txt: ./txt/cord-286613-cmtsu73g.txt cache: ./cache/cord-286613-cmtsu73g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286613-cmtsu73g.txt' === file2bib.sh === id: cord-290034-4b0mshqa author: Le, Yen H. title: Virus detections among patients with severe acute respiratory illness, Northern Vietnam date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-290034-4b0mshqa.txt cache: ./cache/cord-290034-4b0mshqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290034-4b0mshqa.txt' === file2bib.sh === id: cord-281665-6n7aq4k9 author: Qiu, Sangsang title: Is Tuberculosis Treatment Really Free in China? A Study Comparing Two Areas with Different Management Models date: 2015-05-20 pages: extension: .txt txt: ./txt/cord-281665-6n7aq4k9.txt cache: ./cache/cord-281665-6n7aq4k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281665-6n7aq4k9.txt' === file2bib.sh === id: cord-287761-73qgx58i author: Aly, Mahmoud title: Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update date: 2017-10-13 pages: extension: .txt txt: ./txt/cord-287761-73qgx58i.txt cache: ./cache/cord-287761-73qgx58i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287761-73qgx58i.txt' === file2bib.sh === id: cord-291756-ejh1r8h4 author: Pérez-Fuentes, María del Carmen title: Threat of COVID-19 and emotional state during quarantine: Positive and negative affect as mediators in a cross-sectional study of the Spanish population date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-291756-ejh1r8h4.txt cache: ./cache/cord-291756-ejh1r8h4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291756-ejh1r8h4.txt' === file2bib.sh === id: cord-294023-knaxr7t0 author: Murri, Rita title: Social media as a tool for scientific updating at the time of COVID pandemic: Results from a national survey in Italy date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-294023-knaxr7t0.txt cache: ./cache/cord-294023-knaxr7t0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294023-knaxr7t0.txt' === file2bib.sh === id: cord-284016-zb6cv8ik author: Li, Wei title: Activation of Interleukin-32 Pro-Inflammatory Pathway in Response to Influenza A Virus Infection date: 2008-04-16 pages: extension: .txt txt: ./txt/cord-284016-zb6cv8ik.txt cache: ./cache/cord-284016-zb6cv8ik.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284016-zb6cv8ik.txt' === file2bib.sh === id: cord-288502-qqg41daz author: Martini, Katharina title: Patterns of organizing pneumonia and microinfarcts as surrogate for endothelial disruption and microangiopathic thromboembolic events in patients with coronavirus disease 2019 date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-288502-qqg41daz.txt cache: ./cache/cord-288502-qqg41daz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288502-qqg41daz.txt' === file2bib.sh === id: cord-294372-pec1886j author: Greene, Dina N. title: Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-294372-pec1886j.txt cache: ./cache/cord-294372-pec1886j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294372-pec1886j.txt' === file2bib.sh === id: cord-289285-aof7xy13 author: Michaelis, Martin title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression date: 2011-05-17 pages: extension: .txt txt: ./txt/cord-289285-aof7xy13.txt cache: ./cache/cord-289285-aof7xy13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289285-aof7xy13.txt' === file2bib.sh === id: cord-286837-j2sqs20q author: Koetsier, Antonie title: Do Intensive Care Data on Respiratory Infections Reflect Influenza Epidemics? date: 2013-12-31 pages: extension: .txt txt: ./txt/cord-286837-j2sqs20q.txt cache: ./cache/cord-286837-j2sqs20q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286837-j2sqs20q.txt' === file2bib.sh === id: cord-288440-w7g2agaf author: Jia, Rui title: The C-Terminal Sequence of IFITM1 Regulates Its Anti-HIV-1 Activity date: 2015-03-04 pages: extension: .txt txt: ./txt/cord-288440-w7g2agaf.txt cache: ./cache/cord-288440-w7g2agaf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288440-w7g2agaf.txt' === file2bib.sh === id: cord-282668-bs634hti author: Niang, Mbayame Ndiaye title: Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date: 2017-03-22 pages: extension: .txt txt: ./txt/cord-282668-bs634hti.txt cache: ./cache/cord-282668-bs634hti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282668-bs634hti.txt' === file2bib.sh === id: cord-292777-oztmw8jo author: Wong, Michelle title: Microbial Translocation Contribute to Febrile Episodes in Adults with Chemotherapy-Induced Neutropenia date: 2013-07-16 pages: extension: .txt txt: ./txt/cord-292777-oztmw8jo.txt cache: ./cache/cord-292777-oztmw8jo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292777-oztmw8jo.txt' === file2bib.sh === id: cord-000248-zueoyesj author: Berretta, Regina title: Cancer Biomarker Discovery: The Entropic Hallmark date: 2010-08-18 pages: extension: .txt txt: ./txt/cord-000248-zueoyesj.txt cache: ./cache/cord-000248-zueoyesj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000248-zueoyesj.txt' === file2bib.sh === id: cord-290833-m0wodqr3 author: Yuan, Lvfeng title: Synthetic surfactin analogues have improved anti-PEDV properties date: 2019-04-11 pages: extension: .txt txt: ./txt/cord-290833-m0wodqr3.txt cache: ./cache/cord-290833-m0wodqr3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290833-m0wodqr3.txt' === file2bib.sh === id: cord-295352-b8kztgt8 author: Maksimowski, Nicholas title: Kidney ACE2 expression: Implications for chronic kidney disease date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-295352-b8kztgt8.txt cache: ./cache/cord-295352-b8kztgt8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295352-b8kztgt8.txt' === file2bib.sh === id: cord-291417-p49ukyhx author: Mikulska, Malgorzata title: Tocilizumab and steroid treatment in patients with COVID-19 pneumonia date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-291417-p49ukyhx.txt cache: ./cache/cord-291417-p49ukyhx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291417-p49ukyhx.txt' === file2bib.sh === id: cord-295339-nzc47itk author: Baker, Marissa G. title: Estimating the burden of United States workers exposed to infection or disease: A key factor in containing risk of COVID-19 infection date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-295339-nzc47itk.txt cache: ./cache/cord-295339-nzc47itk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295339-nzc47itk.txt' === file2bib.sh === id: cord-286404-eggkqq3b author: Strayer, David R. title: Effect of disease duration in a randomized Phase III trial of rintatolimod, an immune modulator for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-286404-eggkqq3b.txt cache: ./cache/cord-286404-eggkqq3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286404-eggkqq3b.txt' === file2bib.sh === id: cord-292396-8w06oc5i author: Leger, Thomas title: Low-dose chest CT for diagnosing and assessing the extent of lung involvement of SARS-CoV-2 pneumonia using a semi quantitative score date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-292396-8w06oc5i.txt cache: ./cache/cord-292396-8w06oc5i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292396-8w06oc5i.txt' === file2bib.sh === id: cord-282194-0sjmf1yn author: Cherak, Stephana J. title: Impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit: A scoping review date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-282194-0sjmf1yn.txt cache: ./cache/cord-282194-0sjmf1yn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282194-0sjmf1yn.txt' === file2bib.sh === id: cord-292237-45hi4iz2 author: Calvo-Pinilla, Eva title: Establishment of a Bluetongue Virus Infection Model in Mice that Are Deficient in the Alpha/Beta Interferon Receptor date: 2009-04-09 pages: extension: .txt txt: ./txt/cord-292237-45hi4iz2.txt cache: ./cache/cord-292237-45hi4iz2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-292237-45hi4iz2.txt' === file2bib.sh === id: cord-293794-vudufao5 author: Cuthbertson, Leah title: Viral respiratory infections and the oropharyngeal bacterial microbiota in acutely wheezing children date: 2019-10-17 pages: extension: .txt txt: ./txt/cord-293794-vudufao5.txt cache: ./cache/cord-293794-vudufao5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293794-vudufao5.txt' === file2bib.sh === id: cord-290539-8ak2tths author: Cagno, Valeria title: Novel broad spectrum virucidal molecules against enveloped viruses date: 2018-12-07 pages: extension: .txt txt: ./txt/cord-290539-8ak2tths.txt cache: ./cache/cord-290539-8ak2tths.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290539-8ak2tths.txt' === file2bib.sh === id: cord-294768-bs6thjw2 author: Alonso-Fernández, Alberto title: Prevalence of pulmonary embolism in patients with COVID-19 pneumonia and high D-dimer values: A prospective study date: 2020-08-25 pages: extension: .txt txt: ./txt/cord-294768-bs6thjw2.txt cache: ./cache/cord-294768-bs6thjw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294768-bs6thjw2.txt' === file2bib.sh === id: cord-295293-ickp2n47 author: Latsuzbaia, Ardashel title: Evolving social contact patterns during the COVID-19 crisis in Luxembourg date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-295293-ickp2n47.txt cache: ./cache/cord-295293-ickp2n47.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295293-ickp2n47.txt' === file2bib.sh === id: cord-291360-z19ri377 author: Lan, Fan-Yun title: COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-291360-z19ri377.txt cache: ./cache/cord-291360-z19ri377.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291360-z19ri377.txt' === file2bib.sh === id: cord-291176-evb6yt0r author: Giorgi Rossi, Paolo title: Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-291176-evb6yt0r.txt cache: ./cache/cord-291176-evb6yt0r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291176-evb6yt0r.txt' === file2bib.sh === id: cord-290120-fd26t8ja author: Tan, Chew Yee title: First molecular detection and complete sequence analysis of porcine circovirus type 3 (PCV3) in Peninsular Malaysia date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-290120-fd26t8ja.txt cache: ./cache/cord-290120-fd26t8ja.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290120-fd26t8ja.txt' === file2bib.sh === id: cord-293072-giakcaki author: Xu, Wan-Xiang title: A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping date: 2017-10-12 pages: extension: .txt txt: ./txt/cord-293072-giakcaki.txt cache: ./cache/cord-293072-giakcaki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293072-giakcaki.txt' === file2bib.sh === id: cord-289555-1z4vbldd author: Mühldorfer, Kristin title: Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates date: 2011-12-28 pages: extension: .txt txt: ./txt/cord-289555-1z4vbldd.txt cache: ./cache/cord-289555-1z4vbldd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289555-1z4vbldd.txt' === file2bib.sh === id: cord-294645-yzh8h7zo author: Freeman, David W. title: Association between GDF15, poverty and mortality in urban middle-aged African American and white adults date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-294645-yzh8h7zo.txt cache: ./cache/cord-294645-yzh8h7zo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294645-yzh8h7zo.txt' === file2bib.sh === id: cord-289892-yh1lioyz author: Bai, Bingke title: Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date: 2008-07-16 pages: extension: .txt txt: ./txt/cord-289892-yh1lioyz.txt cache: ./cache/cord-289892-yh1lioyz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289892-yh1lioyz.txt' === file2bib.sh === id: cord-289510-spmknns5 author: Curado, Evaldo M. F. title: A discrete-time-evolution model to forecast progress of Covid-19 outbreak date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-289510-spmknns5.txt cache: ./cache/cord-289510-spmknns5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289510-spmknns5.txt' === file2bib.sh === id: cord-295536-dbpt4dhr author: Shook, Natalie J. title: Disease avoidance in the time of COVID-19: The behavioral immune system is associated with concern and preventative health behaviors date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-295536-dbpt4dhr.txt cache: ./cache/cord-295536-dbpt4dhr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295536-dbpt4dhr.txt' === file2bib.sh === id: cord-284501-5i0w74q4 author: Armesto, Maria title: The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date: 2009-10-09 pages: extension: .txt txt: ./txt/cord-284501-5i0w74q4.txt cache: ./cache/cord-284501-5i0w74q4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284501-5i0w74q4.txt' === file2bib.sh === id: cord-294568-12eyo13f author: Fernandes-Matano, Larissa title: Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date: 2017-05-03 pages: extension: .txt txt: ./txt/cord-294568-12eyo13f.txt cache: ./cache/cord-294568-12eyo13f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294568-12eyo13f.txt' === file2bib.sh === id: cord-278099-ypov9ha3 author: Kumar, Surender title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 pages: extension: .txt txt: ./txt/cord-278099-ypov9ha3.txt cache: ./cache/cord-278099-ypov9ha3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278099-ypov9ha3.txt' === file2bib.sh === id: cord-292537-9ra4r6v6 author: Liu, Fenglin title: Predicting and analyzing the COVID-19 epidemic in China: Based on SEIRD, LSTM and GWR models date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-292537-9ra4r6v6.txt cache: ./cache/cord-292537-9ra4r6v6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292537-9ra4r6v6.txt' === file2bib.sh === id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 pages: extension: .txt txt: ./txt/cord-289017-vwye3pk9.txt cache: ./cache/cord-289017-vwye3pk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-289017-vwye3pk9.txt' === file2bib.sh === id: cord-285749-0ejhd9nw author: Hoffmann, Markus title: The Hemagglutinin of Bat-Associated Influenza Viruses Is Activated by TMPRSS2 for pH-Dependent Entry into Bat but Not Human Cells date: 2016-03-30 pages: extension: .txt txt: ./txt/cord-285749-0ejhd9nw.txt cache: ./cache/cord-285749-0ejhd9nw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285749-0ejhd9nw.txt' === file2bib.sh === id: cord-289305-mfjyjjer author: Lee, Min Hye title: A systematic review on the causes of the transmission and control measures of outbreaks in long-term care facilities: Back to basics of infection control date: 2020-03-10 pages: extension: .txt txt: ./txt/cord-289305-mfjyjjer.txt cache: ./cache/cord-289305-mfjyjjer.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289305-mfjyjjer.txt' === file2bib.sh === id: cord-291104-6chpmgry author: Leung, Danny T. M. title: Osteopontin Fragments with Intact Thrombin-Sensitive Site Circulate in Cervical Cancer Patients date: 2016-08-05 pages: extension: .txt txt: ./txt/cord-291104-6chpmgry.txt cache: ./cache/cord-291104-6chpmgry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291104-6chpmgry.txt' === file2bib.sh === id: cord-296635-8r3tm966 author: Breed, Andrew C. title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date: 2011-12-14 pages: extension: .txt txt: ./txt/cord-296635-8r3tm966.txt cache: ./cache/cord-296635-8r3tm966.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296635-8r3tm966.txt' === file2bib.sh === id: cord-293393-kbndie8e author: Braesch-Andersen, Sten title: ApoD Mediates Binding of HDL to LDL and to Growing T24 Carcinoma date: 2014-12-16 pages: extension: .txt txt: ./txt/cord-293393-kbndie8e.txt cache: ./cache/cord-293393-kbndie8e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293393-kbndie8e.txt' === file2bib.sh === id: cord-297835-ukrz8tlv author: Leith, Douglas J. title: Measurement-based evaluation of Google/Apple Exposure Notification API for proximity detection in a light-rail tram date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-297835-ukrz8tlv.txt cache: ./cache/cord-297835-ukrz8tlv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297835-ukrz8tlv.txt' === file2bib.sh === id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 pages: extension: .txt txt: ./txt/cord-289093-si8btsab.txt cache: ./cache/cord-289093-si8btsab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-289093-si8btsab.txt' === file2bib.sh === id: cord-296550-wkmnfph3 author: Hossain, Mohammad Anwar title: Knowledge, attitudes, and fear of COVID-19 during the Rapid Rise Period in Bangladesh date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-296550-wkmnfph3.txt cache: ./cache/cord-296550-wkmnfph3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296550-wkmnfph3.txt' === file2bib.sh === id: cord-293946-4bquxdqa author: Huong, Nguyen Quynh title: Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-293946-4bquxdqa.txt cache: ./cache/cord-293946-4bquxdqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293946-4bquxdqa.txt' === file2bib.sh === id: cord-296691-cg463fbn author: Wang, Ren title: De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing date: 2013-04-09 pages: extension: .txt txt: ./txt/cord-296691-cg463fbn.txt cache: ./cache/cord-296691-cg463fbn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296691-cg463fbn.txt' === file2bib.sh === id: cord-287784-f7usy52w author: Maestre, Ana M. title: Equine Torovirus (BEV) Induces Caspase-Mediated Apoptosis in Infected Cells date: 2011-06-15 pages: extension: .txt txt: ./txt/cord-287784-f7usy52w.txt cache: ./cache/cord-287784-f7usy52w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287784-f7usy52w.txt' === file2bib.sh === id: cord-292475-jrl1fowa author: Abry, Patrice title: Spatial and temporal regularization to estimate COVID-19 reproduction number R(t): Promoting piecewise smoothness via convex optimization date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-292475-jrl1fowa.txt cache: ./cache/cord-292475-jrl1fowa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292475-jrl1fowa.txt' === file2bib.sh === id: cord-299491-8rfm0jxh author: Xiao, Shenglan title: Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date: 2017-07-20 pages: extension: .txt txt: ./txt/cord-299491-8rfm0jxh.txt cache: ./cache/cord-299491-8rfm0jxh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299491-8rfm0jxh.txt' === file2bib.sh === id: cord-299953-sasfvcun author: Whitehead, Ashley B. R. title: Burden of exposure to infectious bursal disease virus, infectious bronchitis virus, Newcastle disease virus, Mycoplasma gallisepticum, and intestinal parasites in introduced broiler chickens on the Galapagos date: 2018-09-24 pages: extension: .txt txt: ./txt/cord-299953-sasfvcun.txt cache: ./cache/cord-299953-sasfvcun.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299953-sasfvcun.txt' === file2bib.sh === id: cord-290446-43h1r4pm author: Vazquez, Leonardo title: Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus date: 2017-07-27 pages: extension: .txt txt: ./txt/cord-290446-43h1r4pm.txt cache: ./cache/cord-290446-43h1r4pm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290446-43h1r4pm.txt' === file2bib.sh === id: cord-297287-0i4nc353 author: Braun, Benjamin title: Simulating phase transitions and control measures for network epidemics caused by infections with presymptomatic, asymptomatic, and symptomatic stages date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-297287-0i4nc353.txt cache: ./cache/cord-297287-0i4nc353.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297287-0i4nc353.txt' === file2bib.sh === id: cord-302189-3xab3yxc author: Tillmann, Ramona Liza title: Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date: 2007-12-26 pages: extension: .txt txt: ./txt/cord-302189-3xab3yxc.txt cache: ./cache/cord-302189-3xab3yxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302189-3xab3yxc.txt' === file2bib.sh === id: cord-302529-43pd2qsp author: El Moussi, Awatef title: Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date: 2013-09-19 pages: extension: .txt txt: ./txt/cord-302529-43pd2qsp.txt cache: ./cache/cord-302529-43pd2qsp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302529-43pd2qsp.txt' === file2bib.sh === id: cord-301180-ndiwmnv0 author: Lin, Min-Hsuan title: Nullbasic, a Potent Anti-HIV Tat Mutant, Induces CRM1-Dependent Disruption of HIV Rev Trafficking date: 2012-12-10 pages: extension: .txt txt: ./txt/cord-301180-ndiwmnv0.txt cache: ./cache/cord-301180-ndiwmnv0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301180-ndiwmnv0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68031 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67447 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68197 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-302200-9gekjgr0 author: Kilich, Eliz title: Factors that influence vaccination decision-making among pregnant women: A systematic review and meta-analysis date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-302200-9gekjgr0.txt cache: ./cache/cord-302200-9gekjgr0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302200-9gekjgr0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67290 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-305547-e66o5j85 author: Bénet, Thomas title: Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study date: 2015-12-22 pages: extension: .txt txt: ./txt/cord-305547-e66o5j85.txt cache: ./cache/cord-305547-e66o5j85.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305547-e66o5j85.txt' === file2bib.sh === id: cord-306466-y4yg42p8 author: Nofal, Ahmed Maged title: Who complies with COVID-19 transmission mitigation behavioral guidelines? date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-306466-y4yg42p8.txt cache: ./cache/cord-306466-y4yg42p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306466-y4yg42p8.txt' === file2bib.sh === id: cord-302355-3se1wp8o author: Chen, Yi-Shiuan title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-302355-3se1wp8o.txt cache: ./cache/cord-302355-3se1wp8o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302355-3se1wp8o.txt' === file2bib.sh === id: cord-298078-uqrwq5qk author: Kwak, Hoyun title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date: 2011-08-30 pages: extension: .txt txt: ./txt/cord-298078-uqrwq5qk.txt cache: ./cache/cord-298078-uqrwq5qk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298078-uqrwq5qk.txt' === file2bib.sh === id: cord-299852-t0mqe7yy author: Janssen, Loes H. C. title: Does the COVID-19 pandemic impact parents’ and adolescents’ well-being? An EMA-study on daily affect and parenting date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-299852-t0mqe7yy.txt cache: ./cache/cord-299852-t0mqe7yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-299852-t0mqe7yy.txt' === file2bib.sh === id: cord-305071-4ck8nd24 author: Calvo, Cristina title: Eight Year Prospective Study of Adenoviruses Infections in Hospitalized Children. Comparison with Other Respiratory Viruses date: 2015-07-06 pages: extension: .txt txt: ./txt/cord-305071-4ck8nd24.txt cache: ./cache/cord-305071-4ck8nd24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305071-4ck8nd24.txt' === file2bib.sh === id: cord-301811-ykpiorgo author: Tanaka, Takuma title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-301811-ykpiorgo.txt cache: ./cache/cord-301811-ykpiorgo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301811-ykpiorgo.txt' === file2bib.sh === id: cord-295559-yc8q62z8 author: Qian, Zhaohui title: Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date: 2013-10-03 pages: extension: .txt txt: ./txt/cord-295559-yc8q62z8.txt cache: ./cache/cord-295559-yc8q62z8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295559-yc8q62z8.txt' === file2bib.sh === id: cord-303331-xolksoy3 author: Pourghasemi, Hamid Reza title: Assessment of the outbreak risk, mapping and infection behavior of COVID-19: Application of the autoregressive integrated-moving average (ARIMA) and polynomial models date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-303331-xolksoy3.txt cache: ./cache/cord-303331-xolksoy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303331-xolksoy3.txt' === file2bib.sh === id: cord-302962-qw6s1t7j author: Hause, Ben M. title: Bovine Rhinitis Viruses Are Common in U.S. Cattle with Bovine Respiratory Disease date: 2015-03-19 pages: extension: .txt txt: ./txt/cord-302962-qw6s1t7j.txt cache: ./cache/cord-302962-qw6s1t7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-302962-qw6s1t7j.txt' === file2bib.sh === id: cord-306958-8bx8kxxh author: Christensen, Sarah R. title: Political and personal reactions to COVID-19 during initial weeks of social distancing in the United States date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-306958-8bx8kxxh.txt cache: ./cache/cord-306958-8bx8kxxh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306958-8bx8kxxh.txt' === file2bib.sh === id: cord-309981-4p3ybrn1 author: Dai, Ling-Ling title: Anxiety and depressive symptoms among COVID-19 patients in Jianghan Fangcang Shelter Hospital in Wuhan, China date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-309981-4p3ybrn1.txt cache: ./cache/cord-309981-4p3ybrn1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309981-4p3ybrn1.txt' === file2bib.sh === id: cord-310061-nro623aa author: Valitutto, Marc T. title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 pages: extension: .txt txt: ./txt/cord-310061-nro623aa.txt cache: ./cache/cord-310061-nro623aa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310061-nro623aa.txt' === file2bib.sh === id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 pages: extension: .txt txt: ./txt/cord-306278-c4q4la5c.txt cache: ./cache/cord-306278-c4q4la5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306278-c4q4la5c.txt' === file2bib.sh === id: cord-305274-mcsdem7y author: Beniac, Daniel R. title: Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date: 2007-10-24 pages: extension: .txt txt: ./txt/cord-305274-mcsdem7y.txt cache: ./cache/cord-305274-mcsdem7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305274-mcsdem7y.txt' === file2bib.sh === id: cord-304993-t4rua95e author: Jung, Kwonil title: The Effects of Simvastatin or Interferon-α on Infectivity of Human Norovirus Using a Gnotobiotic Pig Model for the Study of Antivirals date: 2012-07-23 pages: extension: .txt txt: ./txt/cord-304993-t4rua95e.txt cache: ./cache/cord-304993-t4rua95e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304993-t4rua95e.txt' === file2bib.sh === id: cord-309621-6jj19xpr author: Yu, Pin title: Comparative pathology of rhesus macaque and common marmoset animal models with Middle East respiratory syndrome coronavirus date: 2017-02-24 pages: extension: .txt txt: ./txt/cord-309621-6jj19xpr.txt cache: ./cache/cord-309621-6jj19xpr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309621-6jj19xpr.txt' === file2bib.sh === id: cord-309194-jtouafgd author: Lu, Xiao title: Lung ultrasound score in establishing the timing of intubation in COVID-19 interstitial pneumonia: A preliminary retrospective observational study date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-309194-jtouafgd.txt cache: ./cache/cord-309194-jtouafgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309194-jtouafgd.txt' === file2bib.sh === id: cord-310678-33c3mp1o author: Morgantini, Luca A. title: Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-310678-33c3mp1o.txt cache: ./cache/cord-310678-33c3mp1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310678-33c3mp1o.txt' === file2bib.sh === id: cord-304616-k92fa15l author: Izes, Aaron M. title: Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-304616-k92fa15l.txt cache: ./cache/cord-304616-k92fa15l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304616-k92fa15l.txt' === file2bib.sh === id: cord-306135-pt4jsr6d author: Chan, Kamfai title: A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date: 2016-02-12 pages: extension: .txt txt: ./txt/cord-306135-pt4jsr6d.txt cache: ./cache/cord-306135-pt4jsr6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306135-pt4jsr6d.txt' === file2bib.sh === id: cord-308344-ao9z00t7 author: Diep, Nguyen Van title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date: 2017-01-17 pages: extension: .txt txt: ./txt/cord-308344-ao9z00t7.txt cache: ./cache/cord-308344-ao9z00t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308344-ao9z00t7.txt' === file2bib.sh === id: cord-303034-w72oeoxq author: Haischer, Michael H. title: Who is wearing a mask? Gender-, age-, and location-related differences during the COVID-19 pandemic date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-303034-w72oeoxq.txt cache: ./cache/cord-303034-w72oeoxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303034-w72oeoxq.txt' === file2bib.sh === id: cord-312367-24huwt3y author: Coelho, Camila title: Biochemical screening for SARS-CoV-2 main protease inhibitors date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-312367-24huwt3y.txt cache: ./cache/cord-312367-24huwt3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312367-24huwt3y.txt' === file2bib.sh === id: cord-303490-rixuuytu author: Pazos, Michael A. title: Estrogen Mediates Innate and Adaptive Immune Alterations to Influenza Infection in Pregnant Mice date: 2012-07-05 pages: extension: .txt txt: ./txt/cord-303490-rixuuytu.txt cache: ./cache/cord-303490-rixuuytu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303490-rixuuytu.txt' === file2bib.sh === id: cord-310466-0lbbiq7u author: Fu, Yang-chih title: Representative Contact Diaries for Modeling the Spread of Infectious Diseases in Taiwan date: 2012-10-03 pages: extension: .txt txt: ./txt/cord-310466-0lbbiq7u.txt cache: ./cache/cord-310466-0lbbiq7u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310466-0lbbiq7u.txt' === file2bib.sh === id: cord-311074-j3fw4dfc author: Alviset, Sophie title: Continuous Positive Airway Pressure (CPAP) face-mask ventilation is an easy and cheap option to manage a massive influx of patients presenting acute respiratory failure during the SARS-CoV-2 outbreak: A retrospective cohort study date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-311074-j3fw4dfc.txt cache: ./cache/cord-311074-j3fw4dfc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-311074-j3fw4dfc.txt' === file2bib.sh === id: cord-310790-3ikgmiof author: Cherrak, Sabri Ahmed title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-310790-3ikgmiof.txt cache: ./cache/cord-310790-3ikgmiof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310790-3ikgmiof.txt' === file2bib.sh === id: cord-308261-hxlebas8 author: Broekhuis, Femke title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date: 2019-04-03 pages: extension: .txt txt: ./txt/cord-308261-hxlebas8.txt cache: ./cache/cord-308261-hxlebas8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-308261-hxlebas8.txt' === file2bib.sh === id: cord-303845-y6ws3u6x author: DeLisle, Sylvain title: Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections date: 2010-10-14 pages: extension: .txt txt: ./txt/cord-303845-y6ws3u6x.txt cache: ./cache/cord-303845-y6ws3u6x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303845-y6ws3u6x.txt' === file2bib.sh === id: cord-310438-744r7gc3 author: Chan, Ta-Chien title: The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date: 2010-06-25 pages: extension: .txt txt: ./txt/cord-310438-744r7gc3.txt cache: ./cache/cord-310438-744r7gc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310438-744r7gc3.txt' === file2bib.sh === id: cord-308249-es948mux author: Dokuka, Sofia title: How academic achievement spreads: The role of distinct social networks in academic performance diffusion date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-308249-es948mux.txt cache: ./cache/cord-308249-es948mux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308249-es948mux.txt' === file2bib.sh === id: cord-312493-wbhji81g author: Tay, Ee Laine title: Exploring a Proposed WHO Method to Determine Thresholds for Seasonal Influenza Surveillance date: 2013-10-11 pages: extension: .txt txt: ./txt/cord-312493-wbhji81g.txt cache: ./cache/cord-312493-wbhji81g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312493-wbhji81g.txt' === file2bib.sh === id: cord-308480-t2vukbwp author: Liang, Zhongjie title: Molecular Basis of NDM-1, a New Antibiotic Resistance Determinant date: 2011-08-24 pages: extension: .txt txt: ./txt/cord-308480-t2vukbwp.txt cache: ./cache/cord-308480-t2vukbwp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308480-t2vukbwp.txt' === file2bib.sh === id: cord-307540-dr5m9pfk author: Coelho, Flávio C. title: Assessing the spread of COVID-19 in Brazil: Mobility, morbidity and social vulnerability date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-307540-dr5m9pfk.txt cache: ./cache/cord-307540-dr5m9pfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307540-dr5m9pfk.txt' === file2bib.sh === id: cord-311531-wezrs7gc author: Parčina, Marijo title: Multicenter evaluation of the QIAstat Respiratory Panel—A new rapid highly multiplexed PCR based assay for diagnosis of acute respiratory tract infections date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-311531-wezrs7gc.txt cache: ./cache/cord-311531-wezrs7gc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311531-wezrs7gc.txt' === file2bib.sh === id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 pages: extension: .txt txt: ./txt/cord-317244-4su5on6s.txt cache: ./cache/cord-317244-4su5on6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317244-4su5on6s.txt' === file2bib.sh === id: cord-303187-ny4qr2a2 author: Belo, Vinícius Silva title: Abundance, survival, recruitment and effectiveness of sterilization of free-roaming dogs: A capture and recapture study in Brazil date: 2017-11-01 pages: extension: .txt txt: ./txt/cord-303187-ny4qr2a2.txt cache: ./cache/cord-303187-ny4qr2a2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303187-ny4qr2a2.txt' === file2bib.sh === id: cord-300859-nqklx0vn author: Henderson, Kelley C. title: Specificity and Strain-Typing Capabilities of Nanorod Array-Surface Enhanced Raman Spectroscopy for Mycoplasma pneumoniae Detection date: 2015-06-29 pages: extension: .txt txt: ./txt/cord-300859-nqklx0vn.txt cache: ./cache/cord-300859-nqklx0vn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300859-nqklx0vn.txt' === file2bib.sh === id: cord-312033-iarl77n0 author: López Barreda, Rodrigo title: Poverty, quality of life and psychological wellbeing in adults with congenital heart disease in Chile date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-312033-iarl77n0.txt cache: ./cache/cord-312033-iarl77n0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312033-iarl77n0.txt' === file2bib.sh === id: cord-305811-987dhnf7 author: Cho, Che-Pei title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date: 2013-04-29 pages: extension: .txt txt: ./txt/cord-305811-987dhnf7.txt cache: ./cache/cord-305811-987dhnf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305811-987dhnf7.txt' === file2bib.sh === id: cord-313107-6cfenpxm author: Singh, Anirudh K. title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-313107-6cfenpxm.txt cache: ./cache/cord-313107-6cfenpxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313107-6cfenpxm.txt' === file2bib.sh === id: cord-307934-84zfabti author: Lai, Chao-Kuen title: Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date: 2014-06-06 pages: extension: .txt txt: ./txt/cord-307934-84zfabti.txt cache: ./cache/cord-307934-84zfabti.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307934-84zfabti.txt' === file2bib.sh === id: cord-311065-ie3gty6e author: Gaddi, Pamela J. title: IL-10 Mediated Regulation of Liver Inflammation during Acute Murine Cytomegalovirus Infection date: 2012-08-03 pages: extension: .txt txt: ./txt/cord-311065-ie3gty6e.txt cache: ./cache/cord-311065-ie3gty6e.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311065-ie3gty6e.txt' === file2bib.sh === id: cord-312002-4qhvljpv author: Pacheco-Barrios, Kevin title: COVID-19 pandemic and Farr’s law: A global comparison and prediction of outbreak acceleration and deceleration rates date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-312002-4qhvljpv.txt cache: ./cache/cord-312002-4qhvljpv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312002-4qhvljpv.txt' === file2bib.sh === id: cord-319538-bawzonq1 author: Krause, Martin title: Association between procalcitonin levels and duration of mechanical ventilation in COVID-19 patients date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-319538-bawzonq1.txt cache: ./cache/cord-319538-bawzonq1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319538-bawzonq1.txt' === file2bib.sh === id: cord-305303-82n96ukr author: Shapira, Assaf title: Removal of Hepatitis C Virus-Infected Cells by a Zymogenized Bacterial Toxin date: 2012-02-16 pages: extension: .txt txt: ./txt/cord-305303-82n96ukr.txt cache: ./cache/cord-305303-82n96ukr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305303-82n96ukr.txt' === file2bib.sh === id: cord-307036-n44yml79 author: Ng, Oi-Wing title: Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date: 2014-07-14 pages: extension: .txt txt: ./txt/cord-307036-n44yml79.txt cache: ./cache/cord-307036-n44yml79.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307036-n44yml79.txt' === file2bib.sh === id: cord-316319-m6uha1qn author: Daleno, Cristina title: Phylogenetic Analysis of Human Rhinovirus Isolates Collected from Otherwise Healthy Children with Community-Acquired Pneumonia during Five Successive Years date: 2013-11-19 pages: extension: .txt txt: ./txt/cord-316319-m6uha1qn.txt cache: ./cache/cord-316319-m6uha1qn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316319-m6uha1qn.txt' === file2bib.sh === id: cord-310947-aqau2n7q author: Pan, Ji'An title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 pages: extension: .txt txt: ./txt/cord-310947-aqau2n7q.txt cache: ./cache/cord-310947-aqau2n7q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310947-aqau2n7q.txt' === file2bib.sh === id: cord-317912-v2wovcqd author: Akmatov, Manas K. title: Equivalence of Self- and Staff-Collected Nasal Swabs for the Detection of Viral Respiratory Pathogens date: 2012-11-14 pages: extension: .txt txt: ./txt/cord-317912-v2wovcqd.txt cache: ./cache/cord-317912-v2wovcqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317912-v2wovcqd.txt' === file2bib.sh === id: cord-315343-ywgoqlxj author: Ribeiro, Haroldo V. title: City size and the spreading of COVID-19 in Brazil date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-315343-ywgoqlxj.txt cache: ./cache/cord-315343-ywgoqlxj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315343-ywgoqlxj.txt' === file2bib.sh === id: cord-314651-e4uaw5fy author: Zhao, Guangyu title: Multi-Organ Damage in Human Dipeptidyl Peptidase 4 Transgenic Mice Infected with Middle East Respiratory Syndrome-Coronavirus date: 2015-12-23 pages: extension: .txt txt: ./txt/cord-314651-e4uaw5fy.txt cache: ./cache/cord-314651-e4uaw5fy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-314651-e4uaw5fy.txt' === file2bib.sh === id: cord-310396-jitao9k0 author: Lei, Yu title: MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date: 2009-03-07 pages: extension: .txt txt: ./txt/cord-310396-jitao9k0.txt cache: ./cache/cord-310396-jitao9k0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310396-jitao9k0.txt' === file2bib.sh === id: cord-311941-0dpm35dd author: Jones, Bryony A. title: Calf-Level Factors Associated with Bovine Neonatal Pancytopenia – A Multi-Country Case-Control Study date: 2013-12-02 pages: extension: .txt txt: ./txt/cord-311941-0dpm35dd.txt cache: ./cache/cord-311941-0dpm35dd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-311941-0dpm35dd.txt' === file2bib.sh === id: cord-316703-8kxx3034 author: Parera, Mariona title: Canine Hepacivirus NS3 Serine Protease Can Cleave the Human Adaptor Proteins MAVS and TRIF date: 2012-08-01 pages: extension: .txt txt: ./txt/cord-316703-8kxx3034.txt cache: ./cache/cord-316703-8kxx3034.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316703-8kxx3034.txt' === file2bib.sh === id: cord-312678-81gnmxbk author: Elayeh, Eman title: Before and after case reporting: A comparison of the knowledge, attitude and practices of the Jordanian population towards COVID-19 date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-312678-81gnmxbk.txt cache: ./cache/cord-312678-81gnmxbk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312678-81gnmxbk.txt' === file2bib.sh === id: cord-305900-ht7hb2rc author: van den Brand, Judith M. A. title: Comparison of Temporal and Spatial Dynamics of Seasonal H3N2, Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Virus Infections in Ferrets date: 2012-08-08 pages: extension: .txt txt: ./txt/cord-305900-ht7hb2rc.txt cache: ./cache/cord-305900-ht7hb2rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305900-ht7hb2rc.txt' === file2bib.sh === id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-321855-7b1c2xdh.txt cache: ./cache/cord-321855-7b1c2xdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321855-7b1c2xdh.txt' === file2bib.sh === id: cord-308764-9z4qcoqz author: Wei, Lin title: Transcriptome Analysis of Houttuynia cordata Thunb. by Illumina Paired-End RNA Sequencing and SSR Marker Discovery date: 2014-01-02 pages: extension: .txt txt: ./txt/cord-308764-9z4qcoqz.txt cache: ./cache/cord-308764-9z4qcoqz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308764-9z4qcoqz.txt' === file2bib.sh === id: cord-298131-zolwjl9u author: Xiao, Shuqi title: Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing date: 2010-06-29 pages: extension: .txt txt: ./txt/cord-298131-zolwjl9u.txt cache: ./cache/cord-298131-zolwjl9u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298131-zolwjl9u.txt' === file2bib.sh === id: cord-318614-518giv0m author: Tsai, Jih-Jin title: A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos date: 2019-07-10 pages: extension: .txt txt: ./txt/cord-318614-518giv0m.txt cache: ./cache/cord-318614-518giv0m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318614-518giv0m.txt' === file2bib.sh === id: cord-316853-vaea6siv author: Xie, Nanzhen title: Prevalence of depressive symptoms among nurses in China: A systematic review and meta-analysis date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-316853-vaea6siv.txt cache: ./cache/cord-316853-vaea6siv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316853-vaea6siv.txt' === file2bib.sh === id: cord-319706-2e9jrv0s author: Ebinger, Joseph E. title: Pre-existing traits associated with Covid-19 illness severity date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-319706-2e9jrv0s.txt cache: ./cache/cord-319706-2e9jrv0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319706-2e9jrv0s.txt' === file2bib.sh === id: cord-312817-gskbu0oh author: Witte, Carmel title: Spatiotemporal network structure among “friends of friends” reveals contagious disease process date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-312817-gskbu0oh.txt cache: ./cache/cord-312817-gskbu0oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312817-gskbu0oh.txt' === file2bib.sh === id: cord-315531-2gc2dc46 author: McGarvey, Peter B. title: Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets date: 2009-09-25 pages: extension: .txt txt: ./txt/cord-315531-2gc2dc46.txt cache: ./cache/cord-315531-2gc2dc46.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-315531-2gc2dc46.txt' === file2bib.sh === id: cord-309010-tmfm5u5h author: Dietert, Kristina title: Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia date: 2017-11-20 pages: extension: .txt txt: ./txt/cord-309010-tmfm5u5h.txt cache: ./cache/cord-309010-tmfm5u5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309010-tmfm5u5h.txt' === file2bib.sh === id: cord-311288-6ttux2uu author: Luo, Chen title: What triggers online help-seeking retransmission during the COVID-19 period? Empirical evidence from Chinese social media date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-311288-6ttux2uu.txt cache: ./cache/cord-311288-6ttux2uu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311288-6ttux2uu.txt' === file2bib.sh === id: cord-318008-4s9eoae3 author: Parsons Leigh, Jeanna title: A national cross-sectional survey of public perceptions of the COVID-19 pandemic: Self-reported beliefs, knowledge, and behaviors date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-318008-4s9eoae3.txt cache: ./cache/cord-318008-4s9eoae3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318008-4s9eoae3.txt' === file2bib.sh === id: cord-320466-l7017jis author: Akgun, Emel title: Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-320466-l7017jis.txt cache: ./cache/cord-320466-l7017jis.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320466-l7017jis.txt' === file2bib.sh === id: cord-313506-6bb4q7nv author: Sano, Akiko title: Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date: 2013-10-24 pages: extension: .txt txt: ./txt/cord-313506-6bb4q7nv.txt cache: ./cache/cord-313506-6bb4q7nv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-313506-6bb4q7nv.txt' === file2bib.sh === id: cord-319675-mwy3t1ny author: Gu, Li title: Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date: 2016-08-17 pages: extension: .txt txt: ./txt/cord-319675-mwy3t1ny.txt cache: ./cache/cord-319675-mwy3t1ny.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319675-mwy3t1ny.txt' === file2bib.sh === id: cord-309471-lr68epyb author: Xia, Jingya title: Virus-Specific Immune Memory at Peripheral Sites of Herpes Simplex Virus Type 2 (HSV-2) Infection in Guinea Pigs date: 2014-12-08 pages: extension: .txt txt: ./txt/cord-309471-lr68epyb.txt cache: ./cache/cord-309471-lr68epyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-309471-lr68epyb.txt' === file2bib.sh === id: cord-322414-dpx191xh author: Harke, Nina N. title: To defer or not to defer? A German longitudinal multicentric assessment of clinical practice in urology during the COVID-19 pandemic date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-322414-dpx191xh.txt cache: ./cache/cord-322414-dpx191xh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322414-dpx191xh.txt' === file2bib.sh === id: cord-319190-esjfhztp author: Lu, Xi title: In Vitro Activity of Sodium New Houttuyfonate Alone and in Combination with Oxacillin or Netilmicin against Methicillin-Resistant Staphylococcus aureus date: 2013-07-02 pages: extension: .txt txt: ./txt/cord-319190-esjfhztp.txt cache: ./cache/cord-319190-esjfhztp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319190-esjfhztp.txt' === file2bib.sh === id: cord-309043-dlmx12vt author: von Brunn, Albrecht title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 pages: extension: .txt txt: ./txt/cord-309043-dlmx12vt.txt cache: ./cache/cord-309043-dlmx12vt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309043-dlmx12vt.txt' === file2bib.sh === id: cord-319845-oob2ktnz author: Proença-Modena, José Luiz title: Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date: 2011-06-20 pages: extension: .txt txt: ./txt/cord-319845-oob2ktnz.txt cache: ./cache/cord-319845-oob2ktnz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319845-oob2ktnz.txt' === file2bib.sh === id: cord-321705-6a7avlro author: Hou, Tianya title: Social support and mental health among health care workers during Coronavirus Disease 2019 outbreak: A moderated mediation model date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-321705-6a7avlro.txt cache: ./cache/cord-321705-6a7avlro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321705-6a7avlro.txt' === file2bib.sh === id: cord-305393-96mrxt8a author: Lai, Yvonne title: Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date: 2011-10-10 pages: extension: .txt txt: ./txt/cord-305393-96mrxt8a.txt cache: ./cache/cord-305393-96mrxt8a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305393-96mrxt8a.txt' === file2bib.sh === id: cord-323433-9km824uh author: van den Wijngaard, Cees C. title: Syndromic Surveillance for Local Outbreaks of Lower-Respiratory Infections: Would It Work? date: 2010-04-29 pages: extension: .txt txt: ./txt/cord-323433-9km824uh.txt cache: ./cache/cord-323433-9km824uh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323433-9km824uh.txt' === file2bib.sh === id: cord-319921-uxtydu60 author: Meli, Marina L. title: Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date: 2009-03-09 pages: extension: .txt txt: ./txt/cord-319921-uxtydu60.txt cache: ./cache/cord-319921-uxtydu60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319921-uxtydu60.txt' === file2bib.sh === id: cord-321624-z2mntwef author: Kowitdamrong, Ekasit title: Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-321624-z2mntwef.txt cache: ./cache/cord-321624-z2mntwef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321624-z2mntwef.txt' === file2bib.sh === id: cord-321834-n5w88l23 author: Huang, Cheng-Yang title: Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases date: 2015-05-19 pages: extension: .txt txt: ./txt/cord-321834-n5w88l23.txt cache: ./cache/cord-321834-n5w88l23.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321834-n5w88l23.txt' === file2bib.sh === id: cord-314908-kp2jznwb author: Roczniewska, Marta title: I believe I can craft! introducing Job Crafting Self-Efficacy Scale (JCSES) date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-314908-kp2jznwb.txt cache: ./cache/cord-314908-kp2jznwb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314908-kp2jznwb.txt' === file2bib.sh === id: cord-324359-88vy3dre author: Kamara, Foday Mamoud title: How villagers in central Sierra Leone understand infection risks under threat of Covid-19 date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-324359-88vy3dre.txt cache: ./cache/cord-324359-88vy3dre.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324359-88vy3dre.txt' === file2bib.sh === id: cord-317779-j67vb7f3 author: Irizarry, Kristopher J. L. title: RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes date: 2017-08-28 pages: extension: .txt txt: ./txt/cord-317779-j67vb7f3.txt cache: ./cache/cord-317779-j67vb7f3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-317779-j67vb7f3.txt' === file2bib.sh === id: cord-324410-be2ith3z author: Wang, Qi title: Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry date: 2007-06-13 pages: extension: .txt txt: ./txt/cord-324410-be2ith3z.txt cache: ./cache/cord-324410-be2ith3z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-324410-be2ith3z.txt' === file2bib.sh === id: cord-327257-doygrgrc author: Zhu, Jocelyn title: Deep transfer learning artificial intelligence accurately stages COVID-19 lung disease severity on portable chest radiographs date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-327257-doygrgrc.txt cache: ./cache/cord-327257-doygrgrc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327257-doygrgrc.txt' === file2bib.sh === id: cord-322533-adqqm0n9 author: Sha, Dexuan title: Spatiotemporal analysis of medical resource deficiencies in the U.S. under COVID-19 pandemic date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-322533-adqqm0n9.txt cache: ./cache/cord-322533-adqqm0n9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322533-adqqm0n9.txt' === file2bib.sh === id: cord-322827-h33su548 author: Guan, Lili title: Unlocking Patients with Mental Disorders Who Were in Restraints at Home: A National Follow-Up Study of China’s New Public Mental Health Initiatives date: 2015-04-07 pages: extension: .txt txt: ./txt/cord-322827-h33su548.txt cache: ./cache/cord-322827-h33su548.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322827-h33su548.txt' === file2bib.sh === id: cord-326011-5rmhjbri author: Cui, Dawei title: Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study date: 2016-11-01 pages: extension: .txt txt: ./txt/cord-326011-5rmhjbri.txt cache: ./cache/cord-326011-5rmhjbri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326011-5rmhjbri.txt' === file2bib.sh === id: cord-323330-ghwhgkdm author: Ekundayo, Temitope Cyrus title: A global bibliometric analysis of Plesiomonas-related research (1990 – 2017) date: 2018-11-29 pages: extension: .txt txt: ./txt/cord-323330-ghwhgkdm.txt cache: ./cache/cord-323330-ghwhgkdm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323330-ghwhgkdm.txt' === file2bib.sh === id: cord-321438-llnqzkqt author: Ma, Ruili title: Proteome Profile of Swine Testicular Cells Infected with Porcine Transmissible Gastroenteritis Coronavirus date: 2014-10-21 pages: extension: .txt txt: ./txt/cord-321438-llnqzkqt.txt cache: ./cache/cord-321438-llnqzkqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321438-llnqzkqt.txt' === file2bib.sh === id: cord-331885-8zmuhebu author: Xu, Xiuyan title: Risk factor analysis combined with deep learning in the risk assessment of overseas investment of enterprises date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-331885-8zmuhebu.txt cache: ./cache/cord-331885-8zmuhebu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331885-8zmuhebu.txt' === file2bib.sh === id: cord-324091-nljd2ok1 author: Gordon, Jennifer L. title: The psychological impact of fertility treatment suspensions during the COVID-19 pandemic date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-324091-nljd2ok1.txt cache: ./cache/cord-324091-nljd2ok1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324091-nljd2ok1.txt' === file2bib.sh === id: cord-328206-iylw1bvw author: Yu, Daojun title: Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date: 2012-11-09 pages: extension: .txt txt: ./txt/cord-328206-iylw1bvw.txt cache: ./cache/cord-328206-iylw1bvw.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328206-iylw1bvw.txt' === file2bib.sh === id: cord-318845-w7q5o8wc author: Pendell, Dustin L. title: Economic Assessment of FMDv Releases from the National Bio and Agro Defense Facility date: 2015-06-26 pages: extension: .txt txt: ./txt/cord-318845-w7q5o8wc.txt cache: ./cache/cord-318845-w7q5o8wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318845-w7q5o8wc.txt' === file2bib.sh === id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-325113-sou8xyld.txt cache: ./cache/cord-325113-sou8xyld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325113-sou8xyld.txt' === file2bib.sh === id: cord-330749-xt4aa2ur author: Schilling, Stefan title: Isolation Facilities for Highly Infectious Diseases in Europe – A Cross-Sectional Analysis in 16 Countries date: 2014-10-28 pages: extension: .txt txt: ./txt/cord-330749-xt4aa2ur.txt cache: ./cache/cord-330749-xt4aa2ur.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330749-xt4aa2ur.txt' === file2bib.sh === id: cord-320938-f526k9q1 author: Chen, Hongjun title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 pages: extension: .txt txt: ./txt/cord-320938-f526k9q1.txt cache: ./cache/cord-320938-f526k9q1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-320938-f526k9q1.txt' === file2bib.sh === id: cord-334218-bkjfy66e author: Lin, Jung-Da title: Impact of Mated Female Nonproductive Days in Breeding Herd after Porcine Epidemic Diarrhea Virus Outbreak date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-334218-bkjfy66e.txt cache: ./cache/cord-334218-bkjfy66e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334218-bkjfy66e.txt' === file2bib.sh === id: cord-329727-h47q76y8 author: Sisó-Almirall, Antoni title: Prognostic factors in Spanish COVID-19 patients: A case series from Barcelona date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-329727-h47q76y8.txt cache: ./cache/cord-329727-h47q76y8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329727-h47q76y8.txt' === file2bib.sh === id: cord-326568-twv2i3fb author: Bruminhent, Jackrapong title: Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-326568-twv2i3fb.txt cache: ./cache/cord-326568-twv2i3fb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326568-twv2i3fb.txt' === file2bib.sh === id: cord-327199-ggomuomb author: Moerdyk-Schauwecker, Megan title: Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date: 2014-08-08 pages: extension: .txt txt: ./txt/cord-327199-ggomuomb.txt cache: ./cache/cord-327199-ggomuomb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327199-ggomuomb.txt' === file2bib.sh === id: cord-323133-gdg50omp author: Buzatto, G. P. title: The pathogens profile in children with otitis media with effusion and adenoid hypertrophy date: 2017-02-23 pages: extension: .txt txt: ./txt/cord-323133-gdg50omp.txt cache: ./cache/cord-323133-gdg50omp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-323133-gdg50omp.txt' === file2bib.sh === id: cord-335505-s013j5ex author: Zhang, Chen title: Viral Etiology and Clinical Profiles of Children with Severe Acute Respiratory Infections in China date: 2013-08-22 pages: extension: .txt txt: ./txt/cord-335505-s013j5ex.txt cache: ./cache/cord-335505-s013j5ex.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335505-s013j5ex.txt' === file2bib.sh === id: cord-335859-k37jivp6 author: Wu, Daphne C. title: Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-335859-k37jivp6.txt cache: ./cache/cord-335859-k37jivp6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335859-k37jivp6.txt' === file2bib.sh === id: cord-324405-6uanhe2p author: Burke, Rachel M. title: Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-324405-6uanhe2p.txt cache: ./cache/cord-324405-6uanhe2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324405-6uanhe2p.txt' === file2bib.sh === id: cord-333853-p2kbjwpy author: Smee, Donald F. title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date: 2011-10-13 pages: extension: .txt txt: ./txt/cord-333853-p2kbjwpy.txt cache: ./cache/cord-333853-p2kbjwpy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333853-p2kbjwpy.txt' === file2bib.sh === id: cord-332922-2qjae0x7 author: Mbuvha, Rendani title: Bayesian inference of COVID-19 spreading rates in South Africa date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-332922-2qjae0x7.txt cache: ./cache/cord-332922-2qjae0x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332922-2qjae0x7.txt' === file2bib.sh === id: cord-320091-2lrqubdl author: Badawi, Alaa title: Prevalence of chronic comorbidities in dengue fever and West Nile virus: A systematic review and meta-analysis date: 2018-07-10 pages: extension: .txt txt: ./txt/cord-320091-2lrqubdl.txt cache: ./cache/cord-320091-2lrqubdl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320091-2lrqubdl.txt' === file2bib.sh === id: cord-333208-tibtngy8 author: Muñoz-Moreno, Raquel title: Antiviral Role of IFITM Proteins in African Swine Fever Virus Infection date: 2016-04-26 pages: extension: .txt txt: ./txt/cord-333208-tibtngy8.txt cache: ./cache/cord-333208-tibtngy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333208-tibtngy8.txt' === file2bib.sh === id: cord-323185-n0rubc72 author: Varshney, Bhavna title: SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date: 2012-01-12 pages: extension: .txt txt: ./txt/cord-323185-n0rubc72.txt cache: ./cache/cord-323185-n0rubc72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323185-n0rubc72.txt' === file2bib.sh === id: cord-327534-f2wvh6la author: Zhou, Peng title: IRF7 in the Australian Black Flying Fox, Pteropus alecto: Evidence for a Unique Expression Pattern and Functional Conservation date: 2014-08-06 pages: extension: .txt txt: ./txt/cord-327534-f2wvh6la.txt cache: ./cache/cord-327534-f2wvh6la.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-327534-f2wvh6la.txt' === file2bib.sh === id: cord-339157-wj47xeqj author: Zhang, Chao title: Involvement of the renin-angiotensin system in the progression of severe hand-foot-and-mouth disease date: 2018-05-23 pages: extension: .txt txt: ./txt/cord-339157-wj47xeqj.txt cache: ./cache/cord-339157-wj47xeqj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339157-wj47xeqj.txt' === file2bib.sh === id: cord-336420-1a2u9p4t author: Söderman, Martina title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date: 2016-06-16 pages: extension: .txt txt: ./txt/cord-336420-1a2u9p4t.txt cache: ./cache/cord-336420-1a2u9p4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336420-1a2u9p4t.txt' === file2bib.sh === id: cord-330079-pdaowkop author: Xu, Lin title: Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date: 2012-09-11 pages: extension: .txt txt: ./txt/cord-330079-pdaowkop.txt cache: ./cache/cord-330079-pdaowkop.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330079-pdaowkop.txt' === file2bib.sh === id: cord-335880-m8gecsf0 author: Peci, Adriana title: Epidemiology of Enterovirus D68 in Ontario date: 2015-11-23 pages: extension: .txt txt: ./txt/cord-335880-m8gecsf0.txt cache: ./cache/cord-335880-m8gecsf0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335880-m8gecsf0.txt' === file2bib.sh === id: cord-337585-kpghvb6u author: Moustaqim-Barrette, Amina title: Accessing Take-Home Naloxone in British Columbia and the role of community pharmacies: Results from the analysis of administrative data date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-337585-kpghvb6u.txt cache: ./cache/cord-337585-kpghvb6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337585-kpghvb6u.txt' === file2bib.sh === id: cord-336843-c0sr3six author: Gerritsen, M. G. title: Improving early diagnosis of pulmonary infections in patients with febrile neutropenia using low-dose chest computed tomography date: 2017-02-24 pages: extension: .txt txt: ./txt/cord-336843-c0sr3six.txt cache: ./cache/cord-336843-c0sr3six.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336843-c0sr3six.txt' === file2bib.sh === id: cord-316287-4i1grvlr author: Yim, Sung Sun title: Rapid Isolation of Antibody from a Synthetic Human Antibody Library by Repeated Fluorescence-Activated Cell Sorting (FACS) date: 2014-10-10 pages: extension: .txt txt: ./txt/cord-316287-4i1grvlr.txt cache: ./cache/cord-316287-4i1grvlr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-316287-4i1grvlr.txt' === file2bib.sh === id: cord-333248-5342lyeu author: Elenius, Varpu title: The relationship of serum vitamins A, D, E and LL-37 levels with allergic status, tonsillar virus detection and immune response date: 2017-02-24 pages: extension: .txt txt: ./txt/cord-333248-5342lyeu.txt cache: ./cache/cord-333248-5342lyeu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333248-5342lyeu.txt' === file2bib.sh === id: cord-335404-s48psqth author: Mukandavire, Zindoga title: Quantifying early COVID-19 outbreak transmission in South Africa and exploring vaccine efficacy scenarios date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-335404-s48psqth.txt cache: ./cache/cord-335404-s48psqth.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335404-s48psqth.txt' === file2bib.sh === id: cord-333955-bnzbppof author: Biesold, Susanne E. title: Type I Interferon Reaction to Viral Infection in Interferon-Competent, Immortalized Cell Lines from the African Fruit Bat Eidolon helvum date: 2011-11-30 pages: extension: .txt txt: ./txt/cord-333955-bnzbppof.txt cache: ./cache/cord-333955-bnzbppof.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333955-bnzbppof.txt' === file2bib.sh === id: cord-337795-khqx4t4q author: Pellecchia, Umberto title: Social Consequences of Ebola Containment Measures in Liberia date: 2015-12-09 pages: extension: .txt txt: ./txt/cord-337795-khqx4t4q.txt cache: ./cache/cord-337795-khqx4t4q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337795-khqx4t4q.txt' === file2bib.sh === id: cord-330537-xz0wt1sz author: Biermann, Olivia title: Active case-finding policy development, implementation and scale-up in high-burden countries: A mixed-methods survey with National Tuberculosis Programme managers and document review date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-330537-xz0wt1sz.txt cache: ./cache/cord-330537-xz0wt1sz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330537-xz0wt1sz.txt' === file2bib.sh === id: cord-333650-4towah1t author: Malmo, Jostein title: Cytokine Profiles in Human Metapneumovirus Infected Children: Identification of Genes Involved in the Antiviral Response and Pathogenesis date: 2016-05-12 pages: extension: .txt txt: ./txt/cord-333650-4towah1t.txt cache: ./cache/cord-333650-4towah1t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333650-4towah1t.txt' === file2bib.sh === id: cord-329468-vjsurl60 author: Okino, Cintia Hiromi title: Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles date: 2017-02-15 pages: extension: .txt txt: ./txt/cord-329468-vjsurl60.txt cache: ./cache/cord-329468-vjsurl60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329468-vjsurl60.txt' === file2bib.sh === id: cord-338067-vjyad10p author: Hao, Yan title: Prediction and analysis of Corona Virus Disease 2019 date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-338067-vjyad10p.txt cache: ./cache/cord-338067-vjyad10p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338067-vjyad10p.txt' === file2bib.sh === id: cord-336364-2ust3qoq author: Artigas, Laura title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-336364-2ust3qoq.txt cache: ./cache/cord-336364-2ust3qoq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336364-2ust3qoq.txt' === file2bib.sh === id: cord-339578-eg19rfvi author: Garcia-Garcia, Maria Luz title: Role of viral coinfections in asthma development date: 2017-12-05 pages: extension: .txt txt: ./txt/cord-339578-eg19rfvi.txt cache: ./cache/cord-339578-eg19rfvi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339578-eg19rfvi.txt' === file2bib.sh === id: cord-339327-4422s317 author: Norris, Susan L. title: An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date: 2018-05-30 pages: extension: .txt txt: ./txt/cord-339327-4422s317.txt cache: ./cache/cord-339327-4422s317.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339327-4422s317.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-322446-ddv86eoy author: Sharma, Kulbhushan title: SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date: 2011-05-27 pages: extension: .txt txt: ./txt/cord-322446-ddv86eoy.txt cache: ./cache/cord-322446-ddv86eoy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322446-ddv86eoy.txt' === file2bib.sh === id: cord-333413-8buawes0 author: Liebing, J. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-333413-8buawes0.txt cache: ./cache/cord-333413-8buawes0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-333413-8buawes0.txt' === file2bib.sh === id: cord-340027-6l55rcfm author: Mamode Khan, Naushad title: Studying the trend of the novel coronavirus series in Mauritius and its implications date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-340027-6l55rcfm.txt cache: ./cache/cord-340027-6l55rcfm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340027-6l55rcfm.txt' === file2bib.sh === id: cord-339789-151d1j4n author: Hong, Hyokyoung G. title: Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-339789-151d1j4n.txt cache: ./cache/cord-339789-151d1j4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339789-151d1j4n.txt' === file2bib.sh === id: cord-331652-oc5s1if2 author: Trudeau, Michaela P. title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date: 2016-06-24 pages: extension: .txt txt: ./txt/cord-331652-oc5s1if2.txt cache: ./cache/cord-331652-oc5s1if2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-331652-oc5s1if2.txt' === file2bib.sh === id: cord-339026-eu11larc author: Ryals, Renee C. title: The effects of PEGylation on LNP based mRNA delivery to the eye date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-339026-eu11larc.txt cache: ./cache/cord-339026-eu11larc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339026-eu11larc.txt' === file2bib.sh === id: cord-336441-m6pur6td author: Wang, Changjian title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date: 2019-02-11 pages: extension: .txt txt: ./txt/cord-336441-m6pur6td.txt cache: ./cache/cord-336441-m6pur6td.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336441-m6pur6td.txt' === file2bib.sh === id: cord-329223-f84gjxm1 author: Kouokam, Joseph Calvin title: Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date: 2011-08-02 pages: extension: .txt txt: ./txt/cord-329223-f84gjxm1.txt cache: ./cache/cord-329223-f84gjxm1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329223-f84gjxm1.txt' === file2bib.sh === id: cord-328633-c31xsyeo author: Moser, Michael J. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 pages: extension: .txt txt: ./txt/cord-328633-c31xsyeo.txt cache: ./cache/cord-328633-c31xsyeo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328633-c31xsyeo.txt' === file2bib.sh === id: cord-328627-cf8f71dr author: Jando, Julia title: Expression and regulation of the neutral amino acid transporter B(0)AT1 in rat small intestine date: 2017-09-15 pages: extension: .txt txt: ./txt/cord-328627-cf8f71dr.txt cache: ./cache/cord-328627-cf8f71dr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328627-cf8f71dr.txt' === file2bib.sh === id: cord-338594-wft7yy6j author: Winkler, Michael title: Rhesus macaque IFITM3 gene polymorphisms and SIV infection date: 2017-03-03 pages: extension: .txt txt: ./txt/cord-338594-wft7yy6j.txt cache: ./cache/cord-338594-wft7yy6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338594-wft7yy6j.txt' === file2bib.sh === id: cord-333522-zsdymkjd author: Gruse, Jeannine title: Quercetin Feeding in Newborn Dairy Calves Cannot Compensate Colostrum Deprivation: Study on Metabolic, Antioxidative and Inflammatory Traits date: 2016-01-11 pages: extension: .txt txt: ./txt/cord-333522-zsdymkjd.txt cache: ./cache/cord-333522-zsdymkjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333522-zsdymkjd.txt' === file2bib.sh === id: cord-336615-jfnj6l41 author: Wong, Sarah Sze Wah title: In Vitro and In Vivo Activity of a Novel Antifungal Small Molecule against Candida Infections date: 2014-01-22 pages: extension: .txt txt: ./txt/cord-336615-jfnj6l41.txt cache: ./cache/cord-336615-jfnj6l41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-336615-jfnj6l41.txt' === file2bib.sh === id: cord-340718-amfs4zay author: Zhu, Gengping title: Potential Geographic Distribution of the Novel Avian-Origin Influenza A (H7N9) Virus date: 2014-04-01 pages: extension: .txt txt: ./txt/cord-340718-amfs4zay.txt cache: ./cache/cord-340718-amfs4zay.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340718-amfs4zay.txt' === file2bib.sh === id: cord-330110-pamxy4av author: Teissier, Elodie title: Mechanism of Inhibition of Enveloped Virus Membrane Fusion by the Antiviral Drug Arbidol date: 2011-01-25 pages: extension: .txt txt: ./txt/cord-330110-pamxy4av.txt cache: ./cache/cord-330110-pamxy4av.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330110-pamxy4av.txt' === file2bib.sh === id: cord-335441-bj3me7p8 author: Jourdain, Elsa title: Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date: 2010-01-28 pages: extension: .txt txt: ./txt/cord-335441-bj3me7p8.txt cache: ./cache/cord-335441-bj3me7p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335441-bj3me7p8.txt' === file2bib.sh === id: cord-335245-1eksm537 author: Pattyn, Els title: HyperISGylation of Old World Monkey ISG15 in Human Cells date: 2008-06-18 pages: extension: .txt txt: ./txt/cord-335245-1eksm537.txt cache: ./cache/cord-335245-1eksm537.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335245-1eksm537.txt' === file2bib.sh === id: cord-339724-roj8ksvc author: Lan, Jiaming title: Tailoring Subunit Vaccine Immunity with Adjuvant Combinations and Delivery Routes Using the Middle East Respiratory Coronavirus (MERS-CoV) Receptor-Binding Domain as an Antigen date: 2014-11-18 pages: extension: .txt txt: ./txt/cord-339724-roj8ksvc.txt cache: ./cache/cord-339724-roj8ksvc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339724-roj8ksvc.txt' === file2bib.sh === id: cord-340195-425rd7ul author: Smith, Kristine M. title: Zoonotic Viruses Associated with Illegally Imported Wildlife Products date: 2012-01-10 pages: extension: .txt txt: ./txt/cord-340195-425rd7ul.txt cache: ./cache/cord-340195-425rd7ul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340195-425rd7ul.txt' === file2bib.sh === id: cord-339869-euikj8fv author: Cebey-López, Miriam title: Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date: 2016-04-20 pages: extension: .txt txt: ./txt/cord-339869-euikj8fv.txt cache: ./cache/cord-339869-euikj8fv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339869-euikj8fv.txt' === file2bib.sh === id: cord-337879-liqhbqxl author: Kriesel, John D. title: Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date: 2012-03-08 pages: extension: .txt txt: ./txt/cord-337879-liqhbqxl.txt cache: ./cache/cord-337879-liqhbqxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337879-liqhbqxl.txt' === file2bib.sh === id: cord-334955-gnu92up6 author: Sutton, Jeannette title: COVID-19: Retransmission of official communications in an emerging pandemic date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-334955-gnu92up6.txt cache: ./cache/cord-334955-gnu92up6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334955-gnu92up6.txt' === file2bib.sh === id: cord-335272-jypxi99z author: Sharma, Anupam Joya title: A cross-sectional study of psychological wellbeing of Indian adults during the Covid-19 lockdown: Different strokes for different folks date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-335272-jypxi99z.txt cache: ./cache/cord-335272-jypxi99z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335272-jypxi99z.txt' === file2bib.sh === id: cord-340656-ltd6ueoi author: Grant, Michael C. title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-340656-ltd6ueoi.txt cache: ./cache/cord-340656-ltd6ueoi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340656-ltd6ueoi.txt' === file2bib.sh === id: cord-334695-cjxlw1tu author: Kam, Yiu-Wing title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date: 2009-11-17 pages: extension: .txt txt: ./txt/cord-334695-cjxlw1tu.txt cache: ./cache/cord-334695-cjxlw1tu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334695-cjxlw1tu.txt' === file2bib.sh === id: cord-340937-6mpob1nx author: Varshney, Mohit title: Initial psychological impact of COVID-19 and its correlates in Indian Community: An online (FEEL-COVID) survey date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-340937-6mpob1nx.txt cache: ./cache/cord-340937-6mpob1nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340937-6mpob1nx.txt' === file2bib.sh === id: cord-340627-xyvzgkxl author: Ornaghi, Sara title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-340627-xyvzgkxl.txt cache: ./cache/cord-340627-xyvzgkxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340627-xyvzgkxl.txt' === file2bib.sh === id: cord-340766-aic570x8 author: Kim, Se Jin title: Outcomes of Early Administration of Cidofovir in Non-Immunocompromised Patients with Severe Adenovirus Pneumonia date: 2015-04-15 pages: extension: .txt txt: ./txt/cord-340766-aic570x8.txt cache: ./cache/cord-340766-aic570x8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340766-aic570x8.txt' === file2bib.sh === id: cord-343135-m0pdixw5 author: Marguet, Christophe title: In Very Young Infants Severity of Acute Bronchiolitis Depends On Carried Viruses date: 2009-02-25 pages: extension: .txt txt: ./txt/cord-343135-m0pdixw5.txt cache: ./cache/cord-343135-m0pdixw5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343135-m0pdixw5.txt' === file2bib.sh === id: cord-342476-0rupk21u author: van Rijn, Anneloes L. title: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date: 2019-10-24 pages: extension: .txt txt: ./txt/cord-342476-0rupk21u.txt cache: ./cache/cord-342476-0rupk21u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342476-0rupk21u.txt' === file2bib.sh === id: cord-337630-ojhk5opy author: Tasic, Velibor title: Clinical and Functional Characterization of URAT1 Variants date: 2011-12-16 pages: extension: .txt txt: ./txt/cord-337630-ojhk5opy.txt cache: ./cache/cord-337630-ojhk5opy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337630-ojhk5opy.txt' === file2bib.sh === id: cord-340703-vtuy806l author: Cascio, Antonio title: Low bone mineral density in HIV-positive young Italians and migrants date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-340703-vtuy806l.txt cache: ./cache/cord-340703-vtuy806l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340703-vtuy806l.txt' === file2bib.sh === id: cord-342133-khrljehj author: Principi, Nicola title: Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date: 2015-08-12 pages: extension: .txt txt: ./txt/cord-342133-khrljehj.txt cache: ./cache/cord-342133-khrljehj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342133-khrljehj.txt' === file2bib.sh === id: cord-339392-2ocz784l author: Sharma, Kulbhushan title: Influenza A Virus Nucleoprotein Exploits Hsp40 to Inhibit PKR Activation date: 2011-06-15 pages: extension: .txt txt: ./txt/cord-339392-2ocz784l.txt cache: ./cache/cord-339392-2ocz784l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339392-2ocz784l.txt' === file2bib.sh === id: cord-340713-v5sdowb7 author: Bird, Jordan J. title: Country-level pandemic risk and preparedness classification based on COVID-19 data: A machine learning approach date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-340713-v5sdowb7.txt cache: ./cache/cord-340713-v5sdowb7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340713-v5sdowb7.txt' === file2bib.sh === id: cord-341914-l2bomgji author: Flies, Andrew S. title: Markedly Elevated Antibody Responses in Wild versus Captive Spotted Hyenas Show that Environmental and Ecological Factors Are Important Modulators of Immunity date: 2015-10-07 pages: extension: .txt txt: ./txt/cord-341914-l2bomgji.txt cache: ./cache/cord-341914-l2bomgji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341914-l2bomgji.txt' === file2bib.sh === id: cord-337913-eu2gn4bl author: Stojanov, Ana title: Does Perceived Lack of Control Lead to Conspiracy Theory Beliefs? Findings from an online MTurk sample date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-337913-eu2gn4bl.txt cache: ./cache/cord-337913-eu2gn4bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337913-eu2gn4bl.txt' === file2bib.sh === id: cord-346089-u31n0qxa author: McDade, Thomas W. title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-346089-u31n0qxa.txt cache: ./cache/cord-346089-u31n0qxa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346089-u31n0qxa.txt' === file2bib.sh === id: cord-342519-tjr6dvtt author: Souza, Thiago Moreno L. title: H1N1pdm Influenza Infection in Hospitalized Cancer Patients: Clinical Evolution and Viral Analysis date: 2010-11-30 pages: extension: .txt txt: ./txt/cord-342519-tjr6dvtt.txt cache: ./cache/cord-342519-tjr6dvtt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342519-tjr6dvtt.txt' === file2bib.sh === id: cord-340763-cxnu9g8y author: Grimm, Sebastian K. title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date: 2015-02-17 pages: extension: .txt txt: ./txt/cord-340763-cxnu9g8y.txt cache: ./cache/cord-340763-cxnu9g8y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340763-cxnu9g8y.txt' === file2bib.sh === id: cord-344357-ocyaqs1y author: Fu, Yue-Qiang title: Effect of blood analysis and immune function on the prognosis of patients with COVID-19 date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-344357-ocyaqs1y.txt cache: ./cache/cord-344357-ocyaqs1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344357-ocyaqs1y.txt' === file2bib.sh === id: cord-337067-j8ebslif author: Mades, Andreas title: Role of Human Sec63 in Modulating the Steady-State Levels of Multi-Spanning Membrane Proteins date: 2012-11-15 pages: extension: .txt txt: ./txt/cord-337067-j8ebslif.txt cache: ./cache/cord-337067-j8ebslif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337067-j8ebslif.txt' === file2bib.sh === id: cord-339920-dr5bvpm0 author: Soberman, Roy J. title: CD200R1 Supports HSV-1 Viral Replication and Licenses Pro-Inflammatory Signaling Functions of TLR2 date: 2012-10-17 pages: extension: .txt txt: ./txt/cord-339920-dr5bvpm0.txt cache: ./cache/cord-339920-dr5bvpm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339920-dr5bvpm0.txt' === file2bib.sh === id: cord-344839-r05p9h0e author: Majmundar, Monil title: Efficacy of corticosteroids in non-intensive care unit patients with COVID-19 pneumonia from the New York Metropolitan region date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-344839-r05p9h0e.txt cache: ./cache/cord-344839-r05p9h0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344839-r05p9h0e.txt' === file2bib.sh === id: cord-343973-n5ogyxz7 author: Ip, Andrew title: Hydroxychloroquine and tocilizumab therapy in COVID-19 patients—An observational study date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-343973-n5ogyxz7.txt cache: ./cache/cord-343973-n5ogyxz7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-343973-n5ogyxz7.txt' === file2bib.sh === id: cord-345717-ktajrf7d author: Monagin, Corina title: Serologic and behavioral risk survey of workers with wildlife contact in China date: 2018-04-03 pages: extension: .txt txt: ./txt/cord-345717-ktajrf7d.txt cache: ./cache/cord-345717-ktajrf7d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345717-ktajrf7d.txt' === file2bib.sh === id: cord-340387-ohkjheat author: Wynne, James W. title: Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA date: 2013-01-07 pages: extension: .txt txt: ./txt/cord-340387-ohkjheat.txt cache: ./cache/cord-340387-ohkjheat.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340387-ohkjheat.txt' === file2bib.sh === id: cord-347465-yu6oj30v author: Kurskaya, Olga title: Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date: 2018-09-18 pages: extension: .txt txt: ./txt/cord-347465-yu6oj30v.txt cache: ./cache/cord-347465-yu6oj30v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347465-yu6oj30v.txt' === file2bib.sh === id: cord-345019-i7zm9bt1 author: Al-Waleedi, Ali Ahmed title: The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-345019-i7zm9bt1.txt cache: ./cache/cord-345019-i7zm9bt1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345019-i7zm9bt1.txt' === file2bib.sh === id: cord-346586-fxxceffl author: Razanajatovo, Norosoa Harline title: Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date: 2018-11-21 pages: extension: .txt txt: ./txt/cord-346586-fxxceffl.txt cache: ./cache/cord-346586-fxxceffl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346586-fxxceffl.txt' === file2bib.sh === id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-344782-ond1ziu5.txt cache: ./cache/cord-344782-ond1ziu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344782-ond1ziu5.txt' === file2bib.sh === id: cord-341097-c96hm610 author: Mayer, Craig S. title: Analysis of data dictionary formats of HIV clinical trials date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-341097-c96hm610.txt cache: ./cache/cord-341097-c96hm610.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341097-c96hm610.txt' === file2bib.sh === id: cord-344152-pb1e2w7s author: Kolatkar, Anand title: C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training date: 2008-02-20 pages: extension: .txt txt: ./txt/cord-344152-pb1e2w7s.txt cache: ./cache/cord-344152-pb1e2w7s.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344152-pb1e2w7s.txt' === file2bib.sh === id: cord-350842-4m82l5t8 author: Xing, Jun title: Study of the mental health status of medical personnel dealing with new coronavirus pneumonia date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-350842-4m82l5t8.txt cache: ./cache/cord-350842-4m82l5t8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350842-4m82l5t8.txt' === file2bib.sh === id: cord-346858-18q8rxzg author: Hossain, Md. Tanvir title: Social and electronic media exposure and generalized anxiety disorder among people during COVID-19 outbreak in Bangladesh: A preliminary observation date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-346858-18q8rxzg.txt cache: ./cache/cord-346858-18q8rxzg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346858-18q8rxzg.txt' === file2bib.sh === id: cord-341880-wxliz485 author: Mottaleb, Khondoker Abdul title: COVID-19 induced economic loss and ensuring food security for vulnerable groups: Policy implications from Bangladesh date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-341880-wxliz485.txt cache: ./cache/cord-341880-wxliz485.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-341880-wxliz485.txt' === file2bib.sh === id: cord-348243-e5tdb08v author: Schermer, Bernhard title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-348243-e5tdb08v.txt cache: ./cache/cord-348243-e5tdb08v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348243-e5tdb08v.txt' === file2bib.sh === id: cord-339796-gccnvh0z author: Zhang, Si Min title: Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date: 2015-07-31 pages: extension: .txt txt: ./txt/cord-339796-gccnvh0z.txt cache: ./cache/cord-339796-gccnvh0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-339796-gccnvh0z.txt' === file2bib.sh === id: cord-342639-vf9n2vf9 author: Chang, Chung-ke title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 pages: extension: .txt txt: ./txt/cord-342639-vf9n2vf9.txt cache: ./cache/cord-342639-vf9n2vf9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-342639-vf9n2vf9.txt' === file2bib.sh === id: cord-345695-5vi9wibk author: Hicks, Lorin L. title: A statistical approach to white-nose syndrome surveillance monitoring using acoustic data date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-345695-5vi9wibk.txt cache: ./cache/cord-345695-5vi9wibk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345695-5vi9wibk.txt' === file2bib.sh === id: cord-348807-9xxc5hyl author: Cuomo, Raphael E. title: Sub-national longitudinal and geospatial analysis of COVID-19 tweets date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-348807-9xxc5hyl.txt cache: ./cache/cord-348807-9xxc5hyl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348807-9xxc5hyl.txt' === file2bib.sh === id: cord-346067-zly8p0y7 author: Ruiz-Irastorza, Guillermo title: Second week methyl-prednisolone pulses improve prognosis in patients with severe coronavirus disease 2019 pneumonia: An observational comparative study using routine care data date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-346067-zly8p0y7.txt cache: ./cache/cord-346067-zly8p0y7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346067-zly8p0y7.txt' === file2bib.sh === id: cord-348499-7ll7sd3o author: Manderstedt, Eric title: Genetic variation in the C-type lectin receptor CLEC4M in type 1 von Willebrand Disease patients date: 2018-02-01 pages: extension: .txt txt: ./txt/cord-348499-7ll7sd3o.txt cache: ./cache/cord-348499-7ll7sd3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348499-7ll7sd3o.txt' === file2bib.sh === id: cord-344870-tbgqulpu author: Lloyd-Smith, James O. title: Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases date: 2007-02-14 pages: extension: .txt txt: ./txt/cord-344870-tbgqulpu.txt cache: ./cache/cord-344870-tbgqulpu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344870-tbgqulpu.txt' === file2bib.sh === id: cord-346819-11fkgzaa author: Khan, Mohd Imran title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-346819-11fkgzaa.txt cache: ./cache/cord-346819-11fkgzaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346819-11fkgzaa.txt' === file2bib.sh === id: cord-349029-zyfop43z author: Dobrovolny, Hana M. title: Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-349029-zyfop43z.txt cache: ./cache/cord-349029-zyfop43z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349029-zyfop43z.txt' === file2bib.sh === id: cord-349217-vpih1wvs author: Petropoulos, Fotios title: Forecasting the novel coronavirus COVID-19 date: 2020-03-31 pages: extension: .txt txt: ./txt/cord-349217-vpih1wvs.txt cache: ./cache/cord-349217-vpih1wvs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349217-vpih1wvs.txt' === file2bib.sh === id: cord-342730-b7y8mybg author: Dellagi, Koussay title: Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009 date: 2011-09-29 pages: extension: .txt txt: ./txt/cord-342730-b7y8mybg.txt cache: ./cache/cord-342730-b7y8mybg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342730-b7y8mybg.txt' === file2bib.sh === id: cord-352403-4591ewsa author: Hartwig, Stacey M. title: Depletion of Alveolar Macrophages Ameliorates Virus-Induced Disease following a Pulmonary Coronavirus Infection date: 2014-03-07 pages: extension: .txt txt: ./txt/cord-352403-4591ewsa.txt cache: ./cache/cord-352403-4591ewsa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352403-4591ewsa.txt' === file2bib.sh === id: cord-352222-zq9o66i4 author: Rajatonirina, Soatiana title: Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date: 2013-09-12 pages: extension: .txt txt: ./txt/cord-352222-zq9o66i4.txt cache: ./cache/cord-352222-zq9o66i4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352222-zq9o66i4.txt' === file2bib.sh === id: cord-329999-flzqm3wh author: Buchanan, Tom title: Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-329999-flzqm3wh.txt cache: ./cache/cord-329999-flzqm3wh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329999-flzqm3wh.txt' === file2bib.sh === id: cord-349476-iac9fak3 author: Mao, Liang title: Evaluating the Combined Effectiveness of Influenza Control Strategies and Human Preventive Behavior date: 2011-10-17 pages: extension: .txt txt: ./txt/cord-349476-iac9fak3.txt cache: ./cache/cord-349476-iac9fak3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349476-iac9fak3.txt' === file2bib.sh === id: cord-353866-0r1b44id author: Sun, Hongpeng title: Changes of Adult Population Health Status in China from 2003 to 2008 date: 2011-12-02 pages: extension: .txt txt: ./txt/cord-353866-0r1b44id.txt cache: ./cache/cord-353866-0r1b44id.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353866-0r1b44id.txt' === file2bib.sh === id: cord-349911-dx8wvqkm author: Dahl, Viktor title: Communicable Diseases Prioritized According to Their Public Health Relevance, Sweden, 2013 date: 2015-09-23 pages: extension: .txt txt: ./txt/cord-349911-dx8wvqkm.txt cache: ./cache/cord-349911-dx8wvqkm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349911-dx8wvqkm.txt' === file2bib.sh === id: cord-351387-i0zamkpd author: Witte, Katrin title: The Pelargonium sidoides Extract EPs 7630 Drives the Innate Immune Defense by Activating Selected MAP Kinase Pathways in Human Monocytes date: 2015-09-25 pages: extension: .txt txt: ./txt/cord-351387-i0zamkpd.txt cache: ./cache/cord-351387-i0zamkpd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351387-i0zamkpd.txt' === file2bib.sh === id: cord-353253-kk2q71vg author: Itokawa, Kentaro title: Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-353253-kk2q71vg.txt cache: ./cache/cord-353253-kk2q71vg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353253-kk2q71vg.txt' === file2bib.sh === id: cord-347014-88zmtky7 author: Esposito, Susanna title: Sensitivity and Specificity of Soluble Triggering Receptor Expressed on Myeloid Cells-1, Midregional Proatrial Natriuretic Peptide and Midregional Proadrenomedullin for Distinguishing Etiology and to Assess Severity in Community-Acquired Pneumonia date: 2016-11-15 pages: extension: .txt txt: ./txt/cord-347014-88zmtky7.txt cache: ./cache/cord-347014-88zmtky7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347014-88zmtky7.txt' === file2bib.sh === id: cord-349781-l93978vq author: Cong, Yu title: MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells date: 2018-03-22 pages: extension: .txt txt: ./txt/cord-349781-l93978vq.txt cache: ./cache/cord-349781-l93978vq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349781-l93978vq.txt' === file2bib.sh === id: cord-352522-qnvgg2e9 author: Langille, Morgan G. I. title: BioTorrents: A File Sharing Service for Scientific Data date: 2010-04-14 pages: extension: .txt txt: ./txt/cord-352522-qnvgg2e9.txt cache: ./cache/cord-352522-qnvgg2e9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352522-qnvgg2e9.txt' === file2bib.sh === id: cord-351990-aham72b9 author: Radin, Jennifer M. title: Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date: 2014-12-30 pages: extension: .txt txt: ./txt/cord-351990-aham72b9.txt cache: ./cache/cord-351990-aham72b9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351990-aham72b9.txt' === file2bib.sh === id: cord-355874-nz6eqcdb author: Wang, Le title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-355874-nz6eqcdb.txt cache: ./cache/cord-355874-nz6eqcdb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355874-nz6eqcdb.txt' === file2bib.sh === id: cord-352447-bc1pf272 author: Nishida, Yu title: Novel prognostic biomarkers of pouchitis after ileal pouch-anal anastomosis for ulcerative colitis: Neutrophil-to-lymphocyte ratio date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-352447-bc1pf272.txt cache: ./cache/cord-352447-bc1pf272.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352447-bc1pf272.txt' === file2bib.sh === id: cord-346347-r4ork18p author: Borrion, Hervé title: Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-346347-r4ork18p.txt cache: ./cache/cord-346347-r4ork18p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346347-r4ork18p.txt' === file2bib.sh === id: cord-352564-2j4pjjwk author: Dominguez, Samuel R. title: Human Coronavirus HKU1 Infection of Primary Human Type II Alveolar Epithelial Cells: Cytopathic Effects and Innate Immune Response date: 2013-07-24 pages: extension: .txt txt: ./txt/cord-352564-2j4pjjwk.txt cache: ./cache/cord-352564-2j4pjjwk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352564-2j4pjjwk.txt' === file2bib.sh === id: cord-356132-1nisyl5r author: Wang, Huiyao title: The psychological distress and coping styles in the early stages of the 2019 coronavirus disease (COVID-19) epidemic in the general mainland Chinese population: A web-based survey date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-356132-1nisyl5r.txt cache: ./cache/cord-356132-1nisyl5r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356132-1nisyl5r.txt' === file2bib.sh === id: cord-352200-i05h8csb author: Xu, Yi title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 pages: extension: .txt txt: ./txt/cord-352200-i05h8csb.txt cache: ./cache/cord-352200-i05h8csb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352200-i05h8csb.txt' === file2bib.sh === id: cord-353410-tbmtg88k author: Sharma, Shreela V. title: Using a rapid assessment methodology to identify and address immediate needs among low-income households with children during COVID-19 date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-353410-tbmtg88k.txt cache: ./cache/cord-353410-tbmtg88k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353410-tbmtg88k.txt' === file2bib.sh === id: cord-348055-azlb1zy1 author: Patel, Mira C. title: Enterovirus D-68 Infection, Prophylaxis, and Vaccination in a Novel Permissive Animal Model, the Cotton Rat (Sigmodon hispidus) date: 2016-11-04 pages: extension: .txt txt: ./txt/cord-348055-azlb1zy1.txt cache: ./cache/cord-348055-azlb1zy1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348055-azlb1zy1.txt' === file2bib.sh === id: cord-354000-jxqskt4k author: Warren, Cody J. title: The Antiviral Restriction Factors IFITM1, 2 and 3 Do Not Inhibit Infection of Human Papillomavirus, Cytomegalovirus and Adenovirus date: 2014-05-14 pages: extension: .txt txt: ./txt/cord-354000-jxqskt4k.txt cache: ./cache/cord-354000-jxqskt4k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354000-jxqskt4k.txt' === file2bib.sh === id: cord-353200-5csewb1k author: Jehi, Lara title: Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-353200-5csewb1k.txt cache: ./cache/cord-353200-5csewb1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353200-5csewb1k.txt' === file2bib.sh === id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-352720-z1cvjc2y.txt cache: ./cache/cord-352720-z1cvjc2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352720-z1cvjc2y.txt' === file2bib.sh === id: cord-353245-es7b1rs0 author: Song, Deping title: Molecular Characterization and Phylogenetic Analysis of Porcine Epidemic Diarrhea Viruses Associated with Outbreaks of Severe Diarrhea in Piglets in Jiangxi, China 2013 date: 2015-03-19 pages: extension: .txt txt: ./txt/cord-353245-es7b1rs0.txt cache: ./cache/cord-353245-es7b1rs0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353245-es7b1rs0.txt' === file2bib.sh === id: cord-351868-w4d45fue author: Zuwała, Kaja title: The Nucleocapsid Protein of Human Coronavirus NL63 date: 2015-02-20 pages: extension: .txt txt: ./txt/cord-351868-w4d45fue.txt cache: ./cache/cord-351868-w4d45fue.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351868-w4d45fue.txt' === file2bib.sh === id: cord-353869-l53ms3q8 author: Friesen, Robert H. E. title: New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date: 2010-02-08 pages: extension: .txt txt: ./txt/cord-353869-l53ms3q8.txt cache: ./cache/cord-353869-l53ms3q8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353869-l53ms3q8.txt' === file2bib.sh === id: cord-351098-x729wpp7 author: Long, Rachel B. title: Characterizing trends in human-wildlife conflicts in the American Midwest using wildlife rehabilitation records date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-351098-x729wpp7.txt cache: ./cache/cord-351098-x729wpp7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351098-x729wpp7.txt' === file2bib.sh === id: cord-351142-g20f6bxc author: Kiaghadi, Amin title: Assessing COVID-19 risk, vulnerability and infection prevalence in communities date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-351142-g20f6bxc.txt cache: ./cache/cord-351142-g20f6bxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351142-g20f6bxc.txt' === file2bib.sh === id: cord-350443-ca5avyjf author: Zhang, Lei title: Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date: 2012-02-16 pages: extension: .txt txt: ./txt/cord-350443-ca5avyjf.txt cache: ./cache/cord-350443-ca5avyjf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350443-ca5avyjf.txt' === file2bib.sh === id: cord-351918-pu7i1jfe author: Baek, Yae Jee title: A mathematical model of COVID-19 transmission in a tertiary hospital and assessment of the effects of different intervention strategies date: 2020-10-26 pages: extension: .txt txt: ./txt/cord-351918-pu7i1jfe.txt cache: ./cache/cord-351918-pu7i1jfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351918-pu7i1jfe.txt' === file2bib.sh === id: cord-352511-gkm7i62s author: Yamada, Yoshiyuki title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date: 2009-07-02 pages: extension: .txt txt: ./txt/cord-352511-gkm7i62s.txt cache: ./cache/cord-352511-gkm7i62s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352511-gkm7i62s.txt' === file2bib.sh === id: cord-354052-x4ckzw64 author: Li, Chunhua title: Manipulation of the Porcine Epidemic Diarrhea Virus Genome Using Targeted RNA Recombination date: 2013-08-02 pages: extension: .txt txt: ./txt/cord-354052-x4ckzw64.txt cache: ./cache/cord-354052-x4ckzw64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354052-x4ckzw64.txt' === file2bib.sh === id: cord-356364-ipi81ce3 author: Ho, Bo-Lin title: Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date: 2015-12-14 pages: extension: .txt txt: ./txt/cord-356364-ipi81ce3.txt cache: ./cache/cord-356364-ipi81ce3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-356364-ipi81ce3.txt' === file2bib.sh === id: cord-347317-qcghtkk0 author: Russo, Lucia title: Tracing day-zero and forecasting the COVID-19 outbreak in Lombardy, Italy: A compartmental modelling and numerical optimization approach date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-347317-qcghtkk0.txt cache: ./cache/cord-347317-qcghtkk0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347317-qcghtkk0.txt' === file2bib.sh === id: cord-353596-8iqjugcx author: Bédubourg, Gabriel title: Evaluation and comparison of statistical methods for early temporal detection of outbreaks: A simulation-based study date: 2017-07-17 pages: extension: .txt txt: ./txt/cord-353596-8iqjugcx.txt cache: ./cache/cord-353596-8iqjugcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353596-8iqjugcx.txt' === file2bib.sh === id: cord-354547-eomm1sl5 author: Wang, Jibin title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date: 2009-03-16 pages: extension: .txt txt: ./txt/cord-354547-eomm1sl5.txt cache: ./cache/cord-354547-eomm1sl5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354547-eomm1sl5.txt' === file2bib.sh === id: cord-346314-o9fjpqaj author: Jarboui, Mohamed Ali title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 pages: extension: .txt txt: ./txt/cord-346314-o9fjpqaj.txt cache: ./cache/cord-346314-o9fjpqaj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346314-o9fjpqaj.txt' === file2bib.sh === id: cord-354763-odzrco6q author: Drake, John M. title: Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date: 2006-12-20 pages: extension: .txt txt: ./txt/cord-354763-odzrco6q.txt cache: ./cache/cord-354763-odzrco6q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354763-odzrco6q.txt' === file2bib.sh === id: cord-355259-779czzzx author: Yang, Xiaoyun title: A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date: 2014-10-15 pages: extension: .txt txt: ./txt/cord-355259-779czzzx.txt cache: ./cache/cord-355259-779czzzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355259-779czzzx.txt' === file2bib.sh === id: cord-352219-z245sb3s author: Tallam, Aravind title: Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages date: 2016-02-12 pages: extension: .txt txt: ./txt/cord-352219-z245sb3s.txt cache: ./cache/cord-352219-z245sb3s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352219-z245sb3s.txt' === file2bib.sh === id: cord-351185-3y3gou6v author: Buckles, Thomas C. title: Rapid exposure of macrophages to drugs resolves four classes of effects on the leading edge sensory pseudopod: Non-perturbing, adaptive, disruptive, and activating date: 2020-05-29 pages: extension: .txt txt: ./txt/cord-351185-3y3gou6v.txt cache: ./cache/cord-351185-3y3gou6v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-351185-3y3gou6v.txt' === file2bib.sh === id: cord-353730-owcapg8h author: Dietrich, Jes title: Inducing Dose Sparing with Inactivated Polio Virus Formulated in Adjuvant CAF01 date: 2014-06-23 pages: extension: .txt txt: ./txt/cord-353730-owcapg8h.txt cache: ./cache/cord-353730-owcapg8h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353730-owcapg8h.txt' === file2bib.sh === id: cord-350398-w75flrwv author: Sampath, Rangarajan title: Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date: 2012-06-29 pages: extension: .txt txt: ./txt/cord-350398-w75flrwv.txt cache: ./cache/cord-350398-w75flrwv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350398-w75flrwv.txt' Que is empty; done journal-plosOne-cord === reduce.pl bib === id = cord-000366-u4649rtx author = Shan, Tongling title = Genomic Characterization and High Prevalence of Bocaviruses in Swine date = 2011-04-15 pages = extension = .txt mime = text/plain words = 2887 sentences = 161 flesch = 55 summary = Using random PCR amplification followed by plasmid subcloning and DNA sequencing, we detected bocavirus related sequences in 9 out of 17 porcine stool samples. Using primer walking, we sequenced the nearly complete genomes of two highly divergent bocaviruses we provisionally named porcine bocavirus 1 isolate H18 (PBoV1-H18) and porcine bocavirus 2 isolate A6 (PBoV2-A6) which differed by 51.8% in their NS1 protein. Presently, the bocavirus genus contains eight members: bovine parvovirus, canine minute virus (CnMV), human bocavirus 1-4 (HBoV1-4), a gorilla bocavirus and a partially sequenced chimpanzee bocavirus [1, 6, 7] . In 2009, a porcine bocalike virus (PBo-likeV) was reported in swine feces with postweaning multisystemic wasting syndrome in Sweden and 1854 bp of its partial genome sequenced [27] . Finally, partial genome sequences of 2.4 Kb from another clade of porcine bocaviruses labeled 6V and 7V where also identified yielding three major bocavirus groups in swine (PBo-likeV, PBoV1/PBoV2, and 6V/7V). cache = ./cache/cord-000366-u4649rtx.txt txt = ./txt/cord-000366-u4649rtx.txt === reduce.pl bib === id = cord-000013-pr9i9swk author = Croyle, Maria A. title = Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice date = 2008-10-29 pages = extension = .txt mime = text/plain words = 6509 sentences = 272 flesch = 37 summary = We have previously found that a single dose of a recombinant adenovirus expressing Ebola Zaire GP given by either the oral or the nasal route is capable of affording protection against lethal challenge in naïve mice and that mucosal immunization can stimulate a broad, prolonged T cell-mediated immune response in both the systemic and mucosal compartments [37] . In an effort to correlate markers of immunity with protection against Ebola infection after mucosal immunization, T and B cell specific immune responses against Ebola glycoprotein were analyzed in mice in the presence or absence of pre-existing immunity (PEI) to adenovirus 10 days after vaccination with a first generation adenovirus serotype 5 vector expressing the Zaire Ebola glycoprotein (Ad5-ZGP). A single intranasal dose of a recombinant Ad5 vaccine expressing the Zaire Ebola glycoprotein conferred 100% protection in both naïve mice and those with pre-existing immunity despite the fact that the strength of the immune response generated by this route of administration was quantitatively lower than that seen in animals vaccinated by intramuscular injection. cache = ./cache/cord-000013-pr9i9swk.txt txt = ./txt/cord-000013-pr9i9swk.txt === reduce.pl bib === id = cord-000006-104sqoxz author = Bray, Daniel P. title = Composition and Function of Haemolymphatic Tissues in the European Common Shrew date = 2008-10-15 pages = extension = .txt mime = text/plain words = 5701 sentences = 259 flesch = 46 summary = Here, we examined the unique haemolymphatic system of the European common shrew (Sorex araneus) to investigate the capacity of this short-lived mammal, restricted by a fast metabolism and extremely limited fat reserves, to defend against its unusually diverse parasite fauna, both as a young animal and an adult. We examined and compared the structure, composition and function of relevant haemolymphatic tissues including the pancreas of Aselli, in wild-caught common shrews of different ages pre and post maturation, and the extent and type of inflammatory reactions produced in response to naturally occurring parasitic infections. While some degree of lymphatic exhaustion was obvious in adult animals (perhaps as a result of age-related changes, or reduced investment in immunity as a consequence of breeding effort), there was also evidence of some degree of compensation, in the form of storage of plasma cells particularly in the pancreas of Aselli, possibly as a defence against previously encountered parasites. cache = ./cache/cord-000006-104sqoxz.txt txt = ./txt/cord-000006-104sqoxz.txt === reduce.pl bib === id = cord-000050-tfcerilc author = Rao, Srinivas title = Multivalent HA DNA Vaccination Protects against Highly Pathogenic H5N1 Avian Influenza Infection in Chickens and Mice date = 2008-06-18 pages = extension = .txt mime = text/plain words = 5605 sentences = 256 flesch = 44 summary = METHODOLOGY / PRINCIPAL FINDINGS: The ability of DNA vaccines encoding hemagglutinin (HA) proteins from different HPAI H5N1 serotypes was evaluated for its ability to elicit neutralizing antibodies and to protect against homologous and heterologous HPAI H5N1 strain challenge in mice and chickens after DNA immunization by needle and syringe or with a pressure injection device. After optimization of injection conditions, alternative multivalent DNA vaccine regimens were analyzed and compared for magnitude and breadth of neutralizing antibodies, as well as protective efficacy after challenge in mouse and chicken models of HPAI H5N1 infection. The ability of chickens to generate specific antibodies was assessed with three strains that showed broad cross protection in mouse studies (A/Vietnam/1203/2004, A/Anhui/ 1/2005 and A/Indonesia/05/2005), administered individually or in combination, by different injection methods. cache = ./cache/cord-000050-tfcerilc.txt txt = ./txt/cord-000050-tfcerilc.txt === reduce.pl bib === id = cord-000082-jy7j8sh0 author = Huang, Ting title = Evidence of Recombination and Genetic Diversity in Human Rhinoviruses in Children with Acute Respiratory Infection date = 2009-07-27 pages = extension = .txt mime = text/plain words = 6190 sentences = 271 flesch = 57 summary = Most surprisingly, 20 of the 34 strains classified as HRV-C by comparative analysis of VP4/P2 sequences ( Table 2) were related more closely to HRV-A strains when their 59UTRs were analyzed, and showed incongruent clustering in phylogenetic trees (Figs. When sequencing the VP4/VP2 region of the HRV genome, several recent studies have identified new strains of viruses from children and adults with ARI, asthma, or otitis, which are clustered differently from HRV-A and HRV-B, and have been classified into a novel HRV-C species [7, 8, 17, 18, 19, 20, 21, 25, 26, 27, 28] . In our study, we identified 34 HRVs (51.5%) that clustered differently from HRV-A and HRV-B in a phylogenetic tree that was established on the basis of VP4/VP2 sequences, which were related to recent strains classified in the novel HRV-C species (Fig. 1, Table 2 ). cache = ./cache/cord-000082-jy7j8sh0.txt txt = ./txt/cord-000082-jy7j8sh0.txt === reduce.pl bib === id = cord-000140-5kapn32k author = Wang, Pei-Gang title = Efficient Assembly and Secretion of Recombinant Subviral Particles of the Four Dengue Serotypes Using Native prM and E Proteins date = 2009-12-15 pages = extension = .txt mime = text/plain words = 7780 sentences = 396 flesch = 53 summary = METHODOLOGY/PRINCIPAL FINDINGS: We have used a codon optimization strategy to obtain an efficient expression of native viral proteins and production of recombinant subviral particles (RSPs) for all four dengue virus (DV) serotypes. Pulse chase experiment showed that 8 hours are required for the secretion of DV1 RSPs. We have used HeLa-prME to develop a semi-quantitative assay and screened a human siRNA library targeting genes involved in membrane trafficking. Our data demonstrate that newly synthesized proteins need 8 hours to be translocated through the secretory pathway and released into the supernatant as mature RSPs. To further characterize secreted DV1 RSPs, we performed sucrose gradient fractionation on RSPs concentrated from supernatant of HeLa-prME cells. To identify host factors that could either enhance or reduce production of DV RSPs, we first developed a quantitative assay to relatively quantify levels of secreted particles in supernatant of HeLa-prME cells. cache = ./cache/cord-000140-5kapn32k.txt txt = ./txt/cord-000140-5kapn32k.txt === reduce.pl bib === id = cord-000224-2lz03oqb author = Porter, Kristen A. title = Class II Transactivator (CIITA) Enhances Cytoplasmic Processing of HIV-1 Pr55Gag date = 2010-06-24 pages = extension = .txt mime = text/plain words = 6986 sentences = 313 flesch = 44 summary = METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that both stable and transient expression of CIITA in HIV producer cells does not induce HLA-DR-associated intracellular retention of Gag, but does increase the infectivity of virions. We hypothesized that recapitulating endogenous expression of the entire class II antigen presentation pathway in producer cells via expression of CIITA would restore infectious virus release and provide a more physiologically relevant model for HIV-1 assembly studies. Virus release, both infectious and particle titers) were reduced when cells were transfected with either HLA-DR or other components of the MHC class II antigen presentation pathway ( Figure S2 ), confirming a correlation between Gag retention and reduced virus titers in the presence of HLA-DR, as previously demonstrated [8] . Together, these data suggest CIITA has two effects on the HIV replicative cycle in producer cells, both of which are independent of the MHC II antigen processing pathway; i) it does not induce HLA-DR, mediated intracellular retention of Gag and ii) it increases the infectivity of HIV virions. cache = ./cache/cord-000224-2lz03oqb.txt txt = ./txt/cord-000224-2lz03oqb.txt === reduce.pl bib === id = cord-000255-73nlxqgk author = Hosseini, Parviez title = Predictive Power of Air Travel and Socio-Economic Data for Early Pandemic Spread date = 2010-09-15 pages = extension = .txt mime = text/plain words = 4022 sentences = 184 flesch = 50 summary = CONCLUSIONS/SIGNIFICANCE: We conclude that strategies to prevent pandemic influenza virus emergence and spread in the future should include: 1) enhanced surveillance for strains resulting from reassortment in traded livestock; 2) rapid deployment of control measures in the initial spreading phase to countries where travel data predict the pathogen will reach and to countries where lower healthcare resources will likely cause delays in reporting. Of all the models evaluated, a multivariate model with three predictors, (1) total country-level healthcare spending per capita, (2) estimated passenger volume arriving from Mexico via direct flights (direct flight capacity), and (3) passenger volume from Mexico via indirect, or two-leg, flights (indirect flight capacity), provided the best fit to the data using AIC, as detailed under Methods (Table 1 , DAIC = 0, overall x 2 = 54.33 on 5 degrees of freedom, p-value,0.0001). We validated the model by determining how well a model fit to data up until May 8th predicted reporting dates for fourteen countries where the disease was detected between May 9 th and May 19 th (Supplemental Online Figure S2 ). cache = ./cache/cord-000255-73nlxqgk.txt txt = ./txt/cord-000255-73nlxqgk.txt === reduce.pl bib === id = cord-000176-z76vjkxg author = Nguyen, Jack T. title = Triple Combination of Amantadine, Ribavirin, and Oseltamivir Is Highly Active and Synergistic against Drug Resistant Influenza Virus Strains In Vitro date = 2010-02-22 pages = extension = .txt mime = text/plain words = 7331 sentences = 295 flesch = 45 summary = Our data show that the triple combination was highly synergistic against drug-resistant viruses, and the synergy of the triple combination was significantly greater than the synergy of any double combination tested (P<0.05), including the combination of two NAIs. Surprisingly, amantadine and oseltamivir contributed to the antiviral activity of the TCAD regimen against amantadineand oseltamivir-resistant viruses, respectively, at concentrations where they had no activity as single agents, and at concentrations that were clinically achievable. In an earlier study, we explored the in vitro antiviral activity and synergy of single, double, and triple combinations of amantadine, ribavirin and oseltamivir against a panel of influenza A viruses that were susceptible to these drugs [10] . Statistical analysis of the variability across all replicates from the six experiments for each virus revealed that amantadine made a significant contribution to the synergy of the TCAD regimen at concentrations 0.1 mg/mL and 0.32 mg/mL and above against CA05 and CA10, respectively, compared to the double combination of ribavirin/oseltamivir carboxylate without amantadine ( Figure 1B ). cache = ./cache/cord-000176-z76vjkxg.txt txt = ./txt/cord-000176-z76vjkxg.txt === reduce.pl bib === id = cord-000131-ugbwvy6j author = Jones, James Holland title = Early Assessment of Anxiety and Behavioral Response to Novel Swine-Origin Influenza A(H1N1) date = 2009-12-03 pages = extension = .txt mime = text/plain words = 4322 sentences = 216 flesch = 48 summary = Here, we report the results from an online survey that gathered data (n = 6,249) about risk perception of the outbreak during the first few days of widespread media coverage (April 29 -May 5, 2009) of the emergence of novel swine-origin Influenza A(H1N1). To evaluate the hypothesis that respondents' affective state (subjective anxiety, fatalism about infection) predicts protective measures, we include in the model demographic (age, gender), epidemiological (household size, number of contacts, survey day), and media (source of information on the outbreak) conditioning variables. While our sampling design is subject to many of the usual criticisms of internet-based surveys and is not necessarily representative of the general population, the unparalleled immediacy, longitudinal nature, and the large number of respondents it contains make our data set unique and scientifically important for the study of the spread of information and distribution of risk perception and behavioral change during the most uncertain time (i.e. the initial phase) of an epidemic of a virus novel to the human population. cache = ./cache/cord-000131-ugbwvy6j.txt txt = ./txt/cord-000131-ugbwvy6j.txt === reduce.pl bib === id = cord-000269-v4jochbe author = Wittekindt, Nicola E. title = Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics date = 2010-10-18 pages = extension = .txt mime = text/plain words = 5886 sentences = 314 flesch = 44 summary = cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. The microbial community of mule deer lymph nodes Detection of protein-coding and ribosomal RNA transcripts provides strong support for the presence of viable and replicating microorganisms. As an alternative approach to identifying bacterial microorganisms present in lymph node tissue, we utilized amplicon DNA library sequencing technology. cache = ./cache/cord-000269-v4jochbe.txt txt = ./txt/cord-000269-v4jochbe.txt === reduce.pl bib === id = cord-000143-2xvd5ogf author = Napthine, Sawsan title = Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy date = 2009-12-22 pages = extension = .txt mime = text/plain words = 6886 sentences = 300 flesch = 50 summary = In this process, following translation of an upstream open reading frame (ORF) and termination at the stop codon, a proportion of 40S subunits remain associated with the mRNA and reinitiate at the AUG of a downstream ORF, which is typically in close proximity. Recent studies of termination-reinitiation in the expression of the orthomyxovirus influenza BM2 protein have revealed a requirement for a shorter stretch of mRNA (45 nt) upstream of the stop-start window, but nevertheless, the RNA contains a similar TURBS Motif 1 [19] . Whilst in principle, reinitiation of translation of the MNV 49.7 VP2fluc ORF, following termination, could occur at the next available AUG, this is located 54 amino acids from the natural stop-start signal and initiation here would produce a substantially shorter product that would have been detectable by SDS-PAGE. cache = ./cache/cord-000143-2xvd5ogf.txt txt = ./txt/cord-000143-2xvd5ogf.txt === reduce.pl bib === id = cord-000742-0r4z1zea author = Vittecoq, Marion title = High Influenza A Virus Infection Rates in Mallards Bred for Hunting in the Camargue, South of France date = 2012-08-27 pages = extension = .txt mime = text/plain words = 5923 sentences = 304 flesch = 53 summary = We conducted a 2-year study in the Camargue (Southern France) to investigate the influence of hand-reared Mallard releases on avian influenza virus dynamics in surrounding wildlife. Our results indicate that the potential role of hand-reared Mallards in influenza virus epizootics must be taken into account given the likely risk of viral exchange between game bird facilities and wild habitats, owing to duck rearing conditions. However, to our knowledge no study ever aimed at investigating the potential role of hand-reared Mallards released for hunting in the epidemiology of AIV, despite the very large number of ducks being released in the wild annually. Our results highlighted that: i) GBF represent an epidemiological compartment into which important AIV outbreaks can occur; ii) a significant proportion of Mallards wintering in the Camargue are infected by LPAIV, including H5 strains that are known to be able to evolve to HPAIV in domestic birds [30] . cache = ./cache/cord-000742-0r4z1zea.txt txt = ./txt/cord-000742-0r4z1zea.txt === reduce.pl bib === id = cord-000008-3dgjv0x1 author = Vali, Bahareh title = HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date = 2008-10-20 pages = extension = .txt mime = text/plain words = 5253 sentences = 236 flesch = 47 summary = In response to stimulation with HIV peptide pool, untreated co-infected individuals showed significantly higher frequencies of intra-hepatic CD4 + T-cells producing IFN-c, compared to HCV mono-infected [0.1660.05% vs 0.0260.01%, p,0.05], and HAART-treated co-infected individuals [0.1660.05% vs 0.0360.05%, p,0.05] (Figure 2a ). Therapy naïve co-infected subjects had greater IFN-c producing CD8 + T-cells in response to HIV peptides compared to HCV mono-infected individuals [1.3960.37% vs 0.0260.0%, p,0.05], and HAART was associated with a significant reduction in the frequencies of these cells [1.3960.37% vs 0.3060.26%, p,0.05] (figure 2b). The tetramer cytokine response pattern was shown to be different in the liver compared to blood of the same individual, with diminished intra-hepatic tetramer-specific IFN-c responses and an increase in both CD107a and TNF-a responses, with the majority of SL9 tetramer positive cells expressing these two markers. Therapy naïve co-infected individuals demonstrated a higher frequency of intra-hepatic CD8 + T-cells that produce TNF-a in response to both HCV and HIV antigen stimulation compared to HCV mono-infected individuals. cache = ./cache/cord-000008-3dgjv0x1.txt txt = ./txt/cord-000008-3dgjv0x1.txt === reduce.pl bib === id = cord-000540-bbjmcdo5 author = Hellard, Eléonore title = True versus False Parasite Interactions: A Robust Method to Take Risk Factors into Account and Its Application to Feline Viruses date = 2012-01-03 pages = extension = .txt mime = text/plain words = 7597 sentences = 397 flesch = 45 summary = By combining logistic regressions and chi-square tests, we are able to calculate the expected frequencies of co-infected individuals if parasites are independent considering their risk factors, and to compare them to the observed ones. The corrected chi-square approach is based on the idea that the coefficients of the logistic regression of the two viruses can be used to estimate the number of seronegative, single-and double-seropositive individuals expected if the two pathogens are independent. The two approaches (corrected chi-square and logistic regression) were used for the analysis of the interactions between four cat viruses ( Table 2) . Correcting for all risk factors, no pair of viruses involving the Feline Immunodeficiency Virus (FIV-FHV, FIV-FCV, FIV-FPV) was significantly associated. Table S1 Corrected chi-square tests and logistic regressions to search for feline viruses' interactions using subsets randomly sampled in cat data such that the N F / n ratio takes various values. cache = ./cache/cord-000540-bbjmcdo5.txt txt = ./txt/cord-000540-bbjmcdo5.txt === reduce.pl bib === id = cord-000574-7eflwyxk author = Liu, Yanli title = Effects of a Non-Conservative Sequence on the Properties of β-glucuronidase from Aspergillus terreus Li-20 date = 2012-02-07 pages = extension = .txt mime = text/plain words = 3919 sentences = 216 flesch = 52 summary = The non-conservative N-terminal domain of the protein phosphatase1 (PP1), with 1-8 residues deleted, showed higher sensitivity to three substrates and influenced the structure and properties of PP1 [10] , whereas the truncation of the Cterminal region improved the thermal stability of endo-bglucanase from Bacillus subtilis JA18 [11] . The TIM barrel domain, which is one of the most common catalytic domains, is adopted by about 10% of the enzymes; thus, sequence modification inside or outside the domain to improve the enzymatic property and determine the catalytic mechanism was reported in many studies. In the present research, Atgus and the partial sequence [Atgus(-3t)] without Cterminal non-conservative sequence behind the TIM barrel domain were amplified in order to investigate effects of nonconservative sequence on enzymatic property. Based on the same hydrolyzing mode, relatively higher thermal stability, and especially the enhanced affinity and catalytic efficiency for GL, deletion of the non-conservative sequence behind the TIM barrel domain was a successful evolution of AtGUS. cache = ./cache/cord-000574-7eflwyxk.txt txt = ./txt/cord-000574-7eflwyxk.txt === reduce.pl bib === id = cord-000166-36bfeoqv author = Tracht, Samantha M. title = Mathematical Modeling of the Effectiveness of Facemasks in Reducing the Spread of Novel Influenza A (H1N1) date = 2010-02-10 pages = extension = .txt mime = text/plain words = 5846 sentences = 336 flesch = 59 summary = We construct and analyze a mathematical model for a population in which some people wear facemasks during the pandemic and quantify impact of these masks on the spread of influenza. The results show that if N95 respirators are only 20% effective in reducing susceptibility and infectivity, only 10% of the population would have to wear them to reduce the number of influenza A (H1N1) cases by 20%. With the implementation of N95 respirators Table 3 exhibits a reduction in the cumulative number of cases of almost 200,000, or a 19% decrease, when 10% of the population wears masks and they are 20% effective. With 10% of the population wearing N95 respirators with effectiveness at 20% in reducing both susceptibility and infectivity there is a 19% reduction in the cumulative number of cases. Even at 50% effectiveness in reducing both susceptibility and infectivity and with 50% of the population wearing surgical masks only a 6% reduction in the number of cumulative cases is seen. cache = ./cache/cord-000166-36bfeoqv.txt txt = ./txt/cord-000166-36bfeoqv.txt === reduce.pl bib === id = cord-000063-tex6bgab author = Sui, Hong-Yan title = Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication date = 2009-05-22 pages = extension = .txt mime = text/plain words = 3501 sentences = 189 flesch = 50 summary = Using this vector that also expresses enhanced green fluorescence protein (EGFP) as surrogate marker, stable shRNA-expressing cell lines were successfully established and the inhibition efficiencies of rationally designed siRNAs targeting to conserved regions of influenza A virus genome were assessed. It was further demonstrated that no siRNA-resistant viral mutation appeared in siM2 targeting sequence even after the virus was cultured in the shRNA expressing stable cell line for 40 passages. A recent report by Zhou et al [30] also showed that several siRNAs targeting NP and M genes exhibited effective inhibition against influenza A virus replication in cultured MDCK cells and in animal models. Taken together, all the findings about effective RNAi target, lentiviral vector delivery and the establishment of stable shRNA expressing cell lines in our study provide rational information for the development of siRNAs as prophylaxis and therapy for influenza virus infection in humans. cache = ./cache/cord-000063-tex6bgab.txt txt = ./txt/cord-000063-tex6bgab.txt === reduce.pl bib === id = cord-000720-5b936n3g author = Nannyonga, Betty title = The Dynamics, Causes and Possible Prevention of Hepatitis E Outbreaks date = 2012-07-24 pages = extension = .txt mime = text/plain words = 4405 sentences = 250 flesch = 57 summary = The models designed are fit to data from the Kitgum outbreak, to estimate the basic reproduction number and to relate them to the level of contamination of the environment. Susceptible individuals without bore hole access become infected with the Hepatitis E virus at a rate bc, where b is the transmission rate of HEV from the contaminated environment c, to the human. To estimate model parameters and determine the critical level of control needed to eradicate the epidemic, the model described by the equations in (7) is fit to the data collected during the Kitgum outbreak ( Figure 1 ) During the invasion phase of HEV, the prevalence is approximately Under the above assumption, equations (7) are rewritten to incorporate the malaria dynamics in equation (11) where j is a parameter that models change the increase (or decrease) in susceptibility to Hepatitis E of malaria infected individuals [12] . cache = ./cache/cord-000720-5b936n3g.txt txt = ./txt/cord-000720-5b936n3g.txt === reduce.pl bib === id = cord-000765-r7y1cqou author = Chang, Yu-Ming title = Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis date = 2012-09-21 pages = extension = .txt mime = text/plain words = 5770 sentences = 317 flesch = 54 summary = title: Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. IcaR DNA1 probe duplex of 1 mM was pre-incubated with 2 mM TcaR (dimer) at room temperature for 15 min before mixing with increasing concentration of GC33 ssDNA, followed by the same procedure as described in the legend to Figure 1B . In the EMSA analysis, 1 mM IcaR DNA1 probe duplex was pre-incubated with 1 mM GC33 ssDNA fragment for 15 min at room temperature before mixing with TcaR protein of increasing concentration. cache = ./cache/cord-000765-r7y1cqou.txt txt = ./txt/cord-000765-r7y1cqou.txt === reduce.pl bib === id = cord-000588-3wok0n21 author = Sainz, Juan title = Dectin-1 and DC-SIGN Polymorphisms Associated with Invasive Pulmonary Aspergillosis Infection date = 2012-02-27 pages = extension = .txt mime = text/plain words = 5506 sentences = 293 flesch = 41 summary = The present study was designed to investigate whether the presence of single nucleotide polymorphisms (SNPs) within DC-SIGN, Dectin-1, Dectin-2, CCL2 and CCR2 genes influence the risk of developing Invasive Pulmonary Aspergillosis (IPA). In addition, healthy individuals with this latter genotype showed a significantly decreased level of Dectin-1 mRNA expression compared to C-allele carriers, suggesting a role of the Dectin-1 (rs7309123) polymorphism in determining the levels of Dectin-1 and, consequently, the level of susceptibility to IPA infection. Based on these observations, the objective of the present study was to investigate the role of tagging and potentially functional single-nucleotide polymorphisms (SNPs) located within the DC-SIGN, Dectin-1, Dectin-2, MCP-1/CCL2 and CCR2 genes on IPA susceptibility. Of note is that two SNPs showing genetic interaction in this model were not significantly associated with an increased risk of IPA infection in the univariate analysis (CCR2 rs3918358 and Dectin-2 rs7134303 ). cache = ./cache/cord-000588-3wok0n21.txt txt = ./txt/cord-000588-3wok0n21.txt === reduce.pl bib === id = cord-000501-qz68gtd4 author = Greatorex, Jane S. title = Survival of Influenza A(H1N1) on Materials Found in Households: Implications for Infection Control date = 2011-11-22 pages = extension = .txt mime = text/plain words = 4311 sentences = 194 flesch = 47 summary = METHODOLOGY AND PRINCIPAL FINDINGS: Influenza A/PuertoRico/8/34 (PR8) or A/Cambridge/AHO4/2009 (pandemic H1N1) viruses were inoculated onto a wide range of surfaces used in home and work environments, then sampled at set times following incubation at stabilised temperature and humidity. The potential for transmission of influenza by indirect contact (i.e. via fomites) is linked to the ability of virus to survive in transmissible titres on commonly touched surfaces; however few data exist on this subject. We evaluate the survival of influenza A (H1N1) viruses deliberately applied to a range of commonly touched household and workplace surfaces, using RT-PCR for genome detection and culture methods to determine viability. Our data are consistent with recent findings from a study of environmental deposition of pandemic H1N1 virus in the homes of infected patients, involving our laboratory, when almost 10% of tested surfaces yielded viable virus [15] . cache = ./cache/cord-000501-qz68gtd4.txt txt = ./txt/cord-000501-qz68gtd4.txt === reduce.pl bib === id = cord-000460-h3owwjao author = Xiong, Jing title = Leukocyte- and Platelet-Derived Microvesicle Interactions following In Vitro and In Vivo Activation of Toll-Like Receptor 4 by Lipopolysaccharide date = 2011-09-26 pages = extension = .txt mime = text/plain words = 4313 sentences = 212 flesch = 41 summary = However, with LPS stimulation numbers of platelets staining positive for both plateletand leukocyte-specific antigens increased in blood derived from WT but not dTLR4 mice. Alternatively, comparable activation of leukocyte as well as platelet result in formation of cell-derived microvesicles (MV) which may contribute to increased thrombogenic propensity of the blood, pro-inflammatory immune processes and thus cardiovascular risk [15, 16, 17, 18, 19, 20, 21, 22] . Therefore, the present study was designed to test the hypothesis that acute exposure to a sentinel dose of LPS would induce MV production and exchange of specific proteins/ receptors between platelets and leukocytes via TLR4 activation. The acute effects of LPS on platelet and leukocyte activation were most likely mediated through activation of TLR4 as platelet positive leukocyte antigen was not observed in blood from dTLR4 mice. Platelet-leukocyte interactions require TLR4 signaling as the dual antigen positivity of platelets was observed in blood derived from wild type but not dTLR4 mice. cache = ./cache/cord-000460-h3owwjao.txt txt = ./txt/cord-000460-h3owwjao.txt === reduce.pl bib === id = cord-000266-xwfptmmv author = Liao, Qiuyan title = Situational Awareness and Health Protective Responses to Pandemic Influenza A (H1N1) in Hong Kong: A Cross-Sectional Study date = 2010-10-12 pages = extension = .txt mime = text/plain words = 7129 sentences = 356 flesch = 44 summary = METHODOLOGY: Data from cross-sectional telephone interviews of 1,001 Hong Kong adults in June, 2009 were tested against theory and data-derived hypothesized associations between trust in (formal/informal) information, understanding, self-efficacy, perceived susceptibility and worry, and hand hygiene and social distancing using Structural Equation Modelling with multigroup comparisons. We report on a theoretical model that incorporated elements of influenza causal knowledge, perceived self-efficacy and also social and affective influences ( Figure 1 ) because these latter variables have been less frequently studied in combination, but have theoretical and logical support for their potential importance in the context of RIDs. We tested this model against data collected in the early phase of the influenza A/H1N1 pandemic (Table S1 ) to examine how levels of trust in formal and informal sources of risk/prevention information associated with hand washing and social distancing. cache = ./cache/cord-000266-xwfptmmv.txt txt = ./txt/cord-000266-xwfptmmv.txt === reduce.pl bib === id = cord-000556-uu1oz2ei author = Kumar, Ranjit title = RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” date = 2012-01-20 pages = extension = .txt mime = text/plain words = 4407 sentences = 235 flesch = 46 summary = Whole genome transcriptome analysis is a complementary method to identify "novel" genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. Therefore, genome structural annotation or the identification and demarcation of boundaries of functional elements in a genome (e.g., genes, non-coding RNAs, proteins, and regulatory elements) are critical elements in infectious disease systems biology. Whole genome transcriptome studies (such as whole genome tiling arrays [13, 14, 15] and high throughput sequencing [16, 17] ) are complementary experimental approaches for bacterial genome annotation and can identify ''novel'' genes, gene boundaries, regulatory regions, intergenic regions, and operon structures. We compared the RNA-Seq based transcriptome map with the available genome annotation to identify expressed, novel, and intergenic regions in the genome. The single nucleotide resolution map helped uncover the structure and complexity of this pathogen's transcriptome and led to the identification of novel, small RNAs and protein coding genes as well as gene co-expression. cache = ./cache/cord-000556-uu1oz2ei.txt txt = ./txt/cord-000556-uu1oz2ei.txt === reduce.pl bib === id = cord-000609-dpcgl6ig author = Raju, Sammeta V. title = Suppression of Adenosine-Activated Chloride Transport by Ethanol in Airway Epithelia date = 2012-03-19 pages = extension = .txt mime = text/plain words = 4083 sentences = 253 flesch = 43 summary = Here, air-liquid interface cultures of Calu-3 epithelial cells were basolaterally exposed to physiologically relevant concentrations of ethanol (0, 25, 50 and 100 mM) for 24 hours and adenosine-stimulated ion transport was measured by Ussing chamber. These results imply that ethanol exposure dysregulates CFTR-mediated chloride transport in airways by suppression of adenosine-A(2B)AR-cAMP signaling pathway, which might contribute to alcohol-associated lung infections. The current report directly measured the adenosineinduced chloride secretion of airway epithelia under the exposure of physiologically relevant concentrations of alcohol and found that ethanol attenuates epithelial CFTR-mediated chloride transport by modulating cellular cAMP levels. To explore if ethanol affects adenosine-activated ion transport function of airway epithelium, we employed air-liquid interface cultures of Calu-3 cells, a system widely used to investigate airway epithelial electrophysiological properties [27, 28] . These results not only confirm that ethanol modulates adenosine-cAMP signaling but also suggest that phosphodiesterase inhibitors may be useful as the potential therapeutic agents for improving the airway epithelial ion transport and mucociliary clearance in alcoholic patients. cache = ./cache/cord-000609-dpcgl6ig.txt txt = ./txt/cord-000609-dpcgl6ig.txt === reduce.pl bib === id = cord-000079-533xlisc author = Huszthy, Peter C. title = Remission of Invasive, Cancer Stem-Like Glioblastoma Xenografts Using Lentiviral Vector-Mediated Suicide Gene Therapy date = 2009-07-20 pages = extension = .txt mime = text/plain words = 5427 sentences = 268 flesch = 45 summary = Both, lymphocytic choriomeningitis virus glycoprotein (LCMV-GP) and vesicular stomatitis virus glycoprotein (VSV-G) pseudotyped lentiviral vectors very efficiently transduced human glioblastoma cells in vitro and in vivo. In a therapeutic approach using the suicide gene herpes simplex virus thymidine kinase (HSV-1-tk) fused to eGFP, both lentiviral vectors mediated a complete remission of solid tumors as seen on MRI resulting in a highly significant survival benefit (p<0.001) compared to control groups. Furthermore, we showed a significant therapeutic effect of LCMV-GP pseudotyped lentiviral vectors in the cell-line based 9L rat glioma model using the suicide gene HSV-1-tk. In the presented work, we showed that both, VSV-G and LCMV-GP pseudotyped lentiviruses efficiently transduced human glioma cells in vitro and in vivo, whereas gammaretroviral transduction was inefficient. When analyzed at higher magnification, both LCMV-GP and VSV-G pseudotyped lentiviral vectors showed efficient transgene delivery to nestin-positive tumor cells in solid ( Figure 3B ,E) and invasive tumor areas ( Figure 3C ,F). cache = ./cache/cord-000079-533xlisc.txt txt = ./txt/cord-000079-533xlisc.txt === reduce.pl bib === id = cord-000077-d441jam3 author = Zhang, Hao-Jie title = The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date = 2009-07-03 pages = extension = .txt mime = text/plain words = 5426 sentences = 267 flesch = 54 summary = Reverse transcriptase (RT) of human immunodeficiency virus (HIV)-1 plays a key role in initiating viral replication and is an important target for developing anti-HIV drugs. Our native gel analysis indicated that the mutations at 271 and 274 amino acids might cause conformational changes, leading to the formation of higher order oligomers instead of dimers, resulting in increased protein instability and susceptibility to viral protease. As shown in Fig. 3A , similar levels of Pr160 gag-pol , Gag protein (Pr55 Gag ) and capsid protein p24 (CA p24) were found in cells transfected with the wild type or mutant constructs, indicating that the expression and stability of RT precursor protein were not affected by the mutations. To study if the RTs in the viral particles of Y271A and I274A mutants were degraded by proteolysis that made them undetectable, pseudoviruses of wild type and mutants were generated in the presence or absence of indinavir, a highly specific inhibitor of HIV-1 protease. cache = ./cache/cord-000077-d441jam3.txt txt = ./txt/cord-000077-d441jam3.txt === reduce.pl bib === id = cord-000666-je9t4i6q author = Verbist, Katherine C. title = IL-15 Participates in the Respiratory Innate Immune Response to Influenza Virus Infection date = 2012-05-18 pages = extension = .txt mime = text/plain words = 7210 sentences = 302 flesch = 47 summary = ( Figure 2E) ; however, these animals seemed to regain control of viral replication by day 4 p.i., which perhaps corresponds with the early entry of cells of the adaptive immune response as anti-influenza specific CD8 T cells are first detectable in the lung airways by d6 post infection by flow cytometry ( [34] and data not shown). We observed significant reductions in the numbers of NK cells in the lung airways of influenza-infected animals in which IL-15 was blocked at time points associated with their arrival at the site of infection, and failure of these cell populations to accumulate had implications in early viral control (Figure 2) . doi:10.1371/journal.pone.0037539.g002 frequencies, numbers, CD122 expression, and BrdU incorporation were specific to the lung airways (the sight of treatment), as NK cells isolated from spleens were similar in control and IL-15ctreated animals ( Figure 3C and data not shown). cache = ./cache/cord-000666-je9t4i6q.txt txt = ./txt/cord-000666-je9t4i6q.txt === reduce.pl bib === id = cord-000434-ff2zadol author = Zhao, Rongmao title = Identification of a Highly Conserved H1 Subtype-Specific Epitope with Diagnostic Potential in the Hemagglutinin Protein of Influenza A Virus date = 2011-08-19 pages = extension = .txt mime = text/plain words = 5752 sentences = 307 flesch = 51 summary = The highly conserved H1 subtype-specific immunodominant epitope may form the basis for developing novel assays for sero-diagnosis and active surveillance against H1N1 IAVs. Influenza A viruses (IAVs), members of the Orthomyxoviridae family, are highly contagious to a variety of avian and mammalian species. To confirm that these antibodies can recognize the HA antigen, the reactivity of the anti-peptide sera were evaluated by Western blot and ELISA against the purified HA0 protein of H1N1pdm virus. The sensitivity and specificity of peptide-ELISA versus HI test was 96.5% and 74.4%, respectively, indicating the potential of the peptide-ELISA method in detecting antibody against H1-subtype IAVs. In the present study, we identified immunodominant linear B cell epitopes on the H1N1pdm virus HA protein by a peptide scanning approach using H1N1pdm patients sera. To screen the H1-subtype specific epitopes, a set of 50 peptides spanning the amino acid sequences of the HA protein ectodomain of pandemic A/H1N1 2009 (H1N1pdm) influenza virus strain A/ California/04/2009 were synthesized. cache = ./cache/cord-000434-ff2zadol.txt txt = ./txt/cord-000434-ff2zadol.txt === reduce.pl bib === id = cord-000408-pt3b4yc7 author = Lu, Sydney X. title = Ceacam1 Separates Graft-versus-Host-Disease from Graft-versus-Tumor Activity after Experimental Allogeneic Bone Marrow Transplantation date = 2011-07-06 pages = extension = .txt mime = text/plain words = 5433 sentences = 262 flesch = 48 summary = The accelerated early mortality of Ceacam1 2/2 allo-BMT recipients, together with increased accumulation of donor T cells in GI tract and mesenteric lymph nodes, but decreased numbers peripheral lymph nodes ( Figure 3C ), led us to ask whether Ceacam1 had differential effects in regulating GVHD target organ damage for various target organs and tissues. We analyzed donor WT and Ceacam1 2/2 alloactivated splenic T cells on day 14 after allo-BMT for trafficking molecules, and found that Ceacam1 2/2 CD8 + CD44 + CD62L 2 effector T cells expressed higher levels of integrin b 7 subunit and the gut homing integrin a 4 b 7 ( Figure 5A) , which is important for intestinal GVHD [31, 32, 33] . Ceacam12/2 CD4 effector T cells had similar integrin b 7 subunit expression, yet also accumulated in greater numbers in the gut ( Figure 3A) , suggesting that regulation of target organ damage by Ceacam1 is very likely to involve multiple additional mechanisms beyond trafficking molecule expression. cache = ./cache/cord-000408-pt3b4yc7.txt txt = ./txt/cord-000408-pt3b4yc7.txt === reduce.pl bib === id = cord-000346-9b6yz3f4 author = Holder, Benjamin P. title = Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model date = 2011-03-24 pages = extension = .txt mime = text/plain words = 7494 sentences = 323 flesch = 49 summary = In order to obtain two complementary views of the infection kinetics for the A/Brisbane/59/2007 WT and H275Y mutant strains, virus growth over time was observed in two different in vitro systems: the viral plaque assay and the multiple-cycle viral yield assay. We are left then with two experimental measures -the viral titer growth rate and the plaque velocity -whose values may depend on three unknown infection kinetics parameters: the infecting time, t inf ; the latent infection period, t L ; and the infectious lifespan of a cell, t I . To demonstrate this concept using the A/ Brisbane/59/2007 (H1N1) WT and H275Y mutant strains, we have plotted the experimentally-measured values of plaque velocity and viral titer growth rate as functions of the infecting time and latent infection period, using the model dependence determined above ( Figure 6 ). cache = ./cache/cord-000346-9b6yz3f4.txt txt = ./txt/cord-000346-9b6yz3f4.txt === reduce.pl bib === id = cord-000580-dcid9emx author = Sällman Almén, Markus title = The Dispanins: A Novel Gene Family of Ancient Origin That Contains 14 Human Members date = 2012-02-20 pages = extension = .txt mime = text/plain words = 4662 sentences = 237 flesch = 48 summary = We show that the IFITM genes are a subfamily in a larger family of transmembrane (TM) proteins that we call Dispanins, which refers to a common 2TM structure. We mined 36 eukaryotic species, covering all major eukaryotic groups, and found that the IFITMs form a subfamily in a larger novel family that has ten human members in addition to the four IFITM genes. By combining the results of the phylogenetic analysis and BLAST classification, we created a schematic overview of the organisms' gene repertoire and a schematic picture of the Dispanin family's evolutionary history, which suggests that the invertebrate Dispanins share more similarity towards the DSPC and D subfamilies than DSPA and B ( Figure 2 ). We provide evidence that the four IFITM genes together with ten additional human genes, known as TUSC5, TMEM233, PRRT2, TMEM90A, DSPC2, TMEM90B, TMEM91, AC023157, AL160276 and AC068580, form a novel gene family that we call the Dispanins, which refers to the 2TM membrane topology that is common to all identified members. cache = ./cache/cord-000580-dcid9emx.txt txt = ./txt/cord-000580-dcid9emx.txt === reduce.pl bib === id = cord-000182-ni6iyzdn author = He, Zhisong title = Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features date = 2010-03-11 pages = extension = .txt mime = text/plain words = 6037 sentences = 305 flesch = 46 summary = title: Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features Many researchers have made lots of efforts to develop useful algorithms and softwares to investigate various drug-related biological problems, such as HIV protease cleavage site prediction [18, 19] , identification of GPCR (G protein-coupled receptors) type [20, 21] , protein signal peptide prediction [22] , protein subcellular location prediction [23, 24, 25] , analysis of specificity of GalNAc-transferase protein [26] , identification of protease type [27, 28] , membrane protein type prediction [29, 30, 31, 32] , and a series of relevant webserver predictors as summarized in a recent review [33] . The drug-target benchmark datasets thus obtained for enzymes, ion-channels, GPCRs, and nuclear receptors are given in Online Supporting Information S1, S2, S3, and S4, respectively. Prediction of G-protein-coupled receptor classes based on the concept of Chou's pseudo amino acid composition: an approach from discrete wavelet transform cache = ./cache/cord-000182-ni6iyzdn.txt txt = ./txt/cord-000182-ni6iyzdn.txt === reduce.pl bib === id = cord-000547-adfigzc1 author = Beniac, Daniel R. title = The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date = 2012-01-11 pages = extension = .txt mime = text/plain words = 7782 sentences = 392 flesch = 51 summary = METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. From the same image data set, we combined extracted volumes from tomograms with 2-D single particle processing to determine the structure of the GP spikes ( Figure 5 ) to a resolution of 14 Å as measured by the Fourier Shell Correlation (FSC) 0.5 criterion. Analysis of 2090 distinct intact virions with a nucleocapsid from cryo-electron micrographs shows that the most common class length (53%) of virus particles is 982679 nm ( Figure 1A , Table S1 ). cache = ./cache/cord-000547-adfigzc1.txt txt = ./txt/cord-000547-adfigzc1.txt === reduce.pl bib === id = cord-000736-6f8vyziv author = Pripuzova, Natalia title = Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date = 2012-08-17 pages = extension = .txt mime = text/plain words = 6818 sentences = 328 flesch = 54 summary = FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). The analytical sensitivity of each primer set was determined in the single virus testing using FDA/CBER panels (kindly provided by Dr. Stephen Kerby, FDA/CBER) consisting of various amounts of the viruses (0-1,000 genome copies/ml) spiked into the ''normal'' human plasma. The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Tm and C(t) values obtained with primer sets specific for HIV-1, HCV, or HBV in testing of 17 human clinical samples in the format of PCR array targeting eight different viruses. cache = ./cache/cord-000736-6f8vyziv.txt txt = ./txt/cord-000736-6f8vyziv.txt === reduce.pl bib === id = cord-000725-rafwlw0t author = Hindinger, Claudia title = IFN-γ Signaling to Astrocytes Protects from Autoimmune Mediated Neurological Disability date = 2012-07-27 pages = extension = .txt mime = text/plain words = 5114 sentences = 243 flesch = 37 summary = Experimental autoimmune encephalomyelitis (EAE) was induced in transgenic mice expressing signaling defective dominant-negative interferon gamma (IFN-γ) receptors on astrocytes to determine the influence of inflammation on astrocyte activity. Inhibition of IFN-γ signaling to astrocytes did not influence disease incidence, onset, initial progression of symptoms, blood brain barrier (BBB) integrity or the composition of the acute CNS inflammatory response. GFAPcR1D and wt mice were compared at the peak of acute disease to determine if IFN-c signaling altered astrocyte activation or CNS inflammation. Despite elevated demyelination and axonal loss in the absence of IFN-c signaling to astrocytes, spinal cords showed no evidence of differential astrocyte activation by either immunohistochemistry (Fig. 4 ), or differences in GFAP mRNA expression during the peak of acute disease (Fig. 5 ). Although demyelination was increased in the CNS of GFAPcR1D mice, the extent of astrocyte activation associated with spinal cord white matter lesions was similar in both groups ( Fig. 6 ; ,60 GFAP + cells/mm 2 ). cache = ./cache/cord-000725-rafwlw0t.txt txt = ./txt/cord-000725-rafwlw0t.txt === reduce.pl bib === id = cord-000336-57es391o author = Liao, Qiuyan title = Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study date = 2011-03-11 pages = extension = .txt mime = text/plain words = 7649 sentences = 383 flesch = 39 summary = Greater perceived vaccine benefits (β = 0.15), less concerns regarding vaccine side-effects (β = −0.20), greater adherence to social norms of vaccination (β = 0.39), anticipated higher regret if not vaccinated (β = 0.47), perceived higher self-efficacy for vaccination (β = 0.12) and history of seasonal influenza vaccination (β = 0.12) were associated with higher intention to receive the pH1N1 vaccine, which in turn predicted self-reported vaccination uptake (β = 0.30). The model proposed that attitudes towards vaccination (perceived benefits of pH1N1 vaccination and concerns regarding possible adverse effects of pH1N1 vaccination), perceived social pressures from significant others and other people around regarding pH1N1 vaccination (social norms regarding pH1N1 vaccination), perceived self-efficacy in taking vaccination (perceived self-efficacy), anticipated regret for not taking the pH1N1 vaccination (anticipated regret) and seasonal influenza vaccination history would predict vaccination intention, which in turn predicts vaccination planning and future vaccination uptake; anticipated regret and perceived self-efficacy could also predict vaccination status directly; finally, vaccination planning was proposed to bridge the intention-behavior gap and predict vaccination status directly ( Figure 3 ). cache = ./cache/cord-000336-57es391o.txt txt = ./txt/cord-000336-57es391o.txt === reduce.pl bib === id = cord-000638-ss1435el author = Beq, Stephanie title = Altered Thymic Function during Interferon Therapy in HCV-Infected Patients date = 2012-04-16 pages = extension = .txt mime = text/plain words = 5142 sentences = 237 flesch = 47 summary = The evolution of T-cell subsets and T-cell homeostasis were estimated by flow cytometry while thymic function was measured through quantification of T-cell receptor excision circles (TREC) and estimation of intrathymic precursor T-cell proliferation during the first four months following the initiation of IFNα therapy. In contrast, Arizcorreta and colleagues showed that IFNa and ribavirin therapy induces a substantial reduction of circulating sjTRECs, in HIV/HCV co-infected patients, accompanied by sustained naïve CD4 + T-cell defect, suggesting thymic dysfunction [10] . While the number of RTEs was similar in HCV-infected patients at study entry and healthy individuals ( These data demonstrate that, as early as one month following treatment initiation, IFNa induces stronger alterations of naïve Tcell subsets, and more specifically in the RTE compartment than in any other T-cell subset, suggesting a specific effect on thymopoiesis. cache = ./cache/cord-000638-ss1435el.txt txt = ./txt/cord-000638-ss1435el.txt === reduce.pl bib === id = cord-000321-ee7q7jhv author = Powell, Michael L. title = Further Characterisation of the Translational Termination-Reinitiation Signal of the Influenza B Virus Segment 7 RNA date = 2011-02-08 pages = extension = .txt mime = text/plain words = 9458 sentences = 433 flesch = 51 summary = The features identified in caliciviral TURBS suggest a model for termination-reinitiation in which post-termination 40S subunits are tethered to the mRNA through interactions between the mRNA (through motif 1) and 18S rRNA, initiation factors are recruited and the AUG restart codon located, processes which may require precise RNA folding (involving motif 2) within the TURBS. Analysis of primary and secondary structural features of the BM2 signal has revealed that it contains a short TURBS (of 45 nt) which is largely single-stranded, with motif 1 likely to be located in the apical loop of a metastable stem-loop structure when the ribosome is positioned at the termination codon of the upstream ORF [11] . Importantly, mutation of the motif 1 homologue such that it was fully complementary to yeast 18S rRNA led to a significant (p,0.01) increase in BM2fluc synthesis relative to the wild-type BM2 reporter ( Figure 4C ), supporting the view that mRNA:rRNA base pairing is a key determinant in BM2 ORF expression. cache = ./cache/cord-000321-ee7q7jhv.txt txt = ./txt/cord-000321-ee7q7jhv.txt === reduce.pl bib === id = cord-000715-zl1s82yi author = Shulman, Lester M. title = Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date = 2012-07-16 pages = extension = .txt mime = text/plain words = 4786 sentences = 248 flesch = 50 summary = These samples were selected from among archived stool samples previously tested for enterovirus and MS2 after extraction by QIAamp Viral RNA Mini Kit. A sufficient number of samples with high, intermediate, and low levels of inhibitors were chosen for re-analysis to enable comparison between extraction procedures at each of these levels of inhibition. Analysis of variance ( Fig. 3 , part 2), indicated that there was no significant difference (paired t-test, P.0.05) between the inhibition of rRT-PCR of the MS2 external control and the added enterovirus (P.0.05) for protocols A, C, and D. Stool suspensions (N = 185) prepared for routine analysis of clinical stool samples sent to the Central Virology Laboratory (CVL) at Chaim Sheba Medical Center in Israel were used to evaluate the efficiency of four different RNA extraction systems in excluding inhibitors of rRT-PCR. cache = ./cache/cord-000715-zl1s82yi.txt txt = ./txt/cord-000715-zl1s82yi.txt === reduce.pl bib === id = cord-000208-th0wddvc author = Cornelissen, Lisette A. H. M. title = A Single Immunization with Soluble Recombinant Trimeric Hemagglutinin Protects Chickens against Highly Pathogenic Avian Influenza Virus H5N1 date = 2010-05-14 pages = extension = .txt mime = text/plain words = 5671 sentences = 290 flesch = 49 summary = title: A Single Immunization with Soluble Recombinant Trimeric Hemagglutinin Protects Chickens against Highly Pathogenic Avian Influenza Virus H5N1 Such HA trimers, expressed either in insect or mammalian cells, were indeed shown to elicit neutralizing antibodies [16] and to partially protect mice against HPAI H5N1 challenge infection [19] . In view of their promising potential we have evaluated recombinant soluble HA trimers in chickens and mice for their ability to induce protective immunity against infection with HPAI H5N1. Subsequently, vaccination with the sH5 3 preparation was shown to provide complete protection against challenge with HPAI H5N1 both in mice and in chickens, in the latter already after a single immunization. In the present study we evaluated the vaccine potential of a recombinant soluble H5 protein (sH5 3 ) to protect chickens and mice against a lethal infection with HPAI H5N1. A pseudotype baculovirusmediated vaccine confers protective immunity against lethal challenge with H5N1 avian influenza virus in mice and chickens cache = ./cache/cord-000208-th0wddvc.txt txt = ./txt/cord-000208-th0wddvc.txt === reduce.pl bib === id = cord-000326-a18rch1f author = Zhou, Jun-Wei title = Apolipoprotein M Gene (APOM) Polymorphism Modifies Metabolic and Disease Traits in Type 2 Diabetes date = 2011-02-24 pages = extension = .txt mime = text/plain words = 4829 sentences = 276 flesch = 50 summary = This study aimed at substantiating the associations of the apolipoproein M gene (APOM) with type 2 diabetes (T2D) as well as with metabolic traits in Hong Kong Chinese. Several additional lines of evidence also indicated the possible involvement of APOM in the development of diabetes and metabolic disturbances: 1) the human APOM gene is located within a high susceptibility region (6q21-q23) to type 2 diabetes (T2D) in genome-wide linkage analyses [6] . 2) SNP rs805296 (T-778C) in APOM promoter has been associated with the levels of plasma total cholesterol (TC) and fasting plasma glucose (FPG) in non-diabetic participants, 3) SNP rs805296 has also been associated with the susceptibility to T2D and coronary artery disease among the Northern Chinese [7, 8] . While our results did not support an association between APOM and T2D susceptibility in Hong Kong Chinese, subgroup analyses found SNP as well as haplotype associations between APOM and metabolic traits in T2D. cache = ./cache/cord-000326-a18rch1f.txt txt = ./txt/cord-000326-a18rch1f.txt === reduce.pl bib === id = cord-000554-p4ufea6x author = Gao, Wei title = Distinct Regulation of Host Responses by ERK and JNK MAP Kinases in Swine Macrophages Infected with Pandemic (H1N1) 2009 Influenza Virus date = 2012-01-18 pages = extension = .txt mime = text/plain words = 5516 sentences = 289 flesch = 54 summary = title: Distinct Regulation of Host Responses by ERK and JNK MAP Kinases in Swine Macrophages Infected with Pandemic (H1N1) 2009 Influenza Virus We have also observed cross-talk between MAP kinase and NFkB pathways, and our data indicate that MAP kinase ERK1/2 and JNK1/2 may impact the activation of NFkB through the induction of RIG-1, leading to IFN-b induction in H1N1pdm-infected swine macrophages. To understand the mechanism of proinflammatory cytokine and TNF family ligand induction in H1N1pdm-infected swine macrophages, we investigated how MAP kinases were activated and whether their signaling pathways were involved in the regulation of various cytokines and TNF family ligands in pig immune cells. To evaluate the role of MAP kinases in the regulation of proinflammatory cytokine responses in H1N1pdm-infected swine macrophages, we pre-treated 3D/4 cells with specific inhibitors for ERK1/2, p38, and JNK1/2 1 hr prior to infection. cache = ./cache/cord-000554-p4ufea6x.txt txt = ./txt/cord-000554-p4ufea6x.txt === reduce.pl bib === id = cord-000581-ewx5xhrb author = Rudge, James W. title = Health System Resource Gaps and Associated Mortality from Pandemic Influenza across Six Asian Territories date = 2012-02-21 pages = extension = .txt mime = text/plain words = 5718 sentences = 218 flesch = 36 summary = This study was conducted as part of the AsiaFluCap project (www.asiaflucap.org), the overall aim of which is to conduct health systems analyses to support capacity development for responding to pandemic influenza across six countries and territories in Asia, specifically: Cambodia, Indonesia, Lao PDR, Taiwan, Thailand and Vietnam. Estimating resource needs, gaps, and associated mortality In our baseline scenario, resource gaps were estimated assuming that 12% of ''general'' hospital resources (beds, ventilators and human resources) are available for care of pandemic influenza cases, with the remaining 88% required for maintaining essential healthcare services, as in a previous pilot study for Thailand [20] , and based on previous reports [25] [26] . Figure 1 presents the geographical distribution of estimated resource gaps across provinces (or districts in the case of Indonesia) in each study country for the modeled pandemic influenza scenario, under our baseline assumptions and point estimates for parameter values. cache = ./cache/cord-000581-ewx5xhrb.txt txt = ./txt/cord-000581-ewx5xhrb.txt === reduce.pl bib === id = cord-000721-leedutqo author = Nawaz, Sameena title = Human Bocaviruses Are Not Significantly Associated with Gastroenteritis: Results of Retesting Archive DNA from a Case Control Study in the UK date = 2012-07-24 pages = extension = .txt mime = text/plain words = 3199 sentences = 162 flesch = 50 summary = Human bocavirus (HBoV)s, which are associated with respiratory infections, have also frequently been detected in stool samples in cases of gastroenteritis, and a tentative association between HBoVs, and in particular type-2 HBoVs, and gastroenteritis has previously been made. The aim of this study was to determine the role of HBoVs in gastroenteritis, using archived DNA samples from the case-control Infectious Intestinal Disease Study (IID). In the genotype-specific assays 106 of the 324 HBoV-positive samples were genotyped, with HBoV-1 predominantly found in controls whilst HBoV-2 was more frequently associated with cases of gastroenteritis (p<0.01). The prevalence of HBoV-2 in children in the UK was significantly lower than that reported in a study in Australia, in which HBoV-2 was detected in 17.2% and 8.1% of the cases and controls, respectively [22] . Human bocavirus in children hospitalized for acute gastroenteritis: a case-control study cache = ./cache/cord-000721-leedutqo.txt txt = ./txt/cord-000721-leedutqo.txt === reduce.pl bib === id = cord-001014-8yrpcl94 author = Kitagawa, Hiroshi title = Intranasally Administered Antigen 85B Gene Vaccine in Non-Replicating Human Parainfluenza Type 2 Virus Vector Ameliorates Mouse Atopic Dermatitis date = 2013-07-03 pages = extension = .txt mime = text/plain words = 4451 sentences = 288 flesch = 57 summary = title: Intranasally Administered Antigen 85B Gene Vaccine in Non-Replicating Human Parainfluenza Type 2 Virus Vector Ameliorates Mouse Atopic Dermatitis Ear swelling, dermal cell infiltrations and serum IgE level were significantly suppressed in the rhPIV2/Ag85B treated mouse group accompanied with elevated IFN-γ and IL-10 mRNA expressions, and suppressed IL-4, TNF-α and MIP-2 mRNA expressions. Expression of IL-4 mRNA was significantly decreased in the ear skin of intra-nasally rhPIV2/Ag85B treatment group compared to that of PBS treated mice (Fig. 4A) . mRNA expressions of TNF-a and MIP-2 were significantly decreased in both of intra-nasally and subcutaneously rhPIV2/Ag85B treated groups compared with PBS or vector treated group (Fig. 4E, F) . Ag85B is a conserved protein in mycobacterial species and can elicit a strong Th1-type immune Expressions of IL-4, TNF-a and MIP2-a mRNA were significantly decreased in the ear skin treated with intranasally rhPIV2/Ag85B treated group compared to those of control groups. cache = ./cache/cord-001014-8yrpcl94.txt txt = ./txt/cord-001014-8yrpcl94.txt === reduce.pl bib === === reduce.pl bib === id = cord-000478-88wo4xen author = Gowen, Brian B. title = Use of Recombinant Adenovirus Vectored Consensus IFN-α to Avert Severe Arenavirus Infection date = 2011-10-24 pages = extension = .txt mime = text/plain words = 4407 sentences = 221 flesch = 49 summary = Intranasal administration of DEF201 24 h prior to challenge with Pichindé virus (PICV) was highly effective at protecting animals from mortality and preventing viral replication and liver-associated disease. Interestingly, the 10 7 and 10 8 pfu DEF201 groups presented with little to no day-7 virus burden in the serum, liver, or spleen, while the 10 6 group developed viral titers that were comparable to the rAd EV and placebo controls ( Figure 2B-D) . This may not be the case with hamsters treated with DEF201 24 h prior to challenge since most had no detectable virus titers in spleen, liver, or serum on day 7 of PICV infection ( Figure 2B-D) . Animals were treated i.n. with a single dose 10 8 pfu of DEF201, the rAd EV control virus, or PBS placebo 7 or 14 days prior to PICV infection. cache = ./cache/cord-000478-88wo4xen.txt txt = ./txt/cord-000478-88wo4xen.txt === reduce.pl bib === id = cord-001007-645zegcv author = Kim, Hak title = Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections date = 2013-06-27 pages = extension = .txt mime = text/plain words = 4060 sentences = 189 flesch = 48 summary = This study analyzed parts of the viral genes spanning the 5′ noncoding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. This study aimed to understand and characterize the various recombination events between 5' NCR and VP4/VP2 region of field strains of HRV including species A, B and C, using 105 HRVs identified from two distinctive laboratory surveillance systems, the Acute Respiratory Infectious Network (ARINET) and Severe Lower Respiratory Tract Infections (SLRI) surveillances undertaken from October 2008 to March 2009. In conclusion, this study is the first report describing intraand interspecies genomic recombination in circulating HRV-A and -C isolated from patients with acute or severe respiratory illness and these results will assist in investigating the causes of the diversity and evolution of HRVs arising through recombination events. cache = ./cache/cord-001007-645zegcv.txt txt = ./txt/cord-001007-645zegcv.txt === reduce.pl bib === id = cord-000413-h2e6h076 author = Zhang, Jingyu title = A Conformation-Sensitive Monoclonal Antibody against the A2 Domain of von Willebrand Factor Reduces Its Proteolysis by ADAMTS13 date = 2011-07-11 pages = extension = .txt mime = text/plain words = 4445 sentences = 233 flesch = 56 summary = To investigate whether murine monoclonal antibodies (mAbs) against human VWF affect the susceptibility of VWF to proteolysis by ADAMTS13 in vitro, eight mAbs to different domains of human VWF were used to evaluate the effects on VWF cleavage by ADAMTS13 under fluid shear stress and static/denaturing conditions. The results indicate that mAb SZ34 inhibited proteolytic cleavage of VWF by ADAMTS13 in a concentration-dependent manner under fluid shear stress, but not under static/denaturing conditions. We showed that the decreased amount of the high and intermediate molecular weight multimers were dramatically reduced by mAb SZ34 in a concentration-dependent manner under shear stress (Figure 2 ), further confirming the role of SZ34 in decreasing the susceptibility of VWF to proteolytic cleavage by ADAMTS13 under physiologically relevant conditions. cache = ./cache/cord-000413-h2e6h076.txt txt = ./txt/cord-000413-h2e6h076.txt === reduce.pl bib === id = cord-000837-rdpsxb4n author = Perez-Pepe, Marcelo title = BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis date = 2012-12-20 pages = extension = .txt mime = text/plain words = 7079 sentences = 366 flesch = 50 summary = title: BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. To assess the suitability of BUHO for the analysis of additional cell structures, we investigated several examples of cytoplasmic foci stained with different strategies, including SGs and PBs in mammalian and insect cells, and synapses and Smaug 1-mRNA silencing foci (S-foci) in primary neurons. Moreover, as expected given that SGs and PBs are morphologically similar, we found that prototype SGs were useful to identify PBs. To test the performance of BUHO in analyzing distances between objects, we focused on the presence of synaptic mRNA silencing foci at the synapse surroundings. With minor modifications, we have successfully applied it for processing images of different magnification and resolution of synapses, SGs, PBs and similar foci in mammalian and Drosophila cell lines as well as in primary cultured neurons. cache = ./cache/cord-000837-rdpsxb4n.txt txt = ./txt/cord-000837-rdpsxb4n.txt === reduce.pl bib === id = cord-000237-mticfoic author = Guan, Xuhua title = Pneumonia Incidence and Mortality in Mainland China: Systematic Review of Chinese and English Literature, 1985–2008 date = 2010-07-23 pages = extension = .txt mime = text/plain words = 5405 sentences = 266 flesch = 51 summary = We conducted a systematic review of the Chinese-and Englishlanguage literature in order to describe pneumonia incidence and mortality in China, evaluate the quality of published studies, and identify gaps in the literature that can be addressed through surveillance and epidemiologic research projects in the future. Based on published recommendations for measuring quality of epidemiologic studies of pneumonia [15] , we assessed quality using the following six criteria: (1) geographic location was reported, (2) study was conducted for a period of at least one year or multiples of one year to account for seasonal factors, (3) site of case detection or surveillance location was reported, (4) age and population size of cohort of at least 50 cases were reported, (5) quality assurance and monitoring methods were employed to assure that data was complete and high quality, and (6) a clearly defined case definition (e.g., not based solely on clinical diagnosis) was used and reported. In children aged ,5 years, the highest mortality rates were reported by four studies that were each conducted in multiple regions throughout mainland China (9.55±14.40 deaths from pneumonia per 1,000 live births; Table S3 ) [21, 23, 38, 48] . cache = ./cache/cord-000237-mticfoic.txt txt = ./txt/cord-000237-mticfoic.txt === reduce.pl bib === id = cord-000248-zueoyesj author = Berretta, Regina title = Cancer Biomarker Discovery: The Entropic Hallmark date = 2010-08-18 pages = extension = .txt mime = text/plain words = 33594 sentences = 1678 flesch = 43 summary = These authors cite, for example, ''mitochondrial dysfunction'' [5, 6] (including, but not limited to ''glucose avidity'' [7] and ''a shift in glucosemetabolism from oxidative phosphorylation to glycolysis'' [6, 8] , ''altered glycolysis'' [9] , ''altered bioenergetic function of mitochondria'' [10] ), ''dysregulation of cell cycle and defective genome-integrity checkpoints'' [11] , ''aberrant DNA methylation'' [12] (''promoter hypermethylation of hallmark cancer genes'' [13] and ''CpG island hypermethylation and global genomic hypomethylation'' [14] ), ''shift in cellular metabolism'' [15, 16, 17] , ''regional hypoxia'' [18] , ''microenviroment acidosis'' [19] , ''abnormal microRNA regulation'' [20, 21] , ''aneuploidy'' and ''chromosome aberrations'' [22, 23, 24, 25, 26] , ''disruption of cellular junctions'' [27] , ''avoidance of the immune response'' [28] , ''pre-existing chronic inflammatory conditions'' [29, 30] , ''cancerrelated inflammation'' [29] , ''disabled autophagy'' [28] , ''impaired cellular senescence'' [31] , ''altered NF-kappaB signalling'' [32] , ''altered growth patterns, not altered growth per se'' [33] , ''disregulated DNA methylation and histone modifications'' [34] , ''tissue dedifferentiation'' [35, 36] , and ''somatically heritable molecular alterations'' [37] . cache = ./cache/cord-000248-zueoyesj.txt txt = ./txt/cord-000248-zueoyesj.txt === reduce.pl bib === id = cord-000158-d08buwtu author = Corti, Davide title = Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals date = 2010-01-20 pages = extension = .txt mime = text/plain words = 8060 sentences = 343 flesch = 44 summary = The 2G12 epitope is not present in the majority of clade C isolates [27] , but, of more concern, no 2G12-like activity has been detected in the sera of HIV-1 infected individuals [21, 22] , suggesting that this type of neutralizing antibody may not be generally amenable to elicitation by B cells. By using an improved memory B cell immortalization method [41] , combined with highthroughput parallel screening with a panel of recombinant Envbased antigens, we isolated a panel of 58 human mAbs which we have characterized with regard to epitope specificity and breadth of neutralization. The mAbs were purified and further characterized for binding specificity and neutralizing activity using an extended panel of recombinant Env proteins and pseudoviruses representative of several HIV-1 clades with diverse coreceptor usage, geographic origin and conformation. cache = ./cache/cord-000158-d08buwtu.txt txt = ./txt/cord-000158-d08buwtu.txt === reduce.pl bib === === reduce.pl bib === id = cord-000375-fvfl0bn1 author = Shen, Ching-I title = The Infection of Chicken Tracheal Epithelial Cells with a H6N1 Avian Influenza Virus date = 2011-05-06 pages = extension = .txt mime = text/plain words = 4026 sentences = 208 flesch = 55 summary = This result clearly elucidates the receptor distribution for the avian influenza virus among chicken tracheal epithelial cells and illustrates a primary cell model for evaluating the cell tropisms of respiratory viruses in poultry. In contrast to the finding for MAA/MAL-I, abundant SNA signals were mainly restricted to the mucin + cells (ratio of SNA + /mucin + cells, 0.8560.09, n = 368) ( Fig. 2A) , indicating that the goblet cells expressed SAa2-6Gal terminal glycan. To determine whether a single basal cells can express both SAa2-3Gal and SAa2-6Gal, CTE cells were triple-stained with K14 primary antibody (Cy5-2u Ab, purple), FITC-conjugated MAA (green) and biotin-labeled SNA (detected by Cy3-Streptovidin, red) (Figs. In humans, by contrast, both ciliated and goblet cells can be labeled with MAA/MAL-I and SNA [19, 20] , indicating that these two epithelial cells have both types of influenza viral receptors. cache = ./cache/cord-000375-fvfl0bn1.txt txt = ./txt/cord-000375-fvfl0bn1.txt === reduce.pl bib === id = cord-000265-llilwq1u author = Gao, Rongbao title = A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date = 2010-10-12 pages = extension = .txt mime = text/plain words = 4896 sentences = 253 flesch = 46 summary = Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Although H5N1 virus infection of humans is primarily one of the lower respiratory tract, more recent reports suggested that influenza A H5N1 may in rare, severe cases, disseminate beyond the lungs and infect brain [26, 27] , intestines [20, 27] and lymphoid tissues [27] , and result in extra-pulmonary clinical manifestations including encephalopathy or encephalitis [15, 28] . To better understand the pathogenesis of human H5N1 virus infection, and investigate the route of virus dissemination in vivo, we report on the use of different techniques to detect virus distribution and infection of 5 organ systems in a laboratory confirmed fatal human H5N1 virus infection, and analyze the relationship between viral load in tissues and host response. cache = ./cache/cord-000265-llilwq1u.txt txt = ./txt/cord-000265-llilwq1u.txt === reduce.pl bib === id = cord-000851-uylgyhs8 author = Wang, Zhenya title = Inhibitory Influence of Enterococcus faecium on the Propagation of Swine Influenza A Virus In Vitro date = 2013-01-07 pages = extension = .txt mime = text/plain words = 4519 sentences = 213 flesch = 47 summary = faecium caused a modified cellular expression of selected mediators of defence in 3D4-cells: while the expression of TNF-α, TLR-3 and IL-6 were decreased in the SwIV-infected and probiotic treated cells, IL-10 was found to be increased. The results from quantitative RT-PCR shown in Fig. 5 reveal a decreased expression of these mediators when compared to the non-treated samples (SwIV-infected 3D4/21-cells without E. faecium effectively protects host cells from swine influenza virus infection and are in support of the above author's hypothesis, that probiotics are not only useful to inhibit enteric viruses, but may also have potential for the control of respiratory viruses. faecium before SwIV-infection and a 1 h treatment after completion of virus infection also led to a 2-3 log-unit loss of virus titer, the probiotic must alter host cell factors which apparently results in an inhibition of influenza virus multiplication. faecium in SwIV-infected 3D4/21 cells, the reduced inflammatory response caused by some cytokines at the cellular level may contribute to the antiviral effect of the probiotic. cache = ./cache/cord-000851-uylgyhs8.txt txt = ./txt/cord-000851-uylgyhs8.txt === reduce.pl bib === id = cord-000180-howix091 author = MacLeod, Iain J. title = Binding of Herpes Simplex Virus Type-1 Virions Leads to the Induction of Intracellular Signalling in the Absence of Virus Entry date = 2010-03-05 pages = extension = .txt mime = text/plain words = 6788 sentences = 316 flesch = 49 summary = By taking advantage of the entry-defective phenotype of glycoprotein-deficient HSV-1 virus particles, the results presented here show that binding of virions to cellular receptors on the plasma membrane is sufficient to stimulate a change in cellular gene expression. As induction of the NF-kB reporter construct occurred within one hour of inoculation with DgH virions and peaked at around two-and-a-half hours post-inoculation, then the transcripts previHFFs were stimulated with 1000 particles/cell of DgB, DgD or DgH HSV-1 for six hours and a cDNA microarray corresponding to targets of 19 signalling pathways was used to detect changes in cellular gene expression when compared to mock-infected. Real-time PCR confirmed that changes in transcription associated with the NF-kB, JAK/STAT, JAK/Src and PI3K pathways were modulated as a result of virion binding, all of which required gD on the envelope surface To demonstrate that signalling occurred at physiologically relevant multiplicities of infection, HFFs were inoculated with either 1000, 100, 10 or 1 particles per cell of entry-defective HSV-1. cache = ./cache/cord-000180-howix091.txt txt = ./txt/cord-000180-howix091.txt === reduce.pl bib === === reduce.pl bib === id = cord-001045-jm60nxc2 author = DeLisle, Sylvain title = Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy date = 2013-08-13 pages = extension = .txt mime = text/plain words = 4332 sentences = 209 flesch = 45 summary = METHODS: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The ARI CDA flagged an outpatient visit if the provider assigned it an ARI-related International Disease Classification, 9 th Revision, Clinical Modification (ICD-9) diagnostic code OR issued a prescription for a cough remedy OR documented at least two symptoms from the above ARI case definition in his/her clinical note, as retrieved by computerized text analysis [10] . Discussion Automated text analyses of chest imaging reports improved the performance of EMR-based CDAs that included structured data elements and free-text search for ARI symptoms. cache = ./cache/cord-001045-jm60nxc2.txt txt = ./txt/cord-001045-jm60nxc2.txt === reduce.pl bib === id = cord-000809-9voqa1oy author = Archer, Brett N. title = Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa date = 2012-11-16 pages = extension = .txt mime = text/plain words = 3885 sentences = 208 flesch = 50 summary = We characterize the transmissibility of influenza A(H1N1)pdm09 (hereafter pH1N1) in South Africa during 2009 by estimating the serial interval (SI), the initial effective reproductive number (initial R(t)) and the temporal variation of R(t). In this work we incorporate data collected on all laboratory-confirmed cases detected during the 2009 pH1N1 epidemic in South Africa with the aim of describing the transmissibility characteristics (initial R t and temporal variation of R t ) of the epidemic in the country and compare its dynamics with those observed in other countries in the same year. When estimating initial R t , we focus our analysis on the exponential growth phase of the epidemic in South Africa (i.e. the period from the first occurrence of five consecutive days with confirmed cases reported to the epidemic peak). cache = ./cache/cord-000809-9voqa1oy.txt txt = ./txt/cord-000809-9voqa1oy.txt === reduce.pl bib === id = cord-000536-0mn1gbll author = Hu, Le-Le title = Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions date = 2011-12-29 pages = extension = .txt mime = text/plain words = 5134 sentences = 265 flesch = 48 summary = In this study, based on the information of chemical-chemical interactions, a novel method was developed that can be used to identify which of the following eleven metabolic pathway classes a query compound may be involved with: (1) Carbohydrate Metabolism, (2) Energy Metabolism, (3) Lipid Metabolism, (4) Nucleotide Metabolism, (5) Amino Acid Metabolism, (6) Metabolism of Other Amino Acids, (7) Glycan Biosynthesis and Metabolism, (8) Metabolism of Cofactors and Vitamins, (9) Metabolism of Terpenoids and Polyketides, (10) Biosynthesis of Other Secondary Metabolites, (11) Xenobiotics Biodegradation and Metabolism. In this study, we proposed a multi-target model based on chemical-chemical interactions for predicting the metabolic pathways where compounds participate in. Listed in Table 2 are the accuracies by each of the 11 prediction orders for the 3,137 compounds about their involvement in the 11 metabolic pathway classes using the 5-fold crossvalidation test. cache = ./cache/cord-000536-0mn1gbll.txt txt = ./txt/cord-000536-0mn1gbll.txt === reduce.pl bib === id = cord-000726-tonaaft2 author = Chang, Binggong title = Influence of Mabs on PrP(Sc) Formation Using In Vitro and Cell-Free Systems date = 2012-07-27 pages = extension = .txt mime = text/plain words = 4986 sentences = 239 flesch = 50 summary = Two systems were used to analyze the effect of different antibodies on PrP(Sc) formation: (i) neuroblastoma cells persistently infected with the 22L mouse-adapted scrapie stain, and (ii) protein misfolding cyclic amplification (PMCA), which uses PrP(Sc) as a template or seed, and a series of incubations and sonications, to convert PrP(C) to PrP(Sc). Based on the numerous and varied Mabs analyzed, the inhibitory effect does not appear to be epitope specific, related to PrP(C) conformation, or to cell membrane localization, but is influenced by the targeted PrP region (amino vs carboxy). We compared the effect of individual PrP-specific monoclonal antibodies (Mabs) on the PrP C -PrP Sc conversion process using both an N2a/22L cell culture model and the test-tube PMCA system. To more completely explore the possible therapeutic effect of anti-PrP antibodies, and to establish another system to analyze the influence of Abs on the conversion process, we screened Mabs produced in our laboratory for their capacity to inhibit PrP Sc formation. cache = ./cache/cord-000726-tonaaft2.txt txt = ./txt/cord-000726-tonaaft2.txt === reduce.pl bib === id = cord-000261-ip32y0j5 author = Becker, Pablo D. title = Generation of Human Antigen-Specific Monoclonal IgM Antibodies Using Vaccinated “Human Immune System” Mice date = 2010-10-04 pages = extension = .txt mime = text/plain words = 5816 sentences = 270 flesch = 48 summary = Following immunization, human CD19 + B cells were sorted based on surface CD27 expression, as a marker of memory phenotype, and the isotype of surface Igs. The sorted B cell populations were immortalized in vitro by retroviral transduction with human B cell lymphoma (BCL)-6 and BCL-XL genes and antigen-specific B cell clones were established and characterized. The obtained results provided the proof-of-concept for the usefulness of this generic approach based on HIS mice combined with immortalization of human B cells for the rapid and inexpensive development of human mAbs against a wide range of antigens. Since HIS mice contained broad naïve B cell repertoires, we analyzed the induction of human antigen-specific B cell responses after immunization with commercially available human vaccines. So far, humanized mouse models based on the transplantation of human HSC only -i.e. without additional human tissues -share these limitations, and immunization strategies result in the limited generation of class-switched antigen-specific B cell responses [14, 31, 32] . cache = ./cache/cord-000261-ip32y0j5.txt txt = ./txt/cord-000261-ip32y0j5.txt === reduce.pl bib === id = cord-000959-nk2thkme author = Downer, Eric J. title = Identifying Early Inflammatory Changes in Monocyte-Derived Macrophages from a Population with IQ-Discrepant Episodic Memory date = 2013-05-06 pages = extension = .txt mime = text/plain words = 5396 sentences = 268 flesch = 48 summary = METHODS: This study explored the expression of receptors (CD11b, TLR2 and TLR4) on circulating monocyte-derived macrophages (MDMs) and peripheral blood mononuclear cells (PBMCs) isolated from healthy elderly adults who we classified as either IQ memory-consistent (high-performing, HP) or IQ memory-discrepant (low-performing, LP). The purpose of the study was to compare the expression of receptors (CD11b, TLR2 and TLR4) on circulating monocyte-derived macrophages (MDMs) and the response of these cells to LPS in samples prepared from the LP cohort and a cohort which we classified as IQ memory-consistent (high-performing, HP) individuals. P) TLR4 expression on CD11b + MDMs was increased in the LP group compared with the HP group (P,0.05) and this is also shown in the representative dot plots of TLR4 + cells ( and following LPS stimulation [6] , while pro-inflammatory cytokine [52] and chemokine [53, 54] levels are elevated in peripheral blood monocytes isolated from the elderly after LPS stimulation. cache = ./cache/cord-000959-nk2thkme.txt txt = ./txt/cord-000959-nk2thkme.txt === reduce.pl bib === id = cord-000877-usz7pnvu author = Abdel-Moneim, Ahmed S. title = Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date = 2013-01-30 pages = extension = .txt mime = text/plain words = 1826 sentences = 101 flesch = 51 summary = title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Human bocavirus (HBoV) was first found in children with acute respiratory tract infections in 2005 [1] . The current study aims to screen the epidemiological status and molecular phylogeny of HBoV isolates prevailing in pediatric patients with respiratory infection in Saudi Arabia. The current study investigated the prevalence of HBoV in patients suffering from respiratory tract infections in Saudi Arabia. Furthermore, the phylogenetic analysis results of three selected sequences showed that the Saudi HBoV1 strains obtained from respiratory samples belonged to group I human bocaviruses (Fig. 1) . Detection of human bocavirus in Japanese children with lower respiratory tract infections Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction cache = ./cache/cord-000877-usz7pnvu.txt txt = ./txt/cord-000877-usz7pnvu.txt === reduce.pl bib === id = cord-000642-mkwpuav6 author = Moreira, Rebeca title = Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing date = 2012-04-19 pages = extension = .txt mime = text/plain words = 6848 sentences = 372 flesch = 45 summary = title: Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing The 35 most frequently found contigs included a large number of immune-related genes, and a more detailed analysis showed the presence of putative members of several immune pathways and processes like the apoptosis, the toll like signaling pathway and the complement cascade. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum. Moreover, a few transcripts encoded by genes putatively involved in the clam immune response against Perkinsus olseni have been reported by cDNA library sequencing [18] . philippinarum transcriptome and another four bivalve species sequences were analyzed by comparative genomics (Crassostrea gigas of the family Ostreidae, Bathymodiolus azoricus and Mytilus galloprovincialis of the family Mytilidae and Laternula elliptica of the family Laternulidae). cache = ./cache/cord-000642-mkwpuav6.txt txt = ./txt/cord-000642-mkwpuav6.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-000425-isw6jeir author = Flori, Laurence title = Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation date = 2011-07-29 pages = extension = .txt mime = text/plain words = 7831 sentences = 388 flesch = 46 summary = A study on Yorkshire pigs selected for eight generations for high and low adaptive IR (HIR and LIR, respectively) on an index combining four standardized measures of specific antibodies and cellmediated IR, after stimulation with specific antigens (bacillus Calmette-Guérin and hen egg white lysozyme), has revealed that HIR and LIR animals differ in response to immunization and infection [2, 11, 12, 13, 14] . Finally, several significant QTLs for total leukocyte count ( [20, 21] ; Animal-QTLdb, http://www.animalgenome.org/cgi-bin/QTLdb/index), mitogen-induced proliferation [20] , antibody response [20, 22] , cytokine production (IL10 and IFNc) [23] , complement activity [22] , and acute phase protein serum concentration [22] have been detected and mapped to different pig chromosomes. In this report, we present the results of a global genetic study, combining principal component analysis (PCA), and genetic parameter estimation applied to a large number of innate and adaptive ITs in a pig population vaccinated against Mycoplasma hyopneumoniae (M. cache = ./cache/cord-000425-isw6jeir.txt txt = ./txt/cord-000425-isw6jeir.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-000539-uh3q65we author = Zhang, Yi title = Acute Respiratory Distress Syndrome Induced by a Swine 2009 H1N1 Variant in Mice date = 2012-01-03 pages = extension = .txt mime = text/plain words = 4620 sentences = 247 flesch = 51 summary = BACKGROUND: Acute respiratory distress syndrome (ARDS) induced by pandemic 2009 H1N1 influenza virus has been widely reported and was considered the main cause of death in critically ill patients with 2009 H1N1 infection. Mice infected with SD/09 virus showed typical ARDS symptoms characterized by 60% lethality on days 8–10 post-inoculation, highly edematous lungs, inflammatory cellular infiltration, alveolar and interstitial edema, lung hemorrhage, progressive and severe hypoxemia, and elevated levels of proinflammatory cytokines and chemokines. In the present mouse model, the number of leukocytes observed in the BALF of virus-infected mice significantly increased compared with the control mice on day 8 p.i. Different counts in BALF showed that the proportion of neutrophils dramatically increased. cache = ./cache/cord-000539-uh3q65we.txt txt = ./txt/cord-000539-uh3q65we.txt === reduce.pl bib === === reduce.pl bib === id = cord-000833-m6abyuvx author = Sekiguchi, Satoshi title = Immunization with a Recombinant Vaccinia Virus That Encodes Nonstructural Proteins of the Hepatitis C Virus Suppresses Viral Protein Levels in Mouse Liver date = 2012-12-17 pages = extension = .txt mime = text/plain words = 5915 sentences = 348 flesch = 50 summary = The HCV core protein was expressed consistently in the liver after polyinosinic acid–polycytidylic acid injection, and these mice showed chronic hepatitis C-related pathological findings (hepatocyte abnormalities, accumulation of glycogen, steatosis), liver fibrosis, and hepatocellular carcinoma. These observations, in addition to the modified histology activity index (HAI) scores, indicated that expression of HCV proteins caused chronic hepatitis in the CN2-29 (+/2) /MxCre (+/2) mice because a weak, though persistent, immune response followed an initial bout of acute hepatitis ( Figure S1 ). To determine whether activation of the host immune response caused the reduction with HCV protein levels in the livers of CN2-29 (+/2) /MxCre (+/2) mice, we used a highly attenuated VV strain, LC16m8, to generate three rVVs [12] . To determine whether rVV-N25 treatment induced the same effect in other strains of HCV transgenic mice, we analyzed RzCN5-15 (+/2) /MxCre (+/2) mice, which express all HCV proteins; in these mice, chronic hepatitis was resolved within 28 days of immunization with rVV-N25. cache = ./cache/cord-000833-m6abyuvx.txt txt = ./txt/cord-000833-m6abyuvx.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-000374-gt2pwc9b author = Yang, Albert C. title = Clustering Heart Rate Dynamics Is Associated with β-Adrenergic Receptor Polymorphisms: Analysis by Information-Based Similarity Index date = 2011-05-04 pages = extension = .txt mime = text/plain words = 5304 sentences = 279 flesch = 43 summary = With these considerations in mind, in the present study, we introduce a bottom-up genotype-phenotype analysis to investigate the association between genetic polymorphisms and autonomic control of heart rate dynamics, using three common polymorphisms in genes encoding b-adrenergic receptor (b-AR) as an example. The analyses of the present study were two-fold: 1) a nonrandomness index [17] derived from the IBS method was applied to quantify the nonlinear aspect of HRV according to b-AR genotype and to test the correlation of this index with standard HRV indices; and 2) using agglomerative hierarchical cluster analysis, we unsupervisedly categorized these subjects into clusters based on pairwise dissimilarity among heart rate dynamics, and then we investigated the association of these clustering patterns with b-AR gene polymorphisms. The data presented in this study demonstrate a significant association of a common b 2 -AR polymorphism, Arg16Gly, with the non-randomness index, a nonlinear HRV measure derived from the IBS method. cache = ./cache/cord-000374-gt2pwc9b.txt txt = ./txt/cord-000374-gt2pwc9b.txt === reduce.pl bib === === reduce.pl bib === id = cord-000947-psguw47w author = Feng, Jianyu title = A Study of the Mechanism of the Chaperone-like Function of an scFv of Human Creatine Kinase by Computer Simulation date = 2013-04-24 pages = extension = .txt mime = text/plain words = 4685 sentences = 270 flesch = 54 summary = We built the model of the single chain antibody (scFv-A4) that increased the stability of human creatine kinase (HCK) by the homology modeling method. Epitopes of human creatine kinase were predicted by computer and then the binding of scFv-A4 and HCK was modeled with computer. To elucidate why scFv-A4 had the chaperone-like function, we combined computer modeling and peptide array membrane technique to study the interactions between scFv-A4 and HCK. Firstly, bioinformatics software tools were used to predict the interacting sites between scFv-A4 and HCK and then the results were combined with the peptide array membrane experiment results to build the 3D models of the binding complex. In complex model-I, scFv-A4 exhibits chaperone-like function by assisting the folding of HCK and stabilizing the whole structure. In this study we combined computer modeling and the peptide array membrane method to investigate the interaction between scFv-A4 and HCK. cache = ./cache/cord-000947-psguw47w.txt txt = ./txt/cord-000947-psguw47w.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-001078-5m29nugu author = Chen, Xiaorong title = Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study date = 2013-09-17 pages = extension = .txt mime = text/plain words = 3930 sentences = 200 flesch = 47 summary = title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study OBJECTIVE: The present study aimed to analyze clinical features and factors associated with treatment outcomes of H7N9 influenza A virus infection. Factors analyzed for possible correlation with clinical features and treatment outcomes in patients included 1) baseline characteristics of patients, such as age, sex, occupation, underlying conditions, exposure to poultry and/or wild birds in the past seven days, date of symptom onset and hospital admission, date of specimen collection, and date of positive diagnosis; 2) results from laboratory tests and imaging examinations; 3) treatment regimen including basic supporting therapy, antibiotic therapy, antiviral therapy, traditional Chinese medicine (TCM) therapy, and other therapies if applicable; and 4) current condition of patients including the length of stay in the hospital. cache = ./cache/cord-001078-5m29nugu.txt txt = ./txt/cord-001078-5m29nugu.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-001120-fxd533b4 author = Everitt, Aaron R. title = Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date = 2013-11-21 pages = extension = .txt mime = text/plain words = 4874 sentences = 252 flesch = 47 summary = We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. Here we sought therefore to expand and define the role of Ifitm3 in pathogen restriction by assessing the susceptibility of Ifitm3-deficient (Ifitm3 -/-) mice to bacteria (Salmonella Typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis), a parasite (Plasmodium berghei) and a virus (respiratory syncytial virus, RSV) to determine the specificity of this crucial antimicrobial protein. Similarly, bacterial counts revealed no significant differences between wild type and Ifitm3 -/-mice; together showing that Ifitm3 does not play a role in resistance or susceptibility to Salmonella infection. The experimental challenge revealed there to be no significant difference in phenotype seen in Ifitm3 -/-mice compared with wild type littermate controls, with both showing susceptibility to ECM ( Figure 5A ). cache = ./cache/cord-001120-fxd533b4.txt txt = ./txt/cord-001120-fxd533b4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-001099-jirkkkvy author = Yousuf, Mohammad A. title = Caveolin-1 Associated Adenovirus Entry into Human Corneal Cells date = 2013-10-11 pages = extension = .txt mime = text/plain words = 7110 sentences = 372 flesch = 46 summary = Collectively, these experiments indicate for the first time that HAdV-D37 uses a lipid raft mediated caveolin-1 associated pathway for entry into corneal cells, and connects the processes of viral entry with downstream proinflammatory cell signaling. Initial binding is followed by a secondary interaction between the arginine-glycine-aspartic acid (RGD) motif in the viral capsid penton base and cellular integrins α v β 3 , α v β 5, and α V β 1 [42] [43] [44] [45] This secondary interaction is thought to induce a host cell signaling cascade resulting in clathrin mediated endocytosis [46] [47] [48] , and possibly, activation of the rab5 dependent classical endosomal pathway [49] . Herein, we show that HAdV-D37, an etiologic agent of epidemic keratoconjunctivitis, enters primary human corneal fibroblasts predominantly via lipid rafts and caveolae, suggesting both redundancy and cell specificity in mechanisms of adenoviral entry. To further examine the role of lipid raft microdomains in HAdV-D37 entry, we treated corneal cells with both Cy3-labeled virus and 488-CTXB, and tracked their cellular localization over time ( Figure 1C ). cache = ./cache/cord-001099-jirkkkvy.txt txt = ./txt/cord-001099-jirkkkvy.txt === reduce.pl bib === === reduce.pl bib === id = cord-001199-9khx93c0 author = Liu, Fengchen title = Effect of the One-Child Policy on Influenza Transmission in China: A Stochastic Transmission Model date = 2014-02-06 pages = extension = .txt mime = text/plain words = 6871 sentences = 300 flesch = 48 summary = Changes in household structure and the proportion of children in the population as a result of the one-child policy could have more effects on the AR, and the difference in AR could be as high as 60% under a scenario of very high immunity loss rate per year ( Figures 5(A) ). For each parameter set, we simulated the influenza trajectories under two demographic control policies, and then computed the difference in average annual attack rates over 10 years (2015 to 2024) between two policies. For each parameter set, we simulated the influenza trajectories under two demographic control policies, and then computed the difference in average annual attack rates over 10 years (2015 to 2024) between two policies. For each parameter set, we simulated the influenza trajectories under two demographic control policies, and then computed the difference in average secondary attack rates over 10 years (2015 to 2024) between two policies. cache = ./cache/cord-001199-9khx93c0.txt txt = ./txt/cord-001199-9khx93c0.txt === reduce.pl bib === id = cord-001186-jkg7qkj6 author = Skowronski, Danuta M. title = Randomized Controlled Ferret Study to Assess the Direct Impact of 2008–09 Trivalent Inactivated Influenza Vaccine on A(H1N1)pdm09 Disease Risk date = 2014-01-27 pages = extension = .txt mime = text/plain words = 8871 sentences = 412 flesch = 40 summary = During spring-summer 2009, several observational studies from Canada reported that prior receipt of the 2008-09 trivalent inactivated influenza vaccine (TIV) was associated with increased risk of medically-attended, laboratory-confirmed A(H1N1)pdm09 illness, with estimated risk or odds ratios of 1.4-2.5 compared to those unvaccinated [1] . Protein microarray results were consistent with ELISA but in addition showed vaccine-induced HA1 antibody to the seasonal H1 antigen, for which values were significantly higher in vaccinated animals relative to pre-immunization and compared to placebo from day 28, most pronounced from day 49 after the first TIV dose (i.e. three weeks after two-dose vaccine series completion) ( Figure 2 ). Lower neutralizing antibody to A(H1N1)pdm09 even at Ch+14 among vaccinated versus placebo ferrets, although not statistically significant, is consistent with human immunogenicity trials showing blunting of pandemic H1N1 vaccine-induced responses in association with prior seasonal vaccine receipt [53] [54] [55] [56] . cache = ./cache/cord-001186-jkg7qkj6.txt txt = ./txt/cord-001186-jkg7qkj6.txt === reduce.pl bib === id = cord-001213-gxqufddb author = Butt, Azeem Mehmood title = Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses date = 2014-03-04 pages = extension = .txt mime = text/plain words = 7178 sentences = 371 flesch = 54 summary = Therefore, from the similarity index analysis, we observed that selection pressure from hosts and vectors have contributed to shaping the molecular evolution of CHIKV at the respectively, on the formation of the overall codon usage patterns of CHIKV (Figure 2 ). Although, the nucleotide composition correlation analysis showed that codon usage in CHIKV genomes is mainly caused by compositional constraints or mutational pressure, we were interested to determine the possible influence of other factors, such as natural selection. However, in case of CHIKV genomes, variations in nucleotide base compositions were noted (Table 1 ), indicating that other factors, such as natural selection, could also influence overall synonymous codon usage bias. The RSCU values for all the coding sequences of CHIKV genomes were calculated to determine the characteristics of synonymous codon usage without the confounding influence of amino acid composition and the size of coding sequence of different gene samples, following a previously described method [18] . cache = ./cache/cord-001213-gxqufddb.txt txt = ./txt/cord-001213-gxqufddb.txt === reduce.pl bib === id = cord-001117-llb4f74a author = Ji, Wen-Jie title = Spironolactone Attenuates Bleomycin-Induced Pulmonary Injury Partially via Modulating Mononuclear Phagocyte Phenotype Switching in Circulating and Alveolar Compartments date = 2013-11-19 pages = extension = .txt mime = text/plain words = 4964 sentences = 257 flesch = 34 summary = Moreover, serial flow cytometry analysis in blood, BALF and enzymatically digested lung tissue, revealed that spironolactone could partially inhibit bleomycin-induced circulating Ly6C(hi) monocyte expansion, and reduce alternative activation (F4/80+CD11c+CD206+) of mononuclear phagocyte in alveoli, whereas the phenotype of interstitial macrophage (F4/80+CD11c-) remained unaffected by spironolactone during investigation. CONCLUSIONS/SIGNIFICANCE: The present work provides the experimental evidence that spironolactone could attenuate bleomycin-induced acute pulmonary injury and fibrosis, partially via inhibition of MR-mediated circulating monocyte and alveolar macrophage phenotype switching. Based on current evidence, we speculated that pharmacological inhibition of MR with clinically approved drug, may regulate lung macrophage phenotype switching, as well as their progenitors, bone marrow-derived circulating monocytes, and may confer novel therapeutic potential in a murine model of bleomycin-induced acute pulmonary injury and fibrosis. cache = ./cache/cord-001117-llb4f74a.txt txt = ./txt/cord-001117-llb4f74a.txt === reduce.pl bib === id = cord-001251-forh7lw4 author = Jank, Johanna M. title = The Domain-Specific and Temperature-Dependent Protein Misfolding Phenotype of Variant Medium-Chain acyl-CoA Dehydrogenase date = 2014-04-09 pages = extension = .txt mime = text/plain words = 7785 sentences = 553 flesch = 51 summary = Here we established a comprehensive experimental setup to analyze the structural consequences of eight ACADM missense mutations (p.Ala52Val, p.Tyr67His, p.Tyr158His, p.Arg206Cys, p.Asp266Gly, p.Lys329Glu, p.Arg334Lys, p.Arg413Ser) identified after newborn screening and linked the corresponding protein misfolding phenotype to the site of side-chain replacement with respect to the domain. In a previous study, we provided first experimental evidence for the impact of eight additional ACADM mutations identified in NBS on MCAD structure and function and all of these were clearly associated with conformational derangement and decreased protein stability [16] . Moreover, we summarized and quantified the structural data and visualized the molecular protein misfolding phenotype of the variant MCAD proteins in a 3D plot comparing them to the wild-type, to p.Lys329Glu, the classical severe mutation, and to p.Tyr67His, discussed to be a mild mutation. To visualize results from experiments investigating thermal stability, kinetic stability, and conformation of MCAD wild-type and variants, we combined data and developed relative scores assessing the severity of mutation-induced changes. cache = ./cache/cord-001251-forh7lw4.txt txt = ./txt/cord-001251-forh7lw4.txt === reduce.pl bib === id = cord-001207-yjaiybwf author = Sachsenröder, Jana title = The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date = 2014-02-19 pages = extension = .txt mime = text/plain words = 5919 sentences = 302 flesch = 49 summary = faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations. cache = ./cache/cord-001207-yjaiybwf.txt txt = ./txt/cord-001207-yjaiybwf.txt === reduce.pl bib === id = cord-001129-gi2kswai author = Lemos de Matos, Ana title = Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals date = 2013-11-27 pages = extension = .txt mime = text/plain words = 6978 sentences = 342 flesch = 47 summary = Because viruses are responsible for a great number of severe and lethal diseases, together with the important role that RLRs play in mammalian innate immune system, we expect that RIG-I, MDA5 and LGP2 genes may have been under intense selective pressures in all mammals. Evidence for positive selection on mammalian orthologous for RIG-I ( Figure S7 ), MDA5 ( Figure S8 ) and LGP2 ( Figure S9 ) genes was detected using PAML package [54, 55] site-specific models M1a versus M2a and M7 versus M8. (C) Positively-selected codons are exhibited in the table and numbered according to the mammalian LGP2 deduced protein sequences alignment ( Figure S6 downstream RIG-I and MDA5 signaling, which implies functional constraints, the observed variability across species can be perceived as a great structural plasticity for mammalian CARDs. The helicase domain in the RLR family is generally described as exhibiting affinity for dsRNA [78] . cache = ./cache/cord-001129-gi2kswai.txt txt = ./txt/cord-001129-gi2kswai.txt === reduce.pl bib === id = cord-001162-z8cbbit3 author = Yun, Heather C. title = Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection date = 2014-01-08 pages = extension = .txt mime = text/plain words = 3365 sentences = 160 flesch = 41 summary = title: Pandemic Influenza Virus 2009 H1N1 and Adenovirus in a High Risk Population of Young Adults: Epidemiology, Comparison of Clinical Presentations, and Coinfection While coinfections with viral pathogens including 2009 H1N1 have been described in patients with respiratory infections, few prospective studies have related these to clinical presentation and outcomes in adults since molecular diagnostics became available, and none in the setting of high background rates of adenovirus. [12] [13] [14] [15] [16] [17] We sought to describe the epidemiology of 2009 H1N1 and adenovirus in a basic training population, and to correlate differences in clinical presentations and outcomes with each respective pathogen and in coinfections. Subject enrollment was variable throughout the study period, depending on rates of clinical illness within the training population, as well as availability of study personnel to enroll trainees, and given that 2009 H1N1 influenza virus PCR was done as part of clinical care, there could have been some differences in those who enrolled vs. cache = ./cache/cord-001162-z8cbbit3.txt txt = ./txt/cord-001162-z8cbbit3.txt === reduce.pl bib === id = cord-001145-hc9ssruz author = Akazawa, Yuko title = Endoplasmic Reticulum Stress Contributes to Helicobacter Pylori VacA-Induced Apoptosis date = 2013-12-13 pages = extension = .txt mime = text/plain words = 6256 sentences = 407 flesch = 52 summary = We found that C/EBP homologous protein (CHOP), a key signaling protein of ER stress-induced apoptosis, was transcriptionally up-regulated following incubation of gastric epithelial cells with VacA. Phosphorylation of eukaryotic initiation factor 2 (eIF2)-alpha, which is known to occur downstream of the ER stress sensor PKR-like ER-localized eIF2-alpha kinase (PERK) and to regulate CHOP expression, was also observed following incubation with VacA in the presence of ammonium chloride. Further studies showed that silencing of the PERK gene with siRNA attenuated VacA-mediated phosphorylation of eIF2-alpha, CHOP induction, expression of BH3-only protein Bim and Bax activation, and cell death induced by VacA with ammonium chloride, indicating that ER stress may lead to mitochondrial dysfunction during VacA-induced toxicity. pylori-positive gastric mucosa, as well as transcriptional up-regulation of Bim in AZ-521 cells treated with VacA plus NH 4 Cl. Since knockdown of PERK decreased VacA-mediated Bim mRNA expression, activation of Bim likely occurred downstream of ER stress. cache = ./cache/cord-001145-hc9ssruz.txt txt = ./txt/cord-001145-hc9ssruz.txt === reduce.pl bib === id = cord-001368-ymp1pj3r author = Zhang, Chao title = Recombinant Scorpine Produced Using SUMO Fusion Partner in Escherichia coli Has the Activities against Clinically Isolated Bacteria and Inhibits the Plasmodium falciparum Parasitemia In Vitro date = 2014-07-28 pages = extension = .txt mime = text/plain words = 4430 sentences = 236 flesch = 50 summary = title: Recombinant Scorpine Produced Using SUMO Fusion Partner in Escherichia coli Has the Activities against Clinically Isolated Bacteria and Inhibits the Plasmodium falciparum Parasitemia In Vitro Scorpions are a rich source of antimicrobial peptides: (1) androctonin isolated from the hemolymph of Androctonus australis, shows marked sequence similarity to tachyplesins, polyphemusins and gomesin [3, 4] ; (2) hadrurin from the venom of Hadrurus aztecus, which is hemolytic [5] ; (3) opistoporin-1, which possesses hemolytic activity, and opistoporin-2, both from the venom of the South African scorpion Opistophtalmus carinatus [6] ; (4) scorpine, which is the subject of this study, arising from the venom of Pandinus imperator, was shown to have anti-bacterial and anti-plasmodial activity in vitro [7] , and has shown a potent toxic effect on sexual and asexual stages of Plasmodium berghei and Plasmodium falciparum, respectively, and also a strong inhibition of dengue 2 virus (DENV-2) infection [8] . cache = ./cache/cord-001368-ymp1pj3r.txt txt = ./txt/cord-001368-ymp1pj3r.txt === reduce.pl bib === id = cord-001126-uqr00nzd author = Zhang, Zhicheng title = Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1 date = 2013-11-26 pages = extension = .txt mime = text/plain words = 4902 sentences = 226 flesch = 45 summary = In addition, hierarchical cluster analysis of 41 TTSuV2 isolates based on relative synonymous codon usage (RSCU) values suggested that there was no association between geographic distribution and codon bias of TTSuV2 sequences. To explore whether the evolution of codon usage bias in TTSuV2 CDS had been driven by mutation pressure alone or whether translation selection from its host has also contributed, we first compared the correlation between general nucleotide composition (A%, T%, G%, C%, GC%) and nucleotide composition at the third codon position (A 3S %, T 3S %, G 3S %, C 3S %, GC 3S %) using the Spearman's rank correlation analysis method (Table 4) . These results further support the conclusion that composition constraints under mutational bias is an important factor determining synonymous codon usage pattern in TTSuV2, and but that other factors, such as natural selection, contributed. cache = ./cache/cord-001126-uqr00nzd.txt txt = ./txt/cord-001126-uqr00nzd.txt === reduce.pl bib === id = cord-001254-y2knt8g0 author = Parkhomenko, Taisiya A. title = Comparison of DNA-Hydrolyzing Antibodies from the Cerebrospinal Fluid and Serum of Patients with Multiple Sclerosis date = 2014-04-15 pages = extension = .txt mime = text/plain words = 6739 sentences = 325 flesch = 50 summary = Here we have shown, for the first time, that average concentration of total proteins (132-fold), total IgGs (194-fold) and anti-DNA antibodies (200-fold) in the sera is significantly higher than that in the cerebrospinal fluid (CSF) of fifteen MS patients. We present first evidence showing that IgGs from CSF not only bind but efficiently hydrolyze DNA and that average specific DNase activity of homogeneous antibodies from CSF is unpredictably ∼49-fold higher than that from the sera of the same MS patients. Finally, the relative concentration of total anti-DNA Abs correlated with the relative specific IgG DNase activity better in the sera (CC = +0.51; columns 6 and 12) than in CSF (CC = + 0.11; columns 5 and 11) (Tables 2 and 3 ). cache = ./cache/cord-001254-y2knt8g0.txt txt = ./txt/cord-001254-y2knt8g0.txt === reduce.pl bib === id = cord-001142-puj74k7y author = Crescenzo-Chaigne, Bernadette title = The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date = 2013-11-21 pages = extension = .txt mime = text/plain words = 3355 sentences = 183 flesch = 55 summary = To investigate whether, or not, and how the complete NC regions of a given segment are involved in type specificity, we attempted to rescue, by reverse genetics, type A and C influenza viruses with chimeric non-coding sequences. The sole difference between 5'A/3'C(C5U) and wild-type 5'A/3'A viruses being the 3' distal extremity of the NS segment suggested that the level of NS encoded proteins (i.e. NS1 or/and NS2/NEP) was affected at early stages of infection for this virus (5'A/3'C(C5U)). The major role of the proximal panhandle in type specificity that we identified and the hypothesized involvement of the distal panhandle in transcription need to be tested on the other (2 PFU/cell), viral vRNA and mRNA levels for each segment were evaluated by specific two-step RT-qPCRs previously described [23] . cache = ./cache/cord-001142-puj74k7y.txt txt = ./txt/cord-001142-puj74k7y.txt === reduce.pl bib === id = cord-001219-517gka4h author = Timpka, Toomas title = Intentions to Perform Non-Pharmaceutical Protective Behaviors during Influenza Outbreaks in Sweden: A Cross-Sectional Study following a Mass Vaccination Campaign date = 2014-03-07 pages = extension = .txt mime = text/plain words = 5805 sentences = 247 flesch = 37 summary = We administered a cross-sectional telephone survey to a representative sample (n = 443) of the Swedish adult population to examine whether self-reported intentions to improve personal hygiene and increase social distancing during influenza outbreaks could be explained by trust in official information, self-reported health (SF-8), sociodemographic factors, and determinants postulated in protection motivation theory, namely threat appraisal and coping appraisal. A hypothetical explanatory model was constructed to inform the analysis of the main research question; i.e. to what extent selfreported intentions to perform protective behaviors during influenza outbreaks can be explained by perceptions of threat and the ability to cope as outlined in the PMT, self-assessments of health status, trust in official information, and sociodemiographic factors. cache = ./cache/cord-001219-517gka4h.txt txt = ./txt/cord-001219-517gka4h.txt === reduce.pl bib === id = cord-001280-skavefji author = Choi, Sang-Ho title = Usefulness of Cellular Analysis of Bronchoalveolar Lavage Fluid for Predicting the Etiology of Pneumonia in Critically Ill Patients date = 2014-05-13 pages = extension = .txt mime = text/plain words = 4136 sentences = 204 flesch = 35 summary = This study investigated the ability of cellular analysis of BAL fluid to differentially diagnose bacterial pneumonia from viral pneumonia in adult patients who are admitted to intensive care unit. Exclusion criteria were as follows: (1) patients in whom the pathogen was not identified, (2) patients in whom BAL fluid analysis was impossible (due to severe neutropenia or clotting of specimen) or not performed, (3) patients with a mixed infection (identification of bacteria and virus), (4) patients who were treated with antimicrobial agents for more than 24 hours before bronchoscopic BAL, (5) patients with invasive pulmonary aspergillosis, (6) patients with mycobacterial infection, and (7) patients with Pneumocystis jirovecii pneumonia. Several authors of the current study previously investigated the diagnostic utility of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) in BAL fluid of various patient populations with bilateral lung infiltrates. cache = ./cache/cord-001280-skavefji.txt txt = ./txt/cord-001280-skavefji.txt === reduce.pl bib === id = cord-001359-c1uom5f7 author = Oslund, Karen L. title = Synergistic Up-Regulation of CXCL10 by Virus and IFN γ in Human Airway Epithelial Cells date = 2014-07-17 pages = extension = .txt mime = text/plain words = 4567 sentences = 290 flesch = 53 summary = In this study, we demonstrate the synergistic stimulation of CXCL10 mRNA and protein, a key chemokine responsible for the early immune response to viral infection, following treatment of airway epithelial cells with IFN γ and influenza virus. Therefore, we conclude that IFN γ and dsRNA act in concert to potentiate CXCL10 expression in airway epithelial cells via an NFκB-dependent but IFNAR-STAT independent pathway and it is at least partly regulated at the transcriptional level. In this study, we demonstrate synergistic induction of CXCL10 in well differentiated primary human bronchial epithelial (HBE) cells following influenza virus infection and the treatment with IFN c. As shown in Fig. 1A , well differentiated HBE cells demonstrated significant synergistic induction of CXCL10 mRNA following infection with the MEM influenza virus and treatment with IFN c. These results demonstrate that influenza virus in combination with IFN c synergistically induce CXCL10 mRNA and protein production from primary human airway epithelial cells. cache = ./cache/cord-001359-c1uom5f7.txt txt = ./txt/cord-001359-c1uom5f7.txt === reduce.pl bib === id = cord-001249-awn9ayy6 author = Lasecka, Lidia title = The Nairovirus Nairobi Sheep Disease Virus/Ganjam Virus Induces the Translocation of Protein Disulphide Isomerase-Like Oxidoreductases from the Endoplasmic Reticulum to the Cell Surface and the Extracellular Space date = 2014-04-08 pages = extension = .txt mime = text/plain words = 9953 sentences = 453 flesch = 50 summary = ERp57 while the structure of the ER, ERGIC and Golgi remains unchanged Two isolates of NSDV have been previously described by us [29] : a multiple-times passaged isolate of NSDV from Uganda, which appeared attenuated upon infection of a susceptible animal, and an isolate of GV from India which had been passaged a limited number of times in mouse brain or BHK21 clone 13 cells and which caused haemorrhagic gastroenteritis in sheep upon experimental inoculation. No change to the cellular distribution of calnexin was observed (Figure 2 j-l), indicating that, despite the disappearance of PDI and ERp57, the overall structure of the ER remains unchanged in NSDV-infected cells. Another flavivirus, Dengue virus (DENV) (which, like NSDV, can cause a haemorrhagic fever), increased surface levels of PDI in infected endothelial cells [86] . In this study we have demonstrated that NSDV induces the redistribution of soluble ER oxidoreductases, specifically PDI and ERp57, in infected cells, and that the viral PreGn glycoprotein appears to be involved in this process. cache = ./cache/cord-001249-awn9ayy6.txt txt = ./txt/cord-001249-awn9ayy6.txt === reduce.pl bib === id = cord-001275-a9o2dvke author = Chen, Xue title = A Vaccine of L2 Epitope Repeats Fused with a Modified IgG1 Fc Induced Cross-Neutralizing Antibodies and Protective Immunity against Divergent Human Papillomavirus Types date = 2014-05-06 pages = extension = .txt mime = text/plain words = 5558 sentences = 254 flesch = 47 summary = title: A Vaccine of L2 Epitope Repeats Fused with a Modified IgG1 Fc Induced Cross-Neutralizing Antibodies and Protective Immunity against Divergent Human Papillomavirus Types Current human papillomavirus (HPV) major capsid protein L1 virus-like particles (VLPs)-based vaccines in clinic induce strong HPV type-specific neutralizing antibody responses. To develop pan-HPV vaccines, here, we show that the fusion protein E3R4 consisting of three repeats of HPV16 L2 aa 17–36 epitope (E3) and a modified human IgG1 Fc scaffold (R4) induces cross-neutralizing antibodies and protective immunity against divergent HPV types. In this study, we showed for the first time that fusing HPV16 L2 aa 17-36 epitope repeats to a recombinant ligand for FccRs (designated L2R4, see Figure 1A -B) could significantly increase the immunogenicity of the L2 peptide and induce cross-neutralizing antibodies and protective immunity against a range of phylogenetically distant HPV types. cache = ./cache/cord-001275-a9o2dvke.txt txt = ./txt/cord-001275-a9o2dvke.txt === reduce.pl bib === id = cord-001432-d4zavkcn author = Nishida, Yoriko title = Antibody-Validated Proteins in Inflamed Islets of Fulminant Type 1 Diabetes Profiled by Laser-Capture Microdissection Followed by Mass Spectrometry date = 2014-10-16 pages = extension = .txt mime = text/plain words = 5268 sentences = 306 flesch = 48 summary = PROCEDURES: Proteins expressed in the islets of enterovirus-associated fulminant type 1 diabetes (FT1DM) with extensive insulitis were identified by laser-capture microdissection mass spectrometry using formalin-fixed paraffin-embedded pancreatic tissues. Migratory activity-related proteins, including plastin-2 (LCP1), moesin (MSN), lamin-B1 (LMNB1), Ras GTPase-activating-like protein (IQGAP1) and others, were identified in CD8(+) T cells and CD68(+) macrophages infiltrated to inflamed FT1DM islets. Proteins involved in successive signaling in innate/adaptive immunity were identified, including SAM domain and HD domain-containing protein 1 (SAMHD1), Ras GTPase-activating-like protein (IQGAP1), proteasome activator complex subunit 1 (PSME1), HLA class I histocompatibility antigen (HLA-C), and signal transducer and activator of transcription 1-alpha/beta (STAT1). Actin-related protein 3 (ACTR3) was over-expressed in the cytoplasm and nucleus of MNCs infiltrated to the islets in FT1DM-affected pancreas tissue. Signal transducer and activator of transcription 1-alpha/beta (STAT1) was highly expressed in islet endocrine cells and MNCs in FT1DM tissue ( Figure 2Q, R) . cache = ./cache/cord-001432-d4zavkcn.txt txt = ./txt/cord-001432-d4zavkcn.txt === reduce.pl bib === id = cord-001421-6t5puo6p author = Marfà, Santiago title = Lack of a 5.9 kDa Peptide C-Terminal Fragment of Fibrinogen α Chain Precedes Fibrosis Progression in Patients with Liver Disease date = 2014-10-02 pages = extension = .txt mime = text/plain words = 5057 sentences = 229 flesch = 46 summary = The serum proteomic profile and routine liver and renal function tests were initially analyzed in a training set of 10 HCV-RNA recurrent LT patients 6 months post LT that showed a fibrosis stage F$1 at 1 year after LT. HVPG was assessed in 53 of these patients and the average value was of 5.560.8 mm Hg. All the serum samples showed a quite similar expression pattern and coincidences included both the different peptide fragments detected and the signal intensity of these fragments (Data S4). All serum samples included in the test set showed an intensity m/z 5905 peak well below the values found in both healthy subjects and non recurrent HCV patients. In conclusion, we identified a 5.9 kDa C-terminal fragment of the fibrinogen a chain as a serum biomarker of early fibrogenic processes in patients with liver disease. In conclusion, we identified a 5.9 kDa C-terminal fragment of the fibrinogen a chain as a serum biomarker of early fibrogenic processes in patients with liver disease. cache = ./cache/cord-001421-6t5puo6p.txt txt = ./txt/cord-001421-6t5puo6p.txt === reduce.pl bib === id = cord-001387-2g9dc5z4 author = McIntyre, K. Marie title = A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe date = 2014-08-19 pages = extension = .txt mime = text/plain words = 4582 sentences = 215 flesch = 40 summary = By coupling the H-index method with the EID2, the primary aim of this study was to establish priority lists of human and domestic animal pathogens (including zoonoses) present in Europe. Its potential as a quantitative One Health indicator (i.e. a single measure applicable to both human and animal diseases) was investigated by comparing scores for human-only, zoonotic, and animal-only pathogen groups, including emerging status as this would likely drive research impact. We investigated its value as a proxy for animal disease impact by comparing domestic animal pathogen H-indices with other measures of impact including presence on the OIE list [10] , and inclusion in DISCONTOOLS [11] . The study establishes priority lists of human and domestic animal pathogens (including zoonoses) present in Europe, using the H-index as a proxy measure for impact. cache = ./cache/cord-001387-2g9dc5z4.txt txt = ./txt/cord-001387-2g9dc5z4.txt === reduce.pl bib === id = cord-001537-i34vmfpp author = Lima, Francisco Esmaile de Sales title = Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil date = 2015-02-17 pages = extension = .txt mime = text/plain words = 3874 sentences = 195 flesch = 53 summary = The predicted protein sequences encoded by ORF2 (cap) and ORF1 (rep) of BatCV I-VI genomes were used for phylogenetic analysis with representative and recently discovered circoviruses/cycloviruses; Pepper golden mosaic virus was used as outgroup, as they are somewhat related to other members in the Circoviridae family (Fig. 3A, 3B and 3C ). The phylogenetic analysis constructed based on the alignments of the complete REP and CAP protein confirms that BatCV POA/II and VI cluster into the genus Cyclovirus along with the Chinese cycloviruses sequences clade detected in bat feces [18] and sharing less than 65% of identity at the CAP/REP amino acid level. BatCV POA I and V had a low amino acid identity with CAP (<20%) and REP (<10%) sequences of two other sequences detected in bat feces in this study with known circoviruses/cycloviruses (Table 2) . cache = ./cache/cord-001537-i34vmfpp.txt txt = ./txt/cord-001537-i34vmfpp.txt === reduce.pl bib === id = cord-001435-ebl8yc92 author = Hoppe, Sebastian title = Identification of Antigenic Proteins of the Nosocomial Pathogen Klebsiella pneumoniae date = 2014-10-21 pages = extension = .txt mime = text/plain words = 9619 sentences = 545 flesch = 50 summary = Hence, a cDNA-based expression library was constructed and screened via microarrays to detect novel antigens of Klebsiella pneumoniae, a prominent agent of nosocomial infections well-known for its extensive antibiotics resistance, especially by extended-spectrum beta-lactamases (ESBL). After specificity analysis, homology survey and 3d structural modelling, one epitope sequence GAVVALSTTFA of KPN_00363, an ion channel protein, was identified harboring specificity for K. By identifying several novel antigens and their linear epitope sites, we have paved the way for crucial future research and applications including the design of point-of-care devices, vaccine development and serological screenings for a highly relevant nosocomial pathogen. Incubation with antibodies reactive to either of those two bacterial species resulted in signal intensities in the neighbourhood of the negative control independent of sequence alterations, see Figure 11 . In contrast, the other two proteins displaying linear epitopes, KPN_00363 and KPN_00459, indicated some specificity with the antibodies tested and two linear consensus sequences could be derived, GAVVALSTTFA and GIAFGAVELFD, respectively. cache = ./cache/cord-001435-ebl8yc92.txt txt = ./txt/cord-001435-ebl8yc92.txt === reduce.pl bib === id = cord-001420-b4zcvd04 author = Crescenzo-Chaigne, Bernadette title = Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date = 2014-09-30 pages = extension = .txt mime = text/plain words = 6267 sentences = 296 flesch = 56 summary = Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. The sequence of both ends of each segment of each rescued virus was verified as described [9] , and no Influenza NP Non Coding Region Role in Translation PLOS ONE | www.plosone.org genetics, type A and type C viruses with one or both heterotypic ends. These data based on type A influenza virus NP segment showed that it is possible to obtain virus by reverse genetics when a homotypic proximal panhandle and a homotypic strength of the initial distal panhandle are maintained, and that the length of the 59 end plays an important role in the efficiency of rescue. cache = ./cache/cord-001420-b4zcvd04.txt txt = ./txt/cord-001420-b4zcvd04.txt === reduce.pl bib === id = cord-001455-n7quwr4s author = Rapin, Noreen title = Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans date = 2014-11-12 pages = extension = .txt mime = text/plain words = 3719 sentences = 198 flesch = 50 summary = title: Activation of Innate Immune-Response Genes in Little Brown Bats (Myotis lucifugus) Infected with the Fungus Pseudogymnoascus destructans Using tissue samples collected at the termination of an experiment to explore the pathogenesis of White Nose Syndrome in Little Brown Bats, we determined if hibernating bats infected with the fungus Pseudogymnoascus destructans could respond to infection by activating genes responsible for innate immune and stress responses. We found that bats responded to infection with a significant increase in lungs of transcripts for Cathelicidin (an anti-microbial peptide) as well as the immune modulators tumor necrosis factor alpha and interleukins 10 and 23. We used samples collected during the experiment to address the question: Can hibernating bats respond to infection by activating genes responsible for innate immune and stress responses? We determined levels of transcripts for several immune and stress response genes (Table 1) in lungs from infected and control bats. cache = ./cache/cord-001455-n7quwr4s.txt txt = ./txt/cord-001455-n7quwr4s.txt === reduce.pl bib === id = cord-001599-pfdnmzx2 author = Wee, Yin Shen title = Age-Related Onset of Obesity Corresponds with Metabolic Dysregulation and Altered Microglia Morphology in Mice Deficient for Ifitm Proteins date = 2015-04-09 pages = extension = .txt mime = text/plain words = 6017 sentences = 327 flesch = 45 summary = Analysis of the gene expression profiles in the hypothalamus of IfitmDel animals, compared to WT, demonstrated an altered ratio of Pomc and Npy neuropeptide expression, which likely impairs the satiation response of the IfitmDel animal leading to an increased eating behavior. As we maintain these animals as homozygous deletion lines, over time we have observed a pronounced enhanced weight gain and an obesity phenotype (e.g., [21] [22] [23] ) in older IfitmDel mice compared to C57BL/6 controls. In this report we quantify the obesity phenotype and link this to altered leptin/neuropeptide signaling, and demonstrate abnormal microglia morphology in the IfitmDel animal. Based upon the previously described findings that the absence of the Ifitm proteins can alter cellular induction pathways following type I interferon treatment, we tested whether or not the IfitmDel animals would have an altered response, compared to WT, to chronic Poly I:C treatment. cache = ./cache/cord-001599-pfdnmzx2.txt txt = ./txt/cord-001599-pfdnmzx2.txt === reduce.pl bib === id = cord-001263-hqxiyxfj author = Kam, Yiu-Wing title = Unique Epitopes Recognized by Antibodies Induced in Chikungunya Virus-Infected Non-Human Primates: Implications for the Study of Immunopathology and Vaccine Development date = 2014-04-22 pages = extension = .txt mime = text/plain words = 5676 sentences = 282 flesch = 46 summary = title: Unique Epitopes Recognized by Antibodies Induced in Chikungunya Virus-Infected Non-Human Primates: Implications for the Study of Immunopathology and Vaccine Development In addition to the anti-E2 glycoprotein responses, we also identified new linear B-cell epitopes that were recognized by anti-CHIKV antibodies from CHIKV-infected macaques. Results showed two structural proteins (Capsid protein and E2 glycoprotein) and three nonstructural proteins (nsP1, nsP3 and nsP4 proteins) contained linear epitopes that were recognized by macaque anti-CHIKV antibodies. Here, E2EP3 is one of the major B-cell linear epitopes recognized by antibodies from the sera of all CHIKV-infected macaques during the early phase of disease (amino acids 2800-2818, Table 1 ). Infection of macaques with the LR2006-OPY1 isolate, which encodes K 252 in the E2 glycoprotein, strongly induced anti-CHIKV antibodies against a particular linear B-cell epitope (amino acids 3025-3066) at 16 dpi. cache = ./cache/cord-001263-hqxiyxfj.txt txt = ./txt/cord-001263-hqxiyxfj.txt === reduce.pl bib === id = cord-001343-3euy4u9k author = Wang, Yadong title = A Multi-Method Approach to Curriculum Development for In-Service Training in China’s Newly Established Health Emergency Response Offices date = 2014-06-27 pages = extension = .txt mime = text/plain words = 4088 sentences = 161 flesch = 40 summary = In recognition of the national need for an in-service program to target the''level four'' health staff as defined by WADEM, i.e.'h ealth workers who played lead roles in disaster health management'' [20] , China's Ministry of Health (MoH) commissioned the Capital Medical University in 2010 to develop and implement a competency-based curriculum to help strengthen the performance of the new cadre of HERO staff. We assessed tasks, roles and responsibilities, and training needs of HERO staff through face-to-face interviews of eleven experienced key informants; they included health emergency experts from the government, the military and the academic sector, and senior staff of HEROs. We also explored their awareness of existing training activities and the associated relative strengths and weaknesses, their preferences on modes of curriculum delivery and the optimal duration of in-service training. cache = ./cache/cord-001343-3euy4u9k.txt txt = ./txt/cord-001343-3euy4u9k.txt === reduce.pl bib === id = cord-001446-mpuovmeb author = Bratcher, Preston E. title = Factors Influencing the Measurement of Plasma/Serum Surfactant Protein D Levels by ELISA date = 2014-11-03 pages = extension = .txt mime = text/plain words = 4873 sentences = 226 flesch = 43 summary = Circulating levels of SP-D have been examined for their potential use as a biomarker in various diseases including dermatitis [2, 3] , acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] , periodontitis [14] , interstitial pulmonary fibrosis (IPF) [10, 12, [15] [16] [17] [18] [19] [20] [21] [22] [23] , chronic obstructive pulmonary disease (COPD) [15, [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] , emphysema [37] , cystic fibrosis (CF) [15, 38, 39] , coronary disease [40, 41] , sclerosis [42] [43] [44] [45] [46] , cancer [47, 48] , sarcoidosis [21, 49] , allergies [28, [50] [51] [52] , rheumatoid arthritis [53, 54] , and respiratory infections [18, [55] [56] [57] [58] [59] [60] . Serum levels of surfactant proteins A and D are useful biomarkers for interstitial lung disease in patients with progressive systemic sclerosis cache = ./cache/cord-001446-mpuovmeb.txt txt = ./txt/cord-001446-mpuovmeb.txt === reduce.pl bib === id = cord-001571-drcfdv9z author = Alvarez, Julio title = Impact of Porcine Epidemic Diarrhea on Performance of Growing Pigs date = 2015-03-13 pages = extension = .txt mime = text/plain words = 3100 sentences = 133 flesch = 60 summary = Here, a retrospective cohort study to evaluate the impact of porcine epidemic diarrhea virus (PEDv) infection on growing pigs' performance, as indicated by mortality, average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) was performed using production records from weaned pigs in nursery and wean-to-finish sites from sow farms that became PEDv-infected between May 2013 and June 2014. Collected data included information on the site in which pigs were located, site production type (nursery or wean to finish (WF)), pig source (sow farm from which pigs originated), start and close period on each site, number of pigs per batch, mortality (defined by percentage of total pigs started), average daily gain (ADG), average daily feed intake (ADFI), feed conversion (FCR), and status of the sow farm from which pigs were weaned for PRRS and PED. cache = ./cache/cord-001571-drcfdv9z.txt txt = ./txt/cord-001571-drcfdv9z.txt === reduce.pl bib === id = cord-001363-irysq6pf author = Liu, Zhenjiang title = SELDI-TOF-MS Proteomic Profiling of Serum, Urine, and Amniotic Fluid in Neural Tube Defects date = 2014-07-23 pages = extension = .txt mime = text/plain words = 5113 sentences = 271 flesch = 49 summary = Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is a breakthrough in clinical proteomics, and can detect different protein expression patterns of body fluid and tissue specimens between patients and healthy subjects, and its rapid development provides an alternative tool to search for biomarkers. The purpose of this pilot study was to preliminarily explore the differential protein expression pattern between NTD case mothers and normal control mothers using SELDI-TOF-MS protein profiling and Classification and Regression Tree (CART) analysis, in order to differentiate pregnancies complicated by the presence of an NTD-affected fetus from healthy controls. Analysis of amniotic fluid samples from mothers of NTDaffected fetuses and normal control mothers revealed two major, differentially expressed proteins at 14700 and 13776 Da used in the classification pattern to generate 3 terminal nodes (Fig. 7) . However, when we analyzed the data, we found that only four protein/peptide biomarkers, 4188, 6451, 11744 and 23425 Da, were detected in all serum, urine and amniotic fluid samples. cache = ./cache/cord-001363-irysq6pf.txt txt = ./txt/cord-001363-irysq6pf.txt === reduce.pl bib === id = cord-001447-oi7bkm4z author = Dhanasekaran, Sakthivel title = Toll-Like Receptor Responses to Peste des petits ruminants Virus in Goats and Water Buffalo date = 2014-11-04 pages = extension = .txt mime = text/plain words = 6012 sentences = 318 flesch = 51 summary = We examined the replication of PPRV in peripheral blood mononuclear cells (PBMC) of Indian domestic goats and water buffalo and demonstrated that the levels of TLR3 and TLR7 and downstream signalling molecules correlation with susceptibility vs resistance. Upon stimulation of PBMC with synthetic TLR3 and TLR7 agonists or PPRV, the levels of proinflammatory cytokines were found to be significantly higher while immunosuppressive interleukin (IL) 10 levels were lower in PPRV resistant Kanni and Salem Black breeds and water buffalo at transcriptional level, correlating with reduced viralloads in infected PBMC. Infection of peripheral blood mononuclear cells (PBMC) from four breeds of goats and water buffalo resulted in differential viral replication kinetics and inflammatory cytokine profile including IFNa, IFNc and TNFa with differential activation of TLR3 and TLR7. To determine whether the differential IFN and pro-inflammatory cytokine production between Kanni/Salem vs Barbari/ Tellicherry breeds of goats are dependent on single nucleotide polymorphisms (SNPs) in TLR genes, we examined the complete gene sequence of TLR7. cache = ./cache/cord-001447-oi7bkm4z.txt txt = ./txt/cord-001447-oi7bkm4z.txt === reduce.pl bib === id = cord-001546-ndz3oarf author = Ayithan, Natarajan title = Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date = 2015-02-26 pages = extension = .txt mime = text/plain words = 5128 sentences = 298 flesch = 52 summary = Importantly, proinflammatory cytokine/chemokine expression was much higher in WT mice without VLPs than mice treated with VLPs. In EBOV infected Ifnar(-/-) mice, however, uninhibited viral replication and elevated proinflammatory factor expression ensued, irrespective of VLP treatment, supporting the view that type I IFN signaling helps to limit viral replication and attenuate inflammatory responses. Further analyses showed that VLP protection requires the transcription factor, IRF8 known to amplify type I IFN signaling in dendritic cells and macrophages, the probable sites of initial EBOV infection. The aim of this study was to further investigate molecular bases of postexposure protection by VLPs. Based on our previous report that VLPs stimulate type I IFN expression in DCs and macrophages, in vitro, we focused on the role of type I IFN signaling, and found that post-exposure VLP treatment leads to accelerated activation of IFN signaling, resulting in early induction of ISGs. Significantly, VLP stimulated ISG induction coincided with the attenuation of proinflammatory cytokine surge in EBOV infected mice. cache = ./cache/cord-001546-ndz3oarf.txt txt = ./txt/cord-001546-ndz3oarf.txt === reduce.pl bib === id = cord-001734-bbeznd3r author = Gupta, Garvita title = NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics date = 2015-08-10 pages = extension = .txt mime = text/plain words = 9729 sentences = 418 flesch = 53 summary = Taken together, CD and NMR results define the 172-residue NS3pro domain to be an intrinsically disordered protein which is lacking of both stable secondary and tertiary structures in the absence of the NS2B cofactor [22, [31] [32] [33] [34] [35] [36] . On the other hand, only a small set of broad peaks could be detected in its HSQC spectrum (Fig 4B) , indicating that the NS3B (1-130) in the LMPC micelle undergoes significant conformational exchanges on μs-ms time scale, or/and dynamic aggregation, which thus prevents from further high-resolution NMR studies. Interestingly, although NMR characterization deciphers that the NS3pro domains have different dynamics on the μs-ms time scale in the contexts of being complexed with NS (48-100) in buffer and with NS2B (1-130) in the LMPC micelle, they have very similar enzymatic activities. cache = ./cache/cord-001734-bbeznd3r.txt txt = ./txt/cord-001734-bbeznd3r.txt === reduce.pl bib === id = cord-001605-8p06bpt1 author = Sapmak, Ariya title = The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei date = 2015-04-13 pages = extension = .txt mime = text/plain words = 5165 sentences = 308 flesch = 53 summary = title: The pbrB Gene Encodes a Laccase Required for DHN-Melanin Synthesis in Conidia of Talaromyces (Penicillium) marneffei marneffei genome encodes a number of laccases and this study describes the characterization of one of these, pbrB, during growth and development. The pbrB gene is required for the synthesis of DHN-melanin in conidia and when deleted results in brown pigmented conidia, in contrast to the green conidia of the wild type. marneffei MCO participates in conidial DHN-melanin synthesis, we combined 55 fungal MCO sequences and performed alignments using CLUSTALW (http://www.genome.jp/ tools/clustalw/). marneffei PbrB, this clade comprises of characterized laccases functioning in conidial DHN-melanin synthesis. Talaromyces (Penicillium) marneffei pbrB Gene Cytoplasmic protein extracts from the wild type and ΔpbrB mutant cultured in brain heart infusion broth at 37°C for 3 days were capable of catalyzing L-DOPA (data not shown). cache = ./cache/cord-001605-8p06bpt1.txt txt = ./txt/cord-001605-8p06bpt1.txt === reduce.pl bib === id = cord-001781-afg1nmib author = Saksena, Sumeet title = Evidence for the Convergence Model: The Emergence of Highly Pathogenic Avian Influenza (H5N1) in Viet Nam date = 2015-09-23 pages = extension = .txt mime = text/plain words = 7626 sentences = 395 flesch = 49 summary = We developed and tested a model of the emergence of highly pathogenic avian influenza (HPAI) H5N1 based on suspected convergence factors that are mainly associated with land-use change. The results presented here highlight three main findings: 1) when relevant risk factors are taken into account, urbanization is generally not a significant independent risk factor; but in peri-urban landscapes emergence factors converge, including higher levels of chicken densities, duck and geese flock size diversities, and fraction of land under rice or aquaculture; 2) high land-use diversity landscapes, a variable not previously considered in spatial studies of HPAI H5N1, are at significantly greater risk for HPAI H5N1 outbreaks; as are 3) landscapes where intensive and extensive forms of poultry production are co-located. Hence diseases associated with rice production are likely to peak in peri-urban areas given other risk factors such as land-use diversity, CTI, and distance to infrastructure. cache = ./cache/cord-001781-afg1nmib.txt txt = ./txt/cord-001781-afg1nmib.txt === reduce.pl bib === id = cord-001748-7e8px4vx author = Nobach, Daniel title = Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date = 2015-08-27 pages = extension = .txt mime = text/plain words = 4873 sentences = 249 flesch = 47 summary = The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). In animals caught in 2013 (group 1: female #2, male #5, female #6), after an adaption phase of one month, samples of saliva, lacrimal fluid, skin surface, urine and excrements from the BoDV-1-infected shrews were taken weekly over a period of 4 weeks as necessary veterinary care. The five other shrews did not exhibit any evidence for BoDV-1-infection, neither infectious virus nor viral RNA was detected at any time point investigated. Current data from living shrews provide reliable evidence that natural BoDV-1-infection in these animals is indeed clinically inconspicuous over a long time period as already previously assumed [15, 18] despite persistent infection with shedding of infectious virus via various sites. Distribution of Borna Disease Virus Antigen and RNA in Tissues of naturally infected Bicolored White-Toothed Shrews, Crocidura leucodon, supporting their role as Reservoir Host Species cache = ./cache/cord-001748-7e8px4vx.txt txt = ./txt/cord-001748-7e8px4vx.txt === reduce.pl bib === id = cord-001958-2gt3fwpy author = Meseda, Clement A. title = Percutaneous Vaccination as an Effective Method of Delivery of MVA and MVA-Vectored Vaccines date = 2016-02-19 pages = extension = .txt mime = text/plain words = 8161 sentences = 361 flesch = 43 summary = Our data suggest that MVA administered by percutaneous inoculation, elicited vaccinia-specific antibody responses, and protected mice from lethal vaccinia virus challenge, at levels comparable to or better than subcutaneous or intramuscular inoculation. In the work described here, we demonstrate in mouse models that percutaneous inoculation of MVA elicited protective immune responses against lethal intranasal challenge with the Western Reserve (WR) strain of vaccinia virus, and at low doses of MVA, lower morbidity was recorded in mice that were vaccinated via the percutaneous route than in those immunized via the intramuscular or subcutaneous routes. In a preliminary experiment to investigate the utility of the percutaneous route for the delivery of MVA, we observed that MVA delivered by tail scarification, while statistically insignificant (p = 0.298), elicited a higher vaccinia-specific IgG response and protection in mice than the same dose (10 6 pfu) delivered by the intramuscular route (S1 Fig) . cache = ./cache/cord-001958-2gt3fwpy.txt txt = ./txt/cord-001958-2gt3fwpy.txt === reduce.pl bib === id = cord-001601-tsuz3j40 author = Ngan, Luong Thi My title = Antiviral Activity and Possible Mechanism of Action of Constituents Identified in Paeonia lactiflora Root toward Human Rhinoviruses date = 2015-04-10 pages = extension = .txt mime = text/plain words = 6157 sentences = 328 flesch = 53 summary = An assessment was made of the antiviral activities and mechanisms of action of paeonol (PA) and 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose (PGG) from Paeonia lactiflora root toward HRV-2 and HRV-4 in MRC5 cells using a tetrazolium method and real-time quantitative reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. These findings suggest that PGG and PA may block or reduce the entry of the viruses into the cells to protect the cells from the virus destruction and abate virus replication, which may play an important role in interfering with expressions of rhinovirus receptors (intercellular adhesion molecule-1 and low-density lipoprotein receptor), inflammatory cytokines (interleukin (IL)-6, IL-8, tumor necrosis factor, interferon beta, and IL-1β), and Toll-like receptor, which resulted in diminishing symptoms induced by HRV. In the presence of 100 μg/mL PA or 20 μg/mL PGG in MRC5 cell cultures infected with HRV-2, the RNA replication levels were reduced by 30.1 and 14.3 fold, respectively, compared to the levels in the cell cultures without the compounds (Fig 4A) . cache = ./cache/cord-001601-tsuz3j40.txt txt = ./txt/cord-001601-tsuz3j40.txt === reduce.pl bib === id = cord-001620-yy5gq0ki author = Woo, Hye-Min title = Isolation of Single-Stranded DNA Aptamers That Distinguish Influenza Virus Hemagglutinin Subtype H1 from H5 date = 2015-04-22 pages = extension = .txt mime = text/plain words = 3871 sentences = 213 flesch = 55 summary = These results indicate that the selected aptamers that distinguish H1-HA1 from H5-HA1 can be developed as unique probes for the detection of the H1 subtype of influenza virus. Subtype H5 is known as highly pathogenic in protein (GST-H5-HA1) was incubated with 100 μL of glutathione agarose beads in 100 μL of binding buffer (50 mM Tris/HCl; pH 8.0, 150 mM NaCl, 1.5 mM MgCl 2 , 2 mM DTT, and 1% [w/v] BSA) for 30 min at room temperature with occasional shaking. To select specific ssDNA aptamers that can distinguish H1-HA1 from H5-HA1, counter-SELEX was performed with an ssDNA library of 88-mers containing a randomized sequence region of 45 nucleotides in the center, followed by lambda exonuclease digestion, as shown in Fig 1A. To confirm that the selected aptamers were bound to the sialic acid-binding region of HA1, we performed a flow cytometry analysis (Fig 7) . cache = ./cache/cord-001620-yy5gq0ki.txt txt = ./txt/cord-001620-yy5gq0ki.txt === reduce.pl bib === id = cord-001383-hww0watl author = Li, Wenchao title = Self-Assembly and Release of Peste des Petits Ruminants Virus-Like Particles in an Insect Cell-Baculovirus System and Their Immunogenicity in Mice and Goats date = 2014-08-12 pages = extension = .txt mime = text/plain words = 6541 sentences = 291 flesch = 48 summary = title: Self-Assembly and Release of Peste des Petits Ruminants Virus-Like Particles in an Insect Cell-Baculovirus System and Their Immunogenicity in Mice and Goats For many viral diseases, vaccination with virus-like particles (VLPs) has shown considerable promise as a prophylactic approach; however, the processes of assembly and release of peste des petits ruminants virus (PPRV) VLPs are not well characterized, and their immunogenicity in the host is unknown. In this study, we found that the major structural genes of PPRV can be efficiently expressed in recombinant baculovirus-infected Sf21 insect cells and that these genes can then support the production of PPRV VLPs. The expression of M protein was necessary and sufficient for the formation of VLPs (data not shown); the additional expression of the H or F glycoproteins allowed formation of budding particles with the typical morphology and size of PPRV and related paramyxoviruses. cache = ./cache/cord-001383-hww0watl.txt txt = ./txt/cord-001383-hww0watl.txt === reduce.pl bib === === reduce.pl bib === id = cord-001716-lbtdex4p author = Gilca, Rodica title = Mid-Season Estimates of Influenza Vaccine Effectiveness against Influenza A(H3N2) Hospitalization in the Elderly in Quebec, Canada, January 2015 date = 2015-07-22 pages = extension = .txt mime = text/plain words = 4070 sentences = 189 flesch = 37 summary = Canada's Sentinel Physician Surveillance Network (SPSN) measured vaccine effectiveness (VE) against medically-attended laboratory-confirmed outpatient A(H3N2) illness of -8% (95%CI:-50-23%) overall and 2% (95%CI:-49-36%) in non-elderly (<65-year-old) adults, indicating little or no vaccine protection even among individuals capable of mounting an effective immune response [2] . Although Canadian mid-season inpatient and outpatient VE findings for the 2014/15 season have been consistent with null vaccine effects (statistically non-significant and spanning zero) in both age groups, the CIRN finding of a lower and negative point estimate of VE against A(H3N2) hospitalization in the elderly, more closely broaching statistical significance, warrants further clarification. Multivariable analyses by logistic regression adjusted for age, underlying comorbidity placing individuals at higher risk of influenza-related complications [13] , interval between symptom onset and specimen collection (4 days, 5-7 days), hospital site, epidemic week based on hospital admission date (49-51, 52, 53 and 1-2), and primary residence (community, LTCF or other institutional/group setting). cache = ./cache/cord-001716-lbtdex4p.txt txt = ./txt/cord-001716-lbtdex4p.txt === reduce.pl bib === id = cord-001964-iy6qzq58 author = Muñoz-González, Sara title = Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date = 2016-02-26 pages = extension = .txt mime = text/plain words = 6933 sentences = 319 flesch = 48 summary = The wild boars persistently infected with CSFV were protected from superinfection by the virulent CSFV Margarita strain, as evidenced by the absence of clinical signs and the absence of Margarita RNA detection in serum, swabs and tissue samples. Additionally, in PBMCs, a well-known target for CSFV viral replication, only the primary infecting virus RNA (Cat01 strain) could be detected, even after the isolation in ST cells, demonstrating SIE at the tissue level in vivo. Interestingly, the RNA of the vaccinal C-strain was undetectable by specific RT-PCR [8] in any of the samples analysed after vaccination, including blood, nasal and rectal swabs, or organs throughout the experiment, suggesting a phenomenon of homologous interference, also known as superinfection exclusion (SIE), between the high viral load generated by the primary persistent infection and the CSFV vaccine strain. cache = ./cache/cord-001964-iy6qzq58.txt txt = ./txt/cord-001964-iy6qzq58.txt === reduce.pl bib === id = cord-002141-9mxi4dzi author = Memczak, Henry title = Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding date = 2016-07-14 pages = extension = .txt mime = text/plain words = 8780 sentences = 476 flesch = 51 summary = title: Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding We used complementary experimental and theoretical approaches to select HA binding VH-CDR peptides and to improve their potential to inhibit binding, and finally, infection of cells by influenza A virus. Contribution to the total binding free energy change of every amino acid of PeB GF binding to HA of Aichi H3N2 obtained by MD-simulations is shown in Fig 2B. Our aim was to obtain peptide inhibitors that recognize the conserved region of the sialic acid binding pocket of HA with a broader specificity to cover several influenza virus strains. The three CDRs of the VH-chain of antibody HC19 against hemagglutinin of influenza virus Aichi H3N2 were used as templates to design peptides being a potential inhibitor of virus binding to host cells. As a consequence, the hemagglutination inhibition efficiency may not necessarily be stronger against Aichi H3N2, even though the peptide was derived from an antibody binding to this influenza strain. cache = ./cache/cord-002141-9mxi4dzi.txt txt = ./txt/cord-002141-9mxi4dzi.txt === reduce.pl bib === id = cord-001909-yy9xp5ms author = Buß, O. title = Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters date = 2016-01-05 pages = extension = .txt mime = text/plain words = 6998 sentences = 414 flesch = 49 summary = Two of the tested high throughput screening (HTS) assays depend on coupled enzymatic reactions which detect the alcohol released during ester hydrolysis by luminescence or absorption. The objective of this study is to select an HTS assay to screen for one enzyme for a two-step reaction cascade for the synthesis of β-amino acids. One assay relies on the change of the pH-value, the second is based on enzymatic oxidation of the released ethanol to acetic acid and the third, which we expected to be most sensitive, is based on the oxidation of ethanol to ethanal and hydrogen peroxide which is then converted by horseradish peroxidase (HRP) in a luminescence reaction. According to the other assays a positive control for the evaluation test contained only 2.0 mM ethanol without ester and hydrolase (see also subsection statistical analysis). cache = ./cache/cord-001909-yy9xp5ms.txt txt = ./txt/cord-001909-yy9xp5ms.txt === reduce.pl bib === id = cord-002044-9xgt3tf4 author = Hendiger, Jacek title = Influence of the Pressure Difference and Door Swing on Heavy Contaminants Migration between Rooms date = 2016-05-12 pages = extension = .txt mime = text/plain words = 4537 sentences = 238 flesch = 56 summary = This paper presents the results of investigations whose aim was to describe the influence of the pressure difference level on the ability of contaminants migration between neighbouring rooms in dynamic conditions associated with door swing. In health care facilities, this way of ventilation system operation is utilized in both the Airborne Infection Isolation and Protective Environment Rooms, however, the key difference is the required direction of airflow between the room and the adjacent space, such as a corridor, which determines the application of negative or positive pressure in the protected room, respectively. The research described in the available literature, concerning migration of air between rooms in the conditions of pressure difference was conducted using tracer gases, CFD simulations and smoke visualization. The tests were made with dense smoke visualization in order to investigate the relation between the value of pressure difference, door swing and migration level of heavy contaminants between the rooms. cache = ./cache/cord-002044-9xgt3tf4.txt txt = ./txt/cord-002044-9xgt3tf4.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002094-7tewne3a author = Tago, Damian title = The Impact of Farmers’ Strategic Behavior on the Spread of Animal Infectious Diseases date = 2016-06-14 pages = extension = .txt mime = text/plain words = 6293 sentences = 303 flesch = 53 summary = Incorporating the strategic behavior of farmers in an epidemiologic model reveals that the MRP can trigger premature animal sales by farms at high risk of becoming infected that significantly reduce the efficacy of the policy. The idea behind control strategies such as the MRP and vaccination [7] is that removing infected nodes or immunizing susceptible ones are efficient mechanisms to fight the spread of a disease. If an infectious disease is detected at t = 1, a farmer sufficiently close to the infected zone will face the risk that the restricted zone (RZ) will expand to include his location by the next period (with probability q). In the case of non-vector-borne diseases, i.e. when the transmission channel is restricted to the trade network, the MRP is an effective control strategy. The MRP becomes significantly less efficient when infected nodes that have not been detected spread the disease through both trade and geographic networks. cache = ./cache/cord-002094-7tewne3a.txt txt = ./txt/cord-002094-7tewne3a.txt === reduce.pl bib === === reduce.pl bib === id = cord-002043-z1b7pj3s author = Wang, Xue-Yang title = Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains date = 2016-05-11 pages = extension = .txt mime = text/plain words = 5879 sentences = 359 flesch = 42 summary = obtained numerous differentially expressed genes (DEGs) involved in metabolism, immunity, and inflammatory responses in Microtus fortis following infection with Schistosoma japonicum based on comparative transcriptome analysis [20] . reported that several genes related to physical barriers, immune response, proteolytic/metabolic enzymes, heat-shock proteins, and hormonal signaling were possibly involved in silkworm resistance against Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection; although these genes might be induced by the virus in order to increase infectivity [21] . After BmNPV infection, the expression levels of 4 genes were down-regulation in BC9 and A35 (resistant strain) (Fig 6) , which was consistent with the transcriptome data. Based on their role in apoptosis activation, hosts need to increase the expression level of these genes to promote apoptosis when exposed to a virus; this supposition explains the up-regulation of genes involved in apoptosis in the transcriptome following BmNPV infection. cache = ./cache/cord-002043-z1b7pj3s.txt txt = ./txt/cord-002043-z1b7pj3s.txt === reduce.pl bib === === reduce.pl bib === id = cord-001982-arczqdza author = Khajah, Maitham A. title = Anti-Inflammatory Action of Angiotensin 1-7 in Experimental Colitis date = 2016-03-10 pages = extension = .txt mime = text/plain words = 6218 sentences = 313 flesch = 56 summary = It is thought that the beneficial effects of ACE-inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) on blood pressure control and in delaying/inhibiting the cardiac remodeling process is through increasing serum levels of Ang1-7 [9] [10] [11] [12] . A seven fold decrease in the plasma level of Ang 1-7 was demonstrated in DSS treated mice compared to untreated (UT) group at day 7 post colitis induction (Fig 1A) . The level of phosphorylated forms of three key signaling intermediates, ERK1/2 (Fig 8) , p38 MAPK (Fig 9) and Akt (Fig 10) , were measured by immunofluorescence in sections from resected colon tissue of untreated mice or mice treated with DSS (for 7 days) plus daily Ang 1-7 or saline (vehicle) treatment. cache = ./cache/cord-001982-arczqdza.txt txt = ./txt/cord-001982-arczqdza.txt === reduce.pl bib === id = cord-001761-yvd1n42f author = Yoshimura, Takeo title = Controlled Microwave Heating Accelerates Rolling Circle Amplification date = 2015-09-08 pages = extension = .txt mime = text/plain words = 4411 sentences = 223 flesch = 48 summary = Analysis of the temperature profiles of each RCA component subjected to microwave heating revealed the selectivity heating of buffer components compared with primers, template DNA, dNTP, and RNase-free water. To determine the component of RCA by microwave selectivity heating, we measured the temperatures of the five components (circularized template with primers, dNTPs, ThermoPol Buffer, Bst-LF, and RNase-free water) of the RCA and MW-RCA mixtures for 10 min from 13°C to 60°C. To reveal the effect of the selectivity heating in MW-RCA, we compared the efficiency of DNA amplification in the RCA and MW-RCA reactions mixtures containing a 4-fold excess concentration of each RCA component (dNTP, template-primers, Bst-LF, Tris-HCl, KCl, (NH 4 ) 2 SO 4 , and MgSO 4 ). We performed MW-RCA reactions containing a four-fold higher concentration of each RCA component [dNTP, template-primers, Bst DNA polymerase-LF, Tris-HCl, KCl, (NH 4 ) 2 SO 4 , and MgSO 4 ] to identify a link between microwave selective heating and DNA amplification. cache = ./cache/cord-001761-yvd1n42f.txt txt = ./txt/cord-001761-yvd1n42f.txt === reduce.pl bib === === reduce.pl bib === id = cord-002834-2htnywef author = Tsuchiaka, Shinobu title = Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population date = 2018-01-11 pages = extension = .txt mime = text/plain words = 2976 sentences = 154 flesch = 52 summary = title: Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. The insertion sequences were aligned and compared with those of the PL-CP of EV-G strains from the USA and Belgium and with the PL-VP sequences in the genome of nidoviruses including porcine and bovine toroviruses by phylogenetic analysis and pairwise sequence comparison (Fig 2 and S2 Table) . The G2-PL-CP strain HgYa2-1 showed high homology Genetic diversity and recombination of enterovirus G strains in Japanese pigs to G2 strains in the tree for VP4-VP3 and VP1, whereas HgYa2-1 showed high similarity with G1-PL-CP lineage 1 strains in regions P2 and P3 (Fig 3A) . cache = ./cache/cord-002834-2htnywef.txt txt = ./txt/cord-002834-2htnywef.txt === reduce.pl bib === id = cord-001898-ntqyjqqk author = Huang, Chih-Wei title = Lys-315 at the Interfaces of Diagonal Subunits of δ-Crystallin Plays a Critical Role in the Reversibility of Folding and Subunit Assembly date = 2016-01-05 pages = extension = .txt mime = text/plain words = 6578 sentences = 337 flesch = 47 summary = The changes in tryptophan fluorescence were Dilution of monomeric K315A mutant protein denatured in 5 M GdmCl resulted in refolding to a similar conformation as the original monomeric state (Fig 5A and 5B) . Since refolding of partly unfolded monomeric mutant δ-crystallin resulted in a conformation with high exposure of hydrophobic regions, the occurrence of protein aggregation in the process was determined using light scattering measurement. An increase in fluorescence intensity resulting from binding of ThT with the aggregates over time was observed following dilution of 0.84 and 3 M GdmCl denatured monomeric mutant δ-crystallin into buffer (Fig 6B) . The unique stable conformation from unfolding of K315A mutant protein in the presence of urea suggests that the interactions provided by this residue at the interfaces may play a critical role in stabilization of the quaternary structure of δ-crystallin. cache = ./cache/cord-001898-ntqyjqqk.txt txt = ./txt/cord-001898-ntqyjqqk.txt === reduce.pl bib === === reduce.pl bib === id = cord-002473-2kpxhzbe author = Das, Jayanta Kumar title = Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach date = 2017-03-31 pages = extension = .txt mime = text/plain words = 4613 sentences = 285 flesch = 61 summary = Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. The primary protein sequence is read as consecutive order pairs serially from first amino acid to the end of sequence, and each order pair is nothing but a connected edge between the two nodes where nodes in the graph are involved with different chemical groups of amino acids. Our method of phylogenetic tree formation used the dissimilarity matrix which is obtained for every pair of sequence on the basis of chemical group specific score of amino acids. Based on the phylogenetic tree of five members, we find that the PpcA and PpcD, PpcB and PpcE are mostly closed with regards to the frequency of amino acids of respective eight chemical groups. cache = ./cache/cord-002473-2kpxhzbe.txt txt = ./txt/cord-002473-2kpxhzbe.txt === reduce.pl bib === id = cord-002222-rgqwm3vb author = Olarte-Castillo, Ximena A. title = Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date = 2016-09-23 pages = extension = .txt mime = text/plain words = 7544 sentences = 339 flesch = 46 summary = By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. A total of 20 partial RdRp gene sequences (16 from spotted hyenas, 3 from African lions and 1 from bat-eared foxes) were obtained and used for the phylogenetic analysis, together with publically available sequence data from 25 representatives of all sapovirus genogroups, divergent unclassified sapoviruses, and other genera in the Caliciviridae family, including Norovirus and Vesivirus. cache = ./cache/cord-002222-rgqwm3vb.txt txt = ./txt/cord-002222-rgqwm3vb.txt === reduce.pl bib === id = cord-002100-dt5zvebj author = He, Yonghua title = Transgenic Soybean Production of Bioactive Human Epidermal Growth Factor (EGF) date = 2016-06-17 pages = extension = .txt mime = text/plain words = 6795 sentences = 336 flesch = 45 summary = Phosphorylation and immunohistochemical assays on the EGF receptor in HeLa cells indicate the EGF protein produced in soybean seed is bioactive and comparable to commercially available human EGF. Epidermal growth factor protein from humans was produced in soybean seeds by constructing a plant gene expression cassette that involved a synthetic codon optimized EGF nucleotide sequence (protein sequence from Genbank accession CCQ43157). To assess the bioactivity of soybean-produced hEGF, samples were prepared from both ShEGF transgenic soybean lines and nontransgenic controls that were used to stimulate HeLa cells to induce EGFR internalization, degradation and phosphorylation. In contrast, samples prepared from control nontransgenic soybeans exhibited no apparent bioactivity showing the degradation and phosphorylation of EGFR is the result of EGF binding of either commercial rhEGF added to the media or from the hEGF produced by the transgenic soybeans. cache = ./cache/cord-002100-dt5zvebj.txt txt = ./txt/cord-002100-dt5zvebj.txt === reduce.pl bib === id = cord-002602-2qvyhjlp author = Roy, Amrita title = Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants date = 2017-07-10 pages = extension = .txt mime = text/plain words = 8987 sentences = 456 flesch = 57 summary = Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100) of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Therefore, our results suggest that in the Zika NS2B-NS3pro complex, NS2B has a portion of residues undergo μs-ms dynamics which made their NMR peaks too broad to be detectable; while the rest of NS2B is highly disordered and lacks tight tertiary packing, which results in a narrowly-dispersed HSQC spectrum (S2B Fig) . Together with recent reports on the crystal structures of Zika NS2B-NS3pro complexes in both open and closed conformations [34, 43] , our current results reveal that in solution the NS2B residues over Arg73-Lys100 are highly disordered in the open conformation. Unfortunately, as previously observed on Dengue-2 NS2B-NS3pro complexes [21, 30, 43] , our linked Zika complex also underwent significant μs-ms dynamics, thus making its NMR signals too broad to be detected (Fig 1A and 1B) . cache = ./cache/cord-002602-2qvyhjlp.txt txt = ./txt/cord-002602-2qvyhjlp.txt === reduce.pl bib === id = cord-001843-ceatyj3o author = Huang, Yong title = Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay date = 2015-11-06 pages = extension = .txt mime = text/plain words = 5184 sentences = 231 flesch = 50 summary = PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. The duplex UNDP-PCR assay is suitable for simultaneous detection of RNA and DNA viruses in early viral infection, providing an effective approach for diagnosis of swine diseases. The duplex UNDP-PCR assay developed in this study provided a useful tool for simultaneous detection of RNA (TGEV) and DNA viruses (PCV2) without the need for viral nucleic acid extraction, purification and reverse transcription. cache = ./cache/cord-001843-ceatyj3o.txt txt = ./txt/cord-001843-ceatyj3o.txt === reduce.pl bib === id = cord-002305-qq73gr9y author = Anson, Marie title = Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool date = 2016-11-23 pages = extension = .txt mime = text/plain words = 5422 sentences = 248 flesch = 51 summary = In conclusion, the adoptive cell transfer strategy allowed the development of a primary immune response with B cell activation and expansion, induction of AID expression, class switch recombination, antigen-specific IgM and IgG antibody production and germinal center formation. In this study we show that it is possible to fully reconstitute a primary response and the establishment of antibody memory in immune deficient mice after adoptive transfer of antigen-specific monoclonal B cells together with a population of monoclonal helper T cells. In contrast we showed that after adoptive transfer in immune deficient hosts antigen immunization induced B cell activation and expansion, induction of AID expression, class switch recombination, antigen-specific IgM and IgG antibody production, germinal center formation and the generation of two subsets of AID/YFP + IgM + IgGand AID/YFP + Ig-M -IgG + antigen-experienced B cell subsets able to persist in a lymphopenic environment by cell division mimicking responses obtained in intact non-Tg mice [4] . cache = ./cache/cord-002305-qq73gr9y.txt txt = ./txt/cord-002305-qq73gr9y.txt === reduce.pl bib === === reduce.pl bib === id = cord-002811-5hrydciz author = Hercik, Christine title = A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania date = 2017-12-29 pages = extension = .txt mime = text/plain words = 6511 sentences = 310 flesch = 42 summary = Furthermore, we examined numerous epidemiologic correlates of febrile illness, and conducted demographic, clinical, and behavioral domain-specific multivariate regression to statistically establish associations with agent detection. The objective of this hospital-based syndromic surveillance study was to examine exposure and epidemiologic associations with detection of bloodstream and respiratory agents among patients presenting to clinical settings with acute febrile illness (AFI) in Kilombero, Tanzania. Given the high frequency of detection of Plasmodium, we further examined detection status across three diagnostic platforms, and conducted a non-parametric tests Kruskal-Wallis test to compare mean C t values, as determined by qPCR, for patients grouped within each level of parasite intensity (1+, 2+, 3+, or 4+), as determined by blood smear. Clinical and epidemiologic correlates of agents detected among at least 10% of our patient population were evaluated using an agent-specific filtered multivariate logistic regression approach to determine statistically significant factors among test-positive participants against a test-negative control group. cache = ./cache/cord-002811-5hrydciz.txt txt = ./txt/cord-002811-5hrydciz.txt === reduce.pl bib === id = cord-002901-u4ybz8ds author = Yu, Chanki title = Acral melanoma detection using a convolutional neural network for dermoscopy images date = 2018-03-07 pages = extension = .txt mime = text/plain words = 3513 sentences = 180 flesch = 52 summary = We applied a convolutional neural network to dermoscopy images of acral melanoma and benign nevi on the hands and feet and evaluated its usefulness for the early diagnosis of these conditions. To perform the 2-fold cross validation, we split them into two mutually exclusive subsets: half of the total image dataset was selected for training and the rest for testing, and we calculated the accuracy of diagnosis comparing it with the dermatologist's and non-expert's evaluation. CONCLUSION: Although further data analysis is necessary to improve their accuracy, convolutional neural networks would be helpful to detect acral melanoma from dermoscopy images of the hands and feet. In the result of group B by the training of group A images, CNN also showed a higher diagnostic accuracy (80.23%) than that of the non-expert (62.71%) but was similar to that of the expert (81.64%). cache = ./cache/cord-002901-u4ybz8ds.txt txt = ./txt/cord-002901-u4ybz8ds.txt === reduce.pl bib === id = cord-002624-59nznqsd author = Ti, Jinfeng title = Identification of one B-cell epitope from NS1 protein of duck Tembusu virus with monoclonal antibodies date = 2017-07-26 pages = extension = .txt mime = text/plain words = 4050 sentences = 210 flesch = 53 summary = title: Identification of one B-cell epitope from NS1 protein of duck Tembusu virus with monoclonal antibodies This study describes the identification of one linear B-cell epitope on TMUV NS1 protein with monoclonal antibody (mAb) 3G2 by indirect enzyme-linked immunosorbent assay (ELISA). In this study, one linear B-cell epitope was identified and characterized with one monoclonal antibody against TMUV NS1 protein. To screen the antigenic epitope of TMUV NS1 mAb, 35 short peptide fusion proteins were successfully expressed in prokaryotic expression system and purified. A pane of 16-AA polypeptides of NS1 protein was expressed and one 16-AA polypeptide NS1-27 was screened and identified by 3G2 mAb. In order to accurately map the B-cell epitope, a set of truncated fusion oligopeptides of NS1-27 were expressed. The B-cell epitope of TMUV NS1 protein could apply into the development of detection methods to investigate whether the detected antibody was a result of inactivated vaccine immunization or live virus infection. cache = ./cache/cord-002624-59nznqsd.txt txt = ./txt/cord-002624-59nznqsd.txt === reduce.pl bib === === reduce.pl bib === id = cord-002705-ntokyoai author = Nasir, Nazrila Hairin title = Effectiveness of a fluid chart in outpatient management of suspected dengue fever: A pilot study date = 2017-10-04 pages = extension = .txt mime = text/plain words = 4464 sentences = 229 flesch = 56 summary = However, there have been no published studies looking at self-care intervention measures to improve oral fluid intake among patients suspected of dengue fever. OBJECTIVE: To assess the feasibility and effectiveness of using a fluid chart to improve oral fluid intake in patients with suspected dengue fever in a primary care setting. To assess the feasibility and effectiveness of using a fluid chart to improve oral fluid intake in patients with suspected dengue fever in a primary care setting. A non-randomized controlled study was conducted in Taiwan comparing the effects of oral rehydration with intravenous fluid replacement in adult patients with non-shock dengue haemorrhagic fever [7] . Most importantly, there have been no published studies looking at self-care intervention measures to improve oral fluid intake among patients suspected of dengue fever. Thus, this pilot randomized controlled study aimed to assess the feasibility of using a fluid chart to improve oral fluid intake in patients with suspected dengue fever in a primary care setting. cache = ./cache/cord-002705-ntokyoai.txt txt = ./txt/cord-002705-ntokyoai.txt === reduce.pl bib === id = cord-003507-22ylifqo author = Kelly, J. Daniel title = Projections of Ebola outbreak size and duration with and without vaccine use in Équateur, Democratic Republic of Congo, as of May 27, 2018 date = 2019-03-07 pages = extension = .txt mime = text/plain words = 4481 sentences = 246 flesch = 53 summary = As of May 27, 2018, 6 suspected, 13 probable and 35 confirmed cases of Ebola virus disease (EVD) had been reported in Équateur Province, Democratic Republic of Congo. We modeled Ebola virus transmission using a stochastic branching process model that included reproduction numbers from past Ebola outbreaks and a particle filtering method to generate a probabilistic projection of the outbreak size and duration conditioned on its reported trajectory to date; modeled using high (62%), low (44%), and zero (0%) estimates of vaccination coverage (after deployment). With the stochastic model, using high, low, and zero estimates of vaccination coverage, the median outbreak sizes for probable and confirmed cases were 82 cases (95% prediction interval [PI]: 55, 156), 104 cases (95% PI: 58, 271), and 213 cases (95% PI: 64, 1450), respectively. We modeled Ebola virus transmission using a stochastic branching process model, parameterized by transmission rates estimated from the dynamics of prior EVD outbreaks, and conditioned on agreement with reported case counts from the 2018 EVD outbreak to date. cache = ./cache/cord-003507-22ylifqo.txt txt = ./txt/cord-003507-22ylifqo.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002621-sq5iod1w author = Attia, Mohamed I. title = New hydrazonoindolin-2-ones: Synthesis, exploration of the possible anti-proliferative mechanism of action and encapsulation into PLGA microspheres date = 2017-07-25 pages = extension = .txt mime = text/plain words = 5948 sentences = 280 flesch = 47 summary = Compounds 7b, 7d and 7e were the most active congeners against the tested human cancer cell lines with average IC(50) values of 4.77, 3.39 and 2.37 μM, respectively, as compared with the reference isatin-based drug, sunitinib, which exhibited an average IC(50) value of 8.11 μM. Incorporation of 7e into PLGA microspheres improved its in vitro anti-proliferative activity toward the human cancer cell line A549 after 120 h incubation period with an IC(50) value less than 0.8 μM. The human lung cancer A549 cell line was incubated with various concentrations (0.8, 1.6, 3.13, 6.25, 12.5, 25 and 50 μM) of both free 7e and 7e-loaded microspheres to evaluate the anti-proliferative activity by assessing their effect on cell viability. Synthesis and anticancer activity of certain hydrazonoindolin-2-ones Fig 13B illustrates the obtained results when 7e-loaded microspheres were incubated with the human lung cancer cell lineA549for incubation periods and concentrations similar to that of the free 7e. cache = ./cache/cord-002621-sq5iod1w.txt txt = ./txt/cord-002621-sq5iod1w.txt === reduce.pl bib === === reduce.pl bib === id = cord-002560-pue5q5wp author = Moreno, Paloma S. title = Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date = 2017-06-01 pages = extension = .txt mime = text/plain words = 5137 sentences = 265 flesch = 50 summary = Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, [5] [6] [7] [8] [9] [10] [11] In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, [12] [13] [14] [15] [16] [17] [18] . Another eukaryotic viral family found in one healthy dog sample was Parvoviridae, genetic analysis of the 3 contigs/singletons showed a coverage of approximately 3.5% of the complete genome of canine parvovirus reference sequence (NC_001539), or 9.3% of the polyprotetin Ns1-Ns2. Nucleic acids from a single faecal sample from a dog with acute diarrhoea (DD1), which had 18 contigs/singletons of canine astrovirus (after tBLASTx analysis) was used to determine the complete genome sequence. cache = ./cache/cord-002560-pue5q5wp.txt txt = ./txt/cord-002560-pue5q5wp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004017-gcmpatlb author = Errecaborde, Kaylee Myhre title = Factors that enable effective One Health collaborations - A scoping review of the literature date = 2019-12-04 pages = extension = .txt mime = text/plain words = 9215 sentences = 458 flesch = 34 summary = The review identified 12 factors that support successful One Health collaborations and a coordinated response to health events across three levels: two individual factors (education & training and prior experience & existing relationships), four organizational factors (organizational structures, culture, human resources and, communication), and six network factors (network structures, relationships, leadership, management, available & accessible resources, political environment). In this study, a multidisciplinary team of researchers reviewed a broad scope of literature describing collaborative and multi-sectoral approaches to past health events to understand how such collaborations are commonly described and evaluated and to identify and synthesize enabling factors for One Health collaborations. Starting condition factors reported to enable collaboration at the network level included network structures, existing relationships, available resources in the face of a health event, and the political environment in place to support these efforts. cache = ./cache/cord-004017-gcmpatlb.txt txt = ./txt/cord-004017-gcmpatlb.txt === reduce.pl bib === id = cord-002180-gsdk5x3e author = Davies, Colin title = Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date = 2016-08-24 pages = extension = .txt mime = text/plain words = 4491 sentences = 223 flesch = 52 summary = Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G(0)/G(1) phase as identified for wild-type NS5. Several RNA viruses, including murine norovirus 1 (MNV-1) have been characterized to manipulate cell cycle progression at the G 1 /S restriction point, often creating favorable conditions for viral replication [14] [15] [16] [17] [18] [19] [20] [21] . The effect of NS5 on the host cell cycle was therefore determined by transfection of RAW-Blue cells with RNA transcripts, encoding individual viral genes, NS1-2 from MNV-1 was included as a negative control (Fig 1A) . Furthermore, the NS5(F123A) variant decreased cyclin A protein expression by 67% when compared to the mocktransfected population in a synonymous manner to NS5, strongly implying that the host eukaryotic initiation factor binding domain of NS5 does not play a role in its cell cycle manipulation (Fig 3D) . cache = ./cache/cord-002180-gsdk5x3e.txt txt = ./txt/cord-002180-gsdk5x3e.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002426-5e1xn7kj author = Falcón-Lezama, Jorge Abelardo title = Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico date = 2017-02-22 pages = extension = .txt mime = text/plain words = 5944 sentences = 261 flesch = 49 summary = MATERIALS AND METHODS: We carried out a cohort-nested, case-control study with 126 individuals (42 cases, 42 intradomestic controls and 42 population controls) with the goal of describing human mobility patterns of recently Dengue virus-infected subjects, and comparing them with those of non-infected subjects living in an urban endemic locality. CONCLUSIONS: Results of this study show that human mobility in a small urban setting exceeded that considered by local health authority's administrative limits, and was different between recently infected and non-infected subjects living in the same household. These observations provide important insights about the role that human mobility may have in Dengue virus transmission and persistence across endemic geographic areas that need to be taken into account when planning preventive and control measures. Sample: 126 individuals (42 cases, 42 intradomestic controls and 42 population controls) with age older than 12, and residents in Axochiapan, Morelos State, México, were selected from the cohort "Peridomestic infection as determinant for Dengue virus transmission" [13] . cache = ./cache/cord-002426-5e1xn7kj.txt txt = ./txt/cord-002426-5e1xn7kj.txt === reduce.pl bib === id = cord-003377-9vkhptas author = Wu, Tong title = The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia date = 2018-12-19 pages = extension = .txt mime = text/plain words = 4969 sentences = 267 flesch = 49 summary = title: The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). The indicator for wild bird habitat used in this study was the set of "Important Bird and Biodiversity Areas" (IBAs) for "migratory and congregatory waterbirds" identified by BirdLife The live poultry trade poses different avian influenza risks in different regions of the world Table 1 . Our first specification (Model 1) included a number of factors related to disease risk but excluded both live poultry imports and biosecurity measures. cache = ./cache/cord-003377-9vkhptas.txt txt = ./txt/cord-003377-9vkhptas.txt === reduce.pl bib === === reduce.pl bib === id = cord-002890-g7aje88u author = Wood, Paul L. title = Lipidomic analysis of immune activation in equine leptospirosis and Leptospira-vaccinated horses date = 2018-02-23 pages = extension = .txt mime = text/plain words = 3276 sentences = 177 flesch = 39 summary = In this study, we undertook a lipidomics approach to determine if there are any differences in the serum lipid profiles of horses naturally infected with pathogenic Leptospira spp. Utilizing a high-resolution mass spectrometry serum lipidomics analytical platform, we demonstrate that cyclic phosphatidic acids, diacylglycerols, and hydroperoxide oxidation products of choline plasmalogens are elevated in the serum of naturally infected as well as vaccinated horses. In this study, we asked if differences in host's responses to live, multiplying Leptospira versus killed leptospires, present in the vaccine, are reflected in the serum lipidome of these two groups of horses. Our results show that serum levels of cyclic phosphatidic acids (cPA), diacylglycerols, and hydroperoxide oxidation products of choline plasmalogens were elevated in both vaccinated and naturally infected horses. Our data indicate that the immune response induced by vaccination has a more dramatic effect than leptospiral infection on sphingomyelin synthesis in horses. cache = ./cache/cord-002890-g7aje88u.txt txt = ./txt/cord-002890-g7aje88u.txt === reduce.pl bib === id = cord-003548-zuwt7gk5 author = Cai, Haiming title = Modulating the 3’ end-DNA and the fermentation process for enhanced production and biological activity of porcine interferon-gamma date = 2019-03-26 pages = extension = .txt mime = text/plain words = 6848 sentences = 447 flesch = 56 summary = In this study, we optimized the pIFN-γ gene recombination sequence and mutated the 3' end of the pIFN-γ gene, resulting in a higher expression level and stronger biological activity, as well as a significant upregulation in the expression of the interferon-stimulated genes Mx1 and OAS1 in IPEC-J2 jejunal epithelial cells. These data demonstrated, for the first time, that the expression level of pIFN-γ in Pichia pastoris was improved significantly by gene optimization with 3' end mutation and a fermentation process that maintained good biological activity, which is beneficial to the application of pIFN-γ in animal husbandry. The expression of pIFN-γ protein was maximal when the concentration of DO in the substrate was 30%, especially for the recombinant Pichia pastoris with the optimized pIFN-γ gene and the 3' signaling peptide mutation, which had significantly higher expression than that of the other treatment groups (p<0.05). cache = ./cache/cord-003548-zuwt7gk5.txt txt = ./txt/cord-003548-zuwt7gk5.txt === reduce.pl bib === id = cord-003270-vu9b5a14 author = Panahi, Heidar Ali title = A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins date = 2018-10-24 pages = extension = .txt mime = text/plain words = 7005 sentences = 377 flesch = 50 summary = In the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and in the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens' analyses were carried out successively by different tools. For the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and for the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens analyses were considered. In this study, the binding ability of the first step selected peptides to human and mouse MHC molecules, was analyzed by CABS-dock (http://biocomp.chem.uw.edu.pl/CABSdock/) server. In cancer immunotherapy, the CTL-mediated responses play the central role in eradication of malignant cells, and the binding of epitopes to MHC-I molecules is an essential step for antigen presentation to CTLs. Thus, in this study, predicted epitopes were primarily selected by their MHC-I binding and processing scores. cache = ./cache/cord-003270-vu9b5a14.txt txt = ./txt/cord-003270-vu9b5a14.txt === reduce.pl bib === id = cord-001910-6zfz2ns5 author = Zhang, Xianming title = Abdominal Muscle Activity during Mechanical Ventilation Increases Lung Injury in Severe Acute Respiratory Distress Syndrome date = 2016-01-08 pages = extension = .txt mime = text/plain words = 3991 sentences = 241 flesch = 53 summary = title: Abdominal Muscle Activity during Mechanical Ventilation Increases Lung Injury in Severe Acute Respiratory Distress Syndrome The purpose of this study was to test the hypothesis that abdominal muscle activity during mechanically ventilation increases lung injury in severe ARDS. Therefore, we hypothesized that abdominal muscle activity during mechanically ventilation increases lung injury in severe acute respiratory distress syndrome. In an oleic acid-induced model of experimental ARDS in beagles, our findings suggested that abdominal muscle activity during mechanically ventilation increases lung injury in severe acute respiratory distress syndrome. In an oleic acid-induced ARDS model, our study showed that BIPAP AP had lower mRNA expression of IL-6 and IL-8 in lung tissues and less total cumulative histopathological lung injury scores compared with BIPAP SB group. cache = ./cache/cord-001910-6zfz2ns5.txt txt = ./txt/cord-001910-6zfz2ns5.txt === reduce.pl bib === === reduce.pl bib === id = cord-003125-iptisi1m author = Machablishvili, Ann title = Overview of three influenza seasons in Georgia, 2014–2017 date = 2018-07-27 pages = extension = .txt mime = text/plain words = 3714 sentences = 196 flesch = 48 summary = We aimed to present Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) surveillance data and characterize influenza viruses circulating in the country over three influenza seasons. The objectives were to: (1) define periods of influenza activity in Georgia; (2) assess the proportions of influenza infections among ILI and SARI cases; (3) determine most affected age groups; (4) describe epidemiological characteristics of influenza-associated fatal cases; and (5) determine antigenic and genetic profiles of influenza viruses circulating in the country. Influenza virus detection rates among hospitalized patients were highest, almost equally, in the age groups 30-64 years (55%, OR = 3.48, CI 2.58-4.69, p<0.001) and 15-29 years (53%, OR = 3.03, CI 2.14-4.28, p<0.001) ( Table 1) Among 1,997 sampled SARI cases, only 25 were vaccinated against influenza; of these, three tested positive for A/H1N1pdm09 and three for A/H3N2. cache = ./cache/cord-003125-iptisi1m.txt txt = ./txt/cord-003125-iptisi1m.txt === reduce.pl bib === id = cord-004091-gex0zvoa author = Abdulkareem, Shaheen A. title = Risk perception and behavioral change during epidemics: Comparing models of individual and collective learning date = 2020-01-06 pages = extension = .txt mime = text/plain words = 8379 sentences = 432 flesch = 50 summary = For this study, we ran eight ABMs to test various combinations of individual and group learning, using different information sources-with or without interactions among agents-as factors in the BNs. We investigate the extent to which the epidemic spreads, depending on these different learning approaches regarding risk perception and coping decisions. The empirically-driven BNs model a two-stage decision process of people facing a disease risk: learning to update risk perceptions (threat appraisal, BN1 in Fig 1) and making decisions about how to adapt their behavior during the epidemic (coping appraisal, BN2 in Fig 1) . To evaluate the impact of individual and social intelligence on agents' learning processes regarding risk perception and coping appraisal and the resulting patterns of disease spread, we used four output measures: disease diffusion, risk perception, spatial patterns, and model performance. Finally, in M7, where household agents learned risk perception in decentralized groups and learned to cope individually, 2,911 infected cases were recorded (Table 3) . cache = ./cache/cord-004091-gex0zvoa.txt txt = ./txt/cord-004091-gex0zvoa.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003712-mafz21no author = Perez Vidakovics, Maria Laura A. title = Junín virus induces autophagy in human A549 cells date = 2019-06-19 pages = extension = .txt mime = text/plain words = 6151 sentences = 333 flesch = 47 summary = We found that JUNV infection induces an increment of the LC3-II/LC3-I ratio, an accumulation of punctate pattern in RFP-LC3-transfected cells and the colocalisation of viral nucleoprotein and LC3 protein, suggesting autophagosome formation. Either with the early autophagy inhibitor (3-MA) or the late inhibitor (BAF), the treatment pre or post-infection resulted in reduced expression of N and lower viral titre as compared to JUNV-infected cells that received no treatment (NT) (Fig 4B-4D) . In parallel, experiments performed adding Rap post-infection resulted in a similar increase in viral yields of JUNV, which indicates that the activation of autophagy benefits both viral entry/uncoating and later steps as assembling and viral budding (Fig 4) . When compared to control cells, an increase in the number of mCherry puncta following rapamycin treatment was observed, indicating promoted autophagy and fusion between autophagosomes and acidic compartments (Fig 5C) . cache = ./cache/cord-003712-mafz21no.txt txt = ./txt/cord-003712-mafz21no.txt === reduce.pl bib === id = cord-003062-qm8kalyt author = Chowdhury, Fazle Rabbi title = The association between temperature, rainfall and humidity with common climate-sensitive infectious diseases in Bangladesh date = 2018-06-21 pages = extension = .txt mime = text/plain words = 4997 sentences = 274 flesch = 50 summary = This observational study examined the association of temperature, humidity and rainfall with six common climate-sensitive infectious diseases in adults (malaria, diarrheal disease, enteric fever, encephalitis, pneumonia and bacterial meningitis) in northeastern Bangladesh. Unfortunately, very few studies on the relationship between various environmental variables and trends of infectious disease incidence have been performed so far in Bangladesh, although there are reports of some infections increasing sporadically in different regions of the country [17] [18] [19] . This study examined six infectious diseases based on clinical syndromes and laboratory support (malaria, enteric fever, encephalitis, diarrheal disease, pneumonia and meningitis) to offer a broader scope on the trend of these infectious diseases and their possible relation to climate change in Bangladesh. W.H.O reported dengue, viral encephalitis, diarrheal disease, enteric fever, pneumonia and meningitis as most sensitive to climate factors, and predicted a huge rise of cases in tropical countries [25] . cache = ./cache/cord-003062-qm8kalyt.txt txt = ./txt/cord-003062-qm8kalyt.txt === reduce.pl bib === id = cord-002889-fie121ns author = White, Michael title = Development of improved therapeutic mesothelin-based vaccines for pancreatic cancer date = 2018-02-23 pages = extension = .txt mime = text/plain words = 4872 sentences = 222 flesch = 47 summary = Human and mouse mesothelin share sequence similarity, expression patterns, and biochemical characteristics, [7] , and the homeostatic function of mesothelin in mammals is unknown: the gene can be deleted without apparent effect in mice PLOS C57Bl6 mice and thus can be grown in syngeneic mice to allow for study of an anti-tumor immune response in an immunocompetent mouse model. In order to create a putative therapeutic anti-mesothelin vaccine, we inserted the mouse mesothelin gene into the poxvirus MVA genome under a viral promoter so that mesothelin would be expressed in any cells infected with the recombinant virus. To determine whether the viruses expressing mesothelin protein were able to induce an immune response in mice, we first attempted to measure anti-mesothelin antibody in vaccinated mouse sera. In comparison, there were very few spots (1-3) in response to stimulation with Lewis Lung cells that do not express mouse mesothelin, and mice vaccinated with MVA, MVAmeso and MVAmesoA35Del viruses all had good responses to restimulation with vaccinia virus (124, 147, and 148 spots respectively). cache = ./cache/cord-002889-fie121ns.txt txt = ./txt/cord-002889-fie121ns.txt === reduce.pl bib === === reduce.pl bib === id = cord-004068-d66lwylf author = Shimoda, Tomoko title = Effect of thermal control of dry fomites on regulating the survival of human pathogenic bacteria responsible for nosocomial infections date = 2019-12-27 pages = extension = .txt mime = text/plain words = 4676 sentences = 221 flesch = 43 summary = A specialized handrail device fitted with a heater, which was maintained at normal human body core temperature, successfully prohibited the prolonged survival of bacteria [Enterococcus faecalis (ATCC), E. Furthermore, we propose that fomites warmed to human body core temperature may help to control bacterial survival in dry environments, and that such a strategy may prohibit the emergence of human pathogenic bacteria in hospital environments, eventually reducing the need for antibiotics as well as disinfectants. A heatmap generated with the high-resolution infrared sensor showed that in contrast to the stainless steel pipe without the heater, the surface temperature on the heated pipe was maintained at body core temperature (Fig 5A) , indicating that it is an effective tool to monitor the influence of temperature on bacterial survival on a dry surface. Taken together, we concluded that the handrail device warmed to human body core temperature prohibited the prolonged survival of some bacteria and a yeast-like fungus responsible for nosocomial infections on a dry surface. cache = ./cache/cord-004068-d66lwylf.txt txt = ./txt/cord-004068-d66lwylf.txt === reduce.pl bib === id = cord-003484-ylpa702c author = Blázquez, Elena title = Evaluation of the effectiveness of the SurePure Turbulator ultraviolet-C irradiation equipment on inactivation of different enveloped and non-enveloped viruses inoculated in commercially collected liquid animal plasma date = 2019-02-21 pages = extension = .txt mime = text/plain words = 6990 sentences = 352 flesch = 53 summary = Specifically, Pseudorabies virus (PRV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine epidemic diarrhea virus (PEDV), Bovine viral diarrhea virus (BVDV), Classical swine fever virus (CSFV), Swine influenza virus (SIV) as enveloped viruses and Porcine parvovirus (PPV), Swine vesicular disease virus (SVDV), Porcine circovirus type 2 (PCV-2) and Senecavirus A (SVA) as non-enveloped viruses, were inoculated in bovine or porcine plasma and subjected to different UV-C irradiation doses (0, 750, 1500, 3000, 6000 and 9000 J/L) using an UV-C device developed for opaque liquid working under turbulent flow. The objective of this study was to assess inactivation efficiency of the SurePure Turbulator UV-C irradiation system with selected swine enveloped viruses Pseudorabies virus (PRV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine epidemic diarrhea virus (PEDV), Bovine viral diarrhea virus (BVDV), Swine influenza A virus (SIV) and Classical swine fever virus (CSFV) and non-enveloped viruses Porcine parvovirus (PPV), Swine vesicular disease virus (SVDV), Porcine circovirus 2 (PCV-2) and Senecavirus A (SVA) inoculated in liquid bovine or porcine plasma. cache = ./cache/cord-003484-ylpa702c.txt txt = ./txt/cord-003484-ylpa702c.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-011798-uss38ped author = Li, Guowei title = Intellectual capital and the efficiency of SMEs in the transition economy China; Do financial resources strengthen the routes? date = 2020-07-02 pages = extension = .txt mime = text/plain words = 8759 sentences = 490 flesch = 38 summary = Despite the bourgeoning literature, studies have not yet unleashed the influence of each dimension of intellectual capital; human capital, structural capital and customer capital on SMEs' efficiency with financial resources as a moderator. A survey method was used and collected evidence from 264 Chinese SMEs. The findings exhibit that human capital directly enhances SMEs' efficiency but the presence of financial resources as a moderator weakens the influence. This research recommends that owners and managers of SMEs need to use their financial resources complementary with structural and customer capital while human capital should be used exclusively. Studies have also discussed the role of intellectual capital (IC) (human capital, customer capital and structural capital) in firm competitive advantage and performance in emerging and developed economies [12, 13] Also, studies have assessed the direct and indirect influence of IC on performance [14] [15] [16] . cache = ./cache/cord-011798-uss38ped.txt txt = ./txt/cord-011798-uss38ped.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-251979-j3mme15e author = Kandeel, Amr title = Morbidity, Mortality, and Seasonality of Influenza Hospitalizations in Egypt, November 2007-November 2014 date = 2016-09-08 pages = extension = .txt mime = text/plain words = 4716 sentences = 272 flesch = 43 summary = METHODS: Syndromic case definitions identified individuals with severe acute respiratory infection (SARI) admitted to eight hospitals in Egypt. The aims of this study were to (1) assess the proportion of SARI cases having influenza infection in Egypt; (2) examine the types and subtypes of detected influenza viruses in Egypt; (3) compare demographic and clinical characteristics of influenza-positive SARI cases to those of influenza-negative SARI cases in Egypt; (4) quantify influenza deaths and assess influenza mortality risk factors in Egypt; and (5) establish a defined period of influenza seasonality in Egypt. The odds of death among influenza-positive cases were modeled with logistic regression using different explanatory variables (age group: pediatric <15 years old versus adult 15 years old; sex: male versus female; days from symptom onset to hospitalization: 0-2 versus 3-4 versus 5; chronic conditions: at least one versus none; and influenza type: A versus B). cache = ./cache/cord-251979-j3mme15e.txt txt = ./txt/cord-251979-j3mme15e.txt === reduce.pl bib === === reduce.pl bib === id = cord-048492-4z38v9rg author = Tang, Julian W. title = Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006) date = 2008-07-23 pages = extension = .txt mime = text/plain words = 4458 sentences = 202 flesch = 48 summary = In this study, an analysis is presented of 281 Hong Kong influenza A(H3N2) hemagglutinin (HA) and neuraminidase (NA) full-length, dated sequences collected over 10 years (1997-2006) to assist the ongoing efforts to elucidate the underlying basis for the seasonality of influenza A(H3N2). One example of such possible viral persistence between influenza seasons was found, with HA and NA sequences from the same viruses (5251Jan02 and 5267Jan03, as indicated in Figures S1 and S2 for the HA and NA phylogenetic trees, respectively), showing a similar clustering pattern for both these genes, separated by at least one year. A similar analysis was recently performed using dated whole genome influenza A(H3N2) sequences from New York, New Zealand and Australia, downloaded from publicly available databases, in an attempt to test two competing hypotheses: whether seasonal influenza A(H3N2) viruses continuously 'migrate' around the world, particularly between Northern and Southern hemispheres; or whether the virus remains 'latent' in one location and reactivates each year to produce the familiar pattern of influenza seasonality [19] . cache = ./cache/cord-048492-4z38v9rg.txt txt = ./txt/cord-048492-4z38v9rg.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-252739-1manzf3l author = Zheng, Yueming title = Hexachlorophene Is a Potent KCNQ1/KCNE1 Potassium Channel Activator Which Rescues LQTs Mutants date = 2012-12-12 pages = extension = .txt mime = text/plain words = 4007 sentences = 250 flesch = 56 summary = The voltage-gated KCNQ1 potassium channel is expressed in cardiac tissues, and coassembly of KCNQ1 with an auxiliary KCNE1 subunit mediates a slowly activating current that accelerates the repolarization of action potential in cardiomyocytes. Mutations of KCNQ1 genes that result in reduction or loss of channel activity cause prolongation of repolarization during action potential, thereby causing long QT syndrome (LQTs). Small molecule activators of KCNQ1/KCNE1 are useful both for understanding the mechanism of the complex activity and for developing therapeutics for LQTs. In this study we report that hexachlorophene (HCP), the active component of the topical anti-infective prescription drug pHisoHex, is a KCNQ1/KCNE1 activator. Consistent with previous reports, the effects of KCNE1 on KCNQ1 include increase in overall current amplitude, slowing of the activation and deactivation kinetics, and removal of inactivation (Fig. 4A) . The common phenotype of these mutants is reduction of IKs current, which are commonly thought to be mediated by the KCNQ1/KCNE1 complex [2, 3] , as a result of decrease in either channel activity or trafficking efficiency. cache = ./cache/cord-252739-1manzf3l.txt txt = ./txt/cord-252739-1manzf3l.txt === reduce.pl bib === id = cord-254117-2ttwaegh author = Priest, Patricia C. title = Thermal Image Scanning for Influenza Border Screening: Results of an Airport Screening Study date = 2011-01-05 pages = extension = .txt mime = text/plain words = 4187 sentences = 186 flesch = 44 summary = The prediction by ITIS of tympanic temperature (37.8°C and 37.5°C) and of influenza infection was assessed using Receiver Operating Characteristic (ROC) curves and estimated sensitivity, specificity and positive predictive value (PPV). This evaluation of thermal image scanning was carried out as part of a larger study to measure the prevalence of seasonal influenza infection in arriving airline travellers and the effectiveness of a screening questionnaire for detecting those with influenza infection. To assess the utility of fever as a screening test for influenza infection (MT-PCR result), sensitivity, specificity, and population PPV for influenza were estimated for each tympanic temperature threshold, and the ITIS threshold used above. The greatest potential for the use of ITIS to screen incoming or departing travellers for infectious diseases such as a pandemic strain of influenza would be as the first stage of screening; that is, to identify and select out a high risk group for further assessment, for example by questionnaire, body core temperature measurement, and/or respiratory sample collection. cache = ./cache/cord-254117-2ttwaegh.txt txt = ./txt/cord-254117-2ttwaegh.txt === reduce.pl bib === id = cord-048360-n9sih438 author = Villard, Viviane title = Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif date = 2007-07-25 pages = extension = .txt mime = text/plain words = 4794 sentences = 228 flesch = 45 summary = To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. Here, we focus on the Pf parasite erythrocytic stage, a target of protective antibodies and describe a straightforward, rapid procedure based on bioinformatic analysis of a-helical coiled-coil motifs and peptide synthesis. With regard to the structural features and cellular location prediction of the proteins corresponding to the peptides selected for ADCI assays ( Table 1) , 15 of the proteins contain a pentapeptide conforming to the PEXEL consensus [19, 20; 21, 22] , but that none of these have a position within the amino acid sequence that conforms to the location of known active PEXEL motifs (see Materials and Methods and membrane segments, and none of them has a GPI anchor. In conclusion, an approach combining a genome-wide search by bioinformatics of a-helical coiled coil protein motifs and chemical synthesis can lead to the rapid identification and development of new malaria vaccine candidates. cache = ./cache/cord-048360-n9sih438.txt txt = ./txt/cord-048360-n9sih438.txt === reduce.pl bib === id = cord-013099-j816c3tw author = Blease, Charlotte title = US primary care in 2029: A Delphi survey on the impact of machine learning date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5698 sentences = 303 flesch = 54 summary = To address this research gap, we designed a Delphi survey to explore leading health informaticians' predictions about the impact of machine learning on primary care in the US in 2029. Acknowledging that heterogeneous panels have been shown to result in more accurate estimates [33] , and that what counts as an expert can be influenced by goals, values, and the manner in which knowledge is generated, we aimed to recruit diverse participants from across academia, healthcare, non-profit organizations, and industry; and to strive for panelists with a varied complementarity of interests within health informatics. In the first round, the Delphi survey requested demographic information; this was followed by 5 sections, with 7 open-ended questions, on the impact of machine learning on primary care by 2029 (see S1 Appendix; Table 1 We also included a final comment-box for feedback on the survey. cache = ./cache/cord-013099-j816c3tw.txt txt = ./txt/cord-013099-j816c3tw.txt === reduce.pl bib === id = cord-013334-cptu0k7s author = Holst-Hansen, Joachim A. title = Does the size of rewards influence performance in cognitively demanding tasks? date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6101 sentences = 326 flesch = 55 summary = Empirical studies in sports settings show that athletes generally perform worse when the stakes are higher, while a range of lab studies involving cognitively demanding tasks have led to diverging results, supporting positive, negative and null-effects of higher (vs. Third, if the given task can't be solved more efficiently than the level of performance a low monetary incentive allows, a higher stake can't have an additional positive effect due to a ceiling effect [3] . Studies that have asked participants to solve various forms of cognitively demanding tasks have led to ambiguous findings; some studies find a positive effect on performance of higher stakes compared to lower [6, 16, 17] , some find a negative effect [5, 18] while others find no clear effect when comparing high vs. In order to further investigate how the reward size might influence behavior, we also assess if self-reported measures of effort [6] , intrinsic motivation [7] and focus [5] vary depending on the reward structure the participants have been exposed to. cache = ./cache/cord-013334-cptu0k7s.txt txt = ./txt/cord-013334-cptu0k7s.txt === reduce.pl bib === id = cord-254025-j1l0mder author = de Melo, Andreia C. title = Cancer inpatients with COVID-19: A report from the Brazilian National Cancer Institute date = 2020-10-26 pages = extension = .txt mime = text/plain words = 3366 sentences = 178 flesch = 50 summary = According to the univariate analysis COVID-19-specific mortality was significantly associated with age over 75 years (P = .002), metastatic cancer (p <0.001), two or more sites of metastases (P < .001), the presence of lung (P < .001) or bone metastases (P = .001), non-curative treatment or best supportive care intent (P < .001), higher C-reactive protein levels (P = .002), admission due to COVID-19 (P = .009), and antibiotics use (P = .02). As shown in Table 3 , mortality related to COVID-19 was significantly associated to older age (P < .001 for patients between 60 to 74 years and P = .002 for patients aged 75 years or older), metastatic cancer (P < .001), two or more sites of metastases (P < .001), the presence of lung (P < .001) or bone metastases (P = .001), non-curative treatment or best supportive care intent (P < .001), higher C-reactive protein levels (P = .002), admission due to COVID-19 (P = .009), and antibiotics use (P = .02). cache = ./cache/cord-254025-j1l0mder.txt txt = ./txt/cord-254025-j1l0mder.txt === reduce.pl bib === id = cord-255013-njpuc475 author = He, Xiaocui title = Establishment of Myotis myotis Cell Lines - Model for Investigation of Host-Pathogen Interaction in a Natural Host for Emerging Viruses date = 2014-10-08 pages = extension = .txt mime = text/plain words = 4516 sentences = 263 flesch = 54 summary = The usefulness of these cell lines to study antiviral responses has been confirmed by analysis of their susceptibility to lyssavirus infection and the mRNA patterns of immune-relevant genes after poly I:C stimulation. myotis cell lines present a valuable in vitro model to study the interactions between lyssaviruses and their natural host, and to shed light on the mechanisms of resistance in bat's central nervous system (CNS). To further evaluate the cell line models for study of the different susceptibility between MmBr and other cell lines, mRNA expressions of PRRs and IFN induced genes were investigated in MmTo and MmBr after RABV infection (MOI 0.01 to 1.0). The increased expression of dsRNA receptor TLR3 and IFN induced genes ISG56, ISG43, Mx1 and IFIT3 after stimulation with poly I:C mimicking a viral infection indicates that these cell lines can be used as effective in vitro models to study the bat's innate immune responses to virus infection [32, 44] . cache = ./cache/cord-255013-njpuc475.txt txt = ./txt/cord-255013-njpuc475.txt === reduce.pl bib === id = cord-254313-g2oc32dm author = Klink, Thomas title = Evaluating the diagnostic accuracy of the WHO Severe Acute Respiratory Infection (SARI) criteria in Middle Eastern children under two years over three respiratory seasons date = 2020-04-30 pages = extension = .txt mime = text/plain words = 4499 sentences = 215 flesch = 49 summary = Several studies, including at least nine in the Eastern Mediterranean region, have been published since 2011 using the SARI case definition as inclusion criteria to report a combination of clinical characteristics, risk factors, viral burden, or outcomes in adult and pediatric populations for flu and other respiratory viruses [5] [6] [7] [8] [9] [10] [11] [12] [13] . Only a handful of studies have evaluated the effectiveness of the criteria by including both SARI-positive and SARI-negative patients, allowing them to calculate the diagnostic accuracy of the criteria for detecting flu and respiratory syncytial virus (RSV) [14] [15] [16] [17] [18] [19] . The age distribution differences likely explain these discrepancies as our cohort consists only of children under two years, and the SARI criteria were the least sensitive (15.9%) and most specific (80.5%) for detecting flu in our patients under three months, who make up 45.4% of our study population. cache = ./cache/cord-254313-g2oc32dm.txt txt = ./txt/cord-254313-g2oc32dm.txt === reduce.pl bib === id = cord-253056-765rs3e7 author = Dionne, Audrey title = Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date = 2018-10-17 pages = extension = .txt mime = text/plain words = 3725 sentences = 208 flesch = 45 summary = title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection Children with persistent or recurrent fever 36 hours after the end of intravenous immunoglobulin (IVIG) are considered to be resistant to treatment and are at increased risk for coronary complications. RESULTS: Children with concomitant infection were more likely to have fever 48 hours after initial IVIG treatment (36% vs 20%, p = 0.05) and to be treated with a second dose (33% vs 18%, p = 0.04). Children with concurrent infection had higher rates of IVIG resistance (19 (33%) versus 17 (18%) patients, p = 0.04), and higher temperature at 48 hours (Fig 1) . In this retrospective series, the presence of a concomitant infection was associated with a higher rate of resistance to IVIG treatment. In this study, patients with concomitant infection had a higher rate of resistance to IVIG treatment. cache = ./cache/cord-253056-765rs3e7.txt txt = ./txt/cord-253056-765rs3e7.txt === reduce.pl bib === id = cord-254000-pbzcupjg author = Suvannachart, Pukkapol title = Repeatability, reproducibility, agreement, and safety of Tono-Pen tip cover for intraocular measurement using latex and polyethylene wrap date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3623 sentences = 264 flesch = 60 summary = PURPOSE: To evaluate repeatability, reproducibility, and agreement of intraocular pressure measurement with Tono-Pen using Ocufilm and polyethylene wrap tip cover in human eyes. For the right eye, 4 measurements using polyethylene wrap tip cover were done by two examiners (A and B) in random order to assess intra-observer repeatability and inter-observer reproducibility. For the left eye, 4 measurements were done by examiner A using both polyethylene wrap tip cover and Ocufilm in random order to assess intra-observer repeatability and agreement. RESULTS: For examiner A, the repeatability of polyethylene wrap tip cover was -0.34, 95% limits of agreement (LOA) were -3.04 to 2.36, and ICC was 0.93 in the right eyes. For IOP measurement with TP, our previous eye model and study conducted in canine eyes showed good repeatability and agreement between the custom-made polyethylene wrap (PW) tip cover and OF without causing any ocular surface complications [13, 14] . cache = ./cache/cord-254000-pbzcupjg.txt txt = ./txt/cord-254000-pbzcupjg.txt === reduce.pl bib === id = cord-048339-nzh87aux author = Caley, Peter title = The Waiting Time for Inter-Country Spread of Pandemic Influenza date = 2007-01-03 pages = extension = .txt mime = text/plain words = 5739 sentences = 253 flesch = 45 summary = On the other hand, the model predicts that border screening for symptomatic infection, wearing a protective mask during travel, promoting early presentation of cases arising among arriving passengers and moderate reduction in travel volumes increase the delay only by a matter of days or weeks. In this paper we demonstrate how the delay to importation of an epidemic of pandemic strain influenza may be quantified in terms of the growing infection incidence in the source region, traveler volumes, border screening measures, travel duration, inflight transmission and the delay until an infected arrival initiates a chain of transmission that gathers momentum. For example, if R = 1.5, and we reduce the number of intending travelers from 400 to 10 per day, implement 100% flight-based quarantining, implement compulsory mask wearing during travel and presentation at 6 hours following symptom onset then there is a substantial probability (0.74) that the pandemic strain will never be imported (assuming the epidemic is confined to the source country). cache = ./cache/cord-048339-nzh87aux.txt txt = ./txt/cord-048339-nzh87aux.txt === reduce.pl bib === id = cord-255576-738khdwv author = Van Duyne, Rachel title = Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date = 2012-07-10 pages = extension = .txt mime = text/plain words = 9845 sentences = 517 flesch = 56 summary = We have previously shown that Tax interacts directly with the cellular Rb (Retinoblastoma) protein and targets Rb for degradation via the proteasome pathway, resulting in a decrease in Rb protein expression in HTLV-1 infected cells and a dysregulation of the cell cycle [47] . Collectively, these data indicate that the Drosha in Tax-containing and HTLV-1 infected cells is mostly functionally inactive and the functional suppression of Drosha is dependent on its interaction with a small region of the N-terminus of Tax. We have shown above that Drosha is downregulated, degraded, and mostly inactive in HTLV-1 infected cells, however, it was not clear what effect this dysregulation of Drosha would have on viral replication. Collectively, these data indicate that proteins, such as IKK-b, among others, may directly be regulated by the Tax/Drosha interaction in HTLV infected cells. cache = ./cache/cord-255576-738khdwv.txt txt = ./txt/cord-255576-738khdwv.txt === reduce.pl bib === id = cord-013356-y6vceq2x author = Peace, Angela title = Orchard layout and plant traits influence fruit yield more strongly than pollinator behaviour and density in a dioecious crop date = 2020-10-23 pages = extension = .txt mime = text/plain words = 5864 sentences = 313 flesch = 57 summary = The predictive model provides strategies for improving crop management, such as choosing cultivars which have their peak bloom on the same day, increasing the number of flowers with approximately 70% female flowers in the orchard, and placing enough hives to maintain more than 6 bees per 1000 flowers to optimize yield. We expected that male-female kiwifruit flower ratio and pollinator density will influence fruit yield, along with various parameters of pollinator behavior. The model explicitly tracks pollinators (parameterized here based on data from honey bees), with varying pollen loads as they preferentially visit male and female flowers, as well as A major model output measure is the predicted yield, which is defined as the number of female flowers per ha that became fully pollinated fruit. The model includes preference parameters for pollinators to remain on the type of flower they are visiting, based again on data from honey bee observations. cache = ./cache/cord-013356-y6vceq2x.txt txt = ./txt/cord-013356-y6vceq2x.txt === reduce.pl bib === id = cord-260432-imslfm4l author = Marshall, Jenika D. title = THP-1 macrophage cholesterol efflux is impaired by palmitoleate through Akt activation date = 2020-05-21 pages = extension = .txt mime = text/plain words = 5851 sentences = 287 flesch = 47 summary = Thus, we hypothesized that one or more specific fatty acids that exist within the total FFA component of lipoprotein hydrolysis products that are generated by LPL impair cholesterol efflux through the activation of Akt. To test this hypothesis, using THP-1 macrophages, we examined the activation of Akt in response to various FFA mixtures that contain the concentrations of FFA species that we previously reported to be found within LPL hydrolysis products from total lipoproteins [16] . Lastly, we examined the molecular species of phosphoinositides (PIPx) of THP-1 macrophages treated with palmitoleate, to determine if there were changes to select PIPx species that may contribute to a preferential activation of Akt. We previously showed using antibody arrays that the hydrolysis products liberated by LPL from total lipoproteins (ρ<1.21 g/ml), as well as the reconstituted total FFA component matching that liberated by LPL at a physiological concentration of 0.68 mM, significantly increased the phosphorylation of Akt after 30 minutes within THP-1 macrophages [16] . cache = ./cache/cord-260432-imslfm4l.txt txt = ./txt/cord-260432-imslfm4l.txt === reduce.pl bib === id = cord-257603-ov0b8yub author = Azlan, Arina Anis title = Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia date = 2020-05-21 pages = extension = .txt mime = text/plain words = 4685 sentences = 256 flesch = 54 summary = To measure practices, participants were asked yes/no questions on whether they had avoided going to crowded places such as weddings; wore a face mask when leaving home; and whether they practiced proper hand hygiene in the week before the movement control order (MCO). The first question asked whether or not they agreed that the COVID-19 situation would be successfully controlled; second, whether they thought Malaysia would be able to win its battle against the virus; and third, whether they thought the Malaysian government was handling the health crisis well [Fig 1] . Practices toward COVID-19 were measured using three questions enquiring on: 1) avoidance of crowded places, 2) wearing of face masks; and 3) practising proper hand hygiene in the week before the Movement Control Order (MCO) was implemented in Malaysia [Fig 2] . Public knowledge, attitudes and practices towards COVID-19 in Malaysia residents in the Eastern region and retirees were among the highest percentage of participants who had not practised good hand hygiene in the week before the MCO. cache = ./cache/cord-257603-ov0b8yub.txt txt = ./txt/cord-257603-ov0b8yub.txt === reduce.pl bib === id = cord-254825-c5d0wul9 author = Kim, Sei Won title = Containment of a healthcare-associated COVID-19 outbreak in a university hospital in Seoul, Korea: A single-center experience date = 2020-08-14 pages = extension = .txt mime = text/plain words = 3554 sentences = 205 flesch = 49 summary = In this study, we retrospectively analyzed the results of SARS-CoV-2 RT-PCR testing, contact history, and presence of respiratory symptoms in a single center with a healthcare-associated COVID-19 outbreak. We reviewed the history of patients to assess whether they visited China or other high-risk countries within two weeks prior to the outbreak of healthcare-associated COVID-19, or if they came into contact with confirmed COVID-19 cases. After SARS-CoV-2 infection was confirmed, the Seoul city government announced the closure of the hospital on February 21, 2020, to prevent a healthcare-associated outbreak. After the hospital staff member responsible for transporting patients was confirmed as the first COVID-19 case, people with contact history, fever, or respiratory symptoms were tested for SARS-CoV-2 infection with RT-PCR (Fig 2) . After the first case was reported, epidemiologists from KCDC and the infection control unit of our hospital reviewed electronic medical charts, CCTV, and personal movements to identify individuals with potential contact with confirmed COVID-19 patients. cache = ./cache/cord-254825-c5d0wul9.txt txt = ./txt/cord-254825-c5d0wul9.txt === reduce.pl bib === id = cord-260653-5qwtvm9x author = Chikhlikar, Priya title = DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques date = 2006-12-27 pages = extension = .txt mime = text/plain words = 6117 sentences = 278 flesch = 49 summary = Thomas; Marques, Ernesto T.A. title: DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques Previous studies of HIV-1 p55Gag immunization of mice have demonstrated the usefulness of targeting antigens to the cellular compartment containing the major histocompatibility complex type II (MHC II) complex molecules by use of a DNA antigen formulation encoding Gag as a chimera with the mouse lysosome-associated membrane protein (mLAMP/gag). In the present study, we have analyzed the magnitude and breadth of Gag-specific T-lymphocyte and antibody responses elicited in Rhesus macaques after immunization with DNA encoding a human LAMP/gag (hLAMP/gag) chimera. This study demonstrates that Rhesus macaques immunized with a DNA plasmid vaccine-encoding gag as an hLAMP/gag chimera develops strong antigen-specific humoral responses as well as CD4 + and CD8 + T-cell responses. cache = ./cache/cord-260653-5qwtvm9x.txt txt = ./txt/cord-260653-5qwtvm9x.txt === reduce.pl bib === id = cord-254340-e1x0z3rh author = Cruz, Christian Joy Pattawi title = Exploring the young demographic profile of COVID-19 cases in Hong Kong: Evidence from migration and travel history data date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4963 sentences = 227 flesch = 59 summary = Using detailed case data from Hong Kong's Centre for Health Department and Immigration Department, we analyze the sex and age distribution of the confirmed cases along with their recent travel histories and immigration flows for the period January to April 2020. Our analysis highlights Hong Kong's high proportion of imported cases and large overseas student population in developing COVID-19 hotspot areas such as the United Kingdom. Our study includes an examination of the age and sex distribution of the COVID-19 confirmed cases in Hong Kong and an exploration of how the different measures to combat this outbreak resulted in a relatively low number of cases and deaths. In this paper, we highlight the potential impact of the young profile of the confirmed cases on the total number of mortalities and the effect of early, aggressive policy measures including travel bans, enforced quarantines and contact-tracing imposed by the Hong Kong government as early as January 27, 2020 in containing the spread of the COVID-19. cache = ./cache/cord-254340-e1x0z3rh.txt txt = ./txt/cord-254340-e1x0z3rh.txt === reduce.pl bib === id = cord-259771-653opx0h author = Dwivedi, Varun title = Biodegradable Nanoparticle-Entrapped Vaccine Induces Cross-Protective Immune Response against a Virulent Heterologous Respiratory Viral Infection in Pigs date = 2012-12-11 pages = extension = .txt mime = text/plain words = 5900 sentences = 290 flesch = 45 summary = In a pre-challenge study, intranasal delivery of Nano-KAg resulted in induction of innate immune response at both mucosal and systemic sites, indicated by a significant increase in the frequency of NK cells, DCs, and cd T cells in the lung MNC ( Figure 2 , A-C); and cd T cells and DCs in the PBMC compared to K-Ag vaccinated pigs (Figure 2, H & I) . Lung homogenates of Nano-KAg immunized pigs contained significantly higher levels of virus specific IgA and IgG antibodies compared to unvaccinated and K-Ag vaccinated, MN184 challenged pigs (Figure 4, A & B) . The frequency of cd T cells and CD4 + (but not CD8 + ) T cells in the lungs of Nano-KAg vaccinated animals were significantly increased compared to K-Ag and unvaccinated, virus challenged pigs ( Figure 5 , D, E & F). cache = ./cache/cord-259771-653opx0h.txt txt = ./txt/cord-259771-653opx0h.txt === reduce.pl bib === id = cord-260572-vd65ygtm author = Kim, Curi title = Comparison of Nasopharyngeal and Oropharyngeal Swabs for the Diagnosis of Eight Respiratory Viruses by Real-Time Reverse Transcription-PCR Assays date = 2011-06-30 pages = extension = .txt mime = text/plain words = 3515 sentences = 173 flesch = 52 summary = BACKGROUND: Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP) and/or oropharyngeal (OP) swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach. To evaluate the comparative yields of NP and OP swabs in detecting key respiratory viruses by real-time RT-PCR (qRT-PCR), we conducted a prospective study using paired NP and OP specimens from patients at two respiratory disease surveillance sites in Kenya. NP and OP specimens from each patient were separately tested by singleplex qRT-PCR for eight viral pathogens: adenovirus, influenza A virus, influenza B virus, human metapneumovirus (hMPV), parainfluenza viruses (PIV) 1-3, and respiratory syncytial virus (RSV). cache = ./cache/cord-260572-vd65ygtm.txt txt = ./txt/cord-260572-vd65ygtm.txt === reduce.pl bib === id = cord-256424-t3dtabi4 author = Bousbia, Sabri title = Repertoire of Intensive Care Unit Pneumonia Microbiota date = 2012-02-28 pages = extension = .txt mime = text/plain words = 5641 sentences = 294 flesch = 39 summary = Recently, the bacterial microbiota of patients with cystic fibrosis and ventilator-associated pneumonia (VAP) were studied using 16S rDNA gene amplification followed by clone libraries sequencing [9] [10] [11] . Bacterial microbiota as evaluated by 16S rDNA Molecular assays were positive for at least one bacterium for 129 out of 185 bronchoalveolar lavage (BAL) samples from patients with pneumonia as well as from 13 out of 25 from control individuals (p = 0.07). Fungal microbiota obtained from patients showed the presence of 22 different species belonging to 2 phyla (8 orders, 11 families and 12 genera) among which 6 phylotypes had not been previously identified in BAL fluids from pneumonia. Indeed, our study reveals that some pathogens that till now had been considered typical for ICU pneumonia, such as Pseudomonas aeruginosa and Streptococcus species, or viruses, such CMV and HSV, can be detected as commonly in controls as in patients (Fig. S1 and S2 ). cache = ./cache/cord-256424-t3dtabi4.txt txt = ./txt/cord-256424-t3dtabi4.txt === reduce.pl bib === id = cord-252795-x66zqmgv author = Islam, Md. Akhtarul title = Depression and anxiety among university students during the COVID-19 pandemic in Bangladesh: A web-based cross-sectional survey date = 2020-08-26 pages = extension = .txt mime = text/plain words = 4011 sentences = 214 flesch = 47 summary = title: Depression and anxiety among university students during the COVID-19 pandemic in Bangladesh: A web-based cross-sectional survey Following the detection of first COVID-19 case on March 8, 2020 [6] , Bangladesh like many other countries put the lockdown strategy into effect on March 26, 2020 , to ensure 'social distance' through 'home quarantine' to curb the 'spread' among its population [7] [8] [9] , since a precise treatment or vaccine for the infected and people at risk are yet to achieved by the global health community [10, 11] . The ongoing COVID-19 pandemic is creating a psycho-emotional chaotic situation as countries have been reporting a sharp rise of mental health problems, including anxiety, depression, stress, sleep disorder as well as fear, among its citizens [15] [16] [17] [18] [19] , that eventually increased the substance use [15] and sometimes suicidal behavior [20] [21] [22] . Researchers in China observed that the greater exposure to 'misinformation' through social media are more likely contributing to the development of anxiety, depression, and other mental health problems among its population of different socioeconomic background [23] [24] [25] [26] . cache = ./cache/cord-252795-x66zqmgv.txt txt = ./txt/cord-252795-x66zqmgv.txt === reduce.pl bib === id = cord-262345-hti1jjpn author = Eddy, Lucy H. title = The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review date = 2020-08-25 pages = extension = .txt mime = text/plain words = 8728 sentences = 470 flesch = 50 summary = title: The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review METHODS: A pre-search of 'fundamental movement skills' OR 'fundamental motor skills' in seven online databases (PubMed, Ovid MEDLINE, Ovid Embase, EBSCO CINAHL, EBSCO SPORTDiscus, Ovid PsycINFO and Web of Science) identified 24 assessment tools for school-aged children that: (i) assess FMS; (ii) measure actual motor competence and (iii) evaluate performance on a standard battery of tasks. The psychometric properties of observational assessments of fundamental movement skills for school children correlations to evaluate the concurrent validity between the MOT 4-6 and the KTK, with results showing moderate correlations for children aged 5-6 (mean r = .63), as was hypothesised prior to testing (r >. cache = ./cache/cord-262345-hti1jjpn.txt txt = ./txt/cord-262345-hti1jjpn.txt === reduce.pl bib === id = cord-253436-dz84icdc author = Wille, Michelle title = High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl date = 2016-03-03 pages = extension = .txt mime = text/plain words = 2019 sentences = 103 flesch = 54 summary = In this study we screened 764 samples from 22 avian species of the orders Anseriformes and Charadriiformes in Sweden collected in 2006/2007 for CoV, with an overall CoV prevalence of 18.7%, which is higher than many other wild bird surveys. Coronavirus sequences from Mallards in this study were highly similar to CoV sequences from the sample species and location in 2011, suggesting long-term maintenance in this population. Despite few studies, small samples sizes and differences in prevalence, what is clear, is that in the Northern Hemisphere waterfowl species, especially dabbling and diving ducks are important in the epidemiology of avian CoVs. It is interesting to note that these patterns are very similar to those found in low pathogenic influenza A viruses: high prevalence in waterfowl and gulls in the Northern Hemisphere [30] , and little host species and temporal structuring within waterfowl derived viruses in the conserved polymerase genes (such as PB2, PB1) [31] . cache = ./cache/cord-253436-dz84icdc.txt txt = ./txt/cord-253436-dz84icdc.txt === reduce.pl bib === id = cord-258366-fu9b446y author = Couto, Carla R. title = Fighting Misconceptions to Improve Compliance with Influenza Vaccination among Health Care Workers: An Educational Project date = 2012-02-06 pages = extension = .txt mime = text/plain words = 3287 sentences = 180 flesch = 49 summary = At Hospital das Clinicas, University of Sã o Paulo School of Medical Sciences, a previous study showed a 34% compliance with influenza vaccination among HCWs. In the mentioned study, the main reasons for non-compliance were the perception of vaccine inefficacy and the fear of adverse reactions [4] . To diminish the arguments of fear of adverse events or perception of vaccine inefficacy, this prospective study was conducted to demonstrate to a subset of HCWs from our hospital, that severe adverse events following influenza vaccination are rare and the episodes of respiratory symptoms occurring in the first four months after vaccination are generally caused by other respiratory viruses and not by influenza virus. As expected, no severe adverse event was observed in the present study, and the events more frequently reported, such as headache, myalgia and malaise could be related to influenza vaccine itself as well as to other causes, given their unspecificity. cache = ./cache/cord-258366-fu9b446y.txt txt = ./txt/cord-258366-fu9b446y.txt === reduce.pl bib === id = cord-261908-olcuq6tm author = Lai, Ka-Man title = Propagation of Respiratory Aerosols by the Vuvuzela date = 2011-05-23 pages = extension = .txt mime = text/plain words = 3983 sentences = 199 flesch = 53 summary = The fate of the droplet nuclei on inhalation also depends on their size; particles greater than five microns are likely to remain in the upper airways but smaller particles are more likely to deposit in the alveoli and so may transmit infections of the lower respiratory tract such as tuberculosis [22, 23] . The large number of aerosols emitted by the vuvuzela raises the possibility that, if used by persons with an infection of the respiratory tract, they could act a conduit for the spread of infectious particles. To obtain the desired trumpet sound when blowing the vuvuzela air is forced through the lips into the opening of the instrument which may serve to create further aerosols, or alter the size of droplets produced elsewhere in the respiratory tract. Exhale duration, peak air velocity, particle concentration and mean particle diameter recorded during playing the vuvuzela and shouting by four male and four female volunteers. cache = ./cache/cord-261908-olcuq6tm.txt txt = ./txt/cord-261908-olcuq6tm.txt === reduce.pl bib === id = cord-258243-2utl2mfl author = Chen, Jeng-Wen title = Factors associated with changing indications for adenotonsillectomy: A population-based longitudinal study date = 2018-05-29 pages = extension = .txt mime = text/plain words = 4350 sentences = 230 flesch = 44 summary = We investigated the distribution of the three major categories of surgical indication according to sex, age group (<5 years, 5-11 years, 11-17 years, 18-40 years, and >40 years), hospital level (medical centers, regional hospitals, and local hospitals), and insured residence areas according to the NHI divisions (Taipei, Northern, Central, Southern, Kaoping, and Eastern). In the adult subgroup (Figs 2B and 3B) , the incidence and proportion of AT performed for RICI decreased from 46 (78%) in 1997 to 32 Table 3 indicates the number and percentage of the three categories of surgical indications according to sex, age groups, hospital level, and insured residence areas in the total study population. The trend in the AT rate and the proportion of surgical indications by the calendar year according to sex, age groups, hospital level, and insured residence areas in the total study population are shown in the supplemental data (S1 File). cache = ./cache/cord-258243-2utl2mfl.txt txt = ./txt/cord-258243-2utl2mfl.txt === reduce.pl bib === id = cord-258172-p54j4zzo author = Barker, Harlan title = Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date = 2020-10-28 pages = extension = .txt mime = text/plain words = 8453 sentences = 409 flesch = 48 summary = Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . cache = ./cache/cord-258172-p54j4zzo.txt txt = ./txt/cord-258172-p54j4zzo.txt === reduce.pl bib === id = cord-255351-vp19ydce author = Lanata, Claudio F. title = Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review date = 2013-09-04 pages = extension = .txt mime = text/plain words = 5451 sentences = 221 flesch = 48 summary = We present the results of a systematic literature review of studies of diarrhea etiology in hospitalized children and use these results to estimate the global burden of diarrhea mortality by pathogen for children under 5 years of age for 2011. From 22 643 citations identified in the electronic search, 1 003 articles were selected for further evaluation (Fig. 1) ; 840 articles were excluded because they had one or more of the exclusion criteria (About 35% because they were not longitudinal studies or inappropriate laboratory methods were used, 31% because no data was given for children ,5 years of age, 23% for studies that lasted less than 12 months of duration, and the rest because data were reported after rotavirus vaccine introduction, duplicate publications or reporting results on a pathogen not included in our list). cache = ./cache/cord-255351-vp19ydce.txt txt = ./txt/cord-255351-vp19ydce.txt === reduce.pl bib === id = cord-255588-nh34lgdh author = Guo, Fang title = RO 90-7501 Enhances TLR3 and RLR Agonist Induced Antiviral Response date = 2012-10-03 pages = extension = .txt mime = text/plain words = 4776 sentences = 268 flesch = 51 summary = Recognition of virus infection by innate pattern recognition receptors (PRRs), including membrane-associated toll-like receptors (TLR) and cytoplasmic RIG-I-like receptors (RLR), activates cascades of signal transduction pathways leading to production of type I interferons (IFN) and proinflammatory cytokines that orchestrate the elimination of the viruses. In our efforts to identify small molecules that selectively enhance PRR-mediated antiviral, but not the detrimental inflammatory response, we discovered a compound, RO 90–7501 ('2'-(4-Aminophenyl)-[2,5′-bi-1H-benzimidazol]-5-amine), that significantly promoted both TLR3 and RLR ligand-induced IFN-β gene expression and antiviral response, most likely via selective activation of p38 mitogen-activated protein kinase (MAPK) pathway. In order to discover compounds with the expected pharmacological property, we set out to establish reporter cell lines for high throughput screening of small molecules that selectively enhance TLR3 ligand-induced IFN-b gene expression, but do not affect NFkB activation, which is a central player in the induction of proinflammatory cytokines, but plays a less prominent role in type I IFN gene expression [25] . cache = ./cache/cord-255588-nh34lgdh.txt txt = ./txt/cord-255588-nh34lgdh.txt === reduce.pl bib === id = cord-260843-c97kctjz author = Dai, Lei title = Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake date = 2016-11-16 pages = extension = .txt mime = text/plain words = 4635 sentences = 255 flesch = 46 summary = In vivo, TGEV primarily targets and infects intestinal epithelial cells, which play an important role in glucose absorption via the apical and basolateral transporters Na(+)-dependent glucose transporter 1 (SGLT1) and facilitative glucose transporter 2 (GLUT2), respectively. Our data demonstrate that infection with TGEV resulted in increased glucose uptake and augmented expression of EGFR, SGLT1 and GLUT2. Therefore, in the study, we aimed to examine the in vitro effects of TGEV infection on glucose uptake and the expression of SGLT1 and GLUT2 in porcine intestinal columnar epithelial (IPEC-J2) cells, which have been shown to offer a practical model for studying TGEV infection [11, 12] . Together, these results indicate that EGFR and p-EGFR regulates glucose uptake in mock-infected IPEC-J2 cells by modulation of SGLT1 protein expression. Together, these results indicate that EGFR influences glucose uptake in TGEV-infected cells by promoting both SGLT1 and GLUT2 expression. cache = ./cache/cord-260843-c97kctjz.txt txt = ./txt/cord-260843-c97kctjz.txt === reduce.pl bib === id = cord-260728-4w23kwzu author = Timmermans, Ans title = Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia date = 2016-03-30 pages = extension = .txt mime = text/plain words = 7411 sentences = 381 flesch = 50 summary = Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. Between May 2010 and December 2012, we collected specimens and surveillance data for influenza and other viral respiratory pathogens from a subset of outpatients presenting with influenza-like-illness (ILI) at four sentinel sites-located in five health centers and hospitals in Battambang, Oddar Meanchey, Pailin and Banteay Meanchey provinces in Cambodia (Fig 1) . A subset of 164 culture-negative specimens (collected between May 2010 and April 2012), where we found a higher proportion (5.6%) of non-polio enteroviruses in children less than 5 years old as compared with previous studies (1%) in Cambodia [2] , were tested for enterovirus and rhinovirus by two separate nested RT-PCR methods adapted from Coiras et al., 2004 and Singh et al., 2002 [29,30] , one for simultaneous detection of pan-enteroviruses and rhinoviruses, and the other specific for enterovirus 71 (EV71). cache = ./cache/cord-260728-4w23kwzu.txt txt = ./txt/cord-260728-4w23kwzu.txt === reduce.pl bib === id = cord-260647-7bjhobg7 author = Coudray-Meunier, Coralie title = A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date = 2016-01-29 pages = extension = .txt mime = text/plain words = 5581 sentences = 278 flesch = 48 summary = A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The aim of this study was to develop real time RT-PCR assays for detection of a total of 19 human enteric viruses (including 3 genogroupes of norovirus and 4 coronaviruses) and two control process viruses (mengovirus and murine norovirus) generally used for monitoring the recovery of viral foodstuff extraction methods. The sensitivity of conventional qPCR assays targeting 21 viral genomes was compared to the quantitative digital RT-PCR array and to the qualitative nanofluidic real-time PCR array performed on Fluidigm's BioMark System. Similarly, by testing genomes from viruses in stools and RNA from virus production in cells, the limit of detection (LOD) as determined by RT-dPCR was respectively 1.5 to 3.4 log 10 and 1.6 to 2.1 log 10 lower than the expected copy numbers calculated via the standard curve by RT-qPCR. cache = ./cache/cord-260647-7bjhobg7.txt txt = ./txt/cord-260647-7bjhobg7.txt === reduce.pl bib === id = cord-262759-ec2c25q3 author = Hsieh, Yi-Ting title = Glucose-6-Phosphate Dehydrogenase (G6PD)-Deficient Epithelial Cells Are Less Tolerant to Infection by Staphylococcus aureus date = 2013-11-04 pages = extension = .txt mime = text/plain words = 4838 sentences = 223 flesch = 40 summary = The impairment of ROS removal is predicted to enhance apoptotic activity in G6PD-deficient cells, and this enhanced apoptosis was observed by annexin V/PI staining under a confocal fluorescence microscope and quantified by flow cytometry. We hypothesized that G6PD-deficient cells are less tolerant to oxidative stress upon bacterial infection, leading to the accumulation of more intracellular ROS when compared to the control scramble cells. To determine whether the reduced ROS accumulation and apoptotic activity, particularly in G6PD-deficient cells, was due to deceased αhemolysin expression upon VRSA infection in the presence of vancomycin, the production of intracellular ROS and cell apoptosis when the α-hemolysin inhibitor Oroxylin A was added to the media was quantified by flow cytometry. Our results presented here indicate that expression of active caspase-9, as well as the downstream caspase-3, was much higher in G6PD-deficient cells than in control scramble cells upon VRSA infection, suggesting that mitochondrial dysfunction may be the major cause of the increase in cell apoptosis (Figure 4) . cache = ./cache/cord-262759-ec2c25q3.txt txt = ./txt/cord-262759-ec2c25q3.txt === reduce.pl bib === id = cord-048477-ze511t38 author = Patel, Mahomed S. title = General Practice and Pandemic Influenza: A Framework for Planning and Comparison of Plans in Five Countries date = 2008-05-28 pages = extension = .txt mime = text/plain words = 6918 sentences = 343 flesch = 41 summary = The framework identifies four functional domains: clinical care for influenza and other needs, public health responsibilities, the internal environment and the macro-environment of general practice. Although there is little evidence linking specific preparedness activities to effective system-wide responses to pandemic influenza [5, 6] , change management theories point to a need for dynamic partnerships between general practices and other ambulatory care services, hospitals and public health departments [10] . We aimed to develop a framework that will facilitate systematic planning for the general practice response to pandemic influenza and used it to appraise coverage of key elements in publicly available pandemic plans from Australia, England, USA, New Zealand and Canada. This calls for coordination across general practices and other ambulatory care services to ensure primary health care needs within the community are effectively monitored and addressed; with hospitals to avoid/delay hospitalisation and facilitate early discharge; and with public health units to share responsibilities for contact tracing, monitoring and treating people in home isolation or quarantine, dispensing of anti-viral medications, and participation in mass immunisations against pandemic strains of the virus (when these become available). cache = ./cache/cord-048477-ze511t38.txt txt = ./txt/cord-048477-ze511t38.txt === reduce.pl bib === id = cord-261410-kb91eagd author = Park, Ji Young title = Clinical Features and Courses of Adenovirus Pneumonia in Healthy Young Adults during an Outbreak among Korean Military Personnel date = 2017-01-23 pages = extension = .txt mime = text/plain words = 3504 sentences = 205 flesch = 43 summary = The clinical features of respiratory adenoviral infection among military personnel were described previously; however, HAdV pneumonia in immunocompetent individuals and risk factors of disease progression to severe pneumonia or acute respiratory failure have not been well studied. All military trainees or active duty members, but not officers, were eligible for enrollment if they were !18 years old and had been admitted to the study hospital for pneumonia, defined by acute respiratory symptoms (fever, cough, sputum, dyspnea, and pleuritic chest pain) and pulmonary infiltrates on chest X-rays or computed tomography (CT) scans. Most HAdV pneumonia patients were basic military trainees or personnel who had recently completed training; active duty service personnel were not usually affected, even during outbreak peaks. Our results show that an outbreak of HAdV pneumonia occurred in Korean military training centers and indicate that emergent-type HAdV-55 infections might have caused the outbreak. cache = ./cache/cord-261410-kb91eagd.txt txt = ./txt/cord-261410-kb91eagd.txt === reduce.pl bib === id = cord-256326-3ebcuzd6 author = Liotta, Giuseppe title = Is social connectedness a risk factor for the spreading of COVID-19 among older adults? The Italian paradox date = 2020-05-21 pages = extension = .txt mime = text/plain words = 2364 sentences = 114 flesch = 57 summary = We analyzed several variables to test this hypothesis, such as the percentage of infected patients aged >80 years, available nursing home beds, COVID-19 incidence rate, and the number of days from when the number of positive tests exceeded 50 (epidemic maturity). While there is a very clear association between the case fatality rate and age demographics (Italy has the second oldest population worldwide and has the highest ageing index in Europe [4] with a value of 168.9), we wanted to test the hypothesis that the supposed closeness between younger and older generations in Italian families may have played a major role in the pandemic spread. Additionally, we explored the relationship between the proportion of infected patients aged >80 years and social connectedness indicators, such as the percentage of family comprising one members and household size [5] . cache = ./cache/cord-256326-3ebcuzd6.txt txt = ./txt/cord-256326-3ebcuzd6.txt === reduce.pl bib === id = cord-256837-100ir651 author = Smith, Steven B. title = Identification of Common Biological Pathways and Drug Targets Across Multiple Respiratory Viruses Based on Human Host Gene Expression Analysis date = 2012-03-14 pages = extension = .txt mime = text/plain words = 8447 sentences = 415 flesch = 38 summary = Several recent studies have generated multiple mRNA microarray gene expression datasets derived from experiments involving the infection of human cell-lines or animal models with one or more of the major respiratory viruses [21] [22] [23] . Through a systematic analysis of these respiratory virus-human host gene expression datasets, we determined common sets of genes and pathways involved in host responses to viral infections. A total of seven different respiratory viruses were analyzed, represented by fifteen unique Gene Expression Omnibus (GEO) datasets (indicated by GEO Series or GSE accession numbers), nine different human cell types, and seven different array platforms for a total of 28 unique comparisons. This assumption is based on the occurrence of genes that are differentially expressed in infection models for at least five of the seven respiratory viruses, have involvement in a number of relevant pathways related to host immune response, and encode for known drug targets. cache = ./cache/cord-256837-100ir651.txt txt = ./txt/cord-256837-100ir651.txt === reduce.pl bib === === reduce.pl bib === id = cord-262846-1mhimfsf author = Gray, Nicholas title = Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6023 sentences = 337 flesch = 55 summary = This strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal lockdown measures. To explore the effect of imperfect testing on the disease dynamics when strategies testing regimes are employed to relax lockdown measures, three new classes were added to the model. implement quarantine in their model but do not incorporate the effects on the dynamics from imperfect testing, nor do they consider how the quality and scale of an available test affect the spread of a disease. Wide-scale screening for antibodies in the general population promises significant scientific value, and targeted antibody testing is likely to have value for reducing risks to NHS and care-sector staff, and other key workers who will need to have close contact with COVID-19 sufferers. cache = ./cache/cord-262846-1mhimfsf.txt txt = ./txt/cord-262846-1mhimfsf.txt === reduce.pl bib === id = cord-263276-keyu60in author = Zhou, Weimin title = Prevalence of Herpes and Respiratory Viruses in Induced Sputum among Hospitalized Children with Non Typical Bacterial Community-Acquired Pneumonia date = 2013-11-18 pages = extension = .txt mime = text/plain words = 3813 sentences = 191 flesch = 50 summary = METHODS: Induced sputum (IS) samples were collected from 354 hospitalised patients (infants, n = 205; children, n = 149) with respiratory illness (CAP or non-CAP) admitted to Wenling Hospital of China. The present study was undertaken to describe the profiles of HHVs and other respiratory viruses associated with hospital-based CAP and non-CAP among infants and young children in a rural area of China using comprehensive and sensitive molecular diagnostic techniques. In this study, the viral prevalence in sputum specimens of childhood with non typical bacterial CAP was investigated using sensitive molecular diagnostic methods for HHVs and 15 respiratory viruses, and viruses were detected in 99.6% of the children. In summary, our study on the prevalence of HHVs and other respiratory viruses in infants and young children with CAP identified a detectable virus in more than 99.6% of case participants, in which CMV, HHV-6, EBV, RSV and HBoV were clearly predominant (.25%) and contributed significantly to the spectrum of CAP in a rural area of China. cache = ./cache/cord-263276-keyu60in.txt txt = ./txt/cord-263276-keyu60in.txt === reduce.pl bib === id = cord-263453-7v4y02j6 author = Nishiura, Hiroshi title = Early Epidemiological Assessment of the Virulence of Emerging Infectious Diseases: A Case Study of an Influenza Pandemic date = 2009-08-31 pages = extension = .txt mime = text/plain words = 5350 sentences = 231 flesch = 55 summary = We first examine the approach by analyzing an outbreak of severe acute respiratory syndrome in Hong Kong (2003) with known unbiased cCFR estimate, and then investigate published epidemiological datasets of novel swine-origin influenza A (H1N1) virus infection in the USA and Canada (2009). Nevertheless, a much-used crude estimate of the cCFR, i.e. the ratio of the cumulative number of deaths to cases at calendar time t, tends to yield a biased (and mostly underestimated) cCFR due to the time-delay from onset to death [8] ; similar estimates of such a biased cCFR for severe acute respiratory syndrome (SARS) have shown how such estimates can vary substantially as an epidemic progresses, stabilizing only in the later stages of the outbreak [8, 9] . doi:10.1371/journal.pone.0006852.g003 Figure 6 shows the time course of biased cCFR estimates in the USA and Canada based on the reporting date of confirmed cases and deaths to the World Health Organization. cache = ./cache/cord-263453-7v4y02j6.txt txt = ./txt/cord-263453-7v4y02j6.txt === reduce.pl bib === id = cord-263978-jk82bk1a author = Karaivanov, Alexander title = A social network model of COVID-19 date = 2020-10-29 pages = extension = .txt mime = text/plain words = 11398 sentences = 576 flesch = 57 summary = The proposed network-augmented (NSIR) model allows the evaluation, via simulations, of (i) health and economic policies and outcomes for all or subset of the population: lockdown/distancing, herd immunity, testing, contact tracing; (ii) behavioral responses and/or imposing or lifting policies at specific times or conditional on observed states. I construct and compute a dynamic social network-based model of the COVID-19 epidemic and use it to evaluate a range of simulated health and economic policies-herd immunity, distancing, lockdown, testing, quarantine, and contact tracing. While helpful for simplifying the dynamics and computing outcomes, this population-level random matching assumption abstracts from important elements of realism and locality: (i) people are more likely to interact with members of their social network, broadly defined (e.g., family, work, or distance based); (ii) health and economic policies targeting disease mitigation, as well as individual behavioral responses, can affect the rate of viral transmission via a person's network of contacts vs. cache = ./cache/cord-263978-jk82bk1a.txt txt = ./txt/cord-263978-jk82bk1a.txt === reduce.pl bib === id = cord-257217-f9sdt7ax author = Nunes, Marta C. title = Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date = 2014-02-03 pages = extension = .txt mime = text/plain words = 4629 sentences = 215 flesch = 43 summary = We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and –KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI). METHODS: Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and –uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and influenza A/B. The aim of this study was to identify the prevalence of hBoV, hRV, WUPyV, KIPyV, CoV-OC43, CoV-NL63, CoV-HKU1 and CoV-229E among HIV-infected and -uninfected children who were hospitalized for LRTI using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Very few viral aetiology studies have been conducted in Africa: in a Mozambican study of virus-associated acute respiratory infections (ARI) in infants with an estimated 3-5% HIV prevalence, the most frequently detected viruses were hRV (26%), influenza (15%) and adenovirus (14%) [27] . cache = ./cache/cord-257217-f9sdt7ax.txt txt = ./txt/cord-257217-f9sdt7ax.txt === reduce.pl bib === id = cord-255384-tljyx6ua author = Decaro, Nicola title = Full-Genome Analysis of a Canine Pneumovirus Causing Acute Respiratory Disease in Dogs, Italy date = 2014-01-06 pages = extension = .txt mime = text/plain words = 4629 sentences = 243 flesch = 55 summary = The full-genomic characterisation showed that the causative agent (strain Bari/100-12) was closely related to CnPnVs that have been recently isolated in the USA, as well as to murine pneumovirus, which is responsible for respiratory disease in mice. In order to obtain new insights into the genetic diversity of CnPnV, the Italian prototype strain dog/Bari/100-12/ITA/2012 was submitted to RT-PCR amplification and subsequent sequence analysis of the full-length genome, using oligonucleotide retrieved from previous studies [13] [14] . When the analysis was restricted to the 8,600 and 8,598 nt available for reference CnPnV strains Brne17 and Ane4, respectively, that span from the very 39 end of the L gene to the 59end of the leader region (genome sense), an overall sequence identity of 96.5-96.6% was found against the canine strains. cache = ./cache/cord-255384-tljyx6ua.txt txt = ./txt/cord-255384-tljyx6ua.txt === reduce.pl bib === id = cord-265138-i5m3ax7g author = Wang, Xi-Ling title = Model Selection in Time Series Studies of Influenza-Associated Mortality date = 2012-06-20 pages = extension = .txt mime = text/plain words = 4196 sentences = 240 flesch = 45 summary = METHODS: We assessed four model selection criteria: quasi Akaike information criterion (QAIC), quasi Bayesian information criterion (QBIC), partial autocorrelation functions of residuals (PACF), and generalized cross-validation (GCV), by separately applying them to select the Poisson model best fitted to the mortality datasets that were simulated under the different assumptions of seasonal confounding. CONCLUSIONS: GCV criterion is recommended for selection of Poisson models to estimate influenza-associated mortality and morbidity burden with proper adjustment for confounding. Four model selection criteria were considered in this study: quasi Akaike information criterion (QAIC), quasi Bayesian information criterion (QBIC), partial autocorrelation functions of residuals (PACF), and generalized cross-validation (GCV). Two recent studies in Canada and Hong Kong have demonstrated the estimates of influenza-associated hospitalization derived from Poisson regression models reasonably matched the numbers of patients with laboratory confirmed influenza infections [17, 29] . cache = ./cache/cord-265138-i5m3ax7g.txt txt = ./txt/cord-265138-i5m3ax7g.txt === reduce.pl bib === id = cord-263464-fdosch11 author = Nuvey, Francis Sena title = Evaluation of the sentinel surveillance system for influenza-like illnesses in the Greater Accra region, Ghana, 2018 date = 2019-03-14 pages = extension = .txt mime = text/plain words = 4094 sentences = 227 flesch = 47 summary = We evaluated the ILI surveillance system in the Greater Accra region, Ghana, to assess the system's attributes and its performance on set objectives. In collaboration with the Ghana Health Service (GHS) and the Ministry of Defense (MOD), it currently operates sentinel surveillance for influenza in 27 sites across all regions in Ghana with support from the U.S. Naval Medical Research Unit No. 3 (NAMRU-3), Centers for Disease Control and Prevention (CDC) and WHO [8] . We found that data on patients meeting the ILI case definition (S2 Table) from the sentinel sites are collected together with nasopharyngeal or oropharyngeal specimen. Our study provides evidence, that the ILI sentinel surveillance system in the Greater Accra Region (GAR), Ghana, is only partially meeting its objectives because it did not have thresholds for alerting the health system and does not perform antiviral resistance testing. cache = ./cache/cord-263464-fdosch11.txt txt = ./txt/cord-263464-fdosch11.txt === reduce.pl bib === id = cord-265812-1hcp36cw author = De Jong, Cornelis N. title = Etanercept for steroid-refractory acute graft-versus-host disease: A single center experience date = 2017-10-26 pages = extension = .txt mime = text/plain words = 3168 sentences = 186 flesch = 53 summary = W.; Van der Klift, Marjolein; Cornelissen, Jan J.; Broers, Annoek E. High dose glucocorticosteroids, are currently recommended as first-line treatment for grade II-IV aGVHD resulting in overall complete responses (CR) in 40%-50% of patients. CONCLUSION: Second-line treatment with etanercept does induce responses in SR-aGVHD of the gut but appears to be associated with poor long-term survival even in responding patients. High dose systemic glucocorticosteroids (steroids) are currently recommended as first-line treatment for grade II-IV aGVHD resulting in overall complete responses (CR) in 40%-50% of patients [2, 3] . Studies evaluating second-line treatment with the anti-TFNα agent etanercept have shown promising results with overall response rates of 50-80% [8] [9] [10] . In conclusion, although second-line treatment of SR-aGVHD of the gut with etanercept was associated with a promising initial response rate, overall survival appeared very poor, mainly due to progression of GVHD and opportunistic infections. cache = ./cache/cord-265812-1hcp36cw.txt txt = ./txt/cord-265812-1hcp36cw.txt === reduce.pl bib === id = cord-262832-5iejckwx author = Yen, Muh-Yong title = Taipei's Use of a Multi-Channel Mass Risk Communication Program to Rapidly Reverse an Epidemic of Highly Communicable Disease date = 2009-11-23 pages = extension = .txt mime = text/plain words = 5998 sentences = 285 flesch = 51 summary = In launching countermeasures to bring the AHC outbreak under control, the Taipei Department of Health was also able to test its system and fine-tune its public health response for future EIDs. To evaluate the effectiveness of these intervention measures, daily surveillance was conducted to analyze the incidence rate and temporal-spatial distribution of new AHC cases. This risk communication program focused on communicating directly to the public through three routes: (1) schools delivered a Taipei Department of Health letter signed by the mayor (that detailed AHC information and prevention methods) for students to take home to their parents, (2) the mayor held a press conference to discuss the epidemic and offer guidance to citizens for preventing the spread of the disease, and (3) over 2.2 million short message services (SMS) messages, a communication tool for exchanging short text messages between mobile telephonic devices, were delivered to all Taipei mobile phone numbers. cache = ./cache/cord-262832-5iejckwx.txt txt = ./txt/cord-262832-5iejckwx.txt === reduce.pl bib === id = cord-267189-xq70rn1j author = Wang, Xinyu title = Co-Circulation of Canine Coronavirus I and IIa/b with High Prevalence and Genetic Diversity in Heilongjiang Province, Northeast China date = 2016-01-15 pages = extension = .txt mime = text/plain words = 3037 sentences = 156 flesch = 56 summary = To trace the evolution of canine coronavirus (CCoV), 201 stool samples from diarrheic dogs in northeast China were subjected to reverse transcription-polymerase chain reactions (RT-PCRs) targeting the partial M and S genes of CCoV, followed by an epidemiological analysis. Our data provide evidence that CCoV-I, CCoV-IIa, and CCoV-IIb strains co-circulate in the diarrhoetic dogs in northeast China, high co-infection rates with CaKV and CPV-2 were observed, and the CCoV-II strains exhibited high prevalence and genetic diversity. A phylogenetic analysis using partial S gene sequences demonstrated that the 26 CCoV-IIa strains were closely related to three reference strains, 5281 (Japan), TN-449 (USA), and 1086-IIa (Brazil), and differed genetically from reference strains from China and other countries (Fig 2A) . This result demonstrated that vaccination for other canine viruses did not effect CCoV infections in the dog population in Heilongjiang province, northeast China. cache = ./cache/cord-267189-xq70rn1j.txt txt = ./txt/cord-267189-xq70rn1j.txt === reduce.pl bib === id = cord-263684-3535k3op author = Tang, Julian W. title = Different Types of Door-Opening Motions as Contributing Factors to Containment Failures in Hospital Isolation Rooms date = 2013-06-24 pages = extension = .txt mime = text/plain words = 5292 sentences = 211 flesch = 52 summary = Using colored food dye as a tracer, the qualitative effects of door-opening motions on the dissemination of potentially contaminated air into and out of a single isolation room were visualized and filmed using Reynolds-number-equivalent, small-scale, water-tank models fitted with programmable door-opening and moving human figure motions. This study is part of a longer-term project that aims to demonstrate the effects of door-opening motions using a variety of doors, with and without the passage of a human figure, on the movement of potentially contaminated air into and out of an isolation room, using both a small-scale, Reynolds-number-equivalent model in water, and a full-scale model in air. In the small-scale water-tank models used in these experiments, the compartment outside the isolation room, into or from which The series of 4 snapshots with each dooropening, manikin movement scenario were taken with respect to the following events, rather than at specific times: food dye movement due to door-opening motions alone then with any initial manikin movement -manikin interaction and any entrainment food dye -final food dye movements once the manikin had come to rest at its destination position. cache = ./cache/cord-263684-3535k3op.txt txt = ./txt/cord-263684-3535k3op.txt === reduce.pl bib === id = cord-267644-guzn0peq author = Livadiotis, George title = Statistical analysis of the impact of environmental temperature on the exponential growth rate of cases infected by COVID-19 date = 2020-05-29 pages = extension = .txt mime = text/plain words = 6525 sentences = 326 flesch = 54 summary = We perform a statistical analysis for understanding the effect of the environmental temperature on the exponential growth rate of the cases infected by COVID-19 for US and Italian regions. In particular, we analyze the datasets of regional infected cases, derive the growth rates for regions characterized by a readable exponential growth phase in their evolution spread curve and plot them against the environmental temperatures averaged within the same regions, derive the relationship between temperature and growth rate, and evaluate its statistical confidence. The results clearly support the first reported statistically significant relationship of negative correlation between the average environmental temperature and exponential growth rates of the infected cases. First, we derive the exponential growth rates of the infected cases characterizing each examined region of US and Italy; then, we plot these values against the environmental temperatures of each region, and perform the corresponding statistical analysis. cache = ./cache/cord-267644-guzn0peq.txt txt = ./txt/cord-267644-guzn0peq.txt === reduce.pl bib === id = cord-267519-a0bcmjkn author = Bravi, Francesca title = Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens date = 2020-06-24 pages = extension = .txt mime = text/plain words = 3303 sentences = 144 flesch = 44 summary = AIMS: This retrospective case-control study was aimed at identifying potential independent predictors of severe/lethal COVID-19, including the treatment with Angiotensin-Converting Enzyme inhibitors (ACEi) and/or Angiotensin II Receptor Blockers (ARBs). Observing that human pathogenic coronaviruses bind their target cells through angiotensin-converting enzyme 2 (ACE2) [5] [6] [7] [8] , and that a few studies reported an increase in ACE2 expression mediated by angiotensin II type-I receptor blockers (ARBs) and ACE inhibitors (more consistently on animals than in humans) [9] [10] [11] [12] [13] [14] [15] [16] , some hypothesized that the increased expression of ACE2 would facilitate infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), thus the hypertension treatment with ACE2-stimulating drugs, as well as ACE2 polymorphisms, might increase the risk of developing severe COVID-19 [17] [18] [19] . cache = ./cache/cord-267519-a0bcmjkn.txt txt = ./txt/cord-267519-a0bcmjkn.txt === reduce.pl bib === id = cord-267973-uvz7kavu author = Do, Lien Anh Ha title = Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity date = 2016-08-08 pages = extension = .txt mime = text/plain words = 5921 sentences = 476 flesch = 61 summary = title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. However, information on detailed clinical, epidemiological features and virological characteristics of RSV infections (e.g. disease burden, demographics, seasonal variations of RSV and other viral infections, circulating genotypes and subgroups, viral load) or on the frequency / impact of other respiratory viruses among Vietnamese children under two years old are limited [6] . Here, we aimed to describe the viral etiologies and the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a LRTI, focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. cache = ./cache/cord-267973-uvz7kavu.txt txt = ./txt/cord-267973-uvz7kavu.txt === reduce.pl bib === id = cord-267307-kyh0xsrp author = Kasting, Monica L. title = Public perceptions of the effectiveness of recommended non-pharmaceutical intervention behaviors to mitigate the spread of SARS-CoV-2 date = 2020-11-04 pages = extension = .txt mime = text/plain words = 4343 sentences = 230 flesch = 54 summary = Public health efforts should focus on increasing perceived severity and threat of SARS-CoV-2-related disease, while promoting NPI as effective in reducing threat. A six-item measure was used to assess participants' perceptions of the effectiveness of NPIs to prevent SARS-CoV-2 infection and spread. Three of the six items measured the perceived effectiveness of preventing yourself from spreading COVID-19 to others and included: 1) wearing a mask anytime you leave the house to go out in public, 2) practicing social distancing by leaving at least six feet between you and other people (this does not include people you live with), and 3) covering your mouth when you cough. Any variable that was significant at p<0.01 in bivariate comparisons was included in an adjusted logistic regression model with the binary lower/ higher perceived effectiveness of COVID-19 prevention measures as the outcome. cache = ./cache/cord-267307-kyh0xsrp.txt txt = ./txt/cord-267307-kyh0xsrp.txt === reduce.pl bib === id = cord-266799-t7lqlv41 author = Rotejanaprasert, Chawarat title = Preliminary estimation of temporal and spatiotemporal dynamic measures of COVID-19 transmission in Thailand date = 2020-09-24 pages = extension = .txt mime = text/plain words = 5033 sentences = 265 flesch = 45 summary = This study thus aims to estimate and compare disease dynamic measures in several dimensions that can be augmented with epidemiological summary statistics to monitor the COVID-19 situation for each location and time at different stages of the epidemic. The data in this study were from confirmed COVID-19 cases in 77 provinces of Thailand from January 12 th 2020 through June 30 th 2020 provided in the daily reports of the Department of Disease Control, Thai Ministry of Public Health (MOPH). During the early stage of an epidemic curve caused by emerging diseases, the exponential growth (EG) rate, denoted by r, can be related to the initial reproduction rate and can be described as the change in number of new cases per time unit [15] . We wanted to provide information that could be used to help design effective control strategies for the current COVID-19 situation in Thailand after the disease has spread to different provinces across the country much of which was from cluster outbreaks originating from several super spreader events. cache = ./cache/cord-266799-t7lqlv41.txt txt = ./txt/cord-266799-t7lqlv41.txt === reduce.pl bib === id = cord-262748-v4xue7ha author = Xu, Yongtao title = Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine date = 2015-12-04 pages = extension = .txt mime = text/plain words = 4636 sentences = 253 flesch = 40 summary = Here we developed a support vector machine model using sequence-based statistical scores of self-derived peptide inhibitors as input features to correlate with their activities. The predictive support vector machine model for selfderived peptides of envelope proteins would be useful in development of antiviral peptide inhibitors targeting the virus fusion process. In view of the important role of E proteins in virus fusion process and common mechanism of action of self-derived peptides, we developed a SVM model to predict the antiviral activities of self-derived peptides using sequence-based statistical scores as input features. Because similar sequences are often associated with similar structure and function, the sequence-based property AVPalign would account for the activities of the self-derived peptide inhibitors which regulate the virus fusion by mimicking the binding to E proteins. The prominent performance of EAPscoring model indicates the sequence-based stability feature of self-derived peptides may reflect their potential of binding to E proteins so as to regulate the virus entry process. cache = ./cache/cord-262748-v4xue7ha.txt txt = ./txt/cord-262748-v4xue7ha.txt === reduce.pl bib === id = cord-266797-uglsx7se author = Anastassopoulou, Cleo title = Data-based analysis, modelling and forecasting of the COVID-19 outbreak date = 2020-03-31 pages = extension = .txt mime = text/plain words = 5420 sentences = 235 flesch = 55 summary = Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected and recovered cases in the population most likely are much higher than the reported ones. Based on the released data, we attempted to estimate the mean values of the main epidemiological parameters, i.e. the basic reproduction number R 0 , the case fatality (ĝ) and case recovery (b) ratios, along with their 90% confidence intervals. Then, as described above, we provide coarse estimations of the "effective" per day recovery and mortality rates of the SIRD model based on the reported data by solving the corresponding least squares problems. cache = ./cache/cord-266797-uglsx7se.txt txt = ./txt/cord-266797-uglsx7se.txt === reduce.pl bib === id = cord-267566-gdjl0qmu author = Kweon, Oh Joo title = Antibody kinetics and serologic profiles of SARS-CoV-2 infection using two serologic assays date = 2020-10-22 pages = extension = .txt mime = text/plain words = 3599 sentences = 232 flesch = 51 summary = This study aims to assess the serologic profiles and time kinetics of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients with COVID-19 using two immunoassays. METHODS: A total of 97 samples serially collected from 17 patients with COVID-19 and 137 negative control samples were analyzed for IgM and IgG against SARS-CoV-2 using the AFIAS COVID-19 Ab (Boditech Med Inc., Chuncheon, Republic of Korea) and the EDI(™) Novel Coronavirus COVID-19 ELISA Kit (Epitope Diagnostics, Inc., San Diego, CA). The diagnostic sensitivities of IgM/IgG for ≤14d PSO were 21.4%/35.7~57.1% and increased to 41.2~52.9%/88.2~94.1% at >14 d PSO with specificities of 98.5%/94.2% for AFIAS COVID-19 Ab and 100.0%/96.4% for EDI(™) Novel Coronavirus COVID-19 ELISA Kit. Among 137 negative controls, 12 samples (8.8%) showed positive or indeterminate results. cache = ./cache/cord-267566-gdjl0qmu.txt txt = ./txt/cord-267566-gdjl0qmu.txt === reduce.pl bib === id = cord-268816-nth3o6ot author = Roy, Satyaki title = Factors affecting COVID-19 infected and death rates inform lockdown-related policymaking date = 2020-10-23 pages = extension = .txt mime = text/plain words = 5733 sentences = 363 flesch = 56 summary = The features in the order shown under "Feature name" are: GDP, inter-state distance based on lat-long coordinates, gender, ethnicity, quality of health care facility, number of homeless people, total infected and death, population density, airport passenger traffic, age group, days for infection and death to peak, number of people tested for COVID-19, days elapsed between first reported infection and the imposition of lockdown measures at a given state. Unless otherwise stated, the feature set comprises GDP, gender, ethnicity, health care, homeless, lockdown type, population density, airport activity, and age groups, whereas the output labels consist of infected and death scores on a scale of 0-6. Although proposing a machine learning algorithm that works best on COVID-19 data is not the purpose of this study, it is worth reporting that decision tree classifier (DT) slightly outperforms the other algorithms for both cases of infected and death scores. cache = ./cache/cord-268816-nth3o6ot.txt txt = ./txt/cord-268816-nth3o6ot.txt === reduce.pl bib === id = cord-267605-efb10j3u author = Zheng, Li-Zhen title = Steroid-Associated Hip Joint Collapse in Bipedal Emus date = 2013-10-21 pages = extension = .txt mime = text/plain words = 5851 sentences = 249 flesch = 46 summary = The combination of pulsed LPS and MPS developed in the current study was safe and effective to induce SAON and deterioration of subchondral bone in bipedal emus with subsequent femoral head collapse, a typical clinical feature observed in patients under pulsed steroid treatment. Accordingly, the aim of the current study was to establish a SAON model in bipedal emus, with potentials to bone structural deterioration with subsequent femoral head collapse, a condition seen in SAON patients attributed to similar biomechanics or loading ratio imposed onto the hip joint [23, 24] . Using a combined pulsed LPS and MPS induction protocol previously established for SAON quadrupedal rabbits [11, 13] , the present study established a SAON model in bipedal emus characterized with subchondral bone deterioration and hip joint collapse, an experimental model mimicking human ON often developed at hip joint with femoral head collapse. cache = ./cache/cord-267605-efb10j3u.txt txt = ./txt/cord-267605-efb10j3u.txt === reduce.pl bib === id = cord-272655-qeojdpez author = Remolina, Yuly Andrea title = Viral Infection in Adults with Severe Acute Respiratory Infection in Colombia date = 2015-11-17 pages = extension = .txt mime = text/plain words = 4309 sentences = 204 flesch = 42 summary = OBJECTIVES: To identify the viral aetiology in adult patients with severe acute respiratory infection (SARI) admitted to sentinel surveillance institutions in Bogotá in 2012. DESIGN: A cross-sectional study was conducted in which microarray molecular techniques for viral identification were used on nasopharyngeal samples of adult patients submitted to the surveillance system, and further descriptions of clinical features and relevant clinical outcomes, such as mortality, need for critical care, use of mechanical ventilation and hospital stay, were obtained. Under this initiative, countries have developed surveillance systems by following cases of influenza-like illness and severe acute respiratory infections (SARIs), which are clinically diagnosed among patients with fever, coughing or sore throat, difficulty breathing and the need for hospitalization [3] . In our study, viruses were identified as the most frequent causal agents of SARI requiring hospitalization in 2012, with most cases showing a high rate of viral co-infection, a high degree of morbidity, prolonged hospital stays and frequent needs for ICU management and mechanical ventilation. cache = ./cache/cord-272655-qeojdpez.txt txt = ./txt/cord-272655-qeojdpez.txt === reduce.pl bib === id = cord-268977-hcg2rrhl author = Feikin, Daniel R. title = Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date = 2012-08-24 pages = extension = .txt mime = text/plain words = 6440 sentences = 402 flesch = 53 summary = METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. Compared with other regions, the mortality rate among older children and adults remains several-fold higher in sub-Saharan Africa, where acute respiratory infections (ARI) are a leading cause of this high mortality, as well as associated morbidity [1] . cache = ./cache/cord-268977-hcg2rrhl.txt txt = ./txt/cord-268977-hcg2rrhl.txt === reduce.pl bib === id = cord-262876-civfvk45 author = Su, Tong title = Knowledge Levels and Training Needs of Disaster Medicine among Health Professionals, Medical Students, and Local Residents in Shanghai, China date = 2013-06-24 pages = extension = .txt mime = text/plain words = 4492 sentences = 244 flesch = 43 summary = title: Knowledge Levels and Training Needs of Disaster Medicine among Health Professionals, Medical Students, and Local Residents in Shanghai, China Continuing medical education and public education plans on disaster medicine via media should be practice-oriented, and selectively applied to different populations and take the knowledge levels and training needs into consideration. Three groups of participants in Shanghai, China, were enrolled in this cross-sectional epidemiological study: health professionals, medical students, and community residents. Moreover, the knowledge level was also significantly different among clinicians, public health physicians, nurses, and medical technicians, especially in correctly answering 5 questions (Table S2) . Figure 3 presents the key contents concerning disaster medicine training prioritized by health professionals, medical students, and community residents. Figure 4 presents the most interested contents of disaster medicine training prioritized by health professionals, medical students, and community residents. In this study, we evaluated the current knowledge levels and training needs of disaster medicine among health professionals, medical students, and community residents in Shanghai, China. cache = ./cache/cord-262876-civfvk45.txt txt = ./txt/cord-262876-civfvk45.txt === reduce.pl bib === id = cord-264880-0tmd9knh author = Li, Zhao title = Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids date = 2016-04-13 pages = extension = .txt mime = text/plain words = 5347 sentences = 260 flesch = 46 summary = We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. To avoid thermal cycling, different isothermal amplification methods have been developed that rapidly amplify nucleic acids to detectable levels at a single temperature [42, 43] , such as loop-mediated amplification (LAMP) [44] , rolling circle amplification (RCA) [45] , helicasedependent amplification (HDA) [46] , nucleic acid sequence-based amplification (NASBA) [47] , recombinase polymerase amplification (RPA) [48] , transcription-mediated amplification (TMA) [49] , multiple displacement amplification (MDA) [50] , and strand-displacement amplification (SDA) [51] . Finally, we sealed the PWA chip in a homemade copper chamber filled with oil and successfully performed real-time dRPA on an isothermal incubation setup for the absolute quantification of serial dilutions of a Listeria monocytogenes gDNA stock solution. cache = ./cache/cord-264880-0tmd9knh.txt txt = ./txt/cord-264880-0tmd9knh.txt === reduce.pl bib === id = cord-273343-als886fe author = McClenahan, Shasta D. title = Discovery of a Bovine Enterovirus in Alpaca date = 2013-08-12 pages = extension = .txt mime = text/plain words = 4596 sentences = 214 flesch = 51 summary = A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Analysis of the full polyprotein and the individual capsid, 2A protease, 3C protease, and polymerase proteins of the alpaca-infecting virus relative to sequences of other representative enteroviruses from bovine EV-E (BEV-A serotypes 1-4) and EV-F (BEV-B serotypes 1-4), and sequences from three unclassified EV-F viruses [16] , two from bovine sources (AY724744 and AY724745) [20] , and one from a capped langur (JX538037) [21] , possum, porcine (PEV), and human (HEV) hosts. cache = ./cache/cord-273343-als886fe.txt txt = ./txt/cord-273343-als886fe.txt === reduce.pl bib === id = cord-272445-0xauff51 author = Naaber, Paul title = Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data date = 2020-10-27 pages = extension = .txt mime = text/plain words = 2751 sentences = 150 flesch = 50 summary = title: Evaluation of SARS-CoV-2 IgG antibody response in PCR positive patients: Comparison of nine tests in relation to clinical data The specificity and sensitivity of SARS-CoV-2 antibody tests are known to vary and very few studies have addressed the performance of these tests in COVID-19 patient groups at different time points. We here compared the sensitivity and specificity of seven commercial (SNIBE, Epitope, Euroimmun, Roche, Abbott, DiaSorin, Biosensor) and two in-house LIPS assays (LIPS N and LIPS S-RBD) IgG/total Ab tests in serum samples from 97 COVID-19 patients and 100 controls, and correlated the results with the patients' clinical data and the time-point the test was performed. Our study aimed to compare the performance characteristics of seven commercial and two in-house IgG/total Ab tests, which analyze the reactivity to several target proteins, and to correlate the results with the patients' clinical data (with different symptoms score and age), and time from disease onset. cache = ./cache/cord-272445-0xauff51.txt txt = ./txt/cord-272445-0xauff51.txt === reduce.pl bib === id = cord-268429-drejl99k author = Almberg, Emily S. title = A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community date = 2009-09-16 pages = extension = .txt mime = text/plain words = 7276 sentences = 349 flesch = 52 summary = METHODOLOGY/PRINCIPAL FINDINGS: We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991–2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. Thus we sought to use long-term serological data to identify temporal, spatial, and demographic patterns of pathogen exposure among wolves, coyotes (Canis latrans), and foxes (Vulpes vulpes) in YNP. In summary, the constant high canid exposure to CPV, CAV-1, and CHV in YNP suggest that these pathogens are established in the wolf and coyote populations and that they are unlikely to be causing acute mortality in their hosts [50, 51] . cache = ./cache/cord-268429-drejl99k.txt txt = ./txt/cord-268429-drejl99k.txt === reduce.pl bib === id = cord-273764-itu39mln author = Li, Taisheng title = Long-Term Persistence of Robust Antibody and Cytotoxic T Cell Responses in Recovered Patients Infected with SARS Coronavirus date = 2006-12-20 pages = extension = .txt mime = text/plain words = 2660 sentences = 120 flesch = 49 summary = In this report, we have sequentially monitored 30 recovered patients over a two-year period to characterize temporal changes in SARS-CoV-specific antibody responses as well as cytotoxic T cell (CTL) responses. As show in Fig. 1 , recovered patients clearly experienced two distinct phases of cell restoration in the peripheral blood; an initial rapid phase for all the cell populations studied in the first 3 months after the onset of symptoms followed by a significant slower phase during the subsequent months. To study the sequential changes in CTL responses against SARS-CoV, we used ELISPOT-based technique to quantify the number of INF-c releasing cells in the peripheral blood against peptide pools covering the entire N protein derived from the Urbani strain [3] . We have shown for the first time that recovered patients have persistent and robust binding as well as neutralizing antibody and CTL responses throughout the study period with a moderate decline one year after the onset of symptoms. cache = ./cache/cord-273764-itu39mln.txt txt = ./txt/cord-273764-itu39mln.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-267042-nvwnbp2j author = Gaspard, Philippe title = Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents date = 2019-09-24 pages = extension = .txt mime = text/plain words = 5624 sentences = 290 flesch = 50 summary = This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. In MH stratified analysis (virus, sex (female/male)) adjusted for LOS (<4 or ≥4 years), the odds of being infected remained significant among older residents (≥86 years): NoV+/male (Odds ratio (OR(MH)): 1.64, 95% confidence interval (CI): 1.16–2.30) and Flu+/female and male (respectively OR(MH): 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33). Our objective was to describe GE and RTI infection and all-cause lethality rates according to the individual characteristics of nursing home residents (sex, age, length of stay, autonomy status), and to identify specific susceptibility patterns related to these types of viral outbreaks in these facilities. In the present study, surveillance data obtained during GE and RTI outbreaks in nursing homes were used to construct stratified analyses and to identify specific infection and all-cause lethality rates according to the residents' individual characteristics. cache = ./cache/cord-267042-nvwnbp2j.txt txt = ./txt/cord-267042-nvwnbp2j.txt === reduce.pl bib === id = cord-271660-5sfkhg19 author = Sun, Hsin-Yun title = Impact of introducing fluorescent microscopy on hospital tuberculosis control: A before-after study at a high caseload medical center in Taiwan date = 2020-04-03 pages = extension = .txt mime = text/plain words = 3884 sentences = 192 flesch = 40 summary = METHODS: We measured the impact of switch to fluorescent microscopy on the smear detection rate of culture-confirmed pulmonary TB, timing of respiratory isolation, and total non-isolated infectious person-days in hospital at a high-caseload medical center (approximately 400 TB cases annually) in Taipei. Hospitalized patients had typical presentations of pulmonary TB if they had: (a) a prolonged cough for >3 weeks; (b) clinical suspicion of pulmonary TB based on chest radiography, such as cavitary pulmonary lesions, upper lobe diseases, or miliary lesions; or (c) already received a confirmed diagnosis of pulmonary TB by a positive sputum culture of Mycobacterium tuberculosis, positive acid-fast stain (AFS), or positive TB PCR, before the hospitalization. Our previous survey on age/sex-standardised TB incidence ratio of HCWs (using general population as reference)---the excess TB risk that are attributable to nosocomial TB transmission---in Medical Center A showed a drop of this risk, from 3.11 in 2006 to 1.37 in 2012 [23] , and the decrease in time-to-isolation and total non-isolated infectious patient-days was in parallel in the present study. cache = ./cache/cord-271660-5sfkhg19.txt txt = ./txt/cord-271660-5sfkhg19.txt === reduce.pl bib === id = cord-268524-lr51ubz5 author = Droit-Volet, Sylvie title = Time and Covid-19 stress in the lockdown situation: Time free, «Dying» of boredom and sadness date = 2020-08-10 pages = extension = .txt mime = text/plain words = 5266 sentences = 262 flesch = 56 summary = This time experience was not explained by the levels of perceived stress or anxiety, although these were considerable, but rather by the increase in boredom and sadness felt in the lockdown situation. The aim of the present study was thus to conduct a scale survey on a large sample of an as yet untested population-French people-in order to assess not only the perceived stress related to Covid-19 but also the emotions (happiness, boredom, arousal) felt during as compared to before the lockdown and their links to the subjective experience of time. There is thus a risk in this period of pandemic that the chronic stress related to Covid-19 and its corollaries (anxiety, fear of death) are particularly high and therefore impact the subjective experience of time by speeding up the perceived passage of time. cache = ./cache/cord-268524-lr51ubz5.txt txt = ./txt/cord-268524-lr51ubz5.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-279259-eu80ccm6 author = Pandey, Aseem title = Impact of Preexisting Adenovirus Vector Immunity on Immunogenicity and Protection Conferred with an Adenovirus-Based H5N1 Influenza Vaccine date = 2012-03-14 pages = extension = .txt mime = text/plain words = 4876 sentences = 249 flesch = 47 summary = The immunogenicity and protection results suggest that low levels of vector immunity (<520 virus-neutralization titer) induced by priming mice with up to 10(7) plaque forming units (p.f.u.) of HAd-WT did not adversely impact the protective efficacy of the vaccine. Furthermore, high levels of vector immunity (approximately 1500 virus-neutralization titer) induced by priming mice with 10(8) p.f.u. of HAd-WT were overcome by either increasing the vaccine dose or using alternate routes of vaccination. To determine the level of vector immunity that can be tolerated without significantly affecting the vaccine efficacy, we primed groups of mice with varying doses of wild type (WT) HAd5 via intranasal (i.n.) or intramuscular (i.m.) route of inoculation to generate different levels of HAd5-neutralizing antibody titers. Further increase in the level of vector-specific neutralizing antibody titer to 3040 by i.m. priming with HAd5 only provided partial protection even in the groups receiving a high vaccine dose. cache = ./cache/cord-279259-eu80ccm6.txt txt = ./txt/cord-279259-eu80ccm6.txt === reduce.pl bib === id = cord-270681-6ayciihs author = Bálint, Ádám title = Comparative In Vivo Analysis of Recombinant Type II Feline Coronaviruses with Truncated and Completed ORF3 Region date = 2014-02-20 pages = extension = .txt mime = text/plain words = 4679 sentences = 230 flesch = 49 summary = Our previous in vitro comparative study on a feline coronavirus (FCoV) pair, differing only in the intactness of their ORF3abc regions, showed that the truncated ORF3abc plays an important role in the efficient macrophage/monocyte tropism of type II feline infectious peritonitis virus (FIPV). In the present study using the parent FIPV DF-2 strain and its recombinant derivates we aimed to collect in vivo data how the completed ORF3abc alters virulence, virus shedding, viremia, viral load of organs and humoral immune response against type II FCoV. Shedding of FIPV DF-2 and PBFIPV-DF-2 was detected from day 3 p.i. to euthanasia of the PIP diseased animals at very low and variable amounts of an average value close to the detection limit of the genomic qRT-PCR (1.9610 1 FCoV RNA copies per ml fecal extract) ( Fig. 1) with undetectable virus replication using the subgenomic qRT-PCR assay (data not shown). cache = ./cache/cord-270681-6ayciihs.txt txt = ./txt/cord-270681-6ayciihs.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-276898-ia80cy8j author = Yamanaka, Atsushi title = Imported Case of Acute Respiratory Tract Infection Associated with a Member of Species Nelson Bay Orthoreovirus date = 2014-03-25 pages = extension = .txt mime = text/plain words = 3833 sentences = 190 flesch = 48 summary = Miyazaki-Bali/2007, a strain of the species of Nelson Bay orthoreovirus, was isolated from the patient's throat swab using Vero cells, in which syncytium formation was observed. Here, we report an imported case of an RTI associated with an orthoreovirus, which is classified to the species of Nelson Bay orthoreovirus, in a patient who returned to Japan from Bali, Indonesia in November 2007. Interestingly, S1segment of Miyazaki-Bali/2007 showed 94% homology to that of Kampar virus originated in Malaysia, while it did 48-59% homology to those of the other orthoreoviruses in the genus of Nelson Bay orthoreovirus. S2-segment of Miyazaki-Bali/2007 had the highest homology with being approximately 92-94% in nucleotide sequences to those of HK23629/07, HK46886/09, and HK50842/10, which also seem to have originated in Indonesia [6, 20] , while it showed 83-90% homology to those of Kampar, Melaka, Pulau, Sikamat, and Nelson Bay viruses. cache = ./cache/cord-276898-ia80cy8j.txt txt = ./txt/cord-276898-ia80cy8j.txt === reduce.pl bib === id = cord-280846-bbv6f5gf author = Greninger, Alexander L. title = A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date = 2010-10-18 pages = extension = .txt mime = text/plain words = 8023 sentences = 327 flesch = 44 summary = To determine whether a pan-viral microarray assay was capable of identifying novel 2009 H1N1 in the absence of a priori sequence information, we used the Virochip to comprehensively screen for viruses in 29 nasopharyngeal swab samples from individuals with influenza-like illness. To further characterize the metagenomics of 2009 H1N1 infection in humans, we labeled the 17 influenza samples positive for 2009 H1N1 by Virochip with distinct molecular barcodes and analyzed them by paired-end deep sequencing on three lanes of an Illumina Genome Analyzer IIx. After trimming reads to remove barcodes and exclude low-complexity or primer sequences, 11,427,212 high-quality 60-bp sequence reads were subjected to an iterative BLASTN analysis pipeline (Fig. 1B) . After stratifying by originating location and corresponding method of sample processing (pre-DNase and/or post-DNase treatment), the percentage of total reads aligning to influenza was linearly correlated with calculated viral titers by realtime quantitative RT-PCR for sites in the United States (California) and Canada but not in Mexico (Fig. 5A ). cache = ./cache/cord-280846-bbv6f5gf.txt txt = ./txt/cord-280846-bbv6f5gf.txt === reduce.pl bib === id = cord-278123-mq56em3z author = Hasan, Mohammad Rubayet title = Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date = 2020-07-24 pages = extension = .txt mime = text/plain words = 3924 sentences = 259 flesch = 58 summary = Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. Standard approach for detection of SARS-CoV-2 RNA from nasopharyngeal specimens in our laboratory involves extraction of total nucleic acids from specimens in an IVD-labeled, automated extraction platform followed by RT-qPCR, based on one of the assays (Table 1) suggested by World Health Organization (WHO) [11] . Based on these results, the optimal pre-treatment and reaction conditions for the direct approach were: i) transfer and dilute (4-fold) 10 μl of NPFS specimen in NFW; ii) incubate at 65˚C for 10 min; and iii) test 8 μl of heat lysed specimen in a 20 μl reaction using TaqPath™ 1-Step RT-qPCR Master Mix. The analytical sensitivity of the direct RT-qPCR assay using specimens prepared in this manner was determined by serially diluting a specimen positive for SARS-CoV-2 with a negative specimen as a diluent. cache = ./cache/cord-278123-mq56em3z.txt txt = ./txt/cord-278123-mq56em3z.txt === reduce.pl bib === id = cord-280386-a8qr7nl6 author = Pires, Sara M. title = Aetiology-Specific Estimates of the Global and Regional Incidence and Mortality of Diarrhoeal Diseases Commonly Transmitted through Food date = 2015-12-03 pages = extension = .txt mime = text/plain words = 5931 sentences = 252 flesch = 45 summary = The objective of this study is to provide estimates of the global and regional incidence and mortality of diarrhoeal diseases caused by nine pathogens that are commonly transmitted through foods. METHODS AND FINDINGS: We abstracted data from systematic reviews and, depending on the overall mortality rates of the country, applied either a national incidence estimate approach or a modified Child Health Epidemiology Reference Group (CHERG) approach to estimate the aetiology-specific incidence and mortality of diarrhoeal diseases, by age and region. To identify and prioritize targeted interventions to reduce the public health impact of foodborne diseases, public health policy makers and other stakeholders need aetiology-specific regional and global estimates of the incidence and mortality of diarrhoeal diseases caused by pathogens that are commonly transmitted through foods. While approach 1 analysed national incidence and mortality of disease by pathogens commonly transmitted through foods estimated primarily by correcting surveillance data to account for underreporting and under-diagnosis, approach 2 relied on systematic reviews of studies identifying causative agents in patients with diarrhoea. cache = ./cache/cord-280386-a8qr7nl6.txt txt = ./txt/cord-280386-a8qr7nl6.txt === reduce.pl bib === id = cord-270408-4qqyb8sd author = Pane, Masdalina title = Causes of Mortality for Indonesian Hajj Pilgrims: Comparison between Routine Death Certificate and Verbal Autopsy Findings date = 2013-08-21 pages = extension = .txt mime = text/plain words = 3456 sentences = 182 flesch = 52 summary = title: Causes of Mortality for Indonesian Hajj Pilgrims: Comparison between Routine Death Certificate and Verbal Autopsy Findings This study presents the patterns and causes of death for Indonesian pilgrims, and compares routine death certificates to verbal autopsy findings. In the last two decades, the mortality rate of Indonesian pilgrims, excluding years in which disasters such as stampedes occurred, fluctuated between 200-380 deaths per 100,000 persons during the ten-week Hajj period [5] . The cause of death based on this verbal autopsy method was then recorded in the database and compared to that reported by the hospital or flight doctor death certificate. A greater proportion of deaths were attributed to cardiovascular disease by the flight doctor or hospital death certificate (66%) compared to the cause of death ascertained using the verbal autopsy method (49%, p<0.001). Based on both the death certificates and verbal autopsy categories, cardiovascular disease was the leading cause of Indonesian pilgrim mortality in 2008. cache = ./cache/cord-270408-4qqyb8sd.txt txt = ./txt/cord-270408-4qqyb8sd.txt === reduce.pl bib === id = cord-270647-vn4kirrx author = Romero-Espinoza, Jose A. title = Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 date = 2018-02-15 pages = extension = .txt mime = text/plain words = 3513 sentences = 201 flesch = 48 summary = OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively. Both groups differ with respect to the associated virus and bacteria: while asthma exacerbations have been associated to a specific rhinovirus infection, pneumonia can be related to a wide range of bacterial, fungal and viral agents, with a high prevalence of Respiratory Syncytial Virus (RSV) [2, 7] . Here we describe the virome and bacteriome present in the Upper Respiratory Tract of hospitalized children clinically diagnosed with asthma and pneumonia, during an acute exacerbation and an ARI episode respectively, at the National Institute of Respiratory Diseases (INER, Mexico City) during 2014 and 2015 winter seasons. Prevalence of respiratory viral infection in children hospitalized for acute lower respiratory tract diseases, and association of rhinovirus and influenza virus with asthma exacerbations cache = ./cache/cord-270647-vn4kirrx.txt txt = ./txt/cord-270647-vn4kirrx.txt === reduce.pl bib === id = cord-277357-lpurk7pe author = González-González, Everardo title = Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3999 sentences = 211 flesch = 49 summary = title: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection Here, we demonstrate the use of the miniPCR, a commercial compact and portable PCR device recently available on the market, in combination with a commercial well-plate reader as a diagnostic system for detecting genetic material of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection containing the amplification products of each one of three experiments, where the three different sets of primers (namely N1, N2, and N3) were used to amplify the same range of concentrations of template. Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection others), we observe differences in the performance of each primer pair. cache = ./cache/cord-277357-lpurk7pe.txt txt = ./txt/cord-277357-lpurk7pe.txt === reduce.pl bib === id = cord-278099-ypov9ha3 author = Kumar, Surender title = Molecular characterization of a novel cryptic virus infecting pigeonpea plants date = 2017-08-03 pages = extension = .txt mime = text/plain words = 11403 sentences = 622 flesch = 55 summary = The four dsRNAs eluted from the agarose gel were purified and have been used as templates for RT-PCR amplification employed in SISPA to generate fulllength cDNAs. It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses [12] [13] [14] [15] [16] . We report here the results of elaborated computer-assisted analysis of ArCV-1 replicase which revealed the presence of conserved sequence motifs (A to G) present in the fingers and palm subdomains of the polymerase that are shared in most of the RdRps. Interestingly, ArCV-1 replicase has more structural resemblances with several members of ssRNA (+) mono-partite Picornaviruses (viral replication by primer-dependent initiation), than the de novo dsRNA bacteriophage Փ-6 and reovirus polymerases. Possible functions of the residues of the A to G motifs described for identical RdRps was conserved with respect to the ArCV-1 3Dpol structure and was discussed in structural analysis of ArCVTable 1 ) and the 3' terminus contained the sequence "GCA CCCATATTC". cache = ./cache/cord-278099-ypov9ha3.txt txt = ./txt/cord-278099-ypov9ha3.txt === reduce.pl bib === id = cord-280471-cqypwi5d author = Sun, Hua-Bao title = The changes of the peripheral CD4+ lymphocytes and inflammatory cytokines in Patients with COVID-19 date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4324 sentences = 202 flesch = 57 summary = To investigate the clinical value of changes in the subtypes of peripheral blood lymphocytes and levels of inflammatory cytokines in patients with COVID-19, the total numbers of lymphocytes and CD4+ lymphocytes and the ratio of CD4+/CD8+ lymphocytes were calculated and observed in different groups of patients with COVID-19. Characteristic chest CT imaging patterns, positive nucleic acid detection in nasal and throat swab samples, normal or decreased numbers of peripheral white blood cells, decreased numbers of lymphocytes and increased levels of inflammatory cytokines are the key factors in the diagnosis of COVID-19 [3] . The total number of lymphocytes, the percentages of lymphocyte subtypes and the levels of inflammatory cytokines (TNF-α and IL-6) secreted by CD4+ helper T lymphocytes in the peripheral blood were detected by hematology counter and flow cytometer, respectively. In the COVID-19 patients in the general, severe and critical groups, the numbers of peripheral lymphocytes and CD4+ T lymphocytes and the ratio of CD4+/CD8+ lymphocytes were significantly lower than those in the normal control group. cache = ./cache/cord-280471-cqypwi5d.txt txt = ./txt/cord-280471-cqypwi5d.txt === reduce.pl bib === id = cord-278018-3qemb0x3 author = Li, Li title = Identification of M.tuberculosis-Specific Th1 Cells Expressing CD69 Generated in vivo in Pleural Fluid Cells from Patients with Tuberculous Pleurisy date = 2011-08-22 pages = extension = .txt mime = text/plain words = 5980 sentences = 332 flesch = 57 summary = In the present study, we found that without any stimulation, CD4(+) T cells in pleural fluid cells (PFCs) from patients with TBP expressed significantly higher levels of CD69 than PBMCs from patients with tuberculosis (TB) or healthy donors. The phenotypic and functional analysis of CD69-expressing cells strongly suggested that CD69 could be a useful marker for the identification or enrichment of antigen specific Th1 cells at local sites following MTB infection. However, following stimulation with MTB-specific peptides of ESAT-6/CFP-10, CD4 + CD69 + T cells from the same patients expressed high levels of IFN-c, IL-2 and TNF-a (data not shown). However, following stimulation with MTB-specific peptides of ESAT-6/ CFP-10, CD4 + CD69 + T cells from the same patients with tuberculous pleurisy expressed high levels of IFN-c, IL-2 and TNF-a, indicating that the response was MTB-specific. cache = ./cache/cord-278018-3qemb0x3.txt txt = ./txt/cord-278018-3qemb0x3.txt === reduce.pl bib === id = cord-274241-biqbsggu author = Shaw, Timothy I. title = Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis) date = 2012-11-15 pages = extension = .txt mime = text/plain words = 6003 sentences = 339 flesch = 52 summary = Annotated genes are involved in a broad range of activities ranging from cellular metabolism to genome regulation through ncRNAs. Reciprocal BLAST best hits yielded 8,785 sequences that are orthologous to mouse, rat, cattle, horse and human. Species tree analysis of sequences from 2,378 loci was used to achieve 95% bootstrap support for the placement of bat as sister to the clade containing horse, dog, and cattle. Through substitution rate estimation between bat and human, 32 genes were identified with evidence for positive selection. To address some of these deficiencies, we have performed transcriptome sequencing and analysis of spleen, lung, kidney and poly-IC-stimulated primary kidney cells to identify genes of interest for assessing the host response to TCRV infection. There were 20,145 contigs that mapped to Pteropus alecto, Australian flying fruit bat, and 18,359 that overlapped between genomic and transcriptome sequences for all three datasets ( Figure 5 ). cache = ./cache/cord-274241-biqbsggu.txt txt = ./txt/cord-274241-biqbsggu.txt === reduce.pl bib === id = cord-281815-zvs5qe8x author = Subramanian, Shoba title = Hemoglobin Cleavage Site-Specificity of the Plasmodium falciparum Cysteine Proteases Falcipain-2 and Falcipain-3 date = 2009-04-09 pages = extension = .txt mime = text/plain words = 5953 sentences = 267 flesch = 45 summary = The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 degrade host hemoglobin to provide free amino acids for parasite protein synthesis. Treatment of erythrocytic parasites with cysteine protease inhibitors or disruption of the falcipain-2 gene results in accumulation of undegraded hemoglobin in the food vacuole, confirming a role for this enzyme in hemoglobin hydrolysis [6, 10] . To better characterize the roles of falcipain-2 and falcipain-3, we evaluated activities of these proteases against a library of small peptide substrates, a series of larger peptides spanning the sequences of a and b globin, and intact human hemoglobin. Falcipain-2 and falcipain-3 demonstrated a marked preference for cleavage of small peptide substrates with P 2 Leu, but the enzymes showed less specificity against larger peptides and intact hemoglobin, with hydrolysis at multiple sites. Despite the presence of multiple proteases in the food vacuole, it is noteworthy that treatment of cultured parasites with specific inhibitors of cysteine proteases fully blocked the hydrolysis of hemoglobin, highlighting the key role for the falcipains in this process [22] . cache = ./cache/cord-281815-zvs5qe8x.txt txt = ./txt/cord-281815-zvs5qe8x.txt === reduce.pl bib === id = cord-282303-idh7io9v author = Hassan, Md. Zakiul title = Contamination of hospital surfaces with respiratory pathogens in Bangladesh date = 2019-10-28 pages = extension = .txt mime = text/plain words = 4158 sentences = 203 flesch = 39 summary = With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. With limited infection control practices in overcrowded Bangladeshi hospitals, surfaces may play an important role in the transmission of respiratory pathogens in hospital wards and pose a serious risk of infection for patients, health care workers, caregivers and visitors. Respiratory viral and bacterial pathogens, including Staphylococcus aureus, Streptococcus pyogenes, influenza viruses, respiratory syncytial virus, adenovirus, rhinoviruses and novel coronavirus strains, can survive on hospital surfaces for days, weeks or even months. This study identified that hospital surfaces in these Bangladeshi hospitals, were frequently contaminated with respiratory pathogens and pose a potential threat for fomite-borne transmission of respiratory infections to patients, healthcare workers and family caregivers. cache = ./cache/cord-282303-idh7io9v.txt txt = ./txt/cord-282303-idh7io9v.txt === reduce.pl bib === id = cord-281161-u896icp9 author = Wang, Jing title = The Adjuvanticity of an O. volvulus-Derived rOv-ASP-1 Protein in Mice Using Sequential Vaccinations and in Non-Human Primates date = 2012-05-17 pages = extension = .txt mime = text/plain words = 6854 sentences = 317 flesch = 49 summary = We previously reported that the Onchocerca volvulus recombinant protein rOv-ASP-1 can induce activation and maturation of naïve human DCs and therefore could be used as an innate adjuvant to promote balanced Th1 and Th2 responses to bystander vaccine antigens in mice. As shown in Table 2 , similar IgG1 and IgG2a humoral immune responses against the influenza viruses were induced in the mice vaccinated previously with rRBD plus rOv-ASP-1 adjuvant and those administered with PBS only. As shown in Table 3 , all of the NHPs vaccinated with rRBD protein plus 50 mg (n = 2), 100 mg rOv-ASP-1 (n = 2) or 500 mg CpG (n = 1) as the adjuvant developed RBDspecific IgG antibody response with increasing antibody level after each boost. Secondly, using two concentration of the rOv-ASP-1 adjuvant, 50 or 100 mg, and rRBD as the vaccine antigen, we were able to induce after three immunizations high titers of neutralizing antibodies (1:3,500-1:6,392) that much exceed what is needed for protection against SARS-CoV infection in vivo (.1:500) [56] . cache = ./cache/cord-281161-u896icp9.txt txt = ./txt/cord-281161-u896icp9.txt === reduce.pl bib === id = cord-276372-q1fzxt3r author = Conde, Dalia A. title = Zoos through the Lens of the IUCN Red List: A Global Metapopulation Approach to Support Conservation Breeding Programs date = 2013-12-11 pages = extension = .txt mime = text/plain words = 4780 sentences = 225 flesch = 48 summary = To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. To understand the complexity of maintaining CBPs of threatened species across the ISIS zoo network, we developed a second algorithm to find the optimal radial distance from any given zoo at which the probability of finding a metapopulation size of at least 50, 100 or 250 recruited living individuals was highest relative to that radial distance. As expected, the optimal distance radii and the number of zoos required to maximize the probability of reaching a given population increase with the metapopulation size threshold (.50, .100 and .250 individuals) ( Figure 3) . Therefore, for the zoo community, one of the main challenges of managing their threatened species in CBPs is the complexity of moving individuals across borders and the coordination of conservation efforts among zoos and other institutions at a global level. cache = ./cache/cord-276372-q1fzxt3r.txt txt = ./txt/cord-276372-q1fzxt3r.txt === reduce.pl bib === id = cord-286065-x0g67pnb author = Metzgar, David title = The IRIDICA BAC BSI Assay: Rapid, Sensitive and Culture-Independent Identification of Bacteria and Candida in Blood date = 2016-07-06 pages = extension = .txt mime = text/plain words = 5925 sentences = 240 flesch = 38 summary = We describe the analytical characteristics of the IRIDICA BAC BSI Assay and compare its pre-clinical performance to current standard-of-care methods in a collection of prospectively collected blood specimens from patients with symptoms of sepsis. During the clinical sample study, performed following the sterility and personal protective equipment recommendations of the manufacturer, 61 negative controls were tested and yielded no Other reportable organisms excluding potential contaminants (n = 550) 0 0 0 207 A These 11 culture-negative, IRIDICA BAC BSI Assay-positive detections were supported by later organism-specific ID data which identified the same species as agents of infection (as noted on the subjects' charts). The broad-spectrum nature of the IRIDICA BAC BSI Assay primers, paired with a signal analysis method capable of sensitive and specific detection and identification of one or more species signatures in samples with high background levels of human DNA, make it uniquely suited as a molecular test for bacterial and Candida DNA in blood samples. cache = ./cache/cord-286065-x0g67pnb.txt txt = ./txt/cord-286065-x0g67pnb.txt === reduce.pl bib === id = cord-281124-4nhy35xn author = Soowannayan, Chumporn title = RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date = 2011-08-03 pages = extension = .txt mime = text/plain words = 5596 sentences = 259 flesch = 53 summary = To examine this domain in more detail, the 18 aa peptide (M(11)PVRRPLPPQPPRNARLI(29)) encompassing this sequence was synthesized and found to bind nucleic acids similarly to the full-length N protein in EMSAs. The data indicate a fundamental role for the GAV N protein proline/arginine-rich domain in nucleating genomic ssRNA to form nucleocapsids. In a preliminary attempt to identify an RNA packaging signal in the GAV genome, EMSAs were performed using ssRNAs synthesized to various genome regions including (i) an ORF1b gene 39-region spanning the relative position to the genome packaging signal identified in MHV [28] , (ii) a 39-terminal genome region corresponding in position to the region in the infectious bronchitis virus (IBV) genome reported to contain an RNA binding domain [29] and (iii) the 59-genomic RNA terminus which, in coronaviruses, has also been reported to interact specifically with N protein [30] . cache = ./cache/cord-281124-4nhy35xn.txt txt = ./txt/cord-281124-4nhy35xn.txt === reduce.pl bib === id = cord-282202-q2q4vies author = Banerjee, Amitava title = Clinical academic research in the time of Corona: A simulation study in England and a call for action date = 2020-08-13 pages = extension = .txt mime = text/plain words = 4106 sentences = 229 flesch = 46 summary = DESIGN: A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics). "Learning is difficult in the midst of an emergency" [7] , but our ability to deliver timely, high-impact clinical research, relevant to patients and populations, is critical across the academic spectrum [8] , from "bench to bedside to big data", whether basic biology, repurposed and novel therapeutic approaches, vaccines or modelling. Our aims were to: (i) model potential impact of the pandemic on clinical academic capacity in England relating to COVID-19; and (ii) develop evidence-based recommendations to inform the optimal scientific response to COVID-19. cache = ./cache/cord-282202-q2q4vies.txt txt = ./txt/cord-282202-q2q4vies.txt === reduce.pl bib === id = cord-286708-igu984oc author = Chua, Kaw Bing title = Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date = 2008-11-25 pages = extension = .txt mime = text/plain words = 4359 sentences = 219 flesch = 53 summary = Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Here, we report the discovery and characterization of Kampar virus (KamV), the fourth member in the NBV species group and its isolation from a human patient with fever and acute respiratory illness. Due to the similar CPE morphology ( Figure 1 ) and cell line susceptibility patterns between KamV and the recently discovered Melaka virus (MelV), which also causes acute respiratory diseases in humans [5] , immunofluorescent antibody testing was conducted to examine cross reactivity. cache = ./cache/cord-286708-igu984oc.txt txt = ./txt/cord-286708-igu984oc.txt === reduce.pl bib === id = cord-284275-bqo203pf author = Lu, Roujian title = Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays date = 2012-06-15 pages = extension = .txt mime = text/plain words = 2978 sentences = 165 flesch = 52 summary = title: Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays The etiology and clinical impact of HCoVs in Chinese adults with acute upper respiratory tract infection (URTI) needs to be characterized systematically by molecular detection with excellent sensitivity. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we detected 4 non-SARS related HCoV species by real-time RT-PCR in 981 nasopharyngeal swabs collected from March 2009 to February 2011. Respiratory syncytial virus (RSV), human parainfluenza virus (PIV) and HBoV were detected in very low rate (less than 1%) among adult patients with URTI. CONCLUSIONS/SIGNIFICANCE: All 4 non-SARS-associated HCoVs were more frequently detected by real-time RT-PCR assay in adults with URTI in Beijing and HCoV-229E led to the most prevalent infection. In our retrospective study, a 16.0% detection rate for HCoVs infection was found in adults with URTI; 229E was the most common infection (9.8% of all cases), followed by OC43 (4.3%), HKU1 (1.6%) and NL63 (1.1%). cache = ./cache/cord-284275-bqo203pf.txt txt = ./txt/cord-284275-bqo203pf.txt === reduce.pl bib === id = cord-283976-jgae7r2q author = Armstrong, Melissa J. title = Research priorities of caregivers and individuals with dementia with Lewy bodies: An interview study date = 2020-10-07 pages = extension = .txt mime = text/plain words = 4111 sentences = 208 flesch = 37 summary = BACKGROUND: Funding bodies are placing increased emphasis on patient and public involvement in research, but the research priorities of individuals and caregivers living with dementia with Lewy bodies (DLB) are unknown. Funding should be informed by the priorities of all relevant stakeholders and support research investigating causes, natural history, biomarkers, and treatment in addition to research targeting themes regarding living with disease (e.g. independence, quality of life, caregiving, and education). The study guide queried a variety of research categories and individuals with DLB and caregivers identified topics important for research in all of them-focusing on awareness, determining the cause of DLB, improving diagnosis, investigating what to expect and disease stages, DLB symptoms needing additional research, therapies to prevent, cure, or slow the progression of DLB, targeting daily function and quality of life, caregiving, and improving education. cache = ./cache/cord-283976-jgae7r2q.txt txt = ./txt/cord-283976-jgae7r2q.txt === reduce.pl bib === id = cord-285546-5tjhdczt author = Green, Manfred S. title = The confounded crude case-fatality rates (CFR) for COVID-19 hide more than they reveal—a comparison of age-specific and age-adjusted CFRs between seven countries date = 2020-10-21 pages = extension = .txt mime = text/plain words = 2390 sentences = 142 flesch = 64 summary = title: The confounded crude case-fatality rates (CFR) for COVID-19 hide more than they reveal—a comparison of age-specific and age-adjusted CFRs between seven countries BACKGROUND: Crude case-fatality rates (CFRs) for COVID-19 vary widely between countries. We examined how the age distribution of the cases is responsible for the COVID-19 CFR differences between countries. METHODS: COVID-19 cases and deaths, by ten-year age-groups, were available from the reports of seven countries. The age-adjusted CFRs were computed by the direct method, using the combined number of cases in all seven countries in each age group as the standard population. CONCLUSIONS: The age structure of the cases explains much of differences in the crude CFRs between countries and adjusting for age substantially reduces this variation. The age-specific number of cases, number of deaths and the crude CFRs by country are given in Table 1 . cache = ./cache/cord-285546-5tjhdczt.txt txt = ./txt/cord-285546-5tjhdczt.txt === reduce.pl bib === id = cord-287739-58fth3xl author = Huang, Yhu-Chering title = Successful Control of Methicillin-Resistant Staphylococcus aureus in Endemic Neonatal Intensive Care Units—A 7-Year Campaign date = 2011-08-12 pages = extension = .txt mime = text/plain words = 3821 sentences = 188 flesch = 42 summary = CONCLUSION/SIGNIFICANCE: Through infection control measures, MRSA HAIs can be successfully controlled, even in areas with high levels of endemic MRSA infections such as our NICUs. Methicillin-resistant Staphylococcus aureus (MRSA) is among the most important pathogens of bacteremia in the intensive care units (ICU). To reduce and control healthcare-associated infections (HAIs) caused by MRSA, a ''search and destroy'' strategy, which first detects the patients with MRSA colonization and then decolonizes the MRSA with certain antimicrobial agents, was recently proposed and implemented in some hospitals of different countries, with inconsistent effects [12] [13] [14] [15] [16] . Methicillin-resistant Staphylococcus aureus colonization and its association with infection among infants hospitalized in neonatal intensive care units cache = ./cache/cord-287739-58fth3xl.txt txt = ./txt/cord-287739-58fth3xl.txt === reduce.pl bib === id = cord-279421-rxocrgfu author = Zhang, Dan title = Clinical Evaluation of a Single-Tube Multiple RT-PCR Assay for the Detection of 13 Common Virus Types/Subtypes Associated with Acute Respiratory Infection date = 2016-04-04 pages = extension = .txt mime = text/plain words = 2863 sentences = 134 flesch = 48 summary = title: Clinical Evaluation of a Single-Tube Multiple RT-PCR Assay for the Detection of 13 Common Virus Types/Subtypes Associated with Acute Respiratory Infection In the present study, an improved single-tube multiplex reverse transcription PCR assay for simultaneous detection of 13 respiratory viruses was evaluated and compared with a previously reported two-tube assay as the reference method using clinical nasopharyngeal aspirates samples. In conclusion, our results demonstrates the one-tube assay revealed significant improvements over the two-tube assay in terms of the better sensitivity, more accurate quality control, less nonspecific amplification, more cost-effective and shorter turn-around time and will be a valuable tool for routine surveillance of respiratory virus infection in China. In the present study, we adopted the two-tube assay as a reference, and have been progressively optimized and substantially improved the performance of simultaneous detection of thirteen respiratory viruses types/subtypes, the most frequently detected viral agents of respiratory tract infections documented by Beijing Monitoring Network for Pneumonia between 2012-2014 (unpublished data), in a single-tube assay while maintaining excellent sensitivity and specificity. cache = ./cache/cord-279421-rxocrgfu.txt txt = ./txt/cord-279421-rxocrgfu.txt === reduce.pl bib === id = cord-281364-syg0wo77 author = Caì, Yíngyún title = CD26/DPP4 Cell-Surface Expression in Bat Cells Correlates with Bat Cell Susceptibility to Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection and Evolution of Persistent Infection date = 2014-11-19 pages = extension = .txt mime = text/plain words = 3827 sentences = 178 flesch = 49 summary = title: CD26/DPP4 Cell-Surface Expression in Bat Cells Correlates with Bat Cell Susceptibility to Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection and Evolution of Persistent Infection We found that the susceptibility or resistance of these bat cell lines directly correlates with the presence or absence of cell surface-expressed CD26/DPP4, the functional human receptor for MERS-CoV. Finally, we demonstrate that persistent MERS-CoV infections can be established in permissive bat cell lines after sequential virus passage, leading to downregulation of natural CD26/DPP4 cellsurface expression. None of the four MERS-CoV-resistant cell lines tested in this study (PESU-B5L, R05T, R06E, and Tb1Lu) were recognized by anti-human CD26/DPP4 antibody in this assay, whereas all susceptible bat cells (EidNi/41.3, EpoNi/22.1, HypLu/45.1, HypNi/1.1, RoNi/7.1, and RoNi/7.2) tested positive for CD26/DPP4 expression (Figure 2 ). Our study confirms the role of CD26/DPP4 as receptor for two divergent MERS-CoV isolates and correlates its presence or absence on the surface of bat cells directly with bat cell susceptibility or resistance to productive MERS-CoV infection (Figures 2 and 3 ). cache = ./cache/cord-281364-syg0wo77.txt txt = ./txt/cord-281364-syg0wo77.txt === reduce.pl bib === id = cord-284501-5i0w74q4 author = Armesto, Maria title = The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date = 2009-10-09 pages = extension = .txt mime = text/plain words = 7792 sentences = 322 flesch = 54 summary = The IBV cDNA within pGPT-BeauR-Rep-M41-Struct-3UTR was introduced, by homologous recombination using the transient dominant selection (TDS) ( [25, 37] ), into the IBV Beaudette cDNA within the vaccinia virus genome in rVV-BeauR-Rep-DStruct containing Beau-R-derived sequence corresponding to the replicase gene followed by the first 376 nt of the S gene, part of the N gene and the 39-UTR (Fig. 1) . The samples were analysed for the presence of viable IBV by titration in TOCs or used for RNA extraction using the RNeasy method and analysed by RTThe M41-CK-derived cDNA, representing the M41 structural and accessory genes and the M41 39-UTR, within pGPT-BeauR-Rep-M41-Struct-3UTR was fused to the Beau-R replicase gene in the rVV by a homologous recombination event between the Beau-R replicase sequence common to both constructs. Analysis of the tracheal epithelial cells isolated from the infected chickens, for the presence of IBV by titration on TOCs, had indicated that either there was no Beau-R or rBeauR-Rep-M41-Struct-2 present or that the levels of both viruses were below detection. cache = ./cache/cord-284501-5i0w74q4.txt txt = ./txt/cord-284501-5i0w74q4.txt === reduce.pl bib === id = cord-282668-bs634hti author = Niang, Mbayame Ndiaye title = Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses date = 2017-03-22 pages = extension = .txt mime = text/plain words = 4623 sentences = 243 flesch = 47 summary = In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenzalike Illness cases. From January 2012 to December 2015 we collected specimens (nasal-pharyngeal and oral-pharyngeal swabs) and surveillance data for influenza and other viral respiratory pathogens from outpatients presenting with influenza-like-illness (ILI) at different sentinel sites in Senegal. So the circulation of such HAdV genome types in Senegal emphasizes the need to reinforce HAdV surveillance, especially in hospitalized patients, by including HAdV genome detection and genotyping in the documentation of severe respiratory infections. Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil cache = ./cache/cord-282668-bs634hti.txt txt = ./txt/cord-282668-bs634hti.txt === reduce.pl bib === id = cord-284016-zb6cv8ik author = Li, Wei title = Activation of Interleukin-32 Pro-Inflammatory Pathway in Response to Influenza A Virus Infection date = 2008-04-16 pages = extension = .txt mime = text/plain words = 4188 sentences = 258 flesch = 48 summary = Expression of IL-32 in influenza A virus infected A549 human lung epithelial cells was blocked by either selective COX-2 inhibitor NS398 or Aspirin, a known anti-inflammatory drug, indicating IL-32 was induced through COX-2 in the inflammatory cascade. It has been reported that influenza virus can activate the expression of COX-2 in cell culture systems [26] and that dsRNA can induce the production of COX-2, followed by PGE 2 release [5] . To identify the viral components which play important roles in IV-stimulated pro-inflammatory factors COX-2 and IL-32 expression, we screened all ten proteins of influenza virus: HA, NA, NP, NS1, NS2, M1, M2, PA, PB1, PB2 and poly(IC) (to mimic viral replicative intermediate dsRNA) by luciferase assays. Both influenza A virus infection and poly(IC)+IFN-c treatment in A549 human lung epithelial cells were able to induce COX-2/ IL-32 mRNA and protein expression as well as PGE 2 and IL-32 accumulation in the cell culture supernatants. cache = ./cache/cord-284016-zb6cv8ik.txt txt = ./txt/cord-284016-zb6cv8ik.txt === reduce.pl bib === id = cord-281665-6n7aq4k9 author = Qiu, Sangsang title = Is Tuberculosis Treatment Really Free in China? A Study Comparing Two Areas with Different Management Models date = 2015-05-20 pages = extension = .txt mime = text/plain words = 3982 sentences = 213 flesch = 49 summary = This study describes the economic burden on patients with tuberculosis; identifies related factors by comparing two areas with different management models; and provides policy recommendation for tuberculosis control reform in China. Based on the multivariable linear regression analysis, factors related to the total out-of-pocket costs were study site, age, number of clinical visits, residence, diagnosis delay, hospitalization, intake of liver protective drugs and use of the second-line drugs. This study describes the economic burden on patients with tuberculosis, identifies related factors by comparing two areas with different management models, and provides a policy recommendation for the tuberculosis control system in China. Significant factors related to the total out-of-pocket costs were study setting (t = -3.10, P = 0.002), age (t = -4.04, P < 0.001), number of clinical visits (t = 4.46, P < 0.001), residence (t = 3.19, P = 0.002), diagnosis delay (t = 3.47, P = 0.001), hospitalization (t = 15.04, P < 0.001), intake of liver protective drugs (t = 2.78, P = 0.006) and intake of second-line drugs (t = 2.87, P = 0.004) ( Table 5) . cache = ./cache/cord-281665-6n7aq4k9.txt txt = ./txt/cord-281665-6n7aq4k9.txt === reduce.pl bib === id = cord-287784-f7usy52w author = Maestre, Ana M. title = Equine Torovirus (BEV) Induces Caspase-Mediated Apoptosis in Infected Cells date = 2011-06-15 pages = extension = .txt mime = text/plain words = 8981 sentences = 395 flesch = 45 summary = Based on this finding, we analyzed several apoptotic markers, and observed protein synthesis inhibition, rRNA and DNA degradation, nuclear fragmentation, caspase-mediated cleavage of PARP and eIF4GI, and PKR and eIF2α phosphorylation, all these processes taking place after peak virus production. We did not observe any CPE on the cells treated with UV-inactivated virus (data not shown), and neither of the two caspase substrates was processed in these cells (Fig. 5B) , suggesting that BEV apoptosis triggering is dependent upon viral replication. As a whole, these results indicate that although both cell death receptor and mitochondrial pathways are implicated in the BEV induction of apoptosis, the mitochondrial pathway could be secondarily activated by caspase-8-mediated cleavage of Bid. To further ascertain the involvement of the mitochondrial pathway in BEV-induced apoptosis we analyzed the cellular distribution of cytochrome c at different times postinfection. cache = ./cache/cord-287784-f7usy52w.txt txt = ./txt/cord-287784-f7usy52w.txt === reduce.pl bib === id = cord-289305-mfjyjjer author = Lee, Min Hye title = A systematic review on the causes of the transmission and control measures of outbreaks in long-term care facilities: Back to basics of infection control date = 2020-03-10 pages = extension = .txt mime = text/plain words = 7550 sentences = 417 flesch = 47 summary = title: A systematic review on the causes of the transmission and control measures of outbreaks in long-term care facilities: Back to basics of infection control Three studies on gastrointestinal infection, in which adherence to hand hygiene among HCWs was crucial to prevent its spread, reported control measures including stringent hand hygiene practice and reinforcement of standard precautions [23, 27, 31] . The study on the RSV and HMPV outbreak reported various measures including active surveillance, isolation, contact precaution, antiviral prophylaxis for residents and work restriction for ill staff to control respiratory pathogen transmission [50] . This update for understanding outbreaks in LTCFs by reviewing recent studies indicates that staff members and residents are still at risk for contagious disease outbreaks including influenza, gastroenteritis, and GAS infection. Influenza outbreak control practices and the effectiveness of interventions in long-term care facilities: a systematic review cache = ./cache/cord-289305-mfjyjjer.txt txt = ./txt/cord-289305-mfjyjjer.txt === reduce.pl bib === id = cord-286837-j2sqs20q author = Koetsier, Antonie title = Do Intensive Care Data on Respiratory Infections Reflect Influenza Epidemics? date = 2013-12-31 pages = extension = .txt mime = text/plain words = 4526 sentences = 210 flesch = 49 summary = METHODS: We calculated the time lag and correlation between ILI incidence (from ILI sentinel surveillance, based on general practitioners (GP) consultations) and percentages of ICU admissions with a respiratory infection (from the Dutch National Intensive Care Registry) over the years 2003–2011. In the season 2009/2010 as well as in the season 2010/2011, ILI incidence as measured by GP sentinel practices, reached the epidemic threshold of 5.1 consultations per 10.000 enlisted patients at a time when already more than 100 patients had been hospitalized, with several ICU admissions and deaths from laboratory confirmed Influenza (National Institute for Public Health and the Environment, unpublished surveillance data). In our study we built three additive Poisson GEE regression models with ICU data to predict the incidence of ILI patients, thereby detecting influenza epidemics and aimed at detecting opportunities for enhancing the current national surveillance method. cache = ./cache/cord-286837-j2sqs20q.txt txt = ./txt/cord-286837-j2sqs20q.txt === reduce.pl bib === id = cord-287761-73qgx58i author = Aly, Mahmoud title = Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update date = 2017-10-13 pages = extension = .txt mime = text/plain words = 3389 sentences = 164 flesch = 55 summary = Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. GCC countries including Saudi Arabia now have the infrastructure in place that allows physicians and scientific community to identify and immediately respond to the potential risks posed by new outbreaks of MERS-CoV infections in the region. The emergence of MERS-CoV dates back to July 2012 when an elderly patient of age 60 years died from an acute pneumonia in Saudi Arabia, and a new coronavirus strain was isolated from his lung tissue [1] . With regard to viral origin and transmission, the first case of MERS-CoV infection did not relate it to any particular contact with animals before the disease onset; however, other studies did link it to Dromedary camels [5] [6] [7] [8] . cache = ./cache/cord-287761-73qgx58i.txt txt = ./txt/cord-287761-73qgx58i.txt === reduce.pl bib === id = cord-285433-ehnu83qe author = Sun, Hongliu title = Detection of Cytomegalovirus Antibodies Using a Biosensor Based on Imaging Ellipsometry date = 2015-08-21 pages = extension = .txt mime = text/plain words = 4698 sentences = 265 flesch = 54 summary = METHODS: An antibody analysis method is reported for the detection and identification of CMV antibodies in serum using a biosensor based on high spatial resolution imaging ellipsometry (BIE). As such, the concentration of CMV antibody in serum was quantitatively detected by BIE and then compared using ELISAs. Silicon wafers were purchased from the General Research Institute for Nonferrous Metals (China). Compared to blank controls areas, the purified CMV antibody and patient serum sample detection areas had markedly thicker films, with the average grayscale value displaying significant increases, while negative control areas did not (Fig 1) . Quantitative detection of CMV antibodies in clinical serum 41 CMV patients (Table A in S2 File) with quantitative results by ELISA were tested with BIE (Fig 4) . Thus, this label-free method may avoid some Detection of CMV antibodies in patient serum using BIE. cache = ./cache/cord-285433-ehnu83qe.txt txt = ./txt/cord-285433-ehnu83qe.txt === reduce.pl bib === id = cord-283604-fqc9jp0l author = Chen, Meng title = Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date = 2015-03-27 pages = extension = .txt mime = text/plain words = 3060 sentences = 127 flesch = 39 summary = To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. The comparison results of the penton base, hexon, and fiber gene sequences between the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and the strains from the GenBank database indicated significant conservation and stability of the sequences within the genome across time and space. cache = ./cache/cord-283604-fqc9jp0l.txt txt = ./txt/cord-283604-fqc9jp0l.txt === reduce.pl bib === id = cord-286613-cmtsu73g author = Lee, Sung Woo title = Risk Factors for Acute Kidney Injury and In-Hospital Mortality in Patients Receiving Extracorporeal Membrane Oxygenation date = 2015-10-15 pages = extension = .txt mime = text/plain words = 3601 sentences = 203 flesch = 57 summary = title: Risk Factors for Acute Kidney Injury and In-Hospital Mortality in Patients Receiving Extracorporeal Membrane Oxygenation BACKGROUND AND OBJECTIVES: Although acute kidney injury (AKI) is the most frequent complication in patients receiving extracorporeal membrane oxygenation (ECMO), few studies have been conducted on the risk factors of AKI. CONCLUSION: The initial pump speed of ECMO was a significant risk factor of in-hospital mortality and AKI in patients receiving ECMO. The initial pump speed of ECMO was a significant risk factor of in-hospital mortality and AKI in patients receiving ECMO. The cut-off values of SAPS2, serum sodium level, and ECMO pump speed for in-hospital mortality were a score of 69.5, 147.6 mmol/L, and 2.19 x 10 3 rpm, respectively (Table 3) . We showed that AKI, especially stage 3 AKI, was a significant risk factor for in-hospital mortality in patients receiving ECMO support. In conclusion, AKI is a significant risk factor for in-hospital mortality in patients receiving ECMO support. cache = ./cache/cord-286613-cmtsu73g.txt txt = ./txt/cord-286613-cmtsu73g.txt === reduce.pl bib === id = cord-289555-1z4vbldd author = Mühldorfer, Kristin title = Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates date = 2011-12-28 pages = extension = .txt mime = text/plain words = 5764 sentences = 303 flesch = 44 summary = Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats. In this study, we provide new data on infectious diseases in European bat species, considering factors likely to affect the susceptibility of bats to infectious agents including effects of seasonality, individual and species-specific heterogeneities, and possible intra-and inter-species transmission dynamics. Comparative bacteriologic and histo-pathologic analysis identified 22 different bacterial species that were clearly associated with pathological lesions and/or systemic infection, found in 17% (n = 73) of bats investigated bacteriologically ( Table 5) . cache = ./cache/cord-289555-1z4vbldd.txt txt = ./txt/cord-289555-1z4vbldd.txt === reduce.pl bib === id = cord-289285-aof7xy13 author = Michaelis, Martin title = Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression date = 2011-05-17 pages = extension = .txt mime = text/plain words = 4282 sentences = 270 flesch = 42 summary = title: Glycyrrhizin Exerts Antioxidative Effects in H5N1 Influenza A Virus-Infected Cells and Inhibits Virus Replication and Pro-Inflammatory Gene Expression Here, the effects of an approved parenteral glycyrrhizin preparation (Stronger Neo-Minophafen C) were investigated on highly pathogenic influenza A H5N1 virus replication, H5N1-induced apoptosis, and H5N1-induced pro-inflammatory responses in lung epithelial (A549) cells. The mechanism by which glycyrrhizin interferes with H5N1 replication and H5N1-induced pro-inflammatory gene expression includes inhibition of H5N1-induced formation of reactive oxygen species and (in turn) reduced activation of NFκB, JNK, and p38, redox-sensitive signalling events known to be relevant for influenza A virus replication. Glycyrrhizin 200 mg/ml (the maximum tested concentration) did not affect A549 cell viability (data not shown) but clearly decreased CPE formation in A549 cells infected with the H5N1 influenza strain A/Thailand/1(Kan-1)/04 at MOIs of 0.01, 0.1 or 1 ( Figure 1A ). Here, we show that glycyrrhizin inhibits the replication of highly pathogenic H5N1 influenza A virus, H5N1-induced apoptosis, and H5N1-induced expression of pro-inflammatory cytokines in lung-derived A549 cells. cache = ./cache/cord-289285-aof7xy13.txt txt = ./txt/cord-289285-aof7xy13.txt === reduce.pl bib === id = cord-288440-w7g2agaf author = Jia, Rui title = The C-Terminal Sequence of IFITM1 Regulates Its Anti-HIV-1 Activity date = 2015-03-04 pages = extension = .txt mime = text/plain words = 4902 sentences = 276 flesch = 53 summary = This inhibition appears to be specific to HIV-1, since neither the WT IFITM1 nor its C-terminal truncations affected entry that was mediated by the G protein of vesicular stomatitis virus (VSV) ( Fig. 2A and 2B) . Removing the last 9 or 14 amino acids from C-terminal sequence re-localized the majority of IFITM1 to the cell periphery (Fig. 3A) , indicating that these C-terminus truncated IFITM1 mutants are mostly positioned at the plasma membrane where HIV-1 entry occurs. We recently reported that HIV-1 BH10 became resistant to IFITM1 restriction in the spread infection through acquiring mutations in viral Env and Vpu proteins that together enhance the virus transmission between cells [27] . One possible scenario is that HIV-1 Env protein may modulate virus sensitivity to human IFITM1 restriction by virtue of its ability to mediate and regulate virus cell-to-cell transmission. cache = ./cache/cord-288440-w7g2agaf.txt txt = ./txt/cord-288440-w7g2agaf.txt === reduce.pl bib === id = cord-286404-eggkqq3b author = Strayer, David R. title = Effect of disease duration in a randomized Phase III trial of rintatolimod, an immune modulator for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5439 sentences = 266 flesch = 47 summary = CONCLUSION/SIGNIFICANCE: Analysis of ETT from a Phase III trial has identified within the ITT population, a subset of ME/CFS patients with ≥2 fold increased exercise response to rintatolimod. In the AMP-516 Phase III clinical trial, patients with severe ME/CFS demonstrated significant improvement in the primary endpoint, exercise treadmill tolerance (ETT), compared to placebo controls following the twice weekly for 40 weeks systemic administration [12] of the selective TLR3 dsRNA agonist, rintatolimod (Ampligen 1 ) [10, 11]. Effect of ME/CFS duration in response to rintatolimod fewer patients and reduced statistical power compared to the ITT population (n = 208), the placebo-adjusted mean increase in ETT (Δ = 23.6) within the Target Subset (n = 75) was statistically significant. This post-hoc analysis of the successful AMP-516 double-blind, placebo-controlled, randomized, Phase III trial has identified a subgroup of patients defined primarily by the length of ME/CFS symptoms (2-8 years) with an increased likelihood of a clinically beneficial response to rintatolimod. cache = ./cache/cord-286404-eggkqq3b.txt txt = ./txt/cord-286404-eggkqq3b.txt === reduce.pl bib === id = cord-290773-kgb8r561 author = Ahn, Jong Gyun title = Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus date = 2018-07-03 pages = extension = .txt mime = text/plain words = 2594 sentences = 148 flesch = 47 summary = title: Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus Therefore, in this study, we investigated the epidemiological, clinical, and virological characteristics of HRV infections in children with acute lower respiratory tract infections. This study demonstrates that HRV is an important cause of lower respiratory infection in young children that is associated with symptoms of respiratory distress, such as chest retraction and wheezing. In our study, there were no significant differences in the clinical features, laboratory data or NPA cytokine levels between HRV-A and -C infections. High prevalence of human rhinovirus C infection in Thai children with acute lower respiratory tract disease Human rhinovirus species C infection in young children with acute wheeze is associated with increased acute respiratory hospital admissions Rhinovirus load and disease severity in children with lower respiratory tract infections cache = ./cache/cord-290773-kgb8r561.txt txt = ./txt/cord-290773-kgb8r561.txt === reduce.pl bib === id = cord-289093-si8btsab author = Beard, Philippa M. title = A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date = 2014-06-05 pages = extension = .txt mime = text/plain words = 6578 sentences = 310 flesch = 49 summary = To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. cache = ./cache/cord-289093-si8btsab.txt txt = ./txt/cord-289093-si8btsab.txt === reduce.pl bib === id = cord-289873-6hivjqof author = Lu, Rui title = Patients with mild and general COVID-19 should be negative for at least 3 consecutive nucleic acid tests before discharged date = 2020-10-02 pages = extension = .txt mime = text/plain words = 1693 sentences = 80 flesch = 51 summary = The median time from the onset of COVID-19 to the occurrence of two consecutive negative nucleic acid tests of these patients was 21 days. Thus, we suggested that the patient should be negative for at least 3 consecutive nucleic acid tests before discharge, and the test time should be no earlier than the 23rd day since the onset of the disease. According to the latest COVID-19 clinical diagnosis and treatment guideline [3] , patients who meet the following four criteria can be discharged: (1) the body temperature has returned to normal for more than 3 days; (2) the respiratory symptoms have improved significantly; (3) the pulmonary imaging examination shows that the acute exudative lesions have improved significantly, (4) two consecutive negative nucleic acid test for respiratory specimens such as sputum and nasopharyngeal swabs (sampling interval at least 24 hours). The median time from the onset of COVID-19 to the occurrence of two consecutive negative nucleic acid tests in 845 patients with COVID-19 was 21 days (range: 1-56 days). cache = ./cache/cord-289873-6hivjqof.txt txt = ./txt/cord-289873-6hivjqof.txt === reduce.pl bib === id = cord-289017-vwye3pk9 author = Comach, Guillermo title = Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date = 2012-09-11 pages = extension = .txt mime = text/plain words = 6262 sentences = 301 flesch = 47 summary = CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . cache = ./cache/cord-289017-vwye3pk9.txt txt = ./txt/cord-289017-vwye3pk9.txt === reduce.pl bib === id = cord-290446-43h1r4pm author = Vazquez, Leonardo title = Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus date = 2017-07-27 pages = extension = .txt mime = text/plain words = 8840 sentences = 422 flesch = 53 summary = This spacer provided a reasonably dynamic loop, according to our NMR data, which included narrow chemical shift dispersion (S2A Fig As depicted in Fig 1A, we designed the nsp1 constructs so as to avoid truncating their secondary-structure elements. The full-length nsp1 fusion protein has only a few missing peaks, indicating a well-folded 3D domain, which causes a wide dispersion of chemical shifts and allows straightforward identification of backbone HN signals. The SSP indicates the propensity ranging from -1 to 1 to adopt backbone conformations typical for extended β-strands or helical structures, respectively, according to the effect of these conformations on the chemical shifts of backbone atoms, [39] [40] [41] As shown in Fig 7, with the SSP algorithm it was possible to define very well the secondarystructure elements of the folded globular domain of nsp1 (orange bars in the uppermost graph). cache = ./cache/cord-290446-43h1r4pm.txt txt = ./txt/cord-290446-43h1r4pm.txt === reduce.pl bib === id = cord-289510-spmknns5 author = Curado, Evaldo M. F. title = A discrete-time-evolution model to forecast progress of Covid-19 outbreak date = 2020-10-29 pages = extension = .txt mime = text/plain words = 5920 sentences = 325 flesch = 67 summary = Here, we present a model that can easily incorporate these available data sets and is based on discrete-time equations to forecast the number of confirmed cases by Covid-19 in any given country for the next 14 days. Among its strengths, the presented model: (i) presents low relative error rates, as tested in data from Brazil, South Korea and UK; (ii) provides easily interpretable results, specifically the predicted number of infected people in the next 14 days; (iii) presents results that are directly comparable across countries; and (iv) incorporates the average time related to the disease incubation period (asymptomatic phase) and the average time related to the symptomatic phase, both parameters adjustable according to the pandemics' characteristics. With the intention to test the method and find good values for the parameters α and β, we considered our fictitious t f N ¼ 102-th day, so it is possible to compare the total number of infected people as provided by the original source (JHU) with the predicted data generated by the model. cache = ./cache/cord-289510-spmknns5.txt txt = ./txt/cord-289510-spmknns5.txt === reduce.pl bib === id = cord-285749-0ejhd9nw author = Hoffmann, Markus title = The Hemagglutinin of Bat-Associated Influenza Viruses Is Activated by TMPRSS2 for pH-Dependent Entry into Bat but Not Human Cells date = 2016-03-30 pages = extension = .txt mime = text/plain words = 6025 sentences = 329 flesch = 49 summary = Generation of VSV pseudotypes (VSVpp) was performed as follows: HEK-293T cells were transfected by calcium-phosphate precipitation with expression plasmids encoding viral surface proteins, VSV-G (positive control) , NiV-F/G, FLUAV-HA and/or NA and bat-FLUAV-HAL and/or NAL, or empty plasmid (pCAGGS) as negative control. In order to investigate the potential of human TTSPs to proteolytically activate batFLUAV-HAL for host cell entry, we additionally cotransfected the cells with expression plasmids for TMPRSS2, DESC-1 or MSPL. Notably, three bat cell lines (EidNi/41, HypNi/1.1 and EpoNi/22.1) were susceptible to entry of pseudotypes bearing HAL and NAL of batFLUAV (Fig 2B) , demonstrating that surface glycoproteins of batFLUAV can mediate cellular entry. To assess proteolytic activation of HA/HAL proteins, vesicular stomatitis virus-based pseudotypes (VSVpp) were produced in cells transfected to express the indicated type II transmembrane serine proteases (B) or different amounts of TMPRSS2 (C). cache = ./cache/cord-285749-0ejhd9nw.txt txt = ./txt/cord-285749-0ejhd9nw.txt === reduce.pl bib === id = cord-291756-ejh1r8h4 author = Pérez-Fuentes, María del Carmen title = Threat of COVID-19 and emotional state during quarantine: Positive and negative affect as mediators in a cross-sectional study of the Spanish population date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3766 sentences = 197 flesch = 49 summary = title: Threat of COVID-19 and emotional state during quarantine: Positive and negative affect as mediators in a cross-sectional study of the Spanish population AIMS: The objective of this study was therefore to analyze the effect of exceptionally stressful situations, such as the current health risk, on the cognitive and emotive state of the individual, that is, perceived threat and emotional state on affect and mood. RESULTS: The results showed that the perception of threat from COVID-19 was related positively to negative affect and emotional signs, that is, sadness-depression, anxiety and anger-hostility. The starting hypothesis was that perception of threat in the exceptional state of health emergency caused by COVID-19, affects one's emotional situation (Model 1), and this, in turn, affects perception of risk (Model 2), in which positive and negative affect balances act as mediators in these relationships (Fig 1) . cache = ./cache/cord-291756-ejh1r8h4.txt txt = ./txt/cord-291756-ejh1r8h4.txt === reduce.pl bib === id = cord-289892-yh1lioyz author = Bai, Bingke title = Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date = 2008-07-16 pages = extension = .txt mime = text/plain words = 5451 sentences = 300 flesch = 55 summary = Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. In addition, because in vitro infection model of bat SL-CoV has not so far been established, we intended to use VLPs as an alternative to study the immune responses induced in DCs. Therefore, we compared the phenotypic and functional changes of immature DCs inoculated with BVLPs or with SARS CoV VLPs. The S-specific immune activation was further confirmed in mice using S DNA vaccines. Combining the flow cytometry results in Fig. 2 , it is reasonable to draw a conclusion that the structure of BVLPs, not LPS contamination, contributed to cytokine production in BVLPs-treated DCs. We previously constructed SARS CoV VLPs and investigated the humoral and cellular immune responses induced by SARS CoV VLPs in mice [29] . cache = ./cache/cord-289892-yh1lioyz.txt txt = ./txt/cord-289892-yh1lioyz.txt === reduce.pl bib === id = cord-290120-fd26t8ja author = Tan, Chew Yee title = First molecular detection and complete sequence analysis of porcine circovirus type 3 (PCV3) in Peninsular Malaysia date = 2020-07-24 pages = extension = .txt mime = text/plain words = 6606 sentences = 358 flesch = 53 summary = title: First molecular detection and complete sequence analysis of porcine circovirus type 3 (PCV3) in Peninsular Malaysia Given that PCV3 is increasingly reported in countries including Thailand and U.S. with whom Malaysia shares trade and geographical relationship; and that PCV3 is associated with several clinical presentations that affect productivity, there is a need to study the presence and molecular characteristics of PCV3 in Malaysian swine farms. Results revealed that PCV3 is present in Peninsular Malaysia at a molecular prevalence of 17.02%, with inguinal lymph nodes and lungs showing the highest molecular detection rates of 81.82% and 71.43% respectively. To test for association between PCV3 molecular detection status and age group, health status, farm standing sow population and distance from neighbouring farms, Chi-square tests were performed with statistical significance level set at p < 0.05. PCV3 infection susceptibility has been suggested to be associated with the age of wild boar, with juvenile animals showing statistically lower detection rates, unlike reports described in domestic pigs [37, 48] . cache = ./cache/cord-290120-fd26t8ja.txt txt = ./txt/cord-290120-fd26t8ja.txt === reduce.pl bib === id = cord-288502-qqg41daz author = Martini, Katharina title = Patterns of organizing pneumonia and microinfarcts as surrogate for endothelial disruption and microangiopathic thromboembolic events in patients with coronavirus disease 2019 date = 2020-10-05 pages = extension = .txt mime = text/plain words = 3613 sentences = 207 flesch = 47 summary = BACKGROUND: To evaluate chest-computed-tomography (CT) scans in coronavirus-disease-2019 (COVID-19) patients for signs of organizing pneumonia (OP) and microinfarction as surrogate for microscopic thromboembolic events. 21.1% of COVID-19 patients suspected with PE showed subpleural wedge-shaped consolidation resembling infarct pneumonia, while only 13.2% showed visible filling defects of the pulmonary artery branches on CT-PA. However, patients with suspected PE showed a higher prevalence of lung changes, resembling patterns of infarct pneumonia or OP and CT-signs of pulmonary-artery hypertension. Therefore, the purpose of the study was to investigate possible typical parenchymal lung changes resembling patterns of infarct pneumonia or OP as surrogate for microscopic thromboembolic events in COVID-19 patients. Our hypothesis is further strengthened by the higher presence of CT signs for pulmonary artery hypertension and right heart failure in patients undergoing CT-PA or with CT patterns resembling infarct pneumonia. However, our COVID-19 cohort showed lung changes resembling those of infarct pneumonia and OP as well as CT-signs of pulmonary-artery hypertension. cache = ./cache/cord-288502-qqg41daz.txt txt = ./txt/cord-288502-qqg41daz.txt === reduce.pl bib === id = cord-282194-0sjmf1yn author = Cherak, Stephana J. title = Impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit: A scoping review date = 2020-09-11 pages = extension = .txt mime = text/plain words = 5411 sentences = 276 flesch = 42 summary = title: Impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit: A scoping review The purpose of this scoping review was to summarize existing research on the impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit (ICU). For the purposes of this review, we defined: (1) a caregiver as any informal (i.e., non-clinical) person who regularly provides support to the patient and is in some way directly implicated in the patient's care or directly affected by the patient's health problem (e.g., family, friend); (2) social media as any form of electronic communication that allow users to share information and other content and create online communities; and (3) critically ill patients as any persons who are currently admitted to an intensive care unit (ICU) or had previously been admitted to an ICU. cache = ./cache/cord-282194-0sjmf1yn.txt txt = ./txt/cord-282194-0sjmf1yn.txt === reduce.pl bib === id = cord-290833-m0wodqr3 author = Yuan, Lvfeng title = Synthetic surfactin analogues have improved anti-PEDV properties date = 2019-04-11 pages = extension = .txt mime = text/plain words = 3580 sentences = 195 flesch = 51 summary = In this study, 10 surfactin analogues were obtained by chemical synthesis and evaluated to determine their anti-PEDV activities, hemolytic activities, and critical micelle concentrations. The production of designer surfactins, made by changing the number and composition of amino acids and fatty acids has proven to be an effective strategy for screening large numbers of lipopeptides for biological activity, but most current research focuses on their anticancer [4] , antimicrobial [5] and insulin delivery [6] properties but not on their antiviral potential. Time of addition assays were performed to determine whether the SLP5 exerts its anti-PEDV effect at the same stage during infection as surfactin. As expected for a normal component of the cell membrane, DEPE did not affect PEDV replication at any stage, while SLP5 and surfactin exhibited antiviral activity at specific stages. SLP5 also has two fewer hydrophobic amino acids than surfactin, this reduces the cost of synthesis while having little effect on antiviral activity. cache = ./cache/cord-290833-m0wodqr3.txt txt = ./txt/cord-290833-m0wodqr3.txt === reduce.pl bib === id = cord-290034-4b0mshqa author = Le, Yen H. title = Virus detections among patients with severe acute respiratory illness, Northern Vietnam date = 2020-05-12 pages = extension = .txt mime = text/plain words = 2833 sentences = 145 flesch = 43 summary = To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. There was one case of co-infection with enterovirus and coronavirus 229E including a female military hospital patient 28 years of age. Additionally, our results display enterovirus, adenovirus and coronavirus infections among the SARI cases, suggesting that cities in northern Vietnam could benefit also from local surveillance of non-influenza respiratory viruses. cache = ./cache/cord-290034-4b0mshqa.txt txt = ./txt/cord-290034-4b0mshqa.txt === reduce.pl bib === id = cord-290539-8ak2tths author = Cagno, Valeria title = Novel broad spectrum virucidal molecules against enveloped viruses date = 2018-12-07 pages = extension = .txt mime = text/plain words = 5524 sentences = 276 flesch = 51 summary = To further elucidate the mechanism of action we performed a virucidal assay in which 9d was incubated with the virus at 10 μM 5μM or 1μM concentration for different times (Fig 6A) or for 1h with serial dilutions of compound ( Fig 6B) ; subsequently, the mixture was titrated on cells and the viral titer was evaluated at dilutions at which the compound concentration was known not to be active in plaquing efficiency assays. The irreversibility of the mechanism was also tested with an assay in which the compound was incubated with the virus for 1h and subsequently the mixture has been diluted in drug free medium for additional 1, 2, 3 or 4 hours before the addition on cells (S2 Fig) . cache = ./cache/cord-290539-8ak2tths.txt txt = ./txt/cord-290539-8ak2tths.txt === reduce.pl bib === id = cord-292237-45hi4iz2 author = Calvo-Pinilla, Eva title = Establishment of a Bluetongue Virus Infection Model in Mice that Are Deficient in the Alpha/Beta Interferon Receptor date = 2009-04-09 pages = extension = .txt mime = text/plain words = 4735 sentences = 251 flesch = 53 summary = Furthermore, IFNAR((−/−)) adult mice immunized with a BTV-4 inactivated vaccine showed the induction of neutralizing antibodies against BTV-4 and complete protection against challenge with a lethal dose of this virus. All these data, and the presence of an otherwise intact immune system in these mice [20, 22] suggest that IFNAR (2/2) mice could be a good animal model to study BTV infections and to evaluate vaccine strategies against this virus. By contrast, IFNAR (2/2) mice were susceptible to BTV-4 infection (Fig. 1A) , showing disease symptoms characterized by ocular discharges and apathy starting at 48 h.p.i. Disease progression led to animal death within 60 h.p.i. The LD 50 value was obtained by i.v. inoculation with 10-fold dilutions of BTV-4, resulting in a LD 50 value of 10 2.6 PFU (Fig. 1B) . Infectious viral titers were analyzed in the blood of immunized and nonimmunized IFNAR (2/2) mice by plaque assay after intravenous infection with BTV-4 (Fig. 5C ). cache = ./cache/cord-292237-45hi4iz2.txt txt = ./txt/cord-292237-45hi4iz2.txt === reduce.pl bib === id = cord-291417-p49ukyhx author = Mikulska, Malgorzata title = Tocilizumab and steroid treatment in patients with COVID-19 pneumonia date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4441 sentences = 219 flesch = 44 summary = METHODS: This observational single-center study included patients with COVID-19 pneumonia who were not intubated and received either standard of care (SOC, controls) or SOC plus early (within 3 days from hospital admission) anti-inflammatory treatment. This observational single-center study included patients with COVID-19 pneumonia who were not intubated and received either standard of care (SOC, controls) or SOC plus early (within 3 days from hospital admission) anti-inflammatory treatment. We hypothesized that outcomes such as no need for intubation and survival of patients with severe COVID-19 pneumonia in whom tocilizumab and/or methylprednisolone were administered in addition to standard of care (SOC) could be better than in those who received only SOC. In this observational study in non-intubated patients with mainly severe COVID-19 pneumonia, the early addition of tocilizumab and/or methylprednisolone to SOC resulted in adjusted failure-free survival of 86.5% and 80.8% at day 14 and 30, which was, respectively, 10.7% and 16.7% higher than in SOC patients. cache = ./cache/cord-291417-p49ukyhx.txt txt = ./txt/cord-291417-p49ukyhx.txt === reduce.pl bib === id = cord-293794-vudufao5 author = Cuthbertson, Leah title = Viral respiratory infections and the oropharyngeal bacterial microbiota in acutely wheezing children date = 2019-10-17 pages = extension = .txt mime = text/plain words = 4820 sentences = 255 flesch = 48 summary = No significant difference in bacterial diversity was observed between samples from those with wheeze and healthy controls. Using 16s rRNA gene sequencing of respiratory samples from children presenting to hospital with acute wheezing, this study aimed to examine whether the bacterial community in the airways of children with acute respiratory wheeze was altered compared with that of nonwheezing children. However, when the microbiota in children with bronchiolitis were compared to those closest in age there was a significant reduction in alpha diversity (richness; p = 0.01, Shannon-Weiner, p = 0.003, inverse Simpsons, p = 0.005) that was not associated with change in bacterial biomass (p = 0.874). When those with a diagnosis of bronchiolitis were compared to other cases that wheezed or age matched control subjects, significant differences in alpha and beta diversity were observed however this may have been driven by subjects with bronchiolitis being significantly younger than other groups of subjects. cache = ./cache/cord-293794-vudufao5.txt txt = ./txt/cord-293794-vudufao5.txt === reduce.pl bib === id = cord-293072-giakcaki author = Xu, Wan-Xiang title = A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping date = 2017-10-12 pages = extension = .txt mime = text/plain words = 5303 sentences = 227 flesch = 52 summary = The protocol involves the following core steps: (i) design of plus and minus strands of DNA fragments encoding overlapping 8/18mer peptides; (ii) chemical synthesis of the designed DNA fragments; (iii) development of r-clones using pXXGST-3 vector expressing each 8/18mer peptide fused with truncated GST188 protein; (iv) screening r-clones by running the cell pellets from each induced clone on SDS-PAGE gel followed by sequencing of inserted DNA fragments for each verified r-clone; and (v) Western blotting with either monoclonal antibodies or polyclonal antibodies. cache = ./cache/cord-293072-giakcaki.txt txt = ./txt/cord-293072-giakcaki.txt === reduce.pl bib === id = cord-291360-z19ri377 author = Lan, Fan-Yun title = COVID-19 symptoms predictive of healthcare workers’ SARS-CoV-2 PCR results date = 2020-06-26 pages = extension = .txt mime = text/plain words = 4339 sentences = 251 flesch = 52 summary = Of 509 HCWs with initial negative SARS-CoV-2 assays, nine had symptom progression and positive re-tests, yielding an estimated negative predictive value of 98.2% (95% CI: 96.8–99.0%) for the exclusion of clinically relevant COVID-19. CONCLUSIONS: Symptom and temperature reports are useful screening tools for predicting SARS-CoV-2 assay results in HCWs. Anosmia/ageusia, fever, and myalgia were the strongest independent predictors of positive assays. Therefore, we investigated the presenting symptoms most predictive of positive/negative SARS-CoV-2 RT-PCR results among HCWs. Since March 9, 2020, the occupational health service of a Massachusetts community healthcare system has implemented a staff "hotline" system to maintain a viable/healthy workforce and operational continuity during the pandemic. The clinical COVID-19 attack rate during the study period was calculated as: (the number of initial positive SARS-CoV-2 assays + the number of false negatives) divided by the system's estimated total HCW population (n = 4600). cache = ./cache/cord-291360-z19ri377.txt txt = ./txt/cord-291360-z19ri377.txt === reduce.pl bib === id = cord-292396-8w06oc5i author = Leger, Thomas title = Low-dose chest CT for diagnosing and assessing the extent of lung involvement of SARS-CoV-2 pneumonia using a semi quantitative score date = 2020-11-03 pages = extension = .txt mime = text/plain words = 3373 sentences = 209 flesch = 57 summary = OBJECTIVES: The purpose is to assess the ability of low-dose CT (LDCT) to determine lung involvement in SARS-CoV-2 pneumonia and to describe a COVID19-LDCT severity score. The objective is to evaluate the ability of (LDCT) to analyze well-known imaging abnormalities as well as to establish a COVID19-LDCT score reflecting disease severity and correlate it with clinical risk scores to allow better selection and follow-up of patients. For each patient, the following clinical parameters were recorded: age, sex, date of first symptoms, date of chest CT scan, delay between the first symptom and chest CT scan, fever, cough, dyspnea, diarrhea, myalgia, rhinorrhea, abnormalities at lung auscultation, temperature, heart rate, blood pressure, respiratory rate, oxygen saturation, and oxygen needed. The main findings of the presented work are that 1) LDCT scans can depict the typical features of SARS-CoV-2 pneumonia with limited irradiation; and 2) the COVID19-LDCT score is correlated with the NEWS used routinely to assess disease severity and patient prognosis. cache = ./cache/cord-292396-8w06oc5i.txt txt = ./txt/cord-292396-8w06oc5i.txt === reduce.pl bib === id = cord-291176-evb6yt0r author = Giorgi Rossi, Paolo title = Characteristics and outcomes of a cohort of COVID-19 patients in the Province of Reggio Emilia, Italy date = 2020-08-27 pages = extension = .txt mime = text/plain words = 4559 sentences = 213 flesch = 46 summary = In this report, based on the cohort of all residents in the province of Reggio Emilia who were SARS-CoV-2-positive at nasal and pharyngeal swab and with symptoms (COVID-19 cases) since the inception of the epidemic, we describe patient characteristics and explore their role as putative prognostic factors in predicting the occurrence of hospital admission or death. We considered the following patient characteristics: age, sex, place of birth (Italy or abroad), time span (in days) from symptom onset to diagnosis/ hospitalization, and comorbidities, whose prognostic role was explored both singly (chronic obstructive pulmonary disease, arrhythmia, diabetes, coronary heart disease, heart failure, vascular diseases, obesity) and by computing the Charlson Comorbidity Index, which provides an overall measure of an individual patient's complexity [12] . While in this study we focused on the risk of hospitalization and death in a cohort of COVID-19 patients diagnosed during the epidemic in Northern Italy, it also provided us with the opportunity to describe the pattern of distribution of the disease in the whole population. cache = ./cache/cord-291176-evb6yt0r.txt txt = ./txt/cord-291176-evb6yt0r.txt === reduce.pl bib === id = cord-293393-kbndie8e author = Braesch-Andersen, Sten title = ApoD Mediates Binding of HDL to LDL and to Growing T24 Carcinoma date = 2014-12-16 pages = extension = .txt mime = text/plain words = 6253 sentences = 386 flesch = 60 summary = To investigate the presence of particles containing both apoD and apoB, we performed a dual-specific ELISA using the anti-apoD mAb D554 as a capture antibody and a biotinylated anti-apoB mAb, LDL20, for detection. To determine the importance of having intact lipoprotein particles, we repeated the dual-specific apoD/B ELISA in the presence of detergent, using anti-apoD-D544 as the capture mAb and anti-apoB-LDL20 as the detecting mAb. As seen in Fig. 4A , only small amounts of apoB bound to D544 when detergent was present, indicating that intact lipoprotein particles are needed for the apoD-LDL interaction. In agreement with this latter finding, apoD production was high in confluent, growth-arrested T24 cell cultures (2,5 million cells in 9 ml), but was not detectable in non-confluent proliferating Anti-apoD (D544) was used as the capture antibody and anti-apoB (LDL20-biotin) was used as the detection antibody in a detergent free dualspecific ELISA. cache = ./cache/cord-293393-kbndie8e.txt txt = ./txt/cord-293393-kbndie8e.txt === reduce.pl bib === id = cord-292475-jrl1fowa author = Abry, Patrice title = Spatial and temporal regularization to estimate COVID-19 reproduction number R(t): Promoting piecewise smoothness via convex optimization date = 2020-08-20 pages = extension = .txt mime = text/plain words = 7470 sentences = 386 flesch = 53 summary = The novelty of the proposed approach is twofold: 1) the estimation of the reproduction number is achieved by convex optimization within a proximal-based inverse problem formulation, with constraints aimed at promoting piecewise smoothness; 2) the approach is developed in a multivariate setting, allowing for the simultaneous handling of multiple time series attached to different geographical regions, together with a spatial (graph-based) regularization of their evolutions in time. In that spirit, the overarching goal of the present work is twofold: (1) proposing a new, more versatile framework for the estimation of R(t) within the semi-parametric model of [8, 10] , reformulating its estimation as an inverse problem whose functional is minimized by using non smooth proximal-based convex optimization; (2) inserting this approach in an extended multivariate framework, with applications to various complementary datasets corresponding to different geographical regions. cache = ./cache/cord-292475-jrl1fowa.txt txt = ./txt/cord-292475-jrl1fowa.txt === reduce.pl bib === id = cord-292537-9ra4r6v6 author = Liu, Fenglin title = Predicting and analyzing the COVID-19 epidemic in China: Based on SEIRD, LSTM and GWR models date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5662 sentences = 259 flesch = 52 summary = For the study of infectious diseases like COVID-19, SARS, and Ebola, most of the literature used descriptive research or model methods to assess indicators and analyze the effect of interventions, such as combining migration data to evaluate the potential infection rate [18, 19] , understanding the impact of factors like environmental temperature and vaccines that might be potentially linked to the diseases [20, 21] , using basic and time-varying reproduction number (R 0 & R t ) to estimate changeable transmission dynamics of epidemic conditions [22] [23] [24] [25] [26] [27] , calculating and predicting the fatal risk to display any stage of outbreak [28] [29] [30] , or providing suggestions and interventions from risk management and other related aspects based on the results of modeling tools or historical lessons [31] [32] [33] [34] [35] [36] [37] [38] [39] . cache = ./cache/cord-292537-9ra4r6v6.txt txt = ./txt/cord-292537-9ra4r6v6.txt === reduce.pl bib === id = cord-294568-12eyo13f author = Fernandes-Matano, Larissa title = Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date = 2017-05-03 pages = extension = .txt mime = text/plain words = 4930 sentences = 240 flesch = 45 summary = Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs. Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV) [12] . Therefore, the objective of this study was to determine the viral aetiology of these infections and to analyse the behaviour of non-influenza respiratory viruses in the Mexican population. The importance of the differential diagnosis of other respiratory viruses in samples with negative influenza results becomes apparent when we observe the prevalence of the three main viruses identified in this study as well as their associations with severe cases and deaths, especially in the child population. cache = ./cache/cord-294568-12eyo13f.txt txt = ./txt/cord-294568-12eyo13f.txt === reduce.pl bib === id = cord-294768-bs6thjw2 author = Alonso-Fernández, Alberto title = Prevalence of pulmonary embolism in patients with COVID-19 pneumonia and high D-dimer values: A prospective study date = 2020-08-25 pages = extension = .txt mime = text/plain words = 4652 sentences = 278 flesch = 49 summary = title: Prevalence of pulmonary embolism in patients with COVID-19 pneumonia and high D-dimer values: A prospective study CONCLUSIONS: Patients with COVID-19 pneumonia and D-dimer values higher than 1 μg/mL presented a high prevalence of PE, regardless of clinical suspicion. [12] found, in a retrospective study in 184 intensive care unit (ICU) patients with severe COVID-19 pneumonia, a high prevalence of thrombotic complications and, by far, pulmonary embolism (PE) was the most frequent. Pulmonary embolism in COVID-19 pneumonia with high D-dimer values: A prospective study procoagulant (D-dimer) markers that correlated with the extend of the thromboembolic episode compared to those patients without PE. We included patients with D-dimer values higher than 1 μg/mL, which have been associated with disease severity and in-hospital mortality in patients with COVID-19 infection. Pulmonary embolism in COVID-19 pneumonia with high D-dimer values: A prospective study of our patients, allocated in the non-PE group, was not on enoxaparin prophylaxis during hospitalization. cache = ./cache/cord-294768-bs6thjw2.txt txt = ./txt/cord-294768-bs6thjw2.txt === reduce.pl bib === id = cord-293946-4bquxdqa author = Huong, Nguyen Quynh title = Coronavirus testing indicates transmission risk increases along wildlife supply chains for human consumption in Viet Nam, 2013-2014 date = 2020-08-10 pages = extension = .txt mime = text/plain words = 6229 sentences = 292 flesch = 51 summary = In this study we investigated the presence and diversity of coronavirus sequences in the field rat trade distribution chain, wildlife farms specializing in raising rodents for human consumption, and bat guano "farms" and roosts near human dwellings to better understand the natural hosts of coronaviruses and the risk for these interfaces to facilitate spillover into humans. Out of 70 sites, coronavirus positives were detected at 58 including 100% (24/24) of live rat trade sites, 60.7% (17/28) of rodent wildlife farm sites, 94.1% (16/17) of bat guano farm sites, and at the one natural pteropid bat roost. Significant findings of this study are the high proportion of coronavirus positive wildlife (bats and rodents) and the increasing proportion of positives found along the rat trade supply chain from sub-interfaces close to the capture site (rat traders) to restaurants. cache = ./cache/cord-293946-4bquxdqa.txt txt = ./txt/cord-293946-4bquxdqa.txt === reduce.pl bib === id = cord-291104-6chpmgry author = Leung, Danny T. M. title = Osteopontin Fragments with Intact Thrombin-Sensitive Site Circulate in Cervical Cancer Patients date = 2016-08-05 pages = extension = .txt mime = text/plain words = 6269 sentences = 313 flesch = 58 summary = The possibility that the target epitope recognized by the antibody probe in these assays was absent from the circulating OPN due to protein truncation was supported by gel fractionation of the OPN found in patients' plasma: 60–64 kDa fragments were found instead of the presumably full-length OPN (68 kDa) seen in healthy people. Similar results were found when the serum of these individuals was examined: the cancer patients (424 +/-121 ng/ mL) had significantly (P = 0.0002) higher levels of OPN than healthy subjects (314 +/-98 ng/ mL) (Fig 5B) , the assay sensitivity and specificity being 18% and 97%, respectively. The finding that the mAb 446 inhibition ELISA and the commercial OPN kit could not detect elevated OPN levels in the cancer patients suggested the possibility that the OPN present could be fragmented i.e. the target sites for the antibodies used in these assays could be missing, whereas, by virtue of the design of the mAb 659-based assay, the thrombin-sensitive site must be present. cache = ./cache/cord-291104-6chpmgry.txt txt = ./txt/cord-291104-6chpmgry.txt === reduce.pl bib === id = cord-294645-yzh8h7zo author = Freeman, David W. title = Association between GDF15, poverty and mortality in urban middle-aged African American and white adults date = 2020-08-07 pages = extension = .txt mime = text/plain words = 4977 sentences = 221 flesch = 43 summary = Multivariable adjusted Cox regression models were used to assess the association between log-transformed GDF15 (logGDF15) and 12-year mortality outcomes (all-cause, cardiovascularand cancer-specific outcomes) and interactions with sex, race and poverty status. The objectives of the present study were to assess the association between serum GDF15 and all-cause and cause-specific mortality, and to identify interactions between GDF15 and sex, race and poverty status in a large cohort of community-based middle-aged adults recruited from Baltimore, Maryland. In a community-dwelling cohort of younger urban adults (mean age 49.6) with diverse racial and socioeconomic status, we found that elevated serum GDF15 level was strongly associated with all-cause mortality, CVD-and cancer-specific mortality risk. Our findings of increased risk of mortality due to all-causes and CVD and elevated GDF15 levels in a diverse cohort are consistent with results of previous studies conducted in apparently healthy, community-dwelling adults [12-15, 17, 18] . cache = ./cache/cord-294645-yzh8h7zo.txt txt = ./txt/cord-294645-yzh8h7zo.txt === reduce.pl bib === id = cord-295352-b8kztgt8 author = Maksimowski, Nicholas title = Kidney ACE2 expression: Implications for chronic kidney disease date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3517 sentences = 212 flesch = 54 summary = Angiotensin-converting enzyme 2 (ACE2) has been implicated in the pathogenesis of chronic kidney disease (CKD) and is a membrane receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease (COVID-19), whereas transmembrane protease, serine 2 (TMPRSS2) is involved in viral attachment. Sex, age, body mass index (BMI), and CKD are clinical risk factors for COVID-19 severity, but the relationships between kidney ACE2 and TMPRSS2 expression and these clinical variables are unknown. Tubulointerstitial and glomerular median-centered log2 mRNA expression of ACE2 or TMPRSS2 from renal biopsy samples were compared in CKD and HLD, as well as in male and female subgroups. Mean values for ACE2 mRNA expression in both the tubulointerstitial and glomerular compartments were similar in all of the disease categories represented in the CKD cohort (S1 Fig) . cache = ./cache/cord-295352-b8kztgt8.txt txt = ./txt/cord-295352-b8kztgt8.txt === reduce.pl bib === id = cord-294023-knaxr7t0 author = Murri, Rita title = Social media as a tool for scientific updating at the time of COVID pandemic: Results from a national survey in Italy date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2073 sentences = 115 flesch = 51 summary = title: Social media as a tool for scientific updating at the time of COVID pandemic: Results from a national survey in Italy Seventy percent (n = 261) of respondents reported that their use of social media to find medical information increased during the current pandemic (Fig 1) . In terms of COVID-19 medical practice, information coming from social media were considered "enough" or "much" or "very much" useful by 82.9% (n = 306) of the sample. To the question "During the last week, do you think that information shared on social media had an impact on your clinical practice for patients with COVID?" 28.7% (n = 106) answered "enough" and 47.1% (n = 174) "much" or "very much". Our survey shows that, at the time of COVID pandemic, many clinicians react to their urgent need for updates by seeking information through unconventional sources instead of academic journals publications. cache = ./cache/cord-294023-knaxr7t0.txt txt = ./txt/cord-294023-knaxr7t0.txt === reduce.pl bib === id = cord-292777-oztmw8jo author = Wong, Michelle title = Microbial Translocation Contribute to Febrile Episodes in Adults with Chemotherapy-Induced Neutropenia date = 2013-07-16 pages = extension = .txt mime = text/plain words = 3300 sentences = 179 flesch = 38 summary = In this study we sought to determine the contribution of microbial translocation to febrile episodes with no attributable microbiological cause (Fever of Unknown Origin, FUO) in an adult febrile neutropaenic cohort. In this study we thus sought to determine the contribution of microbial translocation to FUO episodes in an adult febrile neutropaenic cohort using endotoxin and sCD14 concentrations in the plasma as markers for microbial translocation. In this cohort of iatrogenic neutropaenic adults, we found elevated plasma levels of endotoxin and sCD14 in febrile neutropaenic episodes where no other microbiological findings have been documented, implicating microbial translocation as a potential contributor towards their febrile status. Adding to the field, we have, in our study, in addition to measuring plasma endotoxin concentrations, also measured the host receptor for LPS, sCD14 in an attempt to determine the contribution of microbial translocation to fever as a clinical outcome. cache = ./cache/cord-292777-oztmw8jo.txt txt = ./txt/cord-292777-oztmw8jo.txt === reduce.pl bib === id = cord-295339-nzc47itk author = Baker, Marissa G. title = Estimating the burden of United States workers exposed to infection or disease: A key factor in containing risk of COVID-19 infection date = 2020-04-28 pages = extension = .txt mime = text/plain words = 3320 sentences = 139 flesch = 41 summary = METHODS: To estimate the number of United States workers frequently exposed to infection and disease in the workplace, national employment data (by Standard Occupational Classification) maintained by the Bureau of Labor Statistics (BLS) was merged with a BLS O*NET survey measure reporting how frequently workers in each occupation are exposed to infection or disease at work. Given the proportion of the United States workforce exposed to disease or infection at work, this analysis also serves as an important reminder that the workplace is a key locus for public health interventions, which could protect both workers and the communities they serve. To estimate the number of United States workers frequently exposed to infection and disease in the workplace, national employment data (by Standard Occupational Classification) maintained by the Bureau of Labor Statistics (BLS) was merged with a BLS O*NET survey measure reporting how frequently workers in each occupation are exposed to infection or disease at work. cache = ./cache/cord-295339-nzc47itk.txt txt = ./txt/cord-295339-nzc47itk.txt === reduce.pl bib === id = cord-294372-pec1886j author = Greene, Dina N. title = Decreasing median age of COVID-19 cases in the United States—Changing epidemiology or changing surveillance? date = 2020-10-15 pages = extension = .txt mime = text/plain words = 1698 sentences = 103 flesch = 60 summary = Result distributions by age and positivity were compared between early period (March-April 2020) and late periods (June-July 2020) of the COVID-19 pandemic. Overall, this suggests that observed age-related trends are driven by changes in testing patterns rather than true changes in the epidemiology of SARS-CoV-2 infection. In the United States, surveillance data suggest that mean age of infected patients is decreasing compared to the early stages of the COVID-19 pandemic. We used SARS-CoV-2 testing data from a national reference laboratory to characterize the age distribution of detected cases between March and July of 2020. Surveillance data in the United States have shown a trend toward decreasing age among persons with laboratory-confirmed SARS-CoV-2 infection. This study found a similar pattern among patients tested by a national reference laboratory, with the median age among patients testing positive being five years lower in June and early July compared to March and April. cache = ./cache/cord-294372-pec1886j.txt txt = ./txt/cord-294372-pec1886j.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-295536-dbpt4dhr author = Shook, Natalie J. title = Disease avoidance in the time of COVID-19: The behavioral immune system is associated with concern and preventative health behaviors date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4592 sentences = 270 flesch = 40 summary = This study examined whether individual differences in BIS reactivity (germ aversion, pathogen disgust sensitivity) were associated with concern about COVID-19 and engagement in recommended preventative health behaviors (social distancing, handwashing, cleaning/disinfecting, avoiding touching face, wearing facemasks). Germ aversion and pathogen disgust sensitivity were the two variables most consistently associated with COVID-19 concern and preventative health behaviors, while accounting for demographic, health, and psychosocial covariates. In general, younger age, higher income, more populated location of residence, more recent illness, better perceived health, having/had COVID-19, greater religiosity, greater extraversion, greater conscientiousness, greater perceived infectability, greater germ aversion, and greater pathogen disgust sensitivity were associated with engaging in most (at least three) of the preventative health behaviors more frequently. When demographic, health, social, personality, and BIS variables were considered simultaneously, greater germ aversion and pathogen disgust sensitivity were most consistently associated with COVID-19 concern and preventative behaviors. cache = ./cache/cord-295536-dbpt4dhr.txt txt = ./txt/cord-295536-dbpt4dhr.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-297835-ukrz8tlv author = Leith, Douglas J. title = Measurement-based evaluation of Google/Apple Exposure Notification API for proximity detection in a light-rail tram date = 2020-09-30 pages = extension = .txt mime = text/plain words = 5591 sentences = 264 flesch = 58 summary = title: Measurement-based evaluation of Google/Apple Exposure Notification API for proximity detection in a light-rail tram Contact tracing apps based on the Google/Apple Exposure Notification (GAEN) API [4] are currently being rolled out across Europe, with apps already deployed in Italy, Switzerland and Germany. We observe that changing the people holding a pair of handsets, with the location of the handsets otherwise remaining unchanged, can cause variations of ±10dB in the attenuation level reported by the GAEN API. To provide baseline data on the radio propagation environment we also used the standard Android Bluetooth LE scanner API to collect measurements of RSSI as the distance was varied between two Google Pixel 2 handsets placed at a height of approximately 0.5m (about the same height as the tram seating) in the centre aisle of the tram carriage. cache = ./cache/cord-297835-ukrz8tlv.txt txt = ./txt/cord-297835-ukrz8tlv.txt === reduce.pl bib === id = cord-295293-ickp2n47 author = Latsuzbaia, Ardashel title = Evolving social contact patterns during the COVID-19 crisis in Luxembourg date = 2020-08-06 pages = extension = .txt mime = text/plain words = 2976 sentences = 153 flesch = 52 summary = While the number of social contacts was substantially lower during the lockdown by more than 80% compared to the pre-pandemic period, we observed a more recent 121% increase during the post lockdown period showing an increased potential for COVID-19 spread. We repeatedly conducted an internet survey to follow up the impact of the local government interventions on social contact patterns in Luxembourg shortly after the lockdown was implemented due to the rapid local spread of the COVID-19. The average number of contacts reported by Luxembourg residents in a study before the pandemic was 17.5 [4] , suggesting that contacts during lockdown had decreased by 81.7%. Our study suggests that the strict physical distancing measures implemented in Luxembourg had a substantial and immediate impact on social mixing patterns resulting in a large reduction of the average number of contacts per day. In conclusion, our stud shows that physical distance measures resulted in significant reduction in social contacts and therefore decreased the spread of COVID-19 in Luxembourg. cache = ./cache/cord-295293-ickp2n47.txt txt = ./txt/cord-295293-ickp2n47.txt === reduce.pl bib === === reduce.pl bib === id = cord-299852-t0mqe7yy author = Janssen, Loes H. C. title = Does the COVID-19 pandemic impact parents’ and adolescents’ well-being? An EMA-study on daily affect and parenting date = 2020-10-16 pages = extension = .txt mime = text/plain words = 8570 sentences = 476 flesch = 51 summary = In this ecological momentary assessment study, we investigated if the COVID-19 pandemic affected positive and negative affect of parents and adolescents and parenting behaviors (warmth and criticism). However, Intolerance of uncertainty, nor any pandemic related characteristics (i.e. living surface, income, relatives with COVID-19, hours of working at home, helping children with school and contact with COVID-19 patients at work) were linked to the increase of parents' negative affect during COVID-19. In addition, we asked parents and adolescents about daily difficulties and helpful activities during the COVID-19 pandemic that possibly influenced their affect in positive and negative ways. During the COVID-19 pandemic, the most reported daily difficulties across the 14 days of EMA for parents were (1) missing social contact with friends (14.6%), (2) concerns about the coronavirus in general (13.5%), (3) irritations with family members (12.8%), (4) worrying about health of others (8.3%), and (5) coronavirus-related news items (8.0%). cache = ./cache/cord-299852-t0mqe7yy.txt txt = ./txt/cord-299852-t0mqe7yy.txt === reduce.pl bib === id = cord-296635-8r3tm966 author = Breed, Andrew C. title = Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date = 2011-12-14 pages = extension = .txt mime = text/plain words = 4573 sentences = 199 flesch = 47 summary = title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. Hendra virus (HeV) and Nipah virus (NiV) are paramyxoviruses of the genus Henipavirus with pteropid bats (i.e. flying-foxes; Pteropus sp., Family Pteropodidae) being the primary wildlife reservoir [1] . Henipaviruses have the potential to infect a wide range of mammalian species, and Hendra virus has spread from flying-foxes to horses in Australia on at least 20 reported separate occasions (five involving horse-human transmission), most recently in 2011 [5, 6, 7] . [14] on the infection dynamics of HeV in the little red flying-fox, Pteropus scapulatus, in the Northern Territory of Australia suggested that viral transmission may be predominantly horizontal, with pregnancy and lactation suggested as risk factors for infection. cache = ./cache/cord-296635-8r3tm966.txt txt = ./txt/cord-296635-8r3tm966.txt === reduce.pl bib === id = cord-296550-wkmnfph3 author = Hossain, Mohammad Anwar title = Knowledge, attitudes, and fear of COVID-19 during the Rapid Rise Period in Bangladesh date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4576 sentences = 239 flesch = 53 summary = The study aims to determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of fear towards COVID-19 in subjects living in Bangladesh. The study objectives were to determine the level of knowledge, attitudes, and practices related to COVID-19 preventive health habits and the underlying fear of COVID-19 in the Bangladeshi population and how they are affected by socio-demographic factors. The KAP section of the questionnaire related to a total of 12 score knowledge questions on COVID-19, categorical answers to attitudes towards the control of the pandemic, and practices of wearing masks and avoiding public gatherings. This study is similar to one study in China that found a significant relationship between knowledge and age and knowledge and educational level, with males reporting higher levels of knowledge than females regarding COVID-19 symptoms, precautions, and health advisory practices [16] . However, in our study, subjects living in Bangladesh reported similar knowledge for both males and females regarding COVID-19 symptoms, precautions, and health advisory practices. cache = ./cache/cord-296550-wkmnfph3.txt txt = ./txt/cord-296550-wkmnfph3.txt === reduce.pl bib === id = cord-302200-9gekjgr0 author = Kilich, Eliz title = Factors that influence vaccination decision-making among pregnant women: A systematic review and meta-analysis date = 2020-07-09 pages = extension = .txt mime = text/plain words = 6662 sentences = 345 flesch = 38 summary = Previous reviews have established a narrative of evidence that suggests a broad range of factors (vaccine cost, accessibility, maternal knowledge, social influences, context, healthcare professional (HCP) recommendation and the perception of risks and benefits) all contribute to vaccine uptake. Thus, we performed a systematic review and meta-analysis of qualitative and quantitative literature to provide comprehensive evidence on the magnitude of effect that factors influence maternal vaccination decisions globally with the aim to inform policy makers, public health strategists and researchers involved in designing vaccine interventions to increase uptake. For seasonal influenza, the data is inconclusive since women who believed that the disease could be harmful to their pregnancy or baby had four-times greater odds of being vaccinated than those who did not (OR 3.70, 95% CI 1.37-9.94) yet there was no evidence to suggest belief in the risk of the disease generally (OR 1.56, 95% CI 0.88-2.76) or its ability to result in hospitalisation (OR 0.57, 95% CI 0.22-1.45) were related to vaccine uptake. cache = ./cache/cord-302200-9gekjgr0.txt txt = ./txt/cord-302200-9gekjgr0.txt === reduce.pl bib === id = cord-299491-8rfm0jxh author = Xiao, Shenglan title = Role of fomites in SARS transmission during the largest hospital outbreak in Hong Kong date = 2017-07-20 pages = extension = .txt mime = text/plain words = 4765 sentences = 218 flesch = 53 summary = Like many other respiratory viruses, the SARS-CoV is suspected to spread from an infected person to the susceptible via three basic transmission routes, i.e., the long-range airborne, close contact and fomite routes [14] [15] [16] , as shown in Fig 1. Several studies have proposed probable evidence for the airborne spread of the SARS-CoV based on the consistencies between bio-aerosol concentration distributions and reported attack rates [19] [20] [21] , but no mechanism-based investigations exist for the fomite route. To investigate the role the fomite route plays in SARS-CoV transmission, we conducted a detailed modelling study of the largest hospital outbreak in Hong Kong [20] , in which the distribution of reported attack rates of inpatients showed a statistically significant spatial pattern. A multi-agent model ( Fig 2) was developed to simulate the possible spread of the viruses from the index patient to the susceptible by air flow and surface touching, and to calculate the possible exposure doses and infection risks for each hypothesis. cache = ./cache/cord-299491-8rfm0jxh.txt txt = ./txt/cord-299491-8rfm0jxh.txt === reduce.pl bib === id = cord-295559-yc8q62z8 author = Qian, Zhaohui title = Role of the Spike Glycoprotein of Human Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Virus Entry and Syncytia Formation date = 2013-10-03 pages = extension = .txt mime = text/plain words = 7303 sentences = 303 flesch = 50 summary = Coronavirus S proteins are Class I viral fusion proteins like the HIV envelope (env), influenza hemagglutinin (HA) and paramyxovirus fusion (F) glycoproteins [17] , which typically require protease cleavage between the S1 and S2 domains ( Figure 1A ) to permit conformational changes in S2, activated by receptor binding and/or low pH, that mediate membrane fusion leading to virus entry and syncytia formation [3, 17, 18] . In addition to entry by endocytosis, we showed that, like SARS-CoV [21, 22] , MERS pseudovirions could enter susceptible Vero E6 cells at the plasma membrane if virions were first bound to cell surface receptors at 4°C at neutral pH in the presence of NH 4 Cl to inhibit acidification of endosomes, and also treated briefly at room temperature with trypsin to cleave the viral S protein. cache = ./cache/cord-295559-yc8q62z8.txt txt = ./txt/cord-295559-yc8q62z8.txt === reduce.pl bib === id = cord-296691-cg463fbn author = Wang, Ren title = De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing date = 2013-04-09 pages = extension = .txt mime = text/plain words = 5831 sentences = 334 flesch = 46 summary = title: De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing Based on our sequence analysis and published literatures, many putative genes involved in Amaryllidaceae alkaloids synthesis, including PAL, TYDC OMT, NMT, P450, and other potentially important candidate genes, were identified for the first time in this Lycoris. They have played significant roles in functional genomics research for discovery of novel genes together with identifying different protein groups (e.g. proteins with signal peptides) other than the whole genome [27] [28] [29] , developing SSRs and SNPs markers [30] [31] [32] [33] [34] , allowing large-scale expression analysis [35] , improving genome annotation [36] , and elucidating phylogenetic relationships [37] . Hence, determination of the genetic pathways and specific genes involved in Amaryllidaceae alkaloids biosynthesis and some other aspects of Lycoris could be beneficial for humans and enrich our knowledge and understanding of functional genomics and biological research. cache = ./cache/cord-296691-cg463fbn.txt txt = ./txt/cord-296691-cg463fbn.txt === reduce.pl bib === id = cord-299953-sasfvcun author = Whitehead, Ashley B. R. title = Burden of exposure to infectious bursal disease virus, infectious bronchitis virus, Newcastle disease virus, Mycoplasma gallisepticum, and intestinal parasites in introduced broiler chickens on the Galapagos date = 2018-09-24 pages = extension = .txt mime = text/plain words = 4442 sentences = 220 flesch = 55 summary = The objective of the study reported here was to measure the burden of exposure to infectious bursal disease virus (IBDV), infectious bronchitis virus (IBV), Newcastle disease virus (NDV), Mycoplasma gallisepticum (MG), and intestinal parasites in a sample of broiler chickens on 13 farms on Santa Cruz Island and San Cristobal Island in July 2017. Study results are relevant because (i) they provide new baseline data on the burden of exposure to avian pathogens in broiler farms, (ii) justify the need to verify standard operating procedures in hatcheries that supply (non-vaccinated) day-old chicks to the Galapagos and (iii) to implement enhanced biosecurity standards on broiler chicken farms to mitigate risk of disease transmission between broilers, backyard poultry, and wild birds on the Galapagos. cache = ./cache/cord-299953-sasfvcun.txt txt = ./txt/cord-299953-sasfvcun.txt === reduce.pl bib === id = cord-302355-3se1wp8o author = Chen, Yi-Shiuan title = The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date = 2018-07-26 pages = extension = .txt mime = text/plain words = 6004 sentences = 292 flesch = 53 summary = Although XRN1 digestion of a 3'-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Furthermore, the minus-strand templates covering the putative promoter region used for an in vitro RdRp assay gave rise to synthetic products, suggesting that the JEV sfRNA could be initially transcribed from the antigenome and may be further trimmed by XRN1 or other unidentified exoribonucleases. Although efficient RNA replication is required for the detection of any flaviviral RNAs despite which mechanism used for the sfRNA formation, our results were clearly different from the observations from WNV that BHK-21 cells transfected with replicon constructs containing various deletions had no effect on the accumulation of sfRNA when compared to the WT [8] . cache = ./cache/cord-302355-3se1wp8o.txt txt = ./txt/cord-302355-3se1wp8o.txt === reduce.pl bib === id = cord-301180-ndiwmnv0 author = Lin, Min-Hsuan title = Nullbasic, a Potent Anti-HIV Tat Mutant, Induces CRM1-Dependent Disruption of HIV Rev Trafficking date = 2012-12-10 pages = extension = .txt mime = text/plain words = 5161 sentences = 233 flesch = 39 summary = Importantly, treatment of Myc-Rev and Nullbasic-mCherry expressing cells with LMB resulted in the complete restoration of Myc-Rev nucleolar accumulation (Fig. 3, row 6) , suggesting that Nullbasic requires functional CRM1 to mislocalize Rev most likely by an indirect interaction. While expression of Nullbasic-mCherry alone had no apparent effect on the nucleolar localization of either protein (Fig. 6 , rows 2 and 5), coexpression of Nullbasic-mCherry with Myc-Rev induced relocalization of C23 but not fibrillarin from the nucleolus to the nucleoplasm, in a manner concomitant with the redistribution of Myc-Rev (Fig. 6, rows 3 and 6 , respectively). CRM1 is a cellular receptor that recognizes and binds to the leucine-rich NES domain of Rev, an interaction which facilitates the egress of Rev/viral mRNA complexes through nuclear pores [3, 4, 42] and is readily visualized in cells as a colocalization in the nucleolus (Fig. 3, row 2 ). cache = ./cache/cord-301180-ndiwmnv0.txt txt = ./txt/cord-301180-ndiwmnv0.txt === reduce.pl bib === id = cord-304993-t4rua95e author = Jung, Kwonil title = The Effects of Simvastatin or Interferon-α on Infectivity of Human Norovirus Using a Gnotobiotic Pig Model for the Study of Antivirals date = 2012-07-23 pages = extension = .txt mime = text/plain words = 7069 sentences = 369 flesch = 50 summary = At 12 hours after treatment with 80 mM simvastatin, LDLR gene expression levels in IPEC-J2 cells were significantly increased compared to 0 to 20 mM treated groups (Fig. 1B) . Simvastatin Impaired TLR3-mediated Induction of IFN-a in Macrophages or Dendritic Cells, Possibly Due to Lowered Expression of TLR3 after Treatment Our in vivo data showing enhanced early infectivity of HuNoV suggested potential subversion of innate immunity related to simvasatin treatment. Oral treatment of Gn pigs with natural human IFN-a (nhIFN-a) [300 international unit (IU)/ kg/day] reduced or curtailed virus shedding in treated animals during the treatment period (PID 1 to 4), compared to untreated animals ( Fig. 7A-C) . In conclusion, simvastatin treatment increased HuNoV infectivity in the Gn pig model, possibly due to its inhibitory effect on innate immunity as well as its cholesterol lowering effect as reported previously [20] . cache = ./cache/cord-304993-t4rua95e.txt txt = ./txt/cord-304993-t4rua95e.txt === reduce.pl bib === id = cord-300859-nqklx0vn author = Henderson, Kelley C. title = Specificity and Strain-Typing Capabilities of Nanorod Array-Surface Enhanced Raman Spectroscopy for Mycoplasma pneumoniae Detection date = 2015-06-29 pages = extension = .txt mime = text/plain words = 8223 sentences = 331 flesch = 41 summary = title: Specificity and Strain-Typing Capabilities of Nanorod Array-Surface Enhanced Raman Spectroscopy for Mycoplasma pneumoniae Detection pneumoniae with statistically significant specificity and sensitivity in simulated and true clinical throat swab samples, and the ability to distinguish between reference strains of the two main genotypes of M. pneumoniae clinical isolates from globally diverse origins and distinguished these from a panel of 12 other human commensal and pathogenic mycoplasma species with 100% cross-validated statistical accuracy. A total of n = 390 pre-processed NA-SERS spectra collected from both substrates were included in the model, consisting of 20 nanorod substrate background spectra, 20 growth medium control spectra, 25 M129 spectra, 25 FH spectra, and 10 spectra per additional clinical isolate. pneumoniae strains from all 12 other human Mollicutes species and the growth medium control with 100% cross-validated sensitivity and specificity (Fig 3A-3C ). cache = ./cache/cord-300859-nqklx0vn.txt txt = ./txt/cord-300859-nqklx0vn.txt === reduce.pl bib === id = cord-298078-uqrwq5qk author = Kwak, Hoyun title = Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date = 2011-08-30 pages = extension = .txt mime = text/plain words = 5346 sentences = 318 flesch = 56 summary = The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs. Ribosomal frameshifing is a recoding process of translation where a specific messenger RNA (mRNA)-mediated signal directs a ribosome to shift its reading frame and to continue in the new frame. To search for cellular proteins that directly interacted with IBV pseudoknot RNA, a RNA pull down assay was performed in the presence of cell extracts (Figure 2A ). Through the RNA-immunoprecipitation assay, we showed that ANXA2 specifically interacted with wild-type IBV pseudoknot RNA but not with mutant IBV RNA in LNCaP and HEK293T cells ( Figure 3C and 3D). To test how ANXA2 regulates the frameshifting efficiency of IBV pseudoknot RNA, we first overexpressed ANXA2 protein in the presence of the reporters and measured the luciferase activities. cache = ./cache/cord-298078-uqrwq5qk.txt txt = ./txt/cord-298078-uqrwq5qk.txt === reduce.pl bib === id = cord-305303-82n96ukr author = Shapira, Assaf title = Removal of Hepatitis C Virus-Infected Cells by a Zymogenized Bacterial Toxin date = 2012-02-16 pages = extension = .txt mime = text/plain words = 10132 sentences = 431 flesch = 42 summary = As shown in Figure 2 , similar numbers of surviving colonies were observed when the cells were transfected with the plasmids encoding mCherry-NS3 activated MazF or the red fluorescent protein alone, suggesting that expression of NS3-activable ribonuclease in naïve HEK293 T-REx cells (that do not express NS3) cause minimal toxicity, if any. The ER membrane-targeted zymoxin colocalizes with NS3 protease in vivo Previously we described a HEK293 cell line which inducibly expresses (by addition of tetracycline) a fusion between EGFP and the coding sequence of the full length NS3 (including the helicase domain) followed by NS4A from HCV 1a genotype [10] . When infection reached ,50% (about 50% of the cultured cells showed expression of the HCV-core protein, as detected by immuno-staining and fluorescence microscopy), the mixed culture and a culture of uninfected cells were treated with NS3 activated MazF or uncleavable-MazF encoding adenoviruses at MOI of ,3. cache = ./cache/cord-305303-82n96ukr.txt txt = ./txt/cord-305303-82n96ukr.txt === reduce.pl bib === id = cord-306466-y4yg42p8 author = Nofal, Ahmed Maged title = Who complies with COVID-19 transmission mitigation behavioral guidelines? date = 2020-10-08 pages = extension = .txt mime = text/plain words = 5717 sentences = 292 flesch = 36 summary = Particularly, we examine if major personality traits (i.e. conscientiousness, agreeableness, openness to experience, extraversion, and emotional stability) [12] , yield differences in the tendency of people to comply with 21 implemented COVID-19 transmission mitigation behavioral guidelines (see S1 Appendix). However, there has been no work examining the influence of personality traits, such as the big five (i.e. conscientiousness, agreeableness, openness to experience, extraversion, and emotional stability) on the tendency of people to comply with COVID-19 transmission mitigation behavioral guidelines. Connecting literatures of emotional responses to COVID-19 messages, and personalized/tailored communication, we believe that this research not only supports prior work in highlighting the importance of pro-social messages, but also the importance of knowing the specific personality traits that may make individuals less likely to comply with COVID-19 transmission mitigation behavioral guidelines. First, drawing from research on persuasive mass communication [e.g., 19] , we aim to demonstrate if personality traits, specifically, conscientiousness, agreeableness, openness to experience, extraversion, and emotional stability, relate to the tendency of people to comply with COVID-19 transmission mitigation behavioral guidelines. cache = ./cache/cord-306466-y4yg42p8.txt txt = ./txt/cord-306466-y4yg42p8.txt === reduce.pl bib === id = cord-297287-0i4nc353 author = Braun, Benjamin title = Simulating phase transitions and control measures for network epidemics caused by infections with presymptomatic, asymptomatic, and symptomatic stages date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4005 sentences = 204 flesch = 49 summary = Using agent-based simulations on small world networks, we observe phase transitions for epidemic spread related to: 1) Global social distancing with a fixed probability of adherence. Phase transitions and control measures for network epidemics self-isolate in response to one infected social contact) all the way up to 97% with low levels of any type of social distancing. Because our goal is to understand the behavior of phase transitions regarding total number of infections in our model, we conducted secondary simulations on a refined parameter space based on the results of our regression tree analysis. There is also a clear interaction between the social distance probability and viral shedding parameters and the resulting number of infected agents and the length of the epidemic. Social distancing controls in this model exhibit a phase transition regarding total number of infections, either when imposed globally or when based on individual response to infected contacts. cache = ./cache/cord-297287-0i4nc353.txt txt = ./txt/cord-297287-0i4nc353.txt === reduce.pl bib === id = cord-302529-43pd2qsp author = El Moussi, Awatef title = Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date = 2013-09-19 pages = extension = .txt mime = text/plain words = 3251 sentences = 163 flesch = 45 summary = METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses' infection during three seasons in Tunisia. A subset of sentinel primary care physicians participating in virological surveillance schemes in the community submits respiratory samples for virological testing from patients presenting in primary health care with an ILI, as well as all regional emergency centres and hospitals that take on surveillance of influenza from community, hospitalized and fatal cases. Phylogenetic analysis of the HA1 nucleotid sequence of 23 influenza A(H1N1)pdm09 viruses from mild, severe (patients hospitalized with severe pneumonia and severe acute respiratory syndrome) and fatal cases, shows that all viruses characterised in Tunisia during season 2009-2010 were outside the seven genetic groups described in the European Centre for Disease Prevention and Control (ECDC) report [19] . cache = ./cache/cord-302529-43pd2qsp.txt txt = ./txt/cord-302529-43pd2qsp.txt === reduce.pl bib === id = cord-301811-ykpiorgo author = Tanaka, Takuma title = Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5530 sentences = 296 flesch = 55 summary = title: Estimation of the percentages of undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing We estimated the numbers of undiagnosed symptomatic patients and the lower bound of the number of total infected individuals per diagnosed patient before and after the declaration of the state of emergency in Hokkaido, Japan. The present analysis uses the distributions of the cluster size and patients' time from onset to diagnosis, which are released by the health officials, to estimate the model parameters. At the same time, the nodes in the connected component containing the diagnosed node are also removed from the network, which corresponds to the contact tracing of the infected individuals (Fig 2, gray open circles) . In this paper, we have formulated a model to describe the spreading of infection and the quarantine of infected individuals, and estimated the number of undiagnosed symptomatic and asymptomatic COVID-19 patients in Hokkaido. cache = ./cache/cord-301811-ykpiorgo.txt txt = ./txt/cord-301811-ykpiorgo.txt === reduce.pl bib === id = cord-305547-e66o5j85 author = Bénet, Thomas title = Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study date = 2015-12-22 pages = extension = .txt mime = text/plain words = 4161 sentences = 227 flesch = 43 summary = title: Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study pneumoniae (adjusted odds ratio [aOR] = 3.4, 95% confidence interval [95% CI]: 1.6–7.0), human metapneumovirus (aOR = 17.2, 95% CI: 2.0–151.4), respiratory syncytial virus [RSV] (aOR = 7.4, 95% CI: 2.3–23.3), and influenza A virus (aOR = 10.7, 95% CI: 1.0–112.2) were associated with pneumonia, independently of patient age, gender, period, and other pathogens. The primary objective of this prospective case-control study was to assess the etiology and factors associated with community-acquired pneumonia in hospitalized children in Mali. pneumoniae, human metapneumovirus, RSV, and influenza A were the main microbial agents associated with pneumonia among children in Mali, independently of patient age, gender, period, and other pathogens. recently observed, in a pneumonia cases-control study implemented in hospitals of Utah, that detection respiratory syncytial virus, human metapneumovirus and influenza from nasopharyngeal or oropharyngeal sample of patients with pneumonia probably indicates an etiologic role [24] . cache = ./cache/cord-305547-e66o5j85.txt txt = ./txt/cord-305547-e66o5j85.txt === reduce.pl bib === id = cord-303331-xolksoy3 author = Pourghasemi, Hamid Reza title = Assessment of the outbreak risk, mapping and infection behavior of COVID-19: Application of the autoregressive integrated-moving average (ARIMA) and polynomial models date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5988 sentences = 312 flesch = 55 summary = A geographic information system (GIS)-based machine learning algorithm (MLA), support vector machine (SVM), was used for the assessment of the outbreak risk of COVID-19 in Fars Province, Iran whereas the daily observations of infected cases were tested in the—polynomial and the autoregressive integrated moving average (ARIMA) models to examine the patterns of virus infestation in the province and in Iran. The aims of the present study were to analyze the risk factors of coronavirus outbreak and test the SVM model for mapping areas with a high risk of human infection with the virus in Fars Province, Iran. Accordingly, in this research, we selected sixteen most relevant effective factors for the outbreak risk mapping of COVID-19 in Fars Province of Iran, which includes minimum temperature of coldest month (MTCM), maximum temperature of warmest month (MTWM), precipitation in wettest month (PWM), precipitation of driest month (PDM), distance from roads, distance from mosques, distance from hospitals, distance from fuel stations, human footprint, density of cities, distance from bus cache = ./cache/cord-303331-xolksoy3.txt txt = ./txt/cord-303331-xolksoy3.txt === reduce.pl bib === id = cord-298131-zolwjl9u author = Xiao, Shuqi title = Understanding PRRSV Infection in Porcine Lung Based on Genome-Wide Transcriptome Response Identified by Deep Sequencing date = 2010-06-29 pages = extension = .txt mime = text/plain words = 9349 sentences = 429 flesch = 39 summary = Upregulation expression of virus-induced pro-inflammatory cytokines, chemokines, adhesion molecules and inflammatory enzymes and inflammatory cells, antibodies, complement activation were likely to result in the development of inflammatory responses during N-PRRSV infection processes. To investigate the regulation of the host response to the N-PRRSV virus, we considered the global gene expression profiles in lungs using Solexa/Illumina's DGE system, a tag-based transcriptome sequencing method. From the data presented in the paper, a model for the relationship between pulmonary gene expression profiles and infection pathology can be surmised in Figure 7 , N-PRRSV virus replicates and spreads by subverting host innate immune response and hijacking host lipid metabolism as well as inducing an antiapoptotic and anti-inflammatory state, as indicated by suppression expression of SPI IFN, IFN-a, down-regulation expression of proapoptotic genes for BAK, APR-1, SARP3, high levels expression of genes involved in lipid metabolism, such as APOE, LDLB, PIK3C3, anti-apoptotic genes for MCL1, BCL2A1, CHFR, ADM, NFKB, IL10, and anti-inflammatory molecule PGE2 as well as CD163. cache = ./cache/cord-298131-zolwjl9u.txt txt = ./txt/cord-298131-zolwjl9u.txt === reduce.pl bib === id = cord-303187-ny4qr2a2 author = Belo, Vinícius Silva title = Abundance, survival, recruitment and effectiveness of sterilization of free-roaming dogs: A capture and recapture study in Brazil date = 2017-11-01 pages = extension = .txt mime = text/plain words = 7691 sentences = 410 flesch = 44 summary = Despite the perceived need and usefulness of such parameter estimates and recommendations for the most appropriate approaches applicable under such study designs [30] , survival and recruitment estimates of free-ranging dogs had not been obtained using methods of capture and recapture. In this study, we present estimates of abundance, survival and recruitment rates, and the probabilities of capture of two free-roaming dog populations by means of analytical models for open populations, so far unexplored in previous studies. We estimated critical parameters (survival, recruitment and abundance) that describe the population dynamics of free-roaming dogs based on a capture and recapture study design and on models suitable for open populations. Our study demonstrated the increase in population size in both areas, the predominance and greater recruitment of males, the temporal variability in recruitment and in survival probabilities, the lack of effect of sterilization on population dynamics, the influence of abandon and of density-independent factors and a high demographic turnover. cache = ./cache/cord-303187-ny4qr2a2.txt txt = ./txt/cord-303187-ny4qr2a2.txt === reduce.pl bib === id = cord-303490-rixuuytu author = Pazos, Michael A. title = Estrogen Mediates Innate and Adaptive Immune Alterations to Influenza Infection in Pregnant Mice date = 2012-07-05 pages = extension = .txt mime = text/plain words = 6624 sentences = 385 flesch = 43 summary = These data suggest that despite significant morbidity associated with fetal gestation, pregnant mice have an impaired ability to control influenza virus infection in both lethal and nonlethal models. We did not observe any significant differences in the absolute number of cells infiltrating lung tissue during infection with X31 in pregnant ( Figure 5A ) or E2-treated mice (data not shown). In order to determine whether emigration from the lung was impaired, we investigated the number of dendritic cells in the draining mediastinal lymph node at key time points of infection and found no significant differences between pregnant mice and their non-pregnant controls ( Figure 5B ), or between E2-pelleted mice and their placebo controls (data not shown). We found strongly reduced levels of CD86 expression on CD11c+ cells at critical early time points after infection in both pregnancy ( Figure 5C ) and estrogen-treatment ( Figure 5D ), suggesting a deficiency in proper DC maturation. cache = ./cache/cord-303490-rixuuytu.txt txt = ./txt/cord-303490-rixuuytu.txt === reduce.pl bib === id = cord-302962-qw6s1t7j author = Hause, Ben M. title = Bovine Rhinitis Viruses Are Common in U.S. Cattle with Bovine Respiratory Disease date = 2015-03-19 pages = extension = .txt mime = text/plain words = 4948 sentences = 280 flesch = 56 summary = Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD) diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations. The PCR assay specificity was confirmed using bovine rhinitis virus positive samples as determined by metagenomic sequencing as well as with cultures of common BRDC pathogens BVDV, BHV-1, BRSV, BCV, Mannheimia haemolytica, Histophilus somni, Pasteurella multocida and Mycoplasma bovis. As metagenomic sequencing of a nasal swab from a calf with acute respiratory disease identified concurrent infection with two bovine rhinitis virus species, we designed a 5'-nuclease reverse transcription PCR (rtPCR) assay targeting the conserved 3D polymerase gene to investigate the incidence of BRV in BRDC diagnostic submissions. cache = ./cache/cord-302962-qw6s1t7j.txt txt = ./txt/cord-302962-qw6s1t7j.txt === reduce.pl bib === id = cord-307934-84zfabti author = Lai, Chao-Kuen title = Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date = 2014-06-06 pages = extension = .txt mime = text/plain words = 8211 sentences = 465 flesch = 55 summary = Further studies by cofractionation analysis and immunoelectron microscopy of the released particles showed that NS5A-Core complexes, but not NS4B, were present in the low-density fractions, but not in the high-density fractions, of the HCV RNA-containing virions and associated with the internal virion core. Overall, our results suggest that HCV NS5A is associated with the core of the low-density virus particles which exit the cell through a preexisting endosome/exosome pathway and may contribute to HCV natural infection. Both NS5A and Core proteins are found to be closely associated with and co-transported along the microtubules from the perinuclear region of cells via the LDs and endosomes to the plasma membrane. (A) The HCV-infected cells (at day 10 p.i.) were labeled with antibodies specific for Core protein (red) and NS5A (green) (upper row) or NS4B (green) (lower row). cache = ./cache/cord-307934-84zfabti.txt txt = ./txt/cord-307934-84zfabti.txt === reduce.pl bib === id = cord-306278-c4q4la5c author = Esposito, Susanna title = Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date = 2016-04-05 pages = extension = .txt mime = text/plain words = 4660 sentences = 220 flesch = 48 summary = To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. cache = ./cache/cord-306278-c4q4la5c.txt txt = ./txt/cord-306278-c4q4la5c.txt === reduce.pl bib === id = cord-306958-8bx8kxxh author = Christensen, Sarah R. title = Political and personal reactions to COVID-19 during initial weeks of social distancing in the United States date = 2020-09-24 pages = extension = .txt mime = text/plain words = 4271 sentences = 223 flesch = 45 summary = This study examines individual attitudes, behaviors, anxieties, mental health impacts, and knowledge early in the pandemic response, as well as those outcomes by sociodemographic characteristics and political ideology. Four items asked respondents to indicate agreement on a 7-point scale that "events related to COVID-19 had interrupted" their social life, home life, work or vocational life, and/or hurt their mental health. Chi-square, t, and F tests were used to examine the influence of demographic characteristics, political ideology, and mental health on attitudes, knowledge, anxieties, behavior change, and impact variables. Initial covariate selection included all variables that were significant (p <0.05) in bivariate tests, including: political ideology, bias score for consumed news media, attitudes toward global warming and vaccination, sex, race, poverty level, and education. In the adjusted logistic regression model ( Table 2 ) liberals had 5.7 (95%CI: 3.3-9.7) and moderates had 2.5 (95%CI 1.5-4.3) times the odds of responding that the government had not done enough in response to COVID-19 compared to conservatives. cache = ./cache/cord-306958-8bx8kxxh.txt txt = ./txt/cord-306958-8bx8kxxh.txt === reduce.pl bib === id = cord-302189-3xab3yxc author = Tillmann, Ramona Liza title = Sensitive Commercial NASBA Assay for the Detection of Respiratory Syncytial Virus in Clinical Specimen date = 2007-12-26 pages = extension = .txt mime = text/plain words = 1777 sentences = 90 flesch = 45 summary = Thereby, NASBA turned out to be the most sensitive method with a total number of 80 RSV positive samples out of a cohort of 251 nasopharyngeal washings from patients suffering from clinical symptoms, followed by the inhouse RT-PCR (62/251) and ELISA (52/251). Despite an increasing number of newly detected respiratory pathogen the human Respiratory syncytial virus (RSV) remains the single most prevalent etiologic agent in pediatric viral respiratory tract infection [1, 2, 3] . In relation to the positive test results obtained with the NucliSENSH EasyQ NASBA, the relative sensitivity of the RT-PCR was 77,5% compared to 65% obtained with the NOWH RSV ELISA. The results showed that from the three tested methods for molecular diagnosis of RSV the NucliSENSH EasyQ NASBA (bioMerieux, Nürtingen, Germany) detected the most RSV positive samples in a cohort of 251 nasopharyngeal samples of pediatric patients hospitalized with respiratory disease. cache = ./cache/cord-302189-3xab3yxc.txt txt = ./txt/cord-302189-3xab3yxc.txt === reduce.pl bib === id = cord-305274-mcsdem7y author = Beniac, Daniel R. title = Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date = 2007-10-24 pages = extension = .txt mime = text/plain words = 5463 sentences = 254 flesch = 51 summary = We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. The structures of ACE2 bound to a fragment of the SARS spike containing the receptor-binding domain and the pre-and postfusion configurations of the fusion core heptad repeats of the spike have been solved to atomic resolution [2, 3, [24] [25] [26] . In addition, the atomic resolution structures of two neutralizing antibodies bound to the SARS spike receptor-binding domain have been solved [27, 28] showing that blocking of the receptor binding domain, preventing attachment of virions to cell-surface ACE2, is the likely mechanism of virus neutralization by these antibodies. cache = ./cache/cord-305274-mcsdem7y.txt txt = ./txt/cord-305274-mcsdem7y.txt === reduce.pl bib === id = cord-305071-4ck8nd24 author = Calvo, Cristina title = Eight Year Prospective Study of Adenoviruses Infections in Hospitalized Children. Comparison with Other Respiratory Viruses date = 2015-07-06 pages = extension = .txt mime = text/plain words = 3527 sentences = 205 flesch = 49 summary = Human adenovirus (HAdV), a double-stranded DNA virus, causes a wide range of clinical syndromes and is a well-recognized agent of upper and lower respiratory infections in children [1, 2] . Although the literature on adenoviral infections in children is increasing, there are few prospective, long term studies, designed specifically to evaluate the role of HAdV in acute respiratory infections requiring hospitalization. Patients with influenza have fever more frequently (p = 0.028) and have a lower leukocytes count in blood (p<0.001), than children infected by HAdV. HAdV frequently (11% of cases) caused lengthy hospitalizations (more than 7 days) 21% of the single infections were diagnosed with pneumonia. Jin et al [13] , in China, describe similar findings, that children with RSV are younger than patients with HAdV, and have lower respiratory tract infections such as bronchiolitis and bronchitis more frequently. cache = ./cache/cord-305071-4ck8nd24.txt txt = ./txt/cord-305071-4ck8nd24.txt === reduce.pl bib === id = cord-305900-ht7hb2rc author = van den Brand, Judith M. A. title = Comparison of Temporal and Spatial Dynamics of Seasonal H3N2, Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Virus Infections in Ferrets date = 2012-08-08 pages = extension = .txt mime = text/plain words = 9461 sentences = 442 flesch = 47 summary = Therefore, we inoculated ferrets with seasonal H3N2, pandemic H1N1 (pH1N1), and highly pathogenic avian H5N1 influenza virus and performed detailed virological and pathological analyses at time points from 0.5 to 14 days post inoculation (dpi), as well as describing clinical signs and hematological parameters. To this end, we inoculated ferrets with either seasonal human H3N2, pH1N1, or HPAI H5N1 virus, and performed detailed virological and pathological analyses at time points from 0.5 to 14 dpi, as well as measuring virus excretion, clinical signs, and hematological parameters. Comparable with the pattern of antigen expression in the respiratory tissues, high virus titers were seen in the nasal concha from 0.5 to 4 dpi with a peak on 1 dpi (Figure 3) . However, in the current study, we found very little H3N2 infection (based on virus antigen expression) in any cell types of the ferret lower respiratory tract ( Figure 3 ). cache = ./cache/cord-305900-ht7hb2rc.txt txt = ./txt/cord-305900-ht7hb2rc.txt === reduce.pl bib === id = cord-306135-pt4jsr6d author = Chan, Kamfai title = A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date = 2016-02-12 pages = extension = .txt mime = text/plain words = 6292 sentences = 284 flesch = 56 summary = Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. This thermos thermal cycler (TTC) uses a very simple design that performs PCR amplification based on the "archaic" method of hand-transferring reaction tubes through a series of water baths, minimizing the temperature ramping time needed for PCR tubes to reach thermal equilibrium (Fig 1) . The TTC RT-PCR was performed using protocols similar to the HIV test, with PCR tubes transferred between three thermoses (reverse transcription, denaturation, and annealing/extension) and an optional room-temperature water bath. The gel photo in Fig 3 shows that the TTC can produce multiplexed amplicons with the correct sizes and that the yield is similar to a three-step reaction performed in the commercial cycler with same number of PCR cycles. cache = ./cache/cord-306135-pt4jsr6d.txt txt = ./txt/cord-306135-pt4jsr6d.txt === reduce.pl bib === id = cord-309621-6jj19xpr author = Yu, Pin title = Comparative pathology of rhesus macaque and common marmoset animal models with Middle East respiratory syndrome coronavirus date = 2017-02-24 pages = extension = .txt mime = text/plain words = 4645 sentences = 214 flesch = 41 summary = The main histopathological findings in the lungs of rhesus macaques and common marmosets were varying degrees of pulmonary lesions, including pneumonia, pulmonary oedema, haemorrhage, degeneration and necrosis of the pneumocytes and bronchial epithelial cells, and inflammatory cell infiltration. Although there have been several studies in animal models on the pathogenic mechanisms of MERS-CoV infection, little is known about the comparative pathology and inflammatory cell response in rhesus macaques or common marmosets infected with this virus. Pathological findings in the rhesus macaque tissues HE stained tissues from rhesus macaques experimentally infected with MERS-CoV demonstrate that MERS-CoV induces lesions that are primarily observed in the lungs, with varying degrees of inflammation, interstitial pneumonia (Fig 1A) , pulmonary oedema (Fig 1B) , haemorrhaging, degeneration and necrosis of pneumocytes and bronchial epithelial cells (Fig 1C) , and the infiltration of inflammatory cells. Using immunohistochemical techniques and an ISH analysis, we confirmed that MERS-CoV protein and viral RNA were distributed in the lungs of rhesus macaques and common marmosets and that they were primarily located in the pneumocytes and inflammatory cells. cache = ./cache/cord-309621-6jj19xpr.txt txt = ./txt/cord-309621-6jj19xpr.txt === reduce.pl bib === id = cord-303845-y6ws3u6x author = DeLisle, Sylvain title = Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections date = 2010-10-14 pages = extension = .txt mime = text/plain words = 5608 sentences = 246 flesch = 44 summary = Several factors, some of which have already been mentioned, may limit the generalizability of our results: 1) factors related to the performance of our study at the VA health care system: a) the veterans study population is mostly male and excludes the pediatric population, a key target for ARI surveillance [44] ; b) veterans health care utilization may differ from that observed in uninsured or privately insured individuals; c) clinical practices, documentation and coding habits by VA practitioners may differ from those observed in solo or group practices or in health systems subject to different financial or quality-control incentives; 2) factors related to our study period: optimal CDAs could differ outside the respiratory infection season, or during periods of heightened apprehension for an influenza epidemic; 3) factors related to our iterative CDA development process, which may have over adapted CDAs to VA's particular EMR implementation and to our sample dataset in particular, this despite our efforts to maintain a separation between development and validation data subsets; 4) factors related to our text mining approach: a) we did not employ a spell checker prior to applying the NegEx algorithm. cache = ./cache/cord-303845-y6ws3u6x.txt txt = ./txt/cord-303845-y6ws3u6x.txt === reduce.pl bib === id = cord-305811-987dhnf7 author = Cho, Che-Pei title = Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date = 2013-04-29 pages = extension = .txt mime = text/plain words = 5837 sentences = 301 flesch = 49 summary = Because both 59CC-WT and 13363-13520 constructs share 27 identical nucleotides upstream of their slippery sites, the attenuation activity difference is not likely to be caused by an E-site flanking sequences effect [12, 13] but rather by the disruption of the two potential AU base pairs. We noticed a potential to form four extra base pairs between 59and 39-flanking sequences (GACG and CGUU, respectively) of the 6BPGC hairpin stem (and other deletion mutants) due to the existence of a 59 SalI cloning site (Fig. S1A ). The results (Fig. S1C ) indicate that the two potential base pairs involving E-site sequences are not the main cause of observed attenuation activity in 293T cell cultures. Furthermore, mutating two nucleotides (27 nucleotides upstream of the E site) to disrupt Watson-Crick base pairs in the lower hairpin stem dramatically impairs attenuation activity (Fig. 2) , indicating that attenuation is not caused by primary sequencemediated flanking-sequences effects [12, 13] . cache = ./cache/cord-305811-987dhnf7.txt txt = ./txt/cord-305811-987dhnf7.txt === reduce.pl bib === id = cord-308344-ao9z00t7 author = Diep, Nguyen Van title = Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date = 2017-01-17 pages = extension = .txt mime = text/plain words = 4179 sentences = 193 flesch = 52 summary = title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. In this study, variants with large deletions in the S gene were found in eight primary and nine recurrent outbreaks from 16 pig farms, and they mostly (94.1%) coexisted with PEDV strains with an intact S gene. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs cache = ./cache/cord-308344-ao9z00t7.txt txt = ./txt/cord-308344-ao9z00t7.txt === reduce.pl bib === id = cord-305393-96mrxt8a author = Lai, Yvonne title = Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date = 2011-10-10 pages = extension = .txt mime = text/plain words = 9604 sentences = 587 flesch = 60 summary = Recombinant 1b hepatitis C virus polymerase was found to enhance TLR3 signaling in the lung epithelial BEAS-2B cells when added to the media along with either poly(I:C) or viral dsRNAs. The polymerase from the genotype 2a JFH-1 HCV was a poor enhancer of TLR3 signaling until it was mutated to favor a conformation that could bind better to a partially duplexed RNA. These results demonstrate that several viral RNA-binding proteins can enhance the dsRNA-dependent innate immune response initiated by TLR3. Transfection of two plasmids, one containing an interferon stimulated response element (ISRE) promoter-driven firefly luciferase and a second encoding a constitutively expressed Renilla luciferase allow the analysis of TLR3 activation by different RNAs. HEK 293T cells expressing WT TLR3 responded to poly(I:C) (1-2 mg/ml), better than viral dsRNAs (1-2 mg/ml) purified from Reovirus and BPEV (Fig. 1B) . cache = ./cache/cord-305393-96mrxt8a.txt txt = ./txt/cord-305393-96mrxt8a.txt === reduce.pl bib === id = cord-309194-jtouafgd author = Lu, Xiao title = Lung ultrasound score in establishing the timing of intubation in COVID-19 interstitial pneumonia: A preliminary retrospective observational study date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3668 sentences = 191 flesch = 46 summary = PURPOSE: To investigate the role of lung ultrasound score (LUS) in assessing intubation timing for patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia. Lung ultrasound was performed on days 1, 2, 3, 5, and 7 after patients were admitted to the ICU; if the patient was intubated, LUS determination was performed before intubation within 24 h (T1) and on days 1, 2, 5, and 7 after intubation (T2, T3, T4, and T5, respectively).The goal of this study was to evaluate the severity of lung aeration loss in intubated and non-intubated patients with SARS-CoV-2 pneumonia by ultrasound at different time points within one week. Few studies have addressed the timing of intubation for patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia due to the high mortality of patients treated with invasive ventilation. The patient's gender, age, body mass index (BMI index), sequential organ failure assessment (SOFA score), and 28-day mortality rate were recorded; and the evolution of respiratory parameters between the two groups on time point T1 (lung ultrasound performed before intubation within 24 h) were also recorded. cache = ./cache/cord-309194-jtouafgd.txt txt = ./txt/cord-309194-jtouafgd.txt === reduce.pl bib === id = cord-310438-744r7gc3 author = Chan, Ta-Chien title = The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date = 2010-06-25 pages = extension = .txt mime = text/plain words = 5083 sentences = 226 flesch = 40 summary = This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan's influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. The aims of this study were: (1) to evaluate the effectiveness of matching or mismatching influenza vaccine strains on influenzaassociated mortality, (2) to assess whether public health improvements during the post-SARS period might have decreased elderly mortality, and (3) to investigate molecular variation among vaccine-mismatched influenza viruses that may be associated with increased excess influenza-associated mortality. Explanatory variables for the above three outcome measures include monthly meteorological parameters (monthly means of temperature and humidity), annual periodic cycle (i.e., sine/cosine function of seasonal periodicity), monthly virus isolation rates for different subtypes/types of influenza viruses [A (H3N2) or A (H1N1) or B], matching status of different vaccine strains for each subtype/type in each of the studied years, post-SARS effect, and linear temporal monthly trends. cache = ./cache/cord-310438-744r7gc3.txt txt = ./txt/cord-310438-744r7gc3.txt === reduce.pl bib === id = cord-311074-j3fw4dfc author = Alviset, Sophie title = Continuous Positive Airway Pressure (CPAP) face-mask ventilation is an easy and cheap option to manage a massive influx of patients presenting acute respiratory failure during the SARS-CoV-2 outbreak: A retrospective cohort study date = 2020-10-14 pages = extension = .txt mime = text/plain words = 4842 sentences = 254 flesch = 49 summary = title: Continuous Positive Airway Pressure (CPAP) face-mask ventilation is an easy and cheap option to manage a massive influx of patients presenting acute respiratory failure during the SARS-CoV-2 outbreak: A retrospective cohort study From 27th March to 23rd April, consecutive patients who had respiratory failure or were unable to maintain an SpO2 > 90%, despite receiving 10–15 l/min of oxygen with a non-rebreather mask, were treated by continuous positive airway pressure (CPAP) unless the ICU physician judged that immediate intubation was indicated. The following baseline patient characteristics were retrieved from patient electronic medical record: sex, age, comorbidities, body mass index (BMI), withholding / withdrawal of lifesustaining therapies, associated COVID-19 therapies administered before the primary outcome under study occurred (antivirals, corticosteroids, immuno-modulating therapies, prone positioning), oxygen flow rate and SpO2 before and after starting CPAP treatment, duration of CPAP treatment, medical unit where CPAP treatment was performed, duration of invasive mechanical ventilation, SAPS2 score for patients admitted in ICU, driving pressure and P/F ratio on first day of mechanical ventilation. cache = ./cache/cord-311074-j3fw4dfc.txt txt = ./txt/cord-311074-j3fw4dfc.txt === reduce.pl bib === id = cord-307036-n44yml79 author = Ng, Oi-Wing title = Substitution at Aspartic Acid 1128 in the SARS Coronavirus Spike Glycoprotein Mediates Escape from a S2 Domain-Targeting Neutralizing Monoclonal Antibody date = 2014-07-14 pages = extension = .txt mime = text/plain words = 8528 sentences = 392 flesch = 57 summary = Next, to determine if mAb 1A9 exhibits cross-neutralizing activity, S-pseudotyped virus particles, or S-pps, carrying the human SARS-CoV S or the various RBD-modified chimeric S of civet SARS-CoV SZ3 strain and bat SL-CoV Rp3 and Rf1 strains were generated and used to infect CHO-ACE2 cells in the absence or presence of different concentrations (100, 150 and 200 mg/ml) of mAb 1A9. Wild-type S, substitution S mutants, namely D1128A, N1056K, and that containing both D1128A and N1056K, were then expressed in 293 FT cells and Western Blot analysis was performed to determine the effects of these mutations on the binding of the S protein to mAb 1A9. (A) S-pp expressing S protein of humans SARS-CoV HKU39849, civet SARS-CoV SZ3, bat SL-CoV Rp3 and Rf1 and (B) S-pp containing wild-type or mutant D1128A, N1056K or D1128A/ N1056K S were generated and used to infect CHO-ACE2 cells at equal amount (as quantitated using P24 ELISA). cache = ./cache/cord-307036-n44yml79.txt txt = ./txt/cord-307036-n44yml79.txt === reduce.pl bib === id = cord-310061-nro623aa author = Valitutto, Marc T. title = Detection of novel coronaviruses in bats in Myanmar date = 2020-04-09 pages = extension = .txt mime = text/plain words = 3678 sentences = 192 flesch = 48 summary = Historically, bats have been linked to highly pathogenic viruses that pose a serious threat to human health, including the coronaviruses responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), the hemorrhagic ebola and Marburg filoviruses, and paramyxoviruses such as Nipah virus [10, 11, [13] [14] [15] [16] [17] [18] . The 2002-2003 SARS epidemic, the emergence of MERS in people in 2012, and the ongoing COVID-19 pandemic have prompted substantial interest in detecting coronaviruses of bat origin due to public health concern and their pandemic potential [10, [13] [14] [15] [16] [17] [18] . In addition to human-associated CoVs, bats are also hosts of coronaviruses that infect production animals, and have been implicated in the emergence and origin of swine acute diarrhea syndrome (SADS), transmissible gastroenteritis virus (TGEV) in pigs, and porcine epidemic diarrhea (PED), which can cause considerable losses [23] [24] [25] [26] . cache = ./cache/cord-310061-nro623aa.txt txt = ./txt/cord-310061-nro623aa.txt === reduce.pl bib === id = cord-310678-33c3mp1o author = Morgantini, Luca A. title = Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey date = 2020-09-03 pages = extension = .txt mime = text/plain words = 3491 sentences = 214 flesch = 54 summary = INTERPRETATION: Burnout is present at higher than previously reported rates among HCPs working during the COVID-19 pandemic and is related to high workload, job stress, and time pressure, and limited organizational support. Current and future burnout among HCPs could be mitigated by actions from healthcare institutions and other governmental and non-governmental stakeholders aimed at potentially modifiable factors, including providing additional training, organizational support, and support for family, PPE, and mental health resources. assessed 376 Italian HCPs who interacted with COVID-19 infected patients for their reported burnout, psychosomatic symptoms and self-perceived general health, finding in their study population high emotional burnout, physical symptoms, and work-related pressure [7] . Across all countries (Fig 2) , in the multivariable regression analysis, reported burnout was associated with work impacting household activities (RR = 1�57, 95% CI = 1�39-1�78, P<0�001), feeling pushed beyond training (RR = 1�32, 95% CI = 1�20-1�47, P<0�001), exposure to COVID-19 patients (RR = 1�18, 95% CI = 1�05-1�32, P = 0�005), and making life prioritizing decisions due to supply shortages (RR = 1�16, 95% CI = 1�02-1�31, P = 0�03). cache = ./cache/cord-310678-33c3mp1o.txt txt = ./txt/cord-310678-33c3mp1o.txt === reduce.pl bib === id = cord-309981-4p3ybrn1 author = Dai, Ling-Ling title = Anxiety and depressive symptoms among COVID-19 patients in Jianghan Fangcang Shelter Hospital in Wuhan, China date = 2020-08-28 pages = extension = .txt mime = text/plain words = 3554 sentences = 179 flesch = 43 summary = From February 23, 2020, to February 26, 2020, we obtained sociodemographic and clinical characteristics information of COVID-19 patients in Jianghan Fangcang Shelter Hospital (Wuhan, China) and assessed their mental health status and sleep quality. As with other infectious diseases, preliminary evidence suggests that COVID-19 also causes public panic and mental health stress; symptoms of anxiety and depression are common psychological reactions to the COVID-19 pandemic, and may be associated with sociodemographic factors and sleep quality [6] [7] [8] [9] . This cross-sectional study examined the prevalence of anxiety, depression, and poor sleep quality among 307 patients in Jianghan Fangcang Shelter Hospital in Wuhan, China, 2 months after the start of the COVID-19 pandemic. In addition, using one-sample-tests, it was determined that both SAS (42.92±7.30) and SDS (39.77±10.11) scores of the participants of our study were higher than Chinese norms (SAS, 29.78±10.07, n = 1158; SDS, 33.46±8.55, n = 1340) (both P<0.001) [26] , indicating more severe levels of anxiety and depressive symptoms among COVID-19 patients admitted to Fangcang hospitals, compared with the general public. cache = ./cache/cord-309981-4p3ybrn1.txt txt = ./txt/cord-309981-4p3ybrn1.txt === reduce.pl bib === id = cord-304616-k92fa15l author = Izes, Aaron M. title = Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats date = 2020-08-05 pages = extension = .txt mime = text/plain words = 4208 sentences = 234 flesch = 50 summary = title: Assay validation and determination of in vitro binding of mefloquine to plasma proteins from clinically normal and FIP-affected cats As cats with feline infectious peritonitis (FIP) demonstrate altered concentrations of plasma proteins, the proportion of mefloquine binding to plasma proteins in both clinically normal cats and FIP-affected cats was also investigated. Consequently, the aim of this study was two-fold: first, to develop and validate a high pressure liquid chromatography (HPLC) method to detect mefloquine in feline plasma, and second, to determine the in vitro plasma protein binding of mefloquine in both clinically normal and FIP-affected cats. Here, although a significant difference was found between the plasma protein binding of mefloquine in clinically normal and FIP-affected cats, due to the unknown biological variability of the assay, it is likely that this difference is equivocal. This study has validated an accurate and reliable assay to detect mefloquine in feline plasma and demonstrated that mefloquine is highly plasma protein bound in both clinically normal and FIP-affected cats. cache = ./cache/cord-304616-k92fa15l.txt txt = ./txt/cord-304616-k92fa15l.txt === reduce.pl bib === id = cord-309010-tmfm5u5h author = Dietert, Kristina title = Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia date = 2017-11-20 pages = extension = .txt mime = text/plain words = 7842 sentences = 414 flesch = 34 summary = Here, we systematically describe and compare the distinctive histopathological features of established models of acute pneumonia in mice induced by Streptococcus (S.) pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Legionella pneumophila, Escherichia coli, Middle East respiratory syndrome (MERS) coronavirus, influenza A virus (IAV) and superinfection of IAV-incuced pneumonia with S. Systematic comparisons of the models revealed striking differences in the distribution of lesions, the characteristics of pneumonia induced, principal inflammatory cell types, lesions in adjacent tissues, and the detectability of the pathogens in histological sections. Transnasal infection with MERS-CoV following adenoviral transduction of human DPP4 yielded an expansive, (Fig 7A) interstitial pneumonia with severe alveolar epithelial cell necrosis and infiltration of mainly macrophages, lymphocytes, and fewer neutrophils (Fig 7B) . Different mouse models of acute pneumonia differ widely, with an obvious strong dependence on pathogen-specific features of virulence and spread, route of infection, infectious dose and other factors. cache = ./cache/cord-309010-tmfm5u5h.txt txt = ./txt/cord-309010-tmfm5u5h.txt === reduce.pl bib === id = cord-308261-hxlebas8 author = Broekhuis, Femke title = Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date = 2019-04-03 pages = extension = .txt mime = text/plain words = 4771 sentences = 223 flesch = 52 summary = title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya To determine the static interactions between male cheetahs we calculated their space use and the amount of overlap for each dyad to determine the possibility that individuals could encounter each other either directly or indirectly. In general, cheetahs were closer to the encounter location after a possible encounter compared to before for all four time lags, apart from individual M03 in Dyad 3 where the opposite trend was Intraspecific interactions among carnivores: A case study of male cheetahs observed, however none of the results were significant (S1 Table) . Using GPS collar data we documented static and dynamic interactions between male cheetahs in Kenya's Maasai Mara and investigated the outcomes of these interactions in terms of movement behaviour and mortalities. cache = ./cache/cord-308261-hxlebas8.txt txt = ./txt/cord-308261-hxlebas8.txt === reduce.pl bib === id = cord-308249-es948mux author = Dokuka, Sofia title = How academic achievement spreads: The role of distinct social networks in academic performance diffusion date = 2020-07-27 pages = extension = .txt mime = text/plain words = 5043 sentences = 297 flesch = 48 summary = We examine the spread of academic achievements of first-year undergraduate students through friendship and study assistance networks, applying stochastic actor-oriented modeling. In this paper, we analyze the diffusion of academic performance across different types of student social networks. We analyze the spread of academic achievements within two different social networks of first-year undergraduate students. It was shown that achievements spread well within friendship networks, while other types of ties (e.g. online relationships) do not serve as channels for the performance transmission. In this paper, we examine the diffusion of academic achievements in two distinct social networks: friendship and study assistance. We analyze the longitudinal data on friendship and study assistance networks and GPA of a first-year student cohort of the Economics department in one of the leading Russian universities in 2013-2014 academic year. In this paper we explore the academic performance diffusion through two social networks of different natures: friendship and study assistance. cache = ./cache/cord-308249-es948mux.txt txt = ./txt/cord-308249-es948mux.txt === reduce.pl bib === id = cord-310466-0lbbiq7u author = Fu, Yang-chih title = Representative Contact Diaries for Modeling the Spread of Infectious Diseases in Taiwan date = 2012-10-03 pages = extension = .txt mime = text/plain words = 4415 sentences = 204 flesch = 49 summary = To ensure that such diary-based contact patterns provide accurate baseline data for policy implementation in densely populated Taiwan, we collected contact diaries from a national sample, using 3-stage systematic probability sampling and rigorous in-person interviews. Based on such actual and representative data that enable researchers to infer findings to the whole population, our analyses aim to facilitate implementing more appropriate and effective strategies for controlling an emerging or pandemic disease infection. To ensure that such diary-based contact patterns provide accurate baseline data for policy implementation, we collected contact diaries from a representative national sample in Taiwan and extracted realistic parameters for our simulation modeling of disease infections. Our diary-based survey in Taiwan emphasizes the rigorous requirements on both systematic probability sampling and in-person (face-to-face) household interviews to ensure proper inference to the population as a whole. cache = ./cache/cord-310466-0lbbiq7u.txt txt = ./txt/cord-310466-0lbbiq7u.txt === reduce.pl bib === id = cord-312493-wbhji81g author = Tay, Ee Laine title = Exploring a Proposed WHO Method to Determine Thresholds for Seasonal Influenza Surveillance date = 2013-10-11 pages = extension = .txt mime = text/plain words = 4303 sentences = 216 flesch = 49 summary = For all datasets, including the composite datasets, we aligned data on the median week of peak influenza or ILI activity and assigned three threshold levels: seasonal threshold, determined by inspection; and two intensity thresholds termed average and alert thresholds, determined by calculations of means, medians, confidence intervals (CI) and percentiles. Comparison of thresholds revealed variations in defining the start of a season but good agreement in describing the end and intensity of influenza seasons, except in hospital admissions data after the pandemic year of 2009. Four independent surveillance data sources were used: (i) the Victorian GPSS, (ii) sentinel data from the Melbourne Medical Deputising Service (MMDS), (iii) routine laboratoryconfirmed influenza (LAB data) from the Victorian Infectious Diseases Reference Laboratory (VIDRL) and the (iv) Victoria Admitted Episode Dataset (VAED) for hospital admissions. Comparison of thresholds derived from different datasets revealed variations in defining the start of a season but relatively good agreement in describing the end and intensity of influenza seasons, except in the hospital data after the pandemic year. cache = ./cache/cord-312493-wbhji81g.txt txt = ./txt/cord-312493-wbhji81g.txt === reduce.pl bib === id = cord-310790-3ikgmiof author = Cherrak, Sabri Ahmed title = Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3471 sentences = 226 flesch = 50 summary = title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. The three compounds with highest affinity (Fig 2) for the active site are quercetin 3-rhamonoside, myricetin 3-rutinoside and rutin with binding energies of -9.7, -9,3 and -9.2 kcal.mol -1 respectively. Thirty eight flavonoids have been tested in this study by molecular docking against the active site of the SARS-CoV-2Mpro. Glycosylated flavonoids as SARS-CoV-2 Inhibitors: A molecular docking and simulation studies Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies cache = ./cache/cord-310790-3ikgmiof.txt txt = ./txt/cord-310790-3ikgmiof.txt === reduce.pl bib === id = cord-311065-ie3gty6e author = Gaddi, Pamela J. title = IL-10 Mediated Regulation of Liver Inflammation during Acute Murine Cytomegalovirus Infection date = 2012-08-03 pages = extension = .txt mime = text/plain words = 6591 sentences = 328 flesch = 46 summary = Further work has described a role for IL-10 in reducing systemic IFN-c production, CD4+ and CD8+ T cell cytokine responses and viral elimination in the spleen during MCMV infection [28] . The absence of IL-10 during acute MCMV infection results in elevated levels of systemic and local proinflammatory cytokines and chemokines, as well as increased inflammatory cell infiltration into infected livers. MCMV infection in the liver results in increased infiltration of NK cells, T cells and macrophages that contribute to viral clearance through cytokine and chemokine production [20, 23, 27, [38] [39] [40] . Virus-specific CD8+ T cells are recruited to the liver within 4 days of infection and control viral replication through release of cytotoxic molecules and production of cytokines such as IFN-c and TNF-a [18, [21] [22] [23] 26] . cache = ./cache/cord-311065-ie3gty6e.txt txt = ./txt/cord-311065-ie3gty6e.txt === reduce.pl bib === id = cord-310396-jitao9k0 author = Lei, Yu title = MAVS-Mediated Apoptosis and Its Inhibition by Viral Proteins date = 2009-03-07 pages = extension = .txt mime = text/plain words = 6031 sentences = 325 flesch = 46 summary = The mitochondrial antiviral signaling adaptor, MAVS (IPS-1, VISA or Cardif) is critical for host defenses to viral infection by inducing type-1 interferons (IFN-I), however its role in virus-induced apoptotic responses has not been elucidated. A functional screen identifies the hepatitis C virus NS3/4A and the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) nonstructural protein (NSP15) as inhibitors of MAVS-induced apoptosis, possibly as a method of immune evasion. Currently, there are no reports of viral proteins targeting MAVS for inhibition of virus-induced cell death responses. In this report, we describe a novel function of MAVS in mediating virus-induced apoptosis, and identify viral proteins as inhibitors of this response. In addition, the involvement of proteins on IFN axis in virusinduced host cell apoptosis has been implicated in another previous report, in which MAVS has been shown to be critical for reovirus-triggered caspase-3/7 activation in HEK293T cells [46] , however, the study did not evaluate whether MAVS mediates virus-induced apoptosis and what roles type 1 IFNs play in MAVS-mediated apoptosis. cache = ./cache/cord-310396-jitao9k0.txt txt = ./txt/cord-310396-jitao9k0.txt === reduce.pl bib === id = cord-312367-24huwt3y author = Coelho, Camila title = Biochemical screening for SARS-CoV-2 main protease inhibitors date = 2020-10-06 pages = extension = .txt mime = text/plain words = 3351 sentences = 210 flesch = 49 summary = As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). As viral proteases, following polymerases, are the most prominent targets for antiviral drug design [9] , here we describe initial biochemical screenings with recombinant purified SARS-CoV-2 M pro performed in order to define possible candidates which could serve as lead compounds for the design of future COVID-19 therapies. In order to contribute to the ongoing worldwide research and development efforts to contain COVID-19, we cloned, expressed recombinantly in E.coli BL21(DE3) and purified an important drug target of SARS-CoV-2, its main protease (M pro ). From these obtained compounds, esculetin-4-carboxylic acid ethyl ester (IC 50 = 46 μM in M pro inhibition assays), a coumarin derivative and natural product, demonstrated an EC 50 of 112 μM (median toxic concentration TC 50 >800μM) in Vero-cell SARS-CoV assays [13] and MP576 (IC 50 = 2.5 μM), a quinolinecarboxylate, demonstrated an EC 50 of 7 μM (TC 50 >50μM) [15, 17] , thus validating the M pro biochemical screening approach for the development of SARS-CoV drugs. cache = ./cache/cord-312367-24huwt3y.txt txt = ./txt/cord-312367-24huwt3y.txt === reduce.pl bib === id = cord-312033-iarl77n0 author = López Barreda, Rodrigo title = Poverty, quality of life and psychological wellbeing in adults with congenital heart disease in Chile date = 2020-10-08 pages = extension = .txt mime = text/plain words = 4058 sentences = 235 flesch = 51 summary = The objective of this study was to assess the quality of life and psychological wellbeing of adults with congenital heart disease (CHD) in Chile, and to identify other associated factors. They completed a questionnaire, which included a quality of life assessment tool (the Medical Outcome Study 36-Item Short Form Health Survey), a number of psychological scales (the General Health Questionnaire, the Basic Psychological Needs Scales and the Beck Hopelessness Scale), a socioeconomic survey, and some clinical data. The primary aim of this study was to assess the QoL and psychological wellbeing of a population of adults suffering from CHD in Chile. Poverty, quality of life and psychological wellbeing in adults with congenital heart disease in Chile Poverty, quality of life and psychological wellbeing in adults with congenital heart disease in Chile general population [5, 11, 38] . cache = ./cache/cord-312033-iarl77n0.txt txt = ./txt/cord-312033-iarl77n0.txt === reduce.pl bib === id = cord-308480-t2vukbwp author = Liang, Zhongjie title = Molecular Basis of NDM-1, a New Antibiotic Resistance Determinant date = 2011-08-24 pages = extension = .txt mime = text/plain words = 4279 sentences = 206 flesch = 48 summary = In addition, the detailed analysis indicates that the more flexible and hydrophobic loop1, together with the evolution of more positive-charged loop2 leads to NDM-1 positive strain more potent and extensive in antibiotics resistance compared with other MBLs. Furthermore, through biological experiments, we revealed the molecular basis for antibiotics catalysis of NDM-1 on the enzymatic level. Taking two typical antibiotics, imipenem and carbapenem as example, the docked complex structures revealed that although the antibiotics adopted diverse conformations in the active site, the lactam motifs were positioned in the same orientation by coordinating with zinc ions tightly ( Figure 2C ), which suggested that the catalytic mechanisms were highly conserved among B1 subclass enzymes, as shown in Figure 3 . To gain the structural insight into the mechanism of the potent hydrolysis of NDM-1, the intermolecular interactions of three models of NDM-1, VIM-2 and FEZ-1 in complex with antibiotics meropenem were compared and analyzed in details ( Figure 4A -C). cache = ./cache/cord-308480-t2vukbwp.txt txt = ./txt/cord-308480-t2vukbwp.txt === reduce.pl bib === id = cord-303034-w72oeoxq author = Haischer, Michael H. title = Who is wearing a mask? Gender-, age-, and location-related differences during the COVID-19 pandemic date = 2020-10-15 pages = extension = .txt mime = text/plain words = 4429 sentences = 216 flesch = 55 summary = To understand the demographics of mask wearers and resistors, and the impact of mandates on mask-wearing behavior, we observed shoppers (n = 9935) entering retail stores during periods of June, July, and August 2020. Wearing a mask in public is currently a controversial and politicized issue in the United States, even with case evidence from other countries that face coverings help to control the spread of coronavirus disease 2019 (COVID-19) [1] . To facilitate greater understanding and reliable experimental data on whether gender, age, location, and the presence of mask mandates influence mask wearing in the United States, we conducted a direct observational study at retail stores in Wisconsin. It is not surprising that our June data showed that older individuals wear masks more than middle-age and young people because older adults are at higher risk for more severe cases of COVID-19. cache = ./cache/cord-303034-w72oeoxq.txt txt = ./txt/cord-303034-w72oeoxq.txt === reduce.pl bib === id = cord-307540-dr5m9pfk author = Coelho, Flávio C. title = Assessing the spread of COVID-19 in Brazil: Mobility, morbidity and social vulnerability date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3517 sentences = 201 flesch = 52 summary = Probabilistic models were used to calculate the probability of COVID-19 spread from São Paulo and Rio de Janeiro, the initial hotspots, using mobility data from the pre-epidemic period, while multivariate cluster analysis of socio-economic indices was done to identify areas with similar social vulnerability. To identify regions with high geographical and social vulnerability, we proposed a classification scheme based on three main criteria: population mobility, socio-demographic-economic characteristics, and the available health care infrastructure in terms of hospital capacity. To assess the probability of COVID-19 spreading within Brazil, in the absence of mobility restrictions, we first calculated the effective distance (E f (i,j)) between micro-regions using the air travel data. We computed the effective distance, E f (i,j), between each micro-region and the two COVID-19's hotspots, Rio de Janeiro and Sao Paulo. Mostly urban micro-regions, with above-average life expectancy, with comparatively less social inequality, less population living in extreme poverty, better access to water supply and sewage disposal services, higher education. cache = ./cache/cord-307540-dr5m9pfk.txt txt = ./txt/cord-307540-dr5m9pfk.txt === reduce.pl bib === id = cord-312002-4qhvljpv author = Pacheco-Barrios, Kevin title = COVID-19 pandemic and Farr’s law: A global comparison and prediction of outbreak acceleration and deceleration rates date = 2020-09-17 pages = extension = .txt mime = text/plain words = 5434 sentences = 252 flesch = 56 summary = However, a 150-year old epidemics law promulgated by William Farr might be useful as a simple arithmetical model (percent increase [R1] and acceleration [R2] of new cases and deaths) to provide a first sight of the epidemic behavior and to detect regions with high predicted dynamics. In this study, we will model COVID-19 current data (until April 10, 2020) of new confirmed cases and deaths, from 210 countries as to test the assumptions of the 1840 Farr's law, to describe the epidemic dynamics, and also to make predictions to identify areas with high dynamic and suggest preparation and actions of health system in those regions. cache = ./cache/cord-312002-4qhvljpv.txt txt = ./txt/cord-312002-4qhvljpv.txt === reduce.pl bib === id = cord-308764-9z4qcoqz author = Wei, Lin title = Transcriptome Analysis of Houttuynia cordata Thunb. by Illumina Paired-End RNA Sequencing and SSR Marker Discovery date = 2014-01-02 pages = extension = .txt mime = text/plain words = 5253 sentences = 298 flesch = 51 summary = cordata to generate an enormous transcriptome sequence dataset for gene discovery and molecular marker development. cordata; 43 (86%) produced fragments of expected size, suggesting that the unigenes were suitable for specific primer design and of high quality, and the SSR marker could be widely used in marker-assisted selection and molecular breeding of H. cordata and used Illumina paired-end sequencing technology to generate a large-scale EST database and develop a set of SSR markers. For further assessment of the assembly quality and development of new molecular markers, all 63,954 unigenes generated in this study were used to mine potential microsatellites, which were defined as di-to hexa-nucleotide SSRs with a minimum of four repetitions for all motifs. Here, the N50 length of the unigenes was 1,051 bp and the average length was 679 bp, which suggests that the relatively short reads from Illumina paired-end sequencing for this non-model organism have been effectively and accurately assembled. cache = ./cache/cord-308764-9z4qcoqz.txt txt = ./txt/cord-308764-9z4qcoqz.txt === reduce.pl bib === id = cord-311531-wezrs7gc author = Parčina, Marijo title = Multicenter evaluation of the QIAstat Respiratory Panel—A new rapid highly multiplexed PCR based assay for diagnosis of acute respiratory tract infections date = 2020-03-12 pages = extension = .txt mime = text/plain words = 3584 sentences = 179 flesch = 48 summary = The QIAstat Respiratory Panel(®) assay (QIAstat RP) is a multiplexed in vitro diagnostics test for the rapid simultaneous detection of 21 pathogens directly from respiratory samples, including human mastadenovirus A-G, primate bocaparvovirus 1+2, human coronavirus (HKU1, NL63, OC43, 229E), human metapneumovirus A/B, rhinovirus/enterovirus, influenza A virus (no subtype, subtype H1, H1N1/2009, H3), influenza B virus, human respirovirus 1+3, human orthorubulavirus 2+4, human orthopneumovirus, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila. The FilmArray RP is a multiplex sample-to-answer PCR panel that tests for 20 viral and bacterial pathogens on nasopharyngeal swabs in UTM at a time. Before resolution by discrepancy testing, QIAstat RP and FilmArray RP agreed on the detection of 376 pathogens in the 445 samples (Table 3) . After resolution by discrepancy testing on the Allplex RP, a total of 402 pathogen results were considered as true positive (Table 4) , of which QIAstat RP detected 394, for an overall PPA of 98.0% (95%CI 96.0%-99.1%). cache = ./cache/cord-311531-wezrs7gc.txt txt = ./txt/cord-311531-wezrs7gc.txt === reduce.pl bib === id = cord-311941-0dpm35dd author = Jones, Bryony A. title = Calf-Level Factors Associated with Bovine Neonatal Pancytopenia – A Multi-Country Case-Control Study date = 2013-12-02 pages = extension = .txt mime = text/plain words = 5745 sentences = 253 flesch = 56 summary = Bovine neonatal pancytopenia (BNP), a high fatality condition causing haemorrhages in calves aged less than 4 weeks, was first reported in 2007 in Germany and subsequently observed at low incidence in other European countries and New Zealand. A case had 18 times the odds of being born to a dam that was PregSurevaccinated rather than unvaccinated compared with a control, if the dam was first lactation and the calf did not receive colostrum from other cows, adjusting for type of milk fed (amOR 17.8; ci. A case had 3 times the odds of having been fed raw milk only from its dam rather than other types of milk (with or without dams milk) compared with a control (amOR 3.4; ci 1.6, 7.5; p = 0.002) when adjusting for dam PregSure-vaccination, lactation number and source of colostrum. Case control study to investigate risk factors for bovine neonatal pancytopenia (BNP) in young calves in southern Germany cache = ./cache/cord-311941-0dpm35dd.txt txt = ./txt/cord-311941-0dpm35dd.txt === reduce.pl bib === id = cord-310947-aqau2n7q author = Pan, Ji'An title = Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date = 2008-10-01 pages = extension = .txt mime = text/plain words = 6821 sentences = 302 flesch = 43 summary = In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . cache = ./cache/cord-310947-aqau2n7q.txt txt = ./txt/cord-310947-aqau2n7q.txt === reduce.pl bib === id = cord-309471-lr68epyb author = Xia, Jingya title = Virus-Specific Immune Memory at Peripheral Sites of Herpes Simplex Virus Type 2 (HSV-2) Infection in Guinea Pigs date = 2014-12-08 pages = extension = .txt mime = text/plain words = 7010 sentences = 312 flesch = 42 summary = Memory B cells were detected primarily in the spleen and to a lesser extent in bone marrow but not in the genital tract or neural tissues suggesting that the HSV-specific antibody-secreting cells present at peripheral sites of HSV-2 infection represented persisting populations of plasma cells. The presence of memory B cells in the culture is therefore detected as a TLR-agonist-induced increase in the number of antigen-specific, ASCs. To test for the presence of memory B cells at peripheral tissues, we stimulated lymphocyte populations isolated from bone marrow, spleen, vagina/cervix, or spinal cord/sensory ganglia of previously infected guinea pigs with a combination of LPS and CpG oligonucleotides and quantified HSV-specific ASC by ELISPOT. On day 7 post infection, HSV-specific, IFN-c-secreting T cells from the spleen, vagina/cervix, and lumbosacral ganglia and the adjacent spinal cord were quantified using a pair Peripheral Tissue-Resident Immune Memory to HSV-2 of previously described anti-guinea pig IFN-c -specific monoclonal antibodies [27] in an IFN-c ELISPOT assay. cache = ./cache/cord-309471-lr68epyb.txt txt = ./txt/cord-309471-lr68epyb.txt === reduce.pl bib === id = cord-311288-6ttux2uu author = Luo, Chen title = What triggers online help-seeking retransmission during the COVID-19 period? Empirical evidence from Chinese social media date = 2020-11-03 pages = extension = .txt mime = text/plain words = 6202 sentences = 385 flesch = 43 summary = We built an analytical framework that emphasized content characteristics, including information completeness, proximity, support seeking type, disease severity, and emotion of help-seeking messages. For example, harness the social media posts to predict infected case counts and inform timely responses under the infoveillance or infodemiology framework [3, 4] ; analyze the help-seeking posts to identify the characteristics of COVID-19 patients [5] ; More retransmission means more users receiving the message, thus increasing the chance of getting help. There is plenty of research providing conceptual references, such as the depth of self-disclosure [16, 28] , different types of support messages [16, 29] , physical and emotional proximity to the target [30] , the social capital stock of the help seeker [22] . Enlightened by existing experience, we will summarize the impelling factors of help-seeking information diffusion into five dimensions: completeness, proximity, support typology, disease severity, emotion, and elaborate them in the following sections. cache = ./cache/cord-311288-6ttux2uu.txt txt = ./txt/cord-311288-6ttux2uu.txt === reduce.pl bib === id = cord-312678-81gnmxbk author = Elayeh, Eman title = Before and after case reporting: A comparison of the knowledge, attitude and practices of the Jordanian population towards COVID-19 date = 2020-10-15 pages = extension = .txt mime = text/plain words = 5442 sentences = 266 flesch = 52 summary = Our research group initiated a study to ascertain the knowledge, attitude and practices (KAP) of Jordanians toward COVID-19 prior to any initial case report in Jordan. Therefore, the initial aim of this study was to evaluate the overall knowledge, attitude and practices (KAP) of Jordanian citizens to the ongoing international situation regarding the emergence and pandemic nature of COVID-19. where N is the sample size, Zα: type one error = 1.96 when α = 5%; Zβ: type two error = 1.28 when β = 10%; Q = 1-P: expected non-prevalence; P = proportion in the population possessing the characteristic of interest (based on the estimate that 50% of the respondents knew general information about COVID-19, its routes of transmission and the main preventative measures), d = one-half of the desired interval of confidence, in this study d = 5%. cache = ./cache/cord-312678-81gnmxbk.txt txt = ./txt/cord-312678-81gnmxbk.txt === reduce.pl bib === id = cord-314651-e4uaw5fy author = Zhao, Guangyu title = Multi-Organ Damage in Human Dipeptidyl Peptidase 4 Transgenic Mice Infected with Middle East Respiratory Syndrome-Coronavirus date = 2015-12-23 pages = extension = .txt mime = text/plain words = 4167 sentences = 184 flesch = 44 summary = After intranasal inoculation with MERS-CoV, the mice rapidly developed severe pneumonia and multi-organ damage, with viral replication being detected in the lungs on day 5 and in the lungs, kidneys and brains on day 9 post-infection. To assess viral replication and histopathologic damage following MERS-CoV infection, mice were euthanized with overdose inhalational carbon dioxide, and tissues included lungs, kidneys, livers, spleens, intestines and brains were harvested on indicated time points. Although a transgenic mouse model expressing human DPP4 was also established, and its immune response was studied after infection with MERS-CoV [16] , the transgenic mice in the study died on day 6 with only progressive pneumonia and mild perivascular cuffing in brain, and no neurological disorder or other multi-organ damage was observed. cache = ./cache/cord-314651-e4uaw5fy.txt txt = ./txt/cord-314651-e4uaw5fy.txt === reduce.pl bib === id = cord-315531-2gc2dc46 author = McGarvey, Peter B. title = Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets date = 2009-09-25 pages = extension = .txt mime = text/plain words = 7016 sentences = 335 flesch = 39 summary = (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. The centers have generated a heterogeneous set of experimental data using various technologies loosely defined as proteomic, but encompassing genomic, structural, immunology and protein interaction technologies, as well as more standard cell and molecular biology techniques used to validate potential targets identified via high-throughput methods. Here we describe in detail a protein-centric approach for systems integration of such a large and heterogeneous set of data from the NIAID Biodefense Proteomics program, and present scientific case studies to illustrate its application to facilitate the basic understanding of pathogen-host interactions and for the identification of potential candidates for therapeutic or diagnostic targets. cache = ./cache/cord-315531-2gc2dc46.txt txt = ./txt/cord-315531-2gc2dc46.txt === reduce.pl bib === id = cord-313107-6cfenpxm author = Singh, Anirudh K. title = Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2889 sentences = 124 flesch = 50 summary = In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. We hypothesized that testing of pooled respiratory samples, collected from potentially infected individuals, could lead to faster laboratory confirmation and quicker containment of the emerging infection in these districts and, thus, undertook this study to evaluate the diagnostic concordance between the strategies of pooled vs. cache = ./cache/cord-313107-6cfenpxm.txt txt = ./txt/cord-313107-6cfenpxm.txt === reduce.pl bib === id = cord-313506-6bb4q7nv author = Sano, Akiko title = Physiological Level Production of Antigen-Specific Human Immunoglobulin in Cloned Transchromosomic Cattle date = 2013-10-24 pages = extension = .txt mime = text/plain words = 6695 sentences = 313 flesch = 54 summary = We previously showed that transchromosomic (Tc) cattle carrying a human artificial chromosome (HAC) comprising the entire unrearranged human immunoglobulin heavy-chain (hIGH) and kappa-chain (hIGK) germline loci (named as κHAC) are capable of producing functional hpAbs when both of the bovine immunoglobulin mu heavy-chains, bIGHM and bIGHML1, are homozygously inactivated (double knockouts or DKO). Therefore, in an effort to improve B cell development and hIgG production in Tc cattle, we sought to enhance pre-BCR function by engineering a new HAC into which, in addition to the hIGH, hIGK and hIGL chromosome loci that carry the entire human immunoglobulin gene repertoire, the human VpreB (hVPREB1) and λ5 (hIGLL1) genomic loci from human chromosome 22 (hChr22) was incorporated, and part of CH and TM domains, CH2-TM, of hIGHM gene, was replaced by the corresponding bovine gene sequence (bovinization of the CH2-TM domains of hIGHM). doi: 10.1371/journal.pone.0078119.g002 DT40 colonies were screened with genomic PCR (data not shown) for the correctly modified hChr2, and clone K53 was identified and selected for the final HAC construction ( Figure 5 ). cache = ./cache/cord-313506-6bb4q7nv.txt txt = ./txt/cord-313506-6bb4q7nv.txt === reduce.pl bib === id = cord-309043-dlmx12vt author = von Brunn, Albrecht title = Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date = 2007-05-23 pages = extension = .txt mime = text/plain words = 6706 sentences = 341 flesch = 52 summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. cache = ./cache/cord-309043-dlmx12vt.txt txt = ./txt/cord-309043-dlmx12vt.txt === reduce.pl bib === id = cord-315343-ywgoqlxj author = Ribeiro, Haroldo V. title = City size and the spreading of COVID-19 in Brazil date = 2020-09-23 pages = extension = .txt mime = text/plain words = 5473 sentences = 233 flesch = 58 summary = Our results indicate small towns are proportionally more affected by COVID-19 during the initial spread of the disease, such that the cumulative numbers of cases and deaths per capita initially decrease with population size. However, during the long-term course of the pandemic, this urban advantage vanishes and large cities start to exhibit higher incidence of cases and deaths, such that every 1% rise in population is associated with a 0.14% increase in the number of fatalities per capita after about four months since the first two daily deaths. Investigating whether this behavior generalizes to other places and how different quantities such as the number of cases and deaths scale with city size are thus important elements for a better understanding of the spreading of COVID-19 in urban areas. To test for an increasing urban advantage for the treatment of COVID-19 during the initial spread of the disease, we investigate the scaling relation between the number of hospital intensive care unit (ICU) beds and city population. cache = ./cache/cord-315343-ywgoqlxj.txt txt = ./txt/cord-315343-ywgoqlxj.txt === reduce.pl bib === id = cord-314908-kp2jznwb author = Roczniewska, Marta title = I believe I can craft! introducing Job Crafting Self-Efficacy Scale (JCSES) date = 2020-08-10 pages = extension = .txt mime = text/plain words = 9293 sentences = 532 flesch = 53 summary = To better predict these behaviors, we introduce the concept of job crafting self-efficacy (JCSE) and define it as an individual's beliefs about their capability to modify the demands and resources of their job to better fit their needs. In this project we integrate Social Cognitive Theory and the Job Demands-Resources model [6, 7] to introduce the concept of job crafting self-efficacy (JCSE). Based on the assumptions of Social Cognitive Theory, we also expect that these specific beliefs predict matching job-crafting behaviors, for example, individuals who feel self-efficacious with respect to increasing challenging job demands are more likely to start new projects or learn about new developments at work and try them out. cache = ./cache/cord-314908-kp2jznwb.txt txt = ./txt/cord-314908-kp2jznwb.txt === reduce.pl bib === id = cord-312817-gskbu0oh author = Witte, Carmel title = Spatiotemporal network structure among “friends of friends” reveals contagious disease process date = 2020-08-06 pages = extension = .txt mime = text/plain words = 5924 sentences = 274 flesch = 44 summary = These results provide empirical evidence that at least some avian mycobacteriosis infections are transmitted between birds, and provide new methods for detecting contagious processes in large-scale global network structures with indirect contacts, even when transmission pathways, timing of cases, or etiologic agents are unknown. Thus, the population represents a group of birds for which 1) a near-complete social network could be assembled from housing records that tracked dynamic movement over time, and 2) avian mycobacteriosis disease status could be determined for any bird that died. Although disease clustering among friends of friends could represent a contagious process, there is a possibility that some of the association could be explained by homophily, i.e., that connected birds could be more alike than the general bird population in terms of species, behavior, susceptibility, enclosure characteristics, etc. For this test, we evaluated disease clustering between a subject and its friends of friends from different enclosures that could not have transmitted infection based on the timing of the contact. cache = ./cache/cord-312817-gskbu0oh.txt txt = ./txt/cord-312817-gskbu0oh.txt === reduce.pl bib === id = cord-317244-4su5on6s author = Maganga, Gael D. title = Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date = 2014-12-31 pages = extension = .txt mime = text/plain words = 3476 sentences = 191 flesch = 50 summary = In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above. cache = ./cache/cord-317244-4su5on6s.txt txt = ./txt/cord-317244-4su5on6s.txt === reduce.pl bib === === reduce.pl bib === id = cord-316319-m6uha1qn author = Daleno, Cristina title = Phylogenetic Analysis of Human Rhinovirus Isolates Collected from Otherwise Healthy Children with Community-Acquired Pneumonia during Five Successive Years date = 2013-11-19 pages = extension = .txt mime = text/plain words = 3942 sentences = 177 flesch = 53 summary = In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). However, most of these studies were carried out in a single year and involved a relatively small number of patients, and only a few analysed specific LRTIs. Consequently, there are few data concerning the circulation of HRVs over a long period of time or the real role of the different species and genotypes in causing LRTIs. The aim of this study was to evaluate the circulation of the different HRV species and genotypes in Italian children with radiographically confirmed CAP during the winter and early spring of five consecutive years as this information could help to develop tailored strategies for the prevention and treatment of pediatric HRV infections. cache = ./cache/cord-316319-m6uha1qn.txt txt = ./txt/cord-316319-m6uha1qn.txt === reduce.pl bib === id = cord-316853-vaea6siv author = Xie, Nanzhen title = Prevalence of depressive symptoms among nurses in China: A systematic review and meta-analysis date = 2020-07-07 pages = extension = .txt mime = text/plain words = 4363 sentences = 229 flesch = 47 summary = Therefore, the primary aim of this study is to quantitatively assess the prevalence of depressive symptoms in nurses from Chinese mainland and its primary related influencing factors by systematic review and meta-analysis. The following information was extracted from all included studies: title, year of publication, province, sample size, number of positive cases, diagnostic methods and other potential factors that may affect the prevalence of depressive symptoms in nurses and that was provided in the studies. In addition, subgroup analysis was performed based on other potential sources of heterogeneity, such as province, regions (Northwest, Southwest, Northeast, South, Central, East and North China), severity of depressive symptoms, department, gender, age, job title, marriage, education background, shift work and hospital grade (if available). cache = ./cache/cord-316853-vaea6siv.txt txt = ./txt/cord-316853-vaea6siv.txt === reduce.pl bib === id = cord-316703-8kxx3034 author = Parera, Mariona title = Canine Hepacivirus NS3 Serine Protease Can Cleave the Human Adaptor Proteins MAVS and TRIF date = 2012-08-01 pages = extension = .txt mime = text/plain words = 4193 sentences = 220 flesch = 52 summary = The aim of this study was to investigate whether the NS3/4A serine protease of CHV specifically cleaves human mitochondrial antiviral signaling protein (MAVS) and Toll-IL-1 receptor domain-containing adaptor inducing interferon-beta (TRIF). The target specificity for the MAVS and TRIF cleavage sites was tested by coexpressing them with CHV or HCV NS3/4A protease constructs. coli cells coexpressing the lambda cI repressor with either MAVS or TRIF cleavage site and a CHV NS3/4A construct, lambda phage replicated up to 2,000-fold more efficiently than in cells expressing a CHV protease variant that included a substitution in catalytic residue S139 ( Fig. 3A and 3B). In this study, we tested the ability of CHV NS3/4A protease to specifically cleave the human adaptor proteins MAVS and TRIF. Canine orthologs of human MAVS and TRIF differ in sequence at the cleavage site processed by HCV NS3/4A protease; therefore, they were not tested in this study. cache = ./cache/cord-316703-8kxx3034.txt txt = ./txt/cord-316703-8kxx3034.txt === reduce.pl bib === === reduce.pl bib === id = cord-318614-518giv0m author = Tsai, Jih-Jin title = A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos date = 2019-07-10 pages = extension = .txt mime = text/plain words = 4825 sentences = 213 flesch = 49 summary = A pan-dengue virus (DENV) RT-iiPCR, targeting the 5' untranslated region, was validated previously on the semi-automated POCKIT combo system (involving separate devices for nucleic acid extraction and PCR amplification/detection) to offer performance comparable to a laboratory real-time PCR. CONCLUSIONS/SIGNIFICANCE: With performance comparable to a previously validated system, the fully-automated PCR system allows applications of the pan-DENV reagent as a useful tool near points of need to facilitate easy, fast and effective detection of dengue virus and help mitigate versatile public health challenges in the control and management of dengue disease. Testing with the pan-DENV RT-iiPCR, the analytical and clinical performance of the fully automatic POCKIT Central system was comparable to those of the semi-automatic POCKI combo system, which was validated previously to offer performances equivalent to the CDC DENV1-4 real-time RT-PCR for the detection of DENV in human serum [7, 24, 26] . cache = ./cache/cord-318614-518giv0m.txt txt = ./txt/cord-318614-518giv0m.txt === reduce.pl bib === id = cord-317912-v2wovcqd author = Akmatov, Manas K. title = Equivalence of Self- and Staff-Collected Nasal Swabs for the Detection of Viral Respiratory Pathogens date = 2012-11-14 pages = extension = .txt mime = text/plain words = 3488 sentences = 176 flesch = 57 summary = found similar detection rates for respiratory pathogens between self-and staffcollected midturbinate swabs when one staff-collected and one selfcollected swab were taken from opposite nostrils during the same visit to a campus health center [5] . In the study center, a trained staff member (A.G.) obtained a nasal swab (regular flocked swab, Copan, Brescia, Italy, product number 359C) from the participant's left nostril and instructed him/her how to perform a self-swab. Sensitivity and specificity of self-collected swabs, obtained in the study center, to detect viral respiratory pathogens (compared to staff-collected swabs)*. The detection of a viral pathogen was independent of the amount of b-actin DNA in both staff-and self-swabs collected on day 1 (Fig. 4) . This prospective study comparing staff-and self-collected nasal swabs for the detection of ARI pathogens clearly demonstrated the validity of self-swabbing; specifically, self-swabbing was not inferior in terms of acceptance, satisfaction, sample adequacy, and viral detection rate. cache = ./cache/cord-317912-v2wovcqd.txt txt = ./txt/cord-317912-v2wovcqd.txt === reduce.pl bib === id = cord-318008-4s9eoae3 author = Parsons Leigh, Jeanna title = A national cross-sectional survey of public perceptions of the COVID-19 pandemic: Self-reported beliefs, knowledge, and behaviors date = 2020-10-23 pages = extension = .txt mime = text/plain words = 5682 sentences = 268 flesch = 48 summary = We assessed self-reported public perceptions related to COVID-19 including, beliefs (e.g., severity, concerns, health), knowledge (e.g., transmission, information sources), and behaviors (e.g., physical distancing) to understand perspectives in Canada and to inform future public health initiatives. We conducted a national survey of adults residing in Canada to gain a better understanding of public perceptions in several important domains-beliefs (e.g. severity of pandemic, concerns, impact on health), knowledge acquisition (e.g. sources, topics), and behaviors (e.g. isolation and physical distancing)-related to the COVID-19 pandemic. Our study provides a national cross-sectional description of public perceptions, knowledge and behaviors related to COVID-19 in the context of the evolving pandemic, adding to survey data published early in the outbreak [16] [17] [18] . In our survey, respondents from Ontario and Québec reported the least amount of trust in Canadian government and news sources and these were also the same provinces with the highest number of confirmed COVID-19 cases in Canada (32% and 51%, respectively). cache = ./cache/cord-318008-4s9eoae3.txt txt = ./txt/cord-318008-4s9eoae3.txt === reduce.pl bib === id = cord-319706-2e9jrv0s author = Ebinger, Joseph E. title = Pre-existing traits associated with Covid-19 illness severity date = 2020-07-23 pages = extension = .txt mime = text/plain words = 4904 sentences = 219 flesch = 40 summary = For all patients considered to have Covid-19, based on direct or documented laboratory test result and suggestive signs and/or symptoms, we obtained information from the electronic health record (EHR) and verified data for the following demographic and clinical characteristics: age at the time of diagnosis; sex; race; ethnicity; smoking status defined as current versus prior, never, or unknown; comorbidities, including obesity, as clinically assessed and documented by a provider with ICD-10 coding; and, chronic use of angiotensin converting enzyme (ACE) inhibitor or angiotensin II receptor blocker (ARB) medications. For the primary outcome of illness severity, categorized by escalating levels of care (i.e., hospitalization, intensive care, intubation), the pre-existing characteristics that demonstrated statistical significance in age-and sex-adjusted models included older age, male sex, African American race, obesity, hypertension, diabetes mellitus, and the Elixhauser comorbidity score ( Table 2 ; Fig 3) . cache = ./cache/cord-319706-2e9jrv0s.txt txt = ./txt/cord-319706-2e9jrv0s.txt === reduce.pl bib === === reduce.pl bib === id = cord-319538-bawzonq1 author = Krause, Martin title = Association between procalcitonin levels and duration of mechanical ventilation in COVID-19 patients date = 2020-09-18 pages = extension = .txt mime = text/plain words = 2565 sentences = 138 flesch = 35 summary = Based on observational studies from the epicenters of the pandemic in Wuhan, China, the Lombardy region in Italy, and the New York City area in the United States, a significant portion of patients diagnosed with coronavirus disease 2019 (COVID19) were admitted to the intensive care unit (ICU) for ventilatory support: Between 17%-24% of hospitalized patients and up to 72% of patients admitted to the ICU have required invasive mechanical ventilation [2] [3] [4] [5] . We aimed to identify if plasma procalcitonin levels on admission are associated with the duration of mechanical ventilation (primary outcome), 28-day mortality, and time to intubation (secondary outcomes) in a cohort of COVID-19 patients requiring mechanical ventilation. In the univariate analysis of our observational cohort study, procalcitonin levels >0.1 ng/ml on admission were associated with prolonged mechanical ventilation in critically ill COVID-19 patients. cache = ./cache/cord-319538-bawzonq1.txt txt = ./txt/cord-319538-bawzonq1.txt === reduce.pl bib === id = cord-319845-oob2ktnz author = Proença-Modena, José Luiz title = Detection of Human Bocavirus mRNA in Respiratory Secretions Correlates with High Viral Load and Concurrent Diarrhea date = 2011-06-20 pages = extension = .txt mime = text/plain words = 5857 sentences = 269 flesch = 51 summary = Therefore, in order to test whether active viral replication of human bocavirus is associated with respiratory diseases and to understand the clinical impact of this virus in patients with these diseases, we performed a 3-year retrospective hospital-based study of HBoV in outpatients and inpatients with symptoms of Acute Respiratory Infections (ARI) in Brazil. This article reports a cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, in which the shedding of VP1 mRNA in respiratory secretions was used as surrogate marker for active HBoV replication, to look for correlations with viral load, and presence of particular clinical manifestations and simultaneous detection of other respiratory viruses. The results of this cross-sectional study of HBoV in ARI patients from Ribeirão Preto, Brazil, indicate that shedding of VP1 mRNA in respiratory secretions, as a marker of HBoV replication, correlates positively with high viral load, presence of diarrhea, and lack of co-infection by other respiratory viruses. cache = ./cache/cord-319845-oob2ktnz.txt txt = ./txt/cord-319845-oob2ktnz.txt === reduce.pl bib === id = cord-321705-6a7avlro author = Hou, Tianya title = Social support and mental health among health care workers during Coronavirus Disease 2019 outbreak: A moderated mediation model date = 2020-05-29 pages = extension = .txt mime = text/plain words = 5372 sentences = 281 flesch = 46 summary = The current study examined the effect of social support on mental health of health care workers and its underlying mechanisms regarding the mediating role of resilience and moderating role of age during the epidemic. METHODS: Social Support Rating Scale (SSRS), Connor-Davidson Resilience scale (CD-RISC) and Symptom Checklist 90 (SCL-90) were administrated among 1472 health care workers from Jiangsu Province, China during the peak period of COVID-19 outbreak. Thus, the present research employed a sample of Chinese health care workers during COVID-19 outbreak to explore a conceptual model in which, on the one hand, resilience mediated the association between social support and mental health; On the other hand, the indirect relationships between social support and mental health via resilience were moderated by age group. Considering the present study was to compare the indirect effect of social support on mental health via resilience between the young and middle-aged heath care workers, participants aged 50 or over were excluded. cache = ./cache/cord-321705-6a7avlro.txt txt = ./txt/cord-321705-6a7avlro.txt === reduce.pl bib === id = cord-317779-j67vb7f3 author = Irizarry, Kristopher J. L. title = RNA sequencing demonstrates large-scale temporal dysregulation of gene expression in stimulated macrophages derived from MHC-defined chicken haplotypes date = 2017-08-28 pages = extension = .txt mime = text/plain words = 9733 sentences = 443 flesch = 42 summary = Our experimental design leveraged an initial 6 day window for monocytes to differentiate into macrophages, which was followed by IFNγ stimulation between 1 and 24 h to further characterize subsequent RNA gene expression and the molecular basis for dramatically different nitric oxide production and immune function between the B2 and the B19 haplotype chicken macrophages The t-3 day time point, representing 3 days of differentiation in cell culture, exhibited the greatest expression of genes with a total of 11,429 expressed in both B19 and B2 birds while just 4068 genes lacked evidence of expression in both haplotypes. Overall, the gene enrichment analysis of the RNA sequence data provides a cellular-level picture of the specific biological processes that occur over time following activation of monocyte-derived macrophages. cache = ./cache/cord-317779-j67vb7f3.txt txt = ./txt/cord-317779-j67vb7f3.txt === reduce.pl bib === === reduce.pl bib === id = cord-319921-uxtydu60 author = Meli, Marina L. title = Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus) date = 2009-03-09 pages = extension = .txt mime = text/plain words = 5506 sentences = 259 flesch = 48 summary = METHODOLOGY/ PRINCIPAL FINDINGS: We systematically analyzed the prevalence and importance of seven viral, one protozoan (Cytauxzoon felis), and several bacterial (e.g., hemotropic mycoplasma) infections in 77 of approximately 200 remaining free-ranging Iberian lynxes of the Doñana and Sierra Morena areas, in Southern Spain, between 2003 and 2007. Furthermore, the presence of feline leukemia virus (FeLV) provirus was recently reported in six samples originating from both the Doñ ana and Sierra Morena areas in southern Spain between 1994 and 2003 [29] . Thus, in the present study, we report on the prevalence of the aforementioned pathogens and we describe a dramatic FeLV epidemic, which most likely led to the death of 6 Iberian lynxes within a 6-months period in 2007, its possible origin, and its relationship to other infectious agents. However, endogenous FeLV sequences related to those of domestic cats are apparently not present in Iberian lynxes: only 5 of the 77 lynxes tested displayed weak signals by quantitative realtime PCR, which is not compatible with presence of enFeLV sequences. cache = ./cache/cord-319921-uxtydu60.txt txt = ./txt/cord-319921-uxtydu60.txt === reduce.pl bib === id = cord-320938-f526k9q1 author = Chen, Hongjun title = Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date = 2012-09-28 pages = extension = .txt mime = text/plain words = 8614 sentences = 455 flesch = 60 summary = In order to determine whether a Flu PCR amplicon could be transfected into cells and be amplified by the influenza polymerase complex, a PCR product was produced encoding the GFP reporter gene in negative orientation flanked by the influenza segment 7 untranslated regions (UTRs) and further flanked by the human pol1 promoter and the mouse t1 termination signal, pol1EGFPt1 (Fig. 1A, Fig. S1A , Table S1 ). doi:10.1371/journal.pone.0046378.g001 Efficient influenza virus rescue using Flu PCR amplicons in either ''1+7'' or ''2+6'' modes The pol1HA pdm t1 or pol1HA D072 t1 HA PCR amplicons (Table 1) were co-transfected into co-cultured 293T/MDCK cells in a ''1+7'' mode along with 7 RG plasmids encoding the corresponding additional gene segments from the influenza A/Puerto Rico/ 8/1934 (H1N1) strain (PR8). cache = ./cache/cord-320938-f526k9q1.txt txt = ./txt/cord-320938-f526k9q1.txt === reduce.pl bib === id = cord-321855-7b1c2xdh author = Alshami, Alanoud title = Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date = 2020-10-30 pages = extension = .txt mime = text/plain words = 3380 sentences = 190 flesch = 56 summary = title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. cache = ./cache/cord-321855-7b1c2xdh.txt txt = ./txt/cord-321855-7b1c2xdh.txt === reduce.pl bib === id = cord-320466-l7017jis author = Akgun, Emel title = Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date = 2020-10-20 pages = extension = .txt mime = text/plain words = 3722 sentences = 226 flesch = 42 summary = Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified up-regulated proteins Myeloperoxidase, Myeloblastin, Neutrophil Elastase, Cathepsin G, and Azurocidin (MPO, PRTN3, ELANE, CTSG, and AZU1) in nasooropharyngeal swab samples are discussed to highlight the molecular mechanism changes in the site of infection. Pathway analysis of the significantly altered protein levels between COVID-19 positive and negative patients' naso-oropharyngeal swab samples were analyzed using the STRING online database. In SARS-CoV-2 patients' naso-oropharyngeal samples, we have identified azurophilic granule (AG) proteins like Myeloperoxidase (MPO), elastase (ELANE), cathepsin G (CTSG), azurocidin 1 (AZU1) and proteinase 3 (PRTN3) to be highly overexpressed. The alterations of various proteins in SARS-CoV-2 infected patients' naso-oropharyngeal samples depict the molecular changes that govern the host antiviral defense system. cache = ./cache/cord-320466-l7017jis.txt txt = ./txt/cord-320466-l7017jis.txt === reduce.pl bib === id = cord-321438-llnqzkqt author = Ma, Ruili title = Proteome Profile of Swine Testicular Cells Infected with Porcine Transmissible Gastroenteritis Coronavirus date = 2014-10-21 pages = extension = .txt mime = text/plain words = 7110 sentences = 310 flesch = 43 summary = The purpose of this paper was to analyze altered cellular protein levels in porcine transmissible gastroenteritis coronavirus (TGEV)-infected swine testicular (ST) cells in order to determine potential virus-host interactions. To our knowledge, this study is the first time the response profile of ST host cells following TGEV infection has been analyzed using iTRAQ technology, and our description of the late proteomic changes that are occurring after the time of vigorous viral production are novel. Moreover, at the later time point, 64 hpi, our GO term analysis also indicated that a significant number of the differentially expressed proteins were related to cellular stress (p = 8.18E-4), generation of precursor metabolites and energy (p = 2.74E-3), cell motility (p = 6.71E-3), protein complex assembly (p = 4.69E-2), growth (p = 3.87E-2), developmental maturation (p = 1.53E-2), and immune system processes (p = 4.67E-2) ( Table 2) . Prior to proteomic analysis, we determined which time points to investigate following infection by observing the morphological changes and analyzing viral gene expression dynamics in the TGEV infected cells. cache = ./cache/cord-321438-llnqzkqt.txt txt = ./txt/cord-321438-llnqzkqt.txt === reduce.pl bib === id = cord-321834-n5w88l23 author = Huang, Cheng-Yang title = Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases date = 2015-05-19 pages = extension = .txt mime = text/plain words = 5231 sentences = 297 flesch = 47 summary = Although the inhibitory effects of these flavonoids on dihydropyrimidinase were substrate-dependent, dihydromyricetin significantly inhibited dihydropyrimidinase with IC(50) values of 48 and 40 μM for the substrates dihydrouracil and 5-propyl-hydantoin, respectively. In this study, we investigated the effects of the substrates and inhibitors of allantoinase and dihydroorotase, including the flavonols myricetin, quercetin, kaempferol, and galangin, on inhibiting the catalytic activity of a putative dihydropyrimidinase from P. Although dihydromyricetin and myricetin were docked Inhibition of Dihydropyrimidinase by Flavonoids into the active site pocket of dihydropyrimidinase, their binding modes differed. In this study, we showed that dihydromyricetin, a flavonol, significantly inhibited the catalytic activities of dihydropyrimidinase toward both the natural substrate dihydrouracil and xenobiotic substrate 5-propyl-hydantoin (Fig 3) . For example, as shown in Fig 3, the inhibitory effect of kaempferol on the activity of dihydropyrimidinase was significant only with dihydrouracil as a substrate (with IC 50 value of 50 ± 2 μM), but not with 5-propyl-hydantoin. cache = ./cache/cord-321834-n5w88l23.txt txt = ./txt/cord-321834-n5w88l23.txt === reduce.pl bib === id = cord-320091-2lrqubdl author = Badawi, Alaa title = Prevalence of chronic comorbidities in dengue fever and West Nile virus: A systematic review and meta-analysis date = 2018-07-10 pages = extension = .txt mime = text/plain words = 8511 sentences = 411 flesch = 46 summary = The objective of this study is to systematically review the existing literature on the prevalence of the most common non-communicable comorbidities related to the cluster of metabolic syndromes-associated diseases, such as diabetes mellitus, heart diseases, hypertension, asthma, stroke and obesity in flavivirus infections and to evaluate the difference of their prevalence in severe vs. Data extracted from the selected studies in duplicate by two reviewers and included the first author's name, publication date, country, dates of recruitment, total sample size (divided to males and females), age estimates (from reported mean, median or the mid-point for age range of the highest subject frequency), procedures for case identification, type of flavivirus infection, severity of infection, prevalence of clinical manifestations (mild symptoms such as fever, headache, muscle pain, rash, and malaise together with severe symptoms as described below) and percentage of comorbidities including diabetes (both type I and type II, if mentioned), hypertension, heart diseases (due to the small sample size of individual conditions, we (Table 1) . cache = ./cache/cord-320091-2lrqubdl.txt txt = ./txt/cord-320091-2lrqubdl.txt === reduce.pl bib === id = cord-319190-esjfhztp author = Lu, Xi title = In Vitro Activity of Sodium New Houttuyfonate Alone and in Combination with Oxacillin or Netilmicin against Methicillin-Resistant Staphylococcus aureus date = 2013-07-02 pages = extension = .txt mime = text/plain words = 3288 sentences = 185 flesch = 45 summary = title: In Vitro Activity of Sodium New Houttuyfonate Alone and in Combination with Oxacillin or Netilmicin against Methicillin-Resistant Staphylococcus aureus In synergy studies, the combinations of SNH-oxacillin, SNH-cephalothin, SNH-meropenem and SNH-netilmicin showed synergistic effects against 12 MRSA strains with median fractional inhibitory concentration (FIC) indices of 0.38, 0.38, 0.25 and 0.38 in checkerboard assays. Combinations of sub-MIC levels of SNH and oxacillin or netilmicin significantly improved the in vitro antibacterial activity against MRSA compared with either drug alone. In this study, we examined the in vitro activity of SNH and its potential for synergy when combined with antibiotics against a collection of hospital-associated MRSA (HA-MRSA) isolates recovered from various clinical samples in recent years. This study evaluated activity of SNH against MRSA and its potential for synergistic effect when combined with antibiotics. SNH in combination with OXA exhibited synergistic effect for all the five MRSA strains tested in time-kill analysis. cache = ./cache/cord-319190-esjfhztp.txt txt = ./txt/cord-319190-esjfhztp.txt === reduce.pl bib === id = cord-322414-dpx191xh author = Harke, Nina N. title = To defer or not to defer? A German longitudinal multicentric assessment of clinical practice in urology during the COVID-19 pandemic date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3778 sentences = 168 flesch = 43 summary = MATERIAL AND METHODS: An email was sent to 66 urological hospitals with focus on robotic surgery (RS) including a link to a questionnaire (e.g. bed/staff capacity, surgical caseload, protection measures during RS) that covered three time points: a representative baseline week prior to COVID-19, the week of March 16(th)-22(nd) and April 20(th)-26(th) 2020. The complete survey (S1 File) included detailed queries on numbers of available hospital beds and operating room (OR) capacity, staff members, surgical caseloads with subcategorization of surgeries at three different time points: week 1) baseline week that portrays the numbers of a regular/representative week before the outbreak of COVID-19, week 2) March 16 th to 22 nd 2020 which represent the first week after the lockdown in Germany (confirmed cases in Germany on March 16 th 2020: 6,012 with 13 deaths) and week 3) April 20 th to 26 th (confirmed cases in Germany on April 20 th 2020: 141,672; 4,404 deaths and approximately 91,500 recovered) [1] . cache = ./cache/cord-322414-dpx191xh.txt txt = ./txt/cord-322414-dpx191xh.txt === reduce.pl bib === id = cord-318845-w7q5o8wc author = Pendell, Dustin L. title = Economic Assessment of FMDv Releases from the National Bio and Agro Defense Facility date = 2015-06-26 pages = extension = .txt mime = text/plain words = 8168 sentences = 409 flesch = 48 summary = This study evaluates the economic consequences of hypothetical foot-and-mouth disease releases from the future National Bio and Agro Defense Facility in Manhattan, Kansas. To assess the economic impacts of unintentional FMDv releases from NBAF, we follow [4, 7, [21] [22] to link supply shocks from an animal disease spread model with a multi-commodity, multi-market partial equilibrium model. To determine the total economic impact for a scenario, the changes in producer returns to capital and management and consumer welfare, government indemnification and non-indemnification expenditures, and the costs to the non-agricultural regional sector were summed together. Because the duration of the FMD outbreaks and number of animals culled and vaccinated are similar to the aerosol scenarios, the total economic impacts of the transference release scenarios are similar to impacts of an aerosol release, including the distribution of impacts by production types across time. cache = ./cache/cord-318845-w7q5o8wc.txt txt = ./txt/cord-318845-w7q5o8wc.txt === reduce.pl bib === id = cord-319675-mwy3t1ny author = Gu, Li title = Sustained Viremia and High Viral Load in Respiratory Tract Secretions Are Predictors for Death in Immunocompetent Adults with Adenovirus Pneumonia date = 2016-08-17 pages = extension = .txt mime = text/plain words = 3081 sentences = 164 flesch = 56 summary = At admission (on day 5–7 after illness onset), the patients in fatal cases presented higher initial viral loads in respiratory tract secretions (8.578 ± 2.115 vs 6.263 ± 1.225 Log(10) copies/ml, p = 0.023). Our results suggest that a higher initial viral load (10 8 copy/ml) in the respiratory tract samples on day 5-7 after disease onset is a predictor for fatal clinical outcome. In one case, as shown in Fig 2, even though the patient presented with a higher viral load (10 8.32 copies / ml) in tracheal aspiration, which may be associated fatal outcome, his clinical manifestation recovered gradually with a downward trend in the viral load in respiratory tract and whole blood samples. A higher initial viral load (10 8 copy/ml) in the respiratory tract on day 5-7 after disease onset and sustained viremia for 2 weeks or more may be associated with fatal clinical outcomes. cache = ./cache/cord-319675-mwy3t1ny.txt txt = ./txt/cord-319675-mwy3t1ny.txt === reduce.pl bib === id = cord-323433-9km824uh author = van den Wijngaard, Cees C. title = Syndromic Surveillance for Local Outbreaks of Lower-Respiratory Infections: Would It Work? date = 2010-04-29 pages = extension = .txt mime = text/plain words = 4787 sentences = 244 flesch = 49 summary = We evaluated how many LRI-clusters were detected in 1999–2006 and assessed likely causes for the cluster-signals by looking for significantly higher proportions of specific hospital discharge diagnoses (e.g. Legionnaires disease) and overlap with regional influenza elevations. Furthermore, since comparatively few new clusters per year were observed that would prompt investigation, syndromic hospital-surveillance could be a valuable tool for detection of local LRI-outbreaks. Geographic analysis methods -such as space-time scan statistics -may further increase the sensitivity of syndromic surveillance for detection of local outbreaks or of regional differences in regular seasonal epidemic diseases [2, 6] . The objective of this study was to evaluate to what extent syndromic surveillance detects local outbreaks of lower-respiratory infections (LRIs) without swamping true signals by false alarms. Of these, 6 belonged to influenza and/ or RSV related clusters (Figure 2a When repeating the weekly analyses with restricted time or spatial windows, both Legionnaires' disease outbreaks were still detected with the same timeliness. cache = ./cache/cord-323433-9km824uh.txt txt = ./txt/cord-323433-9km824uh.txt === reduce.pl bib === id = cord-324405-6uanhe2p author = Burke, Rachel M. title = Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date = 2020-09-02 pages = extension = .txt mime = text/plain words = 6616 sentences = 242 flesch = 41 summary = To interrupt transmission and facilitate early identification of secondary cases (i.e., transmissions of SARS-CoV-2 from the original travel-related case patient to a close contact), public health authorities at the state, county, and local levels, in consultation with subject-matter experts from the U.S. Centers for Disease Control and Prevention (CDC), mobilized rapidly to place the patients under appropriate isolation and identify contacts exposed to these patients. To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with � 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members and some healthcare personnel. cache = ./cache/cord-324405-6uanhe2p.txt txt = ./txt/cord-324405-6uanhe2p.txt === reduce.pl bib === id = cord-322827-h33su548 author = Guan, Lili title = Unlocking Patients with Mental Disorders Who Were in Restraints at Home: A National Follow-Up Study of China’s New Public Mental Health Initiatives date = 2015-04-07 pages = extension = .txt mime = text/plain words = 5056 sentences = 232 flesch = 50 summary = BACKGROUND: In 2005, China implemented a demonstration program known as "686" to scale-up nation-wide basic mental health services designed to improve access to evidence-based care and to promote human rights for people with severe mental disorders. This program has contributed to improving care for patients with severe mental disorders, including schizophrenia, psychosis, bipolar disorder and schizoaffective disorder, through increasing access to treatment and integrating hospital and community services designed to provide continuity of evidence-based care and to address patients' rights. Patients with severe mental disorders were followed-up about their medication adherence, mental health status, social functioning and family burden in 2009 and 2012 to investigate the changes over time following the unlocking efforts. The finding that more than 92% of those unlocked and entered into continuous treatment by the 686 Program remained free of restraints by 2012 demonstrates the feasibility of improving the human rights of persons with severe mental illness by increasing access to mental health care in the community [22] , even with limited societal resources. cache = ./cache/cord-322827-h33su548.txt txt = ./txt/cord-322827-h33su548.txt === reduce.pl bib === id = cord-322533-adqqm0n9 author = Sha, Dexuan title = Spatiotemporal analysis of medical resource deficiencies in the U.S. under COVID-19 pandemic date = 2020-10-14 pages = extension = .txt mime = text/plain words = 5189 sentences = 232 flesch = 49 summary = The study duration was mainly from February 15, 2020 to May 1, 2020 in the U.S. Multiple data sources were used to extract local population, hospital beds, critical care staff, COVID-19 confirmed case numbers, and hospitalization data at county level. Then, we developed two medical resource deficiency indices that measured the local medical burden based on the number of accumulated active confirmed cases normalized by local maximum potential medical resources, and the number of hospitalized patients that can be supported per ICU bed per critical care staff, respectively. In this report, three fundamental elements or features, i.e. ventilators, ICU beds, and critical care staff (CCS) were identified as medical resources to plan for or manage a COVID-19 pandemic, and it would be wise to consider the interconnections among these factors in a spatiotemporal data analysis framework. cache = ./cache/cord-322533-adqqm0n9.txt txt = ./txt/cord-322533-adqqm0n9.txt === reduce.pl bib === id = cord-323330-ghwhgkdm author = Ekundayo, Temitope Cyrus title = A global bibliometric analysis of Plesiomonas-related research (1990 – 2017) date = 2018-11-29 pages = extension = .txt mime = text/plain words = 4900 sentences = 279 flesch = 40 summary = Here, we carried out a bibliometric survey that aimed to examine publication trends in Plesiomonas-related research by time and place, international collaborative works, identify gaps and suggest directions for future research. The articles were evaluated in terms of annual and country-specific output, theme, domain clusters, international collaboration networks, citations, topical evolution related to keywords and co-occurrence networks, co-authorship, and funding. We used the search term "Plesiomonas shigelloides" to identify primary research articles published between 1990 and 2017. Health emergencies (e.g., outbreaks of infection) relating to emerging viral pathogens including Zika and Chikungunya viruses have driven the generation of new scientific knowledge, resulting in a significant increase in the number of research articles on these subjects [68] . The United States and Sweden dominated the list of top 20 countries most actively researching Plesiomonas in terms of numbers of articles and citations. cache = ./cache/cord-323330-ghwhgkdm.txt txt = ./txt/cord-323330-ghwhgkdm.txt === reduce.pl bib === id = cord-324410-be2ith3z author = Wang, Qi title = Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry date = 2007-06-13 pages = extension = .txt mime = text/plain words = 3772 sentences = 160 flesch = 48 summary = These results demonstrate the significant influence of crystal packing on small molecule complexation and suggest that EUDOC is able to predict small-molecule complexes and that it is useful for the design of new materials, molecular sensors, and multimeric inhibitors of protein-protein interactions. To expand the application of the EUDOC program to supramolecular chemistry, we tested its ability to reproduce the crystal structures of small-molecule guest-host complexes. Herein we report the results of our docking studies with 161 selected crystal structures of small-molecule guest-host complexes using the EUDOC program. These results show that the program is able to reproduce all 161 crystal structures and that the average interaction energy of these small-molecule complexes (250.1 kcal/mol) is nearly half of that of the 153 small molecule-bound protein complexes we studied in previous tests (2108.5 kcal/mol). The results also demonstrate the significant influence of crystal packing on small-molecule complex crystal structures and suggest that the EUDOC program is able to predict 3D structures of small-molecule guest-host complexes with reasonable reliability. cache = ./cache/cord-324410-be2ith3z.txt txt = ./txt/cord-324410-be2ith3z.txt === reduce.pl bib === id = cord-327199-ggomuomb author = Moerdyk-Schauwecker, Megan title = Cellular Proteins Associated with the Interior and Exterior of Vesicular Stomatitis Virus Virions date = 2014-08-08 pages = extension = .txt mime = text/plain words = 6425 sentences = 288 flesch = 43 summary = In another example, the presence of host complement control proteins such as CD46, CD55 and CD59 in the viral envelope has been shown to protect against antibody dependent complement mediated virus lysis in several viruses including human T cell leukemia/ lymphoma virus type I [16] , human cytomegalovirus [16] , hepatitis C virus [17] , HIV-1 [18, 19] , extracellular enveloped vaccinia virus [20] , simian virus 5 [21] and mumps virus [21] . As discussed in the previous section, proteins not associated with the interior of the virion, including proteins embedded in the host derived viral envelope, can be identified by their absence in ProK treated samples or by a size shift upon ProK treatment. While many of the proteins identified in VSV virions appear to be associated with viral assembly, budding or the host-derived viral envelope, they may also have additional functions that affect virus replication. cache = ./cache/cord-327199-ggomuomb.txt txt = ./txt/cord-327199-ggomuomb.txt === reduce.pl bib === id = cord-321624-z2mntwef author = Kowitdamrong, Ekasit title = Antibody responses to SARS-CoV-2 in patients with differing severities of coronavirus disease 2019 date = 2020-10-09 pages = extension = .txt mime = text/plain words = 3382 sentences = 184 flesch = 57 summary = AIM: To investigate SARS-CoV-2 IgA and IgG antibodies in Thai patients with differing severities of COVID-19. The objective of this study was to investigate the response of IgA and IgG antibodies to SARS--CoV-2 in serial blood samples collected from a population of Thai patients with confirmed COVID-19, and the association of these responses with the severity of the illness. The second subgroup included 49 plasma samples collected from May 1 to May 31, 2020, from patients under investigation (PUI) for COVID-19 with RT-PCR results that were negative for SARS-CoV-2. In the present study, 30% of COVID-19 patients developed positive IgA antibodies very early, within 3 days after the onset of symptoms. In the present study, 20% of the patients with mild symptoms did not develop any IgG antibodies specific to COVID-19, even after 2 weeks after the onset of symptoms. cache = ./cache/cord-321624-z2mntwef.txt txt = ./txt/cord-321624-z2mntwef.txt === reduce.pl bib === id = cord-326011-5rmhjbri author = Cui, Dawei title = Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study date = 2016-11-01 pages = extension = .txt mime = text/plain words = 3508 sentences = 172 flesch = 44 summary = title: Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality worldwide in children aged <5 years and older adults with acute lower respiratory infections (ALRIs). Clinical and epidemiologic data pertaining to hospitalized patients of all ages with laboratory-confirmed RSV infection by PCR assay were collected and analyzed in this study. Respiratory syncytial virus (RSV) is a leading cause of viral infection in children and older adults worldwide, particularly young children aged <5 years [1] . In this study, we aimed to evaluate the epidemiology, clinical characteristics and management of ALRIs caused by RSV infection among hospitalized patients of all age groups in eastern China between 2009 and 2013 in a hospital-based surveillance study. Clinical characteristics and risk factors of severe respiratory syncytial virus-associated acute lower respiratory tract infections in hospitalized infants cache = ./cache/cord-326011-5rmhjbri.txt txt = ./txt/cord-326011-5rmhjbri.txt === reduce.pl bib === id = cord-325113-sou8xyld author = Kuiper, Johannes W. P. title = Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date = 2020-11-02 pages = extension = .txt mime = text/plain words = 4973 sentences = 241 flesch = 51 summary = The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. cache = ./cache/cord-325113-sou8xyld.txt txt = ./txt/cord-325113-sou8xyld.txt === reduce.pl bib === id = cord-324091-nljd2ok1 author = Gordon, Jennifer L. title = The psychological impact of fertility treatment suspensions during the COVID-19 pandemic date = 2020-09-18 pages = extension = .txt mime = text/plain words = 4497 sentences = 263 flesch = 49 summary = PURPOSE: To examine the psychological impact of fertility treatment suspensions resulting from the COVID-19 pandemic and to clarify psychosocial predictors of better or worse mental health. Participants completed a battery of questionnaires assessing depressive symptoms, perceived mental health impact, and change in quality of life related to treatment suspensions. Table 2 depicts the correlation between three personality traits (trait optimism, defensive pessimism, and intolerance of uncertainty) that were considered potentially relevant under the current circumstances, in relation to the overall change in quality of life and the mental health impact attributed to fertility treatment suspensions. The psychological impact of fertility treatment suspensions during the COVID-19 pandemic the final subscales are as follows: 1) avoidance, α = 0.82, 2) active coping, α = 0.71, 3) finding meaning, α = 0.72, 4) defensive pessimism, α = 0.66, 5) optimism, α = 0.80, 6) seek social support, α = 0.77, and 7) behavioural engagement, α = 0.67. cache = ./cache/cord-324091-nljd2ok1.txt txt = ./txt/cord-324091-nljd2ok1.txt === reduce.pl bib === id = cord-327534-f2wvh6la author = Zhou, Peng title = IRF7 in the Australian Black Flying Fox, Pteropus alecto: Evidence for a Unique Expression Pattern and Functional Conservation date = 2014-08-06 pages = extension = .txt mime = text/plain words = 7736 sentences = 377 flesch = 52 summary = To explore the role of bat IRF7 in the regulation of the IFN response, we performed sequence and functional analysis of IRF7 from the pteropid bat, Pteropus alecto. Regions containing putative IRF3 or IRF7 binding sites were identified from 2221 to 270 bp from the ATG of the bat IFN-b gene by comparison with human IFN promoters and cloned into the pGL4.1 expression vector (Promega). Analysis of the putative bat IRF7 promoter region around 1000 bp upstream of the start site of the ORF resulted in the identification of two IFN stimulated response elements (ISREs) and one nuclear factor kappa B (NF-kB) binding site. Our results demonstrate that even with a significant difference in its MyD88 binding region, bat IRF7 is still capable of inducing IFN-a transcription via MyD88 ( Figure 5 ). cache = ./cache/cord-327534-f2wvh6la.txt txt = ./txt/cord-327534-f2wvh6la.txt === reduce.pl bib === id = cord-322446-ddv86eoy author = Sharma, Kulbhushan title = SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus date = 2011-05-27 pages = extension = .txt mime = text/plain words = 8437 sentences = 512 flesch = 56 summary = We found that an export signal deficient SARS-CoV 9b protein induces apoptosis in transiently transfected cells and showed elevated caspase-3 activity. Analysis of 9b-YFP localization showed that in addition to the extranuclear region, some amount of 9b was also present within the nucleus similar to the SARS-CoV infected cells (Fig. S1 , panel (i), (ii) and (iii)). Panel (ii) shows that even in in-vitro transport assay, SARS-CoV 9b protein localizes in both cytoplasm as well as nucleus. As shown in panel (v), the SARS-CoV 9b protein was able to enter the nucleus even in the presence of WGA showing that its entry is independent of active transport pathway. The SARS-CoV 9b protein triggers caspase 3 mediated apoptosis when retained in the nucleus of mammalian cells While performing pulse-chase assays, we found that a significant number of Vero E6 cells, in which nuclear export of 9b has been inhibited (either by treating with LMB or using NES deficient 9b), were showing caspase 3 dependent apoptosis. cache = ./cache/cord-322446-ddv86eoy.txt txt = ./txt/cord-322446-ddv86eoy.txt === reduce.pl bib === id = cord-327257-doygrgrc author = Zhu, Jocelyn title = Deep transfer learning artificial intelligence accurately stages COVID-19 lung disease severity on portable chest radiographs date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3686 sentences = 221 flesch = 50 summary = title: Deep transfer learning artificial intelligence accurately stages COVID-19 lung disease severity on portable chest radiographs This study employed deep-learning convolutional neural networks to stage lung disease severity of Coronavirus Disease 2019 (COVID-19) infection on portable chest x-ray (CXR) with radiologist score of disease severity as ground truth. Deep-learning convolutional neural network (CNN) was used to predict lung disease severity scores. In conclusion, deep-learning CNN accurately stages disease severity on portable chest x-ray of COVID-19 lung infection. This study tested the hypothesis that deep-learning convolutional neural networks accurately stage disease severity on portable chest x-rays using radiologists' severity scores as ground truths associated with COVID-19 lung infection. Deep-learning AI, specifically a convolutional neural network, is well suited to extract information from CXR and stage disease severity by training using chest radiologist determination of disease severity scores. In conclusion, deep-learning convolutional neural networks accurately stage lung disease severity on portable chest x-rays associated with COVID-19 lung infection. cache = ./cache/cord-327257-doygrgrc.txt txt = ./txt/cord-327257-doygrgrc.txt === reduce.pl bib === id = cord-323185-n0rubc72 author = Varshney, Bhavna title = SARS Coronavirus 3b Accessory Protein Modulates Transcriptional Activity of RUNX1b date = 2012-01-12 pages = extension = .txt mime = text/plain words = 5667 sentences = 345 flesch = 51 summary = Chromatin immunoprecipitaion (ChIP) and reporter gene assays in 3b expressing jurkat cells showed recruitment of 3b on the RUNX1 binding element that led to an increase in RUNX1b transactivation potential on the IL2 promoter. In this study, we confirmed the putative interaction of 3b and RUNX1b and observed in vivo recruitment of 3b on the RUNX1 binding element on the IL2 promoter in transiently transfected human T, jurkat cells. We next determined the positive effect of 3b-RUNX1b interaction on the expression of RUNX1b regulated chemokine MIP-1a, reported to be upregulated in SARS-CoV infected monocyte derived dendritic cells. To investigate whether 3b-RUNX1b interaction leads to the recruitment of 3b on RUNX1 binding elements on the endogenous IL2 promoter, ChIP assays were performed in RUNX1b/CBFb endogenously expressing jurkat cells that are abortively infected by SARS-CoV. To investigate the effect of SARS-CoV 3b protein on the RUNX1b transcriptional activity, reporter gene assays were performed using the mouse IL2 promoter. cache = ./cache/cord-323185-n0rubc72.txt txt = ./txt/cord-323185-n0rubc72.txt === reduce.pl bib === id = cord-324359-88vy3dre author = Kamara, Foday Mamoud title = How villagers in central Sierra Leone understand infection risks under threat of Covid-19 date = 2020-06-24 pages = extension = .txt mime = text/plain words = 2949 sentences = 163 flesch = 59 summary = We undertook fieldwork in two villages in central Sierra Leone to gain insight into how rural people faced with Covid-19 assess epidemic infection risks. Asked to explain their choices 48% of players cited information on infection risks modelled by the game and 31% stated that their choices reflected awareness of the need for personal action and respect for local regulations. The data relate to rural populations in Sierra Leone exposed both to Ebola Virus Disease (EVD) in 2014-15 and now to Covid-19 in 2020. Three kinds of responses (Table 5 , 89% of all remarks) dominated comments after people made choices in the game-need for rules governing e.g. quarantine, comments on personal capacities to prevent or avoid infection (often made in the context of justifying a choice for disease "mango"), and comments about the relative risks to be inferred from "reading the stones" (i.e. recognition of a pattern in the way the stones were cast, as in divination practices). cache = ./cache/cord-324359-88vy3dre.txt txt = ./txt/cord-324359-88vy3dre.txt === reduce.pl bib === id = cord-328627-cf8f71dr author = Jando, Julia title = Expression and regulation of the neutral amino acid transporter B(0)AT1 in rat small intestine date = 2017-09-15 pages = extension = .txt mime = text/plain words = 8971 sentences = 389 flesch = 50 summary = Protein abundance of B 0 AT1, ACE2 and CD13 along the small intestine was measured by Western blotting performed on brush-border membrane vesicles (bbmv) prepared from duodenum, proximal-, middle-and distal jejunum as well as ileum and quantified relative to the microvilli cytoskeletal protein β-actin,. Additionally, rats fed different diets (NP, HP and AA) were euthanized 3 h after light-onset (ZT3) or 3 h after light-offset The three proteins tested in these bbmv showed a clearly increasing expression level in distal direction along the small intestine, as shown for distal versus proximal jejunum at both time points (Fig 1C, right panels) . This suggested the possibility that rats on a HP or AA diet may have expressed more functional B 0 AT1 along the small intestine and performed a more efficient absorption of neutral amino acids like L-isoleucine. cache = ./cache/cord-328627-cf8f71dr.txt txt = ./txt/cord-328627-cf8f71dr.txt === reduce.pl bib === id = cord-331885-8zmuhebu author = Xu, Xiuyan title = Risk factor analysis combined with deep learning in the risk assessment of overseas investment of enterprises date = 2020-10-02 pages = extension = .txt mime = text/plain words = 3796 sentences = 208 flesch = 43 summary = To evaluate the overseas investment risks of enterprises and expand the application and development of deep learning methods in risk assessment, 15 national clusters are utilized as samples to analyze and discuss the overseas investment risk indicators of enterprises. Second, the Deep Neural Network (DNN) is introduced; a risk evaluation model is constructed for enterprise overseas investment. The results show that the major source of overseas investment risks includes basic resources, political systems, economic and financial development, and environmental protection. To build a risk assessment model for overseas investment of enterprises and evaluate investment risks scientifically and effectively, the Deep Neural Network (DNN) based on deep learning is introduced, which is an innovation. The above analysis suggests that a country's infrastructure, health care conditions, economic development level, environmental protection conditions, and political system are the key components that affect its risks of enterprise overseas investment [29, 30] . cache = ./cache/cord-331885-8zmuhebu.txt txt = ./txt/cord-331885-8zmuhebu.txt === reduce.pl bib === id = cord-326568-twv2i3fb author = Bruminhent, Jackrapong title = Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date = 2020-09-15 pages = extension = .txt mime = text/plain words = 4402 sentences = 245 flesch = 48 summary = To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians' diagnoses. Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. Apart from close contact with an infected case and visiting high-risk places, we found that having no medical coverage and presenting with productive cough were predictors of being diagnosed with COVID-19 among PUIs. SARS-CoV-2 is an emerging respiratory virus that commonly causes no or mild respiratory tract infection and is occasionally complicated by severe pneumonia [1] . cache = ./cache/cord-326568-twv2i3fb.txt txt = ./txt/cord-326568-twv2i3fb.txt === reduce.pl bib === id = cord-329223-f84gjxm1 author = Kouokam, Joseph Calvin title = Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date = 2011-08-02 pages = extension = .txt mime = text/plain words = 8837 sentences = 382 flesch = 47 summary = In contrast to several other antiviral lectins however, GRFT treatment induces only minimal changes in secretion of inflammatory cytokines and chemokines by epithelial cells or human PBMC, has no measureable effect on cell viability and does not significantly upregulate markers of T-cell activation. When freshly-isolated PBMC were pre-incubated for 24 hrs with GRFT at various concentrations, washed and then infected with HIV-1 R5 strain BaL (without adding new compound), GRFT inhibited viral replication for 9 days of cell culture (Fig. 2) . In addition, the numbers of CD4 2 /CD25 + cells were elevated when PBMC were cultured in presence of PHA or ConA compared to their PBS and GRFT counterpart (Fig. 6 , left panel and data not shown). The heat map shown in Fig. 9A indicates that cells exposed for 24 hours to GRFT Lec-(1 and 8 mM), and low concentrations of GRFT (0.1 mM ) and CV-N (0.05 mM) showed comparable gene expression profiles to those that were incubated in presence of PBS alone. cache = ./cache/cord-329223-f84gjxm1.txt txt = ./txt/cord-329223-f84gjxm1.txt === reduce.pl bib === id = cord-328633-c31xsyeo author = Moser, Michael J. title = Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date = 2012-06-04 pages = extension = .txt mime = text/plain words = 7868 sentences = 441 flesch = 54 summary = Most RT-PCR protocols rely on two DNA polymerase (Pol) enzymes; a retroviral reverse transcriptase (RT) to copy RNA into cDNA and a thermostable DNA Pol to amplify the target sequence. Despite their wide use and general reliability, existing twoenzyme RT-PCR systems have several documented performance problems attributed to deficiencies inherent in retroviral RTs: 1) poor reagent stability, 2) low fidelity, 3) frequent rearrangements during cDNA synthesis, 4) secondary enzymatic activities (i.e. RNase H and strand switching), 5) bias for specific primers and templates, and 6) inhibition of PCR Pol enzymes [3, 4, 5, 6, 7] . We describe the discovery and biochemical attributes of one of these, 3173 Pol, its inherent RT activity and its incorporation into a single-enzyme PyroScriptH 2X RT-PCR Master Mix. The sensitivity, specificity and overall performance of this mix were compared to available one-and two-enzyme systems using a control MS2 RNA bacteriophage template, the clinically-relevant influenza A RNA and commonly used reference mRNA transcripts. cache = ./cache/cord-328633-c31xsyeo.txt txt = ./txt/cord-328633-c31xsyeo.txt === reduce.pl bib === id = cord-333208-tibtngy8 author = Muñoz-Moreno, Raquel title = Antiviral Role of IFITM Proteins in African Swine Fever Virus Infection date = 2016-04-26 pages = extension = .txt mime = text/plain words = 5867 sentences = 311 flesch = 45 summary = The interferon-induced transmembrane (IFITM) protein family is a group of antiviral restriction factors that impair flexibility and inhibit membrane fusion at the plasma or the endosomal membrane, restricting viral progression at entry. The role of IFITM2 in the inhibition of ASFV in Vero cells could be related to impaired endocytosis-mediated viral entry and alterations in the cholesterol efflux, suggesting that IFITM2 is acting at the late endosome, preventing the decapsidation stage of ASFV. Thus, our goal in the current work was to test whether the IFITM family of proteins affected early entry steps of ASFV infection in Vero cell cultures using the cell-adapted Ba71V isolate. Confocal microscopy experiments revealed that, IFITM1 was mainly distributed at the plasma membrane and to a lesser extent in perinuclear compartments, resembling endosomal structures (Fig 3C, lower left panel) , while endogenous IFITM1 was barely detected in Vero cells containing the empty vector (Fig 3C, upper left panel) . cache = ./cache/cord-333208-tibtngy8.txt txt = ./txt/cord-333208-tibtngy8.txt === reduce.pl bib === id = cord-328206-iylw1bvw author = Yu, Daojun title = Simultaneous Detection and Differentiation of Human Papillomavirus Genotypes 6, 11, 16 and 18 by AllGlo Quadruplex Quantitative PCR date = 2012-11-09 pages = extension = .txt mime = text/plain words = 4070 sentences = 209 flesch = 48 summary = In this study, applying novel AllGlo fluorescent probes, we established a quadruplex quantitative PCR method to simultaneously detect and differentiate HPV 6, 11, 16 and 18 in a single tube. So AllGlo quadruplex quantitative PCR has the advantages of relatively high throughput, good reproducibility, high sensitivity, high specificity, it is easy for designing the probes and primers of multiplex qPCR and can increase the detection throughput. Two aliquots were used for the detection of HPV6-11 and HPV16-18 mixed types by TaqMan uniplex probe fluorescence quantitative PCR (Guangzhou Da'an Diagnostic Co., Ltd., China). Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. Single-tube AllGlo probe quadruplex fluorescence qPCR could simultaneously type HPV 6, 11, 16, and 18 and quantitatively detect the viral load of each HPV at the same time. cache = ./cache/cord-328206-iylw1bvw.txt txt = ./txt/cord-328206-iylw1bvw.txt === reduce.pl bib === id = cord-316287-4i1grvlr author = Yim, Sung Sun title = Rapid Isolation of Antibody from a Synthetic Human Antibody Library by Repeated Fluorescence-Activated Cell Sorting (FACS) date = 2014-10-10 pages = extension = .txt mime = text/plain words = 6372 sentences = 281 flesch = 51 summary = During the cultivation for regeneration of sorted cells, differential growth rates among various clones (particularly non-specific clones) due to unregulated protein expression and differing cell viability can decrease the library screening efficiency, resulting in more rounds of sorting (longer duration) to isolate the potential antibody candidate [12] . The whole FACS screening rounds of the synthetic human antibody library against each viral antigen could be done in one day, and these results show that repeated FACS screening without regeneration of the sorted cells can be a rapid and efficient method to isolate potential antibody candidates in case of urgent requirements. For the FACS screening of a human synthetic antibody (scFv) library, three fluorescent antigen probes were chemically synthesized: (i) FITC-CRDNWHGSNRPW as an N1 epitope of H1N1 influenza virus [13] ; (ii) FITC-NSTTFHQALLDPRVRGLYF-PAGG as a PreS2 epitope of HBV [14] ; and (iii) FITC-PVTNVRGDLQVLAQK as a VP1 epitope of FMDV [15] . cache = ./cache/cord-316287-4i1grvlr.txt txt = ./txt/cord-316287-4i1grvlr.txt === reduce.pl bib === id = cord-330110-pamxy4av author = Teissier, Elodie title = Mechanism of Inhibition of Enveloped Virus Membrane Fusion by the Antiviral Drug Arbidol date = 2011-01-25 pages = extension = .txt mime = text/plain words = 9268 sentences = 438 flesch = 48 summary = Interestingly, apparent binding affinities between lipids and tryptophan residues are comparable with those of Arb IC50 of the hepatitis C virus (HCV) membrane fusion. By combining surface plasmon resonance, fluorescence and NMR spectroscopy approaches, we showed that Arb directly interacts with the phospholipid membrane interface, with an affinity in the micromolar range, comparable to the concentration inhibiting HCVpp membrane fusion by 50% (IC50). Altogether our results demonstrate that Arb interacts with the polar head of phospholipid membranes and protein motifs enriched in aromatic residues, suggesting that the inhibitory activity of Arb on HCV entry and fusion could involve both types of interactions. Conversely, Arb inhibition of HCVpp membrane fusion, as assessed by a in vitro model system where the only proteins present are the viral glycoproteins, could merely reflect the interaction of Arb on lipids and/or on motifs present in HCV glycoproteins of any genotype. cache = ./cache/cord-330110-pamxy4av.txt txt = ./txt/cord-330110-pamxy4av.txt === reduce.pl bib === id = cord-323133-gdg50omp author = Buzatto, G. P. title = The pathogens profile in children with otitis media with effusion and adenoid hypertrophy date = 2017-02-23 pages = extension = .txt mime = text/plain words = 4243 sentences = 209 flesch = 45 summary = OBJECTIVES: To evaluate the presence of viruses and bacteria in middle ear and adenoids of patients with and without otitis media with effusion (OME). METHODS: Adenoid samples and middle ear washes (MEW) were obtained from children with OME associated with adenoid hypertrophy undergoing adenoidectomy and tympanostomy, and compared to those obtained from patients undergoing cochlear implant surgery, as a control group. Therefore, the present study was carried out to compare the detection of common respiratory viruses and bacteria in adenoids and middle ear fluid in children with OME and in controls. In our study, we used a sensitive method to detect nucleic acid of a comprehensive panel of respiratory viruses and bacteria to compare the microbial colonization of adenoid and its correspondence in the middle ear in both OME children and controls. Concluding, in children with OME and adenoid hypertrophy we observed higher detection rates of potentially pathogenic bacteria, but not respiratory viruses, by real-time PCR in middle ear samples, as compared to control patients without adenoid hypertrophy. cache = ./cache/cord-323133-gdg50omp.txt txt = ./txt/cord-323133-gdg50omp.txt === reduce.pl bib === id = cord-330749-xt4aa2ur author = Schilling, Stefan title = Isolation Facilities for Highly Infectious Diseases in Europe – A Cross-Sectional Analysis in 16 Countries date = 2014-10-28 pages = extension = .txt mime = text/plain words = 4124 sentences = 192 flesch = 41 summary = The term highly infectious diseases (HID) defines mostly viral and bacterial infections that (i) are easily transmissible from person to person; (ii) cause a life-threatening clinical illness with no or few treatment options; and (iii) pose a threat for both health care workers and the public, thus requiring specific infection control measures and public health planning [1] . Despite such efforts, no pooled data on isolation facilities resources, such as infrastructure design, technical equipment, capacity and access to intensive care, do exist. The study presented was performed by the European Network for Highly Infectious Diseases, EuroNHID, and set up to compare the operational management, resources, and technical equipment among isolation facilities with recommendations published. Infection control management of patients with suspected highly infectious diseases in emergency departments: data from a survey in 41 facilities in 14 European countries cache = ./cache/cord-330749-xt4aa2ur.txt txt = ./txt/cord-330749-xt4aa2ur.txt === reduce.pl bib === id = cord-333522-zsdymkjd author = Gruse, Jeannine title = Quercetin Feeding in Newborn Dairy Calves Cannot Compensate Colostrum Deprivation: Study on Metabolic, Antioxidative and Inflammatory Traits date = 2016-01-11 pages = extension = .txt mime = text/plain words = 7010 sentences = 333 flesch = 46 summary = Blood samples were taken repeatedly to measure plasma concentrations of flavonols, glucose, lactate, total protein, albumin, urea, non-esterified fatty acids, triglycerides, cholesterol, insulin, glucagon, cortisol, immunoglobulins, fibrinogen, haptoglobin and serum amyloid A. Basal blood samples were taken before the morning feeding on days 1, 2, 4 and 7 from the jugular vein using evacuated tubes containing either potassium-EDTA (1.2-2 mg/mL EDTA) for analyses of plasma metabolites, insulin, glucagon, immunoglobulins and acute-phase proteins or Li-heparin (12-30 IU heparin) for the determination of the cortisol and flavonol concentrations and the antioxidative status in the plasma. Feed intake, body temperature, heart and respiratory rate and plasma concentrations of metabolites, hormones, flavonols and markers of antioxidative status were analyzed by repeated measurement ANOVA using the MIXED procedure of SAS/STAT software and a model with the fixed factors diet, quercetin and day of life (repeated variable) and all interactions between the fixed factors. cache = ./cache/cord-333522-zsdymkjd.txt txt = ./txt/cord-333522-zsdymkjd.txt === reduce.pl bib === id = cord-335272-jypxi99z author = Sharma, Anupam Joya title = A cross-sectional study of psychological wellbeing of Indian adults during the Covid-19 lockdown: Different strokes for different folks date = 2020-09-03 pages = extension = .txt mime = text/plain words = 9794 sentences = 515 flesch = 52 summary = Moreover, both qualitative and quantitative study findings suggested that greater frequency of calling family members during lockdown could strengthen social relationships and increase social empathy. In response, our study of Indian adults unpacks how social factors such as sexual orientation, relationship status, and residence in high-infection areas, could be linked with several psychological outcomes during the lockdown. Next, we fitted separate multivariable linear regression models to estimate the association of the independent variables (sexual orientation, relationship status, high-risk group, and living in a state with high number of cases) with psychological outcomes (anxiety, depressive symptoms, Internet addiction and pornography consumption) adjusted for the sociodemographic covariates-age, gender, annual income, educational qualification, place of residence-and for individual personal resources (optimism and resilience). Our quantitative and qualitative findings both suggest that LGBT adults, compared to the heterosexuals, are at a higher risk of developing anxiety, depressive symptoms, and using pornography during the lockdown. cache = ./cache/cord-335272-jypxi99z.txt txt = ./txt/cord-335272-jypxi99z.txt === reduce.pl bib === id = cord-333853-p2kbjwpy author = Smee, Donald F. title = Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) date = 2011-10-13 pages = extension = .txt mime = text/plain words = 4585 sentences = 222 flesch = 48 summary = title: Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201) An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. Ad5-vectored mouse interferon (mDEF201) resulted in sustained IFN levels [16] , that completely protected mice from a lethal Western equine encephalitis virus infection when given intramuscularly at 10 7 plaque forming units (PFU)/ mouse up to 7 days prior to virus challenge [16] . The extent of inhibition of lung Intranasal treatments with mDEF201 (10 7 PFU/mouse) were given one time only on the indicated day prior to virus exposure. cache = ./cache/cord-333853-p2kbjwpy.txt txt = ./txt/cord-333853-p2kbjwpy.txt === reduce.pl bib === id = cord-334955-gnu92up6 author = Sutton, Jeannette title = COVID-19: Retransmission of official communications in an emerging pandemic date = 2020-09-16 pages = extension = .txt mime = text/plain words = 7800 sentences = 324 flesch = 41 summary = In this research, we examine message features shown in prior disasters to increase or decrease message retransmission under imminent threat conditions to develop models of official risk communicators' messages shared online from February 1, 2020-April 30, 2020. We develop a lexicon of keywords associated with risk communication about the pandemic response, then use automated coding to identify message content and message structural features. They found that actionable and instructive messages and those that included a visual image were highly shared regardless of the time period; however, daily updates in the form of forecasts or current weather conditions involving little uncertainty, as well as message features that increase interaction, such as direct replies and URLs, decreased message passing. Messages that include information sharing decreases retransmission; however, this content increased post emergency declaration by 61%. cache = ./cache/cord-334955-gnu92up6.txt txt = ./txt/cord-334955-gnu92up6.txt === reduce.pl bib === id = cord-333955-bnzbppof author = Biesold, Susanne E. title = Type I Interferon Reaction to Viral Infection in Interferon-Competent, Immortalized Cell Lines from the African Fruit Bat Eidolon helvum date = 2011-11-30 pages = extension = .txt mime = text/plain words = 5016 sentences = 275 flesch = 51 summary = Here, we investigated interferon (IFN) response, -induction, -secretion and -signaling in epithelial-like cells of the relevant and abundant African fruit bat species, Eidolon helvum (E. Cells from Pteropus species have been shown to produce high amounts of interferon (IFN)-l after stimulation with the double-strand (ds)RNA analogue poly IC, and after infection with the bat-associated paramyxovirus, Tioman [13] . In accordance with the IFN mRNA induction, the highest equivalent amount of bioactive secreted IFN upon RVFV 13 virus infection and poly IC transfection was measured in EidNi/41.3 cells, followed by MEF and MA104 (Figure 3 ). Increases of infectious virus formation were about 1000-fold within 24 hpi, and specific infectivities, expressed as PFU per genome equivalent (PCR units), were highly comparable between cell cultures ( Figure 4C) . cache = ./cache/cord-333955-bnzbppof.txt txt = ./txt/cord-333955-bnzbppof.txt === reduce.pl bib === id = cord-334218-bkjfy66e author = Lin, Jung-Da title = Impact of Mated Female Nonproductive Days in Breeding Herd after Porcine Epidemic Diarrhea Virus Outbreak date = 2016-01-15 pages = extension = .txt mime = text/plain words = 3619 sentences = 176 flesch = 57 summary = title: Impact of Mated Female Nonproductive Days in Breeding Herd after Porcine Epidemic Diarrhea Virus Outbreak The objectives of the present study were to investigate the effects between a 1-year period before and after PEDV outbreak on a sow's reproductive traits on a commercial pig farm in Taiwan. The average number of mated females, average parity of farrowed sows, number of matings, number of farrowings, FR, RR, number of abortions, LMFY, percentage of sows mated by 7 days after weaning, WFSI, FI, NPDs, replacement rates of sows and sow culling rates of preand post-PEDV outbreak periods were compared using a Mann-Whitney test. In the present study, we compared the productivity index of gilts and sows between 1 year pre-and post-PEDV outbreak in a Taiwanese breeding herd. Impact of porcine epidemic diarrhea virus infection at different periods of pregnancy on subsequent reproductive performance in gilts and sows cache = ./cache/cord-334218-bkjfy66e.txt txt = ./txt/cord-334218-bkjfy66e.txt === reduce.pl bib === id = cord-329727-h47q76y8 author = Sisó-Almirall, Antoni title = Prognostic factors in Spanish COVID-19 patients: A case series from Barcelona date = 2020-08-21 pages = extension = .txt mime = text/plain words = 3441 sentences = 201 flesch = 53 summary = CONCLUSION: Determining the clinical, biological and radiological characteristics of patients with suspected COVID-19 infection will be key to early treatment and isolation and the tracing of contacts. Therefore, this study aimed to describe the clinical, biological and radiological manifestations, the evolution, treatments and mortality rate of patients with COVID-19 infection in the population of Barcelona city and determine the most important predictors of a poor prognosis. Signs and symptoms, the main available haematological and biochemical data and the results of imaging tests were recorded, as were comorbidities, the evolution, the hospitalization rate, intensive care unit (ICU) admission and the treatments received. This study summarizes the clinical, biological and radiological characteristics, evolution and prognostic factors of patients with COVID-19 disease in primary and community healthcare. https://doi.org/10.1371/journal.pone.0237960.t002 In bold, statistically significant independent predictive factors associated with hospitalization, death or ICU admission (logistic multivariate regression adjusted for age and sex). cache = ./cache/cord-329727-h47q76y8.txt txt = ./txt/cord-329727-h47q76y8.txt === reduce.pl bib === id = cord-329468-vjsurl60 author = Okino, Cintia Hiromi title = Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles date = 2017-02-15 pages = extension = .txt mime = text/plain words = 5853 sentences = 261 flesch = 48 summary = This study compared the expression profile of genes related to immune responses in tracheal samples after challenge with two Brazilian field isolates (A and B) of IBV from the same genotype, associating these responses with viral replication and with pathological changes in trachea and kidney. Cell-mediated immune (CMI) related genes presented also lower levels of expression in tracheal samples from birds challenged with B isolate at 1dpi. This differential pattern of early immune responses developed after challenge with IBV B isolate, related to the downregulation of TLR7, leading to insufficient pro-inflammatory response and lower CMI responses, seem to have an association with a most severe renal lesion and an enhanced capability of replication of this isolate in chicken. In this study, we found a suppressive effect on expression of some early innate and adaptive cell-mediated immune genes in the primary site of virus replication (trachea) from chickens infected with one of the tested IBV isolates (B). cache = ./cache/cord-329468-vjsurl60.txt txt = ./txt/cord-329468-vjsurl60.txt === reduce.pl bib === id = cord-329999-flzqm3wh author = Buchanan, Tom title = Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date = 2020-10-07 pages = extension = .txt mime = text/plain words = 13812 sentences = 728 flesch = 50 summary = Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Descriptive statistics for participant characteristics (personality, conservatism, new media literacy and age) and their reactions to the stimuli (likelihood of sharing, belief the stories were likely to be true, and rating of likelihood that they had seen them before) are summarised in Table 2 . This evaluated the extent to which digital media literacy (NMLS), authority of the message source, consensus, belief in veracity of the messages, consistency with participant beliefs (operationalised as the total SECS conservatism scale score), age and personality (Extraversion, Conscientiousness, Agreeableness, Openness to Experience and Neuroticism), predicted self-rated likelihood of sharing the posts. cache = ./cache/cord-329999-flzqm3wh.txt txt = ./txt/cord-329999-flzqm3wh.txt === reduce.pl bib === id = cord-333413-8buawes0 author = Liebing, J. title = Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date = 2020-06-16 pages = extension = .txt mime = text/plain words = 5556 sentences = 306 flesch = 51 summary = Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. In 2014 and 2015, the Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Hannover and the Wildlife Research Institute, State Office for Nature, Environment and Consumer Protection of North Rhine-Westphalia caught free-living Ring-necked Pheasant chicks from Lower Saxony (Cuxhaven, Grafschaft Bentheim, Emsland, Osnabrück, Vechta), North Rhine-Westphalia (Coesfeld, Warendorf) and Schleswig-Holstein (Dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations. cache = ./cache/cord-333413-8buawes0.txt txt = ./txt/cord-333413-8buawes0.txt === reduce.pl bib === id = cord-331652-oc5s1if2 author = Trudeau, Michaela P. title = Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) date = 2016-06-24 pages = extension = .txt mime = text/plain words = 5988 sentences = 294 flesch = 52 summary = title: Comparison of Thermal and Non-Thermal Processing of Swine Feed and the Use of Selected Feed Additives on Inactivation of Porcine Epidemic Diarrhea Virus (PEDV) Feed samples were spiked with PEDV and then heated to 120–145°C for up to 30 min or irradiated at 0–50 kGy. Another set of feed samples spiked with PEDV and mixed with Ultracid P (Nutriad), Activate DA (Novus International), KEM-GEST (Kemin Agrifood), Acid Booster (Agri-Nutrition), sugar or salt was incubated at room temperature (~25°C) for up to 21 days. Therefore, the objective of this study was to determine if thermal and non-thermal methods of microbial inactivation, as well as the use of selected feed additives, are effective in reducing the survival of PEDV in experimentally contaminated swine feed. The PEDV showed a high thermal resistance in the dry feed samples and it was completely inactivated (3.0 log reduction) at each of the tested temperatures within 30 min. cache = ./cache/cord-331652-oc5s1if2.txt txt = ./txt/cord-331652-oc5s1if2.txt === reduce.pl bib === id = cord-330537-xz0wt1sz author = Biermann, Olivia title = Active case-finding policy development, implementation and scale-up in high-burden countries: A mixed-methods survey with National Tuberculosis Programme managers and document review date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5668 sentences = 307 flesch = 49 summary = title: Active case-finding policy development, implementation and scale-up in high-burden countries: A mixed-methods survey with National Tuberculosis Programme managers and document review BACKGROUND: The World Health Organization (WHO) stresses the importance of active case-finding (ACF) for early detection of tuberculosis (TB), especially in the 30 high-burden countries that account for almost 90% of cases globally. OBJECTIVE: To describe the attitudes of National TB Programme (NTP) managers related to ACF policy development, implementation and scale-up in the 30 high-burden countries, and to review national TB strategic plans. Moreover, this study focuses on National TB Programme (NTP) managers, key stakeholders in developing and implementing ACF policies [13] . The study comprised a cross-sectional survey with NTP managers from 30 high TB burden countries, which included closed and open-ended questions designed to elicit quantitative and qualitative information, enhancing each other [15] . cache = ./cache/cord-330537-xz0wt1sz.txt txt = ./txt/cord-330537-xz0wt1sz.txt === reduce.pl bib === id = cord-336364-2ust3qoq author = Artigas, Laura title = In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date = 2020-10-02 pages = extension = .txt mime = text/plain words = 5858 sentences = 295 flesch = 45 summary = title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm This has provided 3 sets of proteins related with the infection process: 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lungcells infection set, and 3) acute respiratory distress (ARD) set. According to the findings by GUILDify, we confirm the effect of the combination of pirfenidone and melatonin in the entry points of the SARS-CoV-2 infection, specifically the neighbours of furin and GRP-78, and some proteins associated with ARD. 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lung-cells infection set, and 3) acute respiratory distress (ARD) set that is composed of 6 subsets (Alveolar macrophages, Monocytes, Neutrophils, Intermediate phase ARD, Late phase ARD and ARD cytokine storm). cache = ./cache/cord-336364-2ust3qoq.txt txt = ./txt/cord-336364-2ust3qoq.txt === reduce.pl bib === id = cord-336615-jfnj6l41 author = Wong, Sarah Sze Wah title = In Vitro and In Vivo Activity of a Novel Antifungal Small Molecule against Candida Infections date = 2014-01-22 pages = extension = .txt mime = text/plain words = 7875 sentences = 434 flesch = 54 summary = We screened a library of 50,240 small molecules for inhibitors of yeast-to-hypha transition, a major virulence attribute of Candida albicans. Further examination of the in vitro antifungal and anti-biofilm properties of these compounds, using a range of Candida spp., led to the discovery of SM21, a highly potent antifungal molecule (minimum inhibitory concentration (MIC) 0.2 – 1.6 µg/ml). In vitro, SM21 was toxic to fungi but not to various human cell lines or bacterial species and was active against Candida isolates that are resistant to existing antifungal agents. Second, the increased incidence of invasive candidiasis caused by non-albicans Candida (NAC) species, such as Candida glabrata, Candida tropicalis, Candida krusei or Candida parapsilosis, has been a major concern [13, 14] , because these infections are often associated with higher mortality and antifungal resistance than those caused by C. The antifungal activity of small molecules was assessed by disk diffusion and broth dilution assays (see below) using four groups of Candida isolates. cache = ./cache/cord-336615-jfnj6l41.txt txt = ./txt/cord-336615-jfnj6l41.txt === reduce.pl bib === id = cord-335859-k37jivp6 author = Wu, Daphne C. title = Predictors of self-reported symptoms and testing for COVID-19 in Canada using a nationally representative survey date = 2020-10-21 pages = extension = .txt mime = text/plain words = 3112 sentences = 160 flesch = 52 summary = To understand the socio-demographic predictors of COVID symptoms, we conducted a logistic regression analysis where the outcome was self-reported symptoms suggestive of COVID infection which we defined in this study as the respondent reporting himself/herself and/or at least one member of the household having had a combination of fever (with or without hallucinations) and any of i) difficulty breathing/shortness of breath or ii) dry cough so severe that it disrupts sleep or iii) a loss of a sense of smell in the past month; and the explanatory variables were gender (male, female, or other), education level (high school and under, or some college/ university and higher), province, age, ethnicity (Indigenous, English and other European, or others), visible minority (defined as persons, other than Aboriginal peoples, who are nonwhite in race or colour) [6] , and number of household members. cache = ./cache/cord-335859-k37jivp6.txt txt = ./txt/cord-335859-k37jivp6.txt === reduce.pl bib === id = cord-336420-1a2u9p4t author = Söderman, Martina title = Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study date = 2016-06-16 pages = extension = .txt mime = text/plain words = 4200 sentences = 208 flesch = 46 summary = title: Frequent Respiratory Viral Infections in Children with Febrile Neutropenia A Prospective Follow-Up Study Advances in molecular methods have increased the sensitivity of viral diagnostics tests, with recent studies reporting the detection of respiratory viruses in the nasopharynx in 44-57% of childhood febrile neutropenia episodes using real-time polymerase chain reaction (PCR) [3] [4] [5] 12] . Viral nucleic acids were extracted from the NPA with a MagAttract Virus Mini M48 kit (Qiagen, Sollentuna, Sweden) and analyzed with in-house real-time PCRs for the following 16 viruses: adenovirus (HAdV); bocavirus (HBoV); coronaviruses NL63/OC43/229E/HKU1 (HCoV); enterovirus (EV); influenza virus A, including A(H1N1)pdm09 and B (Flu); metapneumovirus (HMPV); parainfluenza viruses 1-3 (PIV); respiratory syncytial virus (RSV) and rhinovirus (RV) [19] . These results support the theory holding that there is a causal relationship between respiratory viral infections and episodes of febrile neutropenia, but proving this theory will require more longitudinal studies with asymptomatic neutropenic control cohorts. cache = ./cache/cord-336420-1a2u9p4t.txt txt = ./txt/cord-336420-1a2u9p4t.txt === reduce.pl bib === id = cord-337795-khqx4t4q author = Pellecchia, Umberto title = Social Consequences of Ebola Containment Measures in Liberia date = 2015-12-09 pages = extension = .txt mime = text/plain words = 5120 sentences = 277 flesch = 50 summary = INTRODUCTION: In the Ebola Virus Disease (EVD) outbreak in Liberia, two major emergency disease-control measures were cremation of bodies and enforcement of quarantine for asymptomatic individuals suspected of being in contact with a positive case. To address these questions, this study was conducted to assess Liberian community perspectives on State-imposed Ebola public health and outbreak containment measures implemented in 2014 and 2015. The grids were organized according to three main themes: 1) general social perception of the epidemic and community's reactions; 2) funerary and burial practices before and during the epidemic, and opinions on cremation; and 3) health-seeking behaviours and perception of quarantine. Forced quarantine of asymptomatic contacts of positive cases was the main State-imposed measure that transformed social perceptions and practices. Cremation of bodies and forced quarantine, as ways to quickly reduce transmission of Ebola outbreak for the benefit of the larger public, produced social dynamics of resistance in the same population that they wished to protect. cache = ./cache/cord-337795-khqx4t4q.txt txt = ./txt/cord-337795-khqx4t4q.txt === reduce.pl bib === id = cord-335441-bj3me7p8 author = Jourdain, Elsa title = Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date = 2010-01-28 pages = extension = .txt mime = text/plain words = 6354 sentences = 311 flesch = 52 summary = Five of the six ducks excreted viral RNA in their feces on the first day post-inoculation (PI) and all samples (feces, cloacal and oral swabs) from all birds were positive on the second day PI (Figures 4 and S1 ). Intermittent and moderate (high ct-values) viral RNA shedding was detected for all birds in water, fecal or cloacal samples between day 1 and 7 after H7N7 re-inoculation ( Figure 4 ). Active H5 infection was confirmed only in one duck, by expression of H5-specific antibodies and detection of viral RNA in the various sample types (feces, water, oral and cloacal swabs) with a pattern similar to the H5-inoculated control bird. Eight 3-month-old male wild-type mallards (Anas platyrhynchos) of approximately the same body mass and size (measurement of the left wing, the right tarsus length and the distance from bill tip to back of the skull) were selected from a Swedish duck farm known from previous successive sampling to be free from IAV infection. cache = ./cache/cord-335441-bj3me7p8.txt txt = ./txt/cord-335441-bj3me7p8.txt === reduce.pl bib === id = cord-335880-m8gecsf0 author = Peci, Adriana title = Epidemiology of Enterovirus D68 in Ontario date = 2015-11-23 pages = extension = .txt mime = text/plain words = 4030 sentences = 218 flesch = 52 summary = In response to CDC reports, Public Health Ontario Laboratories (PHOL) launched an investigation of patients being tested for enterovirus D-68 (EV-D68) in Ontario, Canada. In order to better understand the epidemiology of this virus, surveillance for EV-D68 should include testing of symptomatic individuals from all treatment settings and patient age groups, with collection and analysis of comprehensive clinical and epidemiological data. Data for this study included specimens submitted for EV-D68 testing at PHOL from patients who presented with respiratory symptoms in different health care settings across Ontario, from September 1, 2014 to October 31, 2014. Percent positivity and descriptions of EV-D68 cases by timing of specimen collection, age, sex, setting, symptoms and local health unit of residence were analysed at the patient level. Bivariate and multivariate logistic regression analyses were performed at the patient level to compare cases and controls in terms of age, sex, settings, symptoms and timing of specimen collection. cache = ./cache/cord-335880-m8gecsf0.txt txt = ./txt/cord-335880-m8gecsf0.txt === reduce.pl bib === id = cord-330079-pdaowkop author = Xu, Lin title = Surveillance and Genome Analysis of Human Bocavirus in Patients with Respiratory Infection in Guangzhou, China date = 2012-09-11 pages = extension = .txt mime = text/plain words = 4469 sentences = 205 flesch = 50 summary = To investigate the epidemiological and genetic variation of HBoV in Guangzhou, South China, we screened 3460 throat swab samples from 1686 children and 1774 adults with acute respiratory infection symptoms for HBoV between March 2010 and February 2011, and analyzed the complete genome sequence of 2 HBoV strains. In our current study, we screened throat swab specimens from patients with acute respiratory tract infection symptoms for HBoV and other common respiratory viruses over a 12-month period using polymerase chain reaction (PCR) methods, and in addition, the molecular phylogeny and complete genome sequences of 2 HBoV strains were also analyzed. Of the 3460 samples collected from patients with respiratory tract infection symptoms and signs enrolled in the study during the period between March 2010 and February 2011, detection for 7 viruses, namely, Influenza, PIV, RSV, HMPV, HCoV, AdV and HBoV, showed that 1275 (36.8%) were found positive for one single virus and 112 (3.2%) were infected by more than one virus. cache = ./cache/cord-330079-pdaowkop.txt txt = ./txt/cord-330079-pdaowkop.txt === reduce.pl bib === id = cord-335505-s013j5ex author = Zhang, Chen title = Viral Etiology and Clinical Profiles of Children with Severe Acute Respiratory Infections in China date = 2013-08-22 pages = extension = .txt mime = text/plain words = 3186 sentences = 173 flesch = 44 summary = BACKGROUND: No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute respiratory infection (SARI) in China during 2009 H1N1 pandemic and post-pandemic period. The RVP Fast assay simultaneously detects the following viruses: respiratory syncytial virus (RSV); influenza(IFV) A (H1, H3, and H5) and B viruses; parainfluenza viruse (PIV) 1, 2, 3, and 4; human metapneumovirus (hMPV); adenovirus(ADV); piconavirus(PIC) which includes enterovirus (EV) and rhinovirus (RV); human coronaviruse(HCoV) NL63, HKU1, 229E, and OC43; and human bocavirus(BoCA). To find the reason that causes severe infection, we performed complete comparison between VSARI patients and the SARI, including clinical signs, number of viral target, gender, and age(Table 3, Figure 2B ). To find the association between virus infection and clinical signs in SARI, binary logistic regression was performed between 4 commonly diagnosed respiratory abnormality, including anhelation, respiratory failure, heart failure and pleural effusion, and the viral target detected by xTAG® RVP FAST. cache = ./cache/cord-335505-s013j5ex.txt txt = ./txt/cord-335505-s013j5ex.txt === reduce.pl bib === id = cord-332922-2qjae0x7 author = Mbuvha, Rendani title = Bayesian inference of COVID-19 spreading rates in South Africa date = 2020-08-05 pages = extension = .txt mime = text/plain words = 3224 sentences = 169 flesch = 52 summary = In this work, we perform Bayesian parameter inference using Markov Chain Monte Carlo (MCMC) methods on the Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological models with time-varying spreading rates for South Africa. The results find two change points in the spreading rate of COVID-19 in South Africa as inferred from the confirmed cases. The second change point coincides with the start of a state-led mass screening and testing programme which has highlighted community-level disease spread that was not well represented in the initial largely traveller based and private laboratory dominated testing data. In this work we combine Bayesian inference with the compartmental SEIR and SIR models to infer time varying spreading rates that allow for quantification of the impact of government interventions in South Africa. SIR and SEIR model parameter inference was performed using confirmed cases data up to and including 20 April 2020 and MCMC samplers described in the methodology section. cache = ./cache/cord-332922-2qjae0x7.txt txt = ./txt/cord-332922-2qjae0x7.txt === reduce.pl bib === id = cord-336441-m6pur6td author = Wang, Changjian title = Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model date = 2019-02-11 pages = extension = .txt mime = text/plain words = 5186 sentences = 282 flesch = 45 summary = title: Features and drivers for energy-related carbon emissions in mega city: The case of Guangzhou, China based on an extended LMDI model Based on the apparent energy consumption data, a systematic and comprehensive city-level total carbon accounting approach was established and applied in Guangzhou, China. g. Stochastic impacts by regression on population, affluence, and technology (STIRPAT) model) are the most commonly applied methods for the scientific evaluation and quantitative analysis of factors influencing city-level carbon emissions, especially the Logarithmic Mean Divisia Index (LMDI) method based on the IDA framework. [51] performed a multi-sectoral decomposition analysis of city-level greenhouse gas emissions in Tianjin from 2001 to 2009, including the agricultural, industrial, transportation, commercial and other sectors, and the results showed that economic growth was the most important driver for emissions increments while energy efficiency was primarily responsible for emissions reductions. cache = ./cache/cord-336441-m6pur6td.txt txt = ./txt/cord-336441-m6pur6td.txt === reduce.pl bib === id = cord-335404-s48psqth author = Mukandavire, Zindoga title = Quantifying early COVID-19 outbreak transmission in South Africa and exploring vaccine efficacy scenarios date = 2020-07-24 pages = extension = .txt mime = text/plain words = 3570 sentences = 183 flesch = 48 summary = We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). Here, we adapt a susceptible-exposed-infected-removed (SEIR) compartmental model to quantify early transmissibility of COVID-19 in South Africa and explore the potential utility of a vaccine in containing the disease. Following a similar approach in [37] , we use a Markov Chain Monte Carlo (MCMC) within a Bayesian framework (in R FME package [38] ) to fit the model to the cumulative data of confirmed COVID-19 cases in South Africa and estimate the magnitude of the epidemic using the basic reproductive number and quantify required vaccines' attributes to stem similar outbreaks. cache = ./cache/cord-335404-s48psqth.txt txt = ./txt/cord-335404-s48psqth.txt === reduce.pl bib === id = cord-333248-5342lyeu author = Elenius, Varpu title = The relationship of serum vitamins A, D, E and LL-37 levels with allergic status, tonsillar virus detection and immune response date = 2017-02-24 pages = extension = .txt mime = text/plain words = 3309 sentences = 206 flesch = 45 summary = We studied how their serum levels were associated with allergy status, intratonsillar/nasopharyngeal virus detection and intratonsillar expression of T celland innate immune response-specific cytokines, transcription factors and type I/II/III interferons in patients undergoing tonsillectomy. We studied how serum vitamins and antimicrobial peptide LL-37 levels and allergic and tonsillar diseases were associated with direct in vivo detection of respiratory viruses and T cell subset-related transcription factors, cytokines as well as type I, II and III interferons in tonsils. The associations of serum levels of vitamins and LL-37, allergy status and virus detection with intratonsillar cytokine and transcription factor expressions were analyzed using univariable and age-adjusted linear regression. This study provides new insights into connections between serum levels of vitamins A, D, and E and antimicrobial peptide LL-37 and several important outcomes: allergy, respiratory virus detection and tonsillar immune responses. cache = ./cache/cord-333248-5342lyeu.txt txt = ./txt/cord-333248-5342lyeu.txt === reduce.pl bib === id = cord-338067-vjyad10p author = Hao, Yan title = Prediction and analysis of Corona Virus Disease 2019 date = 2020-10-05 pages = extension = .txt mime = text/plain words = 4775 sentences = 258 flesch = 59 summary = In this study, the development trend analysis of the cumulative confirmed cases, cumulative deaths, and cumulative cured cases was conducted based on data from Wuhan, Hubei Province, China from January 23, 2020 to April 6, 2020 using an Elman neural network, long short-term memory (LSTM), and support vector machine (SVM). In the present study, three methods, namely, an Elman neural network, LSTM, and SVM are applied to predict and analyze COVID-19 data from January 23, 2020 to April 6, 2020 in Wuhan, Hubei Province, China, including cumulative confirmed cases, confirmed new cases, cumulative deaths, new deaths, and cumulative cured cases and new cured cases. Experimental results showed that the Elman neural network and SVM adopted in this study can accurately predict the development trend of COVID-19, whereas LSTM is more suitable for the prediction of cumulative confirmed cases. cache = ./cache/cord-338067-vjyad10p.txt txt = ./txt/cord-338067-vjyad10p.txt === reduce.pl bib === id = cord-333650-4towah1t author = Malmo, Jostein title = Cytokine Profiles in Human Metapneumovirus Infected Children: Identification of Genes Involved in the Antiviral Response and Pathogenesis date = 2016-05-12 pages = extension = .txt mime = text/plain words = 4659 sentences = 250 flesch = 50 summary = Overall, our data point to cytokines, particularly inflammasome-associated, that might be important in hMPV mediated lung disease and the antiviral response in children with severe infection. To determine the presence of antiviral cytokines in children infected with hMPV and controls, we initially investigated the expression of type I, II and III IFNs. Fig 1A shows that only A2 infected children had slightly elevated mRNA levels of the type I IFN-β compared to the controls. Fig 2 shows the mRNA expression of A) IκBα, a repressor gene induced by NF-κB activation [19] , B) IL-1β, C) IL-18 and D) NLRP3 in hMPV infected children and controls. A previous study comparing the expression of several inflammatory cytokines in hMPV, RSV and influenza virus, detected elevated levels of TNF-α, IL-6 and IL-1β protein in nasal washes from infants with RTI [9] . cache = ./cache/cord-333650-4towah1t.txt txt = ./txt/cord-333650-4towah1t.txt === reduce.pl bib === id = cord-339789-151d1j4n author = Hong, Hyokyoung G. title = Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic date = 2020-07-21 pages = extension = .txt mime = text/plain words = 3934 sentences = 286 flesch = 60 summary = title: Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic However, time-independent parameters in the classical models may not capture the dynamic transmission and removal processes, governed by virus containment strategies taken at various phases of the epidemic. We propose a Poisson model with time-dependent transmission and removal rates to account for possible random errors in reporting and estimate a time-dependent disease reproduction number, which may reflect the effectiveness of virus control strategies. To choose the optimal number of knots for each country when implementing the spline approach, we used 5-fold cross-validation by minimizing the combined mean squared error for the estimated infectious and removed cases. Our model accommodates possible random errors and estimates a timedependent disease reproduction number, R 0 ðtÞ, which can serve as a metric for timely evaluating the effects of health policies. cache = ./cache/cord-339789-151d1j4n.txt txt = ./txt/cord-339789-151d1j4n.txt === reduce.pl bib === id = cord-339026-eu11larc author = Ryals, Renee C. title = The effects of PEGylation on LNP based mRNA delivery to the eye date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4786 sentences = 257 flesch = 46 summary = Similar injections of LNP delivered cre mRNA into Ai9 mice revealed cell-specific protein expression in the retinal pigment epithelium (RPE), confirmed by fundus photography and immunohistochemistry of whole globe cross-sections. Thus far, these particles successfully transfect RPE, Müller cells, the optic nerve head and the trabecular meshwork based on route of administration which can expand the utility of LNP-mediated gene therapies for the eye. Most intriguingly, these particles successfully transfect RPE, Müller glia, the optic nerve head and the trabecular meshwork based on route of administration which can expand the utility of LNP-mediated gene therapies for the eye. Since the subretinal injection places the LNPs in close proximity to the RPE, we utilized this method to understand how PEGylation and size may impact intracellular delivery ( In general, for all particles, luciferase activity in the eye was measurable at 4 hours post-injection, increased to a maximum level at 24 hours post-injection and decreased by 48 hours post-injection (Figs 2B and 3B). cache = ./cache/cord-339026-eu11larc.txt txt = ./txt/cord-339026-eu11larc.txt === reduce.pl bib === id = cord-336843-c0sr3six author = Gerritsen, M. G. title = Improving early diagnosis of pulmonary infections in patients with febrile neutropenia using low-dose chest computed tomography date = 2017-02-24 pages = extension = .txt mime = text/plain words = 4321 sentences = 239 flesch = 49 summary = title: Improving early diagnosis of pulmonary infections in patients with febrile neutropenia using low-dose chest computed tomography We performed a prospective study in patients with chemotherapy induced febrile neutropenia to investigate the diagnostic value of low-dose computed tomography compared to standard chest radiography. Two studies comparing LDCT to CXR in patients with persistent febrile neutropenia demonstrated an increased detection of pulmonary abnormalities. The diagnosis of possible IFD in the patient with a negative LDCT scan was based on abnormalities on HRCT made on day 4 of fever. We conducted a prospective study to evaluate whether pulmonary focus detection would improve using a LDCT scan instead of CXR on the first day of febrile neutropenia. [3] In a retrospective study 1083 adult SCT patients were evaluated, but in none of the 242 CXRs performed in asymptomatic patients with febrile neutropenia pulmonary abnormalities indicative of infection were detected. cache = ./cache/cord-336843-c0sr3six.txt txt = ./txt/cord-336843-c0sr3six.txt === reduce.pl bib === id = cord-339578-eg19rfvi author = Garcia-Garcia, Maria Luz title = Role of viral coinfections in asthma development date = 2017-12-05 pages = extension = .txt mime = text/plain words = 3651 sentences = 190 flesch = 47 summary = OBJECTIVE: Our aim was to compare the frequency of asthma development at 6–8 years in children with previous admission for bronchiolitis associated with single versus double or multiple viral infection. CONCLUSIONS: Asthma at 6–8 years is more frequent and severe in those children previously hospitalized with viral coinfection-bronchiolitis compared with those with single infection. Of the 351 children previously admitted with bronchiolitis, with positive viral detection and current age between 6 and 8 years, 244 (52 coinfections and 192 single infections) could be located and agreed to participate in the study. In conclusion, asthma at the age of 6-8 is more frequent and severe in those children previously hospitalized with viral coinfection bronchiolitis compared with those with single infection. Moreover, viral coinfection, allergic rhinitis and older age at admission seem also to be strong independent risk factors for asthma development in children previously hospitalised because of bronchiolitis. cache = ./cache/cord-339578-eg19rfvi.txt txt = ./txt/cord-339578-eg19rfvi.txt === reduce.pl bib === id = cord-337585-kpghvb6u author = Moustaqim-Barrette, Amina title = Accessing Take-Home Naloxone in British Columbia and the role of community pharmacies: Results from the analysis of administrative data date = 2020-09-11 pages = extension = .txt mime = text/plain words = 4016 sentences = 191 flesch = 50 summary = Individuals not personally at risk of overdose had higher odds of collecting naloxone at a pharmacy site, compared to other community sites (including harm reduction supply distribution sites, peer led organizations, drop-in centers, and supportive housing sites) (Adjusted Odds Ratio (AOR): 2.69; 95% CI: 2.50–2.90). While those at highest risk of overdose may preferentially access naloxone through community sites, naloxone distribution through pharmacies has allowed the BC THN program to expand dramatically, increasing naloxone availability through longer opening hours on evenings and weekends. While analyses from the BCCDC shows that the BC THN program, combined with other harm reduction interventions, has averted thousands of opioid overdose deaths [20, 21] , there is still relatively little data in the published literature examining community reach and barriers to access of naloxone distribution programs in Canada. After evaluating data from 2018, our analysis also finds that individuals at risk of opioid overdose were significantly less likely to collect a naloxone kit at a pharmacy site compared to community-based sites. cache = ./cache/cord-337585-kpghvb6u.txt txt = ./txt/cord-337585-kpghvb6u.txt === reduce.pl bib === id = cord-339157-wj47xeqj author = Zhang, Chao title = Involvement of the renin-angiotensin system in the progression of severe hand-foot-and-mouth disease date = 2018-05-23 pages = extension = .txt mime = text/plain words = 3062 sentences = 174 flesch = 55 summary = RESULTS: The concentrations of Ang II and NA in serum of the HFMD patients with mild or severe symptoms were significantly higher than that in healthy controls. According to the "diagnosis and treatment guideline on hand-foot-and-mouth disease (2010)", patients younger than 60 months with severe symptoms including meningitis, pulmonary edema, and mild cases without any nervous system lesions or pulmonary edema were included in this study. The concentrations of Ang II and NA in serum of the HFMD patients with mild or severe symptoms were significantly higher than that in healthy controls (P<0.001). The concentrations of Ang II and NA in serum of the HFMD patients with mild or severe symptoms were significantly higher than that in healthy controls (P<0.001). In the present study, we found that the concentrations of Ang II and NA were increased in serum of HFMD cases with mild or severe symptoms. cache = ./cache/cord-339157-wj47xeqj.txt txt = ./txt/cord-339157-wj47xeqj.txt === reduce.pl bib === id = cord-338594-wft7yy6j author = Winkler, Michael title = Rhesus macaque IFITM3 gene polymorphisms and SIV infection date = 2017-03-03 pages = extension = .txt mime = text/plain words = 4633 sentences = 277 flesch = 48 summary = In particular, polymorphisms of the human IFITM3 gene have been shown to affect disease severity and progression in influenza A virus (FLUAV) and human immunodeficiency virus (HIV) infection, respectively. Employing previously characterized samples from two cohorts of SIV-infected rhesus macaques, we investigated the relationship between these rhIFITM3 polymorphisms and both AIDS-free survival time and virus load. Polymorphisms in several immune-relevant gene loci such as MHC or KIR are associated with the transmission and course of disease in SIV infected rhesus macaques and HIV-1 infected humans [36, 37] . Immune-related IFITM proteins have been established as important antiviral effectors of the interferon response, and a polymorphism in the human IFITM3 gene has been found to be associated with disease severity and progression in FLUAV and HIV-1 infection [27, 33] . Notably, all polymorphism in the coding region were silent and strong evidence for an association of rhIFITM3 polymorphisms with disease progression and viral load in SIV infected animals was not obtained. cache = ./cache/cord-338594-wft7yy6j.txt txt = ./txt/cord-338594-wft7yy6j.txt === reduce.pl bib === id = cord-335245-1eksm537 author = Pattyn, Els title = HyperISGylation of Old World Monkey ISG15 in Human Cells date = 2008-06-18 pages = extension = .txt mime = text/plain words = 7011 sentences = 419 flesch = 54 summary = Western blot analysis visualized more efficient conjugation of OWmISG15 relative to HuISG15 in human (Hu), monkey and mouse (Mo) cell-lines. Western blot analysis on total cell lysates containing b-ME confirmed ISGylation of UbcH10, H13 and H17 with AgmISG15 but not with HuISG15, as seen by a 15 kDa shift upon staining with anti-V5 Ab detecting the ectopic expressed UbcH proteins (Figure 3a ,b and Figure S2a ). Previous studies using Western blot analysis in HekT cells revealed Hu or MoISG15 conjugation to substrates such as UbcH13 only upon co-transfection of at least UbE1L -and generally also UbcH/M8or upon IFN stimulation. The effect of mutating HuISG15 residues situated near the predicted UbE1L interface and the different allelic variants on conjugation to UbcH proteins is shown in Figure 5a and S3a. As shown in Figure 5c , mutation of D133N and QIT31-33KIA in the HuISG15 N89D variant further enhanced its ISGylation in human HekT cells. cache = ./cache/cord-335245-1eksm537.txt txt = ./txt/cord-335245-1eksm537.txt === reduce.pl bib === id = cord-339327-4422s317 author = Norris, Susan L. title = An evaluation of emergency guidelines issued by the World Health Organization in response to four infectious disease outbreaks date = 2018-05-30 pages = extension = .txt mime = text/plain words = 3690 sentences = 169 flesch = 43 summary = For guidelines, the methods for development were incompletely reported; WHO's quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. For guidelines, the methods for development were incompletely reported; WHO's quality assurance process was rarely used; systematic or other evidence reviews were infrequently referenced; external peer review was not performed; and they scored poorly with AGREE II, particularly for rigour of development and editorial independence. WHO quality standards dictate that guidelines must address a critical public health problem, use transparent and explicit processes minimizing potential sources of bias such as conflicts of interest, include diverse perspectives in the guideline development group, reflect the current state of the evidence, and provide a clear link between the evidence and recommendations taking into consideration the balance of benefits and harms of interventions and other important considerations [2] . cache = ./cache/cord-339327-4422s317.txt txt = ./txt/cord-339327-4422s317.txt === reduce.pl bib === id = cord-334695-cjxlw1tu author = Kam, Yiu-Wing title = Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro date = 2009-11-17 pages = extension = .txt mime = text/plain words = 6404 sentences = 315 flesch = 43 summary = title: Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human Bronchial Epithelial Cells In Vitro We observed that SARS-CoV spike glycoprotein can be efficiently cleaved by several airway proteases and that this processing enhances entry of SARS-CoVpp. Furthermore, we have identified the putative cleavage sites of airway proteases and, by site-directed mutagenesis, have determined the role of specific amino acid residue for proteolytic processing of the envelope glycoprotein, and for SARS-CoVpp entry into human airway epithelial cells (16HBE) in vitro. In an effort to directly demonstrate that airway protease mediated virus entry enhancement is due to the presence of cleavage site on the SARS spike glycoprotein, 16HBE cells were pre-incubated with wild-type (SARS-CoVpp) or mutant (R667App) pseudotypes on ice, which allowed virus attachment but not entry. cache = ./cache/cord-334695-cjxlw1tu.txt txt = ./txt/cord-334695-cjxlw1tu.txt === reduce.pl bib === id = cord-337067-j8ebslif author = Mades, Andreas title = Role of Human Sec63 in Modulating the Steady-State Levels of Multi-Spanning Membrane Proteins date = 2012-11-15 pages = extension = .txt mime = text/plain words = 8726 sentences = 459 flesch = 48 summary = The overexpression of Sec63 reduces the steady-state levels of viral and cellular multi-spanning membrane proteins in a cotranslational mode, while soluble and single-spanning ER reporters are not affected. The specific action of Sec63 is further sustained by our observations that the up-regulation of either Sec62 or two other ER proteins with lumenal J domains, like ERdj1 and ERdj4, does not compromise the steady-state level of a multi-spanning membrane reporter. Similar results were obtained with cell lysates prepared with the denaturing detergent SDS (Fig. 1B) , indicating that the observed down-regulation of HBV.S by excess Sec63 was not merely due to changes in the solubility profile. To analyze whether an up-regulation of these ERdj proteins might also affect the level of a multi-spanning membrane protein, FLAG-tagged versions of ERdj1 and ERdj4 were cotransfected with HBV.S. FLAG-specific Western blotting confirmed the ectopic expression of ERdj1 and ERdj4 in 63 and 25 kDa forms, respectively, consistent with their theoretical molecular masses (Fig. 9) . cache = ./cache/cord-337067-j8ebslif.txt txt = ./txt/cord-337067-j8ebslif.txt === reduce.pl bib === id = cord-340027-6l55rcfm author = Mamode Khan, Naushad title = Studying the trend of the novel coronavirus series in Mauritius and its implications date = 2020-07-10 pages = extension = .txt mime = text/plain words = 3627 sentences = 198 flesch = 52 summary = This paper proposes an integer-valued time series model to analyze the series of COVID-19 cases in Mauritius wherein the corresponding innovation term accommodates for covariate specification. Based on the proposed COM-Poisson mixture models, we could predict the number of COVID-19 cases in Mauritius. The paper therefore proposes an integer-valued auto-regressive model (INAR(1)) with Conway-Maxwell Poisson (COM-Poisson) mixed innovation terms that can accommodate for covariate, random effect and serial auto-correlation specifications. The organization of the paper is as follows: In Section 2, material in terms of time series of COVID-19 in Mauritius and proposed methods principally the INAR(1) Process and the COM-Poisson mixture innovations have been provided. The results of this research revealed that several factors, the most significant being confinement measure, and least one being climatic conditions, affect the number of COVID-19 cases in Mauritius. cache = ./cache/cord-340027-6l55rcfm.txt txt = ./txt/cord-340027-6l55rcfm.txt === reduce.pl bib === id = cord-339724-roj8ksvc author = Lan, Jiaming title = Tailoring Subunit Vaccine Immunity with Adjuvant Combinations and Delivery Routes Using the Middle East Respiratory Coronavirus (MERS-CoV) Receptor-Binding Domain as an Antigen date = 2014-11-18 pages = extension = .txt mime = text/plain words = 5017 sentences = 249 flesch = 49 summary = title: Tailoring Subunit Vaccine Immunity with Adjuvant Combinations and Delivery Routes Using the Middle East Respiratory Coronavirus (MERS-CoV) Receptor-Binding Domain as an Antigen Interestingly, robust RBD-specific antibody and T-cell responses were induced in mice immunized with the rRBD protein in combination with IFA and CpG ODN, but low level of neutralizing antibodies were elicited. In this study, different adjuvants combination regimens including alum, IFA, CpG and poly(I:C) were compared in an effort to promote balance between Th1 and Th2 immune response to bystander rRBD antigen spanning residues 367-606 of MERS-CoV S in a murine model to develop an effective vaccine against MERS-CoV infection. The results indicated that rRBD protein combined with any adjuvant, including alum, IFA, CpG or poly(I:C), could induce a RBD-specific IgG antibody response in the majority of mice after the second immunisation. cache = ./cache/cord-339724-roj8ksvc.txt txt = ./txt/cord-339724-roj8ksvc.txt === reduce.pl bib === id = cord-340763-cxnu9g8y author = Grimm, Sebastian K. title = Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date = 2015-02-17 pages = extension = .txt mime = text/plain words = 7822 sentences = 341 flesch = 45 summary = title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies Because the intrinsic instability and complexity of this trimeric glycoprotein has greatly impeded the development of immunogens that properly represent the structure of native envelope, this platform addresses an essential need for methodologies with the capacity to rapidly engineer HIV spike proteins towards improved homogeneity, stability, and presentation of neutralizing epitopes. The rationally designed d-SOSIP variant and a mutant with disrupted CD4 binding site (CD4bs)-specific Ab binding (d-SOSIP D368R) were displayed as Aga2 fusion proteins on yeast ( Fig. 2A ), and compared for display level and binding to a panel of HIV bnAbs together with the well-characterized and folded YU2 gp120 core [47] and an unrelated viral envelope protein (E2) derived from Hepatitis C virus (HCV E2) as positive and negative controls Fig. 2) . cache = ./cache/cord-340763-cxnu9g8y.txt txt = ./txt/cord-340763-cxnu9g8y.txt === reduce.pl bib === id = cord-337913-eu2gn4bl author = Stojanov, Ana title = Does Perceived Lack of Control Lead to Conspiracy Theory Beliefs? Findings from an online MTurk sample date = 2020-08-17 pages = extension = .txt mime = text/plain words = 7933 sentences = 414 flesch = 48 summary = Across six studies conducted online using MTurk samples, we observed no effect of control manipulations on conspiracy theory beliefs, while replicating previously reported correlational evidence of their association. Given the significance and potential consequences of widespread conspiracy beliefs [38, 39] , and the plausible but largely unsubstantiated role of control in their appeal, we here report three studies to test the effects of lack of control on conspiracy theory beliefs using a standard priming paradigm and a validated measure of conspiracy ideation, which reflects the belief that a powerful entity lies behind significant social or political events and that the conventional (official) truth is not the "real" truth. In a recent meta-analysis of experimental manipulations of control on conspiracy beliefs [68] conducted on 45 effect sizes across 23 studies (including those reported here), we found no moderating effect of sample type (MTurk vs. cache = ./cache/cord-337913-eu2gn4bl.txt txt = ./txt/cord-337913-eu2gn4bl.txt === reduce.pl bib === id = cord-337879-liqhbqxl author = Kriesel, John D. title = Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date = 2012-03-08 pages = extension = .txt mime = text/plain words = 5060 sentences = 296 flesch = 54 summary = Sequences from GB virus C (GBV-C), a flavivirus not previously isolated from brain, were enriched in one of the MS samples. This study shows the feasibility of deep sequencing for the detection of occult viral infections in the brains of deceased persons with MS. Multiple sclerosis (MS) is a chronic demyelinating disease of unknown cause, which affects the brain and spinal cord of about 400,000 individuals in the U.S. A number of viral infections of the CNS can lead to demyelination, including distemper (dogs), measles (SSPE, humans), and influenza (humans). To enhance the detection of non-human sequences, RNA samples that passed the quality control step above were subjected to rRNA removal using the RiboMinus kit (Invitrogen Inc., Carlsbad, CA). One subject who died with primary-progressive MS had .1000 36 bp sequences detected that mapped to GBV-C virus (hepatitis G), a human flavivirus not known to cause any persistent disease and never before detected in human brain. cache = ./cache/cord-337879-liqhbqxl.txt txt = ./txt/cord-337879-liqhbqxl.txt === reduce.pl bib === id = cord-340195-425rd7ul author = Smith, Kristine M. title = Zoonotic Viruses Associated with Illegally Imported Wildlife Products date = 2012-01-10 pages = extension = .txt mime = text/plain words = 4427 sentences = 210 flesch = 48 summary = Initial findings from samples collected at several international airports identified parts originating from nonhuman primate (NHP) and rodent species, including baboon, chimpanzee, mangabey, guenon, green monkey, cane rat and rat. These results are the first demonstration that illegal bushmeat importation into the United States could act as a conduit for pathogen spread, and suggest that implementation of disease surveillance of the wildlife trade will help facilitate prevention of disease emergence. Our study is the first to establish surveillance for zoonotic viruses in wild animal products illegally imported into the United States in an effort to prevent the transmission of infectious agents from these shipments. To date, four groups of HTLV viruses found in humans are believed to have originated from corresponding STLV strains in NHP species (including mangabeys, baboons, and chimpanzees) via multiple transmission events [35] . In summary, our study establishes initial surveillance methodology to detect and identify zoonotic pathogens and species of origin of wildlife products entering the United States. cache = ./cache/cord-340195-425rd7ul.txt txt = ./txt/cord-340195-425rd7ul.txt === reduce.pl bib === id = cord-339920-dr5bvpm0 author = Soberman, Roy J. title = CD200R1 Supports HSV-1 Viral Replication and Licenses Pro-Inflammatory Signaling Functions of TLR2 date = 2012-10-17 pages = extension = .txt mime = text/plain words = 7447 sentences = 406 flesch = 54 summary = We generated CD200R1(−/−) mice and employed them to explore both the role of CD200R1 in regulating macrophage signaling via TLR2 as well as the host response to an in vivo, TLR2-dependent model, herpes simplex virus 1 (HSV-1) infection. CD200R1 2/2 macrophages showed a marked decrease in the generation of both IL-6 and CCL5 (Rantes) in response to stimulation by both Pam 2 CSK 4 and HSV-1, whereas no difference was observed in the generation of any cytokine/chemokine in response to the TLR4 ligand bacterial lipopolysaccharide (LPS). These results indicated that CD200R1 directly controls the inducible surface expression of TLR2 either directly or secondary to decreased viral replication and that it may play a role in the amplification of HSV-1 infection. The lack of difference in brain leukocyte scores, and in CCL2 (MCP-1), CCL5 (Rantes), and IL-6 levels indicated that CD200R1 2/2 mice had equivalent or modestly reduced brain inflammation, rather than an enhanced, inflammatory response to HSV-1 infection compared to CD200R1 +/+ mice (see above). cache = ./cache/cord-339920-dr5bvpm0.txt txt = ./txt/cord-339920-dr5bvpm0.txt === reduce.pl bib === id = cord-339392-2ocz784l author = Sharma, Kulbhushan title = Influenza A Virus Nucleoprotein Exploits Hsp40 to Inhibit PKR Activation date = 2011-06-15 pages = extension = .txt mime = text/plain words = 6208 sentences = 375 flesch = 51 summary = BACKGROUND: Double-stranded RNA dependent protein kinase (PKR) is a key regulator of the anti-viral innate immune response in mammalian cells. In case of influenza A virus (IAV) infection, P58(IPK) is known to dissociate from Hsp40 and inhibit PKR activation. PRINCIPAL FINDINGS: Human heat shock 40 protein (Hsp40) was identified as an interacting partner of Influenza A virus nucleoprotein (IAV NP) using a yeast two-hybrid screen. It is known that under stress conditions the expression level of Hsp40 is enhanced and its cellular localization changes from cytoplasmic to nuclear [38] , however its distribution in influenza virus infected cells was not studied. Taken together, these results suggest that during IAV infection, NP induces the dissociation of the P58 IPK -Hsp40 complex leading to an inhibition of PKR activation and downregulation of eIF2a phosphorylation. In case of influenza virus infection, viral NS1 protein is known to bind directly to PKR and inhibit its activation [20, 21] . cache = ./cache/cord-339392-2ocz784l.txt txt = ./txt/cord-339392-2ocz784l.txt === reduce.pl bib === id = cord-337630-ojhk5opy author = Tasic, Velibor title = Clinical and Functional Characterization of URAT1 Variants date = 2011-12-16 pages = extension = .txt mime = text/plain words = 5356 sentences = 313 flesch = 45 summary = reported that mutations in gene SLC22A12 encoding the URAT1 transporter were responsible for most cases of idiopathic renal hypouricaemia [3] . It is noteworthy that reports of idiopathic renal hypouricaemia secondary to mutations in uric acid transporters URAT1 and GLUT9 were initially reported from Japan, Korea and China [23] . Since the hypouricaemia was associated with an elevated FE urate , we undertook mutational analysis of SLC22A12 which revealed a heterozygous missense mutation, leading to amino acid change R434C. SLC22A12 encodes the protein URAT1 and loss of function mutations are responsible for majority of patients with idiopathic renal hypouricaemia. reported a W258X homozygous mutation in a 7 year old child, whose mother and brother were also heterozygous for W258X and had mild hypouricaemia and abnormally high FE urate , whilst his father who was also heterozygous for W258X, had a normal serum uric acid level of 4.6 mg/dL [23] . cache = ./cache/cord-337630-ojhk5opy.txt txt = ./txt/cord-337630-ojhk5opy.txt === reduce.pl bib === id = cord-341914-l2bomgji author = Flies, Andrew S. title = Markedly Elevated Antibody Responses in Wild versus Captive Spotted Hyenas Show that Environmental and Ecological Factors Are Important Modulators of Immunity date = 2015-10-07 pages = extension = .txt mime = text/plain words = 6626 sentences = 297 flesch = 44 summary = Our results show that wild hyenas have significantly higher serum antibody concentrations, including total IgG and IgM, natural antibodies, and autoantibodies than do captive hyenas; there was no difference in the bacterial killing capacity of sera collected from captive and wild hyenas. The striking differences in serum antibody concentrations observed here suggest that complementing traditional immunology studies, with comparative studies of wild animals in their natural environment may help to uncover links between environment and immune function, and facilitate progress towards answering immunological questions associated with the hygiene hypothesis. A more robust understanding of the effects of ecological variables such as pathogen exposure on immune function might be gained by studying immune function in non-traditional species, and assessing how basic immune defenses differ between wild and captive animals with similar genetic backgrounds. cache = ./cache/cord-341914-l2bomgji.txt txt = ./txt/cord-341914-l2bomgji.txt === reduce.pl bib === id = cord-339796-gccnvh0z author = Zhang, Si Min title = Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date = 2015-07-31 pages = extension = .txt mime = text/plain words = 9073 sentences = 403 flesch = 45 summary = The MPER in the human immunodeficiency virus type I (HIV-1) envelope protein (Env) interacts with the lipid bilayers through a cluster of tryptophan (Trp) residues and a C-terminal cholesterol-interacting motif. We found that elimination of the membrane-active elements in MPER peptides, namely, penta Trp→alanine (Ala) substitutions and the disruption of the C-terminal cholesterol-interacting motif through deletion inhibited the anti-viral effect against the pseudotyped HIV-1. The secondary structure study revealed that the penta-Trp→Ala substitutions also increased the helical content in the MPER sequence, which prompted us to study the biological relevance of such mutations in pre-fusion Env. We observed that Ala mutations of Trp664, Trp668 and Trp670 in MPER moderately lowered the intracellular and intraviral contents of Env while significantly elevating the content of another viral structural protein, p55/Gag and its derivative p24/capsid. Here we describe the roles of the Trp residues in the membrane-active MPER sequence in anti-HIV fusion inhibitor design and a surprising role in the biosynthesis of viral structural proteins. cache = ./cache/cord-339796-gccnvh0z.txt txt = ./txt/cord-339796-gccnvh0z.txt === reduce.pl bib === id = cord-340718-amfs4zay author = Zhu, Gengping title = Potential Geographic Distribution of the Novel Avian-Origin Influenza A (H7N9) Virus date = 2014-04-01 pages = extension = .txt mime = text/plain words = 2395 sentences = 103 flesch = 42 summary = CONCLUSIONS/SIGNIFICANCE: Central-eastern China appears to represent an area of high risk for H7N9 spread, but suitable areas were distributed more spottily in the north and only along the coast in the south; highly suitable areas also were identified in western Taiwan. Since the first case was reported, researchers focused on improving diagnosis, understanding location of origin, and methods of cure; however, little is known about the geographic potential of H7N9 or environmental correlates of its transmission, except Butler [3] and He and Chen [4] , who presented ideas based on lessons from the previous avian influenza threat (i.e. H5N1), and Shi [5] and Fang [6] , who mapped the spread potential of H7N9 using spatial regression method. Effective and predictive risk maps can provide a useful means by which to design targeted surveillance efforts [3] [4] [5] [6] , and ecological niche modeling approaches are offering novel views of the geography of potential for disease transmission [9, 18] . cache = ./cache/cord-340718-amfs4zay.txt txt = ./txt/cord-340718-amfs4zay.txt === reduce.pl bib === id = cord-340713-v5sdowb7 author = Bird, Jordan J. title = Country-level pandemic risk and preparedness classification based on COVID-19 data: A machine learning approach date = 2020-10-28 pages = extension = .txt mime = text/plain words = 5669 sentences = 260 flesch = 53 summary = The three four-class classification problems are then explored and benchmarked through leave-one-country-out cross validation to find the strongest model, producing a Stack of Gradient Boosting and Decision Tree algorithms for risk of transmission, a Stack of Support Vector Machine and Extra Trees for risk of mortality, and a Gradient Boosting algorithm for the risk of inability to test. The classification problem of risk is therefore formulated based on prior knowledge of the pandemic in terms of class only, but the attributes to attempt to classify them are purely country-level information regardless of number of cases, deaths and other coronavirus specific data. Country-level pandemic risk and preparedness classification based on COVID-19 data Fig 10 shows a comparison of other models that were explored. Country-level pandemic risk and preparedness classification based on COVID-19 data Table 1 shows the predicted class values for the best models applied to each of the respective risk classification problems. cache = ./cache/cord-340713-v5sdowb7.txt txt = ./txt/cord-340713-v5sdowb7.txt === reduce.pl bib === id = cord-340703-vtuy806l author = Cascio, Antonio title = Low bone mineral density in HIV-positive young Italians and migrants date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4488 sentences = 230 flesch = 55 summary = We aimed to evaluate the bone mineral density (BMD) in naïve antiretroviral (ARV) treated HIV positive patients comparing native Italian group (ItG) to a Migrants group (MiG) upon arrival in Italy. Lumbar site low BMD is an initial condition of bone loss in HIV young patients, especially in female migrants. Our study aims to emphasize the burden of bone health in naïve ARV HIV positive patients and compare the bone density of the native Italian population group (ItG) with that of HIV Migrants (MiG) upon arrival in Italy. Finally, in Table 3 , we report the logistic regression analysis between Low BMD variable (dichotomous) and the independent variables: Gender (dichotomous), BMI (continuous), Hydroxy-Vitamin D (continuous), CD4 (continuous), and Previous Fractures (dichotomous) for the total sample, ItG, and MiG. Our previous reports [13, 14] on the prevalence of Low-BMD in HIV mono-infected patients who underwent ARV therapy showed higher percentage rates of osteopenia (44.9%) and osteoporosis (20.9%) than an agerelated healthy Italian population (18%) [16] . cache = ./cache/cord-340703-vtuy806l.txt txt = ./txt/cord-340703-vtuy806l.txt === reduce.pl bib === id = cord-340656-ltd6ueoi author = Grant, Michael C. title = The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries date = 2020-06-23 pages = extension = .txt mime = text/plain words = 3435 sentences = 199 flesch = 48 summary = title: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries Furthermore, with few included studies (30 in the largest and most recent [12] ), the range of symptoms were limited and the estimates of prevalence are likely to be upwardly biased because only unwell patients (largely those admitted to hospital) were tested in the early phase of the outbreak. We excluded case reports, articles which failed to disaggregate symptoms in adult and paediatric cohorts, studies of patients with prior respiratory infections (e.g. tuberculosis) or co-infections with other viruses (e.g. similar viruses SARS-CoV-1 or HCoV-EMC/2012, etc) and articles which we are unable to translate to English in a timely fashion. Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: A retrospective single center analysis Epidemiological, clinical and virological characteristics of 74 cases of coronavirus-infected disease 2019 (COVID-19) with gastrointestinal symptoms cache = ./cache/cord-340656-ltd6ueoi.txt txt = ./txt/cord-340656-ltd6ueoi.txt === reduce.pl bib === id = cord-340627-xyvzgkxl author = Ornaghi, Sara title = Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3804 sentences = 228 flesch = 51 summary = title: Performance of an extended triage questionnaire to detect suspected cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in obstetric patients: Experience from two large teaching hospitals in Lombardy, Northern Italy Initially, a targeted SARS-CoV-2 screening approach triggered by a positive questionnaire and based on RT-PCR testing of nasopharyngeal swabs was used in women with hospital admission after accessing the Emergency Department. On April 8 th , we changed our policy and started testing all women for SARS-CoV-2 infection independent of the type of hospital admission and the questionnaire result, in agreement with a disposition of the Lombardy Region Health Care Authority. Our study investigated the accuracy of a comprehensive questionnaire thoroughly assessing obstetric patients upon hospital admission to identify cases suspected for SARS-CoV-2 infection. Our data show that thorough assessment of obstetric patients upon hospital admission by means of an exhaustive questionnaire is feasible and effective in discriminating women at low risk of SARS-CoV-2 infection in the context of both a targeted and a universal screening cache = ./cache/cord-340627-xyvzgkxl.txt txt = ./txt/cord-340627-xyvzgkxl.txt === reduce.pl bib === id = cord-340937-6mpob1nx author = Varshney, Mohit title = Initial psychological impact of COVID-19 and its correlates in Indian Community: An online (FEEL-COVID) survey date = 2020-05-29 pages = extension = .txt mime = text/plain words = 3662 sentences = 217 flesch = 51 summary = The survey collected data on socio-demographic and clinical variables related to COVID-19 (based on the current knowledge); along with measuring psychological impact with the help of Impact of Event–revised (IES-R) scale. The survey collected data on socio-demographic and clinical variables related to COVID-19 (based on the current knowledge); along with measuring psychological impact with the help of Impact of Eventrevised (IES-R) scale. The current study investigated the initial psychological impact of COVID-19 outbreak in Indian population. Despite the limitations, this study provides the first cross-sectional data on actual level of psychological impact among Indian community; and how mental health of people is affected during a pandemic of this nature. Our survey is one of the first mental health related data from India, during the initial phase of COVID-19 pandemic and indicated that a significant proportion of them have had a psychological impact during the crisis. cache = ./cache/cord-340937-6mpob1nx.txt txt = ./txt/cord-340937-6mpob1nx.txt === reduce.pl bib === id = cord-340766-aic570x8 author = Kim, Se Jin title = Outcomes of Early Administration of Cidofovir in Non-Immunocompromised Patients with Severe Adenovirus Pneumonia date = 2015-04-15 pages = extension = .txt mime = text/plain words = 3631 sentences = 196 flesch = 41 summary = The present study describes in detail the clinical characteristics and favorable treatment outcomes of non-immunocompromised adults who had experienced severe AdV pneumonia and received early cidofovir administration. Only non-immunocompromised adult patients who fulfilled the criteria for severe community-acquired pneumonia, set out in the Infectious Diseases Society of America/American Thoracic Society Consensus Guidelines [23] , and admitted to the intensive care unit with progressive respiratory failure, defined as a partial pressure of arterial oxygen (PaO 2 )/fraction of inspired oxygen (FiO 2 ) ratio of < 300 mmHg and/or tachypnea (respiration rate >30 breaths/min) [24] , were included in the analysis. Our data suggest that early administration of cidofovir in the course of treatment for respiratory failure as a result of AdV pneumonia in non-immunocompromised patients could be a treatment strategy worth considering, especially in cases of HAdV-55 infection. Our data suggest that early administration of cidofovir in the course of treatment for respiratory failure as a result of AdV pneumonia in non-immunocompromised patients could be a treatment strategy worth considering, especially in cases of HAdV-55 infection. cache = ./cache/cord-340766-aic570x8.txt txt = ./txt/cord-340766-aic570x8.txt === reduce.pl bib === id = cord-339869-euikj8fv author = Cebey-López, Miriam title = Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date = 2016-04-20 pages = extension = .txt mime = text/plain words = 3325 sentences = 201 flesch = 40 summary = However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory Introduction Molecular techniques including polymerase chain reaction (PCR) have increased the sensitivity of detection for common and emerging respiratory viruses, and often reveal the presence of more than one pathogen in respiratory patients. Our study aims to analyze the relationship between viral or bacterial co-infection detected by molecular methods, and the clinical phenotype of children admitted to hospital with lower tract acute respiratory infections (LT-ARI). PICU admission, disease severity according to different scales, need for respiratory support, and length of hospital stay followed a similar pattern in viral mono-versus co-infected children. cache = ./cache/cord-339869-euikj8fv.txt txt = ./txt/cord-339869-euikj8fv.txt === reduce.pl bib === id = cord-340387-ohkjheat author = Wynne, James W. title = Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA date = 2013-01-07 pages = extension = .txt mime = text/plain words = 7004 sentences = 390 flesch = 52 summary = title: Purification and Characterisation of Immunoglobulins from the Australian Black Flying Fox (Pteropus alecto) Using Anti-Fab Affinity Chromatography Reveals the Low Abundance of IgA To further understand the antibody response of bats, the present study purified and characterised the major immunoglobulin classes from healthy black flying foxes, Pteropus alecto. Considering that in other mammalian species, immunoglobulins IgG, IgM and IgA are present in relatively high abundance in serum and tissues, we anticipated that bats would possess a similar immunoglobulin profile. IgG-depleted samples were fractionated by affinity chromatography on immobilised anti-Fab-specific antibodies adopting the same procedure as that described for immobilised Protein A and G except that the binding and washing buffer consisted of 0.3 M NaCl in 50 mM phosphate buffer, pH 7.4. Two major bands were detected by reducing SDS-PAGE in the eluate from both serum and plasma samples; a 66-70 kDa band representative of IgM H , and a 25 kDa band representative of immunoglobulin light chain ( Fig. 3A and 3B ). cache = ./cache/cord-340387-ohkjheat.txt txt = ./txt/cord-340387-ohkjheat.txt === reduce.pl bib === id = cord-342476-0rupk21u author = van Rijn, Anneloes L. title = The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease date = 2019-10-24 pages = extension = .txt mime = text/plain words = 4036 sentences = 220 flesch = 44 summary = The sensitivity, specificity and predictive values of mNGS were calculated based on 24 PCR positive and 1120 PCR negative target results of 88 samples and the normalized read counts (Table 5 ). The following markers were tested for potential associations with clinical severity of exacerbation (exacerbation severity, self-reported exacerbation severity), length of exacerbation and a decrease/increase in FEV 1 (control visit compared to baseline): mNGS pathogen positive versus negative exacerbation (qPCR targets), the number of normalized reads (log, cutoff of �5normalized reads) for the different target viruses (species level). The Shannon diversity scores for bacteriophages (normalized reads, cut-off of �5normalized reads) were comparable for COPD exacerbations of viral aetiology in PCR positive versus negative patients (Fig 5) . In this study, the respiratory virome in patients with COPD exacerbations was analysed with both mNGS and qPCR, and combined with clinical data. cache = ./cache/cord-342476-0rupk21u.txt txt = ./txt/cord-342476-0rupk21u.txt === reduce.pl bib === id = cord-341880-wxliz485 author = Mottaleb, Khondoker Abdul title = COVID-19 induced economic loss and ensuring food security for vulnerable groups: Policy implications from Bangladesh date = 2020-10-16 pages = extension = .txt mime = text/plain words = 7552 sentences = 365 flesch = 60 summary = This study examines the food security and welfare impacts of the COVID-19 induced lockdown on daily wage workers both in the farm and nonfarm sectors in Bangladesh. Then, applying simple econometric estimation processes, this study estimates the minimum compensation packages for the daily wage-based farm and nonfarm households of Bangladesh that ensure their minimum food security during the lockdown. The estimation suggests a common minimum support at US $ 1 per daily wage-based household in Bangladesh to ensure minimum food security during COVID-19 induced lockdown time. Using information of more than 50,000 respondents from the HIES 2016-17 dataset, this study, firstly quantified the economic loss due to the COVID-19 induced lockdown and suggested the minimum support package to ensure food security of the daily wage-based workers in Bangladesh. cache = ./cache/cord-341880-wxliz485.txt txt = ./txt/cord-341880-wxliz485.txt === reduce.pl bib === id = cord-343135-m0pdixw5 author = Marguet, Christophe title = In Very Young Infants Severity of Acute Bronchiolitis Depends On Carried Viruses date = 2009-02-25 pages = extension = .txt mime = text/plain words = 3344 sentences = 182 flesch = 48 summary = BACKGROUND: RT amplification reaction has revealed that various single viruses or viral co-infections caused acute bronchiolitis in infants, and RV appeared to have a growing involvement in early respiratory diseases. Because remaining controversial, the objective was to determine prospectively the respective role of RSV, RV, hMPV and co-infections on the severity of acute bronchiolitis in very young infants. METHODS AND PRINCIPAL FINDINGS: 209 infants (median age: 2.4 months) were enrolled in a prospective study of infants <1 year old, hospitalized for a first episode of bronchiolitis during the winter epidemic season and with no high risk for severe disease. The aim of this prospective study was to assess the clinical severity and viral etiology in infants hospitalized with a first episode of acute bronchiolitis during the epidemic season. In this study, the clinical severity of dual RSV/RV infection was comparable to that observed with RSV, but differed in a shorter duration of hospitalization in the coinfected infants. cache = ./cache/cord-343135-m0pdixw5.txt txt = ./txt/cord-343135-m0pdixw5.txt === reduce.pl bib === id = cord-342133-khrljehj author = Principi, Nicola title = Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease date = 2015-08-12 pages = extension = .txt mime = text/plain words = 5116 sentences = 243 flesch = 49 summary = To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (2009–2010, 2011–2012, and 2013–2014). To evaluate the circulation of the different hBoV types and the possible relationships between viral load, virus genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children attending the emergency room of the Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection arising between November 1 and March 31 during 3 winters (2009-2010, 2011-2012, and 2013-2014) . Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children cache = ./cache/cord-342133-khrljehj.txt txt = ./txt/cord-342133-khrljehj.txt === reduce.pl bib === id = cord-341097-c96hm610 author = Mayer, Craig S. title = Analysis of data dictionary formats of HIV clinical trials date = 2020-10-05 pages = extension = .txt mime = text/plain words = 6899 sentences = 366 flesch = 57 summary = To facilitate aggregation across studies, we defined three types of data dictionary (data element, forms, and permissible values) and created a simple information model for each type. The presented study is limited to data dictionary analysis, although the motivation is to later analyze a large body of past HIV data elements to inform data-driven consensus on CDEs. This study is part of a larger research project titled 'Identification of Research Common Data Elements in HIV/AIDS using data science methods' [12] . We use the term Forms Data Dictionary (or forms dictionary in shorter form) to refer to a data dictionary that provides a full list of titles and descriptions of all Case Report Forms (CRFs) used in the study (or other relevant metadata for data element grouping). Use of categorical data elements in research is extremely common and, as stated earlier, most studies would be expected to provide a permissible value dictionary. cache = ./cache/cord-341097-c96hm610.txt txt = ./txt/cord-341097-c96hm610.txt === reduce.pl bib === id = cord-342519-tjr6dvtt author = Souza, Thiago Moreno L. title = H1N1pdm Influenza Infection in Hospitalized Cancer Patients: Clinical Evolution and Viral Analysis date = 2010-11-30 pages = extension = .txt mime = text/plain words = 5166 sentences = 293 flesch = 48 summary = The aim of the present study was to evaluate the clinical course, duration of viral shedding, H1N1pdm evolution and emergence of antiviral resistance in hospitalized cancer patients with severe H1N1pdm infections during the winter of 2009 in Brazil. Because the analysis of this novel viral infection in cancer patients is an important component of the 2009 pandemics, we conducted a prospective cohort study aimed at evaluating the clinical course of influenza infection, the duration of viral shedding, H1N1pdm evolution and the emergence of antiviral resistance in hospitalized cancer patients with a severe H1N1pdm infection in a reference cancer center during the winter of 2009 in Brazil. Although prolonged influenza A shedding has been observed for a cancer patient infected with the H3N2 seasonal virus [15] , more detailed data on H1N1pdm secretion in severely ill cancer patients are required. cache = ./cache/cord-342519-tjr6dvtt.txt txt = ./txt/cord-342519-tjr6dvtt.txt === reduce.pl bib === id = cord-344782-ond1ziu5 author = Zhang, Jing title = Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date = 2018-10-24 pages = extension = .txt mime = text/plain words = 6003 sentences = 280 flesch = 49 summary = Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. cache = ./cache/cord-344782-ond1ziu5.txt txt = ./txt/cord-344782-ond1ziu5.txt === reduce.pl bib === id = cord-343973-n5ogyxz7 author = Ip, Andrew title = Hydroxychloroquine and tocilizumab therapy in COVID-19 patients—An observational study date = 2020-08-13 pages = extension = .txt mime = text/plain words = 4322 sentences = 239 flesch = 43 summary = In this retrospective observational cohort study drawn from electronic health records we sought to describe the association between mortality and hydroxychloroquine or tocilizumab therapy among hospitalized COVID-19 patients. Subsequently, an observational cohort study of 1376 hospitalized patients from a New York hospital using propensity modeling found no significant association between hydroxychloroquine use and intubation or death (hazard ratio, 1.04, 95% confidence interval, 0.82 to 1.32) [14] . A recently reported randomized Brazilian trial enrolling 504 hospitalized SARS-CoV-2 confirmed patients with mild-to-moderate disease (defined as not requiring significant supplemental oxygen support) found that a 7-day course of hydroxychloroquine either with azithromycin or alone did not result in better clinical outcomes as measured by a seven-level ordinal scale at 15 days [16] . In this observational cohort study we report our survival outcomes with hydroxychloroquine and tocilizumab among hospitalized patients with COVID-19. cache = ./cache/cord-343973-n5ogyxz7.txt txt = ./txt/cord-343973-n5ogyxz7.txt === reduce.pl bib === id = cord-344357-ocyaqs1y author = Fu, Yue-Qiang title = Effect of blood analysis and immune function on the prognosis of patients with COVID-19 date = 2020-10-30 pages = extension = .txt mime = text/plain words = 4482 sentences = 277 flesch = 58 summary = INTRODUCTION: This retrospective study investigated the implications of changes in blood parameters and cellular immune function in patients with Coronavirus Disease 2019 (COVID-19). The percentage of neutrophil count > 6.3×10 9 /L in death group was significantly higher than that in survival group, and multivariate logistic regression showed neutrophil count > 6.3×10 9 /L was independently associated with mortality. The percentage of neutrophil count > 6.3×10 9 /L in death group was significantly higher than that in survival group, and multivariate logistic regression showed neutrophil count > 6.3×10 9 /L was independently associated with mortality. Another study also indicated that COVID-19 patients in the death group had significantly lower lymphocyte count on admission than the recovered group [8] . Collected information included: age; gender; concomitant disease; symptoms; hemoglobin; platelet; leukocyte, neutrophil, and lymphocyte counts; CRP, CD3+, CD4+, CD8+, CD4/8, CD19+, and CD16+56+;IgG, IgM, IgA, IgE, C3, and C4 chest CT; alanine aminotransferase, creatinine; arterial blood gas; procalcitonin; and the result of the RT-PCR assay of SARS-CoV-2 RNA. cache = ./cache/cord-344357-ocyaqs1y.txt txt = ./txt/cord-344357-ocyaqs1y.txt === reduce.pl bib === id = cord-344839-r05p9h0e author = Majmundar, Monil title = Efficacy of corticosteroids in non-intensive care unit patients with COVID-19 pneumonia from the New York Metropolitan region date = 2020-09-09 pages = extension = .txt mime = text/plain words = 4072 sentences = 235 flesch = 44 summary = OBJECTIVE: The purpose of this study was to evaluate the effect of corticosteroids in non-intensive care unit (ICU) patients with COVID-19 pneumonia complicated by acute hypoxemic respiratory failure (AHRF). The purpose of this study was to evaluate the effect of corticosteroids in non-intensive care unit (ICU) patients with COVID-19 pneumonia complicated by acute hypoxemic respiratory failure (AHRF). The results of our study showed that the administration of corticosteroids in patients admitted to the general medical ward with AHRF and a diagnosis of COVID-19 pneumonia was associated with a lower risk of developing the primary outcome composite of ICU transfer, intubation or death. In our analysis of hospitalized patients in the general ward with COVID-19 pneumonia complicated by acute hypoxic respiratory failure, early use of moderate dose systemic corticosteroid for the shorter duration was associated with a significantly lower rate of the primary outcomes of ICU transfer, intubation, or in-hospital death. cache = ./cache/cord-344839-r05p9h0e.txt txt = ./txt/cord-344839-r05p9h0e.txt === reduce.pl bib === id = cord-344870-tbgqulpu author = Lloyd-Smith, James O. title = Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases date = 2007-02-14 pages = extension = .txt mime = text/plain words = 5997 sentences = 290 flesch = 50 summary = METHODOLOGY: This article presents a simulation study exploring the bias, precision, and confidence interval coverage of maximum-likelihood estimates of k from highly overdispersed distributions. In addition to exploring small-sample bias on negative binomial estimates, the study addresses estimation from datasets influenced by two types of event under-counting, and from disease transmission data subject to selection bias for successful outbreaks. This study uses simulated data to assess the bias and precision of NB parameter estimates and the coverage accuracy of CIs for highly overdispersed datasets, addressing the challenges of small datasets as well as potential biases arising in the data collection process. In the epidemiological context that motivated this study, these values x i correspond to the numbers of secondary cases that were infected by n different infectious individuals, but similar data could arise from many other processes. cache = ./cache/cord-344870-tbgqulpu.txt txt = ./txt/cord-344870-tbgqulpu.txt === reduce.pl bib === id = cord-342730-b7y8mybg author = Dellagi, Koussay title = Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009 date = 2011-09-29 pages = extension = .txt mime = text/plain words = 5974 sentences = 283 flesch = 49 summary = In order to assess at the community level, the actual magnitude of the pH1N1/2009v pandemic and the extent of the herd immunity acquired after passage of the epidemic wave, a prospective population serosurvey was conducted in Reunion Island during the passage of the epidemic wave in the 2009 austral winter season (July-December 2009): prevalence of infection was assessed on a weekly basis and seroconversion rates were measured using paired sera. The CoPanFlu-RUN cohort was set up to conduct a prospective population-based study investigating the herd immunity induced by the 2009 pandemic influenza virus and identifying risk factors for pH1N1/2009v infection from paired sera collected in an entire community. Our study shows that a substantial proportion of Reunion Island's population had pre-existing immunity to 2009 pandemic influenza virus with the highest baseline-proxy seroprevalence rate observed among adults aged of 60 years or more. cache = ./cache/cord-342730-b7y8mybg.txt txt = ./txt/cord-342730-b7y8mybg.txt === reduce.pl bib === id = cord-342639-vf9n2vf9 author = Chang, Chung-ke title = Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date = 2013-05-23 pages = extension = .txt mime = text/plain words = 5386 sentences = 243 flesch = 42 summary = For disulfide trapping experiments, we chose mutation sites that would form disulfide linkages based on the crystal packing structures of the SARS-CoV N protein CTD ( Figure 1 ) [9] . Within the crystal asymmetric unit, the SARS-CoV N protein CTD packs as an octamer which stacks to form a helical arrangement with a continuous positively charged surface that could potentially allow the RNA to bind to it through electrostatic interactions ( Fig. 1 ) [9] . By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that SARS-CoV N protein is capable of transient oligomerization in solution through the CTD in the absence of nucleic acids. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA cache = ./cache/cord-342639-vf9n2vf9.txt txt = ./txt/cord-342639-vf9n2vf9.txt === reduce.pl bib === id = cord-345695-5vi9wibk author = Hicks, Lorin L. title = A statistical approach to white-nose syndrome surveillance monitoring using acoustic data date = 2020-10-22 pages = extension = .txt mime = text/plain words = 5489 sentences = 262 flesch = 48 summary = From these data, we developed site-specific prediction models for bat activity to account for seasonal and annual temperature variation prior to known occurrence of WNS. We propose this model-based method for future monitoring efforts that could be used to trigger targeted sampling of individual bats or hibernacula for WNS, in areas where traditional disease surveillance approaches are logistically difficult to implement or because of human-wildlife transmission concerns from COVID-19. We predicted that bat populations in the western U.S. would have low levels of activity during winter months, high levels of activity during the summer, and that acoustic monitoring could be used as an effective approach for disease surveillance in remote areas of the Intermountain West. The model was fit to data from all 41 sites to estimate among-site and among-year variation in activity, but we use the results to generate prediction intervals for four forest sites to depict how a landowner might implement this approach for WNS surveillance monitoring. cache = ./cache/cord-345695-5vi9wibk.txt txt = ./txt/cord-345695-5vi9wibk.txt === reduce.pl bib === id = cord-345717-ktajrf7d author = Monagin, Corina title = Serologic and behavioral risk survey of workers with wildlife contact in China date = 2018-04-03 pages = extension = .txt mime = text/plain words = 4585 sentences = 241 flesch = 45 summary = We report on a study conducted in Guangdong Province, China, to characterize behaviors and perceptions associated with transmission of pathogens with pandemic potential in highly exposed human populations at the animal-human interface. The present study focuses on the potential for zoonotic viral transfer through contact with wildlife in Guangdong prefectures in China, and seeks to augment our understanding and identification of risky populations, occupations, and behaviors, as well as the perceptions of risk at these interfaces. We performed a serological survey and concurrent behavioral questionnaire of individuals with wildlife contact in Guangdong Province, China, in order to better characterize occupations and community-level behavioral risks that contribute to zoonotic transmission of various wildlife pathogens with pandemic potential. We targeted high-risk individuals, defined as individuals with high levels of exposure to wildlife (wild animal blood or bodily fluids)-primarily hunters, persons working in wet markets and restaurants that butcher wild game, who could be followed over a period of time. cache = ./cache/cord-345717-ktajrf7d.txt txt = ./txt/cord-345717-ktajrf7d.txt === reduce.pl bib === id = cord-346586-fxxceffl author = Razanajatovo, Norosoa Harline title = Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013 date = 2018-11-21 pages = extension = .txt mime = text/plain words = 4150 sentences = 213 flesch = 49 summary = CONCLUSION: The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Following the A/H1N1/2009 influenza pandemic that was associated with a high morbidity and an increased risk of mortality among particular groups [13] , a number of countries have strengthened vigilance for the surveillance of severe diseases and deaths in order to rapidly detect new viruses and to provide information in assessing the impact on the population and having operational preparedness plans. A meta-analysis of data from Africa reported that the incidence of RSV in lower acute respiratory infections that required hospitalization ranged from 10-18 per 1000 person year for infants and 3-9 per 1000 person year for children under 5 years of age [26] . cache = ./cache/cord-346586-fxxceffl.txt txt = ./txt/cord-346586-fxxceffl.txt === reduce.pl bib === id = cord-345019-i7zm9bt1 author = Al-Waleedi, Ali Ahmed title = The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4496 sentences = 236 flesch = 55 summary = A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. For early detection of SARS-CoV-2 in Yemen, as in other countries, a case definition, active surveillance, and contact tracing were required [10, 11] . The first 2 months after confirmation of the SARS-CoV-2 epidemic in Yemen was characterized by a 57% hospitalization rate in the southern and eastern parts of the country included in The First 2 Months of the SARS-CoV-2 Epidemic in Yemen our study, 63% of deaths occurring in individuals aged <60 years, confirmatory testing of <50% of the suspected cases, and majority of cases were not related to a defined chain of transmission. cache = ./cache/cord-345019-i7zm9bt1.txt txt = ./txt/cord-345019-i7zm9bt1.txt === reduce.pl bib === id = cord-344152-pb1e2w7s author = Kolatkar, Anand title = C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training date = 2008-02-20 pages = extension = .txt mime = text/plain words = 5434 sentences = 258 flesch = 45 summary = Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members. For example, protein structure/activity data annotations and images may be kept in paper lab notebooks, manuscripts might be stored electronically in Portable Document Format (PDF), and molecular structure coordinate files may be stored on a hard disk to be viewed and analyzed in graphical molecular viewers, to name a few. Most recently we have developed the Collaborative Molecular Modeling Environment (C-ME), a new collaboratory system that integrates many of the key features available on Kinemage, MICE, iSee, and BioCoRE systems into one thin-client Windows application. cache = ./cache/cord-344152-pb1e2w7s.txt txt = ./txt/cord-344152-pb1e2w7s.txt === reduce.pl bib === id = cord-347465-yu6oj30v author = Kurskaya, Olga title = Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 – 2017) date = 2018-09-18 pages = extension = .txt mime = text/plain words = 3383 sentences = 194 flesch = 45 summary = METHODS: We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. RESULTS: We detected 1128 (72.3%) samples were positive for at least one virus. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. In conclusion, in our study we investigated the etiological structure of acute respiratory viral infections in hospitalized children in Novosibirsk, Russia, and evaluated age and seasonal distribution of the various respiratory viruses. cache = ./cache/cord-347465-yu6oj30v.txt txt = ./txt/cord-347465-yu6oj30v.txt === reduce.pl bib === id = cord-348055-azlb1zy1 author = Patel, Mira C. title = Enterovirus D-68 Infection, Prophylaxis, and Vaccination in a Novel Permissive Animal Model, the Cotton Rat (Sigmodon hispidus) date = 2016-11-04 pages = extension = .txt mime = text/plain words = 7758 sentences = 351 flesch = 50 summary = To determine effect of the EV-D68 infection on the induction of an inflammatory response, we focused on the lung tissue and measured the expression of cotton rat mRNA for several chemokines, Type I and Type II interferons (IFNs), cytokines, and select IFN-inducible genes following VANBT infection. As there are no current animal models for EV-D68 and information regarding relevant disease-related outcomes from human cases is limited, we herein characterized EV-D68 infection in cotton rats by measuring viral load and vRNA (negative or total) in either nose or lung tissues until 4 days p.i., assessing mRNA expression of various chemokines, IFNs, and proinflammatory cytokines, and lung histology. Although the replication cycle of VANBT appeared to be short-lived, its profile of viral titer in the nose over time (showing clear virus eclipse at 4 h, rising quickly and reaching a peak by 10 h p.i.), and their differences with the output virus obtained after infection with different strains demonstrate that VANBT replicates in upper respiratory tract of cotton rats. cache = ./cache/cord-348055-azlb1zy1.txt txt = ./txt/cord-348055-azlb1zy1.txt === reduce.pl bib === id = cord-346089-u31n0qxa author = McDade, Thomas W. title = High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay date = 2020-08-14 pages = extension = .txt mime = text/plain words = 2232 sentences = 140 flesch = 52 summary = title: High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay To address this problem we developed a serological test for SARS-CoV-2 IgG antibodies that requires only a single drop of finger stick capillary whole blood, collected in the home and dried on filter paper (dried blood spot, DBS). Serological testing for SARS-CoV-2 IgG antibodies in DBS samples can facilitate seroprevalence assessment in community settings to address epidemiological questions, monitor duration of antibody responses, and assess if antibodies against the spike protein correlate with protection from reinfection. In addition, we demonstrate the feasibility and utility of quantifying SARS-CoV-2 antibodies in self-collected DBS with results from a community-based sample enriched with health care workers. We have validated a DBS assay to facilitate large-scale serological testing of SARS-CoV-2 IgG antibodies, and results from our feasibility study document a high rate of household transmission. cache = ./cache/cord-346089-u31n0qxa.txt txt = ./txt/cord-346089-u31n0qxa.txt === reduce.pl bib === id = cord-346067-zly8p0y7 author = Ruiz-Irastorza, Guillermo title = Second week methyl-prednisolone pulses improve prognosis in patients with severe coronavirus disease 2019 pneumonia: An observational comparative study using routine care data date = 2020-09-22 pages = extension = .txt mime = text/plain words = 4513 sentences = 221 flesch = 52 summary = title: Second week methyl-prednisolone pulses improve prognosis in patients with severe coronavirus disease 2019 pneumonia: An observational comparative study using routine care data Our therapeutic protocol was updated on April 3 rd 2020, including the recommendation of MP for patients with COVID-19 pneumonia with altered/worsening inflammatory parameters (lymphopenia, thrombocytopenia, rising ferritin, D-dimers and or C-reactive protein) and clinical deterioration, particularly those showing impending respiratory failure with decreasing SpO2/FiO2 values. Other independent predictors of death included a previous diagnosis of arterial hypertension, the use of non-pulse glucocorticoids, a high-risk CURB65 category and SpO2/FiO2 at week 2 ( Table 2 ). Glucocorticoid use, however, should not be indiscriminate, but rather restricted to patients with laboratory evidence of inflammation and progressing respiratory compromise, and best used as short-course pulse therapy (125-250 mg/d of methyl-prednisolone during 3 days) administered during the second week after the onset of symptoms, where the hyperinflammatory reaction takes usually place. cache = ./cache/cord-346067-zly8p0y7.txt txt = ./txt/cord-346067-zly8p0y7.txt === reduce.pl bib === id = cord-346347-r4ork18p author = Borrion, Hervé title = Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China date = 2020-10-14 pages = extension = .txt mime = text/plain words = 7552 sentences = 358 flesch = 49 summary = There are reasons to believe that crime-related performance measures during a pandemic period, or other disasters, may not match the idealised resilience triangle, but rather resemble the dipper-shaped function depicted in Fig 2. Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China RD(n) provides a useful measure to monitor the operating level (%) of offenders. In the case where the crime level in this phase exceeds the pre-Disruptive Event (t DE ) level (μ 7 �μ 1 ), two sub-indicators can be used to measure the ecosystem's resilience during the recovery phase. Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China between τ − and τ + shows it took significantly longer for crime to drop than to return to its expected level. cache = ./cache/cord-346347-r4ork18p.txt txt = ./txt/cord-346347-r4ork18p.txt === reduce.pl bib === id = cord-346819-11fkgzaa author = Khan, Mohd Imran title = Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4405 sentences = 291 flesch = 57 summary = title: Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. The genome analysis of the SARS-CoV-2 strains from 13 different countries showed a large number of mutations within the major structural proteins. This study provides a deeper insight into the emergence of these mutations within the major structural as well as nsp encoded by the SARS-CoV-2 genome from different countries. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations backbone RMSD was also noticed (Fig 4A) . cache = ./cache/cord-346819-11fkgzaa.txt txt = ./txt/cord-346819-11fkgzaa.txt === reduce.pl bib === id = cord-348807-9xxc5hyl author = Cuomo, Raphael E. title = Sub-national longitudinal and geospatial analysis of COVID-19 tweets date = 2020-10-28 pages = extension = .txt mime = text/plain words = 3235 sentences = 143 flesch = 43 summary = METHODS: In an effort to better understand the impacts of COVID-19, we concurrently assessed the geospatial and longitudinal distributions of Twitter messages about COVID-19 which were posted between March 3rd and April 13th and compared these results with the number of confirmed cases reported for sub-national levels of the United States. This study suggests that, across subnational areas within the United States, there exists a highly variable threshold of perceived dangerousness and/or intrusiveness required to activate outbreak-related conversations on social media platforms such as Twitter, a finding that can inform future outbreak communication and health promotion strategies. Concurrent geospatial and longitudinal analyses also indicate that predominantly rural areas of the United States increased engagement in COVID-19 social media conversations at later stages of the study timeframe. This study is unique in that it uses Twitter data as a proxy measure for assessing the concurrent longitudinal and geospatial distributions of attention to COVID-19 across local and regional communities in the United States. cache = ./cache/cord-348807-9xxc5hyl.txt txt = ./txt/cord-348807-9xxc5hyl.txt === reduce.pl bib === id = cord-346314-o9fjpqaj author = Jarboui, Mohamed Ali title = Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date = 2012-11-15 pages = extension = .txt mime = text/plain words = 10004 sentences = 521 flesch = 36 summary = Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. Following the detailed annotation of the quantitative abundance changes in the nucleolar protein composition upon Tat expression, we focussed on the Tat-affected cellular complexes and signalling pathways associated with ribosome biogenesis, spliceosome, molecular chaperones, DNA replication and repair and metabolism and discuss their potential involvement in HIV-1 pathogenesis. In this study, we investigated the quantitative changes in the nucleolar proteome of Jurkat T cells constitutively expressing HIV-1 Tat (86aa) versus their Tat-negative counterpart, using stable isotope labelling with amino acids in cell culture (SILAC) technology, followed by ESI tandem mass spectrometry and implemented the experimental approach described in Figure 1A . cache = ./cache/cord-346314-o9fjpqaj.txt txt = ./txt/cord-346314-o9fjpqaj.txt === reduce.pl bib === id = cord-347014-88zmtky7 author = Esposito, Susanna title = Sensitivity and Specificity of Soluble Triggering Receptor Expressed on Myeloid Cells-1, Midregional Proatrial Natriuretic Peptide and Midregional Proadrenomedullin for Distinguishing Etiology and to Assess Severity in Community-Acquired Pneumonia date = 2016-11-15 pages = extension = .txt mime = text/plain words = 5518 sentences = 247 flesch = 44 summary = STUDY DESIGN: This study aimed to evaluate the diagnostic accuracy of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1), midregional proatrial natriuretic peptide (MR-proANP) and midregional proadrenomedullin (MR-proADM) to distinguish bacterial from viral community-acquired pneumonia (CAP) and to identify severe cases in children hospitalized for radiologically confirmed CAP. CONCLUSIONS: This study indicates that in children with CAP, sTREM-1, MR-proANP, and MR-proADM blood levels have poor abilities to differentiate bacterial from viral diseases or to identify severe cases, highlighting that PCT maintains the main role at this regard. A global evaluation of the results of this study seemed to indicate that in children with CAP, sTREM-1, MR-proANP, and MR-proADM blood levels are unable to differentiate bacterial from viral diseases or to identify severe cases. cache = ./cache/cord-347014-88zmtky7.txt txt = ./txt/cord-347014-88zmtky7.txt === reduce.pl bib === id = cord-348243-e5tdb08v author = Schermer, Bernhard title = Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3958 sentences = 236 flesch = 56 summary = METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays. cache = ./cache/cord-348243-e5tdb08v.txt txt = ./txt/cord-348243-e5tdb08v.txt === reduce.pl bib === id = cord-346858-18q8rxzg author = Hossain, Md. Tanvir title = Social and electronic media exposure and generalized anxiety disorder among people during COVID-19 outbreak in Bangladesh: A preliminary observation date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3462 sentences = 171 flesch = 51 summary = Classified as a pandemic by the World Health Organization, the novel Coronavirus Disease (COVID-19) has spread to Bangladesh since early March of 2020, and people are getting daily updates from the social and electronic media. For this cross-sectional study, data were collected from 880 participants by a self-administered online-based questionnaire relating personal characteristics, self-rate health (SRH), SME, and EME with anxiety. The mental health burden of the COVID-19 infected patients and the healthcare professionals, fearing the persisting social prejudice and stigma generated from 'overexposure' to media 'misinformation,' forced some people to commit suicide [22] [23] [24] . At present, the level of anxiety generated from the exposure to social and electronic media during COVID-19 pandemic is not known in Bangladesh, while some other countries have addressed the issue vigorously [13, 18, 36] . cache = ./cache/cord-346858-18q8rxzg.txt txt = ./txt/cord-346858-18q8rxzg.txt === reduce.pl bib === id = cord-347317-qcghtkk0 author = Russo, Lucia title = Tracing day-zero and forecasting the COVID-19 outbreak in Lombardy, Italy: A compartmental modelling and numerical optimization approach date = 2020-10-30 pages = extension = .txt mime = text/plain words = 9776 sentences = 397 flesch = 51 summary = For the estimation of the day-zero of the outbreak in Lombardy, as well as of the "effective" per-day transmission rate for which no clinical data are available, we have used the proposed SEIIRD simulator to fit the numbers of new daily cases from February 21 to the 8th of March. Among the perplexing problems that mathematical models face when they are used to estimate epidemiological parameters and to forecast the evolution of the outbreak, two stand out: (a) the uncertainty regarding the day-zero of the outbreak, the knowledge of which is crucial to assess the stage and dynamics of the epidemic, especially during the first growth period, and (b) the uncertainty that characterizes the actual number of the asymptomatic infected cases in the total population (see e.g. cache = ./cache/cord-347317-qcghtkk0.txt txt = ./txt/cord-347317-qcghtkk0.txt === reduce.pl bib === id = cord-348499-7ll7sd3o author = Manderstedt, Eric title = Genetic variation in the C-type lectin receptor CLEC4M in type 1 von Willebrand Disease patients date = 2018-02-01 pages = extension = .txt mime = text/plain words = 5449 sentences = 262 flesch = 53 summary = von Willebrand factor (VWF) levels in healthy individuals and in patients with type 1 von Willebrand disease (VWD) are influenced by genetic variation in several genes, e.g. VWF, ABO, STXBP5 and CLEC4M. Additional studies of STXBP5 and STX2 [8] and CLEC4M [9, 10] have confirmed that single nucleotide variants (SNVs) in these genes are associated with the variation observed for plasma levels of VWF. CLEC4M also binds to VWF [9] and variants in this gene contribute to the variation in the VWF level observed both in normal individuals [4] and in type 1 VWD patients [9, 10] . The present study aimed to screen comprehensively for genetic variation in the CLEC4M gene in individuals from 106 unrelated type 1 VWD families by re-sequencing the gene region (excluding exon 4) and genotyping the polymorphic neck region (exon 4) of the gene. cache = ./cache/cord-348499-7ll7sd3o.txt txt = ./txt/cord-348499-7ll7sd3o.txt === reduce.pl bib === id = cord-349029-zyfop43z author = Dobrovolny, Hana M. title = Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date = 2020-08-10 pages = extension = .txt mime = text/plain words = 4596 sentences = 233 flesch = 48 summary = In order to estimate how effective these strategies will be, we will need a better understanding of the role of asymptomatic individuals in SARS-CoV-2 spread and the effect the proportion and relative infectiousness of asymptomatics have on the time course of the epidemic. In this paper, we study a compartmental epidemic model that includes asymptomatic infections to determine the role that asymptomatic individuals might play in the spread of SARS-CoV-2. We apply our model to data from SARS-CoV-2 epidemics in California, Florida, New York, and Texas, finding that a large number of infections in these states are unreported and that relaxing social distancing measures too early will cause a rapid spike in infections driven in part by these hidden infections. For the SARS-CoV epidemics examined here, the model predicts that there are far more asymptomatic or unreported cases at the peak of the infection, suggesting that there might be widespread community transmission if stay-at-home orders are relaxed too early. cache = ./cache/cord-349029-zyfop43z.txt txt = ./txt/cord-349029-zyfop43z.txt === reduce.pl bib === id = cord-349217-vpih1wvs author = Petropoulos, Fotios title = Forecasting the novel coronavirus COVID-19 date = 2020-03-31 pages = extension = .txt mime = text/plain words = 3159 sentences = 185 flesch = 60 summary = Assuming that the data used is reliable and that the future will continue to follow the past pattern of the disease, our forecasts suggest a continuing increase in the confirmed COVID-19 cases with sizable associated uncertainty. While all three data patterns show an exponential increase, the trends of both the confirmed cases and the deaths were reduced in the mid of February; a second exponential increase is observed in late February and March as a result of the increased number of cases in South Korea, Iran, and Europe. The mean estimate (point forecast) for the confirmed cases ten-days-ahead was 209 thousand with the 90% prediction intervals ranging from about 38 to 534 thousand cases. However, the estimated uncertainty by splitting the data is considerably lower, possibly since the confirmed cases outside Mainland China have significantly increased only recently. cache = ./cache/cord-349217-vpih1wvs.txt txt = ./txt/cord-349217-vpih1wvs.txt === reduce.pl bib === id = cord-350842-4m82l5t8 author = Xing, Jun title = Study of the mental health status of medical personnel dealing with new coronavirus pneumonia date = 2020-05-19 pages = extension = .txt mime = text/plain words = 3219 sentences = 150 flesch = 47 summary = Factors affecting the mental health and status of medical personnel based on their significance from high to low are: the degree of suspicion that they were infected when the novel coronavirusrelated symptoms occurred, the level of concern whether they and their family members have been infected, age, whether they have supported in affected areas in Hubei Province, designated hospitals, and other places for the novel coronavirus, and whether family members support them working on the front line (p < 0.05). The results of this study have shown that the factors affecting the mental health status of medical personnel based on the significance from high to low are: the degree of suspicion that they were infected when the novel coronavirus-related symptoms occurred, the level of concern whether they and their family members have been infected, age, whether they have supported in affected areas in Hubei Province, designated hospitals, and other places for the novel coronavirus, and whether their family members support them working on the front line. cache = ./cache/cord-350842-4m82l5t8.txt txt = ./txt/cord-350842-4m82l5t8.txt === reduce.pl bib === id = cord-349781-l93978vq author = Cong, Yu title = MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells date = 2018-03-22 pages = extension = .txt mime = text/plain words = 5653 sentences = 311 flesch = 51 summary = Little is known about the pathogenesis and innate antiviral response in primary human monocyte-derived macrophages (MDMs) and dendritic cells (MDDCs) upon MERS-CoV infection. In this study, we assessed MERS-CoV replication as well as induction of inflammatory cytokines and chemokines in MDMs and immature and mature MDDCs. Immature MDDCs and MDMs were permissive for MERS-CoV infection, while mature MDDCs were not, with stimulation of proinflammatory cytokine and chemokine upregulation in MDMs, but not in MDDCs. To further evaluate the antiviral activity of well-defined drugs in primary antigen presenting cells (APCs), three compounds (chloroquine, chlorpromazine and toremifine), each with broad-spectrum antiviral activity in immortalized cell lines, were evaluated in MDMs and MDDCs to determine their antiviral effect on MERS-CoV infection. However, MERS-CoV continued to propagate in immature MDDCs up to 8 days pi, demonstrating differential infection and replication capabilities in MDMs and immature MDDCs. To compare the ability of MERS-CoV to induce innate immune responses in three types of APCs, the release of cytokines and chemokines was measured from virus-or mock-infected cells. cache = ./cache/cord-349781-l93978vq.txt txt = ./txt/cord-349781-l93978vq.txt === reduce.pl bib === id = cord-349476-iac9fak3 author = Mao, Liang title = Evaluating the Combined Effectiveness of Influenza Control Strategies and Human Preventive Behavior date = 2011-10-17 pages = extension = .txt mime = text/plain words = 4662 sentences = 245 flesch = 43 summary = The simulation outcomes suggest that weaker control strategies could suffice to contain influenza epidemics, because individuals voluntarily adopt preventive behavior, rendering these weaker strategies more effective than would otherwise have been expected. Health policy makers are recommended to review current control strategies and comprehend preventive behavior patterns of local populations before making decisions on influenza containment. The control of influenza primarily involves applying health resources to affected people, known as control strategies, for example, medical treatment for infected individuals, closure of affected workplaces/schools, and travel restriction to affected communities [4] . Results from the influenza-only model indicate the effectiveness of control strategies without individual preventive behavior. Meanwhile, outcomes from the dual-diffusion model show the combined effectiveness of both control strategies and individual preventive behavior. These two modeled effectiveness are compared to a baseline epidemic scenario, which represents a worst situation of no control strategies and no preventive behavior. This research estimates the combined effectiveness of both control strategies and individual preventive behavior. cache = ./cache/cord-349476-iac9fak3.txt txt = ./txt/cord-349476-iac9fak3.txt === reduce.pl bib === id = cord-350443-ca5avyjf author = Zhang, Lei title = Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date = 2012-02-16 pages = extension = .txt mime = text/plain words = 7958 sentences = 383 flesch = 49 summary = This study reviews trends in notifiable infectious diseases in China, in their historical context, discusses the current epidemiological state of these infections and their implications for disease surveillance and public health interventions. The total number of diagnosed and death cases were estimated by multiplying morbidity and mortality rates by the overall Chinese population in the study years. In 2008, the three most frequently reported disease types included viral hepatitis (38.3%), bacterial infections (33.3%) and STIs and HIV (9.8%), which account for 5.4, 4.8 and 1.4 million diagnosed cases respectively during the period 2005-2008 (Table 1) . Second, the rapid rise in the number of notified cases of STIs, especially HIV infection, and viral hepatitis in China is associated with growth of the sex industry, increasingly frequent risky sexual behaviours and an increasing number of sexual partners in the general Chinese population. cache = ./cache/cord-350443-ca5avyjf.txt txt = ./txt/cord-350443-ca5avyjf.txt === reduce.pl bib === id = cord-351868-w4d45fue author = Zuwała, Kaja title = The Nucleocapsid Protein of Human Coronavirus NL63 date = 2015-02-20 pages = extension = .txt mime = text/plain words = 6708 sentences = 421 flesch = 53 summary = Surprisingly, analysis of the subcellular localization of the N protein of HCoV-NL63 revealed that, differently than homologous proteins from other coronaviral species except for SARS-CoV, it is not present in the nucleus of infected or transfected cells. In order to test subcellular localization of the N protein in LLC-MK2 cells, the maxFP-Green-N/NL63-N encoding RNA was prepared based on the original plasmid. For EMSA assay 10 μg of RNA or DNA corresponding in sequence to the N-NL63 gene (prepared in the same manner as for the transfection of eukaryotic cells) was incubated in buffered solution (5 mM Tris, 50 mM NaCl, pH8.0) with 10 μg of the NTD or CTD for 30 minutes at room temperature. The constructs of NTD and CTD used in this study were designed based on literature data, HCoV-NL63 N protein amino acid sequence alignment with known homologs and on the comparative analysis of currently available crystal structures of these homologs. cache = ./cache/cord-351868-w4d45fue.txt txt = ./txt/cord-351868-w4d45fue.txt === reduce.pl bib === id = cord-349911-dx8wvqkm author = Dahl, Viktor title = Communicable Diseases Prioritized According to Their Public Health Relevance, Sweden, 2013 date = 2015-09-23 pages = extension = .txt mime = text/plain words = 4092 sentences = 208 flesch = 49 summary = Ten pathogens in the highest priority group (Borrelia, calicivirus, Campylobacter, Echinococcus multilocularis, hepatitis C virus, HIV, respiratory syncytial virus, SARSand MERS coronavirus, tick-borne encephalitis virus and varicella-zoster virus) did not have any surveillance of typing results. The Public Health Agency of Sweden identified the need to use a structured method that takes relevant aspects into account in order to rationally prioritize between different pathogens when allocating resources for surveillance. The Robert Koch Institute invited ten senior external experts and ten internal experts and asked them to score the pathogens with -1, 0 or 1 for ten variables"Incidence", "Work and school absenteeism", "Health care utilization", "Chronicity of illness or sequelae", "Case fatality rate", "Proportion of events requiring public health actions", "Trend", "Public attention", "Prevention and Treatment possibilities") ( Table 1 ). We used a standardized procedure developed at the Robert Koch Institute to generate a list of pathogens prioritized for surveillance to be used by the Public Health Agency of Sweden. cache = ./cache/cord-349911-dx8wvqkm.txt txt = ./txt/cord-349911-dx8wvqkm.txt === reduce.pl bib === id = cord-351142-g20f6bxc author = Kiaghadi, Amin title = Assessing COVID-19 risk, vulnerability and infection prevalence in communities date = 2020-10-29 pages = extension = .txt mime = text/plain words = 6778 sentences = 313 flesch = 48 summary = A finer spatial resolution is important from a vulnerability and risk standpoint as demonstrated in a recent study that showed that the poorest neighborhoods in Houston, Texas, might be at a higher risk of hospitalization from COVID-19 [14] based on an analysis of the Centers for Disease Control (CDC) underlying risk factors for severe COVID-19 cases [4] that include: asthma, Chronic Obstructive Pulmonary Disease (COPD), heart disease, hypertension, diabetes, and a history of heart attacks or strokes. In this study, we develop a rigorous planning tool at the census tract level that examines influential determinants of vulnerability to COVID-19 in 5 broad categories (with 46 variables) that include: 1) access to medical services, 2) underlying medical conditions, 3) environmental exposures, 4) vulnerability to natural disasters and 5) sociodemographic, behavioral, and lifestyle factors. Fig 9A shows the normalized total number of confirmed COVID-19 cases as of August 16, 2020, in Harris County at the census tract level. cache = ./cache/cord-351142-g20f6bxc.txt txt = ./txt/cord-351142-g20f6bxc.txt === reduce.pl bib === id = cord-352200-i05h8csb author = Xu, Yi title = Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date = 2012-04-27 pages = extension = .txt mime = text/plain words = 5286 sentences = 278 flesch = 47 summary = title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. As a whole, 81388 distinct unigenes have been identified and the results indicated that SRBSDV infection can potentially perturb primary metabolism and the ubiquitin-proteasome pathway of WBPH and activate immune regulatory systems, such as RNA interfering, autophagy and antimicrobial peptide production. However, some unigenes were obtained only from viruliferous or non-viruliferous samples (data not shown) and we believe these differences may be caused by distinctions that arise from long-term ecological adaptation to virus infection. In addition, GO analysis also showed a similar distribution of gene functions for non-viruliferous and viruliferous WBPH (Figure 4 ), indicating that the number of genes expressed in each GO category was not significantly affected by SRBSDV infection. cache = ./cache/cord-352200-i05h8csb.txt txt = ./txt/cord-352200-i05h8csb.txt === reduce.pl bib === id = cord-351387-i0zamkpd author = Witte, Katrin title = The Pelargonium sidoides Extract EPs 7630 Drives the Innate Immune Defense by Activating Selected MAP Kinase Pathways in Human Monocytes date = 2015-09-25 pages = extension = .txt mime = text/plain words = 4360 sentences = 220 flesch = 49 summary = In summary, we demonstrate that EPs 7630 activates human monocytes, induces MAP kinase-dependent pro-inflammatory cytokines in these cells, and specifically modulates their production capacity of mediators known to lead to an increase of acute phase protein production in the liver, neutrophil generation in the bone marrow, and the generation of adaptive Th17 and Th22 cells. In the first setting, PBMCs were stimulated with EPs 7630 (3 and 30 μg/ml), Escherichia coli 0127:B8 lipopolysaccharide (TLR4 ligand; 100 ng/ml; Sigma-Aldrich), polyinosinic-polycytidylic acid [poly (I:C); 10 μg/ml; Sigma-Aldrich], a cytokine mixture of IL-1β, IL-2 and IL-12 (10 ng/ml each; R&D systems), anti-CD3 (Orthoclone; Cilag) and anti-CD28 (R&D systems) monoclonal antibodies (1 μg/ml each), or were left without specific treatment (0.1% ethanol as solvent control) for 4 and 24 h, before cell culture supernatant was recovered for ELISA cytokine production analysis. Our data show that EPs 7630 strongly and dose-dependently induced the production of the pro-inflammatory cytokines TNF-α and IL-6 in human blood immune cells. cache = ./cache/cord-351387-i0zamkpd.txt txt = ./txt/cord-351387-i0zamkpd.txt === reduce.pl bib === id = cord-351185-3y3gou6v author = Buckles, Thomas C. title = Rapid exposure of macrophages to drugs resolves four classes of effects on the leading edge sensory pseudopod: Non-perturbing, adaptive, disruptive, and activating date = 2020-05-29 pages = extension = .txt mime = text/plain words = 10061 sentences = 465 flesch = 45 summary = However, rapid drug addition to cultured macrophages revealed four distinct classes of effects on the leading edge pseudopod: (i) non-perturbing drug exposures yielded no detectable change in pseudopod morphology (acetylsalicylic acid, diclofenac); (ii) adaptive exposures yielded temporary collapse of the extended pseudopod and its signature PI(3,4,5)P(3) lipid signal followed by slow recovery of extended pseudopod morphology (ibuprofen, acetaminophen); (iii) disruptive exposures yielded long-term pseudopod collapse (Gö6976, wortmannin); and (iv) activating exposures yielded pseudopod expansion (PDGF). In contrast, ibuprofen and acetaminophen are classified as adaptive because rapid addition of either drug to polarized cells yields short-term collapse of the leading edge pseudopod and loss of the PIP 3 signal, followed by slow recovery. In contrast to the four therapeutic adaptive drugs, the two non-clinical control inhibitors wortmannin and Gö6976 are each known to directly inhibit key components of the leading edge positive feedback loop and rapid addition is observed herein to trigger long term collapse of the pseudopod with no detected recovery as previously observed [26, 30, [50] [51] [52] [53] [54] . cache = ./cache/cord-351185-3y3gou6v.txt txt = ./txt/cord-351185-3y3gou6v.txt === reduce.pl bib === id = cord-352222-zq9o66i4 author = Rajatonirina, Soatiana title = Outcome Risk Factors during Respiratory Infections in a Paediatric Ward in Antananarivo, Madagascar 2010–2012 date = 2013-09-12 pages = extension = .txt mime = text/plain words = 4137 sentences = 245 flesch = 46 summary = BACKGROUND: Acute respiratory infections are a leading cause of infectious disease-related morbidity, hospitalisation and mortality among children worldwide, and particularly in developing countries. MATERIALS AND METHODS: We conducted a prospective study in a paediatric ward in Antananarivo from November 2010 to July 2012 including patients under 5 years old suffering from respiratory infections. CONCLUSION: Co-mordidity, low-income and age under 6 months increase the risk of severe outcome for children infected by numerous respiratory pathogens. Our study aimed to evaluate the risk factors associated with the evolution and outcome of respiratory illnesses in patients aged under 5 years old hospitalised in one of the four main public hospitals in Antananarivo. In our study, Streptococcus pneumoniae was the most common bacterial pathogen as in other studies of hospitalised patients with acute respiratory illness, and Haemophilus influenzae type B was the next most frequent [16] [17] [18] [19] . cache = ./cache/cord-352222-zq9o66i4.txt txt = ./txt/cord-352222-zq9o66i4.txt === reduce.pl bib === id = cord-352403-4591ewsa author = Hartwig, Stacey M. title = Depletion of Alveolar Macrophages Ameliorates Virus-Induced Disease following a Pulmonary Coronavirus Infection date = 2014-03-07 pages = extension = .txt mime = text/plain words = 3773 sentences = 194 flesch = 55 summary = In addition, a significant increase in the frequency and total number of Tregs in the lung tissue and lung airways was observed following MHV-1 infection in mice depleted of AM. We have previously shown that intranasal MHV-1 infection of C3H/HeJ mice, which harbor a natural mutation in the gene that encodes toll-like receptor 4 (TLR4) [15, 16] , results in increased morbidity and mortality along with severe pulmonary disease as compared to the wild-type C3H/HeN mice [17] . We observed a significant (p,0.05) decrease in the total number of MHV-1-specific IFN-c-producing CD4 T cells in the BAL of CL-treated mice as compared to PBS controls ( Figure 4C ). We also observed a significant increase in the total number and frequency of Tregs following MHV-1 infection in both the airways and lung tissue of the CL-treated mice. cache = ./cache/cord-352403-4591ewsa.txt txt = ./txt/cord-352403-4591ewsa.txt === reduce.pl bib === id = cord-351990-aham72b9 author = Radin, Jennifer M. title = Epidemiology of Pathogen-Specific Respiratory Infections among Three US Populations date = 2014-12-30 pages = extension = .txt mime = text/plain words = 4511 sentences = 220 flesch = 43 summary = METHODS: Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US–Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. This study aimed to describe characteristics associated with specific respiratory pathogens, as well as the etiology, seasonality, and coinfection rates among three US populations: military recruits, Department of Defense (DoD) beneficiaries, and civilians living near the US-Mexico border. Additionally, the following demographic and clinical signs and symptoms were collected from each FRI and SARI case: sex, age, study population, month of illness, pneumonia, sore throat, cough, nausea, shortness of breath, congestion, pink eye, body ache, headache, temperature, number of days of symptoms before seeking care, and date of seeking care. cache = ./cache/cord-351990-aham72b9.txt txt = ./txt/cord-351990-aham72b9.txt === reduce.pl bib === id = cord-351918-pu7i1jfe author = Baek, Yae Jee title = A mathematical model of COVID-19 transmission in a tertiary hospital and assessment of the effects of different intervention strategies date = 2020-10-26 pages = extension = .txt mime = text/plain words = 4902 sentences = 278 flesch = 51 summary = The effects of different intervention strategies such as front door screening, quarantine unit for newly admitted patients, early testing of suspected infected people, and personal protective equipment for both medical staff and visitors were evaluated. The model suggested that the early testing (within eight hours) of infected cases and monitoring the quarantine ward for newly hospitalized patients are effective measures for decreasing the incidence of COVID-19 within a hospital (81.3% and 70% decrease of number of incident cases, respectively, during 60 days). Setting the population vector η as the number of staff, and the stabilized number of inflow and outflow to each department for visitors, we construct the WAIFW matrix, W, by assuming that it is proportional to the contact rate matrix [8, 9] : The diagram for the SEIR (susceptible-exposed-infectious-recovered) model with compartments of doctor, nurse, patient, and caregiver. cache = ./cache/cord-351918-pu7i1jfe.txt txt = ./txt/cord-351918-pu7i1jfe.txt === reduce.pl bib === id = cord-351098-x729wpp7 author = Long, Rachel B. title = Characterizing trends in human-wildlife conflicts in the American Midwest using wildlife rehabilitation records date = 2020-09-11 pages = extension = .txt mime = text/plain words = 6361 sentences = 244 flesch = 37 summary = The purpose of this study was to examine the value of wildlife rehabilitation facility admissions records for informing understanding of local human-wildlife conflicts and wildlife disease trends by 1) identifying the top reasons for admission to this facility, 2) examining how occurrences as measured by admitted cases may fluctuate monthly and across taxa, and 3) analyzing trends in commonly admitted disease cases. To examine how human-wildlife conflict as measured by admissions to this facility may vary seasonally and across taxonomic groups, we assessed changes in mean cases admitted per month via Chi-squared tests. We further examined the top four identified specific causes of admission to the wildlife rehabilitation facility: orphaned, dog attacks, cat attacks, and vehicle strikes. Our study demonstrates the value of wildlife rehabilitation records for characterizing local human-wildlife conflicts and potentially select disease trends, as well as how occurrences may fluctuate seasonally and impact taxa differently. cache = ./cache/cord-351098-x729wpp7.txt txt = ./txt/cord-351098-x729wpp7.txt === reduce.pl bib === id = cord-352564-2j4pjjwk author = Dominguez, Samuel R. title = Human Coronavirus HKU1 Infection of Primary Human Type II Alveolar Epithelial Cells: Cytopathic Effects and Innate Immune Response date = 2013-07-24 pages = extension = .txt mime = text/plain words = 4449 sentences = 199 flesch = 46 summary = Because they are the natural target cells for respiratory virus infection, primary human respiratory epithelial cell cultures provide the ideal in vitro systems for investigation of cell factors required for growth of respiratory human viruses, for analysis of their interactions with viruses and their innate immune responses to infection, and for isolation and propagation of novel respiratory pathogens. Here we demonstrate that HCoV-HKU1 can infect and be serially propagated in primary human alveolar type II cells but not in alveolar type I-like cells or alveolar macrophages at the air-liquid interface. Titers of viral RNA in the wash from the apical surface of the cells were determined by qRT-PCR at the indicated time points, and HCoV-HKU1 Infection of Type II Alveolar Cells PLOS ONE | www.plosone.org cultures were fixed and immunolabeled with antibodies to the HCoV-HKU1 spike glycoprotein to identify infected cells. In summary, HCoV-HKU1 can infect, be serially propagated, and induce an anti-viral response in human alveolar type II cells maintained at an air-liquid interface. cache = ./cache/cord-352564-2j4pjjwk.txt txt = ./txt/cord-352564-2j4pjjwk.txt === reduce.pl bib === id = cord-353200-5csewb1k author = Jehi, Lara title = Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 4344 sentences = 226 flesch = 40 summary = OBJECTIVE: To characterize a large cohort of patients hospitalized with COVID-19, their outcomes, develop and validate a statistical model that allows individualized prediction of future hospitalization risk for a patient newly diagnosed with COVID-19. DESIGN: Retrospective cohort study of patients with COVID-19 applying a least absolute shrinkage and selection operator (LASSO) logistic regression algorithm to retain the most predictive features for hospitalization risk, followed by validation in a temporally distinct patient cohort. MEASUREMENTS: Demographic, clinical, social influencers of health, exposure risk, medical co-morbidities, vaccination history, presenting symptoms, medications, and laboratory values were collected on all patients, and considered in our model development. Hospitalization risk prediction and outcomes in COVID-19 PLOS ONE | https://doi.org/10.1371/journal.pone.0237419 August 11, 2020 2 / 15 ethical restrictions by the Cleveland clinic regulatory bodies including the institutional review Board and legal counsel. We also develop and validate a statistical model that can assist with individualized prediction of hospitalization risk for a patient with COVID-19. cache = ./cache/cord-353200-5csewb1k.txt txt = ./txt/cord-353200-5csewb1k.txt === reduce.pl bib === id = cord-350398-w75flrwv author = Sampath, Rangarajan title = Comprehensive Biothreat Cluster Identification by PCR/Electrospray-Ionization Mass Spectrometry date = 2012-06-29 pages = extension = .txt mime = text/plain words = 11138 sentences = 581 flesch = 50 summary = Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry. In addition to detecting the threat organisms, the biothreat assay described here also detects virulence factors associated with three of the agents: Bacillus anthracis (pXO1 and pXO2), Yersinia pestis (pla and caf), and Vibrio cholera (ctx1). PCR primers were designed to conserved regions within the selected target genes such that the targeted threat agent was clearly identified and differentiated from its near-neighbor species ( Table 1) . In the biothreat assay, the Francisella biocluster is identified by two genus-specific primer pairs targeting the asd (BCT2328) and galE (BCT2332) genes ( Table 1) . cache = ./cache/cord-350398-w75flrwv.txt txt = ./txt/cord-350398-w75flrwv.txt === reduce.pl bib === id = cord-352511-gkm7i62s author = Yamada, Yoshiyuki title = Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date = 2009-07-02 pages = extension = .txt mime = text/plain words = 5731 sentences = 317 flesch = 55 summary = title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells Here we report that acquisition of the cell–cell fusion activity by amino acid mutations in the S protein determines the infectivity of IBV in cultured cells. This study demonstrates that acquisition of the cell–cell fusion activity in S protein determines the selection and/or adaptation of a coronavirus from chicken embryo to cultured cells of human and animal origins. In this study, we report that acquisition of the cell-cell fusion activity by point mutations in the spike (S) protein of avian coronavirus infectious bronchitis virus (IBV) plays a critical role in adaptation and/or selection of a variant that infects cultured cells. Sequence comparison of two S protein constructs, S(EP3) and S(CK), cloned from EP3 and CK-adapted IBV strains, respectively, showed amino acid substitutions at 31 positions (Fig. 1a) . cache = ./cache/cord-352511-gkm7i62s.txt txt = ./txt/cord-352511-gkm7i62s.txt === reduce.pl bib === id = cord-353866-0r1b44id author = Sun, Hongpeng title = Changes of Adult Population Health Status in China from 2003 to 2008 date = 2011-12-02 pages = extension = .txt mime = text/plain words = 3421 sentences = 185 flesch = 54 summary = Stratified analyses revealed significant subpopulation disparities in rate ratios for 2008/2003 in the presence of chronic disease, with greater increases among women, elderly, the Han nationality, unmarried and widow, illiterate, rural, and regions east of China than other groups. This study aimed to describe the male and female adult Chinese population health status in multiple dimensions, including overall morbidity, presence of illness in the last 2 weeks and chronic disease in the last 6 months, and healthy behavior as regards smoking, alcohol consumption, and physical activity, using data from the most recent National Health Services Surveys by the Chinese government in 2003 and 2008. However, overall Chinese adult population health status has not been improved due to short time and small proportion of residents performing frequent exercise; hence it seems that the prevalence and burden of chronic diseases will continue to grow. cache = ./cache/cord-353866-0r1b44id.txt txt = ./txt/cord-353866-0r1b44id.txt === reduce.pl bib === id = cord-352219-z245sb3s author = Tallam, Aravind title = Gene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages date = 2016-02-12 pages = extension = .txt mime = text/plain words = 9117 sentences = 467 flesch = 43 summary = Furthermore, using literature information and transcription factor prediction models, we re-constructed raw gene regulatory networks (GRNs) for IRG1 in mouse and human macrophages. We further implemented a contextualization algorithm that relies on genome-wide gene expression data to infer putative cell type-specific gene regulatory interactions in mouse and human macrophages, which allowed us to predict potential transcriptional regulators of IRG1. Among the computationally identified regulators, siRNA-mediated gene silencing of interferon regulatory factor 1 (IRF1) in macrophages significantly decreased the expression of IRG1/CAD at the gene and protein level, which correlated with a reduced production of itaconic acid. Putative transcriptional regulators of IRG1 were hypothesized from the resulting GRN and tested using siRNA-mediated gene silencing experiments in mouse and human macrophages under LPS stimulation. Although the human data were obtained from primary cells, while the mouse analysis was conducted using the macrophage cell line RAW264.7, it is tempting to speculate that the transcriptional machinery inducing IRG1 expression, with the exception of IRF1, is mostly species-specific, as highlighted by the different transcriptional regulators identified in the two species (Table 1) . cache = ./cache/cord-352219-z245sb3s.txt txt = ./txt/cord-352219-z245sb3s.txt === reduce.pl bib === id = cord-352522-qnvgg2e9 author = Langille, Morgan G. I. title = BioTorrents: A File Sharing Service for Scientific Data date = 2010-04-14 pages = extension = .txt mime = text/plain words = 2994 sentences = 158 flesch = 51 summary = In this study we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. A BitTorrent software client (see Table 1 ) uses the data in the torrent file to contact the tracker and allow transferring of the data between computers containing either full or partial copies of the dataset. Information about each dataset on BioTorrents is supplied on a details page giving a description of the data, number of files, date added, user name of the person who created the dataset, and various other details including a link to the actual torrent file. As the number of datasets and users of BioTorrents increases, and to improve on transfer speeds on a geospatial scale (i.e. across countries and continents), we would encourage other institutions to automatically download and share all or some of the data on BioTorrents. cache = ./cache/cord-352522-qnvgg2e9.txt txt = ./txt/cord-352522-qnvgg2e9.txt === reduce.pl bib === id = cord-352720-z1cvjc2y author = Díaz-Corvillón, Pilar title = Routine screening for SARS CoV-2 in unselected pregnant women at delivery date = 2020-09-29 pages = extension = .txt mime = text/plain words = 4061 sentences = 244 flesch = 49 summary = While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. cache = ./cache/cord-352720-z1cvjc2y.txt txt = ./txt/cord-352720-z1cvjc2y.txt === reduce.pl bib === id = cord-353245-es7b1rs0 author = Song, Deping title = Molecular Characterization and Phylogenetic Analysis of Porcine Epidemic Diarrhea Viruses Associated with Outbreaks of Severe Diarrhea in Piglets in Jiangxi, China 2013 date = 2015-03-19 pages = extension = .txt mime = text/plain words = 4259 sentences = 176 flesch = 55 summary = Compared to the PEDV CV777 strain, CH/JX-1/2013 and CH/JX-2/2013 had some unique genetic characteristics in the proximal region of the 5'-UTRs. Phylogenetic analysis of the complete genomes and the structural proteins revealed that CH/JX-1/2013 and CH/JX-2/2013 had a close relationship with post-2010 Chinese PEDV strains and US strains identified in 2013. Genetic characteristics were observed between the two groups: 1) compared to genome sequences of the members in G1, four insertions, 20803G, 20810CAGGGTGTCAA20820, 20830G, 21042AAT21044 and two deletions, 20842A, 21097CGTGAT21102, existed in the N-terminal domain (NTD) of the S protein in G 2 members; 2) the three field PEDV strains of JS2008, JS2008new and SD-M together with two attenuated PEDV strains, DR13 and vaccine_KC189944, were clustered into subgroup 1b. Notably, an amino acid substitution was found in the middle of one neutralizing epitope Phylogenetic trees based on the complete genome, aa sequences of structural proteins and ORF3 of PEDV strains. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China cache = ./cache/cord-353245-es7b1rs0.txt txt = ./txt/cord-353245-es7b1rs0.txt === reduce.pl bib === id = cord-352447-bc1pf272 author = Nishida, Yu title = Novel prognostic biomarkers of pouchitis after ileal pouch-anal anastomosis for ulcerative colitis: Neutrophil-to-lymphocyte ratio date = 2020-10-26 pages = extension = .txt mime = text/plain words = 3481 sentences = 197 flesch = 47 summary = Despite conflicting results, the development of pouchitis in patients with UC, as reported in several studies, has been linked to various factors, including primary sclerosing cholangitis [2, 4] , other extraintestinal manifestations of inflammatory bowel disease [4, 8, 9] , young age at UC diagnosis [4] , preoperative terminal ileal inflammation [10, 11] , extensive colonic disease [10], presence of interleukin-1 receptor antagonist gene allele 2 [12] , total steroid dose of > 10000 mg [13] , use of infliximab [14] , neutrophil percentage of > 65% [13] , and presence of perinuclear antineutrophil cytoplasmic antibodies [15, 16] . Therefore, our study aimed to evaluate the clinical utility of the NLR for predicting the development of pouchitis after IPAA in patients with UC. Third, we were unable to evaluate the reported pouchitis predictive factors, such as extraintestinal manifestations of inflammatory bowel disease, preoperative terminal ileal inflammation, the presence of interleukin-1 receptor antagonist gene allele 2, total steroid dose of >10000 mg, or presence of perinuclear antineutrophil cytoplasmic antibodies owing to the retrospective design of the study. cache = ./cache/cord-352447-bc1pf272.txt txt = ./txt/cord-352447-bc1pf272.txt === reduce.pl bib === id = cord-353869-l53ms3q8 author = Friesen, Robert H. E. title = New Class of Monoclonal Antibodies against Severe Influenza: Prophylactic and Therapeutic Efficacy in Ferrets date = 2010-02-08 pages = extension = .txt mime = text/plain words = 4680 sentences = 202 flesch = 44 summary = METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the prophylactic and therapeutic efficacy of the human monoclonal antibody CR6261 against lethal challenge with the highly pathogenic avian H5N1 virus in ferrets, the optimal model of human influenza infection. CONCLUSIONS/SIGNIFICANCE: These data demonstrate the prophylactic and therapeutic efficacy of this new class of human monoclonal antibodies in a highly stringent and clinically relevant animal model of influenza and justify clinical development of this approach as intervention for both seasonal and pandemic influenza. Mean decline in body weight at the end of the experiment was 6.2% in the group of ferrets that received CR6261 4 hours after challenge ( Figure 2B) , which was significantly less (p = 0.025) than the 10.1% observed in control animals. These findings were in accordance with the observation that the mean lung weights of ferrets treated with CR6261 at 4 hours post challenge were lower compared to the control group (5.7 g versus 14.9 g, p,0.001; Figure 2F ). cache = ./cache/cord-353869-l53ms3q8.txt txt = ./txt/cord-353869-l53ms3q8.txt === reduce.pl bib === id = cord-356132-1nisyl5r author = Wang, Huiyao title = The psychological distress and coping styles in the early stages of the 2019 coronavirus disease (COVID-19) epidemic in the general mainland Chinese population: A web-based survey date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3022 sentences = 148 flesch = 43 summary = The population with younger age (F = 102.04), unmarried (t = 15.28), with history of visiting Wuhan in the past month (t = -40.86), with history of epidemics occurring in the community (t = -10.25), more concern with media reports (F = 21.84), perceived more impacts of the epidemic outbreak (changes over living situations, F = 331.71; emotional control, F = 1863.07; epidemic-related dreams, F = 1642.78) and negative coping style (t = 37.41) had higher level of psychological distress. The general mainland Chinese population with unmarried, history of visiting Wuhan in the past month, perceived more impacts of the epidemic and negative coping style had higher level of psychological distress in the early stages of COVID-19 epidemic. Unmarried, history of visiting Wuhan, more serious changes over living situations, more difficult of emotional control, higher frequency of epidemic-related dreams, and negative coping style in the general population showed higher level of psychological distress. cache = ./cache/cord-356132-1nisyl5r.txt txt = ./txt/cord-356132-1nisyl5r.txt === reduce.pl bib === id = cord-353253-kk2q71vg author = Itokawa, Kentaro title = Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3327 sentences = 179 flesch = 52 summary = Soon after the pandemic was recognized by epidemiologists, a group of biologists comprising the ARTIC Network, has devised a multiplexed polymerase chain reaction (PCR) protocol and primer set for targeted whole-genome amplification of SARS-CoV-2. In our experience, the low to zero depth for those two amplicons was the most frequent bottleneck for using the ARTIC primer set V1 to sequence all targeted genomic regions from samples with middle to low viral load (Ct > 27). The results indicated that preventing primer dimerformation is an effective measure to improve coverage bias in the ARTIC Network's SARS-CoV-2 genome sequencing protocol, and may be applicable to other PrimalSeq methods in general. The formation of primer-dimers is a major cause of coverage bias in the ARTIC Network's multiplex PCR protocol for SARS-CoV-2 genome sequencing. A proposal of an alternative primer for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing (manuscript version 1) cache = ./cache/cord-353253-kk2q71vg.txt txt = ./txt/cord-353253-kk2q71vg.txt === reduce.pl bib === id = cord-355874-nz6eqcdb author = Wang, Le title = A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia date = 2016-09-14 pages = extension = .txt mime = text/plain words = 3067 sentences = 160 flesch = 54 summary = title: A GeXP-Based Assay for Simultaneous Detection of Multiple Viruses in Hospitalized Children with Community Acquired Pneumonia In this study, we used the GeXP-based assay for simultaneous detection of 20 types/subtypes of viruses in 1699 nasopharyngeal specimens collected from hospitalized children with CAP. To evaluate the sensitivity of the GeXP assay, nucleic acid from all 20 target viruses and the internal control pcDNA3.1 (+) DNA were mixed to make the template pool. In the present study, we applied multiplex RT-PCR together with automated capillary electrophoresis, namely the GeXP-based assay, to detect virus in 1699 nasopharyngeal specimens from hospitalized children with CAP. We showed that the GeXP-based assay had high sensitivity and specificity for simultaneous detection of multiple viruses, and about 65% of cases tested were positive for virus. The development of a GeXP-based multiplex reverse transcription-PCR assay for simultaneous detection of sixteen human respiratory virus types/ subtypes cache = ./cache/cord-355874-nz6eqcdb.txt txt = ./txt/cord-355874-nz6eqcdb.txt === reduce.pl bib === id = cord-353410-tbmtg88k author = Sharma, Shreela V. title = Using a rapid assessment methodology to identify and address immediate needs among low-income households with children during COVID-19 date = 2020-10-01 pages = extension = .txt mime = text/plain words = 3942 sentences = 205 flesch = 56 summary = Due to COVID-19-related school closures, states were under "shelter in place" orders, and Brighter Bites administered a rapid assessment survey to identify social needs among their families. While overall results of the qualitative thematic analysis for the n = 1048 participants are presented elsewhere (Sharma et al., under review) , a qualitative analysis of participant responses in the high-risk group revealed four major themes presented in Table 2 : fear of contracting COVID-19, disruption of employment status, financial hardship, and exacerbated food insecurity. Conducting a COVID-19 rapid response survey was a purposeful decision on part of Brighter Bites to identify those with highest need during this time of crisis and develop a framework to immediately address a variety of social needs among those in the "high risk" category. cache = ./cache/cord-353410-tbmtg88k.txt txt = ./txt/cord-353410-tbmtg88k.txt === reduce.pl bib === id = cord-354000-jxqskt4k author = Warren, Cody J. title = The Antiviral Restriction Factors IFITM1, 2 and 3 Do Not Inhibit Infection of Human Papillomavirus, Cytomegalovirus and Adenovirus date = 2014-05-14 pages = extension = .txt mime = text/plain words = 4420 sentences = 265 flesch = 47 summary = Here, we demonstrate that IFN-α or -β treatment of keratinocytes substantially decreases human papillomavirus 16 (HPV16) infection while robustly inducing IFITM1, 2 and 3 expression. IFITM protein expression induced by type I IFN inhibits infection of many RNA viruses [22] [23] [24] [25] [26] [27] [28] [29] [30] . Therefore, we analyzed induction of IFITM1, 2 and 3 expression by IFN-b treatment in human keratinocytes, the natural host cells for HPV. To determine the effect of IFITMs on HPV16 entry, HeLa cells stably expressing c-Myc-tagged IFITM1, 2 or 3 or with vector alone ( Fig. 2A-B) were infected with HPV16-LucF. Using various epithelial cell lines and primary keratinocytes expressing IFITMs, we show that HPV infection is surprisingly enhanced by IFITM1 and IFITM3 overexpression (Fig. 2) . Taken together, our results suggest that HPV and other DNA viruses may have evolved to avoid IFITM1, 2 and 3 restriction during entry into host cells. cache = ./cache/cord-354000-jxqskt4k.txt txt = ./txt/cord-354000-jxqskt4k.txt === reduce.pl bib === id = cord-356364-ipi81ce3 author = Ho, Bo-Lin title = Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease date = 2015-12-14 pages = extension = .txt mime = text/plain words = 5038 sentences = 277 flesch = 62 summary = In the present study, MERS-CoV main protease (M(pro)) is expressed; the dimerization of the protein and its relationship to catalysis are investigated. The colorimetry-based peptide substrate, TSAVLQ-para-nitroanilide (TQ6-pNA) (purity 95-99% by HPLC; GL Biochem Ltd, Shanghai, China), was used to measure the proteolytic activity of MERS-CoV M pro and its mutants throughout the course of the study as described previously [25, 28] . In addition, although the K d values of wild-type SARS-CoV M pro without or with substrates show no significant difference (Table 2) , it was possible to detect substrate-induced dimerization at a protein concentration of 1 μM by AEC [33] . Biochemical and AUC studies indicated that MERS-CoV M pro shows almost the same proteolytic activity as SARS-CoV M pro ; although it is a monomer in aqueous buffer and displays substrate-induced dimerization (Fig 6) . cache = ./cache/cord-356364-ipi81ce3.txt txt = ./txt/cord-356364-ipi81ce3.txt === reduce.pl bib === id = cord-354052-x4ckzw64 author = Li, Chunhua title = Manipulation of the Porcine Epidemic Diarrhea Virus Genome Using Targeted RNA Recombination date = 2013-08-02 pages = extension = .txt mime = text/plain words = 4932 sentences = 256 flesch = 53 summary = We have established a reverse genetics system for PEDV based on targeted RNA recombination that allows the modification of the 3′-end of the viral genome, which encodes the structural proteins and the ORF3 protein. All mPEDV infected cells stained positive both with the polyclonal MHV serum and with the monoclonal antibody directed against the PEDV nucleocapsid protein confirming the purity and the identity of the chimeric virus. Donor RNAs transcribed from the pPEDV and pPEDV-DORF3 transfer vectors were electroporated into mPEDV-infected L cells after which we were able to recover and purify the r-wtPEDV and PEDV-DORF3 viruses in VERO cells. Thus, the PEDV-DORF3/GFP and PEDV-DORF3/RLuc virus were preincubated with dilutions of serum obtained from an experimentally PEDV-infected pig and control serum, and the mixtures were subsequently added to VERO cells and incubated after which the GFP and Renilla luciferase expression was recorded at 9 and 6 hours p.i., respectively (Fig. 5D) . cache = ./cache/cord-354052-x4ckzw64.txt txt = ./txt/cord-354052-x4ckzw64.txt === reduce.pl bib === id = cord-354763-odzrco6q author = Drake, John M. title = Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date = 2006-12-20 pages = extension = .txt mime = text/plain words = 5739 sentences = 283 flesch = 46 summary = We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. We also retrospectively explore the effect of societal learning during the 2003 outbreak of SARS in Singapore, using weekly data on the time between onset of symptoms and removal of infectious individuals. Finally, we discuss societal and epidemiological factors that might affect societal learning, we observe that a difficult task during the early stages of an outbreak is to estimate the learning rate and suggest that the rate estimated here might be used as prior information in future outbreaks, and we conclude by recommending rapid investment in research at the time of initial detection when actions taken to reduce disease spread can be most efficient and cost effective. cache = ./cache/cord-354763-odzrco6q.txt txt = ./txt/cord-354763-odzrco6q.txt === reduce.pl bib === id = cord-353596-8iqjugcx author = Bédubourg, Gabriel title = Evaluation and comparison of statistical methods for early temporal detection of outbreaks: A simulation-based study date = 2017-07-17 pages = extension = .txt mime = text/plain words = 5603 sentences = 313 flesch = 53 summary = Based on a large dataset of simulated weekly surveillance time series, we performed a systematic assessment of 21 statistical algorithms, 19 implemented in the R package surveillance and two other methods. We estimated false positive rate (FPR), probability of detection (POD), probability of detection during the first week, sensitivity, specificity, negative and positive predictive values and F(1)-measure for each detection method. Then, to identify the factors associated with these performance measures, we ran multivariate Poisson regression models adjusted for the characteristics of the simulated time series (trend, seasonality, dispersion, outbreak sizes, etc.). The objective of this paper is to evaluate the performance of 21 statistical methods applied to large simulated datasets for outbreak detection in weekly health surveillance. Table 2 presents averaged FPR, specificity, POD, POD1week, sensitivity, negative predictive value, positive predictive value and F 1 -measure for all 42 scenarios and all past and current outbreak amplitude and duration and for α = 0.01. cache = ./cache/cord-353596-8iqjugcx.txt txt = ./txt/cord-353596-8iqjugcx.txt === reduce.pl bib === id = cord-355259-779czzzx author = Yang, Xiaoyun title = A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus date = 2014-10-15 pages = extension = .txt mime = text/plain words = 6143 sentences = 324 flesch = 47 summary = Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract. To this purpose, we applied swine influenza virus to a model we previously set up using porcine respiratory mucus, pseudorabies virus (PRV) and single particle tracking (SPT) [20] . This does not only confirm the beneficial effect of neuraminidase on releasing SIV from respiratory mucus, but also highlights bidirectional synergistic interactions between influenza virus and bacterial infections. cache = ./cache/cord-355259-779czzzx.txt txt = ./txt/cord-355259-779czzzx.txt === reduce.pl bib === id = cord-354547-eomm1sl5 author = Wang, Jibin title = Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date = 2009-03-16 pages = extension = .txt mime = text/plain words = 6319 sentences = 295 flesch = 51 summary = title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding In this study, we report that interaction between coronavirus membrane protein (M) and actin with functional implication in facilitating virion assembly and budding. Similarly, analysis of cells expressing the M protein either on its own or together with the Myc-tagged actin by Western blot with anti-M polyclonal antibodies showed the detection of the full-length glycosylated (two upper bands) and unglycosylated (25 kDa) forms of the M protein (Fig. 2, lanes 5 and 6) . In cells transfected with both wild type and MD5 constructs with or without IBV infection, detection of similar amounts of M protein was observed (Fig. 5b, top two panels, lanes 1 and 2) , suggesting that both constructs were expressed at similar efficiencies. cache = ./cache/cord-354547-eomm1sl5.txt txt = ./txt/cord-354547-eomm1sl5.txt === reduce.pl bib === id = cord-353730-owcapg8h author = Dietrich, Jes title = Inducing Dose Sparing with Inactivated Polio Virus Formulated in Adjuvant CAF01 date = 2014-06-23 pages = extension = .txt mime = text/plain words = 7885 sentences = 389 flesch = 53 summary = The CAF01 adjuvant has previously been shown to be a safe and potent adjuvant with several antigens, and here we show that in mice IPV formulated with CAF01 induced increased systemic protective immunity measured by binding and neutralization antibody titers in serum. Based on neutralization titers obtained from mice vaccinated with a range of doses from 30 DU (D-Units) to 0.1 DU (data not shown) we choose 20 DU as a full mouse dose and 2 DU as the dose formulated into the CAF01 adjuvant (indicated dose units in the all experiments correspond to polio virus type-1 D antigen units). Taken together, compared to IM administration a side by side ID+IM administration with a CAF01-adjuvanted vaccine followed by an IM administration did not negatively affect systemic immunity, measured by antibody binding and neutralization titers and T cell IFN-c secretion (Fig. 6) . cache = ./cache/cord-353730-owcapg8h.txt txt = ./txt/cord-353730-owcapg8h.txt ===== Reducing email addresses cord-268524-lr51ubz5 cord-312033-iarl77n0 cord-353200-5csewb1k Creating transaction Updating adr table ===== Reducing keywords cord-000013-pr9i9swk cord-000063-tex6bgab cord-000166-36bfeoqv cord-000050-tfcerilc cord-000079-533xlisc cord-000266-xwfptmmv cord-000131-ugbwvy6j cord-000006-104sqoxz cord-000008-3dgjv0x1 cord-000082-jy7j8sh0 cord-000269-v4jochbe cord-000574-7eflwyxk cord-000255-73nlxqgk cord-000540-bbjmcdo5 cord-000366-u4649rtx cord-000140-5kapn32k cord-000408-pt3b4yc7 cord-000224-2lz03oqb cord-000176-z76vjkxg cord-000077-d441jam3 cord-000460-h3owwjao cord-000588-3wok0n21 cord-000720-5b936n3g cord-000143-2xvd5ogf cord-000765-r7y1cqou cord-000501-qz68gtd4 cord-000547-adfigzc1 cord-000434-ff2zadol cord-000666-je9t4i6q cord-000321-ee7q7jhv cord-000742-0r4z1zea cord-000346-9b6yz3f4 cord-000182-ni6iyzdn cord-000556-uu1oz2ei cord-000736-6f8vyziv cord-000580-dcid9emx cord-000638-ss1435el cord-000267-xroo7z7g cord-000336-57es391o cord-001045-jm60nxc2 cord-000326-a18rch1f cord-001014-8yrpcl94 cord-000725-rafwlw0t cord-000581-ewx5xhrb cord-000721-leedutqo cord-000265-llilwq1u cord-001007-645zegcv cord-000158-d08buwtu cord-000375-fvfl0bn1 cord-000413-h2e6h076 cord-000248-zueoyesj cord-000837-rdpsxb4n cord-000719-o7ttiu97 cord-000478-88wo4xen cord-000715-zl1s82yi cord-000208-th0wddvc cord-000609-dpcgl6ig cord-000851-uylgyhs8 cord-000809-9voqa1oy cord-000536-0mn1gbll cord-000642-mkwpuav6 cord-000689-8lvzab4i cord-000180-howix091 cord-000554-p4ufea6x cord-000877-usz7pnvu cord-000726-tonaaft2 cord-000695-g5sum116 cord-000981-6vloa2w3 cord-000912-6l6c7jpq cord-000895-z5rdf0mi cord-000833-m6abyuvx cord-000352-qzkpik3z cord-000410-av8b8g8c cord-000425-isw6jeir cord-000868-vnwpzsu8 cord-000539-uh3q65we cord-000347-gdra8xhj cord-000979-cav9n18w cord-000359-y0m1utug cord-000261-ip32y0j5 cord-000959-nk2thkme cord-000374-gt2pwc9b cord-000947-psguw47w cord-000322-8ctsa9sd cord-001129-gi2kswai cord-000905-1rhlu59c cord-000723-wo20st5w cord-001011-vjxmrmfc cord-001021-nag4at49 cord-001083-vy1nxax2 cord-000866-dr2uow4m cord-001039-qocuprwb cord-001090-qg2r691d cord-001071-bjx5td52 cord-000786-ofpcgxce cord-001120-fxd533b4 cord-001099-jirkkkvy cord-001123-n2e4s7bu cord-001088-dugsh7mp cord-001199-9khx93c0 cord-001253-3jnkki5z cord-001092-pkps5j8w cord-001162-z8cbbit3 cord-001251-forh7lw4 cord-001145-hc9ssruz cord-001126-uqr00nzd cord-001186-jkg7qkj6 cord-001421-6t5puo6p cord-001455-n7quwr4s cord-001432-d4zavkcn cord-001249-awn9ayy6 cord-001368-ymp1pj3r cord-001207-yjaiybwf cord-001435-ebl8yc92 cord-001219-517gka4h cord-001343-3euy4u9k cord-001263-hqxiyxfj cord-001571-drcfdv9z cord-001446-mpuovmeb cord-001213-gxqufddb cord-001359-c1uom5f7 cord-001363-irysq6pf cord-001843-ceatyj3o cord-001546-ndz3oarf cord-001447-oi7bkm4z cord-001599-pfdnmzx2 cord-001280-skavefji cord-001142-puj74k7y cord-001420-b4zcvd04 cord-001781-afg1nmib cord-001734-bbeznd3r cord-001601-tsuz3j40 cord-001254-y2knt8g0 cord-001620-yy5gq0ki cord-002141-9mxi4dzi cord-001603-vlv8x8l8 cord-001383-hww0watl cord-002624-59nznqsd cord-002094-7tewne3a cord-001707-piyo00yg cord-001639-p9mbmfaq cord-002023-7zd5zhbz cord-001909-yy9xp5ms cord-002044-9xgt3tf4 cord-000237-mticfoic cord-002043-z1b7pj3s cord-001716-lbtdex4p cord-001958-2gt3fwpy cord-001460-eo2bxxbq cord-001117-llb4f74a cord-001748-7e8px4vx cord-000984-64p3wpav cord-001078-5m29nugu cord-001065-j4hvyyoi cord-001982-arczqdza cord-001605-8p06bpt1 cord-001898-ntqyjqqk cord-000937-8vk89i4h cord-001387-2g9dc5z4 cord-000341-d3a06n3f cord-001275-a9o2dvke cord-001964-iy6qzq58 cord-001537-i34vmfpp cord-001761-yvd1n42f cord-002834-2htnywef cord-000813-gagakqw4 cord-002222-rgqwm3vb cord-001983-zo9yngfc cord-001865-ji83zmy7 cord-002473-2kpxhzbe cord-002602-2qvyhjlp cord-002601-d8908t93 cord-002305-qq73gr9y cord-002100-dt5zvebj cord-002811-5hrydciz cord-002901-u4ybz8ds cord-001910-6zfz2ns5 cord-002705-ntokyoai cord-003024-17f1evh3 cord-002398-0a3okta0 cord-002621-sq5iod1w cord-003244-abs3tc3r cord-002890-g7aje88u cord-002913-k5b6abyk cord-002180-gsdk5x3e cord-002426-5e1xn7kj cord-002935-jq1xumrh cord-002560-pue5q5wp cord-002957-gw2cow0d cord-003551-jzfl4xuk cord-003602-wtestt8i cord-002848-w6q1x1zs cord-004017-gcmpatlb cord-003503-t6cnjwpd cord-003125-iptisi1m cord-004091-gex0zvoa cord-003841-7uaj9hmx cord-003062-qm8kalyt cord-003507-22ylifqo cord-010368-plpghewn cord-004068-d66lwylf cord-003484-ylpa702c cord-003548-zuwt7gk5 cord-003270-vu9b5a14 cord-002973-bkr4ndl2 cord-003404-eqgc8v7y cord-002953-4rqoenhr cord-003712-mafz21no cord-002889-fie121ns cord-003377-9vkhptas cord-012387-1ogcxd7b cord-002939-6a3ga6v9 cord-011857-brbqgbpz cord-012461-v8d91fdo cord-048471-7jszm1nd cord-013333-7jx4t0ol cord-012891-heqsfzkm cord-048358-z5klydpi cord-003498-4ct0ywnw cord-048353-hqc7u9w3 cord-012967-w1oc0wdd cord-011798-uss38ped cord-011496-r8e19t0c cord-048446-gaemgm0t cord-048367-yya6w976 cord-013265-qrfi6e5c cord-048483-umvrwgaw cord-012889-dtil5xeo cord-010369-x9z8dg6a cord-254025-j1l0mder cord-013334-cptu0k7s cord-048360-n9sih438 cord-259771-653opx0h cord-254313-g2oc32dm cord-254000-pbzcupjg cord-254117-2ttwaegh cord-252739-1manzf3l cord-255013-njpuc475 cord-255576-738khdwv cord-048339-nzh87aux cord-048492-4z38v9rg cord-251979-j3mme15e cord-252838-av7ducrk cord-253056-765rs3e7 cord-013263-xw611i8k cord-013099-j816c3tw cord-048364-yfn8sy1m cord-252347-vnn4135b cord-254825-c5d0wul9 cord-262345-hti1jjpn cord-013356-y6vceq2x cord-260572-vd65ygtm cord-260432-imslfm4l cord-254340-e1x0z3rh cord-256424-t3dtabi4 cord-257603-ov0b8yub cord-252795-x66zqmgv cord-253436-dz84icdc cord-258366-fu9b446y cord-258172-p54j4zzo cord-260653-5qwtvm9x cord-261908-olcuq6tm cord-258243-2utl2mfl cord-255351-vp19ydce cord-255588-nh34lgdh cord-048477-ze511t38 cord-260843-c97kctjz cord-260728-4w23kwzu cord-261410-kb91eagd cord-262759-ec2c25q3 cord-260647-7bjhobg7 cord-256326-3ebcuzd6 cord-262846-1mhimfsf cord-256837-100ir651 cord-263276-keyu60in cord-257077-cdnkk6ou cord-263453-7v4y02j6 cord-262876-civfvk45 cord-263978-jk82bk1a cord-265138-i5m3ax7g cord-255384-tljyx6ua cord-257217-f9sdt7ax cord-263464-fdosch11 cord-262748-v4xue7ha cord-265812-1hcp36cw cord-267189-xq70rn1j cord-262832-5iejckwx cord-267307-kyh0xsrp cord-267519-a0bcmjkn cord-267644-guzn0peq cord-263684-3535k3op cord-266799-t7lqlv41 cord-267973-uvz7kavu cord-267566-gdjl0qmu cord-267605-efb10j3u cord-266797-uglsx7se cord-268977-hcg2rrhl cord-272655-qeojdpez cord-264880-0tmd9knh cord-272445-0xauff51 cord-273343-als886fe cord-268429-drejl99k cord-269453-30l6rzgo cord-268816-nth3o6ot cord-276763-x3dqi0ym cord-276577-06boh550 cord-278087-0nicp0eq cord-273175-bao8xxe2 cord-273764-itu39mln cord-267042-nvwnbp2j cord-271660-5sfkhg19 cord-272878-6f0q661e cord-268524-lr51ubz5 cord-273594-vmbhok1u cord-270683-982eqtog cord-272971-9luzvzsu cord-269690-6r2bfydw cord-270681-6ayciihs cord-277409-q5wx313k cord-275058-61eof7y8 cord-278224-sq7tokbx cord-277306-r8jki3x4 cord-275395-w2u7fq1g cord-279259-eu80ccm6 cord-280482-o887a7q9 cord-277548-hgmmtew3 cord-274268-0ucqp3uz cord-276898-ia80cy8j cord-278123-mq56em3z cord-280846-bbv6f5gf cord-280386-a8qr7nl6 cord-270647-vn4kirrx cord-270408-4qqyb8sd cord-277357-lpurk7pe cord-278099-ypov9ha3 cord-280471-cqypwi5d cord-278018-3qemb0x3 cord-281815-zvs5qe8x cord-274241-biqbsggu cord-282303-idh7io9v cord-281161-u896icp9 cord-286708-igu984oc cord-276372-q1fzxt3r cord-286065-x0g67pnb cord-281124-4nhy35xn cord-282202-q2q4vies cord-284275-bqo203pf cord-283976-jgae7r2q cord-285546-5tjhdczt cord-287739-58fth3xl cord-279421-rxocrgfu cord-281364-syg0wo77 cord-284501-5i0w74q4 cord-282668-bs634hti cord-284016-zb6cv8ik cord-281665-6n7aq4k9 cord-287784-f7usy52w cord-289305-mfjyjjer cord-287761-73qgx58i cord-285433-ehnu83qe cord-286837-j2sqs20q cord-283604-fqc9jp0l cord-288440-w7g2agaf cord-290446-43h1r4pm cord-289017-vwye3pk9 cord-286404-eggkqq3b cord-290773-kgb8r561 cord-289093-si8btsab cord-289555-1z4vbldd cord-289873-6hivjqof cord-286613-cmtsu73g cord-291756-ejh1r8h4 cord-288502-qqg41daz cord-289285-aof7xy13 cord-285749-0ejhd9nw cord-289510-spmknns5 cord-290833-m0wodqr3 cord-290034-4b0mshqa cord-290120-fd26t8ja cord-289892-yh1lioyz cord-282194-0sjmf1yn cord-290539-8ak2tths cord-292237-45hi4iz2 cord-293794-vudufao5 cord-291417-p49ukyhx cord-291360-z19ri377 cord-291176-evb6yt0r cord-293393-kbndie8e cord-293072-giakcaki cord-294768-bs6thjw2 cord-294645-yzh8h7zo cord-292537-9ra4r6v6 cord-293946-4bquxdqa cord-294023-knaxr7t0 cord-294568-12eyo13f cord-291104-6chpmgry cord-292475-jrl1fowa cord-295352-b8kztgt8 cord-292777-oztmw8jo cord-295781-b831y105 cord-294591-793ywpcd cord-292396-8w06oc5i cord-294372-pec1886j cord-295339-nzc47itk cord-296399-vvbjulm9 cord-295201-u2dola34 cord-294592-zwvr57a0 cord-295536-dbpt4dhr cord-296487-m4xba78g cord-296435-6dergkha cord-299509-7xjdryoq cord-295293-ickp2n47 cord-299852-t0mqe7yy cord-299491-8rfm0jxh cord-294912-xl0wzi16 cord-297835-ukrz8tlv cord-298679-w0yp4u19 cord-296550-wkmnfph3 cord-296635-8r3tm966 cord-295559-yc8q62z8 cord-304993-t4rua95e cord-302355-3se1wp8o cord-302200-9gekjgr0 cord-301180-ndiwmnv0 cord-299953-sasfvcun cord-297287-0i4nc353 cord-305547-e66o5j85 cord-303331-xolksoy3 cord-305303-82n96ukr cord-306466-y4yg42p8 cord-296691-cg463fbn cord-307934-84zfabti cord-302529-43pd2qsp cord-303187-ny4qr2a2 cord-303490-rixuuytu cord-302962-qw6s1t7j cord-301811-ykpiorgo cord-300859-nqklx0vn cord-298131-zolwjl9u cord-298078-uqrwq5qk cord-306958-8bx8kxxh cord-305274-mcsdem7y cord-305071-4ck8nd24 cord-305811-987dhnf7 cord-303845-y6ws3u6x cord-306278-c4q4la5c cord-308344-ao9z00t7 cord-310438-744r7gc3 cord-309621-6jj19xpr cord-306135-pt4jsr6d cord-305393-96mrxt8a cord-305900-ht7hb2rc cord-302189-3xab3yxc cord-309194-jtouafgd cord-309010-tmfm5u5h cord-309981-4p3ybrn1 cord-304616-k92fa15l cord-307036-n44yml79 cord-311074-j3fw4dfc cord-310678-33c3mp1o cord-303034-w72oeoxq cord-308261-hxlebas8 cord-312367-24huwt3y cord-312002-4qhvljpv cord-311065-ie3gty6e cord-308480-t2vukbwp cord-310790-3ikgmiof cord-310466-0lbbiq7u cord-308249-es948mux cord-312493-wbhji81g cord-310061-nro623aa cord-310396-jitao9k0 cord-312033-iarl77n0 cord-309043-dlmx12vt cord-314908-kp2jznwb cord-313107-6cfenpxm cord-309471-lr68epyb cord-311941-0dpm35dd cord-313506-6bb4q7nv cord-315531-2gc2dc46 cord-312678-81gnmxbk cord-317244-4su5on6s cord-311288-6ttux2uu cord-307540-dr5m9pfk cord-315343-ywgoqlxj cord-312817-gskbu0oh cord-316047-d9cpe9yl cord-316319-m6uha1qn cord-316703-8kxx3034 cord-318696-jheb2fnn cord-318008-4s9eoae3 cord-316853-vaea6siv cord-314651-e4uaw5fy cord-319538-bawzonq1 cord-319706-2e9jrv0s cord-311531-wezrs7gc cord-318614-518giv0m cord-308764-9z4qcoqz cord-310947-aqau2n7q cord-317058-anvmj4li cord-317912-v2wovcqd cord-321705-6a7avlro cord-319845-oob2ktnz cord-319921-uxtydu60 cord-319256-7pyinx1a cord-317779-j67vb7f3 cord-321855-7b1c2xdh cord-321438-llnqzkqt cord-320466-l7017jis cord-320938-f526k9q1 cord-320091-2lrqubdl cord-321834-n5w88l23 cord-319675-mwy3t1ny cord-319190-esjfhztp cord-322414-dpx191xh cord-323433-9km824uh cord-322446-ddv86eoy cord-322827-h33su548 cord-324405-6uanhe2p cord-318845-w7q5o8wc cord-322533-adqqm0n9 cord-324410-be2ith3z cord-327199-ggomuomb cord-323330-ghwhgkdm cord-321624-z2mntwef cord-326011-5rmhjbri cord-325113-sou8xyld cord-324091-nljd2ok1 cord-327534-f2wvh6la cord-327257-doygrgrc cord-323185-n0rubc72 cord-324359-88vy3dre cord-328627-cf8f71dr cord-331885-8zmuhebu cord-326568-twv2i3fb cord-329223-f84gjxm1 cord-328633-c31xsyeo cord-333208-tibtngy8 cord-328206-iylw1bvw cord-330110-pamxy4av cord-316287-4i1grvlr cord-323133-gdg50omp cord-335272-jypxi99z cord-330749-xt4aa2ur cord-333853-p2kbjwpy cord-333522-zsdymkjd cord-329727-h47q76y8 cord-334955-gnu92up6 cord-334218-bkjfy66e cord-329468-vjsurl60 cord-333955-bnzbppof cord-329999-flzqm3wh cord-333413-8buawes0 cord-331652-oc5s1if2 cord-330537-xz0wt1sz cord-336364-2ust3qoq cord-336615-jfnj6l41 cord-335859-k37jivp6 cord-336420-1a2u9p4t cord-337795-khqx4t4q cord-335441-bj3me7p8 cord-335880-m8gecsf0 cord-330079-pdaowkop cord-335505-s013j5ex cord-336441-m6pur6td cord-332922-2qjae0x7 cord-333248-5342lyeu cord-335404-s48psqth cord-338067-vjyad10p cord-333650-4towah1t cord-339789-151d1j4n cord-339026-eu11larc cord-339578-eg19rfvi cord-337585-kpghvb6u cord-336843-c0sr3six cord-334695-cjxlw1tu cord-335245-1eksm537 cord-338594-wft7yy6j cord-339327-4422s317 cord-339157-wj47xeqj cord-340027-6l55rcfm cord-339724-roj8ksvc cord-340763-cxnu9g8y cord-337913-eu2gn4bl cord-337879-liqhbqxl cord-340195-425rd7ul cord-339920-dr5bvpm0 cord-339392-2ocz784l cord-337067-j8ebslif cord-339796-gccnvh0z cord-340718-amfs4zay cord-337630-ojhk5opy cord-341914-l2bomgji cord-340713-v5sdowb7 cord-340703-vtuy806l cord-340656-ltd6ueoi cord-340627-xyvzgkxl cord-340937-6mpob1nx cord-340766-aic570x8 cord-339869-euikj8fv cord-341880-wxliz485 cord-342476-0rupk21u cord-340387-ohkjheat cord-342133-khrljehj cord-343135-m0pdixw5 cord-341097-c96hm610 cord-342519-tjr6dvtt cord-344782-ond1ziu5 cord-343973-n5ogyxz7 cord-344839-r05p9h0e cord-342639-vf9n2vf9 cord-344870-tbgqulpu cord-342730-b7y8mybg cord-344357-ocyaqs1y cord-345717-ktajrf7d cord-345695-5vi9wibk cord-345019-i7zm9bt1 cord-344152-pb1e2w7s cord-347465-yu6oj30v cord-346089-u31n0qxa cord-348055-azlb1zy1 cord-346067-zly8p0y7 cord-348807-9xxc5hyl cord-346819-11fkgzaa cord-346347-r4ork18p cord-346314-o9fjpqaj cord-347014-88zmtky7 cord-348243-e5tdb08v cord-346858-18q8rxzg cord-347317-qcghtkk0 cord-348499-7ll7sd3o cord-349029-zyfop43z cord-349217-vpih1wvs cord-349781-l93978vq cord-350443-ca5avyjf cord-350842-4m82l5t8 cord-349476-iac9fak3 cord-349911-dx8wvqkm cord-352222-zq9o66i4 cord-351098-x729wpp7 cord-351142-g20f6bxc cord-351868-w4d45fue cord-351990-aham72b9 cord-352403-4591ewsa cord-352200-i05h8csb cord-346586-fxxceffl cord-353200-5csewb1k cord-351185-3y3gou6v cord-351387-i0zamkpd cord-352564-2j4pjjwk cord-351918-pu7i1jfe cord-352219-z245sb3s cord-353866-0r1b44id cord-352522-qnvgg2e9 cord-350398-w75flrwv cord-352720-z1cvjc2y cord-353245-es7b1rs0 cord-352447-bc1pf272 cord-356132-1nisyl5r cord-354052-x4ckzw64 cord-355259-779czzzx cord-353410-tbmtg88k cord-353253-kk2q71vg cord-354547-eomm1sl5 cord-353869-l53ms3q8 cord-353730-owcapg8h cord-354000-jxqskt4k cord-353596-8iqjugcx cord-355874-nz6eqcdb cord-352511-gkm7i62s cord-354763-odzrco6q cord-356364-ipi81ce3 Creating transaction Updating wrd table ===== Reducing urls cord-000131-ugbwvy6j cord-000269-v4jochbe cord-000366-u4649rtx cord-000588-3wok0n21 cord-000063-tex6bgab cord-000237-mticfoic cord-000143-2xvd5ogf cord-000556-uu1oz2ei cord-001007-645zegcv cord-000736-6f8vyziv cord-000326-a18rch1f cord-000434-ff2zadol cord-000580-dcid9emx cord-000077-d441jam3 cord-000182-ni6iyzdn cord-000536-0mn1gbll cord-000642-mkwpuav6 cord-000208-th0wddvc cord-000425-isw6jeir cord-000347-gdra8xhj cord-000937-8vk89i4h cord-000837-rdpsxb4n cord-000868-vnwpzsu8 cord-000374-gt2pwc9b cord-000912-6l6c7jpq cord-000895-z5rdf0mi cord-000248-zueoyesj cord-001071-bjx5td52 cord-001090-qg2r691d cord-001065-j4hvyyoi cord-001083-vy1nxax2 cord-001092-pkps5j8w cord-001120-fxd533b4 cord-001099-jirkkkvy cord-001213-gxqufddb cord-001126-uqr00nzd cord-001129-gi2kswai cord-001537-i34vmfpp cord-001432-d4zavkcn cord-001275-a9o2dvke cord-001734-bbeznd3r cord-001605-8p06bpt1 cord-001909-yy9xp5ms cord-001639-p9mbmfaq cord-002602-2qvyhjlp cord-003024-17f1evh3 cord-002834-2htnywef cord-002473-2kpxhzbe cord-002100-dt5zvebj cord-002705-ntokyoai cord-001447-oi7bkm4z cord-002601-d8908t93 cord-002043-z1b7pj3s cord-001898-ntqyjqqk cord-003548-zuwt7gk5 cord-002890-g7aje88u cord-002560-pue5q5wp cord-002935-jq1xumrh cord-004017-gcmpatlb cord-003062-qm8kalyt cord-002889-fie121ns cord-003270-vu9b5a14 cord-004091-gex0zvoa cord-003125-iptisi1m cord-003712-mafz21no cord-003503-t6cnjwpd cord-010369-x9z8dg6a cord-003484-ylpa702c cord-012889-dtil5xeo cord-002973-bkr4ndl2 cord-011857-brbqgbpz cord-012891-heqsfzkm cord-012461-v8d91fdo cord-011496-r8e19t0c cord-013333-7jx4t0ol cord-003498-4ct0ywnw cord-048358-z5klydpi cord-013265-qrfi6e5c cord-048492-4z38v9rg cord-048483-umvrwgaw cord-048367-yya6w976 cord-048353-hqc7u9w3 cord-048360-n9sih438 cord-013099-j816c3tw cord-013334-cptu0k7s cord-255013-njpuc475 cord-013356-y6vceq2x cord-260432-imslfm4l cord-256424-t3dtabi4 cord-262345-hti1jjpn cord-258172-p54j4zzo cord-260647-7bjhobg7 cord-262846-1mhimfsf cord-256837-100ir651 cord-257077-cdnkk6ou cord-263978-jk82bk1a cord-260728-4w23kwzu cord-263464-fdosch11 cord-267644-guzn0peq cord-266799-t7lqlv41 cord-267566-gdjl0qmu cord-268816-nth3o6ot cord-269453-30l6rzgo cord-273175-bao8xxe2 cord-273764-itu39mln cord-270683-982eqtog cord-278224-sq7tokbx cord-269690-6r2bfydw cord-275395-w2u7fq1g cord-280386-a8qr7nl6 cord-280846-bbv6f5gf cord-278099-ypov9ha3 cord-280471-cqypwi5d cord-278123-mq56em3z cord-274241-biqbsggu cord-281124-4nhy35xn cord-281665-6n7aq4k9 cord-286837-j2sqs20q cord-287761-73qgx58i cord-283604-fqc9jp0l cord-289555-1z4vbldd cord-282202-q2q4vies cord-290773-kgb8r561 cord-289093-si8btsab cord-289873-6hivjqof cord-282194-0sjmf1yn cord-290833-m0wodqr3 cord-290120-fd26t8ja cord-290446-43h1r4pm cord-289892-yh1lioyz cord-293794-vudufao5 cord-291417-p49ukyhx cord-293946-4bquxdqa cord-292475-jrl1fowa cord-292537-9ra4r6v6 cord-294645-yzh8h7zo cord-292396-8w06oc5i cord-294912-xl0wzi16 cord-295781-b831y105 cord-298078-uqrwq5qk cord-294592-zwvr57a0 cord-296691-cg463fbn cord-302529-43pd2qsp cord-308344-ao9z00t7 cord-298131-zolwjl9u cord-296487-m4xba78g cord-305547-e66o5j85 cord-305274-mcsdem7y cord-309194-jtouafgd cord-295293-ickp2n47 cord-291360-z19ri377 cord-303331-xolksoy3 cord-310678-33c3mp1o cord-311074-j3fw4dfc cord-296399-vvbjulm9 cord-304616-k92fa15l cord-309010-tmfm5u5h cord-310790-3ikgmiof cord-312367-24huwt3y cord-310061-nro623aa cord-303034-w72oeoxq cord-308480-t2vukbwp cord-308764-9z4qcoqz cord-312002-4qhvljpv cord-308249-es948mux cord-307540-dr5m9pfk cord-315531-2gc2dc46 cord-316853-vaea6siv cord-312678-81gnmxbk cord-312817-gskbu0oh cord-316319-m6uha1qn cord-316703-8kxx3034 cord-316047-d9cpe9yl cord-313107-6cfenpxm cord-311941-0dpm35dd cord-317244-4su5on6s cord-318008-4s9eoae3 cord-317779-j67vb7f3 cord-321438-llnqzkqt cord-321834-n5w88l23 cord-319706-2e9jrv0s cord-320466-l7017jis cord-322533-adqqm0n9 cord-322446-ddv86eoy cord-323433-9km824uh cord-323330-ghwhgkdm cord-325113-sou8xyld cord-327257-doygrgrc cord-327534-f2wvh6la cord-328627-cf8f71dr cord-329223-f84gjxm1 cord-326568-twv2i3fb cord-333208-tibtngy8 cord-316287-4i1grvlr cord-330749-xt4aa2ur cord-335272-jypxi99z cord-329727-h47q76y8 cord-329468-vjsurl60 cord-334955-gnu92up6 cord-329999-flzqm3wh cord-339026-eu11larc cord-338067-vjyad10p cord-339789-151d1j4n cord-339157-wj47xeqj cord-335245-1eksm537 cord-340718-amfs4zay cord-340713-v5sdowb7 cord-340627-xyvzgkxl cord-340937-6mpob1nx cord-337879-liqhbqxl cord-337630-ojhk5opy cord-340387-ohkjheat cord-340703-vtuy806l cord-342476-0rupk21u cord-341097-c96hm610 cord-344782-ond1ziu5 cord-342519-tjr6dvtt cord-344839-r05p9h0e cord-344152-pb1e2w7s cord-348243-e5tdb08v cord-346819-11fkgzaa cord-346314-o9fjpqaj cord-348499-7ll7sd3o cord-349217-vpih1wvs cord-346089-u31n0qxa cord-349029-zyfop43z cord-349781-l93978vq cord-351185-3y3gou6v cord-352200-i05h8csb cord-351918-pu7i1jfe cord-351098-x729wpp7 cord-353200-5csewb1k cord-350398-w75flrwv cord-352219-z245sb3s cord-353245-es7b1rs0 cord-356132-1nisyl5r cord-355874-nz6eqcdb cord-354000-jxqskt4k cord-352522-qnvgg2e9 cord-353253-kk2q71vg Creating transaction Updating url table ===== Reducing named entities cord-000008-3dgjv0x1 cord-000166-36bfeoqv cord-000574-7eflwyxk cord-000006-104sqoxz cord-000082-jy7j8sh0 cord-000176-z76vjkxg cord-000079-533xlisc cord-000366-u4649rtx cord-000720-5b936n3g cord-000050-tfcerilc cord-000013-pr9i9swk cord-000266-xwfptmmv cord-000269-v4jochbe cord-000140-5kapn32k cord-000540-bbjmcdo5 cord-000255-73nlxqgk cord-000143-2xvd5ogf cord-000063-tex6bgab cord-000588-3wok0n21 cord-000501-qz68gtd4 cord-000460-h3owwjao cord-000131-ugbwvy6j cord-000182-ni6iyzdn cord-000556-uu1oz2ei cord-000547-adfigzc1 cord-000765-r7y1cqou cord-000224-2lz03oqb cord-000237-mticfoic cord-000321-ee7q7jhv cord-000742-0r4z1zea cord-000736-6f8vyziv cord-000434-ff2zadol cord-000666-je9t4i6q cord-000408-pt3b4yc7 cord-000077-d441jam3 cord-000638-ss1435el cord-000336-57es391o cord-000609-dpcgl6ig cord-000346-9b6yz3f4 cord-000267-xroo7z7g cord-001045-jm60nxc2 cord-000208-th0wddvc cord-000721-leedutqo cord-000581-ewx5xhrb cord-001014-8yrpcl94 cord-000580-dcid9emx cord-000725-rafwlw0t cord-000554-p4ufea6x cord-000265-llilwq1u cord-000715-zl1s82yi cord-000478-88wo4xen cord-000326-a18rch1f cord-000413-h2e6h076 cord-000837-rdpsxb4n cord-000375-fvfl0bn1 cord-000719-o7ttiu97 cord-000158-d08buwtu cord-000536-0mn1gbll cord-000642-mkwpuav6 cord-000248-zueoyesj cord-001007-645zegcv cord-000813-gagakqw4 cord-000851-uylgyhs8 cord-000180-howix091 cord-000809-9voqa1oy cord-000877-usz7pnvu cord-000261-ip32y0j5 cord-000726-tonaaft2 cord-000695-g5sum116 cord-000689-8lvzab4i cord-000959-nk2thkme cord-000981-6vloa2w3 cord-000374-gt2pwc9b cord-000979-cav9n18w cord-000410-av8b8g8c cord-000425-isw6jeir cord-000352-qzkpik3z cord-000912-6l6c7jpq cord-000833-m6abyuvx cord-000868-vnwpzsu8 cord-000895-z5rdf0mi cord-000539-uh3q65we cord-000341-d3a06n3f cord-000347-gdra8xhj cord-000322-8ctsa9sd cord-000947-psguw47w cord-000723-wo20st5w cord-001039-qocuprwb cord-000905-1rhlu59c cord-000359-y0m1utug cord-000786-ofpcgxce cord-000937-8vk89i4h cord-001071-bjx5td52 cord-000866-dr2uow4m cord-000984-64p3wpav cord-001083-vy1nxax2 cord-001021-nag4at49 cord-001065-j4hvyyoi cord-001123-n2e4s7bu cord-001088-dugsh7mp cord-001011-vjxmrmfc cord-001253-3jnkki5z cord-001199-9khx93c0 cord-001162-z8cbbit3 cord-001117-llb4f74a cord-001186-jkg7qkj6 cord-001099-jirkkkvy cord-001078-5m29nugu cord-001251-forh7lw4 cord-001090-qg2r691d cord-001213-gxqufddb cord-001207-yjaiybwf cord-001129-gi2kswai cord-001368-ymp1pj3r cord-001145-hc9ssruz cord-001142-puj74k7y cord-001249-awn9ayy6 cord-001219-517gka4h cord-001280-skavefji cord-001432-d4zavkcn cord-001421-6t5puo6p cord-001254-y2knt8g0 cord-001126-uqr00nzd cord-001387-2g9dc5z4 cord-001435-ebl8yc92 cord-001359-c1uom5f7 cord-001537-i34vmfpp cord-001455-n7quwr4s cord-001420-b4zcvd04 cord-001263-hqxiyxfj cord-001599-pfdnmzx2 cord-001343-3euy4u9k cord-001363-irysq6pf cord-001571-drcfdv9z cord-001446-mpuovmeb cord-001620-yy5gq0ki cord-001958-2gt3fwpy cord-001275-a9o2dvke cord-001546-ndz3oarf cord-001734-bbeznd3r cord-001781-afg1nmib cord-001447-oi7bkm4z cord-001120-fxd533b4 cord-001605-8p06bpt1 cord-001092-pkps5j8w cord-001748-7e8px4vx cord-001601-tsuz3j40 cord-001603-vlv8x8l8 cord-001909-yy9xp5ms cord-002043-z1b7pj3s cord-001460-eo2bxxbq cord-002044-9xgt3tf4 cord-001707-piyo00yg cord-002141-9mxi4dzi cord-001383-hww0watl cord-001964-iy6qzq58 cord-002094-7tewne3a cord-001716-lbtdex4p cord-002023-7zd5zhbz cord-001982-arczqdza cord-002834-2htnywef cord-001639-p9mbmfaq cord-001761-yvd1n42f cord-001898-ntqyjqqk cord-002222-rgqwm3vb cord-001865-ji83zmy7 cord-001983-zo9yngfc cord-001843-ceatyj3o cord-002602-2qvyhjlp cord-002100-dt5zvebj cord-002305-qq73gr9y cord-002811-5hrydciz cord-002601-d8908t93 cord-002473-2kpxhzbe cord-002624-59nznqsd cord-001910-6zfz2ns5 cord-002705-ntokyoai cord-002901-u4ybz8ds cord-003024-17f1evh3 cord-002621-sq5iod1w cord-003244-abs3tc3r cord-002398-0a3okta0 cord-002848-w6q1x1zs cord-003507-22ylifqo cord-002890-g7aje88u cord-002180-gsdk5x3e cord-002913-k5b6abyk cord-002935-jq1xumrh cord-003551-jzfl4xuk cord-002426-5e1xn7kj cord-002957-gw2cow0d cord-002560-pue5q5wp cord-004017-gcmpatlb cord-003602-wtestt8i cord-003377-9vkhptas cord-003548-zuwt7gk5 cord-003270-vu9b5a14 cord-003841-7uaj9hmx cord-003125-iptisi1m cord-004091-gex0zvoa cord-003712-mafz21no cord-003503-t6cnjwpd cord-010368-plpghewn cord-003062-qm8kalyt cord-012387-1ogcxd7b cord-002889-fie121ns cord-004068-d66lwylf cord-003484-ylpa702c cord-012889-dtil5xeo cord-010369-x9z8dg6a cord-002973-bkr4ndl2 cord-002939-6a3ga6v9 cord-012461-v8d91fdo cord-003404-eqgc8v7y cord-011857-brbqgbpz cord-002953-4rqoenhr cord-012891-heqsfzkm cord-013333-7jx4t0ol cord-048471-7jszm1nd cord-011496-r8e19t0c cord-011798-uss38ped cord-012967-w1oc0wdd cord-048358-z5klydpi cord-003498-4ct0ywnw cord-048446-gaemgm0t cord-048353-hqc7u9w3 cord-048364-yfn8sy1m cord-013263-xw611i8k cord-252838-av7ducrk cord-252347-vnn4135b cord-251979-j3mme15e cord-013265-qrfi6e5c cord-048492-4z38v9rg cord-048367-yya6w976 cord-048483-umvrwgaw cord-254025-j1l0mder cord-252739-1manzf3l cord-254117-2ttwaegh cord-048360-n9sih438 cord-013099-j816c3tw cord-013334-cptu0k7s cord-259771-653opx0h cord-254313-g2oc32dm cord-255013-njpuc475 cord-253056-765rs3e7 cord-254000-pbzcupjg cord-048339-nzh87aux cord-255576-738khdwv cord-013356-y6vceq2x cord-260432-imslfm4l cord-260653-5qwtvm9x cord-254825-c5d0wul9 cord-257603-ov0b8yub cord-254340-e1x0z3rh cord-256424-t3dtabi4 cord-260572-vd65ygtm cord-252795-x66zqmgv cord-262345-hti1jjpn cord-258366-fu9b446y cord-253436-dz84icdc cord-258243-2utl2mfl cord-261908-olcuq6tm cord-255351-vp19ydce cord-048477-ze511t38 cord-258172-p54j4zzo cord-255588-nh34lgdh cord-261410-kb91eagd cord-262759-ec2c25q3 cord-260728-4w23kwzu cord-260647-7bjhobg7 cord-256326-3ebcuzd6 cord-262846-1mhimfsf cord-260843-c97kctjz cord-263276-keyu60in cord-256837-100ir651 cord-257077-cdnkk6ou cord-262876-civfvk45 cord-263453-7v4y02j6 cord-263978-jk82bk1a cord-257217-f9sdt7ax cord-255384-tljyx6ua cord-263464-fdosch11 cord-262748-v4xue7ha cord-265138-i5m3ax7g cord-263684-3535k3op cord-262832-5iejckwx cord-267519-a0bcmjkn cord-265812-1hcp36cw cord-266797-uglsx7se cord-267189-xq70rn1j cord-267307-kyh0xsrp cord-267644-guzn0peq cord-266799-t7lqlv41 cord-267973-uvz7kavu cord-272445-0xauff51 cord-267605-efb10j3u cord-268816-nth3o6ot cord-264880-0tmd9knh cord-273343-als886fe cord-269453-30l6rzgo cord-267566-gdjl0qmu cord-278087-0nicp0eq cord-273175-bao8xxe2 cord-273764-itu39mln cord-276577-06boh550 cord-267042-nvwnbp2j cord-276763-x3dqi0ym cord-272878-6f0q661e cord-271660-5sfkhg19 cord-273594-vmbhok1u cord-268524-lr51ubz5 cord-268977-hcg2rrhl cord-272655-qeojdpez cord-268429-drejl99k cord-270683-982eqtog cord-272971-9luzvzsu cord-277409-q5wx313k cord-275058-61eof7y8 cord-278224-sq7tokbx cord-280482-o887a7q9 cord-279259-eu80ccm6 cord-277548-hgmmtew3 cord-276898-ia80cy8j cord-280386-a8qr7nl6 cord-278123-mq56em3z cord-278018-3qemb0x3 cord-277357-lpurk7pe cord-282303-idh7io9v cord-270647-vn4kirrx cord-270408-4qqyb8sd cord-274241-biqbsggu cord-278099-ypov9ha3 cord-280471-cqypwi5d cord-286065-x0g67pnb cord-281161-u896icp9 cord-286708-igu984oc cord-276372-q1fzxt3r cord-280846-bbv6f5gf cord-277306-r8jki3x4 cord-275395-w2u7fq1g cord-274268-0ucqp3uz cord-287739-58fth3xl cord-281124-4nhy35xn cord-279421-rxocrgfu cord-284501-5i0w74q4 cord-281364-syg0wo77 cord-282668-bs634hti cord-284016-zb6cv8ik cord-282202-q2q4vies cord-284275-bqo203pf cord-281665-6n7aq4k9 cord-287761-73qgx58i cord-287784-f7usy52w cord-289305-mfjyjjer cord-286837-j2sqs20q cord-270681-6ayciihs cord-285546-5tjhdczt cord-281815-zvs5qe8x cord-283976-jgae7r2q cord-289093-si8btsab cord-286404-eggkqq3b cord-289555-1z4vbldd cord-289285-aof7xy13 cord-288440-w7g2agaf cord-285433-ehnu83qe cord-289017-vwye3pk9 cord-286613-cmtsu73g cord-290773-kgb8r561 cord-290446-43h1r4pm cord-283604-fqc9jp0l cord-291756-ejh1r8h4 cord-285749-0ejhd9nw cord-282194-0sjmf1yn cord-289873-6hivjqof cord-290833-m0wodqr3 cord-289892-yh1lioyz cord-269690-6r2bfydw cord-290120-fd26t8ja cord-290034-4b0mshqa cord-292237-45hi4iz2 cord-290539-8ak2tths cord-291360-z19ri377 cord-293393-kbndie8e cord-291417-p49ukyhx cord-291176-evb6yt0r cord-293794-vudufao5 cord-288502-qqg41daz cord-292475-jrl1fowa cord-293072-giakcaki cord-292396-8w06oc5i cord-289510-spmknns5 cord-292537-9ra4r6v6 cord-294645-yzh8h7zo cord-294568-12eyo13f cord-295781-b831y105 cord-294591-793ywpcd cord-294023-knaxr7t0 cord-295339-nzc47itk cord-292777-oztmw8jo cord-295536-dbpt4dhr cord-299852-t0mqe7yy cord-295352-b8kztgt8 cord-294372-pec1886j cord-302200-9gekjgr0 cord-296550-wkmnfph3 cord-294768-bs6thjw2 cord-296399-vvbjulm9 cord-296487-m4xba78g cord-295201-u2dola34 cord-295293-ickp2n47 cord-291104-6chpmgry cord-293946-4bquxdqa cord-299509-7xjdryoq cord-296435-6dergkha cord-294912-xl0wzi16 cord-298679-w0yp4u19 cord-297835-ukrz8tlv cord-296635-8r3tm966 cord-294592-zwvr57a0 cord-296691-cg463fbn cord-301180-ndiwmnv0 cord-302355-3se1wp8o cord-305303-82n96ukr cord-295559-yc8q62z8 cord-304993-t4rua95e cord-298078-uqrwq5qk cord-300859-nqklx0vn cord-299953-sasfvcun cord-299491-8rfm0jxh cord-297287-0i4nc353 cord-306466-y4yg42p8 cord-305547-e66o5j85 cord-301811-ykpiorgo cord-303187-ny4qr2a2 cord-303490-rixuuytu cord-298131-zolwjl9u cord-302529-43pd2qsp cord-303331-xolksoy3 cord-302962-qw6s1t7j cord-306278-c4q4la5c cord-307934-84zfabti cord-302189-3xab3yxc cord-305274-mcsdem7y cord-305071-4ck8nd24 cord-306958-8bx8kxxh cord-309621-6jj19xpr cord-303845-y6ws3u6x cord-306135-pt4jsr6d cord-305811-987dhnf7 cord-309194-jtouafgd cord-310438-744r7gc3 cord-305900-ht7hb2rc cord-305393-96mrxt8a cord-308344-ao9z00t7 cord-311074-j3fw4dfc cord-310678-33c3mp1o cord-307036-n44yml79 cord-310061-nro623aa cord-309981-4p3ybrn1 cord-304616-k92fa15l cord-309010-tmfm5u5h cord-308261-hxlebas8 cord-308249-es948mux cord-310466-0lbbiq7u cord-312493-wbhji81g cord-311065-ie3gty6e cord-310790-3ikgmiof cord-310396-jitao9k0 cord-312367-24huwt3y cord-312033-iarl77n0 cord-303034-w72oeoxq cord-307540-dr5m9pfk cord-312002-4qhvljpv cord-308764-9z4qcoqz cord-311531-wezrs7gc cord-308480-t2vukbwp cord-309471-lr68epyb cord-310947-aqau2n7q cord-311288-6ttux2uu cord-311941-0dpm35dd cord-312678-81gnmxbk cord-314651-e4uaw5fy cord-315531-2gc2dc46 cord-313107-6cfenpxm cord-313506-6bb4q7nv cord-314908-kp2jznwb cord-312817-gskbu0oh cord-309043-dlmx12vt cord-315343-ywgoqlxj cord-317244-4su5on6s cord-318696-jheb2fnn cord-316319-m6uha1qn cord-316703-8kxx3034 cord-316853-vaea6siv cord-316047-d9cpe9yl cord-318614-518giv0m cord-318008-4s9eoae3 cord-317912-v2wovcqd cord-319706-2e9jrv0s cord-317058-anvmj4li cord-319538-bawzonq1 cord-321705-6a7avlro cord-319845-oob2ktnz cord-317779-j67vb7f3 cord-319256-7pyinx1a cord-319921-uxtydu60 cord-320938-f526k9q1 cord-321855-7b1c2xdh cord-320466-l7017jis cord-321438-llnqzkqt cord-321834-n5w88l23 cord-320091-2lrqubdl cord-319190-esjfhztp cord-318845-w7q5o8wc cord-322414-dpx191xh cord-319675-mwy3t1ny cord-323433-9km824uh cord-324405-6uanhe2p cord-322446-ddv86eoy cord-322827-h33su548 cord-322533-adqqm0n9 cord-323330-ghwhgkdm cord-324410-be2ith3z cord-327199-ggomuomb cord-326011-5rmhjbri cord-325113-sou8xyld cord-321624-z2mntwef cord-327534-f2wvh6la cord-324091-nljd2ok1 cord-327257-doygrgrc cord-323185-n0rubc72 cord-324359-88vy3dre cord-331885-8zmuhebu cord-326568-twv2i3fb cord-328627-cf8f71dr cord-329223-f84gjxm1 cord-328206-iylw1bvw cord-328633-c31xsyeo cord-333208-tibtngy8 cord-316287-4i1grvlr cord-330110-pamxy4av cord-323133-gdg50omp cord-330749-xt4aa2ur cord-335272-jypxi99z cord-334955-gnu92up6 cord-333955-bnzbppof cord-333853-p2kbjwpy cord-329727-h47q76y8 cord-333522-zsdymkjd cord-333413-8buawes0 cord-329468-vjsurl60 cord-329999-flzqm3wh cord-330537-xz0wt1sz cord-336364-2ust3qoq cord-335859-k37jivp6 cord-331652-oc5s1if2 cord-336615-jfnj6l41 cord-334218-bkjfy66e cord-335441-bj3me7p8 cord-335880-m8gecsf0 cord-337795-khqx4t4q cord-336441-m6pur6td cord-330079-pdaowkop cord-339789-151d1j4n cord-339026-eu11larc cord-333248-5342lyeu cord-336843-c0sr3six cord-338067-vjyad10p cord-339578-eg19rfvi cord-333650-4towah1t cord-337585-kpghvb6u cord-335505-s013j5ex cord-338594-wft7yy6j cord-335245-1eksm537 cord-339327-4422s317 cord-334695-cjxlw1tu cord-337067-j8ebslif cord-332922-2qjae0x7 cord-340763-cxnu9g8y cord-339724-roj8ksvc cord-340027-6l55rcfm cord-337913-eu2gn4bl cord-337879-liqhbqxl cord-340195-425rd7ul cord-337630-ojhk5opy cord-339920-dr5bvpm0 cord-341914-l2bomgji cord-339796-gccnvh0z cord-339392-2ocz784l cord-335404-s48psqth cord-339157-wj47xeqj cord-340718-amfs4zay cord-340713-v5sdowb7 cord-340656-ltd6ueoi cord-340703-vtuy806l cord-340627-xyvzgkxl cord-340766-aic570x8 cord-339869-euikj8fv cord-342476-0rupk21u cord-345717-ktajrf7d cord-348055-azlb1zy1 cord-346089-u31n0qxa cord-346067-zly8p0y7 cord-344839-r05p9h0e cord-336420-1a2u9p4t cord-340937-6mpob1nx cord-341880-wxliz485 cord-345019-i7zm9bt1 cord-342133-khrljehj cord-341097-c96hm610 cord-344782-ond1ziu5 cord-342519-tjr6dvtt cord-344357-ocyaqs1y cord-343973-n5ogyxz7 cord-342639-vf9n2vf9 cord-344870-tbgqulpu cord-342730-b7y8mybg cord-343135-m0pdixw5 cord-340387-ohkjheat cord-346347-r4ork18p cord-347465-yu6oj30v cord-345695-5vi9wibk cord-348243-e5tdb08v cord-349029-zyfop43z cord-346314-o9fjpqaj cord-351868-w4d45fue cord-349911-dx8wvqkm cord-347317-qcghtkk0 cord-349217-vpih1wvs cord-351142-g20f6bxc cord-348499-7ll7sd3o cord-350842-4m82l5t8 cord-349781-l93978vq cord-350443-ca5avyjf cord-346819-11fkgzaa cord-351387-i0zamkpd cord-351185-3y3gou6v cord-347014-88zmtky7 cord-346586-fxxceffl cord-348807-9xxc5hyl cord-344152-pb1e2w7s cord-352222-zq9o66i4 cord-346858-18q8rxzg cord-351990-aham72b9 cord-352200-i05h8csb cord-351098-x729wpp7 cord-352564-2j4pjjwk cord-353200-5csewb1k cord-353866-0r1b44id cord-352511-gkm7i62s cord-349476-iac9fak3 cord-353869-l53ms3q8 cord-355874-nz6eqcdb cord-356132-1nisyl5r cord-353253-kk2q71vg cord-352447-bc1pf272 cord-354763-odzrco6q cord-356364-ipi81ce3 cord-354000-jxqskt4k cord-354052-x4ckzw64 cord-355259-779czzzx cord-353410-tbmtg88k cord-354547-eomm1sl5 cord-352522-qnvgg2e9 cord-353596-8iqjugcx cord-353730-owcapg8h cord-353245-es7b1rs0 cord-352219-z245sb3s cord-351918-pu7i1jfe cord-352403-4591ewsa cord-350398-w75flrwv cord-352720-z1cvjc2y Creating transaction Updating ent table ===== Reducing parts of speech cord-000131-ugbwvy6j cord-000008-3dgjv0x1 cord-000050-tfcerilc cord-000143-2xvd5ogf cord-000063-tex6bgab cord-000006-104sqoxz cord-000588-3wok0n21 cord-000574-7eflwyxk cord-000176-z76vjkxg cord-000166-36bfeoqv cord-000266-xwfptmmv cord-000540-bbjmcdo5 cord-000720-5b936n3g cord-000269-v4jochbe cord-000255-73nlxqgk cord-000082-jy7j8sh0 cord-000501-qz68gtd4 cord-000079-533xlisc cord-000366-u4649rtx cord-000013-pr9i9swk cord-000140-5kapn32k cord-000408-pt3b4yc7 cord-000224-2lz03oqb cord-000742-0r4z1zea cord-000237-mticfoic cord-000208-th0wddvc cord-000434-ff2zadol cord-000336-57es391o cord-000346-9b6yz3f4 cord-001045-jm60nxc2 cord-000077-d441jam3 cord-000765-r7y1cqou cord-000715-zl1s82yi cord-000666-je9t4i6q cord-000460-h3owwjao cord-000581-ewx5xhrb cord-000638-ss1435el cord-000556-uu1oz2ei cord-000580-dcid9emx cord-000736-6f8vyziv cord-000321-ee7q7jhv cord-000609-dpcgl6ig cord-000182-ni6iyzdn cord-000725-rafwlw0t cord-000478-88wo4xen cord-000326-a18rch1f cord-000554-p4ufea6x cord-000265-llilwq1u cord-000413-h2e6h076 cord-000158-d08buwtu cord-000719-o7ttiu97 cord-000375-fvfl0bn1 cord-000267-xroo7z7g cord-001007-645zegcv cord-000721-leedutqo cord-000642-mkwpuav6 cord-000809-9voqa1oy cord-000837-rdpsxb4n cord-000813-gagakqw4 cord-000851-uylgyhs8 cord-001014-8yrpcl94 cord-000536-0mn1gbll cord-000180-howix091 cord-000547-adfigzc1 cord-000689-8lvzab4i cord-000877-usz7pnvu cord-000695-g5sum116 cord-000959-nk2thkme cord-000981-6vloa2w3 cord-000425-isw6jeir cord-000352-qzkpik3z cord-000895-z5rdf0mi cord-000726-tonaaft2 cord-000261-ip32y0j5 cord-000833-m6abyuvx cord-000374-gt2pwc9b cord-000410-av8b8g8c cord-000539-uh3q65we cord-000912-6l6c7jpq cord-000905-1rhlu59c cord-000979-cav9n18w cord-000322-8ctsa9sd cord-000868-vnwpzsu8 cord-000347-gdra8xhj cord-000723-wo20st5w cord-000937-8vk89i4h cord-001083-vy1nxax2 cord-000984-64p3wpav cord-001120-fxd533b4 cord-000866-dr2uow4m cord-000947-psguw47w cord-001088-dugsh7mp cord-001078-5m29nugu cord-001213-gxqufddb cord-001129-gi2kswai cord-001126-uqr00nzd cord-001092-pkps5j8w cord-001162-z8cbbit3 cord-001142-puj74k7y cord-000248-zueoyesj cord-001280-skavefji cord-001145-hc9ssruz cord-001368-ymp1pj3r cord-001359-c1uom5f7 cord-001249-awn9ayy6 cord-001435-ebl8yc92 cord-001387-2g9dc5z4 cord-001432-d4zavkcn cord-001421-6t5puo6p cord-001537-i34vmfpp cord-001455-n7quwr4s cord-001420-b4zcvd04 cord-001571-drcfdv9z cord-001546-ndz3oarf cord-001734-bbeznd3r cord-001781-afg1nmib cord-001605-8p06bpt1 cord-001958-2gt3fwpy cord-001254-y2knt8g0 cord-001599-pfdnmzx2 cord-001748-7e8px4vx cord-001343-3euy4u9k cord-001263-hqxiyxfj cord-001620-yy5gq0ki cord-001383-hww0watl cord-001446-mpuovmeb cord-001603-vlv8x8l8 cord-001363-irysq6pf cord-001447-oi7bkm4z cord-001964-iy6qzq58 cord-002043-z1b7pj3s cord-002094-7tewne3a cord-001639-p9mbmfaq cord-001601-tsuz3j40 cord-001460-eo2bxxbq cord-001898-ntqyjqqk cord-001716-lbtdex4p cord-002222-rgqwm3vb cord-001909-yy9xp5ms cord-001982-arczqdza cord-001865-ji83zmy7 cord-001761-yvd1n42f cord-002834-2htnywef cord-002473-2kpxhzbe cord-002044-9xgt3tf4 cord-001707-piyo00yg cord-001199-9khx93c0 cord-002141-9mxi4dzi cord-001983-zo9yngfc cord-002602-2qvyhjlp cord-002100-dt5zvebj cord-000359-y0m1utug cord-000341-d3a06n3f cord-002811-5hrydciz cord-002601-d8908t93 cord-001843-ceatyj3o cord-001910-6zfz2ns5 cord-001219-517gka4h cord-002848-w6q1x1zs cord-002901-u4ybz8ds cord-001011-vjxmrmfc cord-002023-7zd5zhbz cord-002705-ntokyoai cord-003024-17f1evh3 cord-002426-5e1xn7kj cord-003602-wtestt8i cord-001071-bjx5td52 cord-001123-n2e4s7bu cord-004017-gcmpatlb cord-010368-plpghewn cord-003270-vu9b5a14 cord-003377-9vkhptas cord-004068-d66lwylf cord-003484-ylpa702c cord-012889-dtil5xeo cord-002939-6a3ga6v9 cord-012461-v8d91fdo cord-012891-heqsfzkm cord-003125-iptisi1m cord-004091-gex0zvoa cord-003503-t6cnjwpd cord-012967-w1oc0wdd cord-011857-brbqgbpz cord-048446-gaemgm0t cord-011798-uss38ped cord-010369-x9z8dg6a cord-013263-xw611i8k cord-252347-vnn4135b cord-254025-j1l0mder cord-252838-av7ducrk cord-254117-2ttwaegh cord-013265-qrfi6e5c cord-048364-yfn8sy1m cord-013099-j816c3tw cord-013334-cptu0k7s cord-259771-653opx0h cord-251979-j3mme15e cord-048367-yya6w976 cord-048492-4z38v9rg cord-255013-njpuc475 cord-253056-765rs3e7 cord-254000-pbzcupjg cord-003062-qm8kalyt cord-003548-zuwt7gk5 cord-048360-n9sih438 cord-254313-g2oc32dm cord-048339-nzh87aux cord-003712-mafz21no cord-002889-fie121ns cord-003841-7uaj9hmx cord-012387-1ogcxd7b cord-002953-4rqoenhr cord-001253-3jnkki5z cord-002624-59nznqsd cord-001186-jkg7qkj6 cord-001099-jirkkkvy cord-001275-a9o2dvke cord-002305-qq73gr9y cord-001117-llb4f74a cord-001207-yjaiybwf cord-002973-bkr4ndl2 cord-001039-qocuprwb cord-011496-r8e19t0c cord-001090-qg2r691d cord-002957-gw2cow0d cord-000786-ofpcgxce cord-013333-7jx4t0ol cord-048353-hqc7u9w3 cord-001251-forh7lw4 cord-002621-sq5iod1w cord-003551-jzfl4xuk cord-002913-k5b6abyk cord-001021-nag4at49 cord-255576-738khdwv cord-003244-abs3tc3r cord-002398-0a3okta0 cord-003404-eqgc8v7y cord-048471-7jszm1nd cord-003507-22ylifqo cord-048483-umvrwgaw cord-048358-z5klydpi cord-003498-4ct0ywnw cord-002890-g7aje88u cord-002180-gsdk5x3e cord-001065-j4hvyyoi cord-252739-1manzf3l cord-002560-pue5q5wp cord-013356-y6vceq2x cord-002935-jq1xumrh cord-260432-imslfm4l cord-254825-c5d0wul9 cord-256424-t3dtabi4 cord-257603-ov0b8yub cord-260572-vd65ygtm cord-254340-e1x0z3rh cord-260653-5qwtvm9x cord-252795-x66zqmgv cord-253436-dz84icdc cord-258243-2utl2mfl cord-262345-hti1jjpn cord-258366-fu9b446y cord-261908-olcuq6tm cord-258172-p54j4zzo cord-255351-vp19ydce cord-255588-nh34lgdh cord-048477-ze511t38 cord-261410-kb91eagd cord-260843-c97kctjz cord-262759-ec2c25q3 cord-260728-4w23kwzu cord-260647-7bjhobg7 cord-256326-3ebcuzd6 cord-262846-1mhimfsf cord-263276-keyu60in cord-256837-100ir651 cord-263453-7v4y02j6 cord-262876-civfvk45 cord-265138-i5m3ax7g cord-257077-cdnkk6ou cord-266797-uglsx7se cord-255384-tljyx6ua cord-263464-fdosch11 cord-263978-jk82bk1a cord-257217-f9sdt7ax cord-262748-v4xue7ha cord-265812-1hcp36cw cord-267189-xq70rn1j cord-263684-3535k3op cord-262832-5iejckwx cord-267519-a0bcmjkn cord-267307-kyh0xsrp cord-267644-guzn0peq cord-267973-uvz7kavu cord-267566-gdjl0qmu cord-266799-t7lqlv41 cord-267605-efb10j3u cord-268977-hcg2rrhl cord-268816-nth3o6ot cord-272655-qeojdpez cord-272445-0xauff51 cord-264880-0tmd9knh cord-273343-als886fe cord-269453-30l6rzgo cord-268429-drejl99k cord-276763-x3dqi0ym cord-276577-06boh550 cord-278087-0nicp0eq cord-273175-bao8xxe2 cord-273764-itu39mln cord-272878-6f0q661e cord-267042-nvwnbp2j cord-271660-5sfkhg19 cord-268524-lr51ubz5 cord-273594-vmbhok1u cord-272971-9luzvzsu cord-270683-982eqtog cord-269690-6r2bfydw cord-277409-q5wx313k cord-270681-6ayciihs cord-275058-61eof7y8 cord-278224-sq7tokbx cord-277306-r8jki3x4 cord-279259-eu80ccm6 cord-275395-w2u7fq1g cord-277548-hgmmtew3 cord-280482-o887a7q9 cord-274268-0ucqp3uz cord-276898-ia80cy8j cord-278123-mq56em3z cord-280386-a8qr7nl6 cord-270408-4qqyb8sd cord-270647-vn4kirrx cord-280846-bbv6f5gf cord-277357-lpurk7pe cord-280471-cqypwi5d cord-278018-3qemb0x3 cord-281815-zvs5qe8x cord-276372-q1fzxt3r cord-286065-x0g67pnb cord-286708-igu984oc cord-282303-idh7io9v cord-278099-ypov9ha3 cord-281161-u896icp9 cord-281124-4nhy35xn cord-282202-q2q4vies cord-274241-biqbsggu cord-284275-bqo203pf cord-283976-jgae7r2q cord-287739-58fth3xl cord-285546-5tjhdczt cord-284501-5i0w74q4 cord-279421-rxocrgfu cord-281364-syg0wo77 cord-282668-bs634hti cord-281665-6n7aq4k9 cord-289305-mfjyjjer cord-287761-73qgx58i cord-285433-ehnu83qe cord-283604-fqc9jp0l cord-286613-cmtsu73g cord-289555-1z4vbldd cord-287784-f7usy52w cord-284016-zb6cv8ik cord-289285-aof7xy13 cord-286837-j2sqs20q cord-286404-eggkqq3b cord-290773-kgb8r561 cord-289873-6hivjqof cord-289093-si8btsab cord-288502-qqg41daz cord-289017-vwye3pk9 cord-290446-43h1r4pm cord-291756-ejh1r8h4 cord-285749-0ejhd9nw cord-289510-spmknns5 cord-288440-w7g2agaf cord-282194-0sjmf1yn cord-290833-m0wodqr3 cord-289892-yh1lioyz cord-290539-8ak2tths cord-290120-fd26t8ja cord-290034-4b0mshqa cord-292237-45hi4iz2 cord-293794-vudufao5 cord-293072-giakcaki cord-293393-kbndie8e cord-292396-8w06oc5i cord-292537-9ra4r6v6 cord-294568-12eyo13f cord-294768-bs6thjw2 cord-293946-4bquxdqa cord-294023-knaxr7t0 cord-295352-b8kztgt8 cord-294645-yzh8h7zo cord-291360-z19ri377 cord-291176-evb6yt0r cord-292777-oztmw8jo cord-291104-6chpmgry cord-291417-p49ukyhx cord-292475-jrl1fowa cord-295781-b831y105 cord-294591-793ywpcd cord-295536-dbpt4dhr cord-295339-nzc47itk cord-297835-ukrz8tlv cord-299509-7xjdryoq cord-295293-ickp2n47 cord-295201-u2dola34 cord-296435-6dergkha cord-294592-zwvr57a0 cord-294912-xl0wzi16 cord-302200-9gekjgr0 cord-299491-8rfm0jxh cord-294372-pec1886j cord-306466-y4yg42p8 cord-299953-sasfvcun cord-304993-t4rua95e cord-296691-cg463fbn cord-300859-nqklx0vn cord-302355-3se1wp8o cord-296399-vvbjulm9 cord-302529-43pd2qsp cord-298078-uqrwq5qk cord-301811-ykpiorgo cord-305547-e66o5j85 cord-302962-qw6s1t7j cord-297287-0i4nc353 cord-298679-w0yp4u19 cord-301180-ndiwmnv0 cord-305071-4ck8nd24 cord-303331-xolksoy3 cord-303490-rixuuytu cord-306958-8bx8kxxh cord-296550-wkmnfph3 cord-305303-82n96ukr cord-296487-m4xba78g cord-299852-t0mqe7yy cord-298131-zolwjl9u cord-296635-8r3tm966 cord-307934-84zfabti cord-306278-c4q4la5c cord-303187-ny4qr2a2 cord-305274-mcsdem7y cord-302189-3xab3yxc cord-305900-ht7hb2rc cord-305811-987dhnf7 cord-303845-y6ws3u6x cord-305393-96mrxt8a cord-309194-jtouafgd cord-308344-ao9z00t7 cord-310678-33c3mp1o cord-310438-744r7gc3 cord-310061-nro623aa cord-307036-n44yml79 cord-295559-yc8q62z8 cord-306135-pt4jsr6d cord-309621-6jj19xpr cord-311074-j3fw4dfc cord-309981-4p3ybrn1 cord-304616-k92fa15l cord-309010-tmfm5u5h cord-312493-wbhji81g cord-311065-ie3gty6e cord-310790-3ikgmiof cord-312367-24huwt3y cord-312033-iarl77n0 cord-310396-jitao9k0 cord-311941-0dpm35dd cord-308764-9z4qcoqz cord-311531-wezrs7gc cord-311288-6ttux2uu cord-312002-4qhvljpv cord-310947-aqau2n7q cord-309471-lr68epyb cord-303034-w72oeoxq cord-309043-dlmx12vt cord-315531-2gc2dc46 cord-313506-6bb4q7nv cord-308249-es948mux cord-314908-kp2jznwb cord-310466-0lbbiq7u cord-313107-6cfenpxm cord-308480-t2vukbwp cord-307540-dr5m9pfk cord-312817-gskbu0oh cord-314651-e4uaw5fy cord-317244-4su5on6s cord-318696-jheb2fnn cord-315343-ywgoqlxj cord-316853-vaea6siv cord-316047-d9cpe9yl cord-308261-hxlebas8 cord-317912-v2wovcqd cord-312678-81gnmxbk cord-319706-2e9jrv0s cord-318614-518giv0m cord-318008-4s9eoae3 cord-316319-m6uha1qn cord-319538-bawzonq1 cord-316703-8kxx3034 cord-317058-anvmj4li cord-319256-7pyinx1a cord-321855-7b1c2xdh cord-321705-6a7avlro cord-320466-l7017jis cord-317779-j67vb7f3 cord-320091-2lrqubdl cord-319845-oob2ktnz cord-321834-n5w88l23 cord-319921-uxtydu60 cord-320938-f526k9q1 cord-321438-llnqzkqt cord-322414-dpx191xh cord-322533-adqqm0n9 cord-322446-ddv86eoy cord-323433-9km824uh cord-323330-ghwhgkdm cord-321624-z2mntwef cord-322827-h33su548 cord-324410-be2ith3z cord-319190-esjfhztp cord-319675-mwy3t1ny cord-327199-ggomuomb cord-324091-nljd2ok1 cord-318845-w7q5o8wc cord-326011-5rmhjbri cord-325113-sou8xyld cord-323185-n0rubc72 cord-327257-doygrgrc cord-324359-88vy3dre cord-326568-twv2i3fb cord-328627-cf8f71dr cord-316287-4i1grvlr cord-328206-iylw1bvw cord-328633-c31xsyeo cord-324405-6uanhe2p cord-333208-tibtngy8 cord-329223-f84gjxm1 cord-331885-8zmuhebu cord-323133-gdg50omp cord-330110-pamxy4av cord-330749-xt4aa2ur cord-335272-jypxi99z cord-327534-f2wvh6la cord-334218-bkjfy66e cord-333955-bnzbppof cord-333853-p2kbjwpy cord-333522-zsdymkjd cord-334955-gnu92up6 cord-329999-flzqm3wh cord-329727-h47q76y8 cord-329468-vjsurl60 cord-333413-8buawes0 cord-330537-xz0wt1sz cord-331652-oc5s1if2 cord-335859-k37jivp6 cord-330079-pdaowkop cord-337795-khqx4t4q cord-335880-m8gecsf0 cord-336364-2ust3qoq cord-336615-jfnj6l41 cord-333248-5342lyeu cord-335441-bj3me7p8 cord-332922-2qjae0x7 cord-335404-s48psqth cord-338067-vjyad10p cord-335505-s013j5ex cord-336420-1a2u9p4t cord-339789-151d1j4n cord-339026-eu11larc cord-333650-4towah1t cord-336843-c0sr3six cord-337585-kpghvb6u cord-339157-wj47xeqj cord-339578-eg19rfvi cord-338594-wft7yy6j cord-339327-4422s317 cord-335245-1eksm537 cord-334695-cjxlw1tu cord-337067-j8ebslif cord-340027-6l55rcfm cord-339724-roj8ksvc cord-340763-cxnu9g8y cord-337913-eu2gn4bl cord-336441-m6pur6td cord-337879-liqhbqxl cord-340195-425rd7ul cord-339920-dr5bvpm0 cord-337630-ojhk5opy cord-339392-2ocz784l cord-341914-l2bomgji cord-339796-gccnvh0z cord-340718-amfs4zay cord-340703-vtuy806l cord-340713-v5sdowb7 cord-340656-ltd6ueoi cord-340627-xyvzgkxl cord-340766-aic570x8 cord-340937-6mpob1nx cord-339869-euikj8fv cord-340387-ohkjheat cord-342476-0rupk21u cord-341880-wxliz485 cord-343135-m0pdixw5 cord-342133-khrljehj cord-342519-tjr6dvtt cord-341097-c96hm610 cord-343973-n5ogyxz7 cord-344782-ond1ziu5 cord-344870-tbgqulpu cord-344839-r05p9h0e cord-344357-ocyaqs1y cord-342730-b7y8mybg cord-342639-vf9n2vf9 cord-345717-ktajrf7d cord-346586-fxxceffl cord-344152-pb1e2w7s cord-345019-i7zm9bt1 cord-345695-5vi9wibk cord-347465-yu6oj30v cord-348055-azlb1zy1 cord-346067-zly8p0y7 cord-346089-u31n0qxa cord-346347-r4ork18p cord-348807-9xxc5hyl cord-346819-11fkgzaa cord-347014-88zmtky7 cord-346314-o9fjpqaj cord-346858-18q8rxzg cord-348499-7ll7sd3o cord-349029-zyfop43z cord-350842-4m82l5t8 cord-349476-iac9fak3 cord-349781-l93978vq cord-350443-ca5avyjf cord-351868-w4d45fue cord-351142-g20f6bxc cord-349911-dx8wvqkm cord-352200-i05h8csb cord-348243-e5tdb08v cord-347317-qcghtkk0 cord-351387-i0zamkpd cord-349217-vpih1wvs cord-351185-3y3gou6v cord-352222-zq9o66i4 cord-352403-4591ewsa cord-351990-aham72b9 cord-351918-pu7i1jfe cord-352564-2j4pjjwk cord-351098-x729wpp7 cord-353200-5csewb1k cord-352511-gkm7i62s cord-353866-0r1b44id cord-352522-qnvgg2e9 cord-352720-z1cvjc2y cord-353245-es7b1rs0 cord-352447-bc1pf272 cord-355874-nz6eqcdb cord-353869-l53ms3q8 cord-350398-w75flrwv cord-354052-x4ckzw64 cord-352219-z245sb3s cord-354000-jxqskt4k cord-354763-odzrco6q cord-356132-1nisyl5r cord-353253-kk2q71vg cord-353596-8iqjugcx cord-356364-ipi81ce3 cord-354547-eomm1sl5 cord-353410-tbmtg88k cord-353730-owcapg8h cord-355259-779czzzx Creating transaction Updating pos table Building ./etc/reader.txt cord-000248-zueoyesj cord-001249-awn9ayy6 cord-287784-f7usy52w cord-355259-779czzzx cord-310947-aqau2n7q cord-001420-b4zcvd04 number of items: 672 sum of words: 3,019,971 average size in words: 5,383 average readability score: 48 nouns: cells; virus; infection; study; patients; protein; data; cell; influenza; analysis; disease; time; expression; cases; number; results; viruses; studies; model; samples; control; proteins; health; mice; group; type; gene; infections; levels; population; risk; response; ml; detection; activity; age; sequence; days; children; effect; coronavirus; case; antibody; rate; treatment; sequences; system; role; level; factors verbs: using; shown; including; based; report; increased; find; associated; compared; identified; following; detected; infected; performed; observed; inducing; suggest; indicates; described; contains; provide; determine; binding; expressing; testing; obtained; confirmed; reduced; collected; required; caused; result; related; analyzed; considering; gave; develop; demonstrates; estimating; seen; known; assess; affect; represents; lead; measure; taken; making; according; predicting adjectives: viral; human; respiratory; high; different; specific; clinical; positive; higher; significant; severe; non; acute; anti; first; similar; infectious; immune; low; negative; total; important; new; lower; single; several; infected; molecular; social; large; present; previous; small; novel; early; possible; many; available; multiple; potential; cellular; public; common; primary; bacterial; covid-19; effective; antiviral; like; inflammatory adverbs: also; however; well; respectively; significantly; previously; therefore; highly; even; first; furthermore; recently; approximately; still; moreover; finally; less; directly; prior; together; least; especially; often; relatively; particularly; frequently; similarly; statistically; much; additionally; interestingly; specifically; rather; likely; subsequently; currently; mainly; alone; potentially; indeed; generally; commonly; strongly; almost; fully; briefly; clearly; later; now; overall pronouns: we; it; our; their; its; they; i; them; us; his; one; you; itself; themselves; her; he; my; your; she; me; him; ours; pregn; myself; yourself; imagej; mrnas; ifitm3; em; ourselves; nsp10; ns3/4a; apod; 9b; mg; interleukin-10; il-2rcc; herself; clustalx; stat1; oneself; cav-1b; ĝ; theirs; snoz40; s; rad5; p450s; mine; lc16m8 proper nouns: Fig; RNA; PCR; SARS; COVID-19; C; Table; T; China; IFN; RT; CoV-2; A; Health; CoV; S1; H1N1; mg; HIV; HIV-1; M; USA; PBS; HCV; B; S; HA; CD4; N; MERS; RSV; II; Influenza; NP; Figure; ELISA; H5N1; CD8; PLoS; HRV; sha; United; a1111111111; DNA; Coronavirus; University; D; Disease; E.; pH keywords: covid-19; sars; pcr; rna; cell; virus; patient; respiratory; protein; ifn; influenza; china; dna; infection; h1n1; case; study; rsv; health; model; hiv-1; hcv; bat; mers; hiv; h5n1; table; icu; cd8; cd4; vero; sequence; pneumonia; pedv; lps; gene; viral; usa; sari; sample; risk; ili; ibv; hrv; ebola; united; taiwan; peptide; outbreak; elisa one topic; one dimension: virus file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2565067/ titles(s): HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection three topics; one dimension: study; virus; cells file(s): https://doi.org/10.1371/journal.pone.0239666, https://doi.org/10.1371/journal.pone.0134851, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733918/ titles(s): Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation | Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins | TNF-α Acts as an Immunoregulator in the Mouse Brain by Reducing the Incidence of Severe Disease Following Japanese Encephalitis Virus Infection five topics; three dimensions: covid study health; cells virus cell; respiratory virus influenza; protein proteins using; infection virus mice file(s): https://doi.org/10.1371/journal.pone.0240878, https://www.ncbi.nlm.nih.gov/pubmed/22359682/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712091/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035654/, https://www.ncbi.nlm.nih.gov/pubmed/27556586/ titles(s): A social network model of COVID-19 | Removal of Hepatitis C Virus-Infected Cells by a Zymogenized Bacterial Toxin | Evidence of Recombination and Genetic Diversity in Human Rhinoviruses in Children with Acute Respiratory Infection | Further Characterisation of the Translational Termination-Reinitiation Signal of the Influenza B Virus Segment 7 RNA | Impact of LbSapSal Vaccine in Canine Immunological and Parasitological Features before and after Leishmania chagasi-Challenge Type: cord title: journal-plosOne-cord date: 2021-05-30 time: 15:05 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: facet_journal:"PLoS One" ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-000877-usz7pnvu author: Abdel-Moneim, Ahmed S. title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia date: 2013-01-30 words: 1826.0 sentences: 101.0 pages: flesch: 51.0 cache: ./cache/cord-000877-usz7pnvu.txt txt: ./txt/cord-000877-usz7pnvu.txt summary: title: Detection of Bocavirus in Children Suffering from Acute Respiratory Tract Infections in Saudi Arabia Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Human bocavirus (HBoV) was first found in children with acute respiratory tract infections in 2005 [1] . The current study aims to screen the epidemiological status and molecular phylogeny of HBoV isolates prevailing in pediatric patients with respiratory infection in Saudi Arabia. The current study investigated the prevalence of HBoV in patients suffering from respiratory tract infections in Saudi Arabia. Furthermore, the phylogenetic analysis results of three selected sequences showed that the Saudi HBoV1 strains obtained from respiratory samples belonged to group I human bocaviruses (Fig. 1) . Detection of human bocavirus in Japanese children with lower respiratory tract infections Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction abstract: Human bocavirus (HBoV) was recently discovered in children with respiratory distress and/or diarrhea. To our knowledge, no previous study has reported the existence of bocavirus in Saudi Arabia. Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Real-time polymerase chain reaction was used as a sensitive method to detect the HBoV. Direct gene sequencing was used to determine the genotype of the detected virus isolates. HBoV was detected in 22.5% of the examined patients. The NP1 partial gene sequence from all patients showed that the circulated strains were related to HBoV-1 genotype. Most of HBoV infected patients showed evidence of mixed coinfection with other viral pathogens. The current study clearly demonstrated that genetically conserved HBoV1 circulates in Saudi Arabia. Interestingly, most of the HBoV1 infected cases were associated with high rates of co-infections with other viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3559585/ doi: 10.1371/journal.pone.0055500 id: cord-004091-gex0zvoa author: Abdulkareem, Shaheen A. title: Risk perception and behavioral change during epidemics: Comparing models of individual and collective learning date: 2020-01-06 words: 8379.0 sentences: 432.0 pages: flesch: 50.0 cache: ./cache/cord-004091-gex0zvoa.txt txt: ./txt/cord-004091-gex0zvoa.txt summary: For this study, we ran eight ABMs to test various combinations of individual and group learning, using different information sources-with or without interactions among agents-as factors in the BNs. We investigate the extent to which the epidemic spreads, depending on these different learning approaches regarding risk perception and coping decisions. The empirically-driven BNs model a two-stage decision process of people facing a disease risk: learning to update risk perceptions (threat appraisal, BN1 in Fig 1) and making decisions about how to adapt their behavior during the epidemic (coping appraisal, BN2 in Fig 1) . To evaluate the impact of individual and social intelligence on agents'' learning processes regarding risk perception and coping appraisal and the resulting patterns of disease spread, we used four output measures: disease diffusion, risk perception, spatial patterns, and model performance. Finally, in M7, where household agents learned risk perception in decentralized groups and learned to cope individually, 2,911 infected cases were recorded (Table 3) . abstract: Modern societies are exposed to a myriad of risks ranging from disease to natural hazards and technological disruptions. Exploring how the awareness of risk spreads and how it triggers a diffusion of coping strategies is prominent in the research agenda of various domains. It requires a deep understanding of how individuals perceive risks and communicate about the effectiveness of protective measures, highlighting learning and social interaction as the core mechanisms driving such processes. Methodological approaches that range from purely physics-based diffusion models to data-driven environmental methods rely on agent-based modeling to accommodate context-dependent learning and social interactions in a diffusion process. Mixing agent-based modeling with data-driven machine learning has become popularity. However, little attention has been paid to the role of intelligent learning in risk appraisal and protective decisions, whether used in an individual or a collective process. The differences between collective learning and individual learning have not been sufficiently explored in diffusion modeling in general and in agent-based models of socio-environmental systems in particular. To address this research gap, we explored the implications of intelligent learning on the gradient from individual to collective learning, using an agent-based model enhanced by machine learning. Our simulation experiments showed that individual intelligent judgement about risks and the selection of coping strategies by groups with majority votes were outperformed by leader-based groups and even individuals deciding alone. Social interactions appeared essential for both individual learning and group learning. The choice of how to represent social learning in an agent-based model could be driven by existing cultural and social norms prevalent in a modeled society. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944362/ doi: 10.1371/journal.pone.0226483 id: cord-292475-jrl1fowa author: Abry, Patrice title: Spatial and temporal regularization to estimate COVID-19 reproduction number R(t): Promoting piecewise smoothness via convex optimization date: 2020-08-20 words: 7470.0 sentences: 386.0 pages: flesch: 53.0 cache: ./cache/cord-292475-jrl1fowa.txt txt: ./txt/cord-292475-jrl1fowa.txt summary: The novelty of the proposed approach is twofold: 1) the estimation of the reproduction number is achieved by convex optimization within a proximal-based inverse problem formulation, with constraints aimed at promoting piecewise smoothness; 2) the approach is developed in a multivariate setting, allowing for the simultaneous handling of multiple time series attached to different geographical regions, together with a spatial (graph-based) regularization of their evolutions in time. In that spirit, the overarching goal of the present work is twofold: (1) proposing a new, more versatile framework for the estimation of R(t) within the semi-parametric model of [8, 10] , reformulating its estimation as an inverse problem whose functional is minimized by using non smooth proximal-based convex optimization; (2) inserting this approach in an extended multivariate framework, with applications to various complementary datasets corresponding to different geographical regions. abstract: Among the different indicators that quantify the spread of an epidemic such as the on-going COVID-19, stands first the reproduction number which measures how many people can be contaminated by an infected person. In order to permit the monitoring of the evolution of this number, a new estimation procedure is proposed here, assuming a well-accepted model for current incidence data, based on past observations. The novelty of the proposed approach is twofold: 1) the estimation of the reproduction number is achieved by convex optimization within a proximal-based inverse problem formulation, with constraints aimed at promoting piecewise smoothness; 2) the approach is developed in a multivariate setting, allowing for the simultaneous handling of multiple time series attached to different geographical regions, together with a spatial (graph-based) regularization of their evolutions in time. The effectiveness of the approach is first supported by simulations, and two main applications to real COVID-19 data are then discussed. The first one refers to the comparative evolution of the reproduction number for a number of countries, while the second one focuses on French departments and their joint analysis, leading to dynamic maps revealing the temporal co-evolution of their reproduction numbers. url: https://www.ncbi.nlm.nih.gov/pubmed/32817697/ doi: 10.1371/journal.pone.0237901 id: cord-290773-kgb8r561 author: Ahn, Jong Gyun title: Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus date: 2018-07-03 words: 2594.0 sentences: 148.0 pages: flesch: 47.0 cache: ./cache/cord-290773-kgb8r561.txt txt: ./txt/cord-290773-kgb8r561.txt summary: title: Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus Therefore, in this study, we investigated the epidemiological, clinical, and virological characteristics of HRV infections in children with acute lower respiratory tract infections. This study demonstrates that HRV is an important cause of lower respiratory infection in young children that is associated with symptoms of respiratory distress, such as chest retraction and wheezing. In our study, there were no significant differences in the clinical features, laboratory data or NPA cytokine levels between HRV-A and -C infections. High prevalence of human rhinovirus C infection in Thai children with acute lower respiratory tract disease Human rhinovirus species C infection in young children with acute wheeze is associated with increased acute respiratory hospital admissions Rhinovirus load and disease severity in children with lower respiratory tract infections abstract: The clinical profile of human rhinovirus (HRV) with regard to lower respiratory infections remains unclear. We analyzed the clinical features and cytokine responses of HRV isolates in children with respiratory infections. Quantitative analysis and genotyping of the HRV-positive samples from 601 nasopharyngeal aspirates (NPAs) were performed using VP4/VP2 sequencing. To compare T-helper1 (Th1) type (IFN-γ, TNF-α) and Th2 type (IL-4, IL-10) cytokine responses between HRV-A, B and C, the levels of the four cytokines were measured. The HRV-positive children had shorter fever duration (P = 0.018), and higher frequencies of chest retraction (P = 0.002) and wheezing (P = 0.022) than did the HRV-negative group. HRV-A was identified in 55 cases (58.5%), HRV-B in 8 (8.5%), and HRV-C in 31 (33.0%). There were no significant differences in the clinical data or NPA cytokines levels between patients with HRV-A and HRV-C infections. HRV is an important pathogen of the lower respiratory tract in young children. HRV-A and HRV-C are the dominant species that cause respiratory difficulty in young children. url: https://www.ncbi.nlm.nih.gov/pubmed/29969445/ doi: 10.1371/journal.pone.0198624 id: cord-001145-hc9ssruz author: Akazawa, Yuko title: Endoplasmic Reticulum Stress Contributes to Helicobacter Pylori VacA-Induced Apoptosis date: 2013-12-13 words: 6256.0 sentences: 407.0 pages: flesch: 52.0 cache: ./cache/cord-001145-hc9ssruz.txt txt: ./txt/cord-001145-hc9ssruz.txt summary: We found that C/EBP homologous protein (CHOP), a key signaling protein of ER stress-induced apoptosis, was transcriptionally up-regulated following incubation of gastric epithelial cells with VacA. Phosphorylation of eukaryotic initiation factor 2 (eIF2)-alpha, which is known to occur downstream of the ER stress sensor PKR-like ER-localized eIF2-alpha kinase (PERK) and to regulate CHOP expression, was also observed following incubation with VacA in the presence of ammonium chloride. Further studies showed that silencing of the PERK gene with siRNA attenuated VacA-mediated phosphorylation of eIF2-alpha, CHOP induction, expression of BH3-only protein Bim and Bax activation, and cell death induced by VacA with ammonium chloride, indicating that ER stress may lead to mitochondrial dysfunction during VacA-induced toxicity. pylori-positive gastric mucosa, as well as transcriptional up-regulation of Bim in AZ-521 cells treated with VacA plus NH 4 Cl. Since knockdown of PERK decreased VacA-mediated Bim mRNA expression, activation of Bim likely occurred downstream of ER stress. abstract: Vacuolating cytotoxin A (VacA) is one of the important virulence factors produced by H. pylori. VacA induces apoptotic cell death, which is potentiated by ammonia. VacA also causes cell death by mitochondrial damage, via signaling pathways that are not fully defined. Our aim was to determine whether endoplasmic reticulum (ER) stress is associated with VacA-induced mitochondrial dysfunction and apoptosis. We found that C/EBP homologous protein (CHOP), a key signaling protein of ER stress-induced apoptosis, was transcriptionally up-regulated following incubation of gastric epithelial cells with VacA. The effect of VacA on CHOP induction was significantly enhanced by co-incubation with ammonium chloride. Phosphorylation of eukaryotic initiation factor 2 (eIF2)-alpha, which is known to occur downstream of the ER stress sensor PKR-like ER-localized eIF2-alpha kinase (PERK) and to regulate CHOP expression, was also observed following incubation with VacA in the presence of ammonium chloride. Knockdown of CHOP by siRNA resulted in inhibition of VacA-induced apoptosis. Further studies showed that silencing of the PERK gene with siRNA attenuated VacA-mediated phosphorylation of eIF2-alpha, CHOP induction, expression of BH3-only protein Bim and Bax activation, and cell death induced by VacA with ammonium chloride, indicating that ER stress may lead to mitochondrial dysfunction during VacA-induced toxicity. Activation of ER stress and up-regulation of BH3-only proteins were also observed in human H. pylori-infected gastric mucosa. Collectively, this study reveals a possible association between VacA-induced apoptosis in gastric epithelial cells, and activation of ER stress in H. pylori-positive gastric mucosa. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3862672/ doi: 10.1371/journal.pone.0082322 id: cord-320466-l7017jis author: Akgun, Emel title: Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients date: 2020-10-20 words: 3722.0 sentences: 226.0 pages: flesch: 42.0 cache: ./cache/cord-320466-l7017jis.txt txt: ./txt/cord-320466-l7017jis.txt summary: Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified up-regulated proteins Myeloperoxidase, Myeloblastin, Neutrophil Elastase, Cathepsin G, and Azurocidin (MPO, PRTN3, ELANE, CTSG, and AZU1) in nasooropharyngeal swab samples are discussed to highlight the molecular mechanism changes in the site of infection. Pathway analysis of the significantly altered protein levels between COVID-19 positive and negative patients'' naso-oropharyngeal swab samples were analyzed using the STRING online database. In SARS-CoV-2 patients'' naso-oropharyngeal samples, we have identified azurophilic granule (AG) proteins like Myeloperoxidase (MPO), elastase (ELANE), cathepsin G (CTSG), azurocidin 1 (AZU1) and proteinase 3 (PRTN3) to be highly overexpressed. The alterations of various proteins in SARS-CoV-2 infected patients'' naso-oropharyngeal samples depict the molecular changes that govern the host antiviral defense system. abstract: COVID-19 or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared throughout the World and currently affected more than 9 million people and caused the death of around 470,000 patients. The novel strain of the coronavirus disease is transmittable at a devastating rate with a high rate of severe hospitalization even more so for the elderly population. Naso-oro-pharyngeal swab samples as the first step towards detecting suspected infection of SARS-CoV-2 provides a non-invasive method for PCR testing at a high confidence rate. Furthermore, proteomics analysis of PCR positive and negative naso-oropharyngeal samples provides information on the molecular level which highlights disease pathology. Samples from 15 PCR positive cases and 15 PCR negative cases were analyzed with nanoLC-MS/MS to identify the differentially expressed proteins. Proteomic analyses identified 207 proteins across the sample set and 17 of them were statistically significant. Protein-protein interaction analyses emphasized pathways like Neutrophil degranulation, Innate Immune System, Antimicrobial Peptides. Neutrophil Elastase (ELANE), Azurocidin (AZU1), Myeloperoxidase (MPO), Myeloblastin (PRTN3), Cathepsin G (CTSG) and Transcobalamine-1 (TCN1) were found to be significantly altered in naso-oropharyngeal samples of SARS-CoV-2 patients. The identified proteins are linked to alteration in the innate immune system specifically via neutrophil degranulation and NETosis. url: https://doi.org/10.1371/journal.pone.0240012 doi: 10.1371/journal.pone.0240012 id: cord-317912-v2wovcqd author: Akmatov, Manas K. title: Equivalence of Self- and Staff-Collected Nasal Swabs for the Detection of Viral Respiratory Pathogens date: 2012-11-14 words: 3488.0 sentences: 176.0 pages: flesch: 57.0 cache: ./cache/cord-317912-v2wovcqd.txt txt: ./txt/cord-317912-v2wovcqd.txt summary: found similar detection rates for respiratory pathogens between self-and staffcollected midturbinate swabs when one staff-collected and one selfcollected swab were taken from opposite nostrils during the same visit to a campus health center [5] . In the study center, a trained staff member (A.G.) obtained a nasal swab (regular flocked swab, Copan, Brescia, Italy, product number 359C) from the participant''s left nostril and instructed him/her how to perform a self-swab. Sensitivity and specificity of self-collected swabs, obtained in the study center, to detect viral respiratory pathogens (compared to staff-collected swabs)*. The detection of a viral pathogen was independent of the amount of b-actin DNA in both staff-and self-swabs collected on day 1 (Fig. 4) . This prospective study comparing staff-and self-collected nasal swabs for the detection of ARI pathogens clearly demonstrated the validity of self-swabbing; specifically, self-swabbing was not inferior in terms of acceptance, satisfaction, sample adequacy, and viral detection rate. abstract: BACKGROUND: The need for the timely collection of diagnostic biosamples during symptomatic episodes represents a major obstacle to large-scale studies on acute respiratory infection (ARI) epidemiology. This may be circumvented by having the participants collect their own nasal swabs. We compared self- and staff-collected swabs in terms of swabbing quality and detection of viral respiratory pathogens. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a prospective study among employees of our institution during the ARI season 2010/2011 (December-March). Weekly emails were sent to the participants (n = 84), reminding them to come to the study center in case of new symptoms. The participants self-collected an anterior nasal swab from one nostril, and trained study personnel collected one from the other nostril. The participants self-collected another two swabs (one from each nostril) on a subsequent day. Human β-actin DNA concentration was determined in the swabs as a quality control. Viral respiratory pathogens were detected by multiplex RT-PCR (Seeplex RV15 kit, Seegene, Eschborn, Germany). Of 84 participants, 56 (67%) reported at least one ARI episode, 18 participants two, and one participant three. Self-swabbing was highly accepted by the participants. The amount of β-actin DNA per swab was higher in the self- than in the staff-collected swabs (p = 0.008). β-actin concentration was lower in the self-swabs collected on day 1 than in those collected on a subsequent day (p<0.0001). A respiratory viral pathogen was detected in 31% (23/75) of staff- and in 35% (26/75) of self-collected swabs (p = 0.36). With both approaches, the most frequently identified pathogens were human rhinoviruses A/B/C (12/75 swabs, 16%) and human coronavirus OC43 (4/75 swabs, 5%). There was almost perfect agreement between self- and staff-collected swabs in terms of pathogen detection (agreement = 93%, kappa = 0.85, p<0.0001). CONCLUSIONS/SIGNIFICANCE: Nasal self-swabbing for identification of viral ARI pathogens proved to be equivalent to staff-swabbing in this population in terms of acceptance and pathogen detection. url: https://doi.org/10.1371/journal.pone.0048508 doi: 10.1371/journal.pone.0048508 id: cord-345019-i7zm9bt1 author: Al-Waleedi, Ali Ahmed title: The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data date: 2020-10-29 words: 4496.0 sentences: 236.0 pages: flesch: 55.0 cache: ./cache/cord-345019-i7zm9bt1.txt txt: ./txt/cord-345019-i7zm9bt1.txt summary: A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. For early detection of SARS-CoV-2 in Yemen, as in other countries, a case definition, active surveillance, and contact tracing were required [10, 11] . The first 2 months after confirmation of the SARS-CoV-2 epidemic in Yemen was characterized by a 57% hospitalization rate in the southern and eastern parts of the country included in The First 2 Months of the SARS-CoV-2 Epidemic in Yemen our study, 63% of deaths occurring in individuals aged <60 years, confirmatory testing of <50% of the suspected cases, and majority of cases were not related to a defined chain of transmission. abstract: INTRODUCTION: Yemen was one of the last countries in the world to declare the first case of the pandemic, on 10 April 2020. Fear and concerns of catastrophic outcomes of the epidemic in Yemen were immediately raised, as the country is facing a complex humanitarian crisis. The purpose of this report is to describe the epidemiological situation in Yemen during the first 2 months of the SARS-CoV-2 epidemic. METHODS: We analyzed the epidemiological data from 18 February to 05 June 2020, including the 2 months before the confirmation of the first case. We included in our analysis the data from 10 out of 23 governorates of Yemen, located in southern and eastern part of the country. RESULTS: A total of 469 laboratory confirmed, 552 probable and 55 suspected cases with onset of symptoms between 18 February and 5 June 2020 were reported through the surveillance system. The median age among confirmed cases was 46 years (range: 1–90 years), and 75% of the confirmed cases were male. A total of 111 deaths were reported among those with confirmed infection. The mean age among those who died was 53 years (range: 14–88 years), with 63% of deaths (n = 70) occurring in individuals under the age 60 years. A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths, CONCLUSIONS: The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. The mild and moderate cases were not self-reported to the health facilities and surveillance system due to limited resources, stigma, and other barriers. The mortality appeared to be higher in individuals aged under 60 years, and most fatalities occurred in individuals who were in critical condition when they reached the health facilities. It is unclear whether the presence of other acute comorbidities contributed to the high death rate among SARS-CoV-2 cases. The findings only include the southern and eastern part of the country, which is home to 31% of the total population of Yemen, as the data from the northern part of the country was inaccessible for analysis. This makes our results not generalizable to the rest of the country. url: https://www.ncbi.nlm.nih.gov/pubmed/33119720/ doi: 10.1371/journal.pone.0241260 id: cord-001639-p9mbmfaq author: Alfonso-Morales, Abdulahi title: Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent date: 2015-05-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. METHODOLOGY/PRINCIPAL FINDINGS: Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. CONCLUSIONS/SIGNIFICANCE: This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422720/ doi: 10.1371/journal.pone.0125853 id: cord-268429-drejl99k author: Almberg, Emily S. title: A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community date: 2009-09-16 words: 7276.0 sentences: 349.0 pages: flesch: 52.0 cache: ./cache/cord-268429-drejl99k.txt txt: ./txt/cord-268429-drejl99k.txt summary: METHODOLOGY/PRINCIPAL FINDINGS: We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991–2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. Thus we sought to use long-term serological data to identify temporal, spatial, and demographic patterns of pathogen exposure among wolves, coyotes (Canis latrans), and foxes (Vulpes vulpes) in YNP. In summary, the constant high canid exposure to CPV, CAV-1, and CHV in YNP suggest that these pathogens are established in the wolf and coyote populations and that they are unlikely to be causing acute mortality in their hosts [50, 51] . abstract: BACKGROUND: Gray wolves (Canis lupus) were reintroduced into Yellowstone National Park (YNP) after a >70 year absence, and as part of recovery efforts, the population has been closely monitored. In 1999 and 2005, pup survival was significantly reduced, suggestive of disease outbreaks. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed sympatric wolf, coyote (Canis latrans), and red fox (Vulpes vulpes) serologic data from YNP, spanning 1991–2007, to identify long-term patterns of pathogen exposure, identify associated risk factors, and examine evidence for disease-induced mortality among wolves for which there were survival data. We found high, constant exposure to canine parvovirus (wolf seroprevalence: 100%; coyote: 94%), canine adenovirus-1 (wolf pups [0.5–0.9 yr]: 91%, adults [≥1 yr]: 96%; coyote juveniles [0.5–1.5 yrs]: 18%, adults [≥1.6 yrs]: 83%), and canine herpesvirus (wolf: 87%; coyote juveniles: 23%, young adults [1.6–4.9 yrs]: 51%, old adults [≥5 yrs]: 87%) suggesting that these pathogens were enzootic within YNP wolves and coyotes. An average of 50% of wolves exhibited exposure to the protozoan parasite, Neospora caninum, although individuals’ odds of exposure tended to increase with age and was temporally variable. Wolf, coyote, and fox exposure to canine distemper virus (CDV) was temporally variable, with evidence for distinct multi-host outbreaks in 1999 and 2005, and perhaps a smaller, isolated outbreak among wolves in the interior of YNP in 2002. The years of high wolf-pup mortality in 1999 and 2005 in the northern region of the park were correlated with peaks in CDV seroprevalence, suggesting that CDV contributed to the observed mortality. CONCLUSIONS/SIGNIFICANCE: Of the pathogens we examined, none appear to jeopardize the long-term population of canids in YNP. However, CDV appears capable of causing short-term population declines. Additional information on how and where CDV is maintained and the frequency with which future epizootics might be expected might be useful for future management of the Northern Rocky Mountain wolf population. url: https://doi.org/10.1371/journal.pone.0007042 doi: 10.1371/journal.pone.0007042 id: cord-294768-bs6thjw2 author: Alonso-Fernández, Alberto title: Prevalence of pulmonary embolism in patients with COVID-19 pneumonia and high D-dimer values: A prospective study date: 2020-08-25 words: 4652.0 sentences: 278.0 pages: flesch: 49.0 cache: ./cache/cord-294768-bs6thjw2.txt txt: ./txt/cord-294768-bs6thjw2.txt summary: title: Prevalence of pulmonary embolism in patients with COVID-19 pneumonia and high D-dimer values: A prospective study CONCLUSIONS: Patients with COVID-19 pneumonia and D-dimer values higher than 1 μg/mL presented a high prevalence of PE, regardless of clinical suspicion. [12] found, in a retrospective study in 184 intensive care unit (ICU) patients with severe COVID-19 pneumonia, a high prevalence of thrombotic complications and, by far, pulmonary embolism (PE) was the most frequent. Pulmonary embolism in COVID-19 pneumonia with high D-dimer values: A prospective study procoagulant (D-dimer) markers that correlated with the extend of the thromboembolic episode compared to those patients without PE. We included patients with D-dimer values higher than 1 μg/mL, which have been associated with disease severity and in-hospital mortality in patients with COVID-19 infection. Pulmonary embolism in COVID-19 pneumonia with high D-dimer values: A prospective study of our patients, allocated in the non-PE group, was not on enoxaparin prophylaxis during hospitalization. abstract: INTRODUCTION: Coronavirus disease 2019 (COVID-19) pneumonia is associated to systemic hyper-inflammation and abnormal coagulation profile. D-dimer elevation is particularly frequent, and values higher than 1μg/mL have been associated with disease severity and in-hospital mortality. Previous retrospective studies found a high pulmonary embolism (PE) prevalence, however, it should be highlighted that diagnoses were only completed when PE was clinically suspected. MATERIAL AND METHODS: Single-center prospective cohort study. Between April 6(th) and April 17(th) 2020, consecutive confirmed cases of COVID-19 pneumonia with D-dimer >1 μg/mL underwent computed tomography pulmonary angiography (CTPA) to investigate the presence and magnitude of PE. Demographic and laboratory data, comorbidities, CTPA scores, administered treatments, and, clinical outcomes were analysed and compared between patients with and without PE. RESULTS: Thirty consecutive patients (11 women) were included. PE was diagnosed in 15 patients (50%). In patients with PE, emboli were located mainly in segmental arteries (86%) and bilaterally (60%). Patients with PE were significantly older (median age 67.0 (IQR 63.0–73.0) vs. 57.0 (IQR 48.0–69.0) years, p = .048) and did not differ in sex or risk factors for thromboembolic disease from the non-PE group. D-dimer, platelet count, and, C reactive protein values were significantly higher among PE patients. D-dimer values correlated with the radiologic magnitude of PE (p<0.001). CONCLUSIONS: Patients with COVID-19 pneumonia and D-dimer values higher than 1 μg/mL presented a high prevalence of PE, regardless of clinical suspicion. We consider that these findings could contribute to improve the prognosis of patients with COVID-19 pneumonia, by initiating anticoagulant therapy when a PE is found. url: https://doi.org/10.1371/journal.pone.0238216 doi: 10.1371/journal.pone.0238216 id: cord-321855-7b1c2xdh author: Alshami, Alanoud title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia date: 2020-10-30 words: 3380.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-321855-7b1c2xdh.txt txt: ./txt/cord-321855-7b1c2xdh.txt summary: title: Silent disease and loss of taste and smell are common manifestations of SARS-COV-2 infection in a quarantine facility: Saudi Arabia PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. have examined 24 asymptomatic infected individuals with a history of close contact with SARS-COV-2 confirmed cases and found that only 20% of them developed symptoms. Our findings are in light with a recent study that reported a 59% prevalence of loss of taste and smell in a cohort of COVID-19 patients [15] . Sudden onset of loss of smell and taste were prevalent in our study and were key symptoms of mild disease. abstract: OBJECTIVES: In this study, we aimed to study the clinical presentations, and viral clearance of SARS-COV-2 positive quarantined individuals. DESIGN: Cross-sectional study. SETTING: Governmental- designated facility in the eastern province, Saudi Arabia. PARTICIPANTS: 128 laboratory-confirmed COVID-19 quarantined individuals who had a history of travel abroad in the last 14 days before the quarantine or were in direct contact with laboratory-confirmed cases. The study was from March 18th-till April 16th. PRIMARY AND SECONDARY MEASURES: The clinical presentation, prevalence of asymptomatic carriers among SARS-COV-2 positive quarantined subjects, and the difference between virus clearance among symptomatic and asymptomatic individuals. RESULTS: Sixty-nine of the 128 residents (54%) were completely asymptomatic until the end of the study. The remaining 59 residents (46%) had only mild symptoms. The most common symptom was a sudden loss of smell and taste, accounting for 47.5%. The median time to virus clearance was significantly different between the two groups. Symptomatic residents cleared the virus at a median of 17 days (95% CI, 12.4–21.6) from the first positive PCR vs. 11days (95% CI, 8.7–13.3) in the asymptomatic group (P = 0.011). False-negative test results occurred in 18.8% of the total residents and false-positive results in 3%. CONCLUSION: The prevalence of asymptomatic carriers among quarantined travelers and those identified by contact tracing is high in our study. Therefore, testing, tracing, and isolating travelers and contacts of laboratory-confirmed cases, regardless of symptoms, were very effective measures for early disease identification and containment. Loss of taste and smell were the most common presentations in our mild symptomatic residents and should be used as a screening tool for COVID-19. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control. url: https://doi.org/10.1371/journal.pone.0241258 doi: 10.1371/journal.pone.0241258 id: cord-294912-xl0wzi16 author: Alteri, Claudia title: Detection and quantification of SARS-CoV-2 by droplet digital PCR in real-time PCR negative nasopharyngeal swabs from suspected COVID-19 patients date: 2020-09-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since SARS-CoV-2-based disease (COVID-19) spreads as a pandemic, the necessity of a highly sensitive molecular diagnosis that can drastically reduce false negatives reverse transcription PCR (rtPCR) results, raises as a major clinical need. Here we evaluated the performance of a ddPCR-based assay to quantify SARS-CoV-2 titer in 55 suspected COVID-19 cases with negative rtPCR results thanks to in-house ddPCR assay (targeting RdRp and host RNaseP). Samples were collected at ASST-GOM Niguarda between February and May 2020 at hospital admission. Clinical and imaging data were obtained for clinical staging and definition of disease severity. Patients were mainly female (45.5%) with a median age of 73 (57–84) years. ddPCR-based assay detected SARS-CoV-2 genome in nasopharyngeal samples of 19 (34.5%) patients (median viral-load: 128 copies/mL, IQR: 72–345). In 15 of them (78.9%), chest CT showed a classical COVID-19 bilateral interstitial pneumonia; 14 patients (73.7%) showed severe COVID-19 manifestations. ddPCR did not identify any trace of SARS-CoV-2 genome in the respiratory samples of the remaining 36 patients. The serological assay performed in a subgroup of 34 patients at the later stage of illness (from 3 days to 90 days after) confirmed the presence of SARS-CoV-2 antibodies in all patients tested positive for SARS-CoV-2 in ddPCR (100%). Contrariwise, negative tests were observed in 95.0% ddPCR negative patients (P<0.001). Thanks to a ddPCR-based assay, we achieved a rapid and accurate SARS-CoV-2 diagnosis in rtPCR-negative respiratory samples of individuals with COVID-19 suspect, allowing the rapid taking care and correct management of these patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32898153/ doi: 10.1371/journal.pone.0236311 id: cord-001571-drcfdv9z author: Alvarez, Julio title: Impact of Porcine Epidemic Diarrhea on Performance of Growing Pigs date: 2015-03-13 words: 3100.0 sentences: 133.0 pages: flesch: 60.0 cache: ./cache/cord-001571-drcfdv9z.txt txt: ./txt/cord-001571-drcfdv9z.txt summary: Here, a retrospective cohort study to evaluate the impact of porcine epidemic diarrhea virus (PEDv) infection on growing pigs'' performance, as indicated by mortality, average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) was performed using production records from weaned pigs in nursery and wean-to-finish sites from sow farms that became PEDv-infected between May 2013 and June 2014. Collected data included information on the site in which pigs were located, site production type (nursery or wean to finish (WF)), pig source (sow farm from which pigs originated), start and close period on each site, number of pigs per batch, mortality (defined by percentage of total pigs started), average daily gain (ADG), average daily feed intake (ADFI), feed conversion (FCR), and status of the sow farm from which pigs were weaned for PRRS and PED. abstract: The impact of porcine epidemic diarrhea virus (PEDv) infection on the US pork industry has mainly been attributed to the mortality that it causes in suckling piglets, and, consequently, much effort has been invested in the quantification of its effect in sow farms. However, no information on the performance of surviving pigs that were exposed to the PEDv as piglets is available. Here, a retrospective cohort study to evaluate the impact of porcine epidemic diarrhea virus (PEDv) infection on growing pigs’ performance, as indicated by mortality, average daily gain (ADG), average daily feed intake (ADFI), and feed conversion ratio (FCR) was performed using production records from weaned pigs in nursery and wean-to-finish sites from sow farms that became PEDv-infected between May 2013 and June 2014. Production records from the first batch of growing pigs weaned in infected flows after the PEDv outbreak (“infected batches”) were compared with those from pigs weaned within the previous 14 to 120 days (“control batches”). Performance records from infected and control batches, paired by flow, were compared using non-parametric paired tests. Mortality, ADG and FCR were significantly different in PEDv-positive (infected) compared with PEDv-negative (control) batches, with a mean increase of mortality and FCR of 11% and 0.5, respectively, and a decrease of ADG of 0.16 lb/day. Our results demonstrate a poorer performance of growing pigs weaned after a PEDv outbreak compared with those weaned within the previous 14-120 days, suggesting that in addition to the mortality induced by PEDv in suckling pigs, the disease also impairs the performance of surviving pig. These findings help to quantify the impact of PEDv infection in the US and, ultimately, contribute to efforts to quantify the cost-effectiveness of disease prevention and control measures. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359118/ doi: 10.1371/journal.pone.0120532 id: cord-311074-j3fw4dfc author: Alviset, Sophie title: Continuous Positive Airway Pressure (CPAP) face-mask ventilation is an easy and cheap option to manage a massive influx of patients presenting acute respiratory failure during the SARS-CoV-2 outbreak: A retrospective cohort study date: 2020-10-14 words: 4842.0 sentences: 254.0 pages: flesch: 49.0 cache: ./cache/cord-311074-j3fw4dfc.txt txt: ./txt/cord-311074-j3fw4dfc.txt summary: title: Continuous Positive Airway Pressure (CPAP) face-mask ventilation is an easy and cheap option to manage a massive influx of patients presenting acute respiratory failure during the SARS-CoV-2 outbreak: A retrospective cohort study From 27th March to 23rd April, consecutive patients who had respiratory failure or were unable to maintain an SpO2 > 90%, despite receiving 10–15 l/min of oxygen with a non-rebreather mask, were treated by continuous positive airway pressure (CPAP) unless the ICU physician judged that immediate intubation was indicated. The following baseline patient characteristics were retrieved from patient electronic medical record: sex, age, comorbidities, body mass index (BMI), withholding / withdrawal of lifesustaining therapies, associated COVID-19 therapies administered before the primary outcome under study occurred (antivirals, corticosteroids, immuno-modulating therapies, prone positioning), oxygen flow rate and SpO2 before and after starting CPAP treatment, duration of CPAP treatment, medical unit where CPAP treatment was performed, duration of invasive mechanical ventilation, SAPS2 score for patients admitted in ICU, driving pressure and P/F ratio on first day of mechanical ventilation. abstract: INTRODUCTION: Because of the COVID-19 pandemic, intensive care units (ICU) can be overwhelmed by the number of hypoxemic patients. MATERIAL AND METHODS: This single centre retrospective observational cohort study took place in a French hospital where the number of patients exceeded the ICU capacity despite an increase from 18 to 32 beds. Because of this, 59 (37%) of the 159 patients requiring ICU care were referred to other hospitals. From 27th March to 23rd April, consecutive patients who had respiratory failure or were unable to maintain an SpO2 > 90%, despite receiving 10–15 l/min of oxygen with a non-rebreather mask, were treated by continuous positive airway pressure (CPAP) unless the ICU physician judged that immediate intubation was indicated. We describe the characteristics, clinical course, and outcomes of these patients. The main outcome under study was CPAP discontinuation. RESULTS: CPAP was initiated in 49 patients and performed out of ICU in 41 (84%). Median age was 65 years (IQR = 54–71) and 36 (73%) were men. Median respiratory rate before CPAP was 36 (30–40) and median SpO2 was 92% (90–95) under 10 to 15 L/min oxygen flow. Median duration of CPAP was 3 days (IQR = 1–5). Reasons for discontinuation of CPAP were: intubation in 25 (51%), improvement in 16 (33%), poor tolerance in 6 (12%) and death in 2 (4%) patients. A decision not to intubate had been taken for 8 patients, including the 2 who died while on CPAP. Two patients underwent less than one hour CPAP for poor tolerance. In the end, 15 (38%) out of 39 evaluable patients recovered with only CPAP whereas 24 (62%) were intubated. CONCLUSIONS: CPAP is feasible in a non-ICU environment in the context of massive influx of patients. In our cohort up to 1/3 of the patients presenting with acute respiratory failure recovered without intubation. url: https://www.ncbi.nlm.nih.gov/pubmed/33052968/ doi: 10.1371/journal.pone.0240645 id: cord-287761-73qgx58i author: Aly, Mahmoud title: Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update date: 2017-10-13 words: 3389.0 sentences: 164.0 pages: flesch: 55.0 cache: ./cache/cord-287761-73qgx58i.txt txt: ./txt/cord-287761-73qgx58i.txt summary: Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. GCC countries including Saudi Arabia now have the infrastructure in place that allows physicians and scientific community to identify and immediately respond to the potential risks posed by new outbreaks of MERS-CoV infections in the region. The emergence of MERS-CoV dates back to July 2012 when an elderly patient of age 60 years died from an acute pneumonia in Saudi Arabia, and a new coronavirus strain was isolated from his lung tissue [1] . With regard to viral origin and transmission, the first case of MERS-CoV infection did not relate it to any particular contact with animals before the disease onset; however, other studies did link it to Dromedary camels [5] [6] [7] [8] . abstract: The emergence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections has become a global issue of dire concerns. MERS-CoV infections have been identified in many countries all over the world whereas high level occurrences have been documented in the Middle East and Korea. MERS-CoV is mainly spreading across the geographical region of the Middle East, especially in the Arabian Peninsula, while some imported sporadic cases were reported from the Europe, North America, Africa, and lately Asia. The prevalence of MERS-CoV infections across the Gulf Corporation Council (GCC) countries still remains unclear. Therefore, the objective of the current study was to report the prevalence of MERS-CoV in the GCC countries and to also elucidate on its demographics in the Arabian Peninsula. To date, the World Health Organization (WHO) has reported 1,797 laboratory-confirmed cases of MERS-CoV infection since June 2012, involving 687 deaths in 27 different countries worldwide. Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. Our data comprise a total of 1550 cases (67.1% male and 32.9% female). The age-specific prevalence and distribution of MERS-CoV was as follow: <20 yrs (36 cases: 3.28%), 20–39 yrs (331 cases: 30.15%), 40–59 yrs (314 cases: 28.60%), and the highest-risk elderly group aged ≥60 yrs (417 cases: 37.98%). The case distribution among GCC countries was as follows: Saudi Arabia (1441 cases: 93%), Kuwait (4 cases: 0.3%), Bahrain (1 case: 0.1%), Oman (8 cases: 0.5%), Qatar (16 cases: 1.0%), and United Arab Emirates (80 cases: 5.2%). Thus, MERS-CoV was found to be more prevalent in Saudi Arabia especially in Riyadh, where 756 cases (52.4%) were the worst hit area of the country identified, followed by the western region Makkah where 298 cases (20.6%) were recorded. This prevalence update indicates that the Arabian Peninsula, particularly Saudi Arabia, is the hardest hit region regarding the emerging MERS-CoV infections worldwide. GCC countries including Saudi Arabia now have the infrastructure in place that allows physicians and scientific community to identify and immediately respond to the potential risks posed by new outbreaks of MERS-CoV infections in the region. Given the continuum of emergence and the large magnitude of the disease in our region, more studies will be required to bolster capabilities for timely detection and effective control and prevention of MERS-CoV in our region. url: https://doi.org/10.1371/journal.pone.0183850 doi: 10.1371/journal.pone.0183850 id: cord-266797-uglsx7se author: Anastassopoulou, Cleo title: Data-based analysis, modelling and forecasting of the COVID-19 outbreak date: 2020-03-31 words: 5420.0 sentences: 235.0 pages: flesch: 55.0 cache: ./cache/cord-266797-uglsx7se.txt txt: ./txt/cord-266797-uglsx7se.txt summary: Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected and recovered cases in the population most likely are much higher than the reported ones. Based on the released data, we attempted to estimate the mean values of the main epidemiological parameters, i.e. the basic reproduction number R 0 , the case fatality (ĝ) and case recovery (b) ratios, along with their 90% confidence intervals. Then, as described above, we provide coarse estimations of the "effective" per day recovery and mortality rates of the SIRD model based on the reported data by solving the corresponding least squares problems. abstract: Since the first suspected case of coronavirus disease-2019 (COVID-19) on December 1st, 2019, in Wuhan, Hubei Province, China, a total of 40,235 confirmed cases and 909 deaths have been reported in China up to February 10, 2020, evoking fear locally and internationally. Here, based on the publicly available epidemiological data for Hubei, China from January 11 to February 10, 2020, we provide estimates of the main epidemiological parameters. In particular, we provide an estimation of the case fatality and case recovery ratios, along with their 90% confidence intervals as the outbreak evolves. On the basis of a Susceptible-Infectious-Recovered-Dead (SIDR) model, we provide estimations of the basic reproduction number (R(0)), and the per day infection mortality and recovery rates. By calibrating the parameters of the SIRD model to the reported data, we also attempt to forecast the evolution of the outbreak at the epicenter three weeks ahead, i.e. until February 29. As the number of infected individuals, especially of those with asymptomatic or mild courses, is suspected to be much higher than the official numbers, which can be considered only as a subset of the actual numbers of infected and recovered cases in the total population, we have repeated the calculations under a second scenario that considers twenty times the number of confirmed infected cases and forty times the number of recovered, leaving the number of deaths unchanged. Based on the reported data, the expected value of R(0) as computed considering the period from the 11th of January until the 18th of January, using the official counts of confirmed cases was found to be ∼4.6, while the one computed under the second scenario was found to be ∼3.2. Thus, based on the SIRD simulations, the estimated average value of R(0) was found to be ∼2.6 based on confirmed cases and ∼2 based on the second scenario. Our forecasting flashes a note of caution for the presently unfolding outbreak in China. Based on the official counts for confirmed cases, the simulations suggest that the cumulative number of infected could reach 180,000 (with a lower bound of 45,000) by February 29. Regarding the number of deaths, simulations forecast that on the basis of the up to the 10th of February reported data, the death toll might exceed 2,700 (as a lower bound) by February 29. Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected and recovered cases in the population most likely are much higher than the reported ones. Thus, in a scenario where we have taken twenty times the confirmed number of infected and forty times the confirmed number of recovered cases, the case fatality ratio is around ∼0.15% in the total population. Importantly, based on this scenario, simulations suggest a slow down of the outbreak in Hubei at the end of February. url: https://www.ncbi.nlm.nih.gov/pubmed/32231374/ doi: 10.1371/journal.pone.0230405 id: cord-002305-qq73gr9y author: Anson, Marie title: Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool date: 2016-11-23 words: 5422.0 sentences: 248.0 pages: flesch: 51.0 cache: ./cache/cord-002305-qq73gr9y.txt txt: ./txt/cord-002305-qq73gr9y.txt summary: In conclusion, the adoptive cell transfer strategy allowed the development of a primary immune response with B cell activation and expansion, induction of AID expression, class switch recombination, antigen-specific IgM and IgG antibody production and germinal center formation. In this study we show that it is possible to fully reconstitute a primary response and the establishment of antibody memory in immune deficient mice after adoptive transfer of antigen-specific monoclonal B cells together with a population of monoclonal helper T cells. In contrast we showed that after adoptive transfer in immune deficient hosts antigen immunization induced B cell activation and expansion, induction of AID expression, class switch recombination, antigen-specific IgM and IgG antibody production, germinal center formation and the generation of two subsets of AID/YFP + IgM + IgGand AID/YFP + Ig-M -IgG + antigen-experienced B cell subsets able to persist in a lymphopenic environment by cell division mimicking responses obtained in intact non-Tg mice [4] . abstract: We investigated the ability of monoclonal B cells to restore primary and secondary T-cell dependent antibody responses in adoptive immune-deficient hosts. Priming induced B cell activation and expansion, AID expression, antibody production and the generation of IgM(+)IgG(-) and IgM(-)IgG(+) antigen-experienced B-cell subsets that persisted in the lymphopenic environment by cell division. Upon secondary transfer and recall the IgM(-)IgG(+) cells responded by the production of antigen-specific IgG while the IgM(+) memory cells secreted mainly IgM and little IgG, but generated new B cells expressing germinal center markers. The recall responses were more efficient if the antigenic boost was delayed suggesting that a period of adaptation is necessary before the transferred cells are able to respond. Overall these findings indicate that reconstitution of a functional and complete memory pool requires transfer of all different antigen-experienced B cell subsets. We also found that the size of the memory B cell pool did not rely on the number of the responding naïve B cells, suggesting autonomous homeostatic controls for naïve and memory B cells. By reconstituting a stable memory B cell pool in immune-deficient hosts using a monoclonal high-affinity B cell population we demonstrate the potential value of B cell adoptive immunotherapy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120830/ doi: 10.1371/journal.pone.0167003 id: cord-000809-9voqa1oy author: Archer, Brett N. title: Reproductive Number and Serial Interval of the First Wave of Influenza A(H1N1)pdm09 Virus in South Africa date: 2012-11-16 words: 3885.0 sentences: 208.0 pages: flesch: 50.0 cache: ./cache/cord-000809-9voqa1oy.txt txt: ./txt/cord-000809-9voqa1oy.txt summary: We characterize the transmissibility of influenza A(H1N1)pdm09 (hereafter pH1N1) in South Africa during 2009 by estimating the serial interval (SI), the initial effective reproductive number (initial R(t)) and the temporal variation of R(t). In this work we incorporate data collected on all laboratory-confirmed cases detected during the 2009 pH1N1 epidemic in South Africa with the aim of describing the transmissibility characteristics (initial R t and temporal variation of R t ) of the epidemic in the country and compare its dynamics with those observed in other countries in the same year. When estimating initial R t , we focus our analysis on the exponential growth phase of the epidemic in South Africa (i.e. the period from the first occurrence of five consecutive days with confirmed cases reported to the epidemic peak). abstract: BACKGROUND/OBJECTIVE: Describing transmissibility parameters of past pandemics from diverse geographic sites remains critical to planning responses to future outbreaks. We characterize the transmissibility of influenza A(H1N1)pdm09 (hereafter pH1N1) in South Africa during 2009 by estimating the serial interval (SI), the initial effective reproductive number (initial R(t)) and the temporal variation of R(t). METHODS: We make use of data from a central registry of all pH1N1 laboratory-confirmed cases detected throughout South Africa. Whenever date of symptom onset is missing, we estimate it from the date of specimen collection using a multiple imputation approach repeated 100 times for each missing value. We apply a likelihood-based method (method 1) for simultaneous estimation of initial R(t) and the SI; estimate initial R(t) from SI distributions established from prior field studies (method 2); and the Wallinga and Teunis method (method 3) to model the temporal variation of R(t). RESULTS: 12,360 confirmed pH1N1 cases were reported in the central registry. During the period of exponential growth of the epidemic (June 21 to August 3, 2009), we simultaneously estimate a mean R(t) of 1.47 (95% CI: 1.30–1.72) and mean SI of 2.78 days (95% CI: 1.80–3.75) (method 1). Field studies found a mean SI of 2.3 days between primary cases and laboratory-confirmed secondary cases, and 2.7 days when considering both suspected and confirmed secondary cases. Incorporating the SI estimate from field studies using laboratory-confirmed cases, we found an initial R(t) of 1.43 (95% CI: 1.38–1.49) (method 2). The mean R(t) peaked at 2.91 (95% CI: 0.85–2.91) on June 21, as the epidemic commenced, and R(t)>1 was sustained until August 22 (method 3). CONCLUSIONS: Transmissibility characteristics of pH1N1 in South Africa are similar to estimates reported by countries outside of Africa. Estimations using the likelihood-based method are in agreement with field findings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500305/ doi: 10.1371/journal.pone.0049482 id: cord-002601-d8908t93 author: Arellano-Llamas, Rocío title: Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014 date: 2017-07-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011–2012 winter season and finally, during the 2013–2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease. In this paper, we analyzed the evolution, antigenic and genetic drift of Mexican isolates from 2009, at the beginning of the pandemic, to 2014. We found a clear variation of the virus in Mexico from the 2011–2014 season due to different markers and in accordance with previous reports. In this study, we identified 13 novel substitutions with important biological effects, including virulence, T cell epitope presented by MHC and host specificity shift and some others substitutions might have more than one biological function. The systematic monitoring of mutations on whole genome of influenza A pH1N1 (2009) virus circulating at INER in Mexico City might provide valuable information to predict the emergence of new pathogenic influenza virus url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5503254/ doi: 10.1371/journal.pone.0180419 id: cord-284501-5i0w74q4 author: Armesto, Maria title: The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date: 2009-10-09 words: 7792.0 sentences: 322.0 pages: flesch: 54.0 cache: ./cache/cord-284501-5i0w74q4.txt txt: ./txt/cord-284501-5i0w74q4.txt summary: The IBV cDNA within pGPT-BeauR-Rep-M41-Struct-3UTR was introduced, by homologous recombination using the transient dominant selection (TDS) ( [25, 37] ), into the IBV Beaudette cDNA within the vaccinia virus genome in rVV-BeauR-Rep-DStruct containing Beau-R-derived sequence corresponding to the replicase gene followed by the first 376 nt of the S gene, part of the N gene and the 39-UTR (Fig. 1) . The samples were analysed for the presence of viable IBV by titration in TOCs or used for RNA extraction using the RNeasy method and analysed by RTThe M41-CK-derived cDNA, representing the M41 structural and accessory genes and the M41 39-UTR, within pGPT-BeauR-Rep-M41-Struct-3UTR was fused to the Beau-R replicase gene in the rVV by a homologous recombination event between the Beau-R replicase sequence common to both constructs. Analysis of the tracheal epithelial cells isolated from the infected chickens, for the presence of IBV by titration on TOCs, had indicated that either there was no Beau-R or rBeauR-Rep-M41-Struct-2 present or that the levels of both viruses were below detection. abstract: We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene. url: https://doi.org/10.1371/journal.pone.0007384 doi: 10.1371/journal.pone.0007384 id: cord-283976-jgae7r2q author: Armstrong, Melissa J. title: Research priorities of caregivers and individuals with dementia with Lewy bodies: An interview study date: 2020-10-07 words: 4111.0 sentences: 208.0 pages: flesch: 37.0 cache: ./cache/cord-283976-jgae7r2q.txt txt: ./txt/cord-283976-jgae7r2q.txt summary: BACKGROUND: Funding bodies are placing increased emphasis on patient and public involvement in research, but the research priorities of individuals and caregivers living with dementia with Lewy bodies (DLB) are unknown. Funding should be informed by the priorities of all relevant stakeholders and support research investigating causes, natural history, biomarkers, and treatment in addition to research targeting themes regarding living with disease (e.g. independence, quality of life, caregiving, and education). The study guide queried a variety of research categories and individuals with DLB and caregivers identified topics important for research in all of them-focusing on awareness, determining the cause of DLB, improving diagnosis, investigating what to expect and disease stages, DLB symptoms needing additional research, therapies to prevent, cure, or slow the progression of DLB, targeting daily function and quality of life, caregiving, and improving education. abstract: BACKGROUND: Funding bodies are placing increased emphasis on patient and public involvement in research, but the research priorities of individuals and caregivers living with dementia with Lewy bodies (DLB) are unknown. METHOD: Investigators conducted telephone interviews with individuals living with DLB and caregivers. Participants were recruited from a Lewy Body Dementia Association Research Center of Excellence. Interviews employed a semi-structured questionnaire querying research needs in different categories and then asking participants to select their top priorities. Investigators used a qualitative descriptive approach to analyze transcripts and identify themes. RESULTS: Twenty individuals with DLB and 25 caregivers participated. Seventeen from each group participated as part of a patient-caregiver dyad. Twenty-three of the caregivers were spouses, two were daughters. Individuals with DLB and caregivers identified research needs relating to focusing on awareness, determining the cause of DLB, improving diagnosis, and investigating what to expect/disease stages. Participants also highlighted DLB symptoms needing additional research, therapies to prevent, cure, or slow the progression of DLB, and research targeting daily function and quality of life, caregiving, and improving education. CONCLUSIONS: These findings support the research priorities defined in the National Institutes of Health dementia care summits in addition to ADRD priority-setting summits. Research is needed across all domains of DLB. Funding should be informed by the priorities of all relevant stakeholders and support research investigating causes, natural history, biomarkers, and treatment in addition to research targeting themes regarding living with disease (e.g. independence, quality of life, caregiving, and education). url: https://www.ncbi.nlm.nih.gov/pubmed/33027276/ doi: 10.1371/journal.pone.0239279 id: cord-002953-4rqoenhr author: Arruda, Andréia Gonçalves title: Time-series analysis for porcine reproductive and respiratory syndrome in the United States date: 2018-04-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Industry-driven voluntary disease control programs for swine diseases emerged in North America in the early 2000’s, and, since then, those programs have been used for monitoring diseases of economic importance to swine producers. One example of such initiatives is Dr. Morrison’s Swine Health Monitoring Project, a nation-wide monitoring program for swine diseases including the porcine reproductive and respiratory syndrome (PRRS). PRRS has been extensively reported as a seasonal disease in the U.S., with predictable peaks that start in fall and are extended through the winter season. However, formal time series analysis stratified by geographic region has never been conducted for this important disease across the U.S. The main objective of this study was to use approximately seven years of PRRS incidence data in breeding swine herds to conduct time-series analysis in order to describe the temporal patterns of PRRS outbreaks at the farm level for five major swine-producing states across the U.S. including the states of Minnesota, Iowa, North Carolina, Nebraska and Illinois. Data was aggregated retrospectively at the week level for the number of herds containing animals actively shedding PRRS virus. Basic descriptive statistics were conducted followed by autoregressive integrated moving average (ARIMA) modelling, conducted separately for each of the above-mentioned states. Results showed that there was a difference in the nature of PRRS seasonality among states. Of note, when comparing states, the typical seasonal pattern previously described for PRRS could only be detected for farms located in the states of Minnesota, North Carolina and Nebraska. For the other two states, seasonal peaks every six months were detected within a year. In conclusion, we showed that epidemic patterns are not homogeneous across the U.S, with major peaks of disease occurring through the year. These findings highlight the importance of coordinating alternative control strategies in different regions considering the prevailing epidemiological patterns. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5882168/ doi: 10.1371/journal.pone.0195282 id: cord-336364-2ust3qoq author: Artigas, Laura title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm date: 2020-10-02 words: 5858.0 sentences: 295.0 pages: flesch: 45.0 cache: ./cache/cord-336364-2ust3qoq.txt txt: ./txt/cord-336364-2ust3qoq.txt summary: title: In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm This has provided 3 sets of proteins related with the infection process: 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lungcells infection set, and 3) acute respiratory distress (ARD) set. According to the findings by GUILDify, we confirm the effect of the combination of pirfenidone and melatonin in the entry points of the SARS-CoV-2 infection, specifically the neighbours of furin and GRP-78, and some proteins associated with ARD. 1) coronavirus-host interaction set (including SARS-CoV-2 entry points), 2) lung-cells infection set, and 3) acute respiratory distress (ARD) set that is composed of 6 subsets (Alveolar macrophages, Monocytes, Neutrophils, Intermediate phase ARD, Late phase ARD and ARD cytokine storm). abstract: From January 2020, COVID-19 is spreading around the world producing serious respiratory symptoms in infected patients that in some cases can be complicated by the severe acute respiratory syndrome, sepsis and septic shock, multiorgan failure, including acute kidney injury and cardiac injury. Cost and time efficient approaches to reduce the burthen of the disease are needed. To find potential COVID-19 treatments among the whole arsenal of existing drugs, we combined system biology and artificial intelligence-based approaches. The drug combination of pirfenidone and melatonin has been identified as a candidate treatment that may contribute to reduce the virus infection. Starting from different drug targets the effect of the drugs converges on human proteins with a known role in SARS-CoV-2 infection cycle. Simultaneously, GUILDify v2.0 web server has been used as an alternative method to corroborate the effect of pirfenidone and melatonin against the infection of SARS-CoV-2. We have also predicted a potential therapeutic effect of the drug combination over the respiratory associated pathology, thus tackling at the same time two important issues in COVID-19. These evidences, together with the fact that from a medical point of view both drugs are considered safe and can be combined with the current standard of care treatments for COVID-19 makes this combination very attractive for treating patients at stage II, non-severe symptomatic patients with the presence of virus and those patients who are at risk of developing severe pulmonary complications. url: https://doi.org/10.1371/journal.pone.0240149 doi: 10.1371/journal.pone.0240149 id: cord-002621-sq5iod1w author: Attia, Mohamed I. title: New hydrazonoindolin-2-ones: Synthesis, exploration of the possible anti-proliferative mechanism of action and encapsulation into PLGA microspheres date: 2017-07-25 words: 5948.0 sentences: 280.0 pages: flesch: 47.0 cache: ./cache/cord-002621-sq5iod1w.txt txt: ./txt/cord-002621-sq5iod1w.txt summary: Compounds 7b, 7d and 7e were the most active congeners against the tested human cancer cell lines with average IC(50) values of 4.77, 3.39 and 2.37 μM, respectively, as compared with the reference isatin-based drug, sunitinib, which exhibited an average IC(50) value of 8.11 μM. Incorporation of 7e into PLGA microspheres improved its in vitro anti-proliferative activity toward the human cancer cell line A549 after 120 h incubation period with an IC(50) value less than 0.8 μM. The human lung cancer A549 cell line was incubated with various concentrations (0.8, 1.6, 3.13, 6.25, 12.5, 25 and 50 μM) of both free 7e and 7e-loaded microspheres to evaluate the anti-proliferative activity by assessing their effect on cell viability. Synthesis and anticancer activity of certain hydrazonoindolin-2-ones Fig 13B illustrates the obtained results when 7e-loaded microspheres were incubated with the human lung cancer cell lineA549for incubation periods and concentrations similar to that of the free 7e. abstract: The synthesis and molecular characterization of new isatin-based hydrazonoindolin-2-ones 4a-o and 7a-e are reported. The in vitro anti-proliferative potential of the synthesized compounds 4a-o and 7a-e was examined against HT-29 (colon), ZR-75 (breast) and A549 (lung) human cancer cell lines. Compounds 7b, 7d and 7e were the most active congeners against the tested human cancer cell lines with average IC(50) values of 4.77, 3.39 and 2.37 μM, respectively, as compared with the reference isatin-based drug, sunitinib, which exhibited an average IC(50) value of 8.11 μM. Compound 7e was selected for further pharmacological evaluation in order to gain insight into its possible mechanism of action. It increased caspase 3/7 activity by 2.4- and 1.85-fold between 4 and 8 h of treatment, respectively, at 10 μM and it caused a decrease in the percentage of cells in the G1 phase of the cell cycle with a corresponding increase in the S-phase. In addition, compound 7e increased phosphorylated tyrosine (p-Tyr) levels nearly two-fold with an apparent IC(50) value of 3.8 μM. The 7e-loaded PLGA microspheres were prepared using a modified emulsion-solvent diffusion method. The average encapsulation efficiency of the 7e-loaded PLGA microspheres was 85% ± 1.3. While, the in vitro release profile of the 7e-loaded microspheres was characterized by slow and continuous release of compound 7e during 21 days and the release curve was fitted to zero order kinetics. Incorporation of 7e into PLGA microspheres improved its in vitro anti-proliferative activity toward the human cancer cell line A549 after 120 h incubation period with an IC(50) value less than 0.8 μM. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526551/ doi: 10.1371/journal.pone.0181241 id: cord-001546-ndz3oarf author: Ayithan, Natarajan title: Virus-Like Particles Activate Type I Interferon Pathways to Facilitate Post-Exposure Protection against Ebola Virus Infection date: 2015-02-26 words: 5128.0 sentences: 298.0 pages: flesch: 52.0 cache: ./cache/cord-001546-ndz3oarf.txt txt: ./txt/cord-001546-ndz3oarf.txt summary: Importantly, proinflammatory cytokine/chemokine expression was much higher in WT mice without VLPs than mice treated with VLPs. In EBOV infected Ifnar(-/-) mice, however, uninhibited viral replication and elevated proinflammatory factor expression ensued, irrespective of VLP treatment, supporting the view that type I IFN signaling helps to limit viral replication and attenuate inflammatory responses. Further analyses showed that VLP protection requires the transcription factor, IRF8 known to amplify type I IFN signaling in dendritic cells and macrophages, the probable sites of initial EBOV infection. The aim of this study was to further investigate molecular bases of postexposure protection by VLPs. Based on our previous report that VLPs stimulate type I IFN expression in DCs and macrophages, in vitro, we focused on the role of type I IFN signaling, and found that post-exposure VLP treatment leads to accelerated activation of IFN signaling, resulting in early induction of ISGs. Significantly, VLP stimulated ISG induction coincided with the attenuation of proinflammatory cytokine surge in EBOV infected mice. abstract: Ebola virus (EBOV) causes a severe hemorrhagic disease with high fatality. Virus-like particles (VLPs) are a promising vaccine candidate against EBOV. We recently showed that VLPs protect mice from lethal EBOV infection when given before or after viral infection. To elucidate pathways through which VLPs confer post-exposure protection, we investigated the role of type I interferon (IFN) signaling. We found that VLPs lead to accelerated induction of IFN stimulated genes (ISGs) in liver and spleen of wild type mice, but not in Ifnar(-/-) mice. Accordingly, EBOV infected Ifnar(-/-) mice, unlike wild type mice succumbed to death even after VLP treatment. The ISGs induced in wild type mice included anti-viral proteins and negative feedback factors known to restrict viral replication and excessive inflammatory responses. Importantly, proinflammatory cytokine/chemokine expression was much higher in WT mice without VLPs than mice treated with VLPs. In EBOV infected Ifnar(-/-) mice, however, uninhibited viral replication and elevated proinflammatory factor expression ensued, irrespective of VLP treatment, supporting the view that type I IFN signaling helps to limit viral replication and attenuate inflammatory responses. Further analyses showed that VLP protection requires the transcription factor, IRF8 known to amplify type I IFN signaling in dendritic cells and macrophages, the probable sites of initial EBOV infection. Together, this study indicates that VLPs afford post-exposure protection by promoting expeditious initiation of type I IFN signaling in the host. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342244/ doi: 10.1371/journal.pone.0118345 id: cord-257603-ov0b8yub author: Azlan, Arina Anis title: Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia date: 2020-05-21 words: 4685.0 sentences: 256.0 pages: flesch: 54.0 cache: ./cache/cord-257603-ov0b8yub.txt txt: ./txt/cord-257603-ov0b8yub.txt summary: To measure practices, participants were asked yes/no questions on whether they had avoided going to crowded places such as weddings; wore a face mask when leaving home; and whether they practiced proper hand hygiene in the week before the movement control order (MCO). The first question asked whether or not they agreed that the COVID-19 situation would be successfully controlled; second, whether they thought Malaysia would be able to win its battle against the virus; and third, whether they thought the Malaysian government was handling the health crisis well [Fig 1] . Practices toward COVID-19 were measured using three questions enquiring on: 1) avoidance of crowded places, 2) wearing of face masks; and 3) practising proper hand hygiene in the week before the Movement Control Order (MCO) was implemented in Malaysia [Fig 2] . Public knowledge, attitudes and practices towards COVID-19 in Malaysia residents in the Eastern region and retirees were among the highest percentage of participants who had not practised good hand hygiene in the week before the MCO. abstract: In an effort to mitigate the outbreak of COVID-19, many countries have imposed drastic lockdown, movement control or shelter in place orders on their residents. The effectiveness of these mitigation measures is highly dependent on cooperation and compliance of all members of society. The knowledge, attitudes and practices people hold toward the disease play an integral role in determining a society’s readiness to accept behavioural change measures from health authorities. The aim of this study was to determine the knowledge levels, attitudes and practices toward COVID-19 among the Malaysian public. A cross-sectional online survey of 4,850 Malaysian residents was conducted between 27(th) March and 3(rd) April 2020. The survey instrument consisted of demographic characteristics, 13 items on knowledge, 3 items on attitudes and 3 items on practices, modified from a previously published questionnaire on COVID-19. Descriptive statistics, chi-square tests, t-tests and one-way analysis of variance (ANOVA) were conducted. The overall correct rate of the knowledge questionnaire was 80.5%. Most participants held positive attitudes toward the successful control of COVID-19 (83.1%), the ability of Malaysia to conquer the disease (95.9%) and the way the Malaysian government was handling the crisis (89.9%). Most participants were also taking precautions such as avoiding crowds (83.4%) and practising proper hand hygiene (87.8%) in the week before the movement control order started. However, the wearing of face masks was less common (51.2%). This survey is among the first to assess knowledge, attitudes and practice in response to the COVID-19 pandemic in Malaysia. The results highlight the importance of consistent messaging from health authorities and the government as well as the need for tailored health education programs to improve levels of knowledge, attitudes and practices. url: https://doi.org/10.1371/journal.pone.0233668 doi: 10.1371/journal.pone.0233668 id: cord-320091-2lrqubdl author: Badawi, Alaa title: Prevalence of chronic comorbidities in dengue fever and West Nile virus: A systematic review and meta-analysis date: 2018-07-10 words: 8511.0 sentences: 411.0 pages: flesch: 46.0 cache: ./cache/cord-320091-2lrqubdl.txt txt: ./txt/cord-320091-2lrqubdl.txt summary: The objective of this study is to systematically review the existing literature on the prevalence of the most common non-communicable comorbidities related to the cluster of metabolic syndromes-associated diseases, such as diabetes mellitus, heart diseases, hypertension, asthma, stroke and obesity in flavivirus infections and to evaluate the difference of their prevalence in severe vs. Data extracted from the selected studies in duplicate by two reviewers and included the first author''s name, publication date, country, dates of recruitment, total sample size (divided to males and females), age estimates (from reported mean, median or the mid-point for age range of the highest subject frequency), procedures for case identification, type of flavivirus infection, severity of infection, prevalence of clinical manifestations (mild symptoms such as fever, headache, muscle pain, rash, and malaise together with severe symptoms as described below) and percentage of comorbidities including diabetes (both type I and type II, if mentioned), hypertension, heart diseases (due to the small sample size of individual conditions, we (Table 1) . abstract: BACKGROUND: Flavivirus diseases such as dengue fever (DENV), West Nile virus (WNV), Zika and yellow fever represent a substantial global public health concern. Preexisting chronic conditions such as cardiovascular diseases, diabetes, obesity, and asthma were thought to predict risk of progression to severe infections. OBJECTIVE: We aimed to quantify the frequency of chronic comorbidities in flavivirus diseases to provide an estimate for their prevalence in severe and non-severe infections and examine whether chronic diseases contribute to the increased risk of severe viral expression. METHODS: We conducted a comprehensive search in PubMed, Ovid MEDLINE(R), Embase and Embase Classic and grey literature databases to identify studies reporting prevalence estimates of comorbidities in flavivirus diseases. Study quality was assessed with the risk of bias tool. Age-adjusted odds ratios (ORs) were estimated for severe infection in the presence of chronic comorbidities. RESULTS: We identified 65 studies as eligible for inclusion for DENV (47 studies) and WNV (18 studies). Obesity and overweight (i.e., BMI> 25 kg/m(2), prevalence: 24.5%, 95% CI: 18.6–31.6%), hypertension (17.1%, 13.3–21.8%) and diabetes (13.3%, 9.3–18.8%) were the most prevalent comorbidities in DENV. However, hypertension (45.0%, 39.1–51.0%), diabetes (24.7%, 20.2–29.8%) and heart diseases (25.6%, 19.5–32.7%) were the most prevalent in WNV. ORs of severe flavivirus diseases were about 2 to 4 in infected patients with comorbidities such as diabetes, hypertension and heart diseases. The small number of studies in JEV, YFV and Zika did not permit estimating the prevalence of comorbidities in these infections. CONCLUSION: Higher prevalence of chronic comorbidities was found in severe cases of flavivirus diseases compared to non-severe cases. Findings of the present study may guide public health practitioners and clinicians to evaluate infection severity based on the presence of comorbidity, a critical public health measure that may avert severe disease outcome given the current dearth of clear prevention practices for some flavivirus diseases. url: https://doi.org/10.1371/journal.pone.0200200 doi: 10.1371/journal.pone.0200200 id: cord-351918-pu7i1jfe author: Baek, Yae Jee title: A mathematical model of COVID-19 transmission in a tertiary hospital and assessment of the effects of different intervention strategies date: 2020-10-26 words: 4902.0 sentences: 278.0 pages: flesch: 51.0 cache: ./cache/cord-351918-pu7i1jfe.txt txt: ./txt/cord-351918-pu7i1jfe.txt summary: The effects of different intervention strategies such as front door screening, quarantine unit for newly admitted patients, early testing of suspected infected people, and personal protective equipment for both medical staff and visitors were evaluated. The model suggested that the early testing (within eight hours) of infected cases and monitoring the quarantine ward for newly hospitalized patients are effective measures for decreasing the incidence of COVID-19 within a hospital (81.3% and 70% decrease of number of incident cases, respectively, during 60 days). Setting the population vector η as the number of staff, and the stabilized number of inflow and outflow to each department for visitors, we construct the WAIFW matrix, W, by assuming that it is proportional to the contact rate matrix [8, 9] : The diagram for the SEIR (susceptible-exposed-infectious-recovered) model with compartments of doctor, nurse, patient, and caregiver. abstract: Novel coronavirus (named SARS-CoV-2) can spread widely in confined settings including hospitals, cruise ships, prisons, and places of worship. In particular, a healthcare-associated outbreak could become the epicenter of coronavirus disease (COVID-19). This study aimed to evaluate the effects of different intervention strategies on the hospital outbreak within a tertiary hospital. A mathematical model was developed for the COVID-19 transmission within a 2500-bed tertiary hospital of South Korea. The SEIR (susceptible-exposed-infectious-recovered) model with a compartment of doctor, nurse, patient, and caregiver was constructed. The effects of different intervention strategies such as front door screening, quarantine unit for newly admitted patients, early testing of suspected infected people, and personal protective equipment for both medical staff and visitors were evaluated. The model suggested that the early testing (within eight hours) of infected cases and monitoring the quarantine ward for newly hospitalized patients are effective measures for decreasing the incidence of COVID-19 within a hospital (81.3% and 70% decrease of number of incident cases, respectively, during 60 days). Front door screening for detecting suspected cases had only 42% effectiveness. Screening for prohibiting the admission of COVID-19 patients was more effective than the measures for patients before emergency room or outpatient clinic. This model suggests that under the assumed conditions, some effective measures have a great influence on the incidence of COVID-19 within a hospital. The implementation of the preventive measures could reduce the size of a hospital outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/33104736/ doi: 10.1371/journal.pone.0241169 id: cord-289892-yh1lioyz author: Bai, Bingke title: Virus-Like Particles of SARS-Like Coronavirus Formed by Membrane Proteins from Different Origins Demonstrate Stimulating Activity in Human Dendritic Cells date: 2008-07-16 words: 5451.0 sentences: 300.0 pages: flesch: 55.0 cache: ./cache/cord-289892-yh1lioyz.txt txt: ./txt/cord-289892-yh1lioyz.txt summary: Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. In addition, because in vitro infection model of bat SL-CoV has not so far been established, we intended to use VLPs as an alternative to study the immune responses induced in DCs. Therefore, we compared the phenotypic and functional changes of immature DCs inoculated with BVLPs or with SARS CoV VLPs. The S-specific immune activation was further confirmed in mice using S DNA vaccines. Combining the flow cytometry results in Fig. 2 , it is reasonable to draw a conclusion that the structure of BVLPs, not LPS contamination, contributed to cytokine production in BVLPs-treated DCs. We previously constructed SARS CoV VLPs and investigated the humoral and cellular immune responses induced by SARS CoV VLPs in mice [29] . abstract: The pathogenesis of SARS coronavirus (CoV) remains poorly understood. In the current study, two recombinant baculovirus were generated to express the spike (S) protein of SARS-like coronavirus (SL-CoV) isolated from bats (vAcBS) and the envelope (E) and membrane (M) proteins of SARS-CoV, respectively. Co-infection of insect cells with these two recombinant baculoviruses led to self-assembly of virus-like particles (BVLPs) as demonstrated by electron microscopy. Incorporation of S protein of vAcBS (BS) into VLPs was confirmed by western blot and immunogold labeling. Such BVLPs up-regulated the level of CD40, CD80, CD86, CD83, and enhanced the secretion of IL-6, IL-10 and TNF-α in immature dendritic cells (DCs). Immune responses were compared in immature DCs inoculated with BVLPs or with VLPs formed by S, E and M proteins of human SARS-CoV. BVLPs showed a stronger ability to stimulate DCs in terms of cytokine induction as evidenced by 2 to 6 fold higher production of IL-6 and TNF-α. Further study indicated that IFN-γ+ and IL-4+ populations in CD4+ T cells increased upon co-cultivation with DCs pre-exposed with BVLPs or SARS-CoV VLPs. The observed difference in DC-stimulating activity between BVLPs and SARS CoV VLPs was very likely due to the S protein. In agreement, SL-CoV S DNA vaccine evoked a more vigorous antibody response and a stronger T cell response than SARS-CoV S DNA in mice. Our data have demonstrated for the first time that SL-CoV VLPs formed by membrane proteins of different origins, one from SL-CoV isolated from bats (BS) and the other two from human SARS-CoV (E and M), activated immature DCs and enhanced the expression of co-stimulatory molecules and the secretion of cytokines. Finding in this study may provide important information for vaccine development as well as for understanding the pathogenesis of SARS-like CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/18628832/ doi: 10.1371/journal.pone.0002685 id: cord-295339-nzc47itk author: Baker, Marissa G. title: Estimating the burden of United States workers exposed to infection or disease: A key factor in containing risk of COVID-19 infection date: 2020-04-28 words: 3320.0 sentences: 139.0 pages: flesch: 41.0 cache: ./cache/cord-295339-nzc47itk.txt txt: ./txt/cord-295339-nzc47itk.txt summary: METHODS: To estimate the number of United States workers frequently exposed to infection and disease in the workplace, national employment data (by Standard Occupational Classification) maintained by the Bureau of Labor Statistics (BLS) was merged with a BLS O*NET survey measure reporting how frequently workers in each occupation are exposed to infection or disease at work. Given the proportion of the United States workforce exposed to disease or infection at work, this analysis also serves as an important reminder that the workplace is a key locus for public health interventions, which could protect both workers and the communities they serve. To estimate the number of United States workers frequently exposed to infection and disease in the workplace, national employment data (by Standard Occupational Classification) maintained by the Bureau of Labor Statistics (BLS) was merged with a BLS O*NET survey measure reporting how frequently workers in each occupation are exposed to infection or disease at work. abstract: INTRODUCTION: With the global spread of COVID-19, there is a compelling public health interest in quantifying who is at increased risk of contracting disease. Occupational characteristics, such as interfacing with the public and being in close quarters with other workers, not only put workers at high risk for disease, but also make them a nexus of disease transmission to the community. This can further be exacerbated through presenteeism, the term used to describe the act of coming to work despite being symptomatic for disease. Quantifying the number of workers who are frequently exposed to infection and disease in the workplace, and understanding which occupational groups they represent, can help to prompt public health risk response and management for COVID-19 in the workplace, and subsequent infectious disease outbreaks. METHODS: To estimate the number of United States workers frequently exposed to infection and disease in the workplace, national employment data (by Standard Occupational Classification) maintained by the Bureau of Labor Statistics (BLS) was merged with a BLS O*NET survey measure reporting how frequently workers in each occupation are exposed to infection or disease at work. This allowed us to estimate the number of United States workers, across all occupations, exposed to disease or infection at work more than once a month. RESULTS: Based on our analyses, approximately 10% (14.4 M) of United States workers are employed in occupations where exposure to disease or infection occurs at least once per week. Approximately 18.4% (26.7 M) of all United States workers are employed in occupations where exposure to disease or infection occurs at least once per month. While the majority of exposed workers are employed in healthcare sectors, other occupational sectors also have high proportions of exposed workers. These include protective service occupations (e.g. police officers, correctional officers, firefighters), office and administrative support occupations (e.g. couriers and messengers, patient service representatives), education occupations (e.g. preschool and daycare teachers), community and social services occupations (community health workers, social workers, counselors), and even construction and extraction occupations (e.g. plumbers, septic tank installers, elevator repair). CONCLUSIONS: The large number of persons employed in occupations with frequent exposure to infection and disease underscore the importance of all workplaces developing risk response plans for COVID-19. Given the proportion of the United States workforce exposed to disease or infection at work, this analysis also serves as an important reminder that the workplace is a key locus for public health interventions, which could protect both workers and the communities they serve. url: https://doi.org/10.1371/journal.pone.0232452 doi: 10.1371/journal.pone.0232452 id: cord-282202-q2q4vies author: Banerjee, Amitava title: Clinical academic research in the time of Corona: A simulation study in England and a call for action date: 2020-08-13 words: 4106.0 sentences: 229.0 pages: flesch: 46.0 cache: ./cache/cord-282202-q2q4vies.txt txt: ./txt/cord-282202-q2q4vies.txt summary: DESIGN: A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics). "Learning is difficult in the midst of an emergency" [7] , but our ability to deliver timely, high-impact clinical research, relevant to patients and populations, is critical across the academic spectrum [8] , from "bench to bedside to big data", whether basic biology, repurposed and novel therapeutic approaches, vaccines or modelling. Our aims were to: (i) model potential impact of the pandemic on clinical academic capacity in England relating to COVID-19; and (ii) develop evidence-based recommendations to inform the optimal scientific response to COVID-19. abstract: OBJECTIVES: We aimed to model the impact of coronavirus (COVID-19) on the clinical academic response in England, and to provide recommendations for COVID-related research. DESIGN: A stochastic model to determine clinical academic capacity in England, incorporating the following key factors which affect the ability to conduct research in the COVID-19 climate: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics). SETTING: Clinical academics in primary and secondary care in England. PARTICIPANTS: Equivalent of 3200 full-time clinical academics in England. INTERVENTIONS: Four policy approaches to COVID-19 with differing population infection rates: “Italy model” (6%), “mitigation” (10%), “relaxed mitigation” (40%) and “do-nothing” (80%) scenarios. Low and high strain on the health system (no clinical academics able to do research at 10% and 5% infection rate, respectively. MAIN OUTCOME MEASURES: Number of full-time clinical academics available to conduct clinical research during the pandemic in England. RESULTS: In the “Italy model”, “mitigation”, “relaxed mitigation” and “do-nothing” scenarios, from 5 March 2020 the duration (days) and peak infection rates (%) are 95(2.4%), 115(2.5%), 240(5.3%) and 240(16.7%) respectively. Near complete attrition of academia (87% reduction, <400 clinical academics) occurs 35 days after pandemic start for 11, 34, 62, 76 days respectively—with no clinical academics at all for 37 days in the “do-nothing” scenario. Restoration of normal academic workforce (80% of normal capacity) takes 11, 12, 30 and 26 weeks respectively. CONCLUSIONS: Pandemic COVID-19 crushes the science needed at system level. National policies mitigate, but the academic community needs to adapt. We highlight six key strategies: radical prioritisation (eg 3–4 research ideas per institution), deep resourcing, non-standard leadership (repurposing of key non-frontline teams), rationalisation (profoundly simple approaches), careful site selection (eg protected sites with large academic backup) and complete suspension of academic competition with collaborative approaches. url: https://doi.org/10.1371/journal.pone.0237298 doi: 10.1371/journal.pone.0237298 id: cord-258172-p54j4zzo author: Barker, Harlan title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 words: 8453.0 sentences: 409.0 pages: flesch: 48.0 cache: ./cache/cord-258172-p54j4zzo.txt txt: ./txt/cord-258172-p54j4zzo.txt summary: Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . abstract: The World Health Organization declared the COVID-19 epidemic a public health emergency of international concern on March 11th, 2020, and the pandemic is rapidly spreading worldwide. COVID-19 is caused by a novel coronavirus SARS-CoV-2, which enters human target cells via angiotensin converting enzyme 2 (ACE2). We used a number of bioinformatics tools to computationally characterize ACE2 by determining its cell-specific expression in trachea, lung, and small intestine, derive its putative functions, and predict transcriptional regulation. The small intestine expressed higher levels of ACE2 mRNA than any other organ. By immunohistochemistry, duodenum, kidney and testis showed strong signals, whereas the signal was weak in the respiratory tract. Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Gene ontology analysis suggested that, besides its classical role in the renin-angiotensin system, ACE2 may be functionally associated with angiogenesis/blood vessel morphogenesis. Using a novel tool for the prediction of transcription factor binding sites we identified several putative binding sites within two tissue-specific promoters of the ACE2 gene as well as a new putative short form of ACE2. These include several interferon-stimulated response elements sites for STAT1, IRF8, and IRF9. Our results also confirmed that age and gender play no significant role in the regulation of ACE2 mRNA expression in the lung. url: https://www.ncbi.nlm.nih.gov/pubmed/33112891/ doi: 10.1371/journal.pone.0240647 id: cord-003498-4ct0ywnw author: Bdeir, Najat title: A system for production of defective interfering particles in the absence of infectious influenza A virus date: 2019-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza A virus (IAV) infection poses a serious health threat and novel antiviral strategies are needed. Defective interfering particles (DIPs) can be generated in IAV infected cells due to errors of the viral polymerase and may suppress spread of wild type (wt) virus. The antiviral activity of DIPs is exerted by a DI genomic RNA segment that usually contains a large deletion and suppresses amplification of wt segments, potentially by competing for cellular and viral resources. DI-244 is a naturally occurring prototypic segment 1-derived DI RNA in which most of the PB2 open reading frame has been deleted and which is currently developed for antiviral therapy. At present, coinfection with wt virus is required for production of DI-244 particles which raises concerns regarding biosafety and may complicate interpretation of research results. Here, we show that cocultures of 293T and MDCK cell lines stably expressing codon optimized PB2 allow production of DI-244 particles solely from plasmids and in the absence of helper virus. Moreover, we demonstrate that infectivity of these particles can be quantified using MDCK-PB2 cells. Finally, we report that the DI-244 particles produced in this novel system exert potent antiviral activity against H1N1 and H3N2 IAV but not against the unrelated vesicular stomatitis virus. This is the first report of DIP production in the absence of infectious IAV and may spur efforts to develop DIPs for antiviral therapy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6396908/ doi: 10.1371/journal.pone.0212757 id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 words: 6578.0 sentences: 310.0 pages: flesch: 49.0 cache: ./cache/cord-289093-si8btsab.txt txt: ./txt/cord-289093-si8btsab.txt summary: To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. abstract: Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics. url: https://doi.org/10.1371/journal.pone.0098431 doi: 10.1371/journal.pone.0098431 id: cord-011857-brbqgbpz author: Beasley, Steven A. title: An Angelman syndrome substitution in the HECT E3 ubiquitin ligase C-terminal Lobe of E6AP affects protein stability and activity date: 2020-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Angelman syndrome (AS) is a rare neurodevelopmental disorder characterized by speech impairment, intellectual disability, ataxia, and epilepsy. AS is caused by mutations in the maternal copy of UBE3A located on chromosome 15q11-13. UBE3A codes for E6AP (E6 Associated Protein), a prominent member of the HECT (Homologous to E6AP C-Terminus) E3 ubiquitin ligase family. E6AP catalyzes the posttranslational attachment of ubiquitin via its HECT domain onto various intracellular target proteins to regulate DNA repair and cell cycle progression. The HECT domain consists of an N-lobe, required for E2~ubiquitin recruitment, while the C-lobe contains the conserved catalytic cysteine required for ubiquitin transfer. Previous genetic studies of AS patients have identified point mutations in UBE3A that result in amino acid substitutions or premature termination during translation. An AS transversion mutation (codon change from ATA to AAA) within the region of the gene that codes for the catalytic HECT domain of E6AP has been annotated (I827K), but the molecular basis for this loss of function substitution remained elusive. Here, we demonstrate that the I827K substitution destabilizes the 3D fold causing protein aggregation of the C-terminal lobe of E6AP using a combination of spectropolarimetry and nuclear magnetic resonance (NMR) spectroscopy. Our fluorescent ubiquitin activity assays with E6AP-I827K show decreased ubiquitin thiolester formation and ubiquitin discharge. Using 3D models in combination with our biochemical and biophysical results, we rationalize why the I827K disrupts E6AP-dependent ubiquitylation. This work provides new insight into the E6AP mechanism and how its malfunction can be linked to the AS phenotype. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343168/ doi: 10.1371/journal.pone.0235925 id: cord-000261-ip32y0j5 author: Becker, Pablo D. title: Generation of Human Antigen-Specific Monoclonal IgM Antibodies Using Vaccinated “Human Immune System” Mice date: 2010-10-04 words: 5816.0 sentences: 270.0 pages: flesch: 48.0 cache: ./cache/cord-000261-ip32y0j5.txt txt: ./txt/cord-000261-ip32y0j5.txt summary: Following immunization, human CD19 + B cells were sorted based on surface CD27 expression, as a marker of memory phenotype, and the isotype of surface Igs. The sorted B cell populations were immortalized in vitro by retroviral transduction with human B cell lymphoma (BCL)-6 and BCL-XL genes and antigen-specific B cell clones were established and characterized. The obtained results provided the proof-of-concept for the usefulness of this generic approach based on HIS mice combined with immortalization of human B cells for the rapid and inexpensive development of human mAbs against a wide range of antigens. Since HIS mice contained broad naïve B cell repertoires, we analyzed the induction of human antigen-specific B cell responses after immunization with commercially available human vaccines. So far, humanized mouse models based on the transplantation of human HSC only -i.e. without additional human tissues -share these limitations, and immunization strategies result in the limited generation of class-switched antigen-specific B cell responses [14, 31, 32] . abstract: BACKGROUND: Passive transfer of antibodies not only provides immediate short-term protection against disease, but also can be exploited as a therapeutic tool. However, the ‘humanization’ of murine monoclonal antibodies (mAbs) is a time-consuming and expensive process that has the inherent drawback of potentially altering antigenic specificity and/or affinity. The immortalization of human B cells represents an alternative for obtaining human mAbs, but relies on the availability of biological samples from vaccinated individuals or convalescent patients. In this work we describe a novel approach to generate fully human mAbs by combining a humanized mouse model with a new B cell immortalization technique. METHODOLOGY/PRINCIPAL FINDINGS: After transplantation with CD34(+)CD38(−) human hematopoietic progenitor cells, BALB/c Rag2(−/−)IL-2Rγc(−/−) mice acquire a human immune system and harbor B cells with a diverse IgM repertoire. “Human Immune System” mice were then immunized with two commercial vaccine antigens, tetanus toxoid and hepatitis B surface antigen. Sorted human CD19(+)CD27(+) B cells were retrovirally transduced with the human B cell lymphoma (BCL)-6 and BCL-XL genes, and subsequently cultured in the presence of CD40-ligand and IL-21. This procedure allows generating stable B cell receptor-positive B cells that secrete immunoglobulins. We recovered stable B cell clones that produced IgM specific for tetanus toxoid and the hepatitis B surface antigen, respectively. CONCLUSION/SIGNIFICANCE: This work provides the proof-of-concept for the usefulness of this novel method based on the immunization of humanized mice for the rapid generation of human mAbs against a wide range of antigens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949385/ doi: 10.1371/journal.pone.0013137 id: cord-000895-z5rdf0mi author: Belalov, Ilya S. title: Causes and Implications of Codon Usage Bias in RNA Viruses date: 2013-02-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Choice of synonymous codons depends on nucleotide/dinucleotide composition of the genome (termed mutational pressure) and relative abundance of tRNAs in a cell (translational pressure). Mutational pressure is commonly simplified to genomic GC content; however mononucleotide and dinucleotide frequencies in different genomes or mRNAs may vary significantly, especially in RNA viruses. A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. Total GC content was a poor descriptor of viral genome composition and causes of codon usage bias. Genomic nucleotide content was the single most important factor of synonymous codon usage. Moreover, the choice between compatible amino acids (e.g., leucine and isoleucine) was strongly affected by genomic nucleotide composition. Dinucleotide composition at codon positions 2-3 had additional effect on codon usage. Together with mononucleotide composition bias, it could explain almost the entire codon usage bias in RNA viruses. On the other hand, strong dinucleotide content bias at codon position 3-1 found in some viruses had very little effect on codon usage. A hypothetical innate immunity sensor for CpG in RNA could partially explain the codon usage bias, but due to dependence of virus translation upon biased host translation machinery, experimental studies are required to further explore the source of dinucleotide bias in RNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581513/ doi: 10.1371/journal.pone.0056642 id: cord-303187-ny4qr2a2 author: Belo, Vinícius Silva title: Abundance, survival, recruitment and effectiveness of sterilization of free-roaming dogs: A capture and recapture study in Brazil date: 2017-11-01 words: 7691.0 sentences: 410.0 pages: flesch: 44.0 cache: ./cache/cord-303187-ny4qr2a2.txt txt: ./txt/cord-303187-ny4qr2a2.txt summary: Despite the perceived need and usefulness of such parameter estimates and recommendations for the most appropriate approaches applicable under such study designs [30] , survival and recruitment estimates of free-ranging dogs had not been obtained using methods of capture and recapture. In this study, we present estimates of abundance, survival and recruitment rates, and the probabilities of capture of two free-roaming dog populations by means of analytical models for open populations, so far unexplored in previous studies. We estimated critical parameters (survival, recruitment and abundance) that describe the population dynamics of free-roaming dogs based on a capture and recapture study design and on models suitable for open populations. Our study demonstrated the increase in population size in both areas, the predominance and greater recruitment of males, the temporal variability in recruitment and in survival probabilities, the lack of effect of sterilization on population dynamics, the influence of abandon and of density-independent factors and a high demographic turnover. abstract: The existence of free-roaming dogs raises important issues in animal welfare and in public health. A proper understanding of these animals’ ecology is useful as a necessary input to plan strategies to control these populations. The present study addresses the population dynamics and the effectiveness of the sterilization of unrestricted dogs using capture and recapture procedures suitable for open animal populations. Every two months, over a period of 14 months, we captured, tagged, released and recaptured dogs in two regions in a city in the southeast region of Brazil. In one of these regions the animals were also sterilized. Both regions had similar social, environmental and demographic features. We estimated the presence of 148 females and 227 males during the period of study. The average dog:man ratio was 1 dog for each 42 and 51 human beings, in the areas without and with sterilization, respectively. The animal population size increased in both regions, due mainly to the abandonment of domestic dogs. Mortality rate decreased throughout the study period. Survival probabilities did not differ between genders, but males entered the population in higher numbers. There were no differences in abundance, survival and recruitment between the regions, indicating that sterilization did not affect the population dynamics. Our findings indicate that the observed animal dynamics were influenced by density-independent factors, and that sterilization might not be a viable and effective strategy in regions where availability of resources is low and animal abandonment rates are high. Furthermore, the high demographic turnover rates observed render the canine free-roaming population younger, thus more susceptible to diseases, especially to rabies and leishmaniasis. We conclude by stressing the importance of implementing educational programs to promote responsible animal ownership and effective strategies against abandonment practices. url: https://www.ncbi.nlm.nih.gov/pubmed/29091961/ doi: 10.1371/journal.pone.0187233 id: cord-000547-adfigzc1 author: Beniac, Daniel R. title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date: 2012-01-11 words: 7782.0 sentences: 392.0 pages: flesch: 51.0 cache: ./cache/cord-000547-adfigzc1.txt txt: ./txt/cord-000547-adfigzc1.txt summary: METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. From the same image data set, we combined extracted volumes from tomograms with 2-D single particle processing to determine the structure of the GP spikes ( Figure 5 ) to a resolution of 14 Å as measured by the Fourier Shell Correlation (FSC) 0.5 criterion. Analysis of 2090 distinct intact virions with a nucleocapsid from cryo-electron micrographs shows that the most common class length (53%) of virus particles is 982679 nm ( Figure 1A , Table S1 ). abstract: BACKGROUND: Filoviruses, including Ebola virus, are unusual in being filamentous animal viruses. Structural data on the arrangement, stoichiometry and organisation of the component molecules of filoviruses has until now been lacking, partially due to the need to work under level 4 biological containment. The present study provides unique insights into the structure of this deadly pathogen. METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. We show that the helical Ebola virus inner nucleocapsid containing RNA and nucleoprotein is stabilized by an outer layer of VP24-VP35 bridges. Elucidation of the structure of the membrane-associated glycoprotein in its native state indicates that the putative receptor-binding site is occluded within the molecule, while a major neutralizing epitope is exposed on its surface proximal to the viral envelope. The matrix protein VP40 forms a regular lattice within the envelope, although its contacts with the nucleocapsid are irregular. CONCLUSIONS: The results of this study demonstrate a modular organization in Ebola virus that accommodates a well-ordered, symmetrical nucleocapsid within a flexible, tubular membrane envelope. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256159/ doi: 10.1371/journal.pone.0029608 id: cord-305274-mcsdem7y author: Beniac, Daniel R. title: Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion date: 2007-10-24 words: 5463.0 sentences: 254.0 pages: flesch: 51.0 cache: ./cache/cord-305274-mcsdem7y.txt txt: ./txt/cord-305274-mcsdem7y.txt summary: We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. The structures of ACE2 bound to a fragment of the SARS spike containing the receptor-binding domain and the pre-and postfusion configurations of the fusion core heptad repeats of the spike have been solved to atomic resolution [2, 3, [24] [25] [26] . In addition, the atomic resolution structures of two neutralizing antibodies bound to the SARS spike receptor-binding domain have been solved [27, 28] showing that blocking of the receptor binding domain, preventing attachment of virions to cell-surface ACE2, is the likely mechanism of virus neutralization by these antibodies. abstract: The SARS coronavirus (SARS-CoV) spike is the largest known viral spike molecule, and shares a similar function with all class 1 viral fusion proteins. Previous structural studies of membrane fusion proteins have largely used crystallography of static molecular fragments, in isolation of their transmembrane domains. In this study we have produced purified, irradiated SARS-CoV virions that retain their morphology, and are fusogenic in cell culture. We used cryo-electron microscopy and image processing to investigate conformational changes that occur in the entire spike of intact virions when they bind to the viral receptor, angiotensin-converting enzyme 2 (ACE2). We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. Furthermore, our results show that receptor binding and subsequent membrane fusion are distinct steps, and that each spike can bind up to three ACE2 molecules. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis. url: https://www.ncbi.nlm.nih.gov/pubmed/17957264/ doi: 10.1371/journal.pone.0001082 id: cord-000638-ss1435el author: Beq, Stephanie title: Altered Thymic Function during Interferon Therapy in HCV-Infected Patients date: 2012-04-16 words: 5142.0 sentences: 237.0 pages: flesch: 47.0 cache: ./cache/cord-000638-ss1435el.txt txt: ./txt/cord-000638-ss1435el.txt summary: The evolution of T-cell subsets and T-cell homeostasis were estimated by flow cytometry while thymic function was measured through quantification of T-cell receptor excision circles (TREC) and estimation of intrathymic precursor T-cell proliferation during the first four months following the initiation of IFNα therapy. In contrast, Arizcorreta and colleagues showed that IFNa and ribavirin therapy induces a substantial reduction of circulating sjTRECs, in HIV/HCV co-infected patients, accompanied by sustained naïve CD4 + T-cell defect, suggesting thymic dysfunction [10] . While the number of RTEs was similar in HCV-infected patients at study entry and healthy individuals ( These data demonstrate that, as early as one month following treatment initiation, IFNa induces stronger alterations of naïve Tcell subsets, and more specifically in the RTE compartment than in any other T-cell subset, suggesting a specific effect on thymopoiesis. abstract: Interferon alpha (IFNα) therapy, despite good efficacy in curing HCV infection, leads to major side effects, in particular inducement of a strong peripheral T-cell lymphocytopenia. We here analyze the early consequences of IFNα therapy on both thymic function and peripheral T-cell homeostasis in patients in the acute or chronic phase of HCV-infection as well as in HIV/HCV co-infected patients. The evolution of T-cell subsets and T-cell homeostasis were estimated by flow cytometry while thymic function was measured through quantification of T-cell receptor excision circles (TREC) and estimation of intrathymic precursor T-cell proliferation during the first four months following the initiation of IFNα therapy. Beginning with the first month of therapy, a profound lymphocytopenia was observed for all T-cell subsets, including naïve T-cells and recent thymic emigrants (RTE), associated with inhibition of intrathymic precursor T-cell proliferation. Interleukin (IL)-7 plasma concentration rapidly dropped while lymphocytopenia progressed. This was neither a consequence of higher consumption of the cytokine nor due to its neutralization by soluble CD127. Decrease in IL-7 plasma concentration under IFNα therapy correlated with the decline in HCV viral load, thymic activity and RTE concentration in blood. These data demonstrate that IFNα-based therapy rapidly impacts on thymopoiesis and, consequently, perturbs T-cell homeostasis. Such a side effect might be detrimental for the continuation of IFNα therapy and may lead to an increased level of infectious risk, in particular in HIV/HCV co-infected patients. Altogether, this study suggests the therapeutic potential of IL-7 in the maintenance of peripheral T-cell homeostasis in IFNα-treated patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328332/ doi: 10.1371/journal.pone.0034326 id: cord-000248-zueoyesj author: Berretta, Regina title: Cancer Biomarker Discovery: The Entropic Hallmark date: 2010-08-18 words: 33594.0 sentences: 1678.0 pages: flesch: 43.0 cache: ./cache/cord-000248-zueoyesj.txt txt: ./txt/cord-000248-zueoyesj.txt summary: These authors cite, for example, ''''mitochondrial dysfunction'''' [5, 6] (including, but not limited to ''''glucose avidity'''' [7] and ''''a shift in glucosemetabolism from oxidative phosphorylation to glycolysis'''' [6, 8] , ''''altered glycolysis'''' [9] , ''''altered bioenergetic function of mitochondria'''' [10] ), ''''dysregulation of cell cycle and defective genome-integrity checkpoints'''' [11] , ''''aberrant DNA methylation'''' [12] (''''promoter hypermethylation of hallmark cancer genes'''' [13] and ''''CpG island hypermethylation and global genomic hypomethylation'''' [14] ), ''''shift in cellular metabolism'''' [15, 16, 17] , ''''regional hypoxia'''' [18] , ''''microenviroment acidosis'''' [19] , ''''abnormal microRNA regulation'''' [20, 21] , ''''aneuploidy'''' and ''''chromosome aberrations'''' [22, 23, 24, 25, 26] , ''''disruption of cellular junctions'''' [27] , ''''avoidance of the immune response'''' [28] , ''''pre-existing chronic inflammatory conditions'''' [29, 30] , ''''cancerrelated inflammation'''' [29] , ''''disabled autophagy'''' [28] , ''''impaired cellular senescence'''' [31] , ''''altered NF-kappaB signalling'''' [32] , ''''altered growth patterns, not altered growth per se'''' [33] , ''''disregulated DNA methylation and histone modifications'''' [34] , ''''tissue dedifferentiation'''' [35, 36] , and ''''somatically heritable molecular alterations'''' [37] . abstract: BACKGROUND: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. METHODOLOGY/PRINCIPAL FINDINGS: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. CONCLUSIONS/SIGNIFICANCE: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923618/ doi: 10.1371/journal.pone.0012262 id: cord-330537-xz0wt1sz author: Biermann, Olivia title: Active case-finding policy development, implementation and scale-up in high-burden countries: A mixed-methods survey with National Tuberculosis Programme managers and document review date: 2020-10-28 words: 5668.0 sentences: 307.0 pages: flesch: 49.0 cache: ./cache/cord-330537-xz0wt1sz.txt txt: ./txt/cord-330537-xz0wt1sz.txt summary: title: Active case-finding policy development, implementation and scale-up in high-burden countries: A mixed-methods survey with National Tuberculosis Programme managers and document review BACKGROUND: The World Health Organization (WHO) stresses the importance of active case-finding (ACF) for early detection of tuberculosis (TB), especially in the 30 high-burden countries that account for almost 90% of cases globally. OBJECTIVE: To describe the attitudes of National TB Programme (NTP) managers related to ACF policy development, implementation and scale-up in the 30 high-burden countries, and to review national TB strategic plans. Moreover, this study focuses on National TB Programme (NTP) managers, key stakeholders in developing and implementing ACF policies [13] . The study comprised a cross-sectional survey with NTP managers from 30 high TB burden countries, which included closed and open-ended questions designed to elicit quantitative and qualitative information, enhancing each other [15] . abstract: BACKGROUND: The World Health Organization (WHO) stresses the importance of active case-finding (ACF) for early detection of tuberculosis (TB), especially in the 30 high-burden countries that account for almost 90% of cases globally. OBJECTIVE: To describe the attitudes of National TB Programme (NTP) managers related to ACF policy development, implementation and scale-up in the 30 high-burden countries, and to review national TB strategic plans. METHODS: This was a mixed-methods study with an embedded design: A cross-sectional survey with NTP managers yielded quantitative and qualitative data. A review of national TB strategic plans complemented the results. All data were analyzed in parallel and merged in the interpretation of the findings. RESULTS: 23 of the 30 NTP managers (77%) participated in the survey and 22 (73%) national TB strategic plans were reviewed. NTP managers considered managers in districts and regions key stakeholders for both ACF policy development and implementation. Different types of evidence were used to inform ACF policy, while there was a particular demand for local evidence. The NSPs reflected the NTP managers’ unanimous agreement on the need for ACF scale-up, but not all included explicit aims and targets related to ACF. The NTP managers recognized that ACF may decrease health systems costs in the long-term, while acknowledging the risk for increased health system costs in the short-term. About 90% of the NTP managers declared that financial and human resources were currently lacking, while they also elaborated on strategies to overcome resource constraints. CONCLUSION: NTP managers stated that ACF should be scaled up but reported resource constraints. Strategies to increase resources exist but may not yet have been fully implemented, e.g. generating local evidence including from operational research for advocacy. Managers in districts and regions were identified as key stakeholders whose involvement could help improve ACF policy development, implementation and scale-up. url: https://www.ncbi.nlm.nih.gov/pubmed/33112890/ doi: 10.1371/journal.pone.0240696 id: cord-333955-bnzbppof author: Biesold, Susanne E. title: Type I Interferon Reaction to Viral Infection in Interferon-Competent, Immortalized Cell Lines from the African Fruit Bat Eidolon helvum date: 2011-11-30 words: 5016.0 sentences: 275.0 pages: flesch: 51.0 cache: ./cache/cord-333955-bnzbppof.txt txt: ./txt/cord-333955-bnzbppof.txt summary: Here, we investigated interferon (IFN) response, -induction, -secretion and -signaling in epithelial-like cells of the relevant and abundant African fruit bat species, Eidolon helvum (E. Cells from Pteropus species have been shown to produce high amounts of interferon (IFN)-l after stimulation with the double-strand (ds)RNA analogue poly IC, and after infection with the bat-associated paramyxovirus, Tioman [13] . In accordance with the IFN mRNA induction, the highest equivalent amount of bioactive secreted IFN upon RVFV 13 virus infection and poly IC transfection was measured in EidNi/41.3 cells, followed by MEF and MA104 (Figure 3 ). Increases of infectious virus formation were about 1000-fold within 24 hpi, and specific infectivities, expressed as PFU per genome equivalent (PCR units), were highly comparable between cell cultures ( Figure 4C) . abstract: Bats harbor several highly pathogenic zoonotic viruses including Rabies, Marburg, and henipaviruses, without overt clinical symptoms in the animals. It has been suspected that bats might have evolved particularly effective mechanisms to suppress viral replication. Here, we investigated interferon (IFN) response, -induction, -secretion and -signaling in epithelial-like cells of the relevant and abundant African fruit bat species, Eidolon helvum (E. helvum). Immortalized cell lines were generated; their potential to induce and react on IFN was confirmed, and biological assays were adapted to application in bat cell cultures, enabling comparison of landmark IFN properties with that of common mammalian cell lines. E. helvum cells were fully capable of reacting to viral and artificial IFN stimuli. E. helvum cells showed highest IFN mRNA induction, highly productive IFN protein secretion, and evidence of efficient IFN stimulated gene induction. In an Alphavirus infection model, O'nyong-nyong virus exhibited strong IFN induction but evaded the IFN response by translational rather than transcriptional shutoff, similar to other Alphavirus infections. These novel IFN-competent cell lines will allow comparative research on zoonotic, bat-borne viruses in order to model mechanisms of viral maintenance and emergence in bat reservoirs. url: https://doi.org/10.1371/journal.pone.0028131 doi: 10.1371/journal.pone.0028131 id: cord-340713-v5sdowb7 author: Bird, Jordan J. title: Country-level pandemic risk and preparedness classification based on COVID-19 data: A machine learning approach date: 2020-10-28 words: 5669.0 sentences: 260.0 pages: flesch: 53.0 cache: ./cache/cord-340713-v5sdowb7.txt txt: ./txt/cord-340713-v5sdowb7.txt summary: The three four-class classification problems are then explored and benchmarked through leave-one-country-out cross validation to find the strongest model, producing a Stack of Gradient Boosting and Decision Tree algorithms for risk of transmission, a Stack of Support Vector Machine and Extra Trees for risk of mortality, and a Gradient Boosting algorithm for the risk of inability to test. The classification problem of risk is therefore formulated based on prior knowledge of the pandemic in terms of class only, but the attributes to attempt to classify them are purely country-level information regardless of number of cases, deaths and other coronavirus specific data. Country-level pandemic risk and preparedness classification based on COVID-19 data Fig 10 shows a comparison of other models that were explored. Country-level pandemic risk and preparedness classification based on COVID-19 data Table 1 shows the predicted class values for the best models applied to each of the respective risk classification problems. abstract: In this work we present a three-stage Machine Learning strategy to country-level risk classification based on countries that are reporting COVID-19 information. A K% binning discretisation (K = 25) is used to create four risk groups of countries based on the risk of transmission (coronavirus cases per million population), risk of mortality (coronavirus deaths per million population), and risk of inability to test (coronavirus tests per million population). The four risk groups produced by K% binning are labelled as ‘low’, ‘medium-low’, ‘medium-high’, and ‘high’. Coronavirus-related data are then removed and the attributes for prediction of the three types of risk are given as the geopolitical and demographic data describing each country. Thus, the calculation of class label is based on coronavirus data but the input attributes are country-level information regardless of coronavirus data. The three four-class classification problems are then explored and benchmarked through leave-one-country-out cross validation to find the strongest model, producing a Stack of Gradient Boosting and Decision Tree algorithms for risk of transmission, a Stack of Support Vector Machine and Extra Trees for risk of mortality, and a Gradient Boosting algorithm for the risk of inability to test. It is noted that high risk for inability to test is often coupled with low risks for transmission and mortality, therefore the risk of inability to test should be interpreted first, before consideration is given to the predicted transmission and mortality risks. Finally, the approach is applied to more recent risk levels to data from September 2020 and weaker results are noted due to the growth of international collaboration detracting useful knowledge from country-level attributes which suggests that similar machine learning approaches are more useful prior to situations later unfolding. url: https://doi.org/10.1371/journal.pone.0241332 doi: 10.1371/journal.pone.0241332 id: cord-012891-heqsfzkm author: Blanco Vázquez, Cristina title: Detection of latent forms of Mycobacterium avium subsp. paratuberculosis infection using host biomarker-based ELISAs greatly improves paratuberculosis diagnostic sensitivity date: 2020-09-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bovine paratuberculosis (PTB) is a chronic granulomatous enteritis, caused by Mycobacterium avium subsp. paratuberculosis (MAP), responsible for important economic losses in the dairy industry. Current diagnostic methods have low sensitivities for detection of latent forms of MAP infection, defined by focal granulomatous lesions and scarce humoral response or MAP presence. In contrast, patent infections correspond to multifocal and diffuse types of enteritis where there is increased antibody production, and substantial mycobacterial load. Our previous RNA-Seq analysis allowed the selection of five candidate biomarkers overexpressed in peripheral blood of MAP infected Holstein cows with focal (ABCA13 and MMP8) and diffuse (FAM84A, SPARC and DES) lesions vs. control animals with no detectable PTB-associated lesions in intestine and regional lymph nodes. The aim of the current study was to assess the PTB diagnostic potential of commercial ELISAs designed for the specific detection of these biomarkers. The ability of these ELISAs to identify animals with latent and/or patent forms of MAP infection was investigated using serum from naturally infected cattle (n = 88) and non-infected control animals (n = 67). ROC analysis revealed that the ABCA13-based ELISA showed the highest diagnostic accuracy for the detection of infected animals with focal lesions (AUC 0.837, sensitivity 79.25% and specificity 88.06%) and with any type of histological lesion (AUC 0.793, sensitivity 69.41% and specificity 86.57%) improving on the diagnostic performance of the popular IDEXX ELISA and other conventional diagnostic methods. SPARC and MMP8 showed the highest diagnostic accuracy for the detection of animals with multifocal (AUC 0.852) and diffuse lesions (AUC 0.831), respectively. In conclusion, our results suggest that quantification of ABCA13, SPARC and MMP8 by ELISA has the potential for implementation as a diagnostic tool to reliably identify MAP infection, greatly improving early detection of MAP latent infections when antibody responses and fecal shedding are undetectable using conventional diagnostic methods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470414/ doi: 10.1371/journal.pone.0236336 id: cord-013099-j816c3tw author: Blease, Charlotte title: US primary care in 2029: A Delphi survey on the impact of machine learning date: 2020-10-08 words: 5698.0 sentences: 303.0 pages: flesch: 54.0 cache: ./cache/cord-013099-j816c3tw.txt txt: ./txt/cord-013099-j816c3tw.txt summary: To address this research gap, we designed a Delphi survey to explore leading health informaticians'' predictions about the impact of machine learning on primary care in the US in 2029. Acknowledging that heterogeneous panels have been shown to result in more accurate estimates [33] , and that what counts as an expert can be influenced by goals, values, and the manner in which knowledge is generated, we aimed to recruit diverse participants from across academia, healthcare, non-profit organizations, and industry; and to strive for panelists with a varied complementarity of interests within health informatics. In the first round, the Delphi survey requested demographic information; this was followed by 5 sections, with 7 open-ended questions, on the impact of machine learning on primary care by 2029 (see S1 Appendix; Table 1 We also included a final comment-box for feedback on the survey. abstract: OBJECTIVE: To solicit leading health informaticians’ predictions about the impact of AI/ML on primary care in the US in 2029. DESIGN: A three-round online modified Delphi poll. PARTICIPANTS: Twenty-nine leading health informaticians. METHODS: In September 2019, health informatics experts were selected by the research team, and invited to participate the Delphi poll. Participation in each round was anonymous, and panelists were given between 4–8 weeks to respond to each round. In Round 1 open-ended questions solicited forecasts on the impact of AI/ML on: (1) patient care, (2) access to care, (3) the primary care workforce, (4) technological breakthroughs, and (5) the long-future for primary care physicians. Responses were coded to produce itemized statements. In Round 2, participants were invited to rate their agreement with each item along 7-point Likert scales. Responses were analyzed for consensus which was set at a predetermined interquartile range of ≤ 1. In Round 3 items that did not reach consensus were redistributed. RESULTS: A total of 16 experts participated in Round 1 (16/29, 55%). Of these experts 13/16 (response rate, 81%), and 13/13 (response rate, 100%), responded to Rounds 2 and 3, respectively. As a result of developments in AI/ML by 2029 experts anticipated workplace changes including incursions into the disintermediation of physician expertise, and increased AI/ML training requirements for medical students. Informaticians also forecast that by 2029 AI/ML will increase diagnostic accuracy especially among those with limited access to experts, minorities and those with rare diseases. Expert panelists also predicted that AI/ML-tools would improve access to expert doctor knowledge. CONCLUSIONS: This study presents timely information on informaticians’ consensus views about the impact of AI/ML on US primary care in 2029. Preparation for the near-future of primary care will require improved levels of digital health literacy among patients and physicians. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544100/ doi: 10.1371/journal.pone.0239947 id: cord-003484-ylpa702c author: Blázquez, Elena title: Evaluation of the effectiveness of the SurePure Turbulator ultraviolet-C irradiation equipment on inactivation of different enveloped and non-enveloped viruses inoculated in commercially collected liquid animal plasma date: 2019-02-21 words: 6990.0 sentences: 352.0 pages: flesch: 53.0 cache: ./cache/cord-003484-ylpa702c.txt txt: ./txt/cord-003484-ylpa702c.txt summary: Specifically, Pseudorabies virus (PRV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine epidemic diarrhea virus (PEDV), Bovine viral diarrhea virus (BVDV), Classical swine fever virus (CSFV), Swine influenza virus (SIV) as enveloped viruses and Porcine parvovirus (PPV), Swine vesicular disease virus (SVDV), Porcine circovirus type 2 (PCV-2) and Senecavirus A (SVA) as non-enveloped viruses, were inoculated in bovine or porcine plasma and subjected to different UV-C irradiation doses (0, 750, 1500, 3000, 6000 and 9000 J/L) using an UV-C device developed for opaque liquid working under turbulent flow. The objective of this study was to assess inactivation efficiency of the SurePure Turbulator UV-C irradiation system with selected swine enveloped viruses Pseudorabies virus (PRV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine epidemic diarrhea virus (PEDV), Bovine viral diarrhea virus (BVDV), Swine influenza A virus (SIV) and Classical swine fever virus (CSFV) and non-enveloped viruses Porcine parvovirus (PPV), Swine vesicular disease virus (SVDV), Porcine circovirus 2 (PCV-2) and Senecavirus A (SVA) inoculated in liquid bovine or porcine plasma. abstract: The objective of this study was to evaluate the effectiveness of the SurePure Turbulator ultraviolet-C (UV-C, 254 nm wavelength) irradiation equipment on inactivation of different enveloped and non-enveloped viruses in commercially collected liquid animal plasma. Specifically, Pseudorabies virus (PRV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine epidemic diarrhea virus (PEDV), Bovine viral diarrhea virus (BVDV), Classical swine fever virus (CSFV), Swine influenza virus (SIV) as enveloped viruses and Porcine parvovirus (PPV), Swine vesicular disease virus (SVDV), Porcine circovirus type 2 (PCV-2) and Senecavirus A (SVA) as non-enveloped viruses, were inoculated in bovine or porcine plasma and subjected to different UV-C irradiation doses (0, 750, 1500, 3000, 6000 and 9000 J/L) using an UV-C device developed for opaque liquid working under turbulent flow. The enveloped viruses tested were inactivated at < 3000 J/L of UV-C, being the dose needed to inactivate 4 log TCID(50) (4D) of 1612 J/L for PRV,1004 J/L for PRRSV, 1953 J/L for PEDV, 1639 J/L for SIV, 1641 J/L for CSFV and 1943 J/L for BVDV. The non-enveloped viruses tended to have higher 4D values: 2161 J/L for PPV, 3223 J/L for SVA and 3708 J/L for SVDV. Because the initial viral concentration was <4.0 Log for PCV-2, it was not possible to calculate the 4D value for this virus. In conclusion, these results demonstrated that the SurePure Turbulator UV-C treatment system is capable of inactivating significant levels of swine viruses inoculated in commercially collected porcine or bovine plasma. It was concluded that irradiation with UV-C can provide an additional redundant biosafety feature in the manufacturing process of spray-dried animal plasma. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383881/ doi: 10.1371/journal.pone.0212332 id: cord-001065-j4hvyyoi author: Boncristiani, Humberto F. title: In Vitro Infection of Pupae with Israeli Acute Paralysis Virus Suggests Disturbance of Transcriptional Homeostasis in Honey Bees (Apis mellifera) date: 2013-09-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. The infected pupae developed pronounced but variable patterns of disease. Symptoms varied from complete cessation of development with no visual evidence of disease to rapid darkening of a part or the entire body. Considerable differences in IAPV titer dynamics were observed, suggesting significant variation in resistance to IAPV among and possibly within honey bee colonies. Thus, selective breeding for virus resistance should be possible. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. These results provide first insights into the mechanisms of IAPV pathogenicity. They mirror a transcriptional survey of honey bees afflicted with Colony Collapse Disorder and thus support the hypothesis that viruses play a critical role in declining honey bee health. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3764161/ doi: 10.1371/journal.pone.0073429 id: cord-346347-r4ork18p author: Borrion, Hervé title: Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China date: 2020-10-14 words: 7552.0 sentences: 358.0 pages: flesch: 49.0 cache: ./cache/cord-346347-r4ork18p.txt txt: ./txt/cord-346347-r4ork18p.txt summary: There are reasons to believe that crime-related performance measures during a pandemic period, or other disasters, may not match the idealised resilience triangle, but rather resemble the dipper-shaped function depicted in Fig 2. Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China RD(n) provides a useful measure to monitor the operating level (%) of offenders. In the case where the crime level in this phase exceeds the pre-Disruptive Event (t DE ) level (μ 7 �μ 1 ), two sub-indicators can be used to measure the ecosystem''s resilience during the recovery phase. Measuring the resilience of criminogenic ecosystems to global disruption: A case-study of COVID-19 in China between τ − and τ + shows it took significantly longer for crime to drop than to return to its expected level. abstract: This paper uses resilience as a lens through which to analyse disasters and other major threats to patterns of criminal behaviour. A set of indicators and mathematical models are introduced that aim to quantitatively describe changes in crime levels in comparison to what could otherwise be expected, and what might be expected by way of adaptation and subsequent resumption of those patterns. The validity of the proposed resilience assessment tool is demonstrated using commercial theft data from the COVID-19 pandemic period. A 64 per cent reduction in crime was found in the studied city (China) during an 83-day period, before daily crime levels bounced back to higher than expected values. The proposed resilience indicators are recommended as benchmarking instruments for evaluating and comparing the global impact of COVID-19 policies on crime and public safety. url: https://doi.org/10.1371/journal.pone.0240077 doi: 10.1371/journal.pone.0240077 id: cord-256424-t3dtabi4 author: Bousbia, Sabri title: Repertoire of Intensive Care Unit Pneumonia Microbiota date: 2012-02-28 words: 5641.0 sentences: 294.0 pages: flesch: 39.0 cache: ./cache/cord-256424-t3dtabi4.txt txt: ./txt/cord-256424-t3dtabi4.txt summary: Recently, the bacterial microbiota of patients with cystic fibrosis and ventilator-associated pneumonia (VAP) were studied using 16S rDNA gene amplification followed by clone libraries sequencing [9] [10] [11] . Bacterial microbiota as evaluated by 16S rDNA Molecular assays were positive for at least one bacterium for 129 out of 185 bronchoalveolar lavage (BAL) samples from patients with pneumonia as well as from 13 out of 25 from control individuals (p = 0.07). Fungal microbiota obtained from patients showed the presence of 22 different species belonging to 2 phyla (8 orders, 11 families and 12 genera) among which 6 phylotypes had not been previously identified in BAL fluids from pneumonia. Indeed, our study reveals that some pathogens that till now had been considered typical for ICU pneumonia, such as Pseudomonas aeruginosa and Streptococcus species, or viruses, such CMV and HSV, can be detected as commonly in controls as in patients (Fig. S1 and S2 ). abstract: Despite the considerable number of studies reported to date, the causative agents of pneumonia are not completely identified. We comprehensively applied modern and traditional laboratory diagnostic techniques to identify microbiota in patients who were admitted to or developed pneumonia in intensive care units (ICUs). During a three-year period, we tested the bronchoalveolar lavage (BAL) of patients with ventilator-associated pneumonia, community-acquired pneumonia, non-ventilator ICU pneumonia and aspiration pneumonia, and compared the results with those from patients without pneumonia (controls). Samples were tested by amplification of 16S rDNA, 18S rDNA genes followed by cloning and sequencing and by PCR to target specific pathogens. We also included culture, amoeba co-culture, detection of antibodies to selected agents and urinary antigen tests. Based on molecular testing, we identified a wide repertoire of 160 bacterial species of which 73 have not been previously reported in pneumonia. Moreover, we found 37 putative new bacterial phylotypes with a 16S rDNA gene divergence ≥98% from known phylotypes. We also identified 24 fungal species of which 6 have not been previously reported in pneumonia and 7 viruses. Patients can present up to 16 different microorganisms in a single BAL (mean ± SD; 3.77±2.93). Some pathogens considered to be typical for ICU pneumonia such as Pseudomonas aeruginosa and Streptococcus species can be detected as commonly in controls as in pneumonia patients which strikingly highlights the existence of a core pulmonary microbiota. Differences in the microbiota of different forms of pneumonia were documented. url: https://www.ncbi.nlm.nih.gov/pubmed/22389704/ doi: 10.1371/journal.pone.0032486 id: cord-293393-kbndie8e author: Braesch-Andersen, Sten title: ApoD Mediates Binding of HDL to LDL and to Growing T24 Carcinoma date: 2014-12-16 words: 6253.0 sentences: 386.0 pages: flesch: 60.0 cache: ./cache/cord-293393-kbndie8e.txt txt: ./txt/cord-293393-kbndie8e.txt summary: To investigate the presence of particles containing both apoD and apoB, we performed a dual-specific ELISA using the anti-apoD mAb D554 as a capture antibody and a biotinylated anti-apoB mAb, LDL20, for detection. To determine the importance of having intact lipoprotein particles, we repeated the dual-specific apoD/B ELISA in the presence of detergent, using anti-apoD-D544 as the capture mAb and anti-apoB-LDL20 as the detecting mAb. As seen in Fig. 4A , only small amounts of apoB bound to D544 when detergent was present, indicating that intact lipoprotein particles are needed for the apoD-LDL interaction. In agreement with this latter finding, apoD production was high in confluent, growth-arrested T24 cell cultures (2,5 million cells in 9 ml), but was not detectable in non-confluent proliferating Anti-apoD (D544) was used as the capture antibody and anti-apoB (LDL20-biotin) was used as the detection antibody in a detergent free dualspecific ELISA. abstract: Apolipoprotein (Apo) D is an important protein produced in many parts of the body. It is necessary for the development and repair of the brain and protection from oxidative stress. The purpose of this study was to investigate the extent to which apoD interacts with lipoproteins in human plasma. By using detergent-free ELISA, we show that immobilized monoclonal antibodies against apoD very efficiently bind to low density lipoprotein (LDL) from plasma; this binding is as equally efficient as binding to an anti-apoB monoclonal antibody. Adding detergent to the plasma inhibited the binding, suggesting that the binding is dependent on the presence of intact lipoprotein particles. Reversing the system by using immobilized anti-apoB revealed that the affinity of apoD for LDL is rather low, suggesting that multiple bindings are needed for a durable connection. Biosensor experiments using purified lipoproteins also showed that purified apoD and high density lipoprotein 3 (HDL3), a lipoprotein fraction rich in apoD, were both able to bind LDL very efficiently, indicating that the HDL3-LDL interaction may be a physiological consequence of the affinity of apoD for LDL. Furthermore, we found that apoD increases the binding of HDL to actively growing T24 bladder carcinoma cells but not to quiescent, contact-inhibited, confluent T24 cells. This result is especially intriguing given that the T24 supernatant only contained detectable levels of apoD after growth inhibition, raising the possibility that alternating the expression of apoD and a putative apoD-receptor could give direction to the flow of lipids. In the current paper, we conclude that apoD mediates binding of HDL to LDL and to growing T24 carcinomas, thereby highlighting the importance of apoD in lipid metabolism. url: https://doi.org/10.1371/journal.pone.0115180 doi: 10.1371/journal.pone.0115180 id: cord-001446-mpuovmeb author: Bratcher, Preston E. title: Factors Influencing the Measurement of Plasma/Serum Surfactant Protein D Levels by ELISA date: 2014-11-03 words: 4873.0 sentences: 226.0 pages: flesch: 43.0 cache: ./cache/cord-001446-mpuovmeb.txt txt: ./txt/cord-001446-mpuovmeb.txt summary: Circulating levels of SP-D have been examined for their potential use as a biomarker in various diseases including dermatitis [2, 3] , acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] , periodontitis [14] , interstitial pulmonary fibrosis (IPF) [10, 12, [15] [16] [17] [18] [19] [20] [21] [22] [23] , chronic obstructive pulmonary disease (COPD) [15, [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] , emphysema [37] , cystic fibrosis (CF) [15, 38, 39] , coronary disease [40, 41] , sclerosis [42] [43] [44] [45] [46] , cancer [47, 48] , sarcoidosis [21, 49] , allergies [28, [50] [51] [52] , rheumatoid arthritis [53, 54] , and respiratory infections [18, [55] [56] [57] [58] [59] [60] . Serum levels of surfactant proteins A and D are useful biomarkers for interstitial lung disease in patients with progressive systemic sclerosis abstract: BACKGROUND: Extensive variations in human surfactant protein D (SP-D) levels in circulation as measured by ELISA exist in the published literature. In order to determine the source of these variations, factors influencing the measurement by ELISA were explored. MATERIALS AND METHODS: Peripheral blood from healthy individuals was collected into various vacutainers during the same blood draw. Recombinant SP-D was diluted into different matrices and used for a standard curve. Samples were analyzed by capture ELISA using one of two distinct detection antibodies. RESULTS: The type of matrix had some effects on detection of recombinant SP-D. The type of anticoagulant used and dilution factor had very little effect, except for in plasma collected in EDTA vacutainers. The extent of variation in published values seemed to be due to the ELISA configuration employed, and, in agreement with this, we found that by switching the detection antibody, there was a 50% decrease in the extrapolated SP-D value of serum and plasma samples. Storage of samples resulted in slight changes in measured SP-D levels. CONCLUSIONS: The ELISA configuration employed to measure circulating levels of SP-D has a significant effect on the extrapolated values. In both configurations tested, the use of EDTA as a coagulant resulted in inconsistent values, and we, therefore, suggest the avoidance of this anticoagulant when assaying for SP-D by ELISA. While the demonstrated effects of several factors on measurement of SP-D may not account for all the disparities amongst the previous studies, they stress that variations in methodologies for measuring the same protein can result in very inconsistent results. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4218753/ doi: 10.1371/journal.pone.0111466 id: cord-297287-0i4nc353 author: Braun, Benjamin title: Simulating phase transitions and control measures for network epidemics caused by infections with presymptomatic, asymptomatic, and symptomatic stages date: 2020-09-10 words: 4005.0 sentences: 204.0 pages: flesch: 49.0 cache: ./cache/cord-297287-0i4nc353.txt txt: ./txt/cord-297287-0i4nc353.txt summary: Using agent-based simulations on small world networks, we observe phase transitions for epidemic spread related to: 1) Global social distancing with a fixed probability of adherence. Phase transitions and control measures for network epidemics self-isolate in response to one infected social contact) all the way up to 97% with low levels of any type of social distancing. Because our goal is to understand the behavior of phase transitions regarding total number of infections in our model, we conducted secondary simulations on a refined parameter space based on the results of our regression tree analysis. There is also a clear interaction between the social distance probability and viral shedding parameters and the resulting number of infected agents and the length of the epidemic. Social distancing controls in this model exhibit a phase transition regarding total number of infections, either when imposed globally or when based on individual response to infected contacts. abstract: We investigate phase transitions associated with three control methods for epidemics on small world networks. Motivated by the behavior of SARS-CoV-2, we construct a theoretical SIR model of a virus that exhibits presymptomatic, asymptomatic, and symptomatic stages in two possible pathways. Using agent-based simulations on small world networks, we observe phase transitions for epidemic spread related to: 1) Global social distancing with a fixed probability of adherence. 2) Individually initiated social isolation when a threshold number of contacts are infected. 3) Viral shedding rate. The primary driver of total number of infections is the viral shedding rate, with probability of social distancing being the next critical factor. Individually initiated social isolation was effective when initiated in response to a single infected contact. For each of these control measures, the total number of infections exhibits a sharp phase transition as the strength of the measure is varied. url: https://www.ncbi.nlm.nih.gov/pubmed/32911518/ doi: 10.1371/journal.pone.0238412 id: cord-267519-a0bcmjkn author: Bravi, Francesca title: Predictors of severe or lethal COVID-19, including Angiotensin Converting Enzyme inhibitors and Angiotensin II Receptor Blockers, in a sample of infected Italian citizens date: 2020-06-24 words: 3303.0 sentences: 144.0 pages: flesch: 44.0 cache: ./cache/cord-267519-a0bcmjkn.txt txt: ./txt/cord-267519-a0bcmjkn.txt summary: AIMS: This retrospective case-control study was aimed at identifying potential independent predictors of severe/lethal COVID-19, including the treatment with Angiotensin-Converting Enzyme inhibitors (ACEi) and/or Angiotensin II Receptor Blockers (ARBs). Observing that human pathogenic coronaviruses bind their target cells through angiotensin-converting enzyme 2 (ACE2) [5] [6] [7] [8] , and that a few studies reported an increase in ACE2 expression mediated by angiotensin II type-I receptor blockers (ARBs) and ACE inhibitors (more consistently on animals than in humans) [9] [10] [11] [12] [13] [14] [15] [16] , some hypothesized that the increased expression of ACE2 would facilitate infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), thus the hypertension treatment with ACE2-stimulating drugs, as well as ACE2 polymorphisms, might increase the risk of developing severe COVID-19 [17] [18] [19] . abstract: AIMS: This retrospective case-control study was aimed at identifying potential independent predictors of severe/lethal COVID-19, including the treatment with Angiotensin-Converting Enzyme inhibitors (ACEi) and/or Angiotensin II Receptor Blockers (ARBs). METHODS AND RESULTS: All adults with SARS-CoV-2 infection in two Italian provinces were followed for a median of 24 days. ARBs and/or ACEi treatments, and hypertension, diabetes, cancer, COPD, renal and major cardiovascular diseases (CVD) were extracted from clinical charts and electronic health records, up to two years before infection. The sample consisted of 1603 subjects (mean age 58.0y; 47.3% males): 454 (28.3%) had severe symptoms, 192 (12.0%) very severe or lethal disease (154 deaths; mean age 79.3 years; 70.8% hypertensive, 42.2% with CVD). The youngest deceased person aged 44 years. Among hypertensive subjects (n = 543), the proportion of those treated with ARBs or ACEi were 88.4%, 78.7% and 80.6% among patients with mild, severe and very severe/lethal disease, respectively. At multivariate analysis, no association was observed between therapy and disease severity (Adjusted OR for very severe/lethal COVID-19: 0.87; 95% CI: 0.50–1.49). Significant predictors of severe disease were older age (with AORs largely increasing after 70 years of age), male gender (AOR: 1.76; 1.40–2.23), diabetes (AOR: 1.52; 1.05–2.18), CVD (AOR: 1.88; 1.32–2.70) and COPD (AOR: 1.88; 1.11–3.20). Only gender, age and diabetes also predicted very severe/lethal disease. CONCLUSION: No association was found between COVID-19 severity and treatment with ARBs and/or ACEi, supporting the recommendation to continue medication for all patients unless otherwise advised by their physicians. url: https://www.ncbi.nlm.nih.gov/pubmed/32579597/ doi: 10.1371/journal.pone.0235248 id: cord-000006-104sqoxz author: Bray, Daniel P. title: Composition and Function of Haemolymphatic Tissues in the European Common Shrew date: 2008-10-15 words: 5701.0 sentences: 259.0 pages: flesch: 46.0 cache: ./cache/cord-000006-104sqoxz.txt txt: ./txt/cord-000006-104sqoxz.txt summary: Here, we examined the unique haemolymphatic system of the European common shrew (Sorex araneus) to investigate the capacity of this short-lived mammal, restricted by a fast metabolism and extremely limited fat reserves, to defend against its unusually diverse parasite fauna, both as a young animal and an adult. We examined and compared the structure, composition and function of relevant haemolymphatic tissues including the pancreas of Aselli, in wild-caught common shrews of different ages pre and post maturation, and the extent and type of inflammatory reactions produced in response to naturally occurring parasitic infections. While some degree of lymphatic exhaustion was obvious in adult animals (perhaps as a result of age-related changes, or reduced investment in immunity as a consequence of breeding effort), there was also evidence of some degree of compensation, in the form of storage of plasma cells particularly in the pancreas of Aselli, possibly as a defence against previously encountered parasites. abstract: BACKGROUND: Studies of wild animals responding to their native parasites are essential if we are to understand how the immune system functions in the natural environment. While immune defence may bring increased survival, this may come at a resource cost to other physiological traits, including reproduction. Here, we tested the hypothesis that wild common shrews (Sorex araneus), which produce large numbers of offspring during the one breeding season of their short life span, forgo investment in immunity and immune system maintenance, as increased longevity is unlikely to bring further opportunities for mating. In particular, we predicted that adult shrews, with shorter expected lifespans, would not respond as effectively as young animals to infection. METHODOLOGY/PRINCIPAL FINDINGS: We examined haemolymphatic tissues from wild-caught common shrews using light and transmission electron microscopy, applied in conjunction with immunohistology. We compared composition and function of these tissues in shrews of different ages, and the extent and type of inflammatory reactions observed in response to natural parasitic infections. All ages seemed able to mount systemic, specific immune responses, but adult shrews showed some signs of lymphatic tissue exhaustion: lymphatic follicles in adults (n = 21) were both smaller than those in sub-adults (n = 18; Wald = 11.1, p<0.05) and exhibited greater levels of depletion (Wald = 13.3, p<0.05). CONCLUSIONS/SIGNIFICANCE: Contrary to our expectations, shrews respond effectively to their natural parasites, and show little indication of immunosenescence as adults. The pancreas of Aselli, a unique lymphoid organ, may aid in providing efficient immune responses through the storage of large numbers of plasma cells. This may allow older animals to react effectively to previously encountered parasites, but infection by novel agents, and eventual depletion of plasma cell reserves, could both still be factors in the near-synchronous mortality of adult shrews observed shortly after breeding. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561066/ doi: 10.1371/journal.pone.0003413 id: cord-296635-8r3tm966 author: Breed, Andrew C. title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management date: 2011-12-14 words: 4573.0 sentences: 199.0 pages: flesch: 47.0 cache: ./cache/cord-296635-8r3tm966.txt txt: ./txt/cord-296635-8r3tm966.txt summary: title: Evidence of Endemic Hendra Virus Infection in Flying-Foxes (Pteropus conspicillatus)—Implications for Disease Risk Management This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. Hendra virus (HeV) and Nipah virus (NiV) are paramyxoviruses of the genus Henipavirus with pteropid bats (i.e. flying-foxes; Pteropus sp., Family Pteropodidae) being the primary wildlife reservoir [1] . Henipaviruses have the potential to infect a wide range of mammalian species, and Hendra virus has spread from flying-foxes to horses in Australia on at least 20 reported separate occasions (five involving horse-human transmission), most recently in 2011 [5, 6, 7] . [14] on the infection dynamics of HeV in the little red flying-fox, Pteropus scapulatus, in the Northern Territory of Australia suggested that viral transmission may be predominantly horizontal, with pregnancy and lactation suggested as risk factors for infection. abstract: This study investigated the seroepidemiology of Hendra virus in a spectacled flying-fox (Pteropus conspicillatus) population in northern Australia, near the location of an equine and associated human Hendra virus infection in late 2004. The pattern of infection in the population was investigated using a serial cross-sectional serological study over a 25-month period, with blood sampled from 521 individuals over six sampling sessions. Antibody titres to the virus were determined by virus neutralisation test. In contrast to the expected episodic infection pattern, we observed that seroprevalence gradually increased over the two years suggesting infection was endemic in the population over the study period. Our results suggested age, pregnancy and lactation were significant risk factors for a detectable neutralizing antibody response. Antibody titres were significantly higher in females than males, with the highest titres occurring in pregnant animals. Temporal variation in antibody titres suggests that herd immunity to the virus may wax and wane on a seasonal basis. These findings support an endemic infection pattern of henipaviruses in bat populations suggesting their infection dynamics may differ significantly from the acute, self limiting episodic pattern observed with related viruses (e.g. measles virus, phocine distemper virus, rinderpest virus) hence requiring a much smaller critical host population size to sustain the virus. These findings help inform predictive modelling of henipavirus infection in bat populations, and indicate that the life cycle of the reservoir species should be taken into account when developing risk management strategies for henipaviruses. url: https://doi.org/10.1371/journal.pone.0028816 doi: 10.1371/journal.pone.0028816 id: cord-296399-vvbjulm9 author: Brinkmann, Constantin title: The glycoprotein of vesicular stomatitis virus promotes release of virus-like particles from tetherin-positive cells date: 2017-12-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vesicular stomatitis virus (VSV) release from infected cells is inhibited by the interferon (IFN)-inducible antiviral host cell factor tetherin (BST-2, CD317). However, several viruses encode tetherin antagonists and it is at present unknown whether residual VSV spread in tetherin-positive cells is also promoted by a virus-encoded tetherin antagonist. Here, we show that the viral glycoprotein (VSV-G) antagonizes tetherin in transfected cells, although with reduced efficiency as compared to the HIV-1 Vpu protein. Tetherin antagonism did not involve alteration of tetherin expression and was partially dependent on a GXXXG motif in the transmembrane domain of VSV-G. However, mutation of the GXXXG motif did not modulate tetherin sensitivity of infectious VSV. These results identify VSV-G as a tetherin antagonist in transfected cells but fail to provide evidence for a contribution of tetherin antagonism to viral spread. url: https://www.ncbi.nlm.nih.gov/pubmed/29216247/ doi: 10.1371/journal.pone.0189073 id: cord-308261-hxlebas8 author: Broekhuis, Femke title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya date: 2019-04-03 words: 4771.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-308261-hxlebas8.txt txt: ./txt/cord-308261-hxlebas8.txt summary: title: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: A case study of male cheetahs in the Maasai Mara, Kenya To determine the static interactions between male cheetahs we calculated their space use and the amount of overlap for each dyad to determine the possibility that individuals could encounter each other either directly or indirectly. In general, cheetahs were closer to the encounter location after a possible encounter compared to before for all four time lags, apart from individual M03 in Dyad 3 where the opposite trend was Intraspecific interactions among carnivores: A case study of male cheetahs observed, however none of the results were significant (S1 Table) . Using GPS collar data we documented static and dynamic interactions between male cheetahs in Kenya''s Maasai Mara and investigated the outcomes of these interactions in terms of movement behaviour and mortalities. abstract: Intraspecific interactions between individuals or groups of individuals of the same species are an important component of population dynamics. Interactions can be static, such as spatial overlap, or dynamic based on the interactions of movements, and can be mediated through communication, such as the deployment of scent marks. Interactions and their behavioural outcomes can be difficult to determine, especially for species that live at low densities. With the use of GPS collars we quantify both static and dynamic interactions between male cheetahs (Acinonyx jubatus) and the behavioural outcomes. The 99% home-ranges of males overlapped significantly while there was little overlap of the 50% home-ranges. Despite this overlap, male cheetahs rarely came into close proximity of one another, possibly because presence was communicated through frequent visits to marking posts. The minimum distance between individuals in a dyad ranged from 89m to 196m but the average proximity between individuals ranged from 17,145 ± 6,865m to 26,367 ± 11,288m. Possible interactions took place more frequently at night than by day and occurred mostly in the 50% home-range of one individual of a dyad or where cores of both individuals overlapped. After a possible encounter male cheetahs stayed in close proximity to each other for up to 6 hours, which could be the result of a territory defence strategy or the presence of a receptive female. We believe that one of the encounters between a singleton and a 5-male coalition resulted in the death of the singleton. Our results give new insights into cheetah interactions, which could help our understanding of ecological processes such as disease transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/30943236/ doi: 10.1371/journal.pone.0213910 id: cord-326568-twv2i3fb author: Bruminhent, Jackrapong title: Clinical characteristics and risk factors for coronavirus disease 2019 (COVID-19) among patients under investigation in Thailand date: 2020-09-15 words: 4402.0 sentences: 245.0 pages: flesch: 48.0 cache: ./cache/cord-326568-twv2i3fb.txt txt: ./txt/cord-326568-twv2i3fb.txt summary: To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians'' diagnoses. Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. Apart from close contact with an infected case and visiting high-risk places, we found that having no medical coverage and presenting with productive cough were predictors of being diagnosed with COVID-19 among PUIs. SARS-CoV-2 is an emerging respiratory virus that commonly causes no or mild respiratory tract infection and is occasionally complicated by severe pneumonia [1] . abstract: To manage coronavirus disease 2019 (COVID-19), a national health authority has implemented a case definition of patients under investigation (PUIs) to guide clinicians’ diagnoses. We aimed to determine characteristics among all PUIs and those with and without COVID-19. We retrospectively reviewed clinical characteristics and risk factors for laboratory-confirmed COVID-19 cases among PUIs at a tertiary care center in Bangkok, Thailand, between March 23 and April 7, 2020. Reverse transcription-polymerase chain reaction for SARS-CoV-2 RNA was performed. There were 405 evaluable PUIs; 157 (38.8%) were men, with a mean age ± SD of 36.2 ± 12.6 years. The majority (68.9%) reported no comorbidities. There were 53 (13.1%) confirmed COVID-19 cases. The most common symptoms among those were cough (73.6%), fever (58.5%), sore throat (39.6%), and muscle pain (37.4%). Among these patients, diagnoses were upper respiratory tract infection (69.8%), viral syndrome (15.1%), pneumonia (11.3%), and asymptomatic infection (3.8%). Multivariate analysis identified close contact with an index case (OR, 3.49; 95%CI, 1.49–8.15; P = 0.004), visiting high-risk places (OR, 1.92; 95%CI, 1.03–3.56; P = 0.039), productive cough (OR, 2.03; 95%CI, 1.05–3.92; P = 0.034), and no medical coverage (OR, 3.91; 95%CI, 1.35–11.32; P = 0.012) as independent risk factors for COVID-19 among the PUIs. The majority had favorable outcomes, though one (1.9%) died from severe pneumonia. COVID-19 was identified in 13% of PUIs defined per a national health authority’s case definition. History of contact with a COVID-19 patient, visiting a high-risk place, having no medical coverage, and productive cough may identify individuals at risk of COVID-19 in Thailand. url: https://www.ncbi.nlm.nih.gov/pubmed/32931517/ doi: 10.1371/journal.pone.0239250 id: cord-329999-flzqm3wh author: Buchanan, Tom title: Why do people spread false information online? The effects of message and viewer characteristics on self-reported likelihood of sharing social media disinformation date: 2020-10-07 words: 13812.0 sentences: 728.0 pages: flesch: 50.0 cache: ./cache/cord-329999-flzqm3wh.txt txt: ./txt/cord-329999-flzqm3wh.txt summary: Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Descriptive statistics for participant characteristics (personality, conservatism, new media literacy and age) and their reactions to the stimuli (likelihood of sharing, belief the stories were likely to be true, and rating of likelihood that they had seen them before) are summarised in Table 2 . This evaluated the extent to which digital media literacy (NMLS), authority of the message source, consensus, belief in veracity of the messages, consistency with participant beliefs (operationalised as the total SECS conservatism scale score), age and personality (Extraversion, Conscientiousness, Agreeableness, Openness to Experience and Neuroticism), predicted self-rated likelihood of sharing the posts. abstract: Individuals who encounter false information on social media may actively spread it further, by sharing or otherwise engaging with it. Much of the spread of disinformation can thus be attributed to human action. Four studies (total N = 2,634) explored the effect of message attributes (authoritativeness of source, consensus indicators), viewer characteristics (digital literacy, personality, and demographic variables) and their interaction (consistency between message and recipient beliefs) on self-reported likelihood of spreading examples of disinformation. Participants also reported whether they had shared real-world disinformation in the past. Reported likelihood of sharing was not influenced by authoritativeness of the source of the material, nor indicators of how many other people had previously engaged with it. Participants’ level of digital literacy had little effect on their responses. The people reporting the greatest likelihood of sharing disinformation were those who thought it likely to be true, or who had pre-existing attitudes consistent with it. They were likely to have previous familiarity with the materials. Across the four studies, personality (lower Agreeableness and Conscientiousness, higher Extraversion and Neuroticism) and demographic variables (male gender, lower age and lower education) were weakly and inconsistently associated with self-reported likelihood of sharing. These findings have implications for strategies more or less likely to work in countering disinformation in social media. url: https://doi.org/10.1371/journal.pone.0239666 doi: 10.1371/journal.pone.0239666 id: cord-351185-3y3gou6v author: Buckles, Thomas C. title: Rapid exposure of macrophages to drugs resolves four classes of effects on the leading edge sensory pseudopod: Non-perturbing, adaptive, disruptive, and activating date: 2020-05-29 words: 10061.0 sentences: 465.0 pages: flesch: 45.0 cache: ./cache/cord-351185-3y3gou6v.txt txt: ./txt/cord-351185-3y3gou6v.txt summary: However, rapid drug addition to cultured macrophages revealed four distinct classes of effects on the leading edge pseudopod: (i) non-perturbing drug exposures yielded no detectable change in pseudopod morphology (acetylsalicylic acid, diclofenac); (ii) adaptive exposures yielded temporary collapse of the extended pseudopod and its signature PI(3,4,5)P(3) lipid signal followed by slow recovery of extended pseudopod morphology (ibuprofen, acetaminophen); (iii) disruptive exposures yielded long-term pseudopod collapse (Gö6976, wortmannin); and (iv) activating exposures yielded pseudopod expansion (PDGF). In contrast, ibuprofen and acetaminophen are classified as adaptive because rapid addition of either drug to polarized cells yields short-term collapse of the leading edge pseudopod and loss of the PIP 3 signal, followed by slow recovery. In contrast to the four therapeutic adaptive drugs, the two non-clinical control inhibitors wortmannin and Gö6976 are each known to directly inhibit key components of the leading edge positive feedback loop and rapid addition is observed herein to trigger long term collapse of the pseudopod with no detected recovery as previously observed [26, 30, [50] [51] [52] [53] [54] . abstract: Leukocyte migration is controlled by a membrane-based chemosensory pathway on the leading edge pseudopod that guides cell movement up attractant gradients during the innate immune and inflammatory responses. This study employed single cell and population imaging to investigate drug-induced perturbations of leading edge pseudopod morphology in cultured, polarized RAW macrophages. The drugs tested included representative therapeutics (acetylsalicylic acid, diclofenac, ibuprofen, acetaminophen) as well as control drugs (PDGF, Gö6976, wortmannin). Notably, slow addition of any of the four therapeutics to cultured macrophages, mimicking the slowly increasing plasma concentration reported for standard oral dosage in patients, yielded no detectable change in pseudopod morphology. This finding is consistent with the well established clinical safety of these drugs. However, rapid drug addition to cultured macrophages revealed four distinct classes of effects on the leading edge pseudopod: (i) non-perturbing drug exposures yielded no detectable change in pseudopod morphology (acetylsalicylic acid, diclofenac); (ii) adaptive exposures yielded temporary collapse of the extended pseudopod and its signature PI(3,4,5)P(3) lipid signal followed by slow recovery of extended pseudopod morphology (ibuprofen, acetaminophen); (iii) disruptive exposures yielded long-term pseudopod collapse (Gö6976, wortmannin); and (iv) activating exposures yielded pseudopod expansion (PDGF). The novel observation of adaptive exposures leads us to hypothesize that rapid addition of an adaptive drug overwhelms an intrinsic or extrinsic adaptation system yielding temporary collapse followed by adaptive recovery, while slow addition enables gradual adaptation to counteract the drug perturbation in real time. Overall, the results illustrate an approach that may help identify therapeutic drugs that temporarily inhibit the leading edge pseudopod during extreme inflammation events, and toxic drugs that yield long term inhibition of the pseudopod with negative consequences for innate immunity. Future studies are needed to elucidate the mechanisms of drug-induced pseudopod collapse, as well as the mechanisms of adaptation and recovery following some inhibitory drug exposures. url: https://doi.org/10.1371/journal.pone.0233012 doi: 10.1371/journal.pone.0233012 id: cord-324405-6uanhe2p author: Burke, Rachel M. title: Enhanced contact investigations for nine early travel-related cases of SARS-CoV-2 in the United States date: 2020-09-02 words: 6616.0 sentences: 242.0 pages: flesch: 41.0 cache: ./cache/cord-324405-6uanhe2p.txt txt: ./txt/cord-324405-6uanhe2p.txt summary: To interrupt transmission and facilitate early identification of secondary cases (i.e., transmissions of SARS-CoV-2 from the original travel-related case patient to a close contact), public health authorities at the state, county, and local levels, in consultation with subject-matter experts from the U.S. Centers for Disease Control and Prevention (CDC), mobilized rapidly to place the patients under appropriate isolation and identify contacts exposed to these patients. To understand the prevalence of asymptomatic or pre-symptomatic infection, a convenience sample of actively monitored close contacts was selected from whom to request respiratory (nasopharyngeal [NP] and oropharyngeal [OP]) samples outside of diagnostic specimen collection procedures (i.e., while contacts were asymptomatic or, in some cases, symptomatic with � 1 previous negative SARS-CoV-2 result); some sites were able to request at least one set of samples from all close contacts, but most sites targeted sample collection mainly to close contacts determined to have had high-risk exposures, such as household members and some healthcare personnel. abstract: Coronavirus disease 2019 (COVID-19), the respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. In response to the first cases identified in the United States, close contacts of confirmed COVID-19 cases were investigated to enable early identification and isolation of additional cases and to learn more about risk factors for transmission. Close contacts of nine early travel-related cases in the United States were identified and monitored daily for development of symptoms (active monitoring). Selected close contacts (including those with exposures categorized as higher risk) were targeted for collection of additional exposure information and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction at the Centers for Disease Control and Prevention. Four hundred four close contacts were actively monitored in the jurisdictions that managed the travel-related cases. Three hundred thirty-eight of the 404 close contacts provided at least basic exposure information, of whom 159 close contacts had ≥1 set of respiratory samples collected and tested. Across all actively monitored close contacts, two additional symptomatic COVID-19 cases (i.e., secondary cases) were identified; both secondary cases were in spouses of travel-associated case patients. When considering only household members, all of whom had ≥1 respiratory sample tested for SARS-CoV-2, the secondary attack rate (i.e., the number of secondary cases as a proportion of total close contacts) was 13% (95% CI: 4–38%). The results from these contact tracing investigations suggest that household members, especially significant others, of COVID-19 cases are at highest risk of becoming infected. The importance of personal protective equipment for healthcare workers is also underlined. Isolation of persons with COVID-19, in combination with quarantine of exposed close contacts and practice of everyday preventive behaviors, is important to mitigate spread of COVID-19. url: https://doi.org/10.1371/journal.pone.0238342 doi: 10.1371/journal.pone.0238342 id: cord-001213-gxqufddb author: Butt, Azeem Mehmood title: Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses date: 2014-03-04 words: 7178.0 sentences: 371.0 pages: flesch: 54.0 cache: ./cache/cord-001213-gxqufddb.txt txt: ./txt/cord-001213-gxqufddb.txt summary: Therefore, from the similarity index analysis, we observed that selection pressure from hosts and vectors have contributed to shaping the molecular evolution of CHIKV at the respectively, on the formation of the overall codon usage patterns of CHIKV (Figure 2 ). Although, the nucleotide composition correlation analysis showed that codon usage in CHIKV genomes is mainly caused by compositional constraints or mutational pressure, we were interested to determine the possible influence of other factors, such as natural selection. However, in case of CHIKV genomes, variations in nucleotide base compositions were noted (Table 1 ), indicating that other factors, such as natural selection, could also influence overall synonymous codon usage bias. The RSCU values for all the coding sequences of CHIKV genomes were calculated to determine the characteristics of synonymous codon usage without the confounding influence of amino acid composition and the size of coding sequence of different gene samples, following a previously described method [18] . abstract: Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942501/ doi: 10.1371/journal.pone.0090905 id: cord-323133-gdg50omp author: Buzatto, G. P. title: The pathogens profile in children with otitis media with effusion and adenoid hypertrophy date: 2017-02-23 words: 4243.0 sentences: 209.0 pages: flesch: 45.0 cache: ./cache/cord-323133-gdg50omp.txt txt: ./txt/cord-323133-gdg50omp.txt summary: OBJECTIVES: To evaluate the presence of viruses and bacteria in middle ear and adenoids of patients with and without otitis media with effusion (OME). METHODS: Adenoid samples and middle ear washes (MEW) were obtained from children with OME associated with adenoid hypertrophy undergoing adenoidectomy and tympanostomy, and compared to those obtained from patients undergoing cochlear implant surgery, as a control group. Therefore, the present study was carried out to compare the detection of common respiratory viruses and bacteria in adenoids and middle ear fluid in children with OME and in controls. In our study, we used a sensitive method to detect nucleic acid of a comprehensive panel of respiratory viruses and bacteria to compare the microbial colonization of adenoid and its correspondence in the middle ear in both OME children and controls. Concluding, in children with OME and adenoid hypertrophy we observed higher detection rates of potentially pathogenic bacteria, but not respiratory viruses, by real-time PCR in middle ear samples, as compared to control patients without adenoid hypertrophy. abstract: OBJECTIVES: To evaluate the presence of viruses and bacteria in middle ear and adenoids of patients with and without otitis media with effusion (OME). METHODS: Adenoid samples and middle ear washes (MEW) were obtained from children with OME associated with adenoid hypertrophy undergoing adenoidectomy and tympanostomy, and compared to those obtained from patients undergoing cochlear implant surgery, as a control group. Specific DNA or RNA of 9 respiratory viruses (rhinovirus, influenza virus, picornavirus, syncytial respiratory virus, metapneumovirus, coronavirus, enterovirus, adenovirus and bocavirus) and 5 bacteria (S. pneumoniae, H. influenzae, M. catarrhalis, P. aeruginosa and S. aureus) were extracted and quantified by real-time PCR. RESULTS: 37 OME and 14 cochlear implant children were included in the study. At the adenoid, virus and bacteria were similarly detected in both OME and control patients. At the middle ear washes, however, a higher prevalence of bacteria was observed in patients with OME (p = 0.01). S. pneumoniae (p = 0.01) and M. catarrhalis (p = 0.022) were the bacteria responsible for this difference. Although total virus detection was not statistically different from controls at the middle ear washes (p = 0.065), adenovirus was detected in higher proportions in adenoid samples of OME patients than controls (p = 0.019). CONCLUSIONS: Despite both OME and control patients presented similar rates of viruses and bacteria at the adenoid, children with OME presented higher prevalence of S. pneumonia, M. catarrhalis in middle ear and adenovirus in adenoids when compared to controls. These findings could suggest that these pathogens could contribute to the fluid persistence in the middle ear. url: https://doi.org/10.1371/journal.pone.0171049 doi: 10.1371/journal.pone.0171049 id: cord-001909-yy9xp5ms author: Buß, O. title: Statistical Evaluation of HTS Assays for Enzymatic Hydrolysis of β-Keto Esters date: 2016-01-05 words: 6998.0 sentences: 414.0 pages: flesch: 49.0 cache: ./cache/cord-001909-yy9xp5ms.txt txt: ./txt/cord-001909-yy9xp5ms.txt summary: Two of the tested high throughput screening (HTS) assays depend on coupled enzymatic reactions which detect the alcohol released during ester hydrolysis by luminescence or absorption. The objective of this study is to select an HTS assay to screen for one enzyme for a two-step reaction cascade for the synthesis of β-amino acids. One assay relies on the change of the pH-value, the second is based on enzymatic oxidation of the released ethanol to acetic acid and the third, which we expected to be most sensitive, is based on the oxidation of ethanol to ethanal and hydrogen peroxide which is then converted by horseradish peroxidase (HRP) in a luminescence reaction. According to the other assays a positive control for the evaluation test contained only 2.0 mM ethanol without ester and hydrolase (see also subsection statistical analysis). abstract: β-keto esters are used as precursors for the synthesis of β-amino acids, which are building blocks for some classes of pharmaceuticals. Here we describe the comparison of screening procedures for hydrolases to be used for the hydrolysis of β-keto esters, the first step in the preparation of β-amino acids. Two of the tested high throughput screening (HTS) assays depend on coupled enzymatic reactions which detect the alcohol released during ester hydrolysis by luminescence or absorption. The third assay detects the pH shift due to acid formation using an indicator dye. To choose the most efficient approach for screening, we assessed these assays with different statistical methods—namely, the classical Z’-factor, standardized mean difference (SSMD), the Kolmogorov-Smirnov-test, and t-statistics. This revealed that all three assays are suitable for HTS, the pH assay performing best. Based on our data we discuss the explanatory power of different statistical measures. Finally, we successfully employed the pH assay to identify a very fast hydrolase in an enzyme-substrate screening. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711668/ doi: 10.1371/journal.pone.0146104 id: cord-000981-6vloa2w3 author: Bálint, Zoltán title: Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells date: 2013-06-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Circulating RNA may result from excessive cell damage or acute viral infection and can interact with vascular endothelial cells. Despite the obvious clinical implications associated with the presence of circulating RNA, its pathological effects on endothelial cells and the governing molecular mechanisms are still not fully elucidated. We analyzed the effects of double stranded RNA on primary human pulmonary artery endothelial cells (hPAECs). The effect of natural and synthetic double-stranded RNA (dsRNA) on hPAECs was investigated using trans-endothelial electric resistance, molecule trafficking, calcium (Ca(2+)) homeostasis, gene expression and proliferation studies. Furthermore, the morphology and mechanical changes of the cells caused by synthetic dsRNA was followed by in-situ atomic force microscopy, by vascular-endothelial cadherin and F-actin staining. Our results indicated that exposure of hPAECs to synthetic dsRNA led to functional deficits. This was reflected by morphological and mechanical changes and an increase in the permeability of the endothelial monolayer. hPAECs treated with synthetic dsRNA accumulated in the G1 phase of the cell cycle. Additionally, the proliferation rate of the cells in the presence of synthetic dsRNA was significantly decreased. Furthermore, we found that natural and synthetic dsRNA modulated Ca(2+) signaling in hPAECs by inhibiting the sarco-endoplasmic Ca(2+)-ATPase (SERCA) which is involved in the regulation of the intracellular Ca(2+) homeostasis and thus cell growth. Even upon synthetic dsRNA stimulation silencing of SERCA3 preserved the endothelial monolayer integrity. Our data identify novel mechanisms by which dsRNA can disrupt endothelial barrier function and these may be relevant in inflammatory processes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670875/ doi: 10.1371/journal.pone.0063776 id: cord-270681-6ayciihs author: Bálint, Ádám title: Comparative In Vivo Analysis of Recombinant Type II Feline Coronaviruses with Truncated and Completed ORF3 Region date: 2014-02-20 words: 4679.0 sentences: 230.0 pages: flesch: 49.0 cache: ./cache/cord-270681-6ayciihs.txt txt: ./txt/cord-270681-6ayciihs.txt summary: Our previous in vitro comparative study on a feline coronavirus (FCoV) pair, differing only in the intactness of their ORF3abc regions, showed that the truncated ORF3abc plays an important role in the efficient macrophage/monocyte tropism of type II feline infectious peritonitis virus (FIPV). In the present study using the parent FIPV DF-2 strain and its recombinant derivates we aimed to collect in vivo data how the completed ORF3abc alters virulence, virus shedding, viremia, viral load of organs and humoral immune response against type II FCoV. Shedding of FIPV DF-2 and PBFIPV-DF-2 was detected from day 3 p.i. to euthanasia of the PIP diseased animals at very low and variable amounts of an average value close to the detection limit of the genomic qRT-PCR (1.9610 1 FCoV RNA copies per ml fecal extract) ( Fig. 1) with undetectable virus replication using the subgenomic qRT-PCR assay (data not shown). abstract: Our previous in vitro comparative study on a feline coronavirus (FCoV) pair, differing only in the intactness of their ORF3abc regions, showed that the truncated ORF3abc plays an important role in the efficient macrophage/monocyte tropism of type II feline infectious peritonitis virus (FIPV). In the present study, we describe a challenge experiment with the same recombinant FCoVs in order to gain data on the in vivo characteristics on these viruses. While parent virus FIPV DF-2 developed feline infectious peritonitis in all the infected cats, its recombinant virus PBFIPV-DF-2, differing only in seven nucleotides, proved to be surprisingly low virulent, although caused an acute febrile episode similarly to the original FIPV DF-2. PBFIPV-DF-2 infection induced significantly lower virus neutralization titers than its parent virus, and lacked the second phase of viremia and development of fatal course of the disease. The recombinant PBFIPV-DF-2-R3i with completed ORF3abc gained biological properties that differentiate between the feline enteric coronavirus (FECV) and FIPV biotypes such as intensive replication in the gut, absence of viremia and weak or no serological response. Using reverse genetic approaches our study is the first experimental proof that ORF3abc is indeed responsible for the restriction of FECV replication to the intestine in vivo. url: https://doi.org/10.1371/journal.pone.0088758 doi: 10.1371/journal.pone.0088758 id: cord-353596-8iqjugcx author: Bédubourg, Gabriel title: Evaluation and comparison of statistical methods for early temporal detection of outbreaks: A simulation-based study date: 2017-07-17 words: 5603.0 sentences: 313.0 pages: flesch: 53.0 cache: ./cache/cord-353596-8iqjugcx.txt txt: ./txt/cord-353596-8iqjugcx.txt summary: Based on a large dataset of simulated weekly surveillance time series, we performed a systematic assessment of 21 statistical algorithms, 19 implemented in the R package surveillance and two other methods. We estimated false positive rate (FPR), probability of detection (POD), probability of detection during the first week, sensitivity, specificity, negative and positive predictive values and F(1)-measure for each detection method. Then, to identify the factors associated with these performance measures, we ran multivariate Poisson regression models adjusted for the characteristics of the simulated time series (trend, seasonality, dispersion, outbreak sizes, etc.). The objective of this paper is to evaluate the performance of 21 statistical methods applied to large simulated datasets for outbreak detection in weekly health surveillance. Table 2 presents averaged FPR, specificity, POD, POD1week, sensitivity, negative predictive value, positive predictive value and F 1 -measure for all 42 scenarios and all past and current outbreak amplitude and duration and for α = 0.01. abstract: The objective of this paper is to evaluate a panel of statistical algorithms for temporal outbreak detection. Based on a large dataset of simulated weekly surveillance time series, we performed a systematic assessment of 21 statistical algorithms, 19 implemented in the R package surveillance and two other methods. We estimated false positive rate (FPR), probability of detection (POD), probability of detection during the first week, sensitivity, specificity, negative and positive predictive values and F(1)-measure for each detection method. Then, to identify the factors associated with these performance measures, we ran multivariate Poisson regression models adjusted for the characteristics of the simulated time series (trend, seasonality, dispersion, outbreak sizes, etc.). The FPR ranged from 0.7% to 59.9% and the POD from 43.3% to 88.7%. Some methods had a very high specificity, up to 99.4%, but a low sensitivity. Methods with a high sensitivity (up to 79.5%) had a low specificity. All methods had a high negative predictive value, over 94%, while positive predictive values ranged from 6.5% to 68.4%. Multivariate Poisson regression models showed that performance measures were strongly influenced by the characteristics of time series. Past or current outbreak size and duration strongly influenced detection performances. url: https://www.ncbi.nlm.nih.gov/pubmed/28715489/ doi: 10.1371/journal.pone.0181227 id: cord-305547-e66o5j85 author: Bénet, Thomas title: Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study date: 2015-12-22 words: 4161.0 sentences: 227.0 pages: flesch: 43.0 cache: ./cache/cord-305547-e66o5j85.txt txt: ./txt/cord-305547-e66o5j85.txt summary: title: Etiology and Factors Associated with Pneumonia in Children under 5 Years of Age in Mali: A Prospective Case-Control Study pneumoniae (adjusted odds ratio [aOR] = 3.4, 95% confidence interval [95% CI]: 1.6–7.0), human metapneumovirus (aOR = 17.2, 95% CI: 2.0–151.4), respiratory syncytial virus [RSV] (aOR = 7.4, 95% CI: 2.3–23.3), and influenza A virus (aOR = 10.7, 95% CI: 1.0–112.2) were associated with pneumonia, independently of patient age, gender, period, and other pathogens. The primary objective of this prospective case-control study was to assess the etiology and factors associated with community-acquired pneumonia in hospitalized children in Mali. pneumoniae, human metapneumovirus, RSV, and influenza A were the main microbial agents associated with pneumonia among children in Mali, independently of patient age, gender, period, and other pathogens. recently observed, in a pneumonia cases-control study implemented in hospitals of Utah, that detection respiratory syncytial virus, human metapneumovirus and influenza from nasopharyngeal or oropharyngeal sample of patients with pneumonia probably indicates an etiologic role [24] . abstract: BACKGROUND: There are very limited data on children with pneumonia in Mali. The objective was to assess the etiology and factors associated with community-acquired pneumonia in hospitalized children <5 years of age in Mali. METHODS: A prospective hospital-based case-control study was implemented in the Pediatric department of Gabriel Touré University Hospital at Bamako, Mali, between July 2011-December 2012. Cases were children with radiologically-confirmed pneumonia; Controls were hospitalized children without respiratory features, matched for age and period. Respiratory specimens, were collected to identify 19 viruses and 5 bacteria. Whole blood was collected from cases only. Factors associated with pneumonia were assessed by multivariate logistic regression. RESULTS: Overall, 118 cases and 98 controls were analyzed; 44.1% were female, median age was 11 months. Among pneumonia cases, 30.5% were hypoxemic at admission, mortality was 4.2%. Pneumonia cases differed from the controls regarding clinical signs and symptoms but not in terms of past medical history. Multivariate analysis of nasal swab findings disclosed that S. pneumoniae (adjusted odds ratio [aOR] = 3.4, 95% confidence interval [95% CI]: 1.6–7.0), human metapneumovirus (aOR = 17.2, 95% CI: 2.0–151.4), respiratory syncytial virus [RSV] (aOR = 7.4, 95% CI: 2.3–23.3), and influenza A virus (aOR = 10.7, 95% CI: 1.0–112.2) were associated with pneumonia, independently of patient age, gender, period, and other pathogens. Distribution of S. pneumoniae and RSV differed by season with higher rates of S. pneumoniae in January-June and of RSV in July-September. Pneumococcal serotypes 1 and 5 were more frequent in pneumonia cases than in the controls (P = 0.009, and P = 0.04, respectively). CONCLUSIONS: In this non-PCV population from Mali, pneumonia in children was mainly attributed to S. pneumoniae, RSV, human metapneumovirus, and influenza A virus. Increased pneumococcal conjugate vaccine coverage in children could significantly reduce the burden of pneumonia in sub-Saharan African countries. url: https://doi.org/10.1371/journal.pone.0145447 doi: 10.1371/journal.pone.0145447 id: cord-290539-8ak2tths author: Cagno, Valeria title: Novel broad spectrum virucidal molecules against enveloped viruses date: 2018-12-07 words: 5524.0 sentences: 276.0 pages: flesch: 51.0 cache: ./cache/cord-290539-8ak2tths.txt txt: ./txt/cord-290539-8ak2tths.txt summary: To further elucidate the mechanism of action we performed a virucidal assay in which 9d was incubated with the virus at 10 μM 5μM or 1μM concentration for different times (Fig 6A) or for 1h with serial dilutions of compound ( Fig 6B) ; subsequently, the mixture was titrated on cells and the viral titer was evaluated at dilutions at which the compound concentration was known not to be active in plaquing efficiency assays. The irreversibility of the mechanism was also tested with an assay in which the compound was incubated with the virus for 1h and subsequently the mixture has been diluted in drug free medium for additional 1, 2, 3 or 4 hours before the addition on cells (S2 Fig) . abstract: Viral infections are an important cause of death worldwide. Unfortunately, there is still a lack of antiviral drugs or vaccines for a large number of viruses, and this represents a remarkable challenge particularly for emerging and re-emerging viruses. For this reason, the identification of broad spectrum antiviral compounds provides a valuable opportunity for developing efficient antiviral therapies. Here we report on a class of rhodanine and thiobarbituric derivatives displaying a broad spectrum antiviral activity against seven different enveloped viruses including an HSV-2 acyclovir resistant strain with favorable selectivity indexes. Due to their selective action on enveloped viruses and to their lipid oxidation ability, we hypothesize a mechanism on the viral envelope that affects the fluidity of the lipid bilayer, thus compromising the efficiency of virus-cell fusion and preventing viral entry. url: https://doi.org/10.1371/journal.pone.0208333 doi: 10.1371/journal.pone.0208333 id: cord-003548-zuwt7gk5 author: Cai, Haiming title: Modulating the 3’ end-DNA and the fermentation process for enhanced production and biological activity of porcine interferon-gamma date: 2019-03-26 words: 6848.0 sentences: 447.0 pages: flesch: 56.0 cache: ./cache/cord-003548-zuwt7gk5.txt txt: ./txt/cord-003548-zuwt7gk5.txt summary: In this study, we optimized the pIFN-γ gene recombination sequence and mutated the 3'' end of the pIFN-γ gene, resulting in a higher expression level and stronger biological activity, as well as a significant upregulation in the expression of the interferon-stimulated genes Mx1 and OAS1 in IPEC-J2 jejunal epithelial cells. These data demonstrated, for the first time, that the expression level of pIFN-γ in Pichia pastoris was improved significantly by gene optimization with 3'' end mutation and a fermentation process that maintained good biological activity, which is beneficial to the application of pIFN-γ in animal husbandry. The expression of pIFN-γ protein was maximal when the concentration of DO in the substrate was 30%, especially for the recombinant Pichia pastoris with the optimized pIFN-γ gene and the 3'' signaling peptide mutation, which had significantly higher expression than that of the other treatment groups (p<0.05). abstract: Porcine gamma interferon is a cytokine produced by activated T cells and NK cells with broad-spectrum antiviral activity and immunomodulatory function. However, pIFN-γ is a secretory protein that has a short half-life in organisms and is easily inactivated, making it difficult to apply widely in clinics. Therefore, we tried to optimize the expression of pIFN-γ in Pichia pastoris to obtain a large amount of highly active, easily purified pIFN-γ protein in vitro. Through C-terminal sequence analysis, we found a signal sequence (EKREAEAE) that was easily enzymolysed by a signal peptide enzyme, resulting in degradation and inactivation of the pIFN-γ protein. In this study, we optimized the pIFN-γ gene recombination sequence and mutated the 3' end of the pIFN-γ gene, resulting in a higher expression level and stronger biological activity, as well as a significant upregulation in the expression of the interferon-stimulated genes Mx1 and OAS1 in IPEC-J2 jejunal epithelial cells. Our data also showed that the fermentation process could significantly improve productivity. A recombinant Pichia pastoris strain with the optimized pIFN-γ gene could obtain a high yield of pIFN-γ protein, up to 9536 mg/L, after staged incubation for 0–24 h at 28°C, pH 6.0, and 50% dissolved oxygen (DO), followed by incubation for 24–72 h at 25°C, pH 6.0 and 30% DO. These data demonstrated, for the first time, that the expression level of pIFN-γ in Pichia pastoris was improved significantly by gene optimization with 3' end mutation and a fermentation process that maintained good biological activity, which is beneficial to the application of pIFN-γ in animal husbandry. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435167/ doi: 10.1371/journal.pone.0214319 id: cord-048339-nzh87aux author: Caley, Peter title: The Waiting Time for Inter-Country Spread of Pandemic Influenza date: 2007-01-03 words: 5739.0 sentences: 253.0 pages: flesch: 45.0 cache: ./cache/cord-048339-nzh87aux.txt txt: ./txt/cord-048339-nzh87aux.txt summary: On the other hand, the model predicts that border screening for symptomatic infection, wearing a protective mask during travel, promoting early presentation of cases arising among arriving passengers and moderate reduction in travel volumes increase the delay only by a matter of days or weeks. In this paper we demonstrate how the delay to importation of an epidemic of pandemic strain influenza may be quantified in terms of the growing infection incidence in the source region, traveler volumes, border screening measures, travel duration, inflight transmission and the delay until an infected arrival initiates a chain of transmission that gathers momentum. For example, if R = 1.5, and we reduce the number of intending travelers from 400 to 10 per day, implement 100% flight-based quarantining, implement compulsory mask wearing during travel and presentation at 6 hours following symptom onset then there is a substantial probability (0.74) that the pandemic strain will never be imported (assuming the epidemic is confined to the source country). abstract: BACKGROUND: The time delay between the start of an influenza pandemic and its subsequent initiation in other countries is highly relevant to preparedness planning. We quantify the distribution of this random time in terms of the separate components of this delay, and assess how the delay may be extended by non-pharmaceutical interventions. METHODS AND FINDINGS: The model constructed for this time delay accounts for: (i) epidemic growth in the source region, (ii) the delay until an infected individual from the source region seeks to travel to an at-risk country, (iii) the chance that infected travelers are detected by screening at exit and entry borders, (iv) the possibility of in-flight transmission, (v) the chance that an infected arrival might not initiate an epidemic, and (vi) the delay until infection in the at-risk country gathers momentum. Efforts that reduce the disease reproduction number in the source region below two and severe travel restrictions are most effective for delaying a local epidemic, and under favourable circumstances, could add several months to the delay. On the other hand, the model predicts that border screening for symptomatic infection, wearing a protective mask during travel, promoting early presentation of cases arising among arriving passengers and moderate reduction in travel volumes increase the delay only by a matter of days or weeks. Elevated in-flight transmission reduces the delay only minimally. CONCLUSIONS: The delay until an epidemic of pandemic strain influenza is imported into an at-risk country is largely determined by the course of the epidemic in the source region and the number of travelers attempting to enter the at-risk country, and is little affected by non-pharmaceutical interventions targeting these travelers. Short of preventing international travel altogether, eradicating a nascent pandemic in the source region appears to be the only reliable method of preventing country-to-country spread of a pandemic strain of influenza. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764036/ doi: 10.1371/journal.pone.0000143 id: cord-305071-4ck8nd24 author: Calvo, Cristina title: Eight Year Prospective Study of Adenoviruses Infections in Hospitalized Children. Comparison with Other Respiratory Viruses date: 2015-07-06 words: 3527.0 sentences: 205.0 pages: flesch: 49.0 cache: ./cache/cord-305071-4ck8nd24.txt txt: ./txt/cord-305071-4ck8nd24.txt summary: Human adenovirus (HAdV), a double-stranded DNA virus, causes a wide range of clinical syndromes and is a well-recognized agent of upper and lower respiratory infections in children [1, 2] . Although the literature on adenoviral infections in children is increasing, there are few prospective, long term studies, designed specifically to evaluate the role of HAdV in acute respiratory infections requiring hospitalization. Patients with influenza have fever more frequently (p = 0.028) and have a lower leukocytes count in blood (p<0.001), than children infected by HAdV. HAdV frequently (11% of cases) caused lengthy hospitalizations (more than 7 days) 21% of the single infections were diagnosed with pneumonia. Jin et al [13] , in China, describe similar findings, that children with RSV are younger than patients with HAdV, and have lower respiratory tract infections such as bronchiolitis and bronchitis more frequently. abstract: Human adenovirus (HAdV) cause upper and lower respiratory tract infections. However, there are few large prospective studies focused on HAdVs acute infections requiring hospitalization. From 2005 to 2013 a prospective study was conducted on children admitted with acute respiratory infections. Specimens of nasopharyngeal aspirate were taken for virological study by PCR and clinical data was recorded. HAdV specimens were genotyped. Frequency and clinical course of HAdV infections were compared with RSV, rhinovirus (RV), human bocavirus (HBoV) and influenza in the same population. HAdV was detected in 403 cases of 2371 confirmed viral infections (17.2%) , of which 154 were single virus infections (38%). We genotyped 154 HAdVs. The most frequent genotypes were HAdV-3 (24%), HAdV-6 (21%), and HAdV-5 (20%). A total of 262 children had fever (64.9%); 194 suffered hypoxia (48%), and 147 presented infiltrate in chest x-rays (36.4%). The most frequent diagnoses were recurrent wheezing or asthma (51.7%), bronchiolitis (18.3 %), and pneumonia (11.9%), and 46 (11.4%) episodes required prolonged hospitalization (>7 days) due to the severity. Adenovirus single infections were compared with single infections of 598 RSV, 494 RV, 83 influenza and 78 HBoV. Significant clinical differences were found between HAdV, RSV and RV infections. url: https://doi.org/10.1371/journal.pone.0132162 doi: 10.1371/journal.pone.0132162 id: cord-292237-45hi4iz2 author: Calvo-Pinilla, Eva title: Establishment of a Bluetongue Virus Infection Model in Mice that Are Deficient in the Alpha/Beta Interferon Receptor date: 2009-04-09 words: 4735.0 sentences: 251.0 pages: flesch: 53.0 cache: ./cache/cord-292237-45hi4iz2.txt txt: ./txt/cord-292237-45hi4iz2.txt summary: Furthermore, IFNAR((−/−)) adult mice immunized with a BTV-4 inactivated vaccine showed the induction of neutralizing antibodies against BTV-4 and complete protection against challenge with a lethal dose of this virus. All these data, and the presence of an otherwise intact immune system in these mice [20, 22] suggest that IFNAR (2/2) mice could be a good animal model to study BTV infections and to evaluate vaccine strategies against this virus. By contrast, IFNAR (2/2) mice were susceptible to BTV-4 infection (Fig. 1A) , showing disease symptoms characterized by ocular discharges and apathy starting at 48 h.p.i. Disease progression led to animal death within 60 h.p.i. The LD 50 value was obtained by i.v. inoculation with 10-fold dilutions of BTV-4, resulting in a LD 50 value of 10 2.6 PFU (Fig. 1B) . Infectious viral titers were analyzed in the blood of immunized and nonimmunized IFNAR (2/2) mice by plaque assay after intravenous infection with BTV-4 (Fig. 5C ). abstract: Bluetongue (BT) is a noncontagious, insect-transmitted disease of ruminants caused by the bluetongue virus (BTV). A laboratory animal model would greatly facilitate the studies of pathogenesis, immune response and vaccination against BTV. Herein, we show that adult mice deficient in type I IFN receptor (IFNAR((−/−))) are highly susceptible to BTV-4 and BTV-8 infection when the virus is administered intravenously. Disease was characterized by ocular discharges and apathy, starting at 48 hours post-infection and quickly leading to animal death within 60 hours of inoculation. Infectious virus was recovered from the spleen, lung, thymus, and lymph nodes indicating a systemic infection. In addition, a lymphoid depletion in spleen, and severe pneumonia were observed in the infected mice. Furthermore, IFNAR((−/−)) adult mice immunized with a BTV-4 inactivated vaccine showed the induction of neutralizing antibodies against BTV-4 and complete protection against challenge with a lethal dose of this virus. The data indicate that this mouse model may facilitate the study of BTV pathogenesis, and the development of new effective vaccines for BTV. url: https://doi.org/10.1371/journal.pone.0005171 doi: 10.1371/journal.pone.0005171 id: cord-000352-qzkpik3z author: Carvalho, Gabrielle title: Participation of the Cell Polarity Protein PALS1 to T-Cell Receptor-Mediated NF-κB Activation date: 2011-03-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Beside their established function in shaping cell architecture, some cell polarity proteins were proposed to participate to lymphocyte migration, homing, scanning, as well as activation following antigen receptor stimulation. Although PALS1 is a central component of the cell polarity network, its expression and function in lymphocytes remains unknown. Here we investigated whether PALS1 is present in T cells and whether it contributes to T Cell-Receptor (TCR)-mediated activation. METHODOLOGY/PRINCIPAL FINDINGS: By combining RT-PCR and immunoblot assays, we found that PALS1 is constitutively expressed in human T lymphocytes as well as in Jurkat T cells. siRNA-based knockdown of PALS1 hampered TCR-induced activation and optimal proliferation of lymphocyte. We further provide evidence that PALS1 depletion selectively hindered TCR-driven activation of the transcription factor NF-κB. CONCLUSIONS: The cell polarity protein PALS1 is expressed in T lymphocytes and participates to the optimal activation of NF-κB following TCR stimulation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068181/ doi: 10.1371/journal.pone.0018159 id: cord-340703-vtuy806l author: Cascio, Antonio title: Low bone mineral density in HIV-positive young Italians and migrants date: 2020-09-03 words: 4488.0 sentences: 230.0 pages: flesch: 55.0 cache: ./cache/cord-340703-vtuy806l.txt txt: ./txt/cord-340703-vtuy806l.txt summary: We aimed to evaluate the bone mineral density (BMD) in naïve antiretroviral (ARV) treated HIV positive patients comparing native Italian group (ItG) to a Migrants group (MiG) upon arrival in Italy. Lumbar site low BMD is an initial condition of bone loss in HIV young patients, especially in female migrants. Our study aims to emphasize the burden of bone health in naïve ARV HIV positive patients and compare the bone density of the native Italian population group (ItG) with that of HIV Migrants (MiG) upon arrival in Italy. Finally, in Table 3 , we report the logistic regression analysis between Low BMD variable (dichotomous) and the independent variables: Gender (dichotomous), BMI (continuous), Hydroxy-Vitamin D (continuous), CD4 (continuous), and Previous Fractures (dichotomous) for the total sample, ItG, and MiG. Our previous reports [13, 14] on the prevalence of Low-BMD in HIV mono-infected patients who underwent ARV therapy showed higher percentage rates of osteopenia (44.9%) and osteoporosis (20.9%) than an agerelated healthy Italian population (18%) [16] . abstract: BACKGROUND: Human immunodeficiency virus (HIV) infected individuals may have osteoporosis. We aimed to evaluate the bone mineral density (BMD) in naïve antiretroviral (ARV) treated HIV positive patients comparing native Italian group (ItG) to a Migrants group (MiG) upon arrival in Italy. METHODS: We conducted a cross-sectional study on 83 HIV patients less than 50 years old. We used the dual-energy X-ray absorptiometry (DXA) within six months from the HIV diagnosis. Participants were categorized as having low BMD if the femoral neck or total lumbar spine Z-score was– 2 or less. RESULTS: MiG showed low BMD more often than ItG (37.5% vs.13.6%), especially for the female gender (16.7% vs. 0.0%). A low CD4 rate (<200 cells/μl) was most often detected in MiG than ItG. In particular, we found most often male Italians with abnormal CD4 than male migrants (67.8% vs. 33.3%) and vice versa for females (30.5% vs. 66.7%). We found an abnormal bone mineral density at the lumbar site. Low BMD at the lumbar site was more frequently observed in female migrants than female Italians. Both male and female migrants had a Z-score value significantly lower than male and female Italians, respectively. By logistic regression low vitamin-D level was positively correlated to low BMD in ItG only. All data were verified and validated using a triple code identifier. CONCLUSIONS: Both DXA and vitamin-D evaluation should be offered after the diagnosis of HIV infection. Lumbar site low BMD is an initial condition of bone loss in HIV young patients, especially in female migrants. Vitamin D levels and supplementation may be considered after HIV diagnosis independently of age to improve bone health. HIGHLIGHTS: This study evaluates the frequency of bone mineral density in HIV positive patients naive to antiretroviral therapy. It compares the density of the native Italian population with that of HIV Migrants upon arrival in Italy. The results show that HIV positive migrants, even if younger than 50 years of age, are at risk for osteoporosis, especially if they are female. url: https://doi.org/10.1371/journal.pone.0237984 doi: 10.1371/journal.pone.0237984 id: cord-048358-z5klydpi author: Catic, André title: Screen for ISG15-crossreactive Deubiquitinases date: 2007-07-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The family of ubiquitin-like molecules (UbLs) comprises several members, each of which has sequence, structural, or functional similarity to ubiquitin. ISG15 is a homolog of ubiquitin in vertebrates and is strongly upregulated following induction by type I interferon. ISG15 can be covalently attached to proteins, analogous to ubiquitination and with actual support of ubiquitin conjugating factors. Specific proteases are able to reverse modification with ubiquitin or UbLs by hydrolyzing the covalent bond between their C-termini and substrate proteins. The tail regions of ubiquitin and ISG15 are identical and we therefore hypothesized that promiscuous deubiquitinating proteases (DUBs) might exist, capable of recognizing both ubiquitin and ISG15. RESULTS: We have cloned and expressed 22 human DUBs, representing the major clades of the USP protease family. Utilizing suicide inhibitors based on ubiquitin and ISG15, we have identified USP2, USP5 (IsoT1), USP13 (IsoT3), and USP14 as ISG15-reactive proteases, in addition to the bona fide ISG15-specific protease USP18 (UBP43). USP14 is a proteasome-associated DUB, and its ISG15 isopeptidase activity increases when complexed with the proteasome. CONCLUSIONS: By evolutionary standards, ISG15 is a newcomer among the UbLs and it apparently not only utilizes the conjugating but also the deconjugating machinery of its more established relative ubiquitin. Functional overlap between these two posttranslational modifiers might therefore be more extensive than previously appreciated and explain the rather innocuous phenotype of ISG15 null mice. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1919423/ doi: 10.1371/journal.pone.0000679 id: cord-281364-syg0wo77 author: Caì, Yíngyún title: CD26/DPP4 Cell-Surface Expression in Bat Cells Correlates with Bat Cell Susceptibility to Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection and Evolution of Persistent Infection date: 2014-11-19 words: 3827.0 sentences: 178.0 pages: flesch: 49.0 cache: ./cache/cord-281364-syg0wo77.txt txt: ./txt/cord-281364-syg0wo77.txt summary: title: CD26/DPP4 Cell-Surface Expression in Bat Cells Correlates with Bat Cell Susceptibility to Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Infection and Evolution of Persistent Infection We found that the susceptibility or resistance of these bat cell lines directly correlates with the presence or absence of cell surface-expressed CD26/DPP4, the functional human receptor for MERS-CoV. Finally, we demonstrate that persistent MERS-CoV infections can be established in permissive bat cell lines after sequential virus passage, leading to downregulation of natural CD26/DPP4 cellsurface expression. None of the four MERS-CoV-resistant cell lines tested in this study (PESU-B5L, R05T, R06E, and Tb1Lu) were recognized by anti-human CD26/DPP4 antibody in this assay, whereas all susceptible bat cells (EidNi/41.3, EpoNi/22.1, HypLu/45.1, HypNi/1.1, RoNi/7.1, and RoNi/7.2) tested positive for CD26/DPP4 expression (Figure 2 ). Our study confirms the role of CD26/DPP4 as receptor for two divergent MERS-CoV isolates and correlates its presence or absence on the surface of bat cells directly with bat cell susceptibility or resistance to productive MERS-CoV infection (Figures 2 and 3 ). abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently isolated betacoronavirus identified as the etiologic agent of a frequently fatal disease in Western Asia, Middle East respiratory syndrome. Attempts to identify the natural reservoirs of MERS-CoV have focused in part on dromedaries. Bats are also suspected to be reservoirs based on frequent detection of other betacoronaviruses in these mammals. For this study, ten distinct cell lines derived from bats of divergent species were exposed to MERS-CoV. Plaque assays, immunofluorescence assays, and transmission electron microscopy confirmed that six bat cell lines can be productively infected. We found that the susceptibility or resistance of these bat cell lines directly correlates with the presence or absence of cell surface-expressed CD26/DPP4, the functional human receptor for MERS-CoV. Human anti-CD26/DPP4 antibodies inhibited infection of susceptible bat cells in a dose-dependent manner. Overexpression of human CD26/DPP4 receptor conferred MERS-CoV susceptibility to resistant bat cell lines. Finally, sequential passage of MERS-CoV in permissive bat cells established persistent infection with concomitant downregulation of CD26/DPP4 surface expression. Together, these results imply that bats indeed could be among the MERS-CoV host spectrum, and that cellular restriction of MERS-CoV is determined by CD26/DPP4 expression rather than by downstream restriction factors. url: https://www.ncbi.nlm.nih.gov/pubmed/25409519/ doi: 10.1371/journal.pone.0112060 id: cord-339869-euikj8fv author: Cebey-López, Miriam title: Does Viral Co-Infection Influence the Severity of Acute Respiratory Infection in Children? date: 2016-04-20 words: 3325.0 sentences: 201.0 pages: flesch: 40.0 cache: ./cache/cord-339869-euikj8fv.txt txt: ./txt/cord-339869-euikj8fv.txt summary: However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory Introduction Molecular techniques including polymerase chain reaction (PCR) have increased the sensitivity of detection for common and emerging respiratory viruses, and often reveal the presence of more than one pathogen in respiratory patients. Our study aims to analyze the relationship between viral or bacterial co-infection detected by molecular methods, and the clinical phenotype of children admitted to hospital with lower tract acute respiratory infections (LT-ARI). PICU admission, disease severity according to different scales, need for respiratory support, and length of hospital stay followed a similar pattern in viral mono-versus co-infected children. abstract: BACKGROUND: Multiple viruses are often detected in children with respiratory infection but the significance of co-infection in pathogenesis, severity and outcome is unclear. OBJECTIVES: To correlate the presence of viral co-infection with clinical phenotype in children admitted with acute respiratory infections (ARI). METHODS: We collected detailed clinical information on severity for children admitted with ARI as part of a Spanish prospective multicenter study (GENDRES network) between 2011–2013. A nested polymerase chain reaction (PCR) approach was used to detect respiratory viruses in respiratory secretions. Findings were compared to an independent cohort collected in the UK. RESULTS: 204 children were recruited in the main cohort and 97 in the replication cohort. The number of detected viruses did not correlate with any markers of severity. However, bacterial superinfection was associated with increased severity (OR: 4.356; P-value = 0.005), PICU admission (OR: 3.342; P-value = 0.006), higher clinical score (1.988; P-value = 0.002) respiratory support requirement (OR: 7.484; P-value < 0.001) and longer hospital length of stay (OR: 1.468; P-value < 0.001). In addition, pneumococcal vaccination was found to be a protective factor in terms of degree of respiratory distress (OR: 2.917; P-value = 0.035), PICU admission (OR: 0.301; P-value = 0.011), lower clinical score (-1.499; P-value = 0.021) respiratory support requirement (OR: 0.324; P-value = 0.016) and oxygen necessity (OR: 0.328; P-value = 0.001). All these findings were replicated in the UK cohort. CONCLUSION: The presence of more than one virus in hospitalized children with ARI is very frequent but it does not seem to have a major clinical impact in terms of severity. However bacterial superinfection increases the severity of the disease course. On the contrary, pneumococcal vaccination plays a protective role. url: https://www.ncbi.nlm.nih.gov/pubmed/27096199/ doi: 10.1371/journal.pone.0152481 id: cord-306135-pt4jsr6d author: Chan, Kamfai title: A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics date: 2016-02-12 words: 6292.0 sentences: 284.0 pages: flesch: 56.0 cache: ./cache/cord-306135-pt4jsr6d.txt txt: ./txt/cord-306135-pt4jsr6d.txt summary: Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. This thermos thermal cycler (TTC) uses a very simple design that performs PCR amplification based on the "archaic" method of hand-transferring reaction tubes through a series of water baths, minimizing the temperature ramping time needed for PCR tubes to reach thermal equilibrium (Fig 1) . The TTC RT-PCR was performed using protocols similar to the HIV test, with PCR tubes transferred between three thermoses (reverse transcription, denaturation, and annealing/extension) and an optional room-temperature water bath. The gel photo in Fig 3 shows that the TTC can produce multiplexed amplicons with the correct sizes and that the yield is similar to a three-step reaction performed in the commercial cycler with same number of PCR cycles. abstract: The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC’s ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC’s performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings. url: https://doi.org/10.1371/journal.pone.0149150 doi: 10.1371/journal.pone.0149150 id: cord-310438-744r7gc3 author: Chan, Ta-Chien title: The Impact of Matching Vaccine Strains and Post-SARS Public Health Efforts on Reducing Influenza-Associated Mortality among the Elderly date: 2010-06-25 words: 5083.0 sentences: 226.0 pages: flesch: 40.0 cache: ./cache/cord-310438-744r7gc3.txt txt: ./txt/cord-310438-744r7gc3.txt summary: This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan''s influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. The aims of this study were: (1) to evaluate the effectiveness of matching or mismatching influenza vaccine strains on influenzaassociated mortality, (2) to assess whether public health improvements during the post-SARS period might have decreased elderly mortality, and (3) to investigate molecular variation among vaccine-mismatched influenza viruses that may be associated with increased excess influenza-associated mortality. Explanatory variables for the above three outcome measures include monthly meteorological parameters (monthly means of temperature and humidity), annual periodic cycle (i.e., sine/cosine function of seasonal periodicity), monthly virus isolation rates for different subtypes/types of influenza viruses [A (H3N2) or A (H1N1) or B], matching status of different vaccine strains for each subtype/type in each of the studied years, post-SARS effect, and linear temporal monthly trends. abstract: Public health administrators do not have effective models to predict excess influenza-associated mortality and monitor viral changes associated with it. This study evaluated the effect of matching/mismatching vaccine strains, type/subtype pattern changes in Taiwan's influenza viruses, and the impact of post-SARS (severe acute respiratory syndrome) public health efforts on excess influenza-associated mortalities among the elderly. A negative binomial model was developed to estimate Taiwan's monthly influenza-associated mortality among the elderly. We calculated three winter and annual excess influenza-associated mortalities [pneumonia and influenza (P&I), respiratory and circulatory, and all-cause] from the 1999–2000 through the 2006–2007 influenza seasons. Obtaining influenza virus sequences from the months/years in which death from P&I was excessive, we investigated molecular variation in vaccine-mismatched influenza viruses by comparing hemagglutinin 1 (HA1) of the circulating and vaccine strains. We found that the higher the isolation rate of A (H3N2) and vaccine-mismatched influenza viruses, the greater the monthly P&I mortality. However, this significant positive association became negative for higher matching of A (H3N2) and public health efforts with post-SARS effect. Mean excess P&I mortality for winters was significantly higher before 2003 than after that year [mean ± S.D.: 1.44±1.35 vs. 0.35±1.13, p = 0.04]. Further analysis revealed that vaccine-matched circulating influenza A viruses were significantly associated with lower excess P&I mortality during post-SARS winters (i.e., 2005–2007) than during pre-SARS winters [0.03±0.06 vs. 1.57±1.27, p = 0.01]. Stratification of these vaccine-matching and post-SARS effect showed substantial trends toward lower elderly excess P&I mortalities in winters with either mismatching vaccines during the post-SARS period or matching vaccines during the pre-SARS period. Importantly, all three excess mortalities were at their highest in May, 2003, when inter-hospital nosocomial infections were peaking. Furthermore, vaccine-mismatched H3N2 viruses circulating in the years with high excess P&I mortality exhibited both a lower amino acid identity percentage of HA1 between vaccine and circulating strains and a higher numbers of variations at epitope B. Our model can help future decision makers to estimate excess P&I mortality effectively, select and test virus strains for antigenic variation, and evaluate public health strategy effectiveness. url: https://www.ncbi.nlm.nih.gov/pubmed/20592764/ doi: 10.1371/journal.pone.0011317 id: cord-000726-tonaaft2 author: Chang, Binggong title: Influence of Mabs on PrP(Sc) Formation Using In Vitro and Cell-Free Systems date: 2012-07-27 words: 4986.0 sentences: 239.0 pages: flesch: 50.0 cache: ./cache/cord-000726-tonaaft2.txt txt: ./txt/cord-000726-tonaaft2.txt summary: Two systems were used to analyze the effect of different antibodies on PrP(Sc) formation: (i) neuroblastoma cells persistently infected with the 22L mouse-adapted scrapie stain, and (ii) protein misfolding cyclic amplification (PMCA), which uses PrP(Sc) as a template or seed, and a series of incubations and sonications, to convert PrP(C) to PrP(Sc). Based on the numerous and varied Mabs analyzed, the inhibitory effect does not appear to be epitope specific, related to PrP(C) conformation, or to cell membrane localization, but is influenced by the targeted PrP region (amino vs carboxy). We compared the effect of individual PrP-specific monoclonal antibodies (Mabs) on the PrP C -PrP Sc conversion process using both an N2a/22L cell culture model and the test-tube PMCA system. To more completely explore the possible therapeutic effect of anti-PrP antibodies, and to establish another system to analyze the influence of Abs on the conversion process, we screened Mabs produced in our laboratory for their capacity to inhibit PrP Sc formation. abstract: PrP(Sc) is believed to serve as a template for the conversion of PrP(C) to the abnormal isoform. This process requires contact between the two proteins and implies that there may be critical contact sites that are important for conversion. We hypothesized that antibodies binding to either PrP(c)or PrP(Sc) would hinder or prevent the formation of the PrP(C)–PrP(Sc) complex and thus slow down or prevent the conversion process. Two systems were used to analyze the effect of different antibodies on PrP(Sc) formation: (i) neuroblastoma cells persistently infected with the 22L mouse-adapted scrapie stain, and (ii) protein misfolding cyclic amplification (PMCA), which uses PrP(Sc) as a template or seed, and a series of incubations and sonications, to convert PrP(C) to PrP(Sc). The two systems yielded similar results, in most cases, and demonstrate that PrP-specific monoclonal antibodies (Mabs) vary in their ability to inhibit the PrP(C)–PrP(Sc) conversion process. Based on the numerous and varied Mabs analyzed, the inhibitory effect does not appear to be epitope specific, related to PrP(C) conformation, or to cell membrane localization, but is influenced by the targeted PrP region (amino vs carboxy). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407222/ doi: 10.1371/journal.pone.0041626 id: cord-342639-vf9n2vf9 author: Chang, Chung-ke title: Transient Oligomerization of the SARS-CoV N Protein – Implication for Virus Ribonucleoprotein Packaging date: 2013-05-23 words: 5386.0 sentences: 243.0 pages: flesch: 42.0 cache: ./cache/cord-342639-vf9n2vf9.txt txt: ./txt/cord-342639-vf9n2vf9.txt summary: For disulfide trapping experiments, we chose mutation sites that would form disulfide linkages based on the crystal packing structures of the SARS-CoV N protein CTD ( Figure 1 ) [9] . Within the crystal asymmetric unit, the SARS-CoV N protein CTD packs as an octamer which stacks to form a helical arrangement with a continuous positively charged surface that could potentially allow the RNA to bind to it through electrostatic interactions ( Fig. 1 ) [9] . By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that SARS-CoV N protein is capable of transient oligomerization in solution through the CTD in the absence of nucleic acids. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA abstract: The nucleocapsid (N) phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD). A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization. url: https://www.ncbi.nlm.nih.gov/pubmed/23717688/ doi: 10.1371/journal.pone.0065045 id: cord-000765-r7y1cqou author: Chang, Yu-Ming title: Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis date: 2012-09-21 words: 5770.0 sentences: 317.0 pages: flesch: 54.0 cache: ./cache/cord-000765-r7y1cqou.txt txt: ./txt/cord-000765-r7y1cqou.txt summary: title: Functional Studies of ssDNA Binding Ability of MarR Family Protein TcaR from Staphylococcus epidermidis However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. IcaR DNA1 probe duplex of 1 mM was pre-incubated with 2 mM TcaR (dimer) at room temperature for 15 min before mixing with increasing concentration of GC33 ssDNA, followed by the same procedure as described in the legend to Figure 1B . In the EMSA analysis, 1 mM IcaR DNA1 probe duplex was pre-incubated with 1 mM GC33 ssDNA fragment for 15 min at room temperature before mixing with TcaR protein of increasing concentration. abstract: The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG). Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. Moreover, we show that TcaR preferentially binds 33-mer ssDNA over double-stranded DNA and inhibits viral ssDNA replication. In contrast, such ssDNA binding properties were not observed for other MarR family protein and TetR family protein, suggesting that the results from our studies are not an artifact due to simple charge interactions between TcaR and ssDNA. Overall, these results suggest a novel role for TcaR in regulation of DNA replication. We anticipate that the results of this work will extend our understanding of MarR family protein and broaden the development of new therapeutic strategies for Staphylococci. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448645/ doi: 10.1371/journal.pone.0045665 id: cord-320938-f526k9q1 author: Chen, Hongjun title: Partial and Full PCR-Based Reverse Genetics Strategy for Influenza Viruses date: 2012-09-28 words: 8614.0 sentences: 455.0 pages: flesch: 60.0 cache: ./cache/cord-320938-f526k9q1.txt txt: ./txt/cord-320938-f526k9q1.txt summary: In order to determine whether a Flu PCR amplicon could be transfected into cells and be amplified by the influenza polymerase complex, a PCR product was produced encoding the GFP reporter gene in negative orientation flanked by the influenza segment 7 untranslated regions (UTRs) and further flanked by the human pol1 promoter and the mouse t1 termination signal, pol1EGFPt1 (Fig. 1A, Fig. S1A , Table S1 ). doi:10.1371/journal.pone.0046378.g001 Efficient influenza virus rescue using Flu PCR amplicons in either ''''1+7'''' or ''''2+6'''' modes The pol1HA pdm t1 or pol1HA D072 t1 HA PCR amplicons (Table 1) were co-transfected into co-cultured 293T/MDCK cells in a ''''1+7'''' mode along with 7 RG plasmids encoding the corresponding additional gene segments from the influenza A/Puerto Rico/ 8/1934 (H1N1) strain (PR8). abstract: Since 1999, plasmid-based reverse genetics (RG) systems have revolutionized the way influenza viruses are studied. However, it is not unusual to encounter cloning difficulties for one or more influenza genes while attempting to recover virus de novo. To overcome some of these shortcomings we sought to develop partial or full plasmid-free RG systems. The influenza gene of choice is assembled into a RG competent unit by virtue of overlapping PCR reactions containing a cDNA copy of the viral gene segment under the control of RNA polymerase I promoter (pol1) and termination (t1) signals – herein referred to as Flu PCR amplicons. Transfection of tissue culture cells with either HA or NA Flu PCR amplicons and 7 plasmids encoding the remaining influenza RG units, resulted in efficient virus rescue. Likewise, transfections including both HA and NA Flu PCR amplicons and 6 RG plasmids also resulted in efficient virus rescue. In addition, influenza viruses were recovered from a full set of Flu PCR amplicons without the use of plasmids. url: https://doi.org/10.1371/journal.pone.0046378 doi: 10.1371/journal.pone.0046378 id: cord-258243-2utl2mfl author: Chen, Jeng-Wen title: Factors associated with changing indications for adenotonsillectomy: A population-based longitudinal study date: 2018-05-29 words: 4350.0 sentences: 230.0 pages: flesch: 44.0 cache: ./cache/cord-258243-2utl2mfl.txt txt: ./txt/cord-258243-2utl2mfl.txt summary: We investigated the distribution of the three major categories of surgical indication according to sex, age group (<5 years, 5-11 years, 11-17 years, 18-40 years, and >40 years), hospital level (medical centers, regional hospitals, and local hospitals), and insured residence areas according to the NHI divisions (Taipei, Northern, Central, Southern, Kaoping, and Eastern). In the adult subgroup (Figs 2B and 3B) , the incidence and proportion of AT performed for RICI decreased from 46 (78%) in 1997 to 32 Table 3 indicates the number and percentage of the three categories of surgical indications according to sex, age groups, hospital level, and insured residence areas in the total study population. The trend in the AT rate and the proportion of surgical indications by the calendar year according to sex, age groups, hospital level, and insured residence areas in the total study population are shown in the supplemental data (S1 File). abstract: OBJECTIVE: Adenotonsillectomy (AT) is one of the most common surgical procedures performed in children and adults. We aim to assess the factors associated with changes in the incidence of and indications for AT using population-level data. STUDY DESIGN: This retrospective cohort study investigated patients who underwent AT between 1997 and 2010 by using data from the Taiwan National Health Insurance Research Database. We examined surgical rates and indications by the calendar year as well as age, sex, hospital level, and insured residence areas for the correlating factors. RESULTS: The average annual incidence rate of AT was 14.7 per 100,000 individuals during 1997–2010. Pediatric (<18 years) patients represented 48.2% of the total AT population. More than 99% of the patients underwent the AT procedures as an inpatient intervention. Longitudinal data demonstrated an increasing trend in the pediatric AT rates from 1997 (4.3/100,000) to 2010 (5.7/100,000) (p = 0.029). In the adult subgroup, a decreasing prevalence of infectious indications (p = 0.014) coincided with an increasing neoplastic indications (p = 0.001). In the pediatric subgroup, the prevalence of obstructive indications increased (p = 0.002). The logistic regression analyses indicated that the significant factors associated with the changing surgical indications for AT were the age in the adult subgroup and hospital level in the pediatric subgroup. CONCLUSIONS: This study revealed a low AT rate in Taiwan than that in other countries. Pediatric AT incidence increased during 1997–2010. Although a rising prevalence of obstructive and neoplastic indications was noted, infection remained the most common indications for AT. Age in the adult subgroup and hospital level in the pediatric subgroup were factors associated with the changing indications for AT. url: https://doi.org/10.1371/journal.pone.0193317 doi: 10.1371/journal.pone.0193317 id: cord-283604-fqc9jp0l author: Chen, Meng title: Adenoviruses Associated with Acute Respiratory Diseases Reported in Beijing from 2011 to 2013 date: 2015-03-27 words: 3060.0 sentences: 127.0 pages: flesch: 39.0 cache: ./cache/cord-283604-fqc9jp0l.txt txt: ./txt/cord-283604-fqc9jp0l.txt summary: To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. The comparison results of the penton base, hexon, and fiber gene sequences between the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and the strains from the GenBank database indicated significant conservation and stability of the sequences within the genome across time and space. abstract: BACKGROUND: Adenovirus is one of the most common causes of viral acute respiratory infections. To identify the types of human adenoviruses (HAdVs) causing respiratory illness in Beijing, a sentinel surveillance project on the viral aetiology of acute respiratory infection was initiated in 2011. PRINCIPAL FINDINGS: Through the surveillance project, 4617 cases of respiratory infections were identified during 2011-2013. Throat swabs (pharynx and tonsil secretions) were collected from all the patients, and 15 different respiratory viruses were screened by multiplex one-step PCR method. 45 were identified as adenovirus-positive from sporadic and outbreak cases of respiratory infection by a multiplex one-step RT-PCR method, and a total of 21 adenovirus isolates were obtained. Five HAdV types among three species, including HAdV-3 (species HAdV-B), HAdV-4 (species HAdV-E), HAdV-7 (species HAdV-B), HAdV-55 (species HAdV-B), and an undefined HAdV type (species HAdV-C) were identified. The comparison results of the penton base, hexon, and fiber gene sequences of the Beijing HAdV-3, HAdV-4, HAdV-7, and HAdV-55 strains in this study and those from the GenBank database indicated significant spatial and temporal conservation and stability of sequences within the genome; however, the phylogenetic relationship indicated that both strain BJ04 and strain BJ09 isolated in 2012 and 2013, respectively, may have recombined between HAdV-1 genome and HAdV-2 genome within species HAdV-C, indicating intraspecies recombination. CONCLUSIONS: This study confirmed that at least 5 HAdV types including HAdV-3, HAdV-4, HAdV-7, HAdV-55 and an undefined HAdV type were co-circulating and were the causative agents of respiratory tract infections in recent years in Beijing. HAdV-3, HAdV-4, HAdV-7, and HAdV-55 showed the apparent stability of the genomes, while intraspecies recombination was identified in strain BJ04 and BJ09. The recombinants carrying penton base gene of HAdV-1 as well as hexon and fiber genes of HAdV-2 might be a novel type of HAdV worthy of further study. url: https://www.ncbi.nlm.nih.gov/pubmed/25816320/ doi: 10.1371/journal.pone.0121375 id: cord-001078-5m29nugu author: Chen, Xiaorong title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study date: 2013-09-17 words: 3930.0 sentences: 200.0 pages: flesch: 47.0 cache: ./cache/cord-001078-5m29nugu.txt txt: ./txt/cord-001078-5m29nugu.txt summary: title: Clinical Features and Factors Associated with Outcomes of Patients Infected with a Novel Influenza A (H7N9) Virus: A Preliminary Study OBJECTIVE: The present study aimed to analyze clinical features and factors associated with treatment outcomes of H7N9 influenza A virus infection. Factors analyzed for possible correlation with clinical features and treatment outcomes in patients included 1) baseline characteristics of patients, such as age, sex, occupation, underlying conditions, exposure to poultry and/or wild birds in the past seven days, date of symptom onset and hospital admission, date of specimen collection, and date of positive diagnosis; 2) results from laboratory tests and imaging examinations; 3) treatment regimen including basic supporting therapy, antibiotic therapy, antiviral therapy, traditional Chinese medicine (TCM) therapy, and other therapies if applicable; and 4) current condition of patients including the length of stay in the hospital. abstract: OBJECTIVE: The present study aimed to analyze clinical features and factors associated with treatment outcomes of H7N9 influenza A virus infection. METHODS: The clinical progress in 18 H7N9-infected patients was monitored and recorded. The clinical features of H7N9 infection were noted and factors associated with treatment outcomes were analyzed by univariate analyses. RESULTS: The average ages of patients in recovered and critical conditions were 67.0±10.83 years and 72.75±12.0 years, respectively. Renal insufficiency developed more frequently in critically ill patients (P = 0.023). The duration of traditional Chinese medicine (TCM) therapy was longer in recovered patients than in critically ill patients (P = 0.01). Laboratory tests showed that levels of C-reactive protein, serum creatinine, and myoglobin were significantly higher in critically ill patients than in recovered patients (P = 0.011, 0.04, and 0.016, respectively). Meanwhile, levels of all T cell subsets examined including total CD3(+), CD4(+), CD8(+), and CD45(+) T cells were lower in critically ill patients than in recovered patients (P = 0.033, 0.059, 0.015, and 0.039, respectively). Logistic regression analysis demonstrated that C-reactive protein level, myoglobin level and TCM therapy duration were likely associated with treatment outcomes of H7N9 infection (P = 0.032, 0.041 and 0.017, respectively). CONCLUSION: Elderly people may have increased risk for H7N9 virus infection. T cell-mediated responses play an important role in defense against the H7N9 virus. C-reactive protein level, myoglobin level and TCM duration may be associated with treatment outcomes of H7N9 infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775774/ doi: 10.1371/journal.pone.0073362 id: cord-001275-a9o2dvke author: Chen, Xue title: A Vaccine of L2 Epitope Repeats Fused with a Modified IgG1 Fc Induced Cross-Neutralizing Antibodies and Protective Immunity against Divergent Human Papillomavirus Types date: 2014-05-06 words: 5558.0 sentences: 254.0 pages: flesch: 47.0 cache: ./cache/cord-001275-a9o2dvke.txt txt: ./txt/cord-001275-a9o2dvke.txt summary: title: A Vaccine of L2 Epitope Repeats Fused with a Modified IgG1 Fc Induced Cross-Neutralizing Antibodies and Protective Immunity against Divergent Human Papillomavirus Types Current human papillomavirus (HPV) major capsid protein L1 virus-like particles (VLPs)-based vaccines in clinic induce strong HPV type-specific neutralizing antibody responses. To develop pan-HPV vaccines, here, we show that the fusion protein E3R4 consisting of three repeats of HPV16 L2 aa 17–36 epitope (E3) and a modified human IgG1 Fc scaffold (R4) induces cross-neutralizing antibodies and protective immunity against divergent HPV types. In this study, we showed for the first time that fusing HPV16 L2 aa 17-36 epitope repeats to a recombinant ligand for FccRs (designated L2R4, see Figure 1A -B) could significantly increase the immunogenicity of the L2 peptide and induce cross-neutralizing antibodies and protective immunity against a range of phylogenetically distant HPV types. abstract: Current human papillomavirus (HPV) major capsid protein L1 virus-like particles (VLPs)-based vaccines in clinic induce strong HPV type-specific neutralizing antibody responses. To develop pan-HPV vaccines, here, we show that the fusion protein E3R4 consisting of three repeats of HPV16 L2 aa 17–36 epitope (E3) and a modified human IgG1 Fc scaffold (R4) induces cross-neutralizing antibodies and protective immunity against divergent HPV types. E3R4 was expressed as a secreted protein in baculovirus expression system and could be simply purified by one step Protein A affinity chromatography with the purity above 90%. Vaccination of E3R4 formulated with Freunds adjuvant not only induced cross-neutralizing antibodies against HPV pseudovirus types 16, 18, 45, 52, 58, 6, 11 and 5 in mice, but also protected mice against vaginal challenges with HPV pseudovirus types 16, 45, 52, 58, 11 and 5 for at least eleven months after the first immunization. Moreover, vaccination of E3R4 formulated with FDA approved adjuvant alum plus monophosphoryl lipid A also induced cross-neutralizing antibodies against HPV types 16, 18 and 6 in rabbits. Thus, our results demonstrate that delivery of L2 antigen as a modified Fc-fusion protein may facilitate pan-HPV vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4011685/ doi: 10.1371/journal.pone.0095448 id: cord-302355-3se1wp8o author: Chen, Yi-Shiuan title: The conserved stem-loop II structure at the 3'' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 words: 6004.0 sentences: 292.0 pages: flesch: 53.0 cache: ./cache/cord-302355-3se1wp8o.txt txt: ./txt/cord-302355-3se1wp8o.txt summary: Although XRN1 digestion of a 3''-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Furthermore, the minus-strand templates covering the putative promoter region used for an in vitro RdRp assay gave rise to synthetic products, suggesting that the JEV sfRNA could be initially transcribed from the antigenome and may be further trimmed by XRN1 or other unidentified exoribonucleases. Although efficient RNA replication is required for the detection of any flaviviral RNAs despite which mechanism used for the sfRNA formation, our results were clearly different from the observations from WNV that BHK-21 cells transfected with replicon constructs containing various deletions had no effect on the accumulation of sfRNA when compared to the WT [8] . abstract: Flaviviruses accumulate abundant subgenomic RNA (sfRNA) in infected cells. It has been reported that sfRNA results from stalling of host 5’-to-3’ exoribonuclease XRN1 at the highly structured RNA of the 3’ untranslated region (UTR). Although XRN1 digestion of a 3’-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Mutagenesis studies revealed that the stemloop II (SLII) at the 3’ UTR is required for the accumulation of sfRNA. According to the results of an in vitro RNA-dependent RNA polymerase (RdRp) assay, the (-)10431-10566 RNA fragment, containing the putative promoter on the antigenome for the sfRNA transcription, binds to RdRp protein and exhibits a strong promoter activity. Taken together, our results indicate that the JEV sfRNA could be transcribed initially and then be trimmed by XRN1 or other unidentified exoribonucleases. url: https://doi.org/10.1371/journal.pone.0201250 doi: 10.1371/journal.pone.0201250 id: cord-282194-0sjmf1yn author: Cherak, Stephana J. title: Impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit: A scoping review date: 2020-09-11 words: 5411.0 sentences: 276.0 pages: flesch: 42.0 cache: ./cache/cord-282194-0sjmf1yn.txt txt: ./txt/cord-282194-0sjmf1yn.txt summary: title: Impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit: A scoping review The purpose of this scoping review was to summarize existing research on the impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit (ICU). For the purposes of this review, we defined: (1) a caregiver as any informal (i.e., non-clinical) person who regularly provides support to the patient and is in some way directly implicated in the patient''s care or directly affected by the patient''s health problem (e.g., family, friend); (2) social media as any form of electronic communication that allow users to share information and other content and create online communities; and (3) critically ill patients as any persons who are currently admitted to an intensive care unit (ICU) or had previously been admitted to an ICU. abstract: BACKGROUND: The use of social media in healthcare continues to evolve. The purpose of this scoping review was to summarize existing research on the impact of social media interventions and tools among informal caregivers of critically ill patients after patient admission to the intensive care unit (ICU). METHODS: This review followed established scoping review methods, including an extensive a priori-defined search strategy implemented in the MEDLINE, EMBASE, PsycINFO, CINAHL, and the Cochrane CENTRAL Register of Controlled Trials databases to July 10, 2020. Primary research studies reporting on the use of social media by informal caregivers for critically ill patients were included. RESULTS: We identified 400 unique citations and thirty-one studies met the inclusion criteria. Nine were interventional trials–four randomized controlled trials (RCTs)–and a majority (n = 14) were conducted (i.e., data collected) between 2013 to 2015. Communication platforms (e.g., Text Messaging, Web Camera) were the most commonly used social media tool (n = 17), followed by social networking sites (e.g., Facebook, Instagram) (n = 6), and content communities (e.g., YouTube, SlideShare) (n = 5). Nine studies’ primary objective was caregiver satisfaction, followed by self-care (n = 6), and health literacy (n = 5). Nearly every study reported an outcome on usage feasibility (e.g., user attitudes, preferences, demographics) (n = 30), and twenty-three studies reported an outcome related to patient and caregiver satisfaction. Among the studies that assessed statistical significance (n = 18), 12 reported statistically significant positive effects of social media use. Overall, 16 of the 31 studies reported positive conclusions (e.g., increased knowledge, satisfaction, involvement) regarding the use of social media among informal caregivers for critically ill patients. CONCLUSIONS: Social media has potential benefits for caregivers of the critically ill. More robust and clinically relevant studies are required to identify effective social media strategies used among caregivers for the critically ill. url: https://www.ncbi.nlm.nih.gov/pubmed/32915848/ doi: 10.1371/journal.pone.0238803 id: cord-310790-3ikgmiof author: Cherrak, Sabri Ahmed title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies date: 2020-10-15 words: 3471.0 sentences: 226.0 pages: flesch: 50.0 cache: ./cache/cord-310790-3ikgmiof.txt txt: ./txt/cord-310790-3ikgmiof.txt summary: title: Potential bioactive glycosylated flavonoids as SARS-CoV-2 main protease inhibitors: A molecular docking and simulation studies Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. The three compounds with highest affinity (Fig 2) for the active site are quercetin 3-rhamonoside, myricetin 3-rutinoside and rutin with binding energies of -9.7, -9,3 and -9.2 kcal.mol -1 respectively. Thirty eight flavonoids have been tested in this study by molecular docking against the active site of the SARS-CoV-2Mpro. Glycosylated flavonoids as SARS-CoV-2 Inhibitors: A molecular docking and simulation studies Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies abstract: A novel coronavirus responsible of acute respiratory infection closely related to SARS-CoV has recently emerged. So far there is no consensus for drug treatment to stop the spread of the virus. Discovery of a drug that would limit the virus expansion is one of the biggest challenges faced by the humanity in the last decades. In this perspective, to test existing drugs as inhibitors of SARS-CoV-2 main protease is a good approach. Among natural phenolic compounds found in plants, fruit, and vegetables; flavonoids are the most abundant. Flavonoids, especially in their glycosylated forms, display a number of physiological activities, which makes them interesting to investigate as antiviral molecules. The flavonoids chemical structures were downloaded from PubChem and protease structure 6LU7 was from the Protein Data Bank site. Molecular docking study was performed using AutoDock Vina. Among the tested molecules Quercetin-3-O-rhamnoside showed the highest binding affinity (-9,7 kcal/mol). Docking studies showed that glycosylated flavonoids are good inhibitors for the SARS-CoV-2 protease and could be further investigated by in vitro and in vivo experiments for further validation. MD simulations were further performed to evaluate the dynamic behavior and stability of the protein in complex with the three best hits of docking experiments. Our results indicate that the rutin is a potential drug to inhibit the function of Chymotrypsin-like protease (3CL pro) of Coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/33057452/ doi: 10.1371/journal.pone.0240653 id: cord-260653-5qwtvm9x author: Chikhlikar, Priya title: DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques date: 2006-12-27 words: 6117.0 sentences: 278.0 pages: flesch: 49.0 cache: ./cache/cord-260653-5qwtvm9x.txt txt: ./txt/cord-260653-5qwtvm9x.txt summary: Thomas; Marques, Ernesto T.A. title: DNA Encoding an HIV-1 Gag/Human Lysosome-Associated Membrane Protein-1 Chimera Elicits a Broad Cellular and Humoral Immune Response in Rhesus Macaques Previous studies of HIV-1 p55Gag immunization of mice have demonstrated the usefulness of targeting antigens to the cellular compartment containing the major histocompatibility complex type II (MHC II) complex molecules by use of a DNA antigen formulation encoding Gag as a chimera with the mouse lysosome-associated membrane protein (mLAMP/gag). In the present study, we have analyzed the magnitude and breadth of Gag-specific T-lymphocyte and antibody responses elicited in Rhesus macaques after immunization with DNA encoding a human LAMP/gag (hLAMP/gag) chimera. This study demonstrates that Rhesus macaques immunized with a DNA plasmid vaccine-encoding gag as an hLAMP/gag chimera develops strong antigen-specific humoral responses as well as CD4 + and CD8 + T-cell responses. abstract: Previous studies of HIV-1 p55Gag immunization of mice have demonstrated the usefulness of targeting antigens to the cellular compartment containing the major histocompatibility complex type II (MHC II) complex molecules by use of a DNA antigen formulation encoding Gag as a chimera with the mouse lysosome-associated membrane protein (mLAMP/gag). In the present study, we have analyzed the magnitude and breadth of Gag-specific T-lymphocyte and antibody responses elicited in Rhesus macaques after immunization with DNA encoding a human LAMP/gag (hLAMP/gag) chimera. ELISPOT analyses indicated that the average Gag-specific IFN-γ response elicited by the hLAMP/gag chimera was detectable after only two or three naked DNA immunizations in all five immunized macaques and reached an average of 1000 spot-forming cells (SFC)/10(6) PBMCs. High IFN-γ ELISPOT responses were detected in CD8(+)-depleted cells, indicating that CD4(+) T-cells play a major role in these responses. The T-cell responses of four of the macaques were also tested by use of ELISPOT to 12 overlapping 15-amino acids (aa) peptide pools containing ten peptides each, encompassing the complete Gag protein sequence. The two Mamu 08 immunized macaques responded to eight and twelve of the pools, the Mamu B01 to six, and the other macaque to five pools indicating that the hLAMP/gag DNA antigen formulation elicits a broad T-cell response against Gag. Additionally, there was a strong HIV-1-specific IgG response. The IgG antibody titers increased after each DNA injection, indicating a strong amnestic B-cell response, and were highly elevated in all the macaques after three immunizations. Moreover, the serum of each macaque recognized 13 of the 49 peptides of a 20-aa peptide library covering the complete Gag amino acid sequence. In addition, HIV-1-specific IgA antibodies were present in the plasma and external secretions, including nasal washes. These data support the findings of increased immunogenicity of genetic vaccines encoded as LAMP chimeras, including the response to DNA vaccines by non-human primates. url: https://www.ncbi.nlm.nih.gov/pubmed/17205139/ doi: 10.1371/journal.pone.0000135 id: cord-048353-hqc7u9w3 author: Chis Ster, Irina title: Transmission Parameters of the 2001 Foot and Mouth Epidemic in Great Britain date: 2007-06-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite intensive ongoing research, key aspects of the spatial-temporal evolution of the 2001 foot and mouth disease (FMD) epidemic in Great Britain (GB) remain unexplained. Here we develop a Markov Chain Monte Carlo (MCMC) method for estimating epidemiological parameters of the 2001 outbreak for a range of simple transmission models. We make the simplifying assumption that infectious farms were completely observed in 2001, equivalent to assuming that farms that were proactively culled but not diagnosed with FMD were not infectious, even if some were infected. We estimate how transmission parameters varied through time, highlighting the impact of the control measures on the progression of the epidemic. We demonstrate statistically significant evidence for assortative contact patterns between animals of the same species. Predictive risk maps of the transmission potential in different geographic areas of GB are presented for the fitted models. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876810/ doi: 10.1371/journal.pone.0000502 id: cord-305811-987dhnf7 author: Cho, Che-Pei title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date: 2013-04-29 words: 5837.0 sentences: 301.0 pages: flesch: 49.0 cache: ./cache/cord-305811-987dhnf7.txt txt: ./txt/cord-305811-987dhnf7.txt summary: Because both 59CC-WT and 13363-13520 constructs share 27 identical nucleotides upstream of their slippery sites, the attenuation activity difference is not likely to be caused by an E-site flanking sequences effect [12, 13] but rather by the disruption of the two potential AU base pairs. We noticed a potential to form four extra base pairs between 59and 39-flanking sequences (GACG and CGUU, respectively) of the 6BPGC hairpin stem (and other deletion mutants) due to the existence of a 59 SalI cloning site (Fig. S1A ). The results (Fig. S1C ) indicate that the two potential base pairs involving E-site sequences are not the main cause of observed attenuation activity in 293T cell cultures. Furthermore, mutating two nucleotides (27 nucleotides upstream of the E site) to disrupt Watson-Crick base pairs in the lower hairpin stem dramatically impairs attenuation activity (Fig. 2) , indicating that attenuation is not caused by primary sequencemediated flanking-sequences effects [12, 13] . abstract: RNA structures are unwound for decoding. In the process, they can pause the elongating ribosome for regulation. An example is the stimulation of -1 programmed ribosomal frameshifting, leading to 3′ direction slippage of the reading-frame during elongation, by specific pseudoknot stimulators downstream of the frameshifting site. By investigating a recently identified regulatory element upstream of the SARS coronavirus (SARS-CoV) −1 frameshifting site, it is shown that a minimal functional element with hairpin forming potential is sufficient to down-regulate−1 frameshifting activity. Mutagenesis to disrupt or restore base pairs in the potential hairpin stem reveals that base-pair formation is required for−1 frameshifting attenuation in vitro and in 293T cells. The attenuation efficiency of a hairpin is determined by its stability and proximity to the frameshifting site; however, it is insensitive to E site sequence variation. Additionally, using a dual luciferase assay, it can be shown that a hairpin stimulated +1 frameshifting when placed upstream of a +1 shifty site in yeast. The investigations indicate that the hairpin is indeed a cis-acting programmed reading-frame switch modulator. This result provides insight into mechanisms governing−1 frameshifting stimulation and attenuation. Since the upstream hairpin is unwound (by a marching ribosome) before the downstream stimulator, this study’s findings suggest a new mode of translational regulation that is mediated by the reformed stem of a ribosomal unwound RNA hairpin during elongation. url: https://doi.org/10.1371/journal.pone.0062283 doi: 10.1371/journal.pone.0062283 id: cord-001280-skavefji author: Choi, Sang-Ho title: Usefulness of Cellular Analysis of Bronchoalveolar Lavage Fluid for Predicting the Etiology of Pneumonia in Critically Ill Patients date: 2014-05-13 words: 4136.0 sentences: 204.0 pages: flesch: 35.0 cache: ./cache/cord-001280-skavefji.txt txt: ./txt/cord-001280-skavefji.txt summary: This study investigated the ability of cellular analysis of BAL fluid to differentially diagnose bacterial pneumonia from viral pneumonia in adult patients who are admitted to intensive care unit. Exclusion criteria were as follows: (1) patients in whom the pathogen was not identified, (2) patients in whom BAL fluid analysis was impossible (due to severe neutropenia or clotting of specimen) or not performed, (3) patients with a mixed infection (identification of bacteria and virus), (4) patients who were treated with antimicrobial agents for more than 24 hours before bronchoscopic BAL, (5) patients with invasive pulmonary aspergillosis, (6) patients with mycobacterial infection, and (7) patients with Pneumocystis jirovecii pneumonia. Several authors of the current study previously investigated the diagnostic utility of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1) in BAL fluid of various patient populations with bilateral lung infiltrates. abstract: BACKGROUND: The usefulness of bronchoalveolar lavage (BAL) fluid cellular analysis in pneumonia has not been adequately evaluated. This study investigated the ability of cellular analysis of BAL fluid to differentially diagnose bacterial pneumonia from viral pneumonia in adult patients who are admitted to intensive care unit. METHODS: BAL fluid cellular analysis was evaluated in 47 adult patients who underwent bronchoscopic BAL following less than 24 hours of antimicrobial agent exposure. The abilities of BAL fluid total white blood cell (WBC) counts and differential cell counts to differentiate between bacterial and viral pneumonia were evaluated using receiver operating characteristic (ROC) curve analysis. RESULTS: Bacterial pneumonia (n = 24) and viral pneumonia (n = 23) were frequently associated with neutrophilic pleocytosis in BAL fluid. BAL fluid median total WBC count (2,815/µL vs. 300/µL, P<0.001) and percentage of neutrophils (80.5% vs. 54.0%, P = 0.02) were significantly higher in the bacterial pneumonia group than in the viral pneumonia group. In ROC curve analysis, BAL fluid total WBC count showed the best discrimination, with an area under the curve of 0.855 (95% CI, 0.750–0.960). BAL fluid total WBC count ≥510/µL had a sensitivity of 83.3%, specificity of 78.3%, positive likelihood ratio (PLR) of 3.83, and negative likelihood ratio (NLR) of 0.21. When analyzed in combination with serum procalcitonin or C-reactive protein, sensitivity was 95.8%, specificity was 95.7%, PLR was 8.63, and NLR was 0.07. BAL fluid total WBC count ≥510/µL was an independent predictor of bacterial pneumonia with an adjusted odds ratio of 13.5 in multiple logistic regression analysis. CONCLUSIONS: Cellular analysis of BAL fluid can aid early differential diagnosis of bacterial pneumonia from viral pneumonia in critically ill patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019586/ doi: 10.1371/journal.pone.0097346 id: cord-003244-abs3tc3r author: Chong, Ka Chun title: Monitoring the age-specificity of measles transmissions during 2009-2016 in Southern China date: 2018-10-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Despite several immunization efforts, China saw a resurgence of measles in 2012. Monitoring of transmissions of individuals from different age groups could offer information that would be valuable for planning adequate disease control strategies. We compared the age-specific effective reproductive numbers (R) of measles during 2009–2016 in Guangdong, China. METHODS: We estimated the age-specific R values for 7 age groups: 0–8 months, 9–18 months, 19 months to 6 years, 7–15 years, 16–25 years, 26–45 years, and ≥46 years adapting the contact matrix of China. The daily numbers of laboratory and clinically confirmed cases reported to the Center for Disease Control and Prevention of Guangdong were used. RESULTS: The peak R values of the entire population were above unity from 2012 to 2016, indicating the persistence of measles in the population. In general, children aged 0–6 years and adults aged 26–45 years had larger values of R when comparing with other age groups after 2012. While the peaks of R values for children aged 0–6 years dropped steadily after 2013, the peaks of R values for adults aged 26–45 years kept at a high range every year. CONCLUSIONS: Although the provincial supplementary immunization activities (SIAs) conducted in 2009 and 2010 were able to reduce the transmissions from 2009 to 2011, larger values of R for children aged 0–6 years were observed after 2012, indicating that the benefits of the SIAs were short-lived. In addition, the transmissions from adults aged between 26 and 45 years increased over time. Disease control strategies should target children and adult groups that carry high potential for measles transmission. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6175510/ doi: 10.1371/journal.pone.0205339 id: cord-274268-0ucqp3uz author: Chorus, Caspar title: Diabolical dilemmas of COVID-19: An empirical study into Dutch society’s trade-offs between health impacts and other effects of the lockdown date: 2020-09-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We report and interpret preferences of a sample of the Dutch adult population for different strategies to end the so-called ‘intelligent lockdown’ which their government had put in place in response to the COVID-19 pandemic. Using a discrete choice experiment, we invited participants to make a series of choices between policy scenarios aimed at relaxing the lockdown, which were specified not in terms of their nature (e.g. whether or not to allow schools to re-open) but in terms of their effects along seven dimensions. These included health-related effects, but also impacts on the economy, education, and personal income. From the observed choices, we were able to infer the implicit trade-offs made by the Dutch between these policy effects. For example, we find that the average citizen, in order to avoid one fatality directly or indirectly related to COVID-19, is willing to accept a lasting lag in the educational performance of 18 children, or a lasting (>3 years) and substantial (>15%) reduction in net income of 77 households. We explore heterogeneity across individuals in terms of these trade-offs by means of latent class analysis. Our results suggest that most citizens are willing to trade-off health-related and other effects of the lockdown, implying a consequentialist ethical perspective. Somewhat surprisingly, we find that the elderly, known to be at relatively high risk of being affected by the virus, are relatively reluctant to sacrifice economic pain and educational disadvantages for the younger generation, to avoid fatalities. We also identify a so-called taboo trade-off aversion amongst a substantial share of our sample, being an aversion to accept morally problematic policies that simultaneously imply higher fatality numbers and lower taxes. We explain various ways in which our results can be of value to policy makers in the context of the COVID-19 and future pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32936815/ doi: 10.1371/journal.pone.0238683 id: cord-003062-qm8kalyt author: Chowdhury, Fazle Rabbi title: The association between temperature, rainfall and humidity with common climate-sensitive infectious diseases in Bangladesh date: 2018-06-21 words: 4997.0 sentences: 274.0 pages: flesch: 50.0 cache: ./cache/cord-003062-qm8kalyt.txt txt: ./txt/cord-003062-qm8kalyt.txt summary: This observational study examined the association of temperature, humidity and rainfall with six common climate-sensitive infectious diseases in adults (malaria, diarrheal disease, enteric fever, encephalitis, pneumonia and bacterial meningitis) in northeastern Bangladesh. Unfortunately, very few studies on the relationship between various environmental variables and trends of infectious disease incidence have been performed so far in Bangladesh, although there are reports of some infections increasing sporadically in different regions of the country [17] [18] [19] . This study examined six infectious diseases based on clinical syndromes and laboratory support (malaria, enteric fever, encephalitis, diarrheal disease, pneumonia and meningitis) to offer a broader scope on the trend of these infectious diseases and their possible relation to climate change in Bangladesh. W.H.O reported dengue, viral encephalitis, diarrheal disease, enteric fever, pneumonia and meningitis as most sensitive to climate factors, and predicted a huge rise of cases in tropical countries [25] . abstract: Bangladesh is one of the world’s most vulnerable countries for climate change. This observational study examined the association of temperature, humidity and rainfall with six common climate-sensitive infectious diseases in adults (malaria, diarrheal disease, enteric fever, encephalitis, pneumonia and bacterial meningitis) in northeastern Bangladesh. Subjects admitted to the adult medicine ward of a tertiary referral hospital in Sylhet, Bangladesh from 2008 to 2012 with a diagnosis of one of the six chosen climate-sensitive infectious diseases were enrolled in the study. Climate-related data were collected from the Bangladesh Meteorological Institute. Disease incidence was then analyzed against mean temperature, humidity and average rainfall for the Sylhet region. Statistical significance was determined using Mann-Whitney test, Chi-square test and ANOVA testing. 5033 patients were enrolled (58% male, 42% female, ratio 1.3:1). All six diseases showed highly significant (p = 0.01) rises in incidence between the study years 2008 (540 cases) and 2012 (1330 cases), compared with no significant rise in overall all-cause hospital admissions in the same period (p = 0.19). The highest number of malaria (135), diarrhea (266) and pneumonia (371) cases occurred during the rainy season. On the other hand, the maximum number of enteric fever (408), encephalitis (183) and meningitis (151) cases occurred during autumn, which follows the rainy season. A positive (P = 0.01) correlation was observed between increased temperature and the incidence of malaria, enteric fever and diarrhea, and a negative correlation with encephalitis, meningitis and pneumonia. Higher humidity correlated (P = 0.01) with a higher number of cases of malaria and diarrhea, but inversely correlated with meningitis and encephalitis. Higher incidences of encephalitis and meningitis occurred while there was low rainfall. Incidences of diarrhea, malaria and enteric fever, increased with rainfall, and then gradually decreased. The findings support a relationship between weather patterns and disease incidence, and provide essential baseline data for future large prospective studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013221/ doi: 10.1371/journal.pone.0199579 id: cord-306958-8bx8kxxh author: Christensen, Sarah R. title: Political and personal reactions to COVID-19 during initial weeks of social distancing in the United States date: 2020-09-24 words: 4271.0 sentences: 223.0 pages: flesch: 45.0 cache: ./cache/cord-306958-8bx8kxxh.txt txt: ./txt/cord-306958-8bx8kxxh.txt summary: This study examines individual attitudes, behaviors, anxieties, mental health impacts, and knowledge early in the pandemic response, as well as those outcomes by sociodemographic characteristics and political ideology. Four items asked respondents to indicate agreement on a 7-point scale that "events related to COVID-19 had interrupted" their social life, home life, work or vocational life, and/or hurt their mental health. Chi-square, t, and F tests were used to examine the influence of demographic characteristics, political ideology, and mental health on attitudes, knowledge, anxieties, behavior change, and impact variables. Initial covariate selection included all variables that were significant (p <0.05) in bivariate tests, including: political ideology, bias score for consumed news media, attitudes toward global warming and vaccination, sex, race, poverty level, and education. In the adjusted logistic regression model ( Table 2 ) liberals had 5.7 (95%CI: 3.3-9.7) and moderates had 2.5 (95%CI 1.5-4.3) times the odds of responding that the government had not done enough in response to COVID-19 compared to conservatives. abstract: OBJECTIVE: To examine perceptions, behaviors, and impacts surrounding COVID-19 early in the pandemic response. MATERIALS AND METHODS: A cross-sectional survey of 1,030 U.S. adults was administered on March 31st, 2020. This survey examined attitudes toward media, government, and community responses to COVID-19 by political ideology and sociodemographic factors. Knowledge, anxieties, and impacts of COVID-19 were also assessed. RESULTS: Conservatives were more likely to report that COVID-19 was receiving too much media coverage and people were generally overreacting; liberals were more likely to report the government had not done enough in response to the pandemic. Females and those with lower income experienced more COVID-19 related economic anxieties. Those working and with children at home reported higher social, home, and work disruption. Social distancing behaviors were more common among liberals and were associated with increases in depressive symptoms. General knowledge about COVID-19 was widely exhibited across the sample, however, Black and Hispanic respondents were less likely to correctly answer questions about the availability of a vaccine and modes of transmission. CONCLUSIONS: Public health experts should consider the political climate in crafting messaging that appeals to the values of those across the political spectrum. Research on the COVID-19 pandemic should continue to monitor the effects of social distancing on mental health and among vulnerable populations. url: https://doi.org/10.1371/journal.pone.0239693 doi: 10.1371/journal.pone.0239693 id: cord-000786-ofpcgxce author: Chua, Brendon Y. title: Hepatitis C VLPs Delivered to Dendritic Cells by a TLR2 Targeting Lipopeptide Results in Enhanced Antibody and Cell-Mediated Responses date: 2012-10-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although many studies provide strong evidence supporting the development of HCV virus-like particle (VLP)-based vaccines, the fact that heterologous viral vectors and/or multiple dosing regimes are required to induce protective immunity indicates that it is necessary to improve their immunogenicity. In this study, we have evaluated the use of an anionic self-adjuvanting lipopeptide containing the TLR2 agonist Pam(2)Cys (E(8)Pam(2)Cys) to enhance the immunogenicity of VLPs containing the HCV structural proteins (core, E1 and E2) of genotype 1a. While co-formulation of this lipopeptide with VLPs only resulted in marginal improvements in dendritic cell (DC) uptake, its ability to concomitantly induce DC maturation at very small doses is a feature not observed using VLPs alone or in the presence of an aluminium hydroxide-based adjuvant (Alum). Dramatically improved VLP and E2-specific antibody responses were observed in VLP+E(8)Pam(2)Cys vaccinated mice where up to 3 doses of non-adjuvanted or traditionally alum-adjuvanted VLPs was required to match the antibody titres obtained with a single dose of VLPs formulated with this lipopeptide. This result also correlated with significantly higher numbers of specific antibody secreting cells that was detected in the spleens of VLP+E(8)Pam(2)Cys vaccinated mice and greater ability of sera from these mice to neutralise the binding and uptake of VLPs by Huh7 cells. Moreover, vaccination of HLA-A2 transgenic mice with this formulation also induced better VLP-specific IFN-γ-mediated responses compared to non-adjuvanted VLPs but comparable levels to that achieved when coadministered with complete freund’s adjuvant. These results suggest overall that the immunogenicity of HCV VLPs can be significantly improved by the addition of this novel adjuvant by targeting their delivery to DCs and could therefore constitute a viable vaccine strategy for the treatment of HCV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472981/ doi: 10.1371/journal.pone.0047492 id: cord-286708-igu984oc author: Chua, Kaw Bing title: Identification and Characterization of a New Orthoreovirus from Patients with Acute Respiratory Infections date: 2008-11-25 words: 4359.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-286708-igu984oc.txt txt: ./txt/cord-286708-igu984oc.txt summary: Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Here, we report the discovery and characterization of Kampar virus (KamV), the fourth member in the NBV species group and its isolation from a human patient with fever and acute respiratory illness. Due to the similar CPE morphology ( Figure 1 ) and cell line susceptibility patterns between KamV and the recently discovered Melaka virus (MelV), which also causes acute respiratory diseases in humans [5] , immunofluorescent antibody testing was conducted to examine cross reactivity. abstract: First discovered in the early 1950s, reoviruses (respiratory enteric orphan viruses) were not associated with any known disease, and hence named orphan viruses. Recently, our group reported the isolation of the Melaka virus from a patient with acute respiratory disease and provided data suggesting that this new orthoreovirus is capable of human-to-human transmission and is probably of bat origin. Here we report yet another Melaka-like reovirus (named Kampar virus) isolated from the throat swab of a 54 year old male patient in Kampar, Perak, Malaysia who was suffering from high fever, acute respiratory disease and vomiting at the time of virus isolation. Serological studies indicated that Kampar virus was transmitted from the index case to at least one other individual and caused respiratory disease in the contact case. Sequence analysis of the four small class genome segments indicated that Kampar and Melaka viruses are closely related. This was confirmed by virus neutralization assay, showing an effective two-way cross neutralization, i.e., the serum against one virus was able to neutralize the other. Although the exact origin of Kampar virus is unknown, epidemiological tracing revealed that the house of the index case is surrounded by fruit trees frequently visited by fruit bats. There is a high probability that Kampar virus originated from bats and was transmitted to humans via bat droppings or contaminated fruits. The discovery of Kampar virus highlights the increasing trend of emergence of bat zoonotic viruses and the need to expand our understanding of bats as a source of many unknown viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/19030226/ doi: 10.1371/journal.pone.0003803 id: cord-003551-jzfl4xuk author: Ciejka, Justyna title: Synthetic sulfonated derivatives of poly(allylamine hydrochloride) as inhibitors of human metapneumovirus date: 2019-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human metapneumovirus (hMPV) is a widely distributed pathogen responsible for acute upper and lower respiratory infections of varying severity. Previously, we reported that N-sulfonated derivatives of poly(allylamine hydrochloride) (NSPAHs) efficiently inhibit replication of the influenza virus in vitro and ex vivo. Here, we show a dose dependent inhibition of hMPV infection by NSPAHs in LLC-MK2 cells. The results showed strong antiviral properties of NSPAHs. While the activity of NSPAHs is comparable to those of carrageenans, they show better physicochemical properties and may be delivered at high concentrations. The functional assays showed that tested polymers block hMPV release from infected cells and, consequently, constrain virus spread. Moreover, further studies on viruses utilizing different egress mechanisms suggest that observed antiviral effect depend on selective inhibition of viruses budding from the cell surface. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438514/ doi: 10.1371/journal.pone.0214646 id: cord-312367-24huwt3y author: Coelho, Camila title: Biochemical screening for SARS-CoV-2 main protease inhibitors date: 2020-10-06 words: 3351.0 sentences: 210.0 pages: flesch: 49.0 cache: ./cache/cord-312367-24huwt3y.txt txt: ./txt/cord-312367-24huwt3y.txt summary: As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). As viral proteases, following polymerases, are the most prominent targets for antiviral drug design [9] , here we describe initial biochemical screenings with recombinant purified SARS-CoV-2 M pro performed in order to define possible candidates which could serve as lead compounds for the design of future COVID-19 therapies. In order to contribute to the ongoing worldwide research and development efforts to contain COVID-19, we cloned, expressed recombinantly in E.coli BL21(DE3) and purified an important drug target of SARS-CoV-2, its main protease (M pro ). From these obtained compounds, esculetin-4-carboxylic acid ethyl ester (IC 50 = 46 μM in M pro inhibition assays), a coumarin derivative and natural product, demonstrated an EC 50 of 112 μM (median toxic concentration TC 50 >800μM) in Vero-cell SARS-CoV assays [13] and MP576 (IC 50 = 2.5 μM), a quinolinecarboxylate, demonstrated an EC 50 of 7 μM (TC 50 >50μM) [15, 17] , thus validating the M pro biochemical screening approach for the development of SARS-CoV drugs. abstract: The Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic represents a global challenge. SARS-CoV-2's ability to replicate in host cells relies on the action of its non-structural proteins, like its main protease (M(pro)). This cysteine protease acts by processing the viruses' precursor polyproteins. As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 M(pro). A fluorescent assay was used to identify inhibitors in a compound library containing known drugs, bioactive molecules and natural products. These screens led to the identification of 13 inhibitors with IC(50) values ranging from 0.2 μM to 23 μM. The screens confirmed several known SARS-CoV M(pro) inhibitors as inhibitors of SARS-CoV-2 M(pro), such as the organo-mercuric compounds thimerosal and phenylmercuric acetate. Benzophenone derivatives could also be identified among the most potent screening hits. Additionally, Evans blue, a sulfonic acid-containing dye, could be identified as an M(pro) inhibitor. The obtained compounds could be of interest as lead compounds for the development of future SARS-CoV-2 drugs. url: https://doi.org/10.1371/journal.pone.0240079 doi: 10.1371/journal.pone.0240079 id: cord-307540-dr5m9pfk author: Coelho, Flávio C. title: Assessing the spread of COVID-19 in Brazil: Mobility, morbidity and social vulnerability date: 2020-09-18 words: 3517.0 sentences: 201.0 pages: flesch: 52.0 cache: ./cache/cord-307540-dr5m9pfk.txt txt: ./txt/cord-307540-dr5m9pfk.txt summary: Probabilistic models were used to calculate the probability of COVID-19 spread from São Paulo and Rio de Janeiro, the initial hotspots, using mobility data from the pre-epidemic period, while multivariate cluster analysis of socio-economic indices was done to identify areas with similar social vulnerability. To identify regions with high geographical and social vulnerability, we proposed a classification scheme based on three main criteria: population mobility, socio-demographic-economic characteristics, and the available health care infrastructure in terms of hospital capacity. To assess the probability of COVID-19 spreading within Brazil, in the absence of mobility restrictions, we first calculated the effective distance (E f (i,j)) between micro-regions using the air travel data. We computed the effective distance, E f (i,j), between each micro-region and the two COVID-19''s hotspots, Rio de Janeiro and Sao Paulo. Mostly urban micro-regions, with above-average life expectancy, with comparatively less social inequality, less population living in extreme poverty, better access to water supply and sewage disposal services, higher education. abstract: Brazil detected community transmission of COVID-19 on March 13, 2020. In this study we identified which areas in the country were the most vulnerable for COVID-19, both in terms of the risk of arrival of cases, the risk of sustained transmission and their social vulnerability. Probabilistic models were used to calculate the probability of COVID-19 spread from São Paulo and Rio de Janeiro, the initial hotspots, using mobility data from the pre-epidemic period, while multivariate cluster analysis of socio-economic indices was done to identify areas with similar social vulnerability. The results consist of a series of maps of effective distance, outbreak probability, hospital capacity and social vulnerability. They show areas in the North and Northeast with high risk of COVID-19 outbreak that are also highly socially vulnerable. Later, these areas would be found the most severely affected. The maps produced were sent to health authorities to aid in their efforts to prioritize actions such as resource allocation to mitigate the effects of the pandemic. In the discussion, we address how predictions compared to the observed dynamics of the disease. url: https://doi.org/10.1371/journal.pone.0238214 doi: 10.1371/journal.pone.0238214 id: cord-001092-pkps5j8w author: Coleman, Ryan G. title: Ligand Pose and Orientational Sampling in Molecular Docking date: 2013-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×10(10) to 4×10(10) to 1×10(11) to 2×10(11) to 5×10(11) mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787967/ doi: 10.1371/journal.pone.0075992 id: cord-289017-vwye3pk9 author: Comach, Guillermo title: Sentinel Surveillance of Influenza-Like Illness in Two Hospitals in Maracay, Venezuela: 2006–2010 date: 2012-09-11 words: 6262.0 sentences: 301.0 pages: flesch: 47.0 cache: ./cache/cord-289017-vwye3pk9.txt txt: ./txt/cord-289017-vwye3pk9.txt summary: CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Recent prospective studies, which utilized more sensitive methods for detecting respiratory viruses such as multiplex polymerase chain reaction (PCR), have similarly demonstrated that the highest rates of viral respiratory infection occur among children and the frequency of infection tends to decrease with age due to increasing acquired immunity [8] . On the other hand, the percentage of influenza viruses (not including pH1N1) detected in our study during a similar period of time, but in different years accounted for the significant differences found in both studies: a) the collection, preservation and further processing of respiratory samples, and b) the type of cells and IFA reagents used for virus isolation and identification. In contrast, a prospective study of ILI among Brazilian adults, which utilized viral isolation and RT-PCR testing on respiratory samples, detected rhinoviruses in 19.6% of patients [14] . abstract: BACKGROUND: Limited information exists on the epidemiology of acute febrile respiratory illnesses in tropical South American countries such as Venezuela. The objective of the present study was to examine the epidemiology of influenza-like illness (ILI) in two hospitals in Maracay, Venezuela. METHODOLOGY/PRINCIPAL FINDINGS: We performed a prospective surveillance study of persons with ILI who presented for care at two hospitals in Maracay, Venezuela, from October 2006 to December 2010. A respiratory specimen and clinical information were obtained from each participant. Viral isolation and identification with immunofluorescent antibodies and molecular methods were employed to detect respiratory viruses such as adenovirus, influenza A and B, parainfluenza, and respiratory sincytial virus, among others. There were 916 participants in the study (median age: 17 years; range: 1 month – 86 years). Viruses were identified in 143 (15.6%) subjects, and one participant was found to have a co-infection with more than one virus. Influenza viruses, including pandemic H1N1 2009, were the most frequently detected pathogens, accounting for 67.4% (97/144) of the viruses detected. Adenovirus (15/144), parainfluenza virus (13/144), and respiratory syncytial virus (11/144) were also important causes of ILI in this study. Pandemic H1N1 2009 virus became the most commonly isolated influenza virus during its initial appearance in 2009. Two waves of the pandemic were observed: the first which peaked in August 2009 and the second - higher than the preceding - that peaked in October 2009. In 2010, influenza A/H3N2 re-emerged as the most predominant respiratory virus detected. CONCLUSIONS/SIGNIFICANCE: Influenza viruses were the most commonly detected viral organisms among patients with acute febrile respiratory illnesses presenting at two hospitals in Maracay, Venezuela. Pandemic H1N1 2009 influenza virus did not completely replace other circulating influenza viruses during its initial appearance in 2009. Seasonal influenza A/H3N2 was the most common influenza virus in the post-pandemic phase. url: https://www.ncbi.nlm.nih.gov/pubmed/22984519/ doi: 10.1371/journal.pone.0044511 id: cord-276372-q1fzxt3r author: Conde, Dalia A. title: Zoos through the Lens of the IUCN Red List: A Global Metapopulation Approach to Support Conservation Breeding Programs date: 2013-12-11 words: 4780.0 sentences: 225.0 pages: flesch: 48.0 cache: ./cache/cord-276372-q1fzxt3r.txt txt: ./txt/cord-276372-q1fzxt3r.txt summary: To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. To understand the complexity of maintaining CBPs of threatened species across the ISIS zoo network, we developed a second algorithm to find the optimal radial distance from any given zoo at which the probability of finding a metapopulation size of at least 50, 100 or 250 recruited living individuals was highest relative to that radial distance. As expected, the optimal distance radii and the number of zoos required to maximize the probability of reaching a given population increase with the metapopulation size threshold (.50, .100 and .250 individuals) ( Figure 3) . Therefore, for the zoo community, one of the main challenges of managing their threatened species in CBPs is the complexity of moving individuals across borders and the coordination of conservation efforts among zoos and other institutions at a global level. abstract: Given current extinction trends, the number of species requiring conservation breeding programs (CBPs) is likely to increase dramatically. To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. Our results show that 695 of the 3,955 (23%) terrestrial vertebrate species in ISIS zoos are threatened. Only two of the 59 taxonomic orders show a higher proportion of threatened species in ISIS zoos than would be expected if species were selected at random. In addition, for most taxa, the management of a zoo metapopulation of more than 250 individuals will require the coordination of a cluster of 11 to 24 ISIS zoos within a radius of 2,000 km. Thus, in the zoo network, the representation of species that may require CBPs is currently low and the spatial distribution of these zoo populations makes management difficult. Although the zoo community may have the will and the logistical potential to contribute to conservation actions, including CBPs, to do so will require greater collaboration between zoos and other institutions, alongside the development of international agreements that facilitate cross-border movement of zoo animals. To maximize the effectiveness of integrated conservation actions that include CBPs, it is fundamental that the non-zoo conservation community acknowledges and integrates the expertise and facilities of zoos where it can be helpful. url: https://doi.org/10.1371/journal.pone.0080311 doi: 10.1371/journal.pone.0080311 id: cord-349781-l93978vq author: Cong, Yu title: MERS-CoV pathogenesis and antiviral efficacy of licensed drugs in human monocyte-derived antigen-presenting cells date: 2018-03-22 words: 5653.0 sentences: 311.0 pages: flesch: 51.0 cache: ./cache/cord-349781-l93978vq.txt txt: ./txt/cord-349781-l93978vq.txt summary: Little is known about the pathogenesis and innate antiviral response in primary human monocyte-derived macrophages (MDMs) and dendritic cells (MDDCs) upon MERS-CoV infection. In this study, we assessed MERS-CoV replication as well as induction of inflammatory cytokines and chemokines in MDMs and immature and mature MDDCs. Immature MDDCs and MDMs were permissive for MERS-CoV infection, while mature MDDCs were not, with stimulation of proinflammatory cytokine and chemokine upregulation in MDMs, but not in MDDCs. To further evaluate the antiviral activity of well-defined drugs in primary antigen presenting cells (APCs), three compounds (chloroquine, chlorpromazine and toremifine), each with broad-spectrum antiviral activity in immortalized cell lines, were evaluated in MDMs and MDDCs to determine their antiviral effect on MERS-CoV infection. However, MERS-CoV continued to propagate in immature MDDCs up to 8 days pi, demonstrating differential infection and replication capabilities in MDMs and immature MDDCs. To compare the ability of MERS-CoV to induce innate immune responses in three types of APCs, the release of cytokines and chemokines was measured from virus-or mock-infected cells. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) presents an emerging threat to public health worldwide by causing severe respiratory disease in humans with high virulence and case fatality rate (about 35%) since 2012. Little is known about the pathogenesis and innate antiviral response in primary human monocyte-derived macrophages (MDMs) and dendritic cells (MDDCs) upon MERS-CoV infection. In this study, we assessed MERS-CoV replication as well as induction of inflammatory cytokines and chemokines in MDMs and immature and mature MDDCs. Immature MDDCs and MDMs were permissive for MERS-CoV infection, while mature MDDCs were not, with stimulation of proinflammatory cytokine and chemokine upregulation in MDMs, but not in MDDCs. To further evaluate the antiviral activity of well-defined drugs in primary antigen presenting cells (APCs), three compounds (chloroquine, chlorpromazine and toremifine), each with broad-spectrum antiviral activity in immortalized cell lines, were evaluated in MDMs and MDDCs to determine their antiviral effect on MERS-CoV infection. While chloroquine was not active in these primary cells, chlorpromazine showed strong anti-MERS-CoV activity, but it was associated with high cytotoxicity narrowing the potential window for drug utilization. Unlike in established cells, toremifene had marginal activity when tested in antigen presenting cells, with high apparent cytotoxicity, also limiting its potential as a therapeutic option. These results demonstrate the value of testing drugs in primary cells, in addition to established cell lines, before initiating preclinical or clinical studies for MERS treatment and the importance of carefully assessing cytotoxicity in drug screen assays. Furthermore, these studies also highlight the role of APCs in stimulating a robust protective immune response to MERS-CoV infection. url: https://doi.org/10.1371/journal.pone.0194868 doi: 10.1371/journal.pone.0194868 id: cord-000208-th0wddvc author: Cornelissen, Lisette A. H. M. title: A Single Immunization with Soluble Recombinant Trimeric Hemagglutinin Protects Chickens against Highly Pathogenic Avian Influenza Virus H5N1 date: 2010-05-14 words: 5671.0 sentences: 290.0 pages: flesch: 49.0 cache: ./cache/cord-000208-th0wddvc.txt txt: ./txt/cord-000208-th0wddvc.txt summary: title: A Single Immunization with Soluble Recombinant Trimeric Hemagglutinin Protects Chickens against Highly Pathogenic Avian Influenza Virus H5N1 Such HA trimers, expressed either in insect or mammalian cells, were indeed shown to elicit neutralizing antibodies [16] and to partially protect mice against HPAI H5N1 challenge infection [19] . In view of their promising potential we have evaluated recombinant soluble HA trimers in chickens and mice for their ability to induce protective immunity against infection with HPAI H5N1. Subsequently, vaccination with the sH5 3 preparation was shown to provide complete protection against challenge with HPAI H5N1 both in mice and in chickens, in the latter already after a single immunization. In the present study we evaluated the vaccine potential of a recombinant soluble H5 protein (sH5 3 ) to protect chickens and mice against a lethal infection with HPAI H5N1. A pseudotype baculovirusmediated vaccine confers protective immunity against lethal challenge with H5N1 avian influenza virus in mice and chickens abstract: BACKGROUND: The highly pathogenic avian influenza (HPAI) virus H5N1 causes multi-organ disease and death in poultry, resulting in significant economic losses in the poultry industry. In addition, it poses a major public health threat as it can be transmitted directly from infected poultry to humans with very high (60%) mortality rate. Effective vaccination against HPAI H5N1 would protect commercial poultry and would thus provide an important control measure by reducing the likelihood of bird-to-bird and bird-to-human transmission. METHODOLOGY/PRINCIPAL FINDINGS: In the present study we evaluated the vaccine potential of recombinant soluble trimeric subtype 5 hemagglutinin (sH5(3)) produced in mammalian cells. The secreted, purified sH5(3) was biologically active as demonstrated by its binding to ligands in a sialic acid-dependent manner. It was shown to protect chickens, in a dose-dependent manner, against a lethal challenge with H5N1 after a single vaccination. Protected animals did not shed challenge virus as determined by a quantitative RT-PCR on RNA isolated from trachea and cloaca swabs. Also in mice, vaccination with sH5(3) provided complete protection against challenge with HPAI H5N1. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that sH5(3) constitutes an attractive vaccine antigen for protection of chickens and mammals against HPAI H5N1. As these recombinant soluble hemagglutinin preparations can be produced with high yields and with relatively short lead time, they enable a rapid response to circulating and potentially pandemic influenza viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871037/ doi: 10.1371/journal.pone.0010645 id: cord-000158-d08buwtu author: Corti, Davide title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals date: 2010-01-20 words: 8060.0 sentences: 343.0 pages: flesch: 44.0 cache: ./cache/cord-000158-d08buwtu.txt txt: ./txt/cord-000158-d08buwtu.txt summary: The 2G12 epitope is not present in the majority of clade C isolates [27] , but, of more concern, no 2G12-like activity has been detected in the sera of HIV-1 infected individuals [21, 22] , suggesting that this type of neutralizing antibody may not be generally amenable to elicitation by B cells. By using an improved memory B cell immortalization method [41] , combined with highthroughput parallel screening with a panel of recombinant Envbased antigens, we isolated a panel of 58 human mAbs which we have characterized with regard to epitope specificity and breadth of neutralization. The mAbs were purified and further characterized for binding specificity and neutralizing activity using an extended panel of recombinant Env proteins and pseudoviruses representative of several HIV-1 clades with diverse coreceptor usage, geographic origin and conformation. abstract: BACKGROUND: The isolation of human monoclonal antibodies (mAbs) that neutralize a broad spectrum of primary HIV-1 isolates and the characterization of the human neutralizing antibody B cell response to HIV-1 infection are important goals that are central to the design of an effective antibody-based vaccine. METHODS AND FINDINGS: We immortalized IgG(+) memory B cells from individuals infected with diverse clades of HIV-1 and selected on the basis of plasma neutralization profiles that were cross-clade and relatively potent. Culture supernatants were screened using various recombinant forms of the envelope glycoproteins (Env) in multiple parallel assays. We isolated 58 mAbs that were mapped to different Env surfaces, most of which showed neutralizing activity. One mAb in particular (HJ16) specific for a novel epitope proximal to the CD4 binding site on gp120 selectively neutralized a multi-clade panel of Tier-2 HIV-1 pseudoviruses, and demonstrated reactivity that was comparable in breadth, but distinct in neutralization specificity, to that of the other CD4 binding site-specific neutralizing mAb b12. A second mAb (HGN194) bound a conserved epitope in the V3 crown and neutralized all Tier-1 and a proportion of Tier-2 pseudoviruses tested, irrespective of clade. A third mAb (HK20) with broad neutralizing activity, particularly as a Fab fragment, recognized a highly conserved epitope in the HR-1 region of gp41, but showed striking assay-dependent selectivity in its activity. CONCLUSIONS: This study reveals that by using appropriate screening methods, a large proportion of memory B cells can be isolated that produce mAbs with HIV-1 neutralizing activity. Three of these mAbs show unusual breadth of neutralization and therefore add to the current panel of HIV-1 neutralizing antibodies with potential for passive protection and template-based vaccine design. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808385/ doi: 10.1371/journal.pone.0008805 id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 words: 5581.0 sentences: 278.0 pages: flesch: 48.0 cache: ./cache/cord-260647-7bjhobg7.txt txt: ./txt/cord-260647-7bjhobg7.txt summary: A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The aim of this study was to develop real time RT-PCR assays for detection of a total of 19 human enteric viruses (including 3 genogroupes of norovirus and 4 coronaviruses) and two control process viruses (mengovirus and murine norovirus) generally used for monitoring the recovery of viral foodstuff extraction methods. The sensitivity of conventional qPCR assays targeting 21 viral genomes was compared to the quantitative digital RT-PCR array and to the qualitative nanofluidic real-time PCR array performed on Fluidigm''s BioMark System. Similarly, by testing genomes from viruses in stools and RNA from virus production in cells, the limit of detection (LOD) as determined by RT-dPCR was respectively 1.5 to 3.4 log 10 and 1.6 to 2.1 log 10 lower than the expected copy numbers calculated via the standard curve by RT-qPCR. abstract: Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log(10). Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log(10). Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log(10) lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log(10). Conversely, sensitivity was only 0.30 log(10) better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health. url: https://www.ncbi.nlm.nih.gov/pubmed/26824897/ doi: 10.1371/journal.pone.0147832 id: cord-258366-fu9b446y author: Couto, Carla R. title: Fighting Misconceptions to Improve Compliance with Influenza Vaccination among Health Care Workers: An Educational Project date: 2012-02-06 words: 3287.0 sentences: 180.0 pages: flesch: 49.0 cache: ./cache/cord-258366-fu9b446y.txt txt: ./txt/cord-258366-fu9b446y.txt summary: At Hospital das Clinicas, University of Sã o Paulo School of Medical Sciences, a previous study showed a 34% compliance with influenza vaccination among HCWs. In the mentioned study, the main reasons for non-compliance were the perception of vaccine inefficacy and the fear of adverse reactions [4] . To diminish the arguments of fear of adverse events or perception of vaccine inefficacy, this prospective study was conducted to demonstrate to a subset of HCWs from our hospital, that severe adverse events following influenza vaccination are rare and the episodes of respiratory symptoms occurring in the first four months after vaccination are generally caused by other respiratory viruses and not by influenza virus. As expected, no severe adverse event was observed in the present study, and the events more frequently reported, such as headache, myalgia and malaise could be related to influenza vaccine itself as well as to other causes, given their unspecificity. abstract: The compliance with influenza vaccination is poor among health care workers (HCWs) due to misconceptions about safety and effectiveness of influenza vaccine. We proposed an educational prospective study to demonstrate to HCWs that influenza vaccine is safe and that other respiratory viruses (RV) are the cause of respiratory symptoms in the months following influenza vaccination. 398 HCWs were surveyed for adverse events (AE) occurring within 48 h of vaccination. AE were reported by 30% of the HCWs. No severe AE was observed. A subset of 337 HCWs was followed up during four months, twice a week, for the detection of respiratory symptoms. RV was diagnosed by direct immunofluorescent assay (DFA) and real time PCR in symptomatic HCWs. Influenza A was detected in five episodes of respiratory symptoms (5.3%) and other RV in 26 (27.9%) episodes. The incidence density of influenza and other RV was 4.3 and 10.8 episodes per 100 HCW-month, respectively. The educational nature of the present study may persuade HCWs to develop a more positive attitude to influenza vaccination. url: https://doi.org/10.1371/journal.pone.0030670 doi: 10.1371/journal.pone.0030670 id: cord-001142-puj74k7y author: Crescenzo-Chaigne, Bernadette title: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression date: 2013-11-21 words: 3355.0 sentences: 183.0 pages: flesch: 55.0 cache: ./cache/cord-001142-puj74k7y.txt txt: ./txt/cord-001142-puj74k7y.txt summary: To investigate whether, or not, and how the complete NC regions of a given segment are involved in type specificity, we attempted to rescue, by reverse genetics, type A and C influenza viruses with chimeric non-coding sequences. The sole difference between 5''A/3''C(C5U) and wild-type 5''A/3''A viruses being the 3'' distal extremity of the NS segment suggested that the level of NS encoded proteins (i.e. NS1 or/and NS2/NEP) was affected at early stages of infection for this virus (5''A/3''C(C5U)). The major role of the proximal panhandle in type specificity that we identified and the hypothesized involvement of the distal panhandle in transcription need to be tested on the other (2 PFU/cell), viral vRNA and mRNA levels for each segment were evaluated by specific two-step RT-qPCRs previously described [23] . abstract: Exchange of the extremities of the NS segment of type A and C influenza viruses in reverse genetics systems was used to assess their putative role in type specificity. Restoration of each specific proximal panhandle was mandatory to allow the rescue of viruses with heterotypic extremities. Moreover, the transcription level of the modified segment seemed to be directly affected by the distal panhandle strength. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858493/ doi: 10.1371/journal.pone.0081550 id: cord-001420-b4zcvd04 author: Crescenzo-Chaigne, Bernadette title: Chimeric NP Non Coding Regions between Type A and C Influenza Viruses Reveal Their Role in Translation Regulation date: 2014-09-30 words: 6267.0 sentences: 296.0 pages: flesch: 56.0 cache: ./cache/cord-001420-b4zcvd04.txt txt: ./txt/cord-001420-b4zcvd04.txt summary: Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. The sequence of both ends of each segment of each rescued virus was verified as described [9] , and no Influenza NP Non Coding Region Role in Translation PLOS ONE | www.plosone.org genetics, type A and type C viruses with one or both heterotypic ends. These data based on type A influenza virus NP segment showed that it is possible to obtain virus by reverse genetics when a homotypic proximal panhandle and a homotypic strength of the initial distal panhandle are maintained, and that the length of the 59 end plays an important role in the efficiency of rescue. abstract: Exchange of the non coding regions of the NP segment between type A and C influenza viruses was used to demonstrate the importance not only of the proximal panhandle, but also of the initial distal panhandle strength in type specificity. Both elements were found to be compulsory to rescue infectious virus by reverse genetics systems. Interestingly, in type A influenza virus infectious context, the length of the NP segment 5′ NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182659/ doi: 10.1371/journal.pone.0109046 id: cord-000013-pr9i9swk author: Croyle, Maria A. title: Nasal Delivery of an Adenovirus-Based Vaccine Bypasses Pre-Existing Immunity to the Vaccine Carrier and Improves the Immune Response in Mice date: 2008-10-29 words: 6509.0 sentences: 272.0 pages: flesch: 37.0 cache: ./cache/cord-000013-pr9i9swk.txt txt: ./txt/cord-000013-pr9i9swk.txt summary: We have previously found that a single dose of a recombinant adenovirus expressing Ebola Zaire GP given by either the oral or the nasal route is capable of affording protection against lethal challenge in naïve mice and that mucosal immunization can stimulate a broad, prolonged T cell-mediated immune response in both the systemic and mucosal compartments [37] . In an effort to correlate markers of immunity with protection against Ebola infection after mucosal immunization, T and B cell specific immune responses against Ebola glycoprotein were analyzed in mice in the presence or absence of pre-existing immunity (PEI) to adenovirus 10 days after vaccination with a first generation adenovirus serotype 5 vector expressing the Zaire Ebola glycoprotein (Ad5-ZGP). A single intranasal dose of a recombinant Ad5 vaccine expressing the Zaire Ebola glycoprotein conferred 100% protection in both naïve mice and those with pre-existing immunity despite the fact that the strength of the immune response generated by this route of administration was quantitatively lower than that seen in animals vaccinated by intramuscular injection. abstract: Pre-existing immunity to human adenovirus serotype 5 (Ad5) is common in the general population. Bypassing pre-existing immunity could maximize Ad5 vaccine efficacy. Vaccination by the intramuscular (I.M.), nasal (I.N.) or oral (P.O.) route with Ad5 expressing Ebola Zaire glycoprotein (Ad5-ZGP) fully protected naïve mice against lethal challenge with Ebola. In the presence of pre-existing immunity, only mice vaccinated I.N. survived. The frequency of IFN-γ+ CD8+ T cells was reduced by 80% and by 15% in animals vaccinated by the I.M. and P.O. routes respectively. Neutralizing antibodies could not be detected in serum from either treatment group. Pre-existing immunity did not compromise the frequency of IFN-γ+ CD8+ T cells (3.9±1% naïve vs. 3.6±1% pre-existing immunity, PEI) nor anti-Ebola neutralizing antibody (NAB, 40±10 reciprocal dilution, both groups). The number of INF-γ+ CD8+ cells detected in bronchioalveolar lavage fluid (BAL) after I.N. immunization was not compromised by pre-existing immunity to Ad5 (146±14, naïve vs. 120±16 SFC/million MNCs, PEI). However, pre-existing immunity reduced NAB levels in BAL by ∼25% in this group. To improve the immune response after oral vaccination, the Ad5-based vaccine was PEGylated. Mice given the modified vaccine did not survive challenge and had reduced levels of IFN-γ+ CD8+ T cells 10 days after administration (0.3±0.3% PEG vs. 1.7±0.5% unmodified). PEGylation did increase NAB levels 2-fold. These results provide some insight about the degree of T and B cell mediated immunity necessary for protection against Ebola virus and suggest that modification of the virus capsid can influence the type of immune response elicited by an Ad5-based vaccine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2569416/ doi: 10.1371/journal.pone.0003548 id: cord-254340-e1x0z3rh author: Cruz, Christian Joy Pattawi title: Exploring the young demographic profile of COVID-19 cases in Hong Kong: Evidence from migration and travel history data date: 2020-06-26 words: 4963.0 sentences: 227.0 pages: flesch: 59.0 cache: ./cache/cord-254340-e1x0z3rh.txt txt: ./txt/cord-254340-e1x0z3rh.txt summary: Using detailed case data from Hong Kong''s Centre for Health Department and Immigration Department, we analyze the sex and age distribution of the confirmed cases along with their recent travel histories and immigration flows for the period January to April 2020. Our analysis highlights Hong Kong''s high proportion of imported cases and large overseas student population in developing COVID-19 hotspot areas such as the United Kingdom. Our study includes an examination of the age and sex distribution of the COVID-19 confirmed cases in Hong Kong and an exploration of how the different measures to combat this outbreak resulted in a relatively low number of cases and deaths. In this paper, we highlight the potential impact of the young profile of the confirmed cases on the total number of mortalities and the effect of early, aggressive policy measures including travel bans, enforced quarantines and contact-tracing imposed by the Hong Kong government as early as January 27, 2020 in containing the spread of the COVID-19. abstract: This paper investigates the profile of COVID-19 cases in Hong Kong, highlighting the unique age structure of confirmed cases compared to other territories. While the majority of cases in most territories around the world have fitted an older age profile, our analysis shows that positive cases in Hong Kong have been concentrated among younger age groups, with the largest incidence of cases reported in the 15–24 age group. This is despite the population’s rapidly aging structure and extremely high levels of population density. Using detailed case data from Hong Kong’s Centre for Health Department and Immigration Department, we analyze the sex and age distribution of the confirmed cases along with their recent travel histories and immigration flows for the period January to April 2020. Our analysis highlights Hong Kong’s high proportion of imported cases and large overseas student population in developing COVID-19 hotspot areas such as the United Kingdom. Combined with community action and targeted and aggressive early policy measures taken to contain the virus, these factors may have contributed to the uniquely younger age structure of COVID-19 cases in the city. Consequently, this young profile of confirmed cases may have prevented fatalities in the territory. Recent research has highlighted the importance of a demographic approach to understanding COVID-19 transmission and fatality rates. The experience in Hong Kong shows that while an older population age structure may be important for understanding COVID-19 fatality, it is not a given. From a social science perspective at least, there is ‘no easy answer’ to why one area should experience COVID-19 differently from another. url: https://www.ncbi.nlm.nih.gov/pubmed/32589645/ doi: 10.1371/journal.pone.0235306 id: cord-326011-5rmhjbri author: Cui, Dawei title: Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study date: 2016-11-01 words: 3508.0 sentences: 172.0 pages: flesch: 44.0 cache: ./cache/cord-326011-5rmhjbri.txt txt: ./txt/cord-326011-5rmhjbri.txt summary: title: Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality worldwide in children aged <5 years and older adults with acute lower respiratory infections (ALRIs). Clinical and epidemiologic data pertaining to hospitalized patients of all ages with laboratory-confirmed RSV infection by PCR assay were collected and analyzed in this study. Respiratory syncytial virus (RSV) is a leading cause of viral infection in children and older adults worldwide, particularly young children aged <5 years [1] . In this study, we aimed to evaluate the epidemiology, clinical characteristics and management of ALRIs caused by RSV infection among hospitalized patients of all age groups in eastern China between 2009 and 2013 in a hospital-based surveillance study. Clinical characteristics and risk factors of severe respiratory syncytial virus-associated acute lower respiratory tract infections in hospitalized infants abstract: Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality worldwide in children aged <5 years and older adults with acute lower respiratory infections (ALRIs). However, few studies regarding the epidemiology of hospitalizations for RSV infection have been performed previously in China. Here, we aimed to describe the clinical and epidemiologic characteristics of hospitalized patients with laboratory-confirmed RSV infection in eastern China. Active surveillance for hospitalized ALRI patients using a broad case definition based on symptoms was performed from 2009–2013 in 12 sentinel hospitals in eastern China. Clinical and epidemiologic data pertaining to hospitalized patients of all ages with laboratory-confirmed RSV infection by PCR assay were collected and analyzed in this study. From 2009 to 2013, 1046 hospitalized patients with laboratory-confirmed RSV infection were enrolled in this study, and 14.7% of patients had subtype A, 24.2% of patients had subtype B, 23.8% of patients with subtype not performed, and 37.3% of patients had RSV coinfections with other viruses. RSV and influenza coinfections (33.3%) were the most common coinfections noted in this study. Moreover, young children aged <5 years (89.1%, 932/1046), particularly young infants aged <1 year (43.3%, 453/1046), represented the highest proportion of patients with RSV infections. In contrast, older adults aged ≥60 years (1.1%, 12/1046) represented the lowest proportion of patients with RSV infections among enrolled patients. The peak RSV infection period occurred mainly during autumn and winter, and 57% and 66% of patients exhibited symptoms such as fever (body temperature ≥38°C) and cough separately. Additionally, only a small number of patients were treated with broad-spectrum antiviral drugs, and most of patients were treated with antimicrobial drugs that were not appropriate for RSV infection. RSV is a leading viral pathogen and a common cause of viral infection in young children aged <5 years with ALRIs in eastern China. Effective vaccines and antiviral agents targeting RSV are needed to mitigate its large public health impact. url: https://www.ncbi.nlm.nih.gov/pubmed/27802292/ doi: 10.1371/journal.pone.0165437 id: cord-348807-9xxc5hyl author: Cuomo, Raphael E. title: Sub-national longitudinal and geospatial analysis of COVID-19 tweets date: 2020-10-28 words: 3235.0 sentences: 143.0 pages: flesch: 43.0 cache: ./cache/cord-348807-9xxc5hyl.txt txt: ./txt/cord-348807-9xxc5hyl.txt summary: METHODS: In an effort to better understand the impacts of COVID-19, we concurrently assessed the geospatial and longitudinal distributions of Twitter messages about COVID-19 which were posted between March 3rd and April 13th and compared these results with the number of confirmed cases reported for sub-national levels of the United States. This study suggests that, across subnational areas within the United States, there exists a highly variable threshold of perceived dangerousness and/or intrusiveness required to activate outbreak-related conversations on social media platforms such as Twitter, a finding that can inform future outbreak communication and health promotion strategies. Concurrent geospatial and longitudinal analyses also indicate that predominantly rural areas of the United States increased engagement in COVID-19 social media conversations at later stages of the study timeframe. This study is unique in that it uses Twitter data as a proxy measure for assessing the concurrent longitudinal and geospatial distributions of attention to COVID-19 across local and regional communities in the United States. abstract: OBJECTIVES: According to current reporting, the number of active coronavirus disease 2019 (COVID-19) infections is not evenly distributed, both spatially and temporally. Reported COVID-19 infections may not have properly conveyed the full extent of attention to the pandemic. Furthermore, infection metrics are unlikely to illustrate the full scope of negative consequences of the pandemic and its associated risk to communities. METHODS: In an effort to better understand the impacts of COVID-19, we concurrently assessed the geospatial and longitudinal distributions of Twitter messages about COVID-19 which were posted between March 3rd and April 13th and compared these results with the number of confirmed cases reported for sub-national levels of the United States. Geospatial hot spot analysis was also conducted to detect geographic areas that might be at elevated risk of spread based on both volume of tweets and number of reported cases. RESULTS: Statistically significant aberrations of high numbers of tweets were detected in approximately one-third of US states, most of which had relatively high proportions of rural inhabitants. Geospatial trends toward becoming hotspots for tweets related to COVID-19 were observed for specific rural states in the United States. DISCUSSION: Population-adjusted results indicate that rural areas in the U.S. may not have engaged with the COVID-19 topic until later stages of an outbreak. Future studies should explore how this dynamic can inform future outbreak communication and health promotion. url: https://doi.org/10.1371/journal.pone.0241330 doi: 10.1371/journal.pone.0241330 id: cord-289510-spmknns5 author: Curado, Evaldo M. F. title: A discrete-time-evolution model to forecast progress of Covid-19 outbreak date: 2020-10-29 words: 5920.0 sentences: 325.0 pages: flesch: 67.0 cache: ./cache/cord-289510-spmknns5.txt txt: ./txt/cord-289510-spmknns5.txt summary: Here, we present a model that can easily incorporate these available data sets and is based on discrete-time equations to forecast the number of confirmed cases by Covid-19 in any given country for the next 14 days. Among its strengths, the presented model: (i) presents low relative error rates, as tested in data from Brazil, South Korea and UK; (ii) provides easily interpretable results, specifically the predicted number of infected people in the next 14 days; (iii) presents results that are directly comparable across countries; and (iv) incorporates the average time related to the disease incubation period (asymptomatic phase) and the average time related to the symptomatic phase, both parameters adjustable according to the pandemics'' characteristics. With the intention to test the method and find good values for the parameters α and β, we considered our fictitious t f N ¼ 102-th day, so it is possible to compare the total number of infected people as provided by the original source (JHU) with the predicted data generated by the model. abstract: Here we present a discrete-time-evolution model with one day interval to forecast the propagation of Covid-19. The proposed model can be easily implemented with daily updated data sets of the pandemic publicly available by distinct online sources. It has only two adjustable parameters and it predicts the evolution of the total number of infected people in a country for the next 14 days if parameters do not change during the analyzed period. The model incorporates the main aspects of the disease such as the fact that there are asymptomatic and symptomatic phases (both capable of propagating the virus), and that these phases take almost two weeks before the infected person status evolves to the next (asymptomatic becomes symptomatic or symptomatic becomes either recovered or dead). A striking advantage of the model for its implementation by the health sector is that it gives directly the number of total infected people in each day (in thousands, tens of thousands or hundred of thousands). Here, the model is tested with data from Brazil, UK and South Korea, presenting low error rates on the prediction of the evolution of the disease in all analyzed countries. We hope this model may be a useful tool to estimate the propagation of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/33119708/ doi: 10.1371/journal.pone.0241472 id: cord-293794-vudufao5 author: Cuthbertson, Leah title: Viral respiratory infections and the oropharyngeal bacterial microbiota in acutely wheezing children date: 2019-10-17 words: 4820.0 sentences: 255.0 pages: flesch: 48.0 cache: ./cache/cord-293794-vudufao5.txt txt: ./txt/cord-293794-vudufao5.txt summary: No significant difference in bacterial diversity was observed between samples from those with wheeze and healthy controls. Using 16s rRNA gene sequencing of respiratory samples from children presenting to hospital with acute wheezing, this study aimed to examine whether the bacterial community in the airways of children with acute respiratory wheeze was altered compared with that of nonwheezing children. However, when the microbiota in children with bronchiolitis were compared to those closest in age there was a significant reduction in alpha diversity (richness; p = 0.01, Shannon-Weiner, p = 0.003, inverse Simpsons, p = 0.005) that was not associated with change in bacterial biomass (p = 0.874). When those with a diagnosis of bronchiolitis were compared to other cases that wheezed or age matched control subjects, significant differences in alpha and beta diversity were observed however this may have been driven by subjects with bronchiolitis being significantly younger than other groups of subjects. abstract: Acute viral wheeze in children is a major cause of hospitalisation and a major risk factor for the development of asthma. However, the role of the respiratory tract microbiome in the development of acute wheeze is unclear. To investigate whether severe wheezing episodes in children are associated with bacterial dysbiosis in the respiratory tract, oropharyngeal swabs were collected from 109 children with acute wheezing attending the only tertiary paediatric hospital in Perth, Australia. The bacterial community from these samples was explored using next generation sequencing and compared to samples from 75 non-wheezing controls. No significant difference in bacterial diversity was observed between samples from those with wheeze and healthy controls. Within the wheezing group, attendance at kindergarten or preschool was however, associated with increased bacterial diversity. Rhinovirus (RV) infection did not have a significant effect on bacterial community composition. A significant difference in bacterial richness was observed between children with RV-A and RV-C infection, however this is likely due to the differences in age group between the patient cohorts. The bacterial community within the oropharynx was found to be diverse and heterogeneous. Age and attendance at day care or kindergarten were important factors in driving bacterial diversity. However, wheeze and viral infection were not found to significantly relate to the bacterial community. Bacterial airway microbiome is highly variable in early life and its role in wheeze remains less clear than viral influences. url: https://www.ncbi.nlm.nih.gov/pubmed/31622414/ doi: 10.1371/journal.pone.0223990 id: cord-000905-1rhlu59c author: Cyktor, Joshua C. title: Clonal Expansions of CD8(+) T Cells with IL-10 Secreting Capacity Occur during Chronic Mycobacterium tuberculosis Infection date: 2013-03-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The exact role of CD8(+) T cells during Mycobacterium tuberculosis (Mtb) infection has been heavily debated, yet it is generally accepted that CD8(+) T cells contribute to protection against Mtb. In this study, however, we show that the Mtb-susceptible CBA/J mouse strain accumulates large numbers of CD8(+) T cells in the lung as infection progresses, and that these cells display a dysfunctional and immunosuppressive phenotype (PD-1(+), Tim-3(+), CD122(+)). CD8(+) T cell expansions from the lungs of Mtb-infected CBA/J mice were also capable of secreting the immunosuppressive cytokine interleukin-10 (IL-10), although in vivo CD8(+) T cell depletion did not significantly alter Mtb burden. Further analysis revealed that pulmonary CD8(+) T cells from Mtb-infected CBA/J mice were clonally expanded, preferentially expressing T cell receptor (TcR) Vβ chain 8 (8.2, 8.3) or Vβ 14. Although Vβ8(+) CD8(+) T cells were responsible for the majority of IL-10 production, in vivo depletion of Vβ8(+) did not significantly change the outcome of Mtb infection, which we hypothesize was a consequence of their dual IL-10/IFN-γ secreting profiles. Our data demonstrate that IL-10-secreting CD8(+) T cells can arise during chronic Mtb infection, although the significance of this T cell population in tuberculosis pathogenesis remains unclear. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589362/ doi: 10.1371/journal.pone.0058612 id: cord-349911-dx8wvqkm author: Dahl, Viktor title: Communicable Diseases Prioritized According to Their Public Health Relevance, Sweden, 2013 date: 2015-09-23 words: 4092.0 sentences: 208.0 pages: flesch: 49.0 cache: ./cache/cord-349911-dx8wvqkm.txt txt: ./txt/cord-349911-dx8wvqkm.txt summary: Ten pathogens in the highest priority group (Borrelia, calicivirus, Campylobacter, Echinococcus multilocularis, hepatitis C virus, HIV, respiratory syncytial virus, SARSand MERS coronavirus, tick-borne encephalitis virus and varicella-zoster virus) did not have any surveillance of typing results. The Public Health Agency of Sweden identified the need to use a structured method that takes relevant aspects into account in order to rationally prioritize between different pathogens when allocating resources for surveillance. The Robert Koch Institute invited ten senior external experts and ten internal experts and asked them to score the pathogens with -1, 0 or 1 for ten variables"Incidence", "Work and school absenteeism", "Health care utilization", "Chronicity of illness or sequelae", "Case fatality rate", "Proportion of events requiring public health actions", "Trend", "Public attention", "Prevention and Treatment possibilities") ( Table 1 ). We used a standardized procedure developed at the Robert Koch Institute to generate a list of pathogens prioritized for surveillance to be used by the Public Health Agency of Sweden. abstract: To establish strategic priorities for the Public Health Agency of Sweden we prioritized pathogens according to their public health relevance in Sweden in order to guide resource allocation. We then compared the outcome to ongoing surveillance. We used a modified prioritization method developed at the Robert Koch Institute in Germany. In a Delphi process experts scored pathogens according to ten variables. We ranked the pathogens according to the total score and divided them into four priority groups. We then compared the priority groups to self-reported time spent on surveillance by epidemiologists and ongoing programmes for surveillance through mandatory and/or voluntary notifications and for surveillance of typing results. 106 pathogens were scored. The result of the prioritization process was similar to the outcome of the prioritization in Germany. Common pathogens such as calicivirus and Influenza virus as well as blood-borne pathogens such as human immunodeficiency virus, hepatitis B and C virus, gastro-intestinal infections such as Campylobacter and Salmonella and vector-borne pathogens such as Borrelia were all in the highest priority group. 63% of time spent by epidemiologists on surveillance was spent on pathogens in the highest priority group and all pathogens in the highest priority group, except for Borrelia and varicella-zoster virus, were under surveillance through notifications. Ten pathogens in the highest priority group (Borrelia, calicivirus, Campylobacter, Echinococcus multilocularis, hepatitis C virus, HIV, respiratory syncytial virus, SARS- and MERS coronavirus, tick-borne encephalitis virus and varicella-zoster virus) did not have any surveillance of typing results. We will evaluate the possibilities of surveillance for the pathogens in the highest priority group where we currently do not have any ongoing surveillance and evaluate the need of surveillance for the pathogens from the low priority group where there is ongoing surveillance in order to focus our work on the pathogens with the highest relevance. url: https://doi.org/10.1371/journal.pone.0136353 doi: 10.1371/journal.pone.0136353 id: cord-260843-c97kctjz author: Dai, Lei title: Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake date: 2016-11-16 words: 4635.0 sentences: 255.0 pages: flesch: 46.0 cache: ./cache/cord-260843-c97kctjz.txt txt: ./txt/cord-260843-c97kctjz.txt summary: In vivo, TGEV primarily targets and infects intestinal epithelial cells, which play an important role in glucose absorption via the apical and basolateral transporters Na(+)-dependent glucose transporter 1 (SGLT1) and facilitative glucose transporter 2 (GLUT2), respectively. Our data demonstrate that infection with TGEV resulted in increased glucose uptake and augmented expression of EGFR, SGLT1 and GLUT2. Therefore, in the study, we aimed to examine the in vitro effects of TGEV infection on glucose uptake and the expression of SGLT1 and GLUT2 in porcine intestinal columnar epithelial (IPEC-J2) cells, which have been shown to offer a practical model for studying TGEV infection [11, 12] . Together, these results indicate that EGFR and p-EGFR regulates glucose uptake in mock-infected IPEC-J2 cells by modulation of SGLT1 protein expression. Together, these results indicate that EGFR influences glucose uptake in TGEV-infected cells by promoting both SGLT1 and GLUT2 expression. abstract: Transmissible gastroenteritis virus (TGEV) is a coronavirus that causes villus atrophy, followed by crypt hyperplasia, reduces the activities of intestinal digestive enzymes, and disrupts the absorption of intestinal nutrients. In vivo, TGEV primarily targets and infects intestinal epithelial cells, which play an important role in glucose absorption via the apical and basolateral transporters Na(+)-dependent glucose transporter 1 (SGLT1) and facilitative glucose transporter 2 (GLUT2), respectively. In this study, we therefore sought to evaluate the effects of TGEV infection on glucose uptake and SGLT1 and GLUT2 expression. Our data demonstrate that infection with TGEV resulted in increased glucose uptake and augmented expression of EGFR, SGLT1 and GLUT2. Moreover, inhibition studies showed that EGFR modulated glucose uptake in control and TGEV infected cells. Finally, high glucose absorption was subsequently found to promote TGEV replication. url: https://www.ncbi.nlm.nih.gov/pubmed/27851758/ doi: 10.1371/journal.pone.0165585 id: cord-309981-4p3ybrn1 author: Dai, Ling-Ling title: Anxiety and depressive symptoms among COVID-19 patients in Jianghan Fangcang Shelter Hospital in Wuhan, China date: 2020-08-28 words: 3554.0 sentences: 179.0 pages: flesch: 43.0 cache: ./cache/cord-309981-4p3ybrn1.txt txt: ./txt/cord-309981-4p3ybrn1.txt summary: From February 23, 2020, to February 26, 2020, we obtained sociodemographic and clinical characteristics information of COVID-19 patients in Jianghan Fangcang Shelter Hospital (Wuhan, China) and assessed their mental health status and sleep quality. As with other infectious diseases, preliminary evidence suggests that COVID-19 also causes public panic and mental health stress; symptoms of anxiety and depression are common psychological reactions to the COVID-19 pandemic, and may be associated with sociodemographic factors and sleep quality [6] [7] [8] [9] . This cross-sectional study examined the prevalence of anxiety, depression, and poor sleep quality among 307 patients in Jianghan Fangcang Shelter Hospital in Wuhan, China, 2 months after the start of the COVID-19 pandemic. In addition, using one-sample-tests, it was determined that both SAS (42.92±7.30) and SDS (39.77±10.11) scores of the participants of our study were higher than Chinese norms (SAS, 29.78±10.07, n = 1158; SDS, 33.46±8.55, n = 1340) (both P<0.001) [26] , indicating more severe levels of anxiety and depressive symptoms among COVID-19 patients admitted to Fangcang hospitals, compared with the general public. abstract: Fangcang shelter hospitals were established in China during the coronavirus disease 2019 (COVID-19) pandemic as a countermeasure to stop the spread of the disease. To our knowledge, no research has been conducted on mental health problems among patients in Fangcang shelter hospitals. This study aimed to determine the prevalence and major influencing factors of anxiety and depressive symptoms among COVID-19 patients admitted to Fangcang shelter hospitals. From February 23, 2020, to February 26, 2020, we obtained sociodemographic and clinical characteristics information of COVID-19 patients in Jianghan Fangcang Shelter Hospital (Wuhan, China) and assessed their mental health status and sleep quality. Data were obtained with an online questionnaire. The questionnaire consisted of a set of items on demographic characteristics, a set of items on clinical characteristics, the Self-Rating Anxiety Scale, Self-Rating Depression Scale, and Pittsburgh Sleep Quality Index. Three hundred seven COVID-19 patients who were admitted to Jianghan Fangcang Shelter Hospital participated in this study. The prevalence of anxiety and depressive symptoms were 18.6% and 13.4%, respectively. Poor sleep quality and having ≥ two current physical symptoms were independent risk factors for anxiety symptoms. Female sex, having a family member with confirmed COVID-19, and having ≥ two current physical symptoms were independent risk factors for depressive symptoms. Anxiety and depressive symptoms were found to be common among COVID-19 patients in Fangcang Shelter Hospital, with some patients being at high risk. url: https://www.ncbi.nlm.nih.gov/pubmed/32857826/ doi: 10.1371/journal.pone.0238416 id: cord-316319-m6uha1qn author: Daleno, Cristina title: Phylogenetic Analysis of Human Rhinovirus Isolates Collected from Otherwise Healthy Children with Community-Acquired Pneumonia during Five Successive Years date: 2013-11-19 words: 3942.0 sentences: 177.0 pages: flesch: 53.0 cache: ./cache/cord-316319-m6uha1qn.txt txt: ./txt/cord-316319-m6uha1qn.txt summary: In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). However, most of these studies were carried out in a single year and involved a relatively small number of patients, and only a few analysed specific LRTIs. Consequently, there are few data concerning the circulation of HRVs over a long period of time or the real role of the different species and genotypes in causing LRTIs. The aim of this study was to evaluate the circulation of the different HRV species and genotypes in Italian children with radiographically confirmed CAP during the winter and early spring of five consecutive years as this information could help to develop tailored strategies for the prevention and treatment of pediatric HRV infections. abstract: In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify HRV, and the HRV-positive samples were used for sequencing analysis and to reconstruct the phylogenetic tree. HRV was identified in 198 samples (42.2%), and the VP4/VP2 region was successfully amplified in 151 (76.3%). HRV-A was identified in 78 samples (51.6%), HRV-B in 14 (9.3%) and HRV-C in 59 (39.1%). Forty-seven (31.1%) of the children with HRV infection were aged <1 year, 71 (47.0%) were aged 1-3 years, and 33 (21.9%) were aged ≥4 years. Blast and phylogenetic analyses showed that the HRV strains were closely related to a total of 66 reference genotypes, corresponding to 29 HRV-A, 9 HRV-B and 28 HRV-C strains. Nucleotide variability was 37% between HRV-A and HRV-B, 37.3% between HRV-A and HRV-C, and 39.9% between HRV-B and HRV-C. A number of sequences clustered with known serotypes and, within these clusters, there were strains circulating during several seasons. The most frequently detected genotypes were HRV-A78 (n=17), HRV-A12 (n=9) and HRV-C2 (n=5). This study shows that, although it is mainly associated with HRV-A, pediatric CAP can also be diagnosed in subjects infected by HRV-C and, more rarely, by HRV-B. Moreover, a large number of genotypes may be involved in causing pediatric CAP and can be different from year to year. Although the prolonged circulation of the same genotypes can sometimes be associated with a number of CAP episodes in different years. url: https://doi.org/10.1371/journal.pone.0080614 doi: 10.1371/journal.pone.0080614 id: cord-002473-2kpxhzbe author: Das, Jayanta Kumar title: Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach date: 2017-03-31 words: 4613.0 sentences: 285.0 pages: flesch: 61.0 cache: ./cache/cord-002473-2kpxhzbe.txt txt: ./txt/cord-002473-2kpxhzbe.txt summary: Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. The primary protein sequence is read as consecutive order pairs serially from first amino acid to the end of sequence, and each order pair is nothing but a connected edge between the two nodes where nodes in the graph are involved with different chemical groups of amino acids. Our method of phylogenetic tree formation used the dissimilarity matrix which is obtained for every pair of sequence on the basis of chemical group specific score of amino acids. Based on the phylogenetic tree of five members, we find that the PpcA and PpcD, PpcB and PpcE are mostly closed with regards to the frequency of amino acids of respective eight chemical groups. abstract: Periplasmic c7 type cytochrome A (PpcA) protein is determined in Geobacter sulfurreducens along with its other four homologs (PpcB-E). From the crystal structure viewpoint the observation emerges that PpcA protein can bind with Deoxycholate (DXCA), while its other homologs do not. But it is yet to be established with certainty the reason behind this from primary protein sequence information. This study is primarily based on primary protein sequence analysis through the chemical basis of embedded amino acids. Firstly, we look for the chemical group specific score of amino acids. Along with this, we have developed a new methodology for the phylogenetic analysis based on chemical group dissimilarities of amino acids. This new methodology is applied to the cytochrome c7 family members and pinpoint how a particular sequence is differing with others. Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. Thirdly, we search for unique patterns as subsequences which are common among the group or specific individual member. In all the cases, we are able to show some distinct features of PpcA that emerges PpcA as an outstanding protein compared to its other homologs, resulting towards its binding with deoxycholate. Similarly, some notable features for the structurally dissimilar protein PpcD compared to the other homologs are also brought out. Further, the five members of cytochrome family being homolog proteins, they must have some common significant features which are also enumerated in this study. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376323/ doi: 10.1371/journal.pone.0175031 id: cord-002180-gsdk5x3e author: Davies, Colin title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date: 2016-08-24 words: 4491.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-002180-gsdk5x3e.txt txt: ./txt/cord-002180-gsdk5x3e.txt summary: Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G(0)/G(1) phase as identified for wild-type NS5. Several RNA viruses, including murine norovirus 1 (MNV-1) have been characterized to manipulate cell cycle progression at the G 1 /S restriction point, often creating favorable conditions for viral replication [14] [15] [16] [17] [18] [19] [20] [21] . The effect of NS5 on the host cell cycle was therefore determined by transfection of RAW-Blue cells with RNA transcripts, encoding individual viral genes, NS1-2 from MNV-1 was included as a negative control (Fig 1A) . Furthermore, the NS5(F123A) variant decreased cyclin A protein expression by 67% when compared to the mocktransfected population in a synonymous manner to NS5, strongly implying that the host eukaryotic initiation factor binding domain of NS5 does not play a role in its cell cycle manipulation (Fig 3D) . abstract: Murine norovirus-1 (MNV-1) is known to subvert host cell division inducing an accumulation of cells in the G(0)/G(1) phase, creating conditions where viral replication is favored. This study identified that NS5 (VPg), is capable of inducing cell cycle arrest in the absence of viral replication or other viral proteins in an analogous manner to MNV-1 infection. NS5 expression induced an accumulation of cells in the G(0)/G(1) phase in an asynchronous population by inhibiting progression at the G(1)/S restriction point. Furthermore, NS5 expression resulted in a down-regulation of cyclin A expression in asynchronous cells and inhibited cyclin A expression in cells progressing from G(1) to S phase. The activity of NS5 on the host cell cycle occurs through an uncharacterized function. Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G(0)/G(1) phase as identified for wild-type NS5. To the best of our knowledge, this is the first report of a VPg protein manipulating the host cell cycle. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996510/ doi: 10.1371/journal.pone.0161582 id: cord-265812-1hcp36cw author: De Jong, Cornelis N. title: Etanercept for steroid-refractory acute graft-versus-host disease: A single center experience date: 2017-10-26 words: 3168.0 sentences: 186.0 pages: flesch: 53.0 cache: ./cache/cord-265812-1hcp36cw.txt txt: ./txt/cord-265812-1hcp36cw.txt summary: W.; Van der Klift, Marjolein; Cornelissen, Jan J.; Broers, Annoek E. High dose glucocorticosteroids, are currently recommended as first-line treatment for grade II-IV aGVHD resulting in overall complete responses (CR) in 40%-50% of patients. CONCLUSION: Second-line treatment with etanercept does induce responses in SR-aGVHD of the gut but appears to be associated with poor long-term survival even in responding patients. High dose systemic glucocorticosteroids (steroids) are currently recommended as first-line treatment for grade II-IV aGVHD resulting in overall complete responses (CR) in 40%-50% of patients [2, 3] . Studies evaluating second-line treatment with the anti-TFNα agent etanercept have shown promising results with overall response rates of 50-80% [8] [9] [10] . In conclusion, although second-line treatment of SR-aGVHD of the gut with etanercept was associated with a promising initial response rate, overall survival appeared very poor, mainly due to progression of GVHD and opportunistic infections. abstract: BACKGROUND: Acute graft-versus-host disease (aGVHD) is an important complication of allogeneic stem cell transplantation (alloSCT). High dose glucocorticosteroids, are currently recommended as first-line treatment for grade II-IV aGVHD resulting in overall complete responses (CR) in 40%-50% of patients. No standard second-line regimen has been established. Different options have been reported, including anti-TNFα antibodies. METHODS: We retrospectively reviewed the outcome of 15 patients with steroid-refractory (SR) aGVHD treated with etanercept at our institution. Patients were transplanted for a hematological malignancy and received either a myeloablative or a non-myeloablative conditioning regimen. Prophylaxis of GVHD consisted of cyclosporin A and mycophenolic acid. RESULTS: Acute GVHD was diagnosed at a median of 61 days post-transplantation. All patients had grade III aGVHD of the gut. Second-line treatment with etanercept was started at a median of 13 days after initiation of first-line therapy. Overall response rate was 53%, with CR in 3 patients and PR in 5 patients. Median overall survival after initiation of treatment with etanercept was 66 days (range 5–267) for the entire group. Median overall survival was 99 days (range 47–267 days) for responders and 17 days (range 5–66 days) for non-responders (p<0.01). Nevertheless, all patients died. Causes of death were progressive GVHD in 7 patients (47%), infection in 6 patients (40%), cardiac death in 1 patient (6.7%) and relapse in 1 patient (6,7%). CONCLUSION: Second-line treatment with etanercept does induce responses in SR-aGVHD of the gut but appears to be associated with poor long-term survival even in responding patients. url: https://www.ncbi.nlm.nih.gov/pubmed/29073260/ doi: 10.1371/journal.pone.0187184 id: cord-269690-6r2bfydw author: De Lorenzo, Rebecca title: Residual clinical damage after COVID-19: A retrospective and prospective observational cohort study date: 2020-10-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Data on residual clinical damage after Coronavirus disease-2019 (COVID-19) are lacking. The aims of this study were to investigate whether COVID-19 leaves behind residual dysfunction, and identify patients who might benefit from post-discharge monitoring. All patients aged ≥18 years admitted to the Emergency Department (ED) for COVID-19, and evaluated at post-discharge follow-up between 7 April and 7 May, 2020, were enrolled. Primary outcome was need of follow-up, defined as the presence at follow-up of at least one among: respiratory rate (RR) >20 breaths/min, uncontrolled blood pressure (BP) requiring therapeutic change, moderate to very severe dyspnoea, malnutrition, or new-onset cognitive impairment, according to validated scores. Post-traumatic stress disorder (PTSD) served as secondary outcome. 185 patients were included. Median [interquartile range] time from hospital discharge to follow-up was 23 [20–29] days. 109 (58.9%) patients needed follow-up. At follow-up evaluation, 58 (31.3%) patients were dyspnoeic, 41 (22.2%) tachypnoeic, 10 (5.4%) malnourished, 106 (57.3%) at risk for malnutrition. Forty (21.6%) patients had uncontrolled BP requiring therapeutic change, and 47 (25.4%) new-onset cognitive impairment. PTSD was observed in 41 (22.2%) patients. At regression tree analysis, the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO(2)/FiO(2)) and body mass index (BMI) at ED presentation, and age emerged as independent predictors of the need of follow-up. Patients with PaO(2)/FiO(2) <324 and BMI ≥33 Kg/m(2) had the highest odds to require follow-up. Among hospitalised patients, age ≥63 years, or age <63 plus non-invasive ventilation or diabetes identified those with the highest probability to need follow-up. PTSD was independently predicted by female gender and hospitalisation, the latter being protective (odds ratio, OR, 4.03, 95% confidence interval, CI, 1.76 to 9.47, p 0.0011; OR 0.37, 95% CI 0.14 to 0.92, p 0.033, respectively). COVID-19 leaves behind physical and psychological dysfunctions. Follow-up programmes should be implemented for selected patients. url: https://www.ncbi.nlm.nih.gov/pubmed/33052920/ doi: 10.1371/journal.pone.0239570 id: cord-001045-jm60nxc2 author: DeLisle, Sylvain title: Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy date: 2013-08-13 words: 4332.0 sentences: 209.0 pages: flesch: 45.0 cache: ./cache/cord-001045-jm60nxc2.txt txt: ./txt/cord-001045-jm60nxc2.txt summary: METHODS: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The ARI CDA flagged an outpatient visit if the provider assigned it an ARI-related International Disease Classification, 9 th Revision, Clinical Modification (ICD-9) diagnostic code OR issued a prescription for a cough remedy OR documented at least two symptoms from the above ARI case definition in his/her clinical note, as retrieved by computerized text analysis [10] . Discussion Automated text analyses of chest imaging reports improved the performance of EMR-based CDAs that included structured data elements and free-text search for ARI symptoms. abstract: BACKGROUND: Timely information about disease severity can be central to the detection and management of outbreaks of acute respiratory infections (ARI), including influenza. We asked if two resources: 1) free text, and 2) structured data from an electronic medical record (EMR) could complement each other to identify patients with pneumonia, an ARI severity landmark. METHODS: A manual EMR review of 2747 outpatient ARI visits with associated chest imaging identified x-ray reports that could support the diagnosis of pneumonia (kappa score = 0.88 (95% CI 0.82∶0.93)), along with attendant cases with Possible Pneumonia (adds either cough, sputum, fever/chills/night sweats, dyspnea or pleuritic chest pain) or with Pneumonia-in-Plan (adds pneumonia stated as a likely diagnosis by the provider). The x-ray reports served as a reference to develop a text classifier using machine-learning software that did not require custom coding. To identify pneumonia cases, the classifier was combined with EMR-based structured data and with text analyses aimed at ARI symptoms in clinical notes. RESULTS: 370 reference cases with Possible Pneumonia and 250 with Pneumonia-in-Plan were identified. The x-ray report text classifier increased the positive predictive value of otherwise identical EMR-based case-detection algorithms by 20–70%, while retaining sensitivities of 58–75%. These performance gains were independent of the case definitions and of whether patients were admitted to the hospital or sent home. Text analyses seeking ARI symptoms in clinical notes did not add further value. CONCLUSION: Specialized software development is not required for automated text analyses to help identify pneumonia patients. These results begin to map an efficient, replicable strategy through which EMR data can be used to stratify ARI severity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3742728/ doi: 10.1371/journal.pone.0070944 id: cord-303845-y6ws3u6x author: DeLisle, Sylvain title: Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections date: 2010-10-14 words: 5608.0 sentences: 246.0 pages: flesch: 44.0 cache: ./cache/cord-303845-y6ws3u6x.txt txt: ./txt/cord-303845-y6ws3u6x.txt summary: Several factors, some of which have already been mentioned, may limit the generalizability of our results: 1) factors related to the performance of our study at the VA health care system: a) the veterans study population is mostly male and excludes the pediatric population, a key target for ARI surveillance [44] ; b) veterans health care utilization may differ from that observed in uninsured or privately insured individuals; c) clinical practices, documentation and coding habits by VA practitioners may differ from those observed in solo or group practices or in health systems subject to different financial or quality-control incentives; 2) factors related to our study period: optimal CDAs could differ outside the respiratory infection season, or during periods of heightened apprehension for an influenza epidemic; 3) factors related to our iterative CDA development process, which may have over adapted CDAs to VA''s particular EMR implementation and to our sample dataset in particular, this despite our efforts to maintain a separation between development and validation data subsets; 4) factors related to our text mining approach: a) we did not employ a spell checker prior to applying the NegEx algorithm. abstract: BACKGROUND: The electronic medical record (EMR) contains a rich source of information that could be harnessed for epidemic surveillance. We asked if structured EMR data could be coupled with computerized processing of free-text clinical entries to enhance detection of acute respiratory infections (ARI). METHODOLOGY: A manual review of EMR records related to 15,377 outpatient visits uncovered 280 reference cases of ARI. We used logistic regression with backward elimination to determine which among candidate structured EMR parameters (diagnostic codes, vital signs and orders for tests, imaging and medications) contributed to the detection of those reference cases. We also developed a computerized free-text search to identify clinical notes documenting at least two non-negated ARI symptoms. We then used heuristics to build case-detection algorithms that best combined the retained structured EMR parameters with the results of the text analysis. PRINCIPAL FINDINGS: An adjusted grouping of diagnostic codes identified reference ARI patients with a sensitivity of 79%, a specificity of 96% and a positive predictive value (PPV) of 32%. Of the 21 additional structured clinical parameters considered, two contributed significantly to ARI detection: new prescriptions for cough remedies and elevations in body temperature to at least 38°C. Together with the diagnostic codes, these parameters increased detection sensitivity to 87%, but specificity and PPV declined to 95% and 25%, respectively. Adding text analysis increased sensitivity to 99%, but PPV dropped further to 14%. Algorithms that required satisfying both a query of structured EMR parameters as well as text analysis disclosed PPVs of 52–68% and retained sensitivities of 69–73%. CONCLUSION: Structured EMR parameters and free-text analyses can be combined into algorithms that can detect ARI cases with new levels of sensitivity or precision. These results highlight potential paths by which repurposed EMR information could facilitate the discovery of epidemics before they cause mass casualties. url: https://doi.org/10.1371/journal.pone.0013377 doi: 10.1371/journal.pone.0013377 id: cord-255384-tljyx6ua author: Decaro, Nicola title: Full-Genome Analysis of a Canine Pneumovirus Causing Acute Respiratory Disease in Dogs, Italy date: 2014-01-06 words: 4629.0 sentences: 243.0 pages: flesch: 55.0 cache: ./cache/cord-255384-tljyx6ua.txt txt: ./txt/cord-255384-tljyx6ua.txt summary: The full-genomic characterisation showed that the causative agent (strain Bari/100-12) was closely related to CnPnVs that have been recently isolated in the USA, as well as to murine pneumovirus, which is responsible for respiratory disease in mice. In order to obtain new insights into the genetic diversity of CnPnV, the Italian prototype strain dog/Bari/100-12/ITA/2012 was submitted to RT-PCR amplification and subsequent sequence analysis of the full-length genome, using oligonucleotide retrieved from previous studies [13] [14] . When the analysis was restricted to the 8,600 and 8,598 nt available for reference CnPnV strains Brne17 and Ane4, respectively, that span from the very 39 end of the L gene to the 59end of the leader region (genome sense), an overall sequence identity of 96.5-96.6% was found against the canine strains. abstract: An outbreak of canine infectious respiratory disease (CIRD) associated to canine pneumovirus (CnPnV) infection is reported. The outbreak occurred in a shelter of the Apulia region and involved 37 out of 350 dogs that displayed cough and/or nasal discharge with no evidence of fever. The full-genomic characterisation showed that the causative agent (strain Bari/100-12) was closely related to CnPnVs that have been recently isolated in the USA, as well as to murine pneumovirus, which is responsible for respiratory disease in mice. The present study represents a useful contribution to the knowledge of the pathogenic potential of CnPnV and its association with CIRD in dogs. Further studies will elucidate the pathogenicity and epidemiology of this novel pneumovirus, thus addressing the eventual need for specific vaccines. url: https://doi.org/10.1371/journal.pone.0085220 doi: 10.1371/journal.pone.0085220 id: cord-013263-xw611i8k author: Dederichs, Melina title: Students’ perspectives on interventions to reduce stress in medical school: A qualitative study date: 2020-10-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The mental health of medical students remains to be a matter of concern. Numerous setting-based and individual-based interventions for student mental health have been proposed in the literature. However, the student perspective on those interventions has been largely neglected. This study aims to explore how medical students perceive different interventions and if they desire any additional changes with regard to their studies. Eight focus groups with 71 participants were conducted at a large German medical school. Focus groups were recorded, transcribed and content-analyzed using MAXQDA 18. We found that medical students prefer setting-based interventions. Most proposed interventions were on a setting-based level. For instance, students asked for more information on the university’s psychosocial counseling services and for better information management regarding contact persons. Interventions proposed in the literature received mixed reactions: Several participants did not favour a pass/fail grading system. Students considered a peer-to-peer mentoring program for freshmen very helpful. Students had diverse attitudes towards Balint groups. They approved of several self-management courses, most of them being related to time or stress management. Interestingly, the most urgently wanted interventions appear to be rather easy to implement (e.g. a mentoring program). This study explored the medical student perspective on student mental health interventions. Additionally, our study illustrates the benefit and feasibility of involving students early on in the conception of interventions. Further research with a representative sample is needed to obtain broader information on the acceptance of the suggested interventions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561099/ doi: 10.1371/journal.pone.0240587 id: cord-342730-b7y8mybg author: Dellagi, Koussay title: Pandemic Influenza Due to pH1N1/2009 Virus: Estimation of Infection Burden in Reunion Island through a Prospective Serosurvey, Austral Winter 2009 date: 2011-09-29 words: 5974.0 sentences: 283.0 pages: flesch: 49.0 cache: ./cache/cord-342730-b7y8mybg.txt txt: ./txt/cord-342730-b7y8mybg.txt summary: In order to assess at the community level, the actual magnitude of the pH1N1/2009v pandemic and the extent of the herd immunity acquired after passage of the epidemic wave, a prospective population serosurvey was conducted in Reunion Island during the passage of the epidemic wave in the 2009 austral winter season (July-December 2009): prevalence of infection was assessed on a weekly basis and seroconversion rates were measured using paired sera. The CoPanFlu-RUN cohort was set up to conduct a prospective population-based study investigating the herd immunity induced by the 2009 pandemic influenza virus and identifying risk factors for pH1N1/2009v infection from paired sera collected in an entire community. Our study shows that a substantial proportion of Reunion Island''s population had pre-existing immunity to 2009 pandemic influenza virus with the highest baseline-proxy seroprevalence rate observed among adults aged of 60 years or more. abstract: BACKGROUND: To date, there is little information that reflects the true extent of spread of the pH1N1/2009v influenza pandemic at the community level as infection often results in mild or no clinical symptoms. This study aimed at assessing through a prospective study, the attack rate of pH1N1/2009 virus in Reunion Island and risk factors of infection, during the 2009 season. METHODOLOGY/PRINCIPAL FINDINGS: A serosurvey was conducted during the 2009 austral winter, in the frame of a prospective population study. Pairs of sera were collected from 1687 individuals belonging to 772 households, during and after passage of the pandemic wave. Antibodies to pH1N1/2009v were titered using the hemagglutination inhibition assay (HIA) with titers ≥1/40 being considered positive. Seroprevalence during the first two weeks of detection of pH1N1/2009v in Reunion Island was 29.8% in people under 20 years of age, 35.6% in adults (20–59 years) and 73.3% in the elderly (≥60 years) (P<0.0001). Baseline corrected cumulative incidence rates, were 42.9%, 13.9% and 0% in these age groups respectively (P<0.0001). A significant decline in antibody titers occurred soon after the passage of the epidemic wave. Seroconversion rates to pH1N1/2009 correlated negatively with age: 63.2%, 39.4% and 16.7%, in each age group respectively (P<0.0001). Seroconversion occurred in 65.2% of individuals who were seronegative at inclusion compared to 6.8% in those who were initially seropositive. CONCLUSIONS: Seroincidence of pH1N1/2009v infection was three times that estimated from clinical surveillance, indicating that almost two thirds of infections occurring at the community level have escaped medical detection. People under 20 years of age were the most affected group. Pre-epidemic titers ≥1/40 prevented seroconversion and are likely protective against infection. A concern was raised about the long term stability of the antibody responses. url: https://www.ncbi.nlm.nih.gov/pubmed/21980532/ doi: 10.1371/journal.pone.0025738 id: cord-003841-7uaj9hmx author: Desmonts de Lamache, D. title: Immuno-modulating properties of Tulathromycin in porcine monocyte-derived macrophages infected with porcine reproductive and respiratory syndrome virus date: 2019-08-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is a positive-stranded RNA virus that grows in macrophages and causes acute pneumonia in pigs. PRRSV causes devastating losses to the porcine industry. However, due to its high antigenic variability and poorly understood immunopathogenesis, there is currently no effective vaccine or treatment to control PRRSV infection. The common occurrence of PRRSV infection with bacterial infections as well as its inflammatory-driven pathobiology raises the question of the value of antibiotics with immunomodulating properties for the treatment of the disease it causes. The macrolide antibiotic Tulathromycin (TUL) has been found to exhibit potent anti-inflammatory and immunomodulating properties in cattle and pigs. The aim of this study was to characterize the anti-viral and immunomodulating properties of TUL in PRRSV-infected porcine macrophages. Our findings indicate that blood monocyte-derived macrophages are readily infected by PRRSV and can be used as an effective cellular model to study PRRSV pathogenesis. TUL did not change intracellular or extracellular viral titers, not did it alter viral receptors (CD163 and CD169) expression on porcine macrophages. In contrast, TUL exhibited potent immunomodulating properties, which therefore occurred in the absence of any direct antiviral effects against PRRSV. TUL had an additive effect with PRRSV on the induction of macrophage apoptosis, and inhibited virus-induced necrosis. TUL significantly attenuated PRRSV-induced macrophage pro-inflammatory signaling (CXCL-8 and mitochondrial ROS production) and prevented PRRSV inhibition of non-opsonized and opsonized phagocytic function. Together, these data demonstrate that TUL inhibits PRRSV-induced inflammatory responses in porcine macrophages and protects against the phagocytic impairment caused by the virus. Research in live pigs is warranted to assess the potential clinical benefits of this antibiotic in the context of virally induced inflammation and tissue injury. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707645/ doi: 10.1371/journal.pone.0221560 id: cord-001447-oi7bkm4z author: Dhanasekaran, Sakthivel title: Toll-Like Receptor Responses to Peste des petits ruminants Virus in Goats and Water Buffalo date: 2014-11-04 words: 6012.0 sentences: 318.0 pages: flesch: 51.0 cache: ./cache/cord-001447-oi7bkm4z.txt txt: ./txt/cord-001447-oi7bkm4z.txt summary: We examined the replication of PPRV in peripheral blood mononuclear cells (PBMC) of Indian domestic goats and water buffalo and demonstrated that the levels of TLR3 and TLR7 and downstream signalling molecules correlation with susceptibility vs resistance. Upon stimulation of PBMC with synthetic TLR3 and TLR7 agonists or PPRV, the levels of proinflammatory cytokines were found to be significantly higher while immunosuppressive interleukin (IL) 10 levels were lower in PPRV resistant Kanni and Salem Black breeds and water buffalo at transcriptional level, correlating with reduced viralloads in infected PBMC. Infection of peripheral blood mononuclear cells (PBMC) from four breeds of goats and water buffalo resulted in differential viral replication kinetics and inflammatory cytokine profile including IFNa, IFNc and TNFa with differential activation of TLR3 and TLR7. To determine whether the differential IFN and pro-inflammatory cytokine production between Kanni/Salem vs Barbari/ Tellicherry breeds of goats are dependent on single nucleotide polymorphisms (SNPs) in TLR genes, we examined the complete gene sequence of TLR7. abstract: Ovine rinderpest or goat plague is an economically important and contagious viral disease of sheep and goats, caused by the Peste des petits ruminants virus (PPRV). Differences in susceptibility to goat plague among different breeds and water buffalo exist. The host innate immune system discriminates between pathogen associated molecular patterns and self antigens through surveillance receptors known as Toll like receptors (TLR). We investigated the role of TLR and cytokines in differential susceptibility of goat breeds and water buffalo to PPRV. We examined the replication of PPRV in peripheral blood mononuclear cells (PBMC) of Indian domestic goats and water buffalo and demonstrated that the levels of TLR3 and TLR7 and downstream signalling molecules correlation with susceptibility vs resistance. Naturally susceptible goat breeds, Barbari and Tellichery, had dampened innate immune responses to PPRV and increased viral loads with lower basal expression levels of TLR 3/7. Upon stimulation of PBMC with synthetic TLR3 and TLR7 agonists or PPRV, the levels of proinflammatory cytokines were found to be significantly higher while immunosuppressive interleukin (IL) 10 levels were lower in PPRV resistant Kanni and Salem Black breeds and water buffalo at transcriptional level, correlating with reduced viralloads in infected PBMC. Water buffalo produced higher levels of interferon (IFN) α in comparison with goats at transcriptional and translational levels. Pre-treatment of Vero cells with human IFNα resulted in reduction of PPRV replication, confirming the role of IFNα in limiting PPRV replication. Treatment with IRS66, a TLR7 antagonist, resulted in the reduction of IFNα levels, with increased PPRV replication confirming the role of TLR7. Single nucleotide polymorphism analysis of TLR7 of these goat breeds did not show any marked nucleotide differences that might account for susceptibility vs resistance to PPRV. Analyzing other host genetic factors might provide further insights on susceptibility to PPRV and genetic polymorphisms in the host. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4219731/ doi: 10.1371/journal.pone.0111609 id: cord-308344-ao9z00t7 author: Diep, Nguyen Van title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation date: 2017-01-17 words: 4179.0 sentences: 193.0 pages: flesch: 52.0 cache: ./cache/cord-308344-ao9z00t7.txt txt: ./txt/cord-308344-ao9z00t7.txt summary: title: Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. In this study, variants with large deletions in the S gene were found in eight primary and nine recurrent outbreaks from 16 pig farms, and they mostly (94.1%) coexisted with PEDV strains with an intact S gene. Cell culture isolation and sequence analysis of genetically diverse US porcine epidemic diarrhea virus strains including a novel strain with a large deletion in the spike gene New porcine epidemic diarrhoea virus variant with a large deletion in the spike gene identified in domestic pigs abstract: Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28–714 (10–238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/28095455/ doi: 10.1371/journal.pone.0170126 id: cord-309010-tmfm5u5h author: Dietert, Kristina title: Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia date: 2017-11-20 words: 7842.0 sentences: 414.0 pages: flesch: 34.0 cache: ./cache/cord-309010-tmfm5u5h.txt txt: ./txt/cord-309010-tmfm5u5h.txt summary: Here, we systematically describe and compare the distinctive histopathological features of established models of acute pneumonia in mice induced by Streptococcus (S.) pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Legionella pneumophila, Escherichia coli, Middle East respiratory syndrome (MERS) coronavirus, influenza A virus (IAV) and superinfection of IAV-incuced pneumonia with S. Systematic comparisons of the models revealed striking differences in the distribution of lesions, the characteristics of pneumonia induced, principal inflammatory cell types, lesions in adjacent tissues, and the detectability of the pathogens in histological sections. Transnasal infection with MERS-CoV following adenoviral transduction of human DPP4 yielded an expansive, (Fig 7A) interstitial pneumonia with severe alveolar epithelial cell necrosis and infiltration of mainly macrophages, lymphocytes, and fewer neutrophils (Fig 7B) . Different mouse models of acute pneumonia differ widely, with an obvious strong dependence on pathogen-specific features of virulence and spread, route of infection, infectious dose and other factors. abstract: Pneumonia may be caused by a wide range of pathogens and is considered the most common infectious cause of death in humans. Murine acute lung infection models mirror human pathologies in many aspects and contribute to our understanding of the disease and the development of novel treatment strategies. Despite progress in other fields of tissue imaging, histopathology remains the most conclusive and practical read out tool for the descriptive and semiquantitative evaluation of mouse pneumonia and therapeutic interventions. Here, we systematically describe and compare the distinctive histopathological features of established models of acute pneumonia in mice induced by Streptococcus (S.) pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Legionella pneumophila, Escherichia coli, Middle East respiratory syndrome (MERS) coronavirus, influenza A virus (IAV) and superinfection of IAV-incuced pneumonia with S. pneumoniae. Systematic comparisons of the models revealed striking differences in the distribution of lesions, the characteristics of pneumonia induced, principal inflammatory cell types, lesions in adjacent tissues, and the detectability of the pathogens in histological sections. We therefore identified core criteria for each model suitable for practical semiquantitative scoring systems that take into account the pathogen- and model-specific patterns of pneumonia. Other critical factors that affect experimental pathologies are discussed, including infectious dose, time kinetics, and the genetic background of the mouse strain. The substantial differences between the model-specific pathologies underscore the necessity of pathogen- and model-adapted criteria for the comparative quantification of experimental outcomes. These criteria also allow for the standardized validation and comparison of treatment strategies in preclinical models. url: https://doi.org/10.1371/journal.pone.0188251 doi: 10.1371/journal.pone.0188251 id: cord-353730-owcapg8h author: Dietrich, Jes title: Inducing Dose Sparing with Inactivated Polio Virus Formulated in Adjuvant CAF01 date: 2014-06-23 words: 7885.0 sentences: 389.0 pages: flesch: 53.0 cache: ./cache/cord-353730-owcapg8h.txt txt: ./txt/cord-353730-owcapg8h.txt summary: The CAF01 adjuvant has previously been shown to be a safe and potent adjuvant with several antigens, and here we show that in mice IPV formulated with CAF01 induced increased systemic protective immunity measured by binding and neutralization antibody titers in serum. Based on neutralization titers obtained from mice vaccinated with a range of doses from 30 DU (D-Units) to 0.1 DU (data not shown) we choose 20 DU as a full mouse dose and 2 DU as the dose formulated into the CAF01 adjuvant (indicated dose units in the all experiments correspond to polio virus type-1 D antigen units). Taken together, compared to IM administration a side by side ID+IM administration with a CAF01-adjuvanted vaccine followed by an IM administration did not negatively affect systemic immunity, measured by antibody binding and neutralization titers and T cell IFN-c secretion (Fig. 6) . abstract: The development of new low cost inactivated polio virus based vaccines (IPV) is a high priority, and will be required to eradicate polio. In addition, such a vaccine constitutes the only realistic polio vaccine in the post-eradication era. One way to reduce the cost of a vaccine is to increase immunogenicity by use of adjuvants. The CAF01 adjuvant has previously been shown to be a safe and potent adjuvant with several antigens, and here we show that in mice IPV formulated with CAF01 induced increased systemic protective immunity measured by binding and neutralization antibody titers in serum. CAF01 also influenced the kinetics of both the cellular and humoral response against IPV to produce a faster, as well as a stronger, response, dominated by IgG2a, IgG2b, and IgG2c isotypes as well as IPV specific T cells secreting IFN-γ/IL-2. Finally, as intestinal immunity is also a priority of polio vaccines, we present a vaccine strategy based on simultaneous priming at an intradermal and an intramuscular site that generate intestinal immune responses against polio virus. Taken together, the IPV-CAF01 formulation constitutes a new promising vaccine against polio with the ability to generate strong humoral and cellular immunity against the polio virus. url: https://doi.org/10.1371/journal.pone.0100879 doi: 10.1371/journal.pone.0100879 id: cord-253056-765rs3e7 author: Dionne, Audrey title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection date: 2018-10-17 words: 3725.0 sentences: 208.0 pages: flesch: 45.0 cache: ./cache/cord-253056-765rs3e7.txt txt: ./txt/cord-253056-765rs3e7.txt summary: title: Profile of resistance to IVIG treatment in patients with Kawasaki disease and concomitant infection Children with persistent or recurrent fever 36 hours after the end of intravenous immunoglobulin (IVIG) are considered to be resistant to treatment and are at increased risk for coronary complications. RESULTS: Children with concomitant infection were more likely to have fever 48 hours after initial IVIG treatment (36% vs 20%, p = 0.05) and to be treated with a second dose (33% vs 18%, p = 0.04). Children with concurrent infection had higher rates of IVIG resistance (19 (33%) versus 17 (18%) patients, p = 0.04), and higher temperature at 48 hours (Fig 1) . In this retrospective series, the presence of a concomitant infection was associated with a higher rate of resistance to IVIG treatment. In this study, patients with concomitant infection had a higher rate of resistance to IVIG treatment. abstract: INTRODUCTION: Kawasaki disease (KD) can be associated with concomitant viral or bacterial infections. Children with persistent or recurrent fever 36 hours after the end of intravenous immunoglobulin (IVIG) are considered to be resistant to treatment and are at increased risk for coronary complications. Although concomitant infection does not affect coronary outcome, it is unknown how it influences the response to IVIG treatment. METHODOLOGY: Retrospective cohort study between 2008 and 2016 in a tertiary pediatric university hospital, including 154 children, of which 59 (38%) had concomitant infection. RESULTS: Children with concomitant infection were more likely to have fever 48 hours after initial IVIG treatment (36% vs 20%, p = 0.05) and to be treated with a second dose (33% vs 18%, p = 0.04). Children with infection had higher C-reactive protein at the time of diagnosis (148 vs 112 mg/L, p = 0.04), and 48 hours after IVIG administration (111 vs 59 mg/L, p = 0.003). Nevertheless, there was no statistically significant difference in the prevalence of coronary complications (Z-score > 2.5) between children with and without concomitant infection (36% vs 39%, p = 0.68). CONCLUSION: Children with KD and concomitant infection are more likely to have persistent fever and elevated inflammatory markers after treatment. This association increases the likelihood of receiving a second dose of IVIG but not the risk of coronary complication. Accordingly, prospective studies to distinguish true IVIG resistance from infection induced persistent fever is warranted. url: https://www.ncbi.nlm.nih.gov/pubmed/30332473/ doi: 10.1371/journal.pone.0206001 id: cord-267973-uvz7kavu author: Do, Lien Anh Ha title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity date: 2016-08-08 words: 5921.0 sentences: 476.0 pages: flesch: 61.0 cache: ./cache/cord-267973-uvz7kavu.txt txt: ./txt/cord-267973-uvz7kavu.txt summary: title: Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. However, information on detailed clinical, epidemiological features and virological characteristics of RSV infections (e.g. disease burden, demographics, seasonal variations of RSV and other viral infections, circulating genotypes and subgroups, viral load) or on the frequency / impact of other respiratory viruses among Vietnamese children under two years old are limited [6] . Here, we aimed to describe the viral etiologies and the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a LRTI, focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. abstract: BACKGROUND: Despite a high burden of respiratory syncytial virus (RSV) infections among children, data on demographic and clinical characteristics of RSV are scarce in low and middle income countries. This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. METHODS: A prospective study among children under two years of age, hospitalized with LRTI was conducted in two referral pediatric hospitals in Ho Chi Minh City, Vietnam, from May 2009 to December 2010. Socio-demographic, clinical data and nasopharyngeal swabs were collected on enrolment and discharge. Multiplex real-time RT-PCR (13 viruses) and quantitative RSV RT-PCR were used to identify viral pathogens, RSV load and subgroups. RESULTS: Among 632 cases, 48% were RSV positive. RSV infections occurred at younger age than three other leading viral infections i.e rhinovirus (RV), metapneumovirus (MPV), parainfluenza virus (PIV-3) and were significantly more frequent in the first 6 months of life. Clinical severity score of RSV infection was significantly higher than PIV-3 but not for RV or MPV. In multivariate analysis, RV infection was significantly associated with severity while RSV infection was not. Among RSV infections, neither viral load nor viral co-infections were significantly associated with severity. Young age and having fever at admission were significantly associated with both RSV and LRTI severity. A shift in RSV subgroup predominance was observed during two consecutive rainy seasons but was not associated with severity. CONCLUSION: We report etiologies, the epidemiological and clinical characteristics of LRTI among hospitalized children under two years of age and risk factors of RSV and LRTI severity. url: https://doi.org/10.1371/journal.pone.0160606 doi: 10.1371/journal.pone.0160606 id: cord-349029-zyfop43z author: Dobrovolny, Hana M. title: Modeling the role of asymptomatics in infection spread with application to SARS-CoV-2 date: 2020-08-10 words: 4596.0 sentences: 233.0 pages: flesch: 48.0 cache: ./cache/cord-349029-zyfop43z.txt txt: ./txt/cord-349029-zyfop43z.txt summary: In order to estimate how effective these strategies will be, we will need a better understanding of the role of asymptomatic individuals in SARS-CoV-2 spread and the effect the proportion and relative infectiousness of asymptomatics have on the time course of the epidemic. In this paper, we study a compartmental epidemic model that includes asymptomatic infections to determine the role that asymptomatic individuals might play in the spread of SARS-CoV-2. We apply our model to data from SARS-CoV-2 epidemics in California, Florida, New York, and Texas, finding that a large number of infections in these states are unreported and that relaxing social distancing measures too early will cause a rapid spike in infections driven in part by these hidden infections. For the SARS-CoV epidemics examined here, the model predicts that there are far more asymptomatic or unreported cases at the peak of the infection, suggesting that there might be widespread community transmission if stay-at-home orders are relaxed too early. abstract: SARS-CoV-2 started causing infections in humans in late 2019 and has spread rapidly around the world. While the number of symptomatically infected and severely ill people is high and has overwhelmed the medical systems of many countries, there is mounting evidence that some of the rapid spread of this virus has been driven by asymptomatic infections. In this study, we use a compartmental mathematical model of a viral epidemic that includes asymptomatic infection to examine the role of asymptomatic individuals in the spread of the infection. We apply the model to epidemics in California, Florida, New York, and Texas, finding that asymptomatic infections far outnumber reported symptomatic infections at the peak of the epidemic in all four states. The model suggests that relaxing of social distancing measures too quickly could lead to a rapid rise in the number of cases, driven in part by asymptomatic infections. url: https://doi.org/10.1371/journal.pone.0236976 doi: 10.1371/journal.pone.0236976 id: cord-308249-es948mux author: Dokuka, Sofia title: How academic achievement spreads: The role of distinct social networks in academic performance diffusion date: 2020-07-27 words: 5043.0 sentences: 297.0 pages: flesch: 48.0 cache: ./cache/cord-308249-es948mux.txt txt: ./txt/cord-308249-es948mux.txt summary: We examine the spread of academic achievements of first-year undergraduate students through friendship and study assistance networks, applying stochastic actor-oriented modeling. In this paper, we analyze the diffusion of academic performance across different types of student social networks. We analyze the spread of academic achievements within two different social networks of first-year undergraduate students. It was shown that achievements spread well within friendship networks, while other types of ties (e.g. online relationships) do not serve as channels for the performance transmission. In this paper, we examine the diffusion of academic achievements in two distinct social networks: friendship and study assistance. We analyze the longitudinal data on friendship and study assistance networks and GPA of a first-year student cohort of the Economics department in one of the leading Russian universities in 2013-2014 academic year. In this paper we explore the academic performance diffusion through two social networks of different natures: friendship and study assistance. abstract: Behavior diffusion through social networks is a key social process. It may be guided by various factors such as network topology, type of propagated behavior, and the strength of network connections. In this paper, we claim that the type of social interactions is also an important ingredient of behavioral diffusion. We examine the spread of academic achievements of first-year undergraduate students through friendship and study assistance networks, applying stochastic actor-oriented modeling. We show that informal social connections transmit performance while instrumental connections do not. The results highlight the importance of friendship in educational environments and contribute to debates on the behavior spread in social networks. url: https://doi.org/10.1371/journal.pone.0236737 doi: 10.1371/journal.pone.0236737 id: cord-352564-2j4pjjwk author: Dominguez, Samuel R. title: Human Coronavirus HKU1 Infection of Primary Human Type II Alveolar Epithelial Cells: Cytopathic Effects and Innate Immune Response date: 2013-07-24 words: 4449.0 sentences: 199.0 pages: flesch: 46.0 cache: ./cache/cord-352564-2j4pjjwk.txt txt: ./txt/cord-352564-2j4pjjwk.txt summary: Because they are the natural target cells for respiratory virus infection, primary human respiratory epithelial cell cultures provide the ideal in vitro systems for investigation of cell factors required for growth of respiratory human viruses, for analysis of their interactions with viruses and their innate immune responses to infection, and for isolation and propagation of novel respiratory pathogens. Here we demonstrate that HCoV-HKU1 can infect and be serially propagated in primary human alveolar type II cells but not in alveolar type I-like cells or alveolar macrophages at the air-liquid interface. Titers of viral RNA in the wash from the apical surface of the cells were determined by qRT-PCR at the indicated time points, and HCoV-HKU1 Infection of Type II Alveolar Cells PLOS ONE | www.plosone.org cultures were fixed and immunolabeled with antibodies to the HCoV-HKU1 spike glycoprotein to identify infected cells. In summary, HCoV-HKU1 can infect, be serially propagated, and induce an anti-viral response in human alveolar type II cells maintained at an air-liquid interface. abstract: Because they are the natural target for respiratory pathogens, primary human respiratory epithelial cells provide the ideal in vitro system for isolation and study of human respiratory viruses, which display a high degree of cell, tissue, and host specificity. Human coronavirus HKU1, first discovered in 2005, has a worldwide prevalence and is associated with both upper and lower respiratory tract disease in both children and adults. Research on HCoV-HKU1 has been difficult because of its inability to be cultured on continuous cell lines and only recently it was isolated from clinical specimens using primary human, ciliated airway epithelial cells. Here we demonstrate that HCoV-HKU1 can infect and be serially propagated in primary human alveolar type II cells at the air-liquid interface. We were not able to infect alveolar type I-like cells or alveolar macrophages. Type II alveolar cells infected with HCoV-HKU1 demonstrated formation of large syncytium. At 72 hours post inoculation, HCoV-HKU1 infection of type II cells induced increased levels of mRNAs encoding IL29,CXCL10, CCL5, and IL-6 with no significant increases in the levels of IFNβ. These studies demonstrate that type II cells are a target cell for HCoV-HKU1 infection in the lower respiratory tract, that type II alveolar cells are immune-competent in response to infection exhibiting a type III interferon and proinflammatory chemokine response, and that cell to cell spread may be a major factor for spread of infection. Furthermore, these studies demonstrate that human alveolar cells can be used to isolate and study novel human respiratory viruses that cause lower respiratory tract disease. url: https://www.ncbi.nlm.nih.gov/pubmed/23894604/ doi: 10.1371/journal.pone.0070129 id: cord-000959-nk2thkme author: Downer, Eric J. title: Identifying Early Inflammatory Changes in Monocyte-Derived Macrophages from a Population with IQ-Discrepant Episodic Memory date: 2013-05-06 words: 5396.0 sentences: 268.0 pages: flesch: 48.0 cache: ./cache/cord-000959-nk2thkme.txt txt: ./txt/cord-000959-nk2thkme.txt summary: METHODS: This study explored the expression of receptors (CD11b, TLR2 and TLR4) on circulating monocyte-derived macrophages (MDMs) and peripheral blood mononuclear cells (PBMCs) isolated from healthy elderly adults who we classified as either IQ memory-consistent (high-performing, HP) or IQ memory-discrepant (low-performing, LP). The purpose of the study was to compare the expression of receptors (CD11b, TLR2 and TLR4) on circulating monocyte-derived macrophages (MDMs) and the response of these cells to LPS in samples prepared from the LP cohort and a cohort which we classified as IQ memory-consistent (high-performing, HP) individuals. P) TLR4 expression on CD11b + MDMs was increased in the LP group compared with the HP group (P,0.05) and this is also shown in the representative dot plots of TLR4 + cells ( and following LPS stimulation [6] , while pro-inflammatory cytokine [52] and chemokine [53, 54] levels are elevated in peripheral blood monocytes isolated from the elderly after LPS stimulation. abstract: BACKGROUND: Cells of the innate immune system including monocytes and macrophages are the first line of defence against infections and are critical regulators of the inflammatory response. These cells express toll-like receptors (TLRs), innate immune receptors which govern tailored inflammatory gene expression patterns. Monocytes, which produce pro-inflammatory mediators, are readily recruited to the central nervous system (CNS) in neurodegenerative diseases. METHODS: This study explored the expression of receptors (CD11b, TLR2 and TLR4) on circulating monocyte-derived macrophages (MDMs) and peripheral blood mononuclear cells (PBMCs) isolated from healthy elderly adults who we classified as either IQ memory-consistent (high-performing, HP) or IQ memory-discrepant (low-performing, LP). RESULTS: The expression of CD11b, TLR4 and TLR2 was increased in MDMs from the LP group when compared to HP cohort. MDMs from both groups responded robustly to treatment with the TLR4 activator, lipopolysaccharide (LPS), in terms of cytokine production. Significantly, MDMs from the LP group displayed hypersensitivity to LPS exposure. INTERPRETATION: Overall these findings define differential receptor expression and cytokine profiles that occur in MDMs derived from a cohort of IQ memory-discrepant individuals. These changes are indicative of inflammation and may be involved in the prodromal processes leading to the development of neurodegenerative disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646027/ doi: 10.1371/journal.pone.0063194 id: cord-354763-odzrco6q author: Drake, John M. title: Societal Learning in Epidemics: Intervention Effectiveness during the 2003 SARS Outbreak in Singapore date: 2006-12-20 words: 5739.0 sentences: 283.0 pages: flesch: 46.0 cache: ./cache/cord-354763-odzrco6q.txt txt: ./txt/cord-354763-odzrco6q.txt summary: We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. We also retrospectively explore the effect of societal learning during the 2003 outbreak of SARS in Singapore, using weekly data on the time between onset of symptoms and removal of infectious individuals. Finally, we discuss societal and epidemiological factors that might affect societal learning, we observe that a difficult task during the early stages of an outbreak is to estimate the learning rate and suggest that the rate estimated here might be used as prior information in future outbreaks, and we conclude by recommending rapid investment in research at the time of initial detection when actions taken to reduce disease spread can be most efficient and cost effective. abstract: BACKGROUND: Rapid response to outbreaks of emerging infectious diseases is impeded by uncertain diagnoses and delayed communication. Understanding the effect of inefficient response is a potentially important contribution of epidemic theory. To develop this understanding we studied societal learning during emerging outbreaks wherein patient removal accelerates as information is gathered and disseminated. METHODS AND FINDINGS: We developed an extension of a standard outbreak model, the simple stochastic epidemic, which accounts for societal learning. We obtained expressions for the expected outbreak size and the distribution of epidemic duration. We found that rapid learning noticeably affects the final outbreak size even when learning exhibits diminishing returns (relaxation). As an example, we estimated the learning rate for the 2003 outbreak of severe acute respiratory syndrome (SARS) in Singapore. Evidence for relaxation during the first eight weeks of the outbreak was inconclusive. We estimated that if societal learning had occurred at half the actual rate, the expected final size of the outbreak would have reached nearly 800 cases, more than three times the observed number of infections. By contrast, the expected outbreak size for societal learning twice as effective was 116 cases. CONCLUSION: These results show that the rate of societal learning can greatly affect the final size of disease outbreaks, justifying investment in early warning systems and attentiveness to disease outbreak by both government authorities and the public. We submit that the burden of emerging infections, including the risk of a global pandemic, could be efficiently reduced by improving procedures for rapid detection of outbreaks, alerting public health officials, and aggressively educating the public at the start of an outbreak. url: https://www.ncbi.nlm.nih.gov/pubmed/17183647/ doi: 10.1371/journal.pone.0000020 id: cord-268524-lr51ubz5 author: Droit-Volet, Sylvie title: Time and Covid-19 stress in the lockdown situation: Time free, «Dying» of boredom and sadness date: 2020-08-10 words: 5266.0 sentences: 262.0 pages: flesch: 56.0 cache: ./cache/cord-268524-lr51ubz5.txt txt: ./txt/cord-268524-lr51ubz5.txt summary: This time experience was not explained by the levels of perceived stress or anxiety, although these were considerable, but rather by the increase in boredom and sadness felt in the lockdown situation. The aim of the present study was thus to conduct a scale survey on a large sample of an as yet untested population-French people-in order to assess not only the perceived stress related to Covid-19 but also the emotions (happiness, boredom, arousal) felt during as compared to before the lockdown and their links to the subjective experience of time. There is thus a risk in this period of pandemic that the chronic stress related to Covid-19 and its corollaries (anxiety, fear of death) are particularly high and therefore impact the subjective experience of time by speeding up the perceived passage of time. abstract: A lockdown of people has been used as an efficient public health measure to fight against the exponential spread of the coronavirus disease (Covid-19) and allows the health system to manage the number of patients. The aim of this study (clinicaltrials.gov NCT 0430818) was to evaluate the impact of both perceived stress aroused by Covid-19 and of emotions triggered by the lockdown situation on the individual experience of time. A large sample of the French population responded to a survey on their experience of the passage of time during the lockdown compared to before the lockdown. The perceived stress resulting from Covid-19 and stress at work and home were also assessed, as were the emotions felt. The results showed that people have experienced a slowing down of time during the lockdown. This time experience was not explained by the levels of perceived stress or anxiety, although these were considerable, but rather by the increase in boredom and sadness felt in the lockdown situation. The increased anger and fear of death only explained a small part of variance in the time judgment. The conscious experience of time therefore reflected the psychological difficulties experienced during lockdown and was not related to their perceived level of stress or anxiety. url: https://doi.org/10.1371/journal.pone.0236465 doi: 10.1371/journal.pone.0236465 id: cord-259771-653opx0h author: Dwivedi, Varun title: Biodegradable Nanoparticle-Entrapped Vaccine Induces Cross-Protective Immune Response against a Virulent Heterologous Respiratory Viral Infection in Pigs date: 2012-12-11 words: 5900.0 sentences: 290.0 pages: flesch: 45.0 cache: ./cache/cord-259771-653opx0h.txt txt: ./txt/cord-259771-653opx0h.txt summary: In a pre-challenge study, intranasal delivery of Nano-KAg resulted in induction of innate immune response at both mucosal and systemic sites, indicated by a significant increase in the frequency of NK cells, DCs, and cd T cells in the lung MNC ( Figure 2 , A-C); and cd T cells and DCs in the PBMC compared to K-Ag vaccinated pigs (Figure 2, H & I) . Lung homogenates of Nano-KAg immunized pigs contained significantly higher levels of virus specific IgA and IgG antibodies compared to unvaccinated and K-Ag vaccinated, MN184 challenged pigs (Figure 4, A & B) . The frequency of cd T cells and CD4 + (but not CD8 + ) T cells in the lungs of Nano-KAg vaccinated animals were significantly increased compared to K-Ag and unvaccinated, virus challenged pigs ( Figure 5 , D, E & F). abstract: Biodegradable nanoparticle-based vaccine development research is unexplored in large animals and humans. In this study, we illustrated the efficacy of nanoparticle-entrapped UV-killed virus vaccine against an economically important respiratory viral disease of pigs called porcine reproductive and respiratory syndrome virus (PRRSV). We entrapped PLGA [poly (lactide-co-glycolides)] nanoparticles with killed PRRSV antigens (Nano-KAg) and detected its phagocytosis by pig alveolar macrophages. Single doses of Nano-KAg vaccine administered intranasally to pigs upregulated innate and PRRSV specific adaptive responses. In a virulent heterologous PRRSV challenge study, Nano-KAg vaccine significantly reduced the lung pathology and viremia, and the viral load in the lungs. Immunologically, enhanced innate and adaptive immune cell population and associated cytokines with decreased secretion of immunosuppressive mediators were observed at both mucosal sites and blood. In summary, we demonstrated the benefits of intranasal delivery of nanoparticle-based viral vaccine in eliciting cross-protective immune response in pigs, a potential large animal model. url: https://www.ncbi.nlm.nih.gov/pubmed/23240064/ doi: 10.1371/journal.pone.0051794 id: cord-352720-z1cvjc2y author: Díaz-Corvillón, Pilar title: Routine screening for SARS CoV-2 in unselected pregnant women at delivery date: 2020-09-29 words: 4061.0 sentences: 244.0 pages: flesch: 49.0 cache: ./cache/cord-352720-z1cvjc2y.txt txt: ./txt/cord-352720-z1cvjc2y.txt summary: While initial evidence suggests that pregnant women were not at increased risk for COVID-19, neither developed a more severe disease compared to non-pregnant adults [3, 4] , recent reports suggest increased rates of preterm birth [5] , pneumonia and intensive care unit admission [6] , and maternal mortality [6, 7] . The main objective of this study was to assess point-prevalence of SARS CoV-2 infection in unselected obstetrical population at the time of delivery and to describe the presentation and clinical evolution of confirmed cases. women were screened for COVID-19 clinical symptoms including fever, cough and shortness of breath by trained personnel, and RT-PCR for SARS CoV-2 (Allplex TM 2019-nCoV Assay [17] ) was performed by nasopharyngeal swab, unless a prior test with no more than 48 hours to admission was reported. abstract: BACKGROUND: South America has become the epicenter of coronavirus pandemic. It seems that asymptomatic population may contribute importantly to the spread of the disease. Transmission from asymptomatic pregnant patients’ needs to be characterized in larger population cohorts and symptom assessment needs to be standardized. OBJECTIVE: To assess the prevalence of SARS CoV-2 infection in an unselected obstetrical population and to describe their presentation and clinical evolution. METHODS: A cross-sectional study was designed. Medical records of pregnant women admitted at the Obstetrics & Gynecology department of Clínica Dávila for labor & delivery, between April 27(th) and June 7(th), 2020 were reviewed. All patients were screened with RT-PCR for SARS CoV-2 at admission. After delivery, positive cases were inquired by the researchers for clinical symptoms presented before admission and clinical evolution. All neonates born from mothers with confirmed SARS CoV-2 were isolated and tested for SARS CoV-2 infection. RESULTS: A total of 586 patients were tested for SARS CoV-2 during the study period. Outcomes were obtained from 583 patients which were included in the study. Thirty-seven pregnant women had a positive test for SARS CoV-2 at admission. Cumulative prevalence of confirmed SARS CoV-2 infection was 6.35% (37/583) [CI 95%: 4.63–8.65]. From confirmed cases, 43.2% (16/37) were asymptomatic. From symptomatic patients 85.7% (18/21) had mild symptoms and evolved without complications and 14.3% (3/21) presented severe symptoms requiring admission to intensive care unit. Only 5.4% (2/37) of the neonates born to mothers with a positive test at admission had a positive RT-PCR for SARS CoV-2. CONCLUSION: In our study nearly half of pregnant patients with SARS CoV-2 were asymptomatic at the time of delivery. Universal screening, in endemic areas, is necessary for adequate patient isolation, prompt neonatal testing and targeted follow-up. url: https://www.ncbi.nlm.nih.gov/pubmed/32991621/ doi: 10.1371/journal.pone.0239887 id: cord-012967-w1oc0wdd author: Eberle, Jaelyn J. title: Using tooth enamel microstructure to identify mammalian fossils at an Eocene Arctic forest date: 2020-09-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lower Eocene (Wasatchian-aged) sediments of the Margaret Formation on Ellesmere Island in Canada’s High Arctic preserve evidence of a rainforest inhabited by alligators, turtles, and a diverse mammalian fauna. The mammalian fossils are fragmentary and often poorly preserved. Here, we offer an alternative method for their identification. Among the best preserved and extensive of the Eocene Arctic forests is the Strathcona Fiord Fossil Forest, which contains permineralized in situ tree stumps protruding from a prominent coal seam, but a paucity of vertebrate fossils. In 2010 and 2018, we recovered mammalian tooth fragments at the fossil forest, but they are so incomplete as to be undiagnostic by using their external morphology. We used a combination of light microscopy and SEM analysis to study the enamel microstructure of two tooth fragments from the fossil forest—NUFV2092B and 2092E. The results of our analysis indicate that NUFV2092B and 2092E have Coryphodon-enamel, which is characterized by vertical bodies that manifest as bands of nested chevrons or treelike structures visible in the tangential section under light microscopy. This enamel type is not found in other mammals known from the Arctic. Additionally, when studied under SEM, the enamel of NUFV2092B and 2092E has rounded prisms that open to one side and are surrounded by interprismatic matrix that is nearly parallel to the prisms, which also occurs in Coryphodon enamel, based on prior studies. The tooth fragments reported here, along with some poorly preserved bone fragments, thus far are the only documented vertebrate fossils from the Strathcona Fiord Fossil Forest. However, fossils of Coryphodon occur elsewhere in the Margaret Formation, so its presence at the fossil forest is not surprising. What is novel in our study is the way in which we identified the fossils using their enamel microstructure. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511010/ doi: 10.1371/journal.pone.0239073 id: cord-319706-2e9jrv0s author: Ebinger, Joseph E. title: Pre-existing traits associated with Covid-19 illness severity date: 2020-07-23 words: 4904.0 sentences: 219.0 pages: flesch: 40.0 cache: ./cache/cord-319706-2e9jrv0s.txt txt: ./txt/cord-319706-2e9jrv0s.txt summary: For all patients considered to have Covid-19, based on direct or documented laboratory test result and suggestive signs and/or symptoms, we obtained information from the electronic health record (EHR) and verified data for the following demographic and clinical characteristics: age at the time of diagnosis; sex; race; ethnicity; smoking status defined as current versus prior, never, or unknown; comorbidities, including obesity, as clinically assessed and documented by a provider with ICD-10 coding; and, chronic use of angiotensin converting enzyme (ACE) inhibitor or angiotensin II receptor blocker (ARB) medications. For the primary outcome of illness severity, categorized by escalating levels of care (i.e., hospitalization, intensive care, intubation), the pre-existing characteristics that demonstrated statistical significance in age-and sex-adjusted models included older age, male sex, African American race, obesity, hypertension, diabetes mellitus, and the Elixhauser comorbidity score ( Table 2 ; Fig 3) . abstract: IMPORTANCE: Certain individuals, when infected by SARS-CoV-2, tend to develop the more severe forms of Covid-19 illness for reasons that remain unclear. OBJECTIVE: To determine the demographic and clinical characteristics associated with increased severity of Covid-19 infection. DESIGN: Retrospective observational study. We curated data from the electronic health record, and used multivariable logistic regression to examine the association of pre-existing traits with a Covid-19 illness severity defined by level of required care: need for hospital admission, need for intensive care, and need for intubation. SETTING: A large, multihospital healthcare system in Southern California. PARTICIPANTS: All patients with confirmed Covid-19 infection (N = 442). RESULTS: Of all patients studied, 48% required hospitalization, 17% required intensive care, and 12% required intubation. In multivariable-adjusted analyses, patients requiring a higher levels of care were more likely to be older (OR 1.5 per 10 years, P<0.001), male (OR 2.0, P = 0.001), African American (OR 2.1, P = 0.011), obese (OR 2.0, P = 0.021), with diabetes mellitus (OR 1.8, P = 0.037), and with a higher comorbidity index (OR 1.8 per SD, P<0.001). Several clinical associations were more pronounced in younger compared to older patients (P(interaction)<0.05). Of all hospitalized patients, males required higher levels of care (OR 2.5, P = 0.003) irrespective of age, race, or morbidity profile. CONCLUSIONS AND RELEVANCE: In our healthcare system, greater Covid-19 illness severity is seen in patients who are older, male, African American, obese, with diabetes, and with greater overall comorbidity burden. Certain comorbidities paradoxically augment risk to a greater extent in younger patients. In hospitalized patients, male sex is the main determinant of needing more intensive care. Further investigation is needed to understand the mechanisms underlying these findings. url: https://doi.org/10.1371/journal.pone.0236240 doi: 10.1371/journal.pone.0236240 id: cord-262345-hti1jjpn author: Eddy, Lucy H. title: The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review date: 2020-08-25 words: 8728.0 sentences: 470.0 pages: flesch: 50.0 cache: ./cache/cord-262345-hti1jjpn.txt txt: ./txt/cord-262345-hti1jjpn.txt summary: title: The validity and reliability of observational assessment tools available to measure fundamental movement skills in school-age children: A systematic review METHODS: A pre-search of ''fundamental movement skills'' OR ''fundamental motor skills'' in seven online databases (PubMed, Ovid MEDLINE, Ovid Embase, EBSCO CINAHL, EBSCO SPORTDiscus, Ovid PsycINFO and Web of Science) identified 24 assessment tools for school-aged children that: (i) assess FMS; (ii) measure actual motor competence and (iii) evaluate performance on a standard battery of tasks. The psychometric properties of observational assessments of fundamental movement skills for school children correlations to evaluate the concurrent validity between the MOT 4-6 and the KTK, with results showing moderate correlations for children aged 5-6 (mean r = .63), as was hypothesised prior to testing (r >. abstract: BACKGROUND: Fundamental Movement Skills (FMS) play a critical role in ontogenesis. Many children have insufficient FMS, highlighting the need for universal screening in schools. There are many observational FMS assessment tools, but their psychometric properties are not readily accessible. A systematic review was therefore undertaken to compile evidence of the validity and reliability of observational FMS assessments, to evaluate their suitability for screening. METHODS: A pre-search of ‘fundamental movement skills’ OR ‘fundamental motor skills’ in seven online databases (PubMed, Ovid MEDLINE, Ovid Embase, EBSCO CINAHL, EBSCO SPORTDiscus, Ovid PsycINFO and Web of Science) identified 24 assessment tools for school-aged children that: (i) assess FMS; (ii) measure actual motor competence and (iii) evaluate performance on a standard battery of tasks. Studies were subsequently identified that: (a) used these tools; (b) quantified validity or reliability and (c) sampled school-aged children. Study quality was assessed using COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) checklists. RESULTS: Ninety studies were included following the screening of 1863 articles. Twenty-one assessment tools had limited or no evidence to support their psychometric properties. The Test of Gross Motor Development (TGMD, n = 34) and the Movement Assessment Battery for Children (MABC, n = 37) were the most researched tools. Studies consistently reported good evidence for validity, reliability for the TGMD, whilst only 64% of studies reported similarly promising results for the MABC. Twelve studies found good evidence for the reliability and validity of the Bruininks-Oseretsky Test of Motor Proficiency but poor study quality appeared to inflate results. Considering all assessment tools, those with promising psychometric properties often measured limited aspects of validity/reliability, and/or had limited feasibility for large scale deployment in a school-setting. CONCLUSION: There is insufficient evidence to justify the use of any observational FMS assessment tools for universal screening in schools, in their current form. url: https://www.ncbi.nlm.nih.gov/pubmed/32841268/ doi: 10.1371/journal.pone.0237919 id: cord-000868-vnwpzsu8 author: Eissmann, Kristin title: HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop date: 2013-01-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A strategy for antiviral drug discovery is the elucidation and imitation of viral interference mechanisms. HIV-1 patients benefit from a coinfection with GB Virus C (GBV-C), since HIV-positive individuals with long-term GBV-C viraemia show better survival rates than HIV-1 patients without persisting GBV-C. A direct influence of GBV-C on HIV-1 replication has been shown in coinfection experiments. GBV-C is a human non-pathogenic member of the flaviviridae family that can replicate in T and B cells. Therefore, GBV-C shares partly the same ecological niche with HIV-1. In earlier work we have demonstrated that recombinant glycoprotein E2 of GBV-C and peptides derived from the E2 N-terminus interfere with HIV entry. In this study we investigated the underlying mechanism. Performing a virus-cell fusion assay and temperature-arrested HIV-infection kinetics, we provide evidence that the HIV-inhibitory E2 peptides interfere with late HIV-1 entry steps after the engagement of gp120 with CD4 receptor and coreceptor. Binding and competition experiments revealed that the N-terminal E2 peptides bind to the disulfide loop region of HIV-1 transmembrane protein gp41. In conjunction with computational analyses, we identified sequence similarities between the N-termini of GBV-C E2 and the HIV-1 glycoprotein gp120. This similarity appears to enable the GBV-C E2 N-terminus to interact with the HIV-1 gp41 disulfide loop, a crucial domain involved in the gp120-gp41 interface. Furthermore, the results of the present study provide initial proof of concept that peptides targeted to the gp41 disulfide loop are able to inhibit HIV fusion and should inspire the development of this new class of HIV-1 entry inhibitors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551756/ doi: 10.1371/journal.pone.0054452 id: cord-323330-ghwhgkdm author: Ekundayo, Temitope Cyrus title: A global bibliometric analysis of Plesiomonas-related research (1990 – 2017) date: 2018-11-29 words: 4900.0 sentences: 279.0 pages: flesch: 40.0 cache: ./cache/cord-323330-ghwhgkdm.txt txt: ./txt/cord-323330-ghwhgkdm.txt summary: Here, we carried out a bibliometric survey that aimed to examine publication trends in Plesiomonas-related research by time and place, international collaborative works, identify gaps and suggest directions for future research. The articles were evaluated in terms of annual and country-specific output, theme, domain clusters, international collaboration networks, citations, topical evolution related to keywords and co-occurrence networks, co-authorship, and funding. We used the search term "Plesiomonas shigelloides" to identify primary research articles published between 1990 and 2017. Health emergencies (e.g., outbreaks of infection) relating to emerging viral pathogens including Zika and Chikungunya viruses have driven the generation of new scientific knowledge, resulting in a significant increase in the number of research articles on these subjects [68] . The United States and Sweden dominated the list of top 20 countries most actively researching Plesiomonas in terms of numbers of articles and citations. abstract: Plesiomonas shigelloides is an emerging pathogen with damaging effects on human health such as gastroenteritis and extraintestinal infections. Here, we carried out a bibliometric survey that aimed to examine publication trends in Plesiomonas-related research by time and place, international collaborative works, identify gaps and suggest directions for future research. The search term “Plesiomonas shigelloides” was used to retrieve articles published between 1990 and 2017 from the Web of Science database. Only primary research articles were included in the analysis. A total of 155 articles were published within the survey period, with an average of 5.54±2.66 articles per year and an annual growth rate of −0.8%. Research output peaked in 2000 and 2006 (each accounting for 7.7% of the total). The United States ranked first in terms of numbers of articles (n = 29, 18.1%) and total citations (n = 451). Cameroon, Canada, Cuba, Switzerland and Turkey co-shared the 10(th) position each with 2 articles (1.3%). Research collaboration was low (collaboration index = 3. 32). In addition to Plesiomonas shigelloides (n = 82, 52.9%), the top Authors Keywords and research focus included lipopolysaccharide and nuclear magnetic resonance (n = 13, 8.4%). Diarrhea (n = 43, 27.7%), Aeromonas species (n = 41, 26.5%) and infections (n = 31, 20.0%) were also highly represented in Keywords-Plus. Authors’ collaborations and coupling networks formed two mega-clusters which nodes were shared solely by authors from high-income countries. The common conceptual framework in retrieved articles determined by K-means clustering revealed three clusters with sizes of 7, 16, and 29, representing research responses focused on extraintestinal and gastroenteritis, P. shigelloides lipopolysaccharide structure, and co-infections, respectively. Our bibliometric analysis revealed a global diminishing research in Plesiomonas; greater research outcomes from high-income countries compared to others and low collaboration with developing countries. url: https://doi.org/10.1371/journal.pone.0207655 doi: 10.1371/journal.pone.0207655 id: cord-302529-43pd2qsp author: El Moussi, Awatef title: Virological Surveillance of Influenza Viruses during the 2008–09, 2009–10 and 2010–11 Seasons in Tunisia date: 2013-09-19 words: 3251.0 sentences: 163.0 pages: flesch: 45.0 cache: ./cache/cord-302529-43pd2qsp.txt txt: ./txt/cord-302529-43pd2qsp.txt summary: METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses'' infection during three seasons in Tunisia. A subset of sentinel primary care physicians participating in virological surveillance schemes in the community submits respiratory samples for virological testing from patients presenting in primary health care with an ILI, as well as all regional emergency centres and hospitals that take on surveillance of influenza from community, hospitalized and fatal cases. Phylogenetic analysis of the HA1 nucleotid sequence of 23 influenza A(H1N1)pdm09 viruses from mild, severe (patients hospitalized with severe pneumonia and severe acute respiratory syndrome) and fatal cases, shows that all viruses characterised in Tunisia during season 2009-2010 were outside the seven genetic groups described in the European Centre for Disease Prevention and Control (ECDC) report [19] . abstract: BACKGROUND: The data contribute to a better understanding of the circulation of influenza viruses especially in North-Africa. OBJECTIVE: The objective of this surveillance was to detect severe influenza cases, identify their epidemiological and virological characteristics and assess their impact on the healthcare system. METHOD: We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses' infection during three seasons in Tunisia. RESULTS: The 2008–09 winter influenza season is underway in Tunisia, with co-circulation of influenza A/H3N2 (56.25%), influenza A(H1N1) (32.5%), and a few sporadic influenza B viruses (11.25%). In 2010–11 season the circulating strains are predominantly the 2009 pandemic influenza A(H1N1)pdm09 (70%) and influenza B viruses (22%). And sporadic viruses were sub-typed as A/H3N2 and unsubtyped influenza A, 5% and 3%, respectively. Unlike other countries, highest prevalence of influenza B virus Yamagata-like lineage has been reported in Tunisia (76%) localised into the clade B/Bangladesh/3333/2007. In the pandemic year, influenza A(H1N1)pdm09 predominated over other influenza viruses (95%). Amino acid changes D222G and D222E were detected in the HA gene of A(H1N1)pdm09 virus in two severe cases, one fatal case and one mild case out of 50 influenza A(H1N1)pdm09 viruses studied. The most frequently reported respiratory virus other than influenza in three seasons was RSV (45.29%). CONCLUSION: This article summarises the surveillance and epidemiology of influenza viruses and other respiratory viruses, showing how rapid improvements in influenza surveillance were feasible by connecting the existing structure in the health care system for patient records to electronic surveillance system for reporting ILI cases. url: https://www.ncbi.nlm.nih.gov/pubmed/24069267/ doi: 10.1371/journal.pone.0074064 id: cord-312678-81gnmxbk author: Elayeh, Eman title: Before and after case reporting: A comparison of the knowledge, attitude and practices of the Jordanian population towards COVID-19 date: 2020-10-15 words: 5442.0 sentences: 266.0 pages: flesch: 52.0 cache: ./cache/cord-312678-81gnmxbk.txt txt: ./txt/cord-312678-81gnmxbk.txt summary: Our research group initiated a study to ascertain the knowledge, attitude and practices (KAP) of Jordanians toward COVID-19 prior to any initial case report in Jordan. Therefore, the initial aim of this study was to evaluate the overall knowledge, attitude and practices (KAP) of Jordanian citizens to the ongoing international situation regarding the emergence and pandemic nature of COVID-19. where N is the sample size, Zα: type one error = 1.96 when α = 5%; Zβ: type two error = 1.28 when β = 10%; Q = 1-P: expected non-prevalence; P = proportion in the population possessing the characteristic of interest (based on the estimate that 50% of the respondents knew general information about COVID-19, its routes of transmission and the main preventative measures), d = one-half of the desired interval of confidence, in this study d = 5%. abstract: Coronavirus disease- 2019 (COVID-19) is an emerging contagious infectious disease. It is pandemic and has affected more than 21 million people and resulted in more than 750,000 deaths worldwide (https://www.worldometers.info/coronavirus/#countries; 14/08/20). Our research group initiated a study to ascertain the knowledge, attitude and practices (KAP) of Jordanians toward COVID-19 prior to any initial case report in Jordan. This project was underway when the first Jordanian case was reported. We extended our study to identify how case reporting would alter public KAP towards COVID-19. This cross-sectional study randomly selected and recruited 2104 Jordanian adults. A four-section questionnaire was devised to address the sociodemographic characteristics of the subjects and their KAP toward COVID-19. The mean knowledge score for the study population was 15.9 ± 2.2 (out of the 20 knowledge questions), with 60.9% of the participants having good knowledge about COVID-19. Participants’ practices to prevent transmission of COVID-19 were adequate in more than 60% of participants. Most participants had positive attitudes regarding their role in preventing COVID-19 and many of the participants’ attitudes and practices changed to more appropriate ones after reporting the first case of COVID-19 in Jordan. The percentage of participants who trust the government in confronting COVID-19 increased significantly (p value < 0.001). However, one alarming and unexpected finding was that the prevention practice score of participants working in the medical field was similar to those from the general population. This may necessitate stricter training and guidelines for this group who will be in the frontline in combating the disease. Impact of this study: The data generated from this study shows that when cases of disease were reported, the public’s attitudes and practices improved in many aspects, and that confidence in the government to contain the disease was boosted. We believe that this study is important in allowing other, international governments to develop an understanding of public KAP during pandemic disease outbreaks. url: https://doi.org/10.1371/journal.pone.0240780 doi: 10.1371/journal.pone.0240780 id: cord-333248-5342lyeu author: Elenius, Varpu title: The relationship of serum vitamins A, D, E and LL-37 levels with allergic status, tonsillar virus detection and immune response date: 2017-02-24 words: 3309.0 sentences: 206.0 pages: flesch: 45.0 cache: ./cache/cord-333248-5342lyeu.txt txt: ./txt/cord-333248-5342lyeu.txt summary: We studied how their serum levels were associated with allergy status, intratonsillar/nasopharyngeal virus detection and intratonsillar expression of T celland innate immune response-specific cytokines, transcription factors and type I/II/III interferons in patients undergoing tonsillectomy. We studied how serum vitamins and antimicrobial peptide LL-37 levels and allergic and tonsillar diseases were associated with direct in vivo detection of respiratory viruses and T cell subset-related transcription factors, cytokines as well as type I, II and III interferons in tonsils. The associations of serum levels of vitamins and LL-37, allergy status and virus detection with intratonsillar cytokine and transcription factor expressions were analyzed using univariable and age-adjusted linear regression. This study provides new insights into connections between serum levels of vitamins A, D, and E and antimicrobial peptide LL-37 and several important outcomes: allergy, respiratory virus detection and tonsillar immune responses. abstract: BACKGROUND: Tonsils have an active role in immune defence and inducing and maintaining tolerance to allergens. Vitamins A, D, and E, and antimicrobial peptide LL-37 may have immunomodulatory effects. We studied how their serum levels were associated with allergy status, intratonsillar/nasopharyngeal virus detection and intratonsillar expression of T cell- and innate immune response-specific cytokines, transcription factors and type I/II/III interferons in patients undergoing tonsillectomy. METHODS: 110 elective tonsillectomy patients participated. Serum levels of vitamins A, 25(OH)D, and E, LL-37 and allergen-specific IgE as well as nasopharyngeal/intratonsillar respiratory viruses were analyzed. The mRNA expression of IFN-α, IFN-β, IFN-γ, IL-10, IL-13, IL-17, IL-28, IL-29, IL-37, TGF-β, FOXP3, GATA3, RORC2 and Tbet in tonsils were analyzed by quantitative RT-PCR. RESULTS: The median age of the patients was 16 years (range 3–60), 28% of subjects had atopy, and 57% carried ≥1 respiratory virus in nasopharynx. Detection of viruses decreased by age. Higher vitamin A levels showed borderline significance with less viral detection (P = 0.056). Higher 25(OH)D was associated with less allergic rhinitis and atopy (P < 0.05) and higher vitamin E with less self-reported allergy (P < 0.05). In gene expression analyses, 25(OH)D was associated with higher IL-37, vitamin A with higher IFN-γ and vitamin E with less IL-28 (P < 0.05). LL-37 was associated with less FOXP3, RORC2 and IL-17 in tonsils (P < 0.05). CONCLUSIONS: Vitamin D and E levels were associated with less allergic disorders. Vitamin A was linked to antiviral and vitamin D with anti-inflammatory activity. LL-37 and was linked to T regulatory cell effects. url: https://doi.org/10.1371/journal.pone.0172350 doi: 10.1371/journal.pone.0172350 id: cord-004017-gcmpatlb author: Errecaborde, Kaylee Myhre title: Factors that enable effective One Health collaborations - A scoping review of the literature date: 2019-12-04 words: 9215.0 sentences: 458.0 pages: flesch: 34.0 cache: ./cache/cord-004017-gcmpatlb.txt txt: ./txt/cord-004017-gcmpatlb.txt summary: The review identified 12 factors that support successful One Health collaborations and a coordinated response to health events across three levels: two individual factors (education & training and prior experience & existing relationships), four organizational factors (organizational structures, culture, human resources and, communication), and six network factors (network structures, relationships, leadership, management, available & accessible resources, political environment). In this study, a multidisciplinary team of researchers reviewed a broad scope of literature describing collaborative and multi-sectoral approaches to past health events to understand how such collaborations are commonly described and evaluated and to identify and synthesize enabling factors for One Health collaborations. Starting condition factors reported to enable collaboration at the network level included network structures, existing relationships, available resources in the face of a health event, and the political environment in place to support these efforts. abstract: Advocates for a One Health approach recognize that global health challenges require multidisciplinary collaborative efforts. While past publications have looked at interdisciplinary competency training for collaboration, few have identified the factors and conditions that enable operational One Health. Through a scoping review of the literature, a multidisciplinary team of researchers analyzed peer-reviewed publications describing multisectoral collaborations around infectious disease-related health events. The review identified 12 factors that support successful One Health collaborations and a coordinated response to health events across three levels: two individual factors (education & training and prior experience & existing relationships), four organizational factors (organizational structures, culture, human resources and, communication), and six network factors (network structures, relationships, leadership, management, available & accessible resources, political environment). The researchers also identified the stage of collaboration during which these factors were most critical, further organizing into starting condition or process-based factors. The research found that publications on multisectoral collaboration for health events do not uniformly report on successes or challenges of collaboration and rarely identify outputs or outcomes of the collaborative process. This paper proposes a common language and framework to enable more uniform reporting, implementation, and evaluation of future One Health collaborations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892547/ doi: 10.1371/journal.pone.0224660 id: cord-306278-c4q4la5c author: Esposito, Susanna title: Epidemiology and Clinical Characteristics of Respiratory Infections Due to Adenovirus in Children Living in Milan, Italy, during 2013 and 2014 date: 2016-04-05 words: 4660.0 sentences: 220.0 pages: flesch: 48.0 cache: ./cache/cord-306278-c4q4la5c.txt txt: ./txt/cord-306278-c4q4la5c.txt summary: To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. To evaluate the circulation of the different HAdV types and the possible relationship between viral load, viral genetic characteristics, and the severity of infection, nasopharyngeal swabs were collected from otherwise healthy children consecutively attending the Emergency Room of the Fondazione IRCCS Ca'' Granda Ospedale Maggiore Policlinico, University of Milan, Italy, due to a respiratory tract infection. However, further studies are needed to identify the potential pathogenetic role of the different species and types of HAdV and the importance of viral load in the severity of infection. abstract: To evaluate the predominant human adenovirus (HAdV) species and types associated with pediatric respiratory infections, nasopharyngeal swabs were collected from otherwise healthy children attending an emergency room in Milan, Italy, due to a respiratory tract infection from January 1 to February 28 of two subsequent years, 2013 and 2014. The HAdVs were detected using a respiratory virus panel fast assay (xTAG RVP FAST v2) and with a HAdV-specific real-time polymerase chain reaction; their nucleotides were sequenced, and they were tested for positive selection. Among 307 nasopharyngeal samples, 61 (19.9%) tested positive for HAdV. HAdV was the only virus detected in 31/61 (50.8%) cases, whereas it was found in association with one other virus in 25 (41.0%) cases and with two or more viruses in 5 (8.2%) cases. Human Enterovirus/human rhinovirus and respiratory syncytial virus were the most common co-infecting viral agents and were found in 12 (19.7%) and 7 (11.5%) samples, respectively. Overall, the HAdV strain sequences analyzed were highly conserved. In comparison to HAdV-negative children, those infected with HAdV had a reduced frequency of lower respiratory tract involvement (36.1% vs 55.2%; p = 0.007), wheezing (0.0% vs 12.5%; p = 0.004), and hospitalization (27.9% vs 56.1%; p<0.001). Antibiotic therapy and white blood cell counts were more frequently prescribed (91.9% vs 57.1%; p = 0.04) and higher (17,244 ± 7,737 vs 9,565 ± 3,211 cells/μL; p = 0.04), respectively, in children infected by HAdV-C than among those infected by HAdV-B. On the contrary, those infected by HAdV-B had more frequently lower respiratory tract involvement (57.1% vs 29.7%) but difference did not reach statistical significant (p = 0.21). Children with high viral load were absent from child care attendance for a longer period of time (14.5 ± 7.5 vs 5.5 ± 3.2 days; p = 0.002) and had higher C reactive protein levels (41.3 ± 78.5 vs 5.4 ± 9.6 μg/dL; p = 0.03). This study has shown that HAdV infections are diagnosed more commonly than usually thought and that HAdVs are stable infectious agents that do not frequently cause severe diseases. A trend toward more complex disease in cases due to HAdV species C and in those with higher viral load was demonstrated. However, further studies are needed to clarify factors contributing to disease severity to understand how to develop adequate preventive and therapeutic measures. url: https://www.ncbi.nlm.nih.gov/pubmed/27045588/ doi: 10.1371/journal.pone.0152375 id: cord-347014-88zmtky7 author: Esposito, Susanna title: Sensitivity and Specificity of Soluble Triggering Receptor Expressed on Myeloid Cells-1, Midregional Proatrial Natriuretic Peptide and Midregional Proadrenomedullin for Distinguishing Etiology and to Assess Severity in Community-Acquired Pneumonia date: 2016-11-15 words: 5518.0 sentences: 247.0 pages: flesch: 44.0 cache: ./cache/cord-347014-88zmtky7.txt txt: ./txt/cord-347014-88zmtky7.txt summary: STUDY DESIGN: This study aimed to evaluate the diagnostic accuracy of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1), midregional proatrial natriuretic peptide (MR-proANP) and midregional proadrenomedullin (MR-proADM) to distinguish bacterial from viral community-acquired pneumonia (CAP) and to identify severe cases in children hospitalized for radiologically confirmed CAP. CONCLUSIONS: This study indicates that in children with CAP, sTREM-1, MR-proANP, and MR-proADM blood levels have poor abilities to differentiate bacterial from viral diseases or to identify severe cases, highlighting that PCT maintains the main role at this regard. A global evaluation of the results of this study seemed to indicate that in children with CAP, sTREM-1, MR-proANP, and MR-proADM blood levels are unable to differentiate bacterial from viral diseases or to identify severe cases. abstract: STUDY DESIGN: This study aimed to evaluate the diagnostic accuracy of soluble triggering receptor expressed on myeloid cells-1 (sTREM-1), midregional proatrial natriuretic peptide (MR-proANP) and midregional proadrenomedullin (MR-proADM) to distinguish bacterial from viral community-acquired pneumonia (CAP) and to identify severe cases in children hospitalized for radiologically confirmed CAP. Index test results were compared with those derived from routine diagnostic tests, i.e., white blood cell (WBC) counts, neutrophil percentages, and serum C-reactive protein (CRP) and procalcitonin (PCT) levels. METHODS: This prospective, multicenter study was carried out in the most important children’s hospitals (n = 11) in Italy and 433 otherwise healthy children hospitalized for radiologically confirmed CAP were enrolled. Among cases for whom etiology could be determined, CAP was ascribed to bacteria in 235 (54.3%) children and to one or more viruses in 111 (25.6%) children. A total of 312 (72.2%) children had severe disease. RESULTS: CRP and PCT had the best performances for both bacterial and viral CAP identification. The cut-off values with the highest combined sensitivity and specificity for the identification of bacterial and viral infections using CRP were ≥7.98 mg/L and ≤7.5 mg/L, respectively. When PCT was considered, the cut-off values with the highest combined sensitivity and specificity were ≥0.188 ng/mL for bacterial CAP and ≤0.07 ng/mL for viral CAP. For the identification of severe cases, the best results were obtained with evaluations of PCT and MR-proANP. However, in both cases, the biomarker cut-off with the highest combined sensitivity and specificity (≥0.093 ng/mL for PCT and ≥33.8 pmol/L for proANP) had a relatively good sensitivity (higher than 70%) but a limited specificity (of approximately 55%). CONCLUSIONS: This study indicates that in children with CAP, sTREM-1, MR-proANP, and MR-proADM blood levels have poor abilities to differentiate bacterial from viral diseases or to identify severe cases, highlighting that PCT maintains the main role at this regard. url: https://doi.org/10.1371/journal.pone.0163262 doi: 10.1371/journal.pone.0163262 id: cord-001120-fxd533b4 author: Everitt, Aaron R. title: Defining the Range of Pathogens Susceptible to Ifitm3 Restriction Using a Knockout Mouse Model date: 2013-11-21 words: 4874.0 sentences: 252.0 pages: flesch: 47.0 cache: ./cache/cord-001120-fxd533b4.txt txt: ./txt/cord-001120-fxd533b4.txt summary: We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. Here we sought therefore to expand and define the role of Ifitm3 in pathogen restriction by assessing the susceptibility of Ifitm3-deficient (Ifitm3 -/-) mice to bacteria (Salmonella Typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis), a parasite (Plasmodium berghei) and a virus (respiratory syncytial virus, RSV) to determine the specificity of this crucial antimicrobial protein. Similarly, bacterial counts revealed no significant differences between wild type and Ifitm3 -/-mice; together showing that Ifitm3 does not play a role in resistance or susceptibility to Salmonella infection. The experimental challenge revealed there to be no significant difference in phenotype seen in Ifitm3 -/-mice compared with wild type littermate controls, with both showing susceptibility to ECM ( Figure 5A ). abstract: The interferon-inducible transmembrane (IFITM) family of proteins has been shown to restrict a broad range of viruses in vitro and in vivo by halting progress through the late endosomal pathway. Further, single nucleotide polymorphisms (SNPs) in its sequence have been linked with risk of developing severe influenza virus infections in humans. The number of viruses restricted by this host protein has continued to grow since it was first demonstrated as playing an antiviral role; all of which enter cells via the endosomal pathway. We therefore sought to test the limits of antimicrobial restriction by Ifitm3 using a knockout mouse model. We showed that Ifitm3 does not impact on the restriction or pathogenesis of bacterial (Salmonella typhimurium, Citrobacter rodentium, Mycobacterium tuberculosis) or protozoan (Plasmodium berghei) pathogens, despite in vitro evidence. However, Ifitm3 is capable of restricting respiratory syncytial virus (RSV) in vivo either through directly restricting RSV cell infection, or by exerting a previously uncharacterised function controlling disease pathogenesis. This represents the first demonstration of a virus that enters directly through the plasma membrane, without the need for the endosomal pathway, being restricted by the IFITM family; therefore further defining the role of these antiviral proteins. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836756/ doi: 10.1371/journal.pone.0080723 id: cord-002426-5e1xn7kj author: Falcón-Lezama, Jorge Abelardo title: Analysis of spatial mobility in subjects from a Dengue endemic urban locality in Morelos State, Mexico date: 2017-02-22 words: 5944.0 sentences: 261.0 pages: flesch: 49.0 cache: ./cache/cord-002426-5e1xn7kj.txt txt: ./txt/cord-002426-5e1xn7kj.txt summary: MATERIALS AND METHODS: We carried out a cohort-nested, case-control study with 126 individuals (42 cases, 42 intradomestic controls and 42 population controls) with the goal of describing human mobility patterns of recently Dengue virus-infected subjects, and comparing them with those of non-infected subjects living in an urban endemic locality. CONCLUSIONS: Results of this study show that human mobility in a small urban setting exceeded that considered by local health authority''s administrative limits, and was different between recently infected and non-infected subjects living in the same household. These observations provide important insights about the role that human mobility may have in Dengue virus transmission and persistence across endemic geographic areas that need to be taken into account when planning preventive and control measures. Sample: 126 individuals (42 cases, 42 intradomestic controls and 42 population controls) with age older than 12, and residents in Axochiapan, Morelos State, México, were selected from the cohort "Peridomestic infection as determinant for Dengue virus transmission" [13] . abstract: INTRODUCTION: Mathematical models and field data suggest that human mobility is an important driver for Dengue virus transmission. Nonetheless little is known on this matter due the lack of instruments for precise mobility quantification and study design difficulties. MATERIALS AND METHODS: We carried out a cohort-nested, case-control study with 126 individuals (42 cases, 42 intradomestic controls and 42 population controls) with the goal of describing human mobility patterns of recently Dengue virus-infected subjects, and comparing them with those of non-infected subjects living in an urban endemic locality. Mobility was quantified using a GPS-data logger registering waypoints at 60-second intervals for a minimum of 15 natural days. RESULTS: Although absolute displacement was highly biased towards the intradomestic and peridomestic areas, occasional displacements exceeding a 100-Km radius from the center of the studied locality were recorded for all three study groups and individual displacements were recorded traveling across six states from central Mexico. Additionally, cases had a larger number of visits out of the municipality´s administrative limits when compared to intradomestic controls (cases: 10.4 versus intradomestic controls: 2.9, p = 0.0282). We were able to identify extradomestic places within and out of the locality that were independently visited by apparently non-related infected subjects, consistent with houses, working and leisure places. CONCLUSIONS: Results of this study show that human mobility in a small urban setting exceeded that considered by local health authority’s administrative limits, and was different between recently infected and non-infected subjects living in the same household. These observations provide important insights about the role that human mobility may have in Dengue virus transmission and persistence across endemic geographic areas that need to be taken into account when planning preventive and control measures. Finally, these results are a valuable reference when setting the parameters for future mathematical modeling studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321279/ doi: 10.1371/journal.pone.0172313 id: cord-268977-hcg2rrhl author: Feikin, Daniel R. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 words: 6440.0 sentences: 402.0 pages: flesch: 53.0 cache: ./cache/cord-268977-hcg2rrhl.txt txt: ./txt/cord-268977-hcg2rrhl.txt summary: METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. Compared with other regions, the mortality rate among older children and adults remains several-fold higher in sub-Saharan Africa, where acute respiratory infections (ARI) are a leading cause of this high mortality, as well as associated morbidity [1] . abstract: BACKGROUND: Few comprehensive data exist on disease incidence for specific etiologies of acute respiratory illness (ARI) in older children and adults in Africa. METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). We also collected swabs from asymptomatic controls, from which we calculated pathogen-attributable fractions, adjusting for age, season, and HIV-status, in logistic regression. We calculated incidence by pathogen, adjusting for health-seeking for ARI and pathogen-attributable fractions. Among 3,406 ARI patients >5 years old (adjusted annual incidence 12.0 per 100 person-years), influenza A virus was the most common virus (22% overall; 11% inpatients, 27% outpatients) and Streptococcus pneumoniae was the most common bacteria (16% overall; 23% inpatients, 14% outpatients), yielding annual incidences of 2.6 and 1.7 episodes per 100 person-years, respectively. Influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human metapneumovirus were more prevalent in swabs among cases (22%, 6%, 8% and 5%, respectively) than controls. Adenovirus, parainfluenza viruses, rhinovirus/enterovirus, parechovirus, and Mycoplasma pneumoniae were not more prevalent among cases than controls. Pneumococcus and non-typhi Salmonella were more prevalent among HIV-infected adults, but prevalence of viruses was similar among HIV-infected and HIV-negative individuals. ARI incidence was highest during peak malaria season. CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. url: https://www.ncbi.nlm.nih.gov/pubmed/22937071/ doi: 10.1371/journal.pone.0043656 id: cord-000947-psguw47w author: Feng, Jianyu title: A Study of the Mechanism of the Chaperone-like Function of an scFv of Human Creatine Kinase by Computer Simulation date: 2013-04-24 words: 4685.0 sentences: 270.0 pages: flesch: 54.0 cache: ./cache/cord-000947-psguw47w.txt txt: ./txt/cord-000947-psguw47w.txt summary: We built the model of the single chain antibody (scFv-A4) that increased the stability of human creatine kinase (HCK) by the homology modeling method. Epitopes of human creatine kinase were predicted by computer and then the binding of scFv-A4 and HCK was modeled with computer. To elucidate why scFv-A4 had the chaperone-like function, we combined computer modeling and peptide array membrane technique to study the interactions between scFv-A4 and HCK. Firstly, bioinformatics software tools were used to predict the interacting sites between scFv-A4 and HCK and then the results were combined with the peptide array membrane experiment results to build the 3D models of the binding complex. In complex model-I, scFv-A4 exhibits chaperone-like function by assisting the folding of HCK and stabilizing the whole structure. In this study we combined computer modeling and the peptide array membrane method to investigate the interaction between scFv-A4 and HCK. abstract: A new application of antibodies is to use them as macromolecular chaperones. Protein antigens usually have multiple epitopes, thus, there may be a plurality of antibodies binding to one antigen. However, not all antibodies that bind to one antigen could act as a chaperone. Experiments show that some screened anti-human creatine kinase single chain antibodies (scFV) could assist in the folding and stabilizing of the enzyme, while others could not. We built the model of the single chain antibody (scFv-A4) that increased the stability of human creatine kinase (HCK) by the homology modeling method. Epitopes of human creatine kinase were predicted by computer and then the binding of scFv-A4 and HCK was modeled with computer. The calculation results were further combined with the peptide array membrane experiment results to obtain reliable models for the scFv-A4-HCK complex. Based on the above study we gave an explanation about how scFv-A4 could act as a macromolecular chaperone assisting the folding of HCK. This study provides an approach for predicting antigen-antibody binding mode and also a useful theoretical guidance for the study of antibodies' chaperone-like function. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634753/ doi: 10.1371/journal.pone.0062147 id: cord-294568-12eyo13f author: Fernandes-Matano, Larissa title: Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico date: 2017-05-03 words: 4930.0 sentences: 240.0 pages: flesch: 45.0 cache: ./cache/cord-294568-12eyo13f.txt txt: ./txt/cord-294568-12eyo13f.txt summary: Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs. Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV) [12] . Therefore, the objective of this study was to determine the viral aetiology of these infections and to analyse the behaviour of non-influenza respiratory viruses in the Mexican population. The importance of the differential diagnosis of other respiratory viruses in samples with negative influenza results becomes apparent when we observe the prevalence of the three main viruses identified in this study as well as their associations with severe cases and deaths, especially in the child population. abstract: BACKGROUND: Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections. METHODS: This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR. RESULTS: The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age. CONCLUSION: In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/28467515/ doi: 10.1371/journal.pone.0176298 id: cord-341914-l2bomgji author: Flies, Andrew S. title: Markedly Elevated Antibody Responses in Wild versus Captive Spotted Hyenas Show that Environmental and Ecological Factors Are Important Modulators of Immunity date: 2015-10-07 words: 6626.0 sentences: 297.0 pages: flesch: 44.0 cache: ./cache/cord-341914-l2bomgji.txt txt: ./txt/cord-341914-l2bomgji.txt summary: Our results show that wild hyenas have significantly higher serum antibody concentrations, including total IgG and IgM, natural antibodies, and autoantibodies than do captive hyenas; there was no difference in the bacterial killing capacity of sera collected from captive and wild hyenas. The striking differences in serum antibody concentrations observed here suggest that complementing traditional immunology studies, with comparative studies of wild animals in their natural environment may help to uncover links between environment and immune function, and facilitate progress towards answering immunological questions associated with the hygiene hypothesis. A more robust understanding of the effects of ecological variables such as pathogen exposure on immune function might be gained by studying immune function in non-traditional species, and assessing how basic immune defenses differ between wild and captive animals with similar genetic backgrounds. abstract: Evolutionary processes have shaped the vertebrate immune system over time, but proximal mechanisms control the onset, duration, and intensity of immune responses. Based on testing of the hygiene hypothesis, it is now well known that microbial exposure is important for proper development and regulation of the immune system. However, few studies have examined the differences between wild animals in their natural environments, in which they are typically exposed to a wide array of potential pathogens, and their conspecifics living in captivity. Wild spotted hyenas (Crocuta crocuta) are regularly exposed to myriad pathogens, but there is little evidence of disease-induced mortality in wild hyena populations, suggesting that immune defenses are robust in this species. Here we assessed differences in immune defenses between wild spotted hyenas that inhabit their natural savanna environment and captive hyenas that inhabit a captive environment where pathogen control programs are implemented. Importantly, the captive population of spotted hyenas was derived directly from the wild population and has been in captivity for less than four generations. Our results show that wild hyenas have significantly higher serum antibody concentrations, including total IgG and IgM, natural antibodies, and autoantibodies than do captive hyenas; there was no difference in the bacterial killing capacity of sera collected from captive and wild hyenas. The striking differences in serum antibody concentrations observed here suggest that complementing traditional immunology studies, with comparative studies of wild animals in their natural environment may help to uncover links between environment and immune function, and facilitate progress towards answering immunological questions associated with the hygiene hypothesis. url: https://doi.org/10.1371/journal.pone.0137679 doi: 10.1371/journal.pone.0137679 id: cord-000425-isw6jeir author: Flori, Laurence title: Immunity Traits in Pigs: Substantial Genetic Variation and Limited Covariation date: 2011-07-29 words: 7831.0 sentences: 388.0 pages: flesch: 46.0 cache: ./cache/cord-000425-isw6jeir.txt txt: ./txt/cord-000425-isw6jeir.txt summary: A study on Yorkshire pigs selected for eight generations for high and low adaptive IR (HIR and LIR, respectively) on an index combining four standardized measures of specific antibodies and cellmediated IR, after stimulation with specific antigens (bacillus Calmette-Guérin and hen egg white lysozyme), has revealed that HIR and LIR animals differ in response to immunization and infection [2, 11, 12, 13, 14] . Finally, several significant QTLs for total leukocyte count ( [20, 21] ; Animal-QTLdb, http://www.animalgenome.org/cgi-bin/QTLdb/index), mitogen-induced proliferation [20] , antibody response [20, 22] , cytokine production (IL10 and IFNc) [23] , complement activity [22] , and acute phase protein serum concentration [22] have been detected and mapped to different pig chromosomes. In this report, we present the results of a global genetic study, combining principal component analysis (PCA), and genetic parameter estimation applied to a large number of innate and adaptive ITs in a pig population vaccinated against Mycoplasma hyopneumoniae (M. abstract: BACKGROUND: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs). Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment. METHODOLOGY/PRINCIPAL FINDINGS: Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA) and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNα, TNFα, IL6, IL8, IL12, IFNγ, IL2, IL4, IL10), phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.1