Carrel name: keyword-strain-cord Creating study carrel named keyword-strain-cord Initializing database file: cache/cord-255857-y9wjp0aj.json key: cord-255857-y9wjp0aj authors: Yuan, Shishan; Mickelson, Daniel; Murtaugh, Michael P.; Faaberg, Kay S. title: Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date: 2001-11-05 journal: Virus Res DOI: 10.1016/s0168-1702(01)00295-7 sha: doc_id: 255857 cord_uid: y9wjp0aj file: cache/cord-009764-m9flptcv.json key: cord-009764-m9flptcv authors: Bossé, Ynuk title: The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity date: 2019-01-18 journal: J Eng Sci Med Diagn Ther DOI: 10.1115/1.4042309 sha: doc_id: 9764 cord_uid: m9flptcv file: cache/cord-000820-5b29wtim.json key: cord-000820-5b29wtim authors: Borriello, Giorgia; Lucibelli, Maria G; Pesciaroli, Michele; Carullo, Maria R; Graziani, Caterina; Ammendola, Serena; Battistoni, Andrea; Ercolini, Danilo; Pasquali, Paolo; Galiero, Giorgio title: Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis date: 2012-10-25 journal: BMC Vet Res DOI: 10.1186/1746-6148-8-201 sha: doc_id: 820 cord_uid: 5b29wtim file: cache/cord-014461-2ubh9u8r.json key: cord-014461-2ubh9u8r authors: Nelson, Oranmiyan W.; Garrity, George M. title: Genome sequences published outside of Standards in Genomic Sciences, July - October 2012 date: 2012-10-10 journal: Stand Genomic Sci DOI: 10.4056/sigs.3416907 sha: doc_id: 14461 cord_uid: 2ubh9u8r file: cache/cord-002561-7j43yic1.json key: cord-002561-7j43yic1 authors: Donato, Celeste; Vijaykrishna, Dhanasekaran title: The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses date: 2017-05-10 journal: Viruses DOI: 10.3390/v9050102 sha: doc_id: 2561 cord_uid: 7j43yic1 file: cache/cord-012054-bpgb7tgo.json key: cord-012054-bpgb7tgo authors: Ferreira, Maria Isabel M.; Marchesi, Julian R.; Janssen, Dick B. title: Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1 date: 2008-03-01 journal: Appl Microbiol Biotechnol DOI: 10.1007/s00253-008-1343-3 sha: doc_id: 12054 cord_uid: bpgb7tgo file: cache/cord-004116-ckms25na.json key: cord-004116-ckms25na authors: Moser, Kara A.; Drábek, Elliott F.; Dwivedi, Ankit; Stucke, Emily M.; Crabtree, Jonathan; Dara, Antoine; Shah, Zalak; Adams, Matthew; Li, Tao; Rodrigues, Priscila T.; Koren, Sergey; Phillippy, Adam M.; Munro, James B.; Ouattara, Amed; Sparklin, Benjamin C.; Dunning Hotopp, Julie C.; Lyke, Kirsten E.; Sadzewicz, Lisa; Tallon, Luke J.; Spring, Michele D.; Jongsakul, Krisada; Lon, Chanthap; Saunders, David L.; Ferreira, Marcelo U.; Nyunt, Myaing M.; Laufer, Miriam K.; Travassos, Mark A.; Sauerwein, Robert W.; Takala-Harrison, Shannon; Fraser, Claire M.; Sim, B. Kim Lee; Hoffman, Stephen L.; Plowe, Christopher V.; Silva, Joana C. title: Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential date: 2020-01-08 journal: Genome Med DOI: 10.1186/s13073-019-0708-9 sha: doc_id: 4116 cord_uid: ckms25na file: cache/cord-004751-4vl0cvyq.json key: cord-004751-4vl0cvyq authors: Mostow, S. R.; Tyrrell, D. A. J. title: The behaviour in vitro of attenuated recombinant influenza viruses date: 1973 journal: Arch Gesamte Virusforsch DOI: 10.1007/bf01556156 sha: doc_id: 4751 cord_uid: 4vl0cvyq file: cache/cord-255137-utg8k7qs.json key: cord-255137-utg8k7qs authors: Yinda, Claude Kwe; Vanhulle, Emiel; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Shi, Chenyan; Ghogomu, Stephen Mbigha; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle title: Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date: 2019-01-23 journal: mSphere DOI: 10.1128/msphere.00585-18 sha: doc_id: 255137 cord_uid: utg8k7qs file: cache/cord-281172-7di6eub3.json key: cord-281172-7di6eub3 authors: Biswas, Kaushiki; Chatterjee, Dhriti; Addya, Sankar; Khan, Reas S.; Kenyon, Lawrence C.; Choe, Alexander; Cohrs, Randall J.; Shindler, Kenneth S.; Das Sarma, Jayasri title: Demyelinating strain of mouse hepatitis virus infection bridging innate and adaptive immune response in the induction of demyelination date: 2016-07-06 journal: Clin Immunol DOI: 10.1016/j.clim.2016.07.004 sha: doc_id: 281172 cord_uid: 7di6eub3 file: cache/cord-005057-deq5tv1d.json key: cord-005057-deq5tv1d authors: Bergström, T.; Alestig, K.; Svennerholm, B.; Horal, P.; Sköldenberg, B.; Vahlne, A. title: Neurovirulence of herpes simplex virus types 1 and 2 isolates in diseases of the central nervous system date: 1990 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/bf02184688 sha: doc_id: 5057 cord_uid: deq5tv1d 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-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-259959-qzd3hf8y.json key: cord-259959-qzd3hf8y authors: Alhatami, Abdullah O.; Alaraji, Furkan; Abdulwahab, Husam Muhsen; Khudhair, Yahia Ismail title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date: 2020-07-16 journal: Vet World DOI: 10.14202/vetworld.2020.1358-1362 sha: doc_id: 259959 cord_uid: qzd3hf8y file: cache/cord-010187-ymhcfyxx.json key: cord-010187-ymhcfyxx authors: Gromeier, Matthias; Lu, Hui-Hua; Wimmer, Eckard title: Mouse neuropathogenic poliovirus strains cause damage in the central nervous system distinct from poliomyelitis date: 2005-03-25 journal: Microb Pathog DOI: 10.1016/s0882-4010(05)80002-6 sha: doc_id: 10187 cord_uid: ymhcfyxx file: cache/cord-288451-npefpo3t.json key: cord-288451-npefpo3t authors: Yinda, Claude Kwe; Zeller, Mark; Conceição-Neto, Nádia; Maes, Piet; Deboutte, Ward; Beller, Leen; Heylen, Elisabeth; Ghogomu, Stephen Mbigha; Van Ranst, Marc; Matthijnssens, Jelle title: Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis date: 2016-09-26 journal: Sci Rep DOI: 10.1038/srep34209 sha: doc_id: 288451 cord_uid: npefpo3t file: cache/cord-003908-wbawzbhz.json key: cord-003908-wbawzbhz authors: Matsushima, Yuki; Mizukoshi, Fuminori; Sakon, Naomi; Doan, Yen Hai; Ueki, Yo; Ogawa, Yasutaka; Motoya, Takumi; Tsukagoshi, Hiroyuki; Nakamura, Noriko; Shigemoto, Naoki; Yoshitomi, Hideaki; Okamoto-Nakagawa, Reiko; Suzuki, Rieko; Tsutsui, Rika; Terasoma, Fumio; Takahashi, Tomoko; Sadamasu, Kenji; Shimizu, Hideaki; Okabe, Nobuhiko; Nagasawa, Koo; Aso, Jumpei; Ishii, Haruyuki; Kuroda, Makoto; Ryo, Akihide; Katayama, Kazuhiko; Kimura, Hirokazu title: Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017 date: 2019-09-27 journal: Front Microbiol DOI: 10.3389/fmicb.2019.02189 sha: doc_id: 3908 cord_uid: wbawzbhz file: cache/cord-291510-jh2fdks4.json key: cord-291510-jh2fdks4 authors: Jiang, Yi; Cheng, Xu; Zhao, Xiumei; Yu, Yan; Gao, Mingyan; Zhou, Sheng title: Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity date: 2020-02-11 journal: Vaccine DOI: 10.1016/j.vaccine.2020.01.001 sha: doc_id: 291510 cord_uid: jh2fdks4 file: cache/cord-289623-7oc1ykds.json key: cord-289623-7oc1ykds authors: Gendy, Sherif; Chauhan, Ashvini; Agarwal, Meenakshi; Pathak, Ashish; Rathore, Rajesh Singh; Jaswal, Rajneesh title: Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018 date: 2020-08-20 journal: Front Microbiol DOI: 10.3389/fmicb.2020.01923 sha: doc_id: 289623 cord_uid: 7oc1ykds file: cache/cord-022383-pz0htccp.json key: cord-022383-pz0htccp authors: Kohn, Dennis F.; Barthold, Stephen W. title: Biology and Diseases of Rats date: 2013-11-17 journal: Laboratory Animal Medicine DOI: 10.1016/b978-0-12-263620-2.50010-0 sha: doc_id: 22383 cord_uid: pz0htccp file: cache/cord-355492-0zvqvumc.json key: cord-355492-0zvqvumc authors: Hamm, Ronda L; Kaufman, Phillip E; Reasor, Colleen A; Rutz, Donald A; Scott, Jeffrey G title: Resistance to cyfluthrin and tetrachlorvinphos in the lesser mealworm, Alphitobius diaperinus, collected from the eastern United States date: 2006-06-12 journal: Pest Manag Sci DOI: 10.1002/ps.1230 sha: doc_id: 355492 cord_uid: 0zvqvumc file: cache/cord-294509-txk1qic1.json key: cord-294509-txk1qic1 authors: Li, Zi; He, Wenqi; Lan, Yungang; Zhao, Kui; Lv, Xiaoling; Lu, Huijun; Ding, Ning; Zhang, Jing; Shi, Junchao; Shan, Changjian; Gao, Feng title: The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets date: 2016-09-15 journal: PeerJ DOI: 10.7717/peerj.2443 sha: doc_id: 294509 cord_uid: txk1qic1 file: cache/cord-271897-9oqzsd70.json key: cord-271897-9oqzsd70 authors: Domanska-Blicharz, Katarzyna; Lisowska, Anna; Sajewicz-Krukowska, Joanna title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017 date: 2020-01-07 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2020.104177 sha: doc_id: 271897 cord_uid: 9oqzsd70 file: cache/cord-306976-p2521bl4.json key: cord-306976-p2521bl4 authors: Gao, Mengying; Wang, Qiuling; Zhao, Wenjun; Chen, Yuqiu; Zhang, Tingting; Han, Zongxi; Xu, Qianqian; Kong, Xiangang; Liu, Shengwang title: Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date: 2016-08-15 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2016.05.018 sha: doc_id: 306976 cord_uid: p2521bl4 file: cache/cord-010641-hk90qx1k.json key: cord-010641-hk90qx1k authors: Rodrigues, Juliana Falcão; Lourenço, Rogério Ferreira; Maeda, Denicar Lina Nascimento Fabris; de Jesus Cintra, Mariana; Nakao, Naomi; Mathias-Santos, Camila; Luiz, Wilson Barros; de Souza Ferreira, Luís Carlos title: Strain-specific transcriptional and posttranscriptional regulation of heat-labile toxin expression by enterotoxigenic Escherichia coli date: 2020-02-03 journal: Braz J Microbiol DOI: 10.1007/s42770-020-00231-2 sha: doc_id: 10641 cord_uid: hk90qx1k file: cache/cord-018061-jy3km0fr.json key: cord-018061-jy3km0fr authors: AL KASSAA, Imad title: Antiviral Probiotics: A New Concept in Medical Sciences date: 2016-12-02 journal: New Insights on Antiviral Probiotics DOI: 10.1007/978-3-319-49688-7_1 sha: doc_id: 18061 cord_uid: jy3km0fr file: cache/cord-291930-n7wq09rq.json key: cord-291930-n7wq09rq authors: Arden, K.E.; Faux, C.E.; O’Neill, N.T.; McErlean, P.; Nitsche, A.; Lambert, S.B.; Nissen, M.D.; Sloots, T.P.; Mackay, I.M. title: Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003 date: 2010-01-27 journal: J Clin Virol DOI: 10.1016/j.jcv.2010.01.001 sha: doc_id: 291930 cord_uid: n7wq09rq file: cache/cord-296611-ma32oz4o.json key: cord-296611-ma32oz4o authors: Ma, Tianxin; Xu, Liwen; Ren, Mengting; Shen, Jie; Han, Zongxi; Sun, Junfeng; Zhao, Yan; Liu, Shengwang title: Novel genotype of infectious bronchitis virus isolated in China date: 2019-01-29 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2019.01.020 sha: doc_id: 296611 cord_uid: ma32oz4o file: cache/cord-355119-sdg9zdc1.json key: cord-355119-sdg9zdc1 authors: Lin, Huixing; Chen, Lei; Gao, Lu; Yuan, Xiaomin; Ma, Zhe; Fan, Hongjie title: Epidemic strain YC2014 of porcine epidemic diarrhea virus could provide piglets against homologous challenge date: 2016-04-22 journal: Virol J DOI: 10.1186/s12985-016-0529-z sha: doc_id: 355119 cord_uid: sdg9zdc1 file: cache/cord-279495-zxerb7de.json key: cord-279495-zxerb7de authors: Liu, Xiaoli; Shao, Yuhao; Ma, Huijie; Sun, Chuyang; Zhang, Xiaonan; Li, Chengren; Han, Zongxi; Yan, Baolong; Kong, Xiangang; Liu, Shengwang title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date: 2012-11-21 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2012.09.016 sha: doc_id: 279495 cord_uid: zxerb7de file: cache/cord-269892-bmdpbkni.json key: cord-269892-bmdpbkni authors: Tabares, Paula; Pimentel-Elardo, Sheila M.; Schirmeister, Tanja; Hünig, Thomas; Hentschel, Ute title: Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges date: 2011-01-11 journal: Mar Biotechnol (NY) DOI: 10.1007/s10126-010-9349-0 sha: doc_id: 269892 cord_uid: bmdpbkni file: cache/cord-009664-kb9fnbgy.json key: cord-009664-kb9fnbgy authors: nan title: Oral presentations date: 2014-12-24 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2009.02857.x sha: doc_id: 9664 cord_uid: kb9fnbgy file: cache/cord-301301-ilsenpus.json key: cord-301301-ilsenpus authors: Mihalov-Kovács, Eszter; Martella, Vito; Lanave, Gianvito; Bodnar, Livia; Fehér, Enikő; Marton, Szilvia; Kemenesi, Gábor; Jakab, Ferenc; Bányai, Krisztián title: Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission date: 2017-03-15 journal: Virus Res DOI: 10.1016/j.virusres.2016.12.005 sha: doc_id: 301301 cord_uid: ilsenpus file: cache/cord-347644-4qenzjiu.json key: cord-347644-4qenzjiu authors: Shorter, John R.; Maurizio, Paul L.; Bell, Timothy A.; Shaw, Ginger D.; Miller, Darla R.; Gooch, Terry J.; Spence, Jason S.; McMillan, Leonard; Valdar, William; Pardo-Manuel de Villena, Fernando title: A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size date: 2019-03-15 journal: G3 (Bethesda) DOI: 10.1534/g3.118.200847 sha: doc_id: 347644 cord_uid: 4qenzjiu file: cache/cord-301347-22lt6h40.json key: cord-301347-22lt6h40 authors: Jarvis, Matthew C.; Lam, Ham Ching; Zhang, Yan; Wang, Leyi; Hesse, Richard A.; Hause, Ben M.; Vlasova, Anastasia; Wang, Qiuhong; Zhang, Jianqiang; Nelson, Martha I.; Murtaugh, Michael P.; Marthaler, Douglas title: Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus date: 2016-01-01 journal: Prev Vet Med DOI: 10.1016/j.prevetmed.2015.10.020 sha: doc_id: 301347 cord_uid: 22lt6h40 file: cache/cord-299763-ttb7o8lv.json key: cord-299763-ttb7o8lv authors: Choi, Jeong-Won; Jung, Ji-Youl; Lee, Jae-Il; Lee, Kyoung-Ki; Oem, Jae-Ku title: Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date: 2016-06-01 journal: Arch Virol DOI: 10.1007/s00705-016-2895-7 sha: doc_id: 299763 cord_uid: ttb7o8lv file: cache/cord-323463-osf6t7cw.json key: cord-323463-osf6t7cw authors: Cercenado, Emilia; Garau, Javier; Almirante, Benito; Ramón Azanza, José; Cantón, Rafael; Cisterna, Ramón; María Eiros, José; Fariñas, Carmen; Fortún, Jesús; Gudiol, Francisco; Mensa, José; Pachón, Jerónimo; Pascual, Álvaro; Luis Pérez, José; Rodríguez, Alejandro; Sánchez, Miguel; Vila, Jordi title: Update on bacterial pathogens: virulence and resistance date: 2008-04-30 journal: Enfermedades Infecciosas y Microbiología Clínica DOI: 10.1016/s0213-005x(08)76378-x sha: doc_id: 323463 cord_uid: osf6t7cw file: cache/cord-280334-7b7rvr25.json key: cord-280334-7b7rvr25 authors: Abrantes, Joana; Droillard, Clément; Lopes, Ana M.; Lemaitre, Evelyne; Lucas, Pierrick; Blanchard, Yannick; Marchandeau, Stéphane; Esteves, Pedro J.; Le Gall-Reculé, Ghislaine title: Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2 date: 2020-09-02 journal: Sci Rep DOI: 10.1038/s41598-020-71303-4 sha: doc_id: 280334 cord_uid: 7b7rvr25 file: cache/cord-353190-7qcoxl81.json key: cord-353190-7qcoxl81 authors: Nicklas, Werner; Bleich, André; Mähler, Michael title: Viral Infections of Laboratory Mice date: 2012-05-17 journal: The Laboratory Mouse DOI: 10.1016/b978-0-12-382008-2.00019-2 sha: doc_id: 353190 cord_uid: 7qcoxl81 file: cache/cord-267671-ys43n672.json key: cord-267671-ys43n672 authors: Whary, Mark T.; Baumgarth, Nicole; Fox, James G.; Barthold, Stephen W. title: Biology and Diseases of Mice date: 2015-07-10 journal: Laboratory Animal Medicine DOI: 10.1016/b978-0-12-409527-4.00003-1 sha: doc_id: 267671 cord_uid: ys43n672 file: cache/cord-023592-w96h4rir.json key: cord-023592-w96h4rir authors: nan title: Abstracts cont. date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2004.0902c.x sha: doc_id: 23592 cord_uid: w96h4rir file: cache/cord-019490-m1cuuehi.json key: cord-019490-m1cuuehi authors: nan title: Abstracts cont. date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1469-0691.2005.clm_1134_02.x sha: doc_id: 19490 cord_uid: m1cuuehi file: cache/cord-008777-i2reanan.json key: cord-008777-i2reanan authors: nan title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 journal: J Biotechnol DOI: 10.1016/j.jbiotec.2005.06.005 sha: doc_id: 8777 cord_uid: i2reanan file: cache/cord-022501-9wnmdvg5.json key: cord-022501-9wnmdvg5 authors: nan title: P1460 – P1884 date: 2015-12-28 journal: Clin Microbiol Infect DOI: 10.1111/j.1470-9465.2006.12_4_1431.x sha: doc_id: 22501 cord_uid: 9wnmdvg5 file: cache/cord-007890-bie1veti.json key: cord-007890-bie1veti authors: nan title: ECC-4 Abstracts date: 2002-04-16 journal: Int J Antimicrob Agents DOI: 10.1016/s0924-8579(02)00033-x sha: doc_id: 7890 cord_uid: bie1veti Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-strain-cord parallel: Warning: No more processes: Decreasing number of running jobs to 44. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 44. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.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: 59494 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: 59576 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: 59725 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: 59915 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: 60094 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 44. 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: 60548 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: 61056 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 44. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 43. 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: 61646 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: 60251 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: 61966 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: 60558 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 42. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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/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/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 /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: 61916 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: 61559 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.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: 62476 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: 62485 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: 62482 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: 64157 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: 64812 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: 63593 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: 66034 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: 65580 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: 65510 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: 66809 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: 64733 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: 65074 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: 59399 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: 66979 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: 68245 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-255857-y9wjp0aj author: Yuan, Shishan title: Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date: 2001-11-05 pages: extension: .txt txt: ./txt/cord-255857-y9wjp0aj.txt cache: ./cache/cord-255857-y9wjp0aj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-255857-y9wjp0aj.txt' === file2bib.sh === id: cord-000820-5b29wtim author: Borriello, Giorgia title: Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis date: 2012-10-25 pages: extension: .txt txt: ./txt/cord-000820-5b29wtim.txt cache: ./cache/cord-000820-5b29wtim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-000820-5b29wtim.txt' === file2bib.sh === id: cord-299763-ttb7o8lv author: Choi, Jeong-Won title: Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date: 2016-06-01 pages: extension: .txt txt: ./txt/cord-299763-ttb7o8lv.txt cache: ./cache/cord-299763-ttb7o8lv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-299763-ttb7o8lv.txt' === file2bib.sh === id: cord-301347-22lt6h40 author: Jarvis, Matthew C. title: Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus date: 2016-01-01 pages: extension: .txt txt: ./txt/cord-301347-22lt6h40.txt cache: ./cache/cord-301347-22lt6h40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301347-22lt6h40.txt' === file2bib.sh === id: cord-279495-zxerb7de author: Liu, Xiaoli title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date: 2012-11-21 pages: extension: .txt txt: ./txt/cord-279495-zxerb7de.txt cache: ./cache/cord-279495-zxerb7de.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279495-zxerb7de.txt' === file2bib.sh === id: cord-269892-bmdpbkni author: Tabares, Paula title: Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges date: 2011-01-11 pages: extension: .txt txt: ./txt/cord-269892-bmdpbkni.txt cache: ./cache/cord-269892-bmdpbkni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269892-bmdpbkni.txt' === file2bib.sh === id: cord-018061-jy3km0fr author: AL KASSAA, Imad title: Antiviral Probiotics: A New Concept in Medical Sciences date: 2016-12-02 pages: extension: .txt txt: ./txt/cord-018061-jy3km0fr.txt cache: ./cache/cord-018061-jy3km0fr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018061-jy3km0fr.txt' === file2bib.sh === id: cord-323463-osf6t7cw author: Cercenado, Emilia title: Update on bacterial pathogens: virulence and resistance date: 2008-04-30 pages: extension: .txt txt: ./txt/cord-323463-osf6t7cw.txt cache: ./cache/cord-323463-osf6t7cw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323463-osf6t7cw.txt' === file2bib.sh === id: cord-022383-pz0htccp author: Kohn, Dennis F. title: Biology and Diseases of Rats date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022383-pz0htccp.txt cache: ./cache/cord-022383-pz0htccp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022383-pz0htccp.txt' === file2bib.sh === id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 pages: extension: .txt txt: ./txt/cord-353190-7qcoxl81.txt cache: ./cache/cord-353190-7qcoxl81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-353190-7qcoxl81.txt' === file2bib.sh === id: cord-009664-kb9fnbgy author: nan title: Oral presentations date: 2014-12-24 pages: extension: .txt txt: ./txt/cord-009664-kb9fnbgy.txt cache: ./cache/cord-009664-kb9fnbgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-009664-kb9fnbgy.txt' === file2bib.sh === id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 pages: extension: .txt txt: ./txt/cord-267671-ys43n672.txt cache: ./cache/cord-267671-ys43n672.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-267671-ys43n672.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-023592-w96h4rir author: nan title: Abstracts cont. date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-023592-w96h4rir.txt cache: ./cache/cord-023592-w96h4rir.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-023592-w96h4rir.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-007890-bie1veti author: nan title: ECC-4 Abstracts date: 2002-04-16 pages: extension: .txt txt: ./txt/cord-007890-bie1veti.txt cache: ./cache/cord-007890-bie1veti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 303 resourceName b'cord-007890-bie1veti.txt' === file2bib.sh === id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-019490-m1cuuehi.txt cache: ./cache/cord-019490-m1cuuehi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-019490-m1cuuehi.txt' === file2bib.sh === id: cord-022501-9wnmdvg5 author: nan title: P1460 – P1884 date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-022501-9wnmdvg5.txt cache: ./cache/cord-022501-9wnmdvg5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022501-9wnmdvg5.txt' === file2bib.sh === id: cord-008777-i2reanan author: nan title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 pages: extension: .txt txt: ./txt/cord-008777-i2reanan.txt cache: ./cache/cord-008777-i2reanan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-008777-i2reanan.txt' Que is empty; done keyword-strain-cord === reduce.pl bib === id = cord-255857-y9wjp0aj author = Yuan, Shishan title = Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date = 2001-11-05 pages = extension = .txt mime = text/plain words = 4283 sentences = 235 flesch = 56 summary = Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. However, the cluster of amino acid mutations located near the carboxyl terminal end suggests that the replicase region was altered during passage to result in a more fit virus for replication in cell culture, as evidenced by the in vitro one-step growth curve comparison shown in Fig. 4 . Sequence analysis of strains VR-2332 and RespPRRS indicated that there were 15 nucleotide changes in this region, and all but one of which resulted in amino acid alterations. Attenuation can result from changes in many areas of viral genomes and the 41 nucleotide mutations described include alterations in several key PRRSV regions. cache = ./cache/cord-255857-y9wjp0aj.txt txt = ./txt/cord-255857-y9wjp0aj.txt === reduce.pl bib === === reduce.pl bib === id = cord-000820-5b29wtim author = Borriello, Giorgia title = Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis date = 2012-10-25 pages = extension = .txt mime = text/plain words = 4319 sentences = 237 flesch = 47 summary = RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The current study investigated the intestinal contents collected from 248 water buffalo calves affected by gastroenteritis with lethal outcome to: (i) evaluate the prevalence of Salmonella spp., and (ii) perform a polyphasic characterization of the collected isolates of S. The genetic characterization (Table 2) included five loci (avrA, ssaQ, mgtC, siiD, and sopB) located on SPI 1-5, respectively [8] , eight loci (gipA, gtgB, sopE, sodC1, gtgE, gogB, sspH1, and sspH2) of prophage origin [9] [10] [11] [12] [13] , the gene spvC, located on a virulence plasmid [12] , and nine genes (stfE, safC, csgA, ipfD, bcfC, stbD, pefA, fimA, and agfA) coding for bacterial fimbriae, involved in surface adhesion and gut colonization [5] . cache = ./cache/cord-000820-5b29wtim.txt txt = ./txt/cord-000820-5b29wtim.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 === === reduce.pl bib === id = cord-022383-pz0htccp author = Kohn, Dennis F. title = Biology and Diseases of Rats date = 2013-11-17 pages = extension = .txt mime = text/plain words = 20181 sentences = 1195 flesch = 50 summary = The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. cache = ./cache/cord-022383-pz0htccp.txt txt = ./txt/cord-022383-pz0htccp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-018061-jy3km0fr author = AL KASSAA, Imad title = Antiviral Probiotics: A New Concept in Medical Sciences date = 2016-12-02 pages = extension = .txt mime = text/plain words = 13236 sentences = 747 flesch = 42 summary = rhamnosus GG (LGG), a famous probiotic strain, was evaluated and showed an anti-infl uenza virus activity on intranasal and oral administration [ 26 , 27 ] . Moreover, the antiviral effect of probiotics by immunomodulatory mechanisms depends on the immune system status, which can be explained in the study conducted by Lehtoranta et al., who showed that the combination of four probiotic strains worked very well in children but not in the elderly [ 61 ] . The role of commensal bacteria in the persistence of enteric viral infections has previously been shown in a series of recent studies published in 2011, using poliovirus, reovirus and mouse mammary tumor virus (MMTV) as EnV models [ 99 -101 ] . Differential effects of Escherichia coli Nissle and Lactobacillus rhamnosus Strain GG on human rotavirus binding, infection, and B cell immunity cache = ./cache/cord-018061-jy3km0fr.txt txt = ./txt/cord-018061-jy3km0fr.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-279495-zxerb7de author = Liu, Xiaoli title = Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date = 2012-11-21 pages = extension = .txt mime = text/plain words = 5235 sentences = 258 flesch = 56 summary = Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-279495-zxerb7de.txt txt = ./txt/cord-279495-zxerb7de.txt === reduce.pl bib === id = cord-269892-bmdpbkni author = Tabares, Paula title = Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges date = 2011-01-11 pages = extension = .txt mime = text/plain words = 5401 sentences = 298 flesch = 47 summary = Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. The first group of sponges (Aplysina fistularis, Plakortis sp., Amphimedon compressa, Aiolochroia crassa, Agelas clathrodes, Agelas cerebrum, Ircinia felix, Scopalina ruetzleri, Erylus formosus, Chondrilla nucula, and Aplysina archeri) was collected by SCUBA diving at depths of 3-20 m in Bahamas in July 2008 (GPS-26°27′3.25″ N, 77°5 4′14.59″ W). In terms of actinomycete diversity, the 79 cultivated strains are represented by 20 different genera namely Microbacterium (21 isolates), Rhodococcus (10), Streptomyces (5), Mycobacterium (6), Micromonospora (5), Knoellia (4), Gordonia (4), Curtobacterium (4), Arthrobacter (4) Salinispora (3), Saccharopolyspora (2), Nocardioides (2), Citromicrobium (2), Sanguibacter (1), Lapillicoccus (1), Kocuria (1), Dietzia (1), Cellulosimicrobium (1) Cellulomonas (1), and Agrococcus (1; Supplementary Table 1) . A family of aeruginosin inhibitors is active against human serine proteases and was isolated from marine sponges and cyanobacterial waterblooms (Ersmark et al. Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes cache = ./cache/cord-269892-bmdpbkni.txt txt = ./txt/cord-269892-bmdpbkni.txt === reduce.pl bib === id = cord-009664-kb9fnbgy author = nan title = Oral presentations date = 2014-12-24 pages = extension = .txt mime = text/plain words = 71112 sentences = 3948 flesch = 47 summary = Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically. cache = ./cache/cord-009664-kb9fnbgy.txt txt = ./txt/cord-009664-kb9fnbgy.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-301347-22lt6h40 author = Jarvis, Matthew C. title = Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus date = 2016-01-01 pages = extension = .txt mime = text/plain words = 4256 sentences = 218 flesch = 52 summary = Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States 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 cache = ./cache/cord-301347-22lt6h40.txt txt = ./txt/cord-301347-22lt6h40.txt === reduce.pl bib === id = cord-323463-osf6t7cw author = Cercenado, Emilia title = Update on bacterial pathogens: virulence and resistance date = 2008-04-30 pages = extension = .txt mime = text/plain words = 15021 sentences = 679 flesch = 42 summary = This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. Although predictions during the 20th century indicated that the incidence of infectious diseases would diminish as a result of improvements in sanitation and by the introduction of many vaccines and antibiotics, at the beginning of the 21st century the rates of infections produced by new pathogens or by reemerging microorganisms possessing new virulence or resistance phenotypes is increasing, threatening the overall human health [1] [2] [3] [4] [5] . It is in this scenario where community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as the most common pathogen isolated from patients with skin and soft-tissue infections attending to the emergency departments in many United States and Australian cities 8, 9 , and at present, its incidence is increasing in other parts of the world 10, 11 . cache = ./cache/cord-323463-osf6t7cw.txt txt = ./txt/cord-323463-osf6t7cw.txt === reduce.pl bib === id = cord-299763-ttb7o8lv author = Choi, Jeong-Won title = Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date = 2016-06-01 pages = extension = .txt mime = text/plain words = 2615 sentences = 128 flesch = 49 summary = Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains cache = ./cache/cord-299763-ttb7o8lv.txt txt = ./txt/cord-299763-ttb7o8lv.txt === reduce.pl bib === === reduce.pl bib === id = cord-353190-7qcoxl81 author = Nicklas, Werner title = Viral Infections of Laboratory Mice date = 2012-05-17 pages = extension = .txt mime = text/plain words = 27775 sentences = 1482 flesch = 39 summary = This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler's murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi's sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. cache = ./cache/cord-353190-7qcoxl81.txt txt = ./txt/cord-353190-7qcoxl81.txt === reduce.pl bib === id = cord-267671-ys43n672 author = Whary, Mark T. title = Biology and Diseases of Mice date = 2015-07-10 pages = extension = .txt mime = text/plain words = 63666 sentences = 3678 flesch = 40 summary = Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. cache = ./cache/cord-267671-ys43n672.txt txt = ./txt/cord-267671-ys43n672.txt === reduce.pl bib === id = cord-019490-m1cuuehi author = nan title = Abstracts cont. date = 2015-12-28 pages = extension = .txt mime = text/plain words = 93588 sentences = 5683 flesch = 50 summary = Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. cache = ./cache/cord-019490-m1cuuehi.txt txt = ./txt/cord-019490-m1cuuehi.txt === reduce.pl bib === id = cord-008777-i2reanan author = nan title = ECB12: 12th European Congess on Biotechnology date = 2005-07-19 pages = extension = .txt mime = text/plain words = 151383 sentences = 7577 flesch = 43 summary = Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins. cache = ./cache/cord-008777-i2reanan.txt txt = ./txt/cord-008777-i2reanan.txt === reduce.pl bib === id = cord-022501-9wnmdvg5 author = nan title = P1460 – P1884 date = 2015-12-28 pages = extension = .txt mime = text/plain words = 128256 sentences = 7808 flesch = 51 summary = Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). cache = ./cache/cord-022501-9wnmdvg5.txt txt = ./txt/cord-022501-9wnmdvg5.txt === reduce.pl bib === id = cord-023592-w96h4rir author = nan title = Abstracts cont. date = 2015-12-28 pages = extension = .txt mime = text/plain words = 67857 sentences = 4136 flesch = 52 summary = Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined. cache = ./cache/cord-023592-w96h4rir.txt txt = ./txt/cord-023592-w96h4rir.txt === reduce.pl bib === id = cord-007890-bie1veti author = nan title = ECC-4 Abstracts date = 2002-04-16 pages = extension = .txt mime = text/plain words = 85992 sentences = 5665 flesch = 50 summary = Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children's Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. cache = ./cache/cord-007890-bie1veti.txt txt = ./txt/cord-007890-bie1veti.txt ===== Reducing email addresses cord-008777-i2reanan Creating transaction Updating adr table ===== Reducing keywords cord-255857-y9wjp0aj cord-009764-m9flptcv cord-000820-5b29wtim cord-014461-2ubh9u8r cord-002561-7j43yic1 cord-255137-utg8k7qs cord-012054-bpgb7tgo cord-004751-4vl0cvyq cord-004116-ckms25na cord-005057-deq5tv1d cord-281172-7di6eub3 cord-000347-gdra8xhj cord-267189-xq70rn1j cord-259959-qzd3hf8y cord-288451-npefpo3t cord-010187-ymhcfyxx cord-003908-wbawzbhz cord-291510-jh2fdks4 cord-289623-7oc1ykds cord-022383-pz0htccp cord-355492-0zvqvumc cord-294509-txk1qic1 cord-271897-9oqzsd70 cord-306976-p2521bl4 cord-010641-hk90qx1k cord-018061-jy3km0fr cord-291930-n7wq09rq cord-296611-ma32oz4o cord-355119-sdg9zdc1 cord-279495-zxerb7de cord-269892-bmdpbkni cord-009664-kb9fnbgy cord-301301-ilsenpus cord-347644-4qenzjiu cord-301347-22lt6h40 cord-299763-ttb7o8lv cord-323463-osf6t7cw cord-280334-7b7rvr25 cord-353190-7qcoxl81 cord-267671-ys43n672 cord-023592-w96h4rir cord-019490-m1cuuehi cord-008777-i2reanan cord-022501-9wnmdvg5 cord-007890-bie1veti Creating transaction Updating wrd table ===== Reducing urls cord-004116-ckms25na cord-259959-qzd3hf8y cord-281172-7di6eub3 cord-255137-utg8k7qs cord-000347-gdra8xhj cord-003908-wbawzbhz cord-291510-jh2fdks4 cord-288451-npefpo3t cord-289623-7oc1ykds cord-294509-txk1qic1 cord-306976-p2521bl4 cord-271897-9oqzsd70 cord-296611-ma32oz4o cord-279495-zxerb7de cord-009664-kb9fnbgy cord-301301-ilsenpus cord-347644-4qenzjiu cord-301347-22lt6h40 cord-267671-ys43n672 cord-353190-7qcoxl81 cord-019490-m1cuuehi cord-008777-i2reanan cord-022501-9wnmdvg5 Creating transaction Updating url table ===== Reducing named entities cord-255857-y9wjp0aj cord-000820-5b29wtim cord-009764-m9flptcv cord-014461-2ubh9u8r cord-002561-7j43yic1 cord-012054-bpgb7tgo cord-004751-4vl0cvyq cord-004116-ckms25na cord-255137-utg8k7qs cord-005057-deq5tv1d cord-281172-7di6eub3 cord-267189-xq70rn1j cord-000347-gdra8xhj cord-259959-qzd3hf8y cord-288451-npefpo3t cord-010187-ymhcfyxx cord-003908-wbawzbhz cord-291510-jh2fdks4 cord-022383-pz0htccp cord-289623-7oc1ykds cord-294509-txk1qic1 cord-355492-0zvqvumc cord-271897-9oqzsd70 cord-306976-p2521bl4 cord-010641-hk90qx1k cord-018061-jy3km0fr cord-291930-n7wq09rq cord-355119-sdg9zdc1 cord-296611-ma32oz4o cord-279495-zxerb7de cord-269892-bmdpbkni cord-301301-ilsenpus cord-299763-ttb7o8lv cord-347644-4qenzjiu cord-301347-22lt6h40 cord-280334-7b7rvr25 cord-323463-osf6t7cw cord-353190-7qcoxl81 cord-009664-kb9fnbgy cord-267671-ys43n672 cord-023592-w96h4rir cord-007890-bie1veti cord-019490-m1cuuehi cord-022501-9wnmdvg5 cord-008777-i2reanan Creating transaction Updating ent table ===== Reducing parts of speech cord-255857-y9wjp0aj cord-000820-5b29wtim cord-014461-2ubh9u8r cord-259959-qzd3hf8y cord-005057-deq5tv1d cord-012054-bpgb7tgo cord-267189-xq70rn1j cord-002561-7j43yic1 cord-288451-npefpo3t cord-355492-0zvqvumc cord-281172-7di6eub3 cord-010187-ymhcfyxx cord-003908-wbawzbhz cord-255137-utg8k7qs cord-004116-ckms25na cord-004751-4vl0cvyq cord-291510-jh2fdks4 cord-009764-m9flptcv cord-000347-gdra8xhj cord-289623-7oc1ykds cord-294509-txk1qic1 cord-271897-9oqzsd70 cord-010641-hk90qx1k cord-306976-p2521bl4 cord-291930-n7wq09rq cord-355119-sdg9zdc1 cord-269892-bmdpbkni cord-279495-zxerb7de cord-301301-ilsenpus cord-301347-22lt6h40 cord-299763-ttb7o8lv cord-280334-7b7rvr25 cord-347644-4qenzjiu cord-018061-jy3km0fr cord-022383-pz0htccp cord-323463-osf6t7cw cord-353190-7qcoxl81 cord-267671-ys43n672 cord-023592-w96h4rir cord-009664-kb9fnbgy cord-007890-bie1veti cord-019490-m1cuuehi cord-022501-9wnmdvg5 cord-008777-i2reanan cord-296611-ma32oz4o Creating transaction Updating pos table Building ./etc/reader.txt cord-007890-bie1veti cord-019490-m1cuuehi cord-022501-9wnmdvg5 cord-022501-9wnmdvg5 cord-019490-m1cuuehi cord-007890-bie1veti number of items: 45 sum of words: 764,176 average size in words: 44,951 average readability score: 47 nouns: strains; patients; infection; results; mice; isolates; resistance; strain; virus; study; methods; infections; gene; treatment; analysis; activity; cells; genes; disease; samples; cell; sequence; data; species; group; production; cases; days; time; protein; mouse; type; method; use; aureus; studies; susceptibility; bacteria; years; control; acid; blood; therapy; detection; effect; laboratory; system; antibiotics; presence; culture verbs: using; shows; includes; isolated; found; determine; detected; identify; increased; compared; associated; causes; performed; based; obtained; following; produced; tested; occurred; observed; developed; report; contained; study; suggest; infected; evaluate; related; indicate; described; treated; revealed; investigated; resulted; reducing; considered; provide; collect; carried; presented; induced; according; known; confirms; give; involved; remaining; received; requiring; demonstrate adjectives: clinical; resistant; different; high; positive; human; specific; non; antibiotic; bacterial; viral; new; negative; significant; respiratory; common; important; genetic; antimicrobial; susceptible; several; low; infectious; molecular; first; present; higher; similar; acute; many; severe; major; single; immune; effective; large; available; natural; novel; active; experimental; multiple; recombinant; possible; various; infected; small; lower; total; oral adverbs: also; respectively; however; well; significantly; therefore; highly; often; previously; especially; recently; usually; frequently; even; commonly; furthermore; currently; particularly; clinically; still; mainly; moreover; less; genetically; approximately; now; relatively; first; closely; rapidly; probably; together; almost; generally; directly; prior; widely; least; alone; potentially; nt; finally; additionally; naturally; subsequently; later; rather; experimentally; easily; worldwide pronouns: we; it; their; our; its; they; them; i; he; us; his; she; her; one; itself; themselves; my; mg; me; you; fusb; your; rh120-s1/; esat-6; ch/; Þ; ya; y; thereof; thee; talens; sngr; rhli; putk2; pm230; met198ile; lmb415; ldha; kf442963; kaz)objectives; ka.max; igg2c; igfbp2; hp6a; himself; h120; fusr; facieum; exou; ermb proper nouns: S.; PCR; mg; C.; E.; MRSA; L; C; University; MIC; P.; B.; RNA; M.; Staphylococcus; A; M; S; L.; IBV; Fig; Department; A.; B; T; H.; ESBL; K.; USA; China; Genome; PFGE; Pseudomonas; II; RT; NCCLS; Hospital; IV; imipenem; Escherichia; ELISA; D; Salmonella; DNA; ICU; R.; Europe; CA; Institute; HIV keywords: strain; pcr; isolate; infection; study; result; patient; mrsa; ibv; gram; virus; method; esbl; dna; china; staphylococcus; resistance; mic; pfge; objective; nccls; mouse; university; salmonella; pvl; pedv; mhv; medicine; lcmv; institute; icu; grn; gene; escherichia; elisa; effect; disease; department; cfu; cell; canine; candida; bat; bacillus; animal; 16s; yc2014; vr-2332; vp7; vp1 one topic; one dimension: strains file(s): https://www.ncbi.nlm.nih.gov/pubmed/11551659/ titles(s): Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” three topics; one dimension: strains; production; mice file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134330/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164505/ titles(s): P1460 – P1884 | ECB12: 12th European Congess on Biotechnology | The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity five topics; three dimensions: patients strains isolates; production using used; mice infection virus; strains strain sequence; airway strain asm file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134330/, https://api.elsevier.com/content/article/pii/B9780124095274000031, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950926/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164505/ titles(s): P1460 – P1884 | ECB12: 12th European Congess on Biotechnology | Biology and Diseases of Mice | Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential | The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity Type: cord title: keyword-strain-cord date: 2021-05-25 time: 16:49 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:strain ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-018061-jy3km0fr author: AL KASSAA, Imad title: Antiviral Probiotics: A New Concept in Medical Sciences date: 2016-12-02 words: 13236.0 sentences: 747.0 pages: flesch: 42.0 cache: ./cache/cord-018061-jy3km0fr.txt txt: ./txt/cord-018061-jy3km0fr.txt summary: rhamnosus GG (LGG), a famous probiotic strain, was evaluated and showed an anti-infl uenza virus activity on intranasal and oral administration [ 26 , 27 ] . Moreover, the antiviral effect of probiotics by immunomodulatory mechanisms depends on the immune system status, which can be explained in the study conducted by Lehtoranta et al., who showed that the combination of four probiotic strains worked very well in children but not in the elderly [ 61 ] . The role of commensal bacteria in the persistence of enteric viral infections has previously been shown in a series of recent studies published in 2011, using poliovirus, reovirus and mouse mammary tumor virus (MMTV) as EnV models [ 99 -101 ] . Differential effects of Escherichia coli Nissle and Lactobacillus rhamnosus Strain GG on human rotavirus binding, infection, and B cell immunity abstract: In recent decades, probiotics have shown beneficial effects on animal and human health. Probiotics can protect the host against several health threats, including infectious diseases. Before 1995, researchers believed that the effect of probiotics was only on gut microbiota which can restore the gut flora and thus prevent pathogenic bacteria from triggering gastroenteritis. Recent studies have shown that the immunomodulatory activity is the most important mechanism of action of probiotics. From this information, researchers started to evaluate the effect of some immunobiotics, not only on pathogenic bacteria but also on viruses, including enteric and respiratory viruses. Several studies have confirmed the potential antiviral activity of some probiotics due to the immunomodulatory effect. These studies were conducted on humans (clinical trials) and in animal models. In this chapter, probiotics with antiviral effect against respiratory and enteric viruses will be presented and discussed, as well as their mechanisms of action. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122849/ doi: 10.1007/978-3-319-49688-7_1 id: cord-280334-7b7rvr25 author: Abrantes, Joana title: Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2 date: 2020-09-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution. url: https://www.ncbi.nlm.nih.gov/pubmed/32879332/ doi: 10.1038/s41598-020-71303-4 id: cord-259959-qzd3hf8y author: Alhatami, Abdullah O. title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date: 2020-07-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND AND AIM: Infectious bronchitis (IB) has an influential economic impact on the poultry industry, causing huge losses each year due to the condemnation of infected chickens. Despite the use of many kinds of vaccines in Iraq, it is common to find IB problems in vaccinated chickens. Information about the strains that affect Iraqi chickens is very limited. Therefore, we aimed to detect the currently circulating strains of IB virus that cause frequent outbreaks in egg layers despite the use of vaccination against the virus. MATERIALS AND METHODS: Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples). RESULTS: The isolated strain was different from other strains, especially the strain isolated in the North of Iraq (Sulemania Strain) and shares 98% homology with an Israeli strain (Israel variant 2, IS 1494). CONCLUSION: Although more studies are needed to detect IB virus strains circulating in Iraq, this work lays the foundation for making a good strategy to control the disease and selecting vaccines that should be used in farms. url: https://www.ncbi.nlm.nih.gov/pubmed/32848311/ doi: 10.14202/vetworld.2020.1358-1362 id: cord-291930-n7wq09rq author: Arden, K.E. title: Molecular characterization and distinguishing features of a novel human rhinovirus (HRV) C, HRVC-QCE, detected in children with fever, cough and wheeze during 2003 date: 2010-01-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human rhinoviruses (HRVs) are associated with more acute respiratory tract infections than any other viral group yet we know little about viral diversity, epidemiology or clinical outcome resulting from infection by strains, in particular the recently identified HRVs. OBJECTIVES: To determine whether HRVC-QCE was a distinct HRV-C strain, by determining its genome and prevalence, by cataloguing genomic features for strain discrimination and by observing clinical features in positive patients. STUDY DESIGN: Novel real-time RT-PCRs and retrospective chart reviews were used to investigate a well-defined population of 1247 specimen extracts to observe the prevalence and the clinical features of each HRV-QCE positive case from an in- and out-patient pediatric, hospital-based population during 2003. An objective illness severity score was determined for each HRVC-QCE positive patient. RESULTS: Differences in overall polyprotein and VP1 binding pocket residues and the predicted presence of a cis-acting replication element in 1B defined HRVC-QCE as a novel HRV-C strain. Twelve additional HRVC-QCE detections (1.0% prevalence) occurred among infants and toddlers (1–24 months) suffering mild to moderate illness, including fever and cough, who were often hospitalized. HRVC-QCE was frequently detected in the absence of another virus and was the only virus detected in three (23% of HRVC-QCE positives) children with asthma exacerbation and in two (15%) toddlers with febrile convulsion. CONCLUSIONS: HRVC-QCE is a newly identified, genetically distinct HRV strain detected in hospitalized children with a range of clinical features. HRV strains should be independently considered to ensure we do not overestimate the HRVs in asymptomatic illness. url: https://doi.org/10.1016/j.jcv.2010.01.001 doi: 10.1016/j.jcv.2010.01.001 id: cord-005057-deq5tv1d author: Bergström, T. title: Neurovirulence of herpes simplex virus types 1 and 2 isolates in diseases of the central nervous system date: 1990 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Herpes simplex virus (HSV) isolates derived from the central nervous system of ten patients with HSV-1-induced encephalitis, one patient with multiple sclerosis, and 14 patients with HSV-2-induced meningitis were investigated for neurovirulence by assaying the LD(50) after nose and intracerebral (i.c.) inoculation of mice. HSV-1 encephalitis strains were significantly more virulent after nose inoculation (i.e. neuroinvasive) when compared with HSV-1 isolates from patients with oral lesions only, whereas HSV-2 meningitis strains were significantly more virulent after i.c. inoculation when compared with HSV-2 isolates from patients with genital lesions only. No correlation between high neurovirulence (defined as low LD(50) for both routes of infection) and replication in cell cultures of neuronal and non-neuronal cell lines was found, but the weakly neurovirulent HSV-1 strain isolated from a patient with multiple sclerosis gave low replication yields. After nose inoculation, a highly neuroinvasive HSV-1 laboratory reference strain replicated to high titers in nose tissue, the trigeminal ganglia and brainstem, while a strain with low neuroinvasiveness but high i.c. virulence replicated less well in the brainstem. Neuroinvasiveness of the virus strain might be one factor of relevance in the pathogenesis of HSV-1 encephalitis in man. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088202/ doi: 10.1007/bf02184688 id: cord-281172-7di6eub3 author: Biswas, Kaushiki title: Demyelinating strain of mouse hepatitis virus infection bridging innate and adaptive immune response in the induction of demyelination date: 2016-07-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The presence of immunoglobulin oligoclonal bands in the cerebrospinal fluid of Multiple Sclerosis (MS) patients supports the hypothesis of an infectious etiology, although the antigenic targets remain elusive. Neurotropic mouse hepatitis virus (MHV) infection in mice provides a useful tool for studying mechanisms of demyelination in a virus-induced experimental model of MS. This study uses Affymetrix microarray analysis to compare differential spinal cord mRNA levels between mice infected with demyelinating and non-demyelinating strains of MHV to identify host immune genes expressed in this demyelinating disease model. The study reveals that during the acute stage of infection, both strains induce inflammatory innate immune response genes, whereas upregulation of several immunoglobulin genes during chronic stage infection is unique to infection with the demyelinating strain. Results suggest that the demyelinating strain induced an innate-immune response during acute infection that may promote switching of Ig isotype genes during chronic infection, potentially playing a role in antibody-mediated progressive demyelination even after viral clearance. url: https://api.elsevier.com/content/article/pii/S1521661616301589 doi: 10.1016/j.clim.2016.07.004 id: cord-000820-5b29wtim author: Borriello, Giorgia title: Diversity of Salmonella spp. serovars isolated from the intestines of water buffalo calves with gastroenteritis date: 2012-10-25 words: 4319.0 sentences: 237.0 pages: flesch: 47.0 cache: ./cache/cord-000820-5b29wtim.txt txt: ./txt/cord-000820-5b29wtim.txt summary: RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The current study investigated the intestinal contents collected from 248 water buffalo calves affected by gastroenteritis with lethal outcome to: (i) evaluate the prevalence of Salmonella spp., and (ii) perform a polyphasic characterization of the collected isolates of S. The genetic characterization (Table 2) included five loci (avrA, ssaQ, mgtC, siiD, and sopB) located on SPI 1-5, respectively [8] , eight loci (gipA, gtgB, sopE, sodC1, gtgE, gogB, sspH1, and sspH2) of prophage origin [9] [10] [11] [12] [13] , the gene spvC, located on a virulence plasmid [12] , and nine genes (stfE, safC, csgA, ipfD, bcfC, stbD, pefA, fimA, and agfA) coding for bacterial fimbriae, involved in surface adhesion and gut colonization [5] . abstract: BACKGROUND: Salmonellosis in water buffalo (Bubalus bubalis) calves is a widespread disease characterized by severe gastrointestinal lesions, profuse diarrhea and severe dehydration, occasionally exhibiting a systemic course. Several Salmonella serovars seem to be able to infect water buffalo, but Salmonella isolates collected from this animal species have been poorly characterized. In the present study, the prevalence of Salmonella spp. in water buffalo calves affected by lethal gastroenteritis was assessed, and a polyphasic characterization of isolated strains of S. Typhimurium was performed. RESULTS: The microbiological analysis of the intestinal contents obtained from 248 water buffalo calves affected by lethal gastroenteritis exhibited a significant prevalence of Salmonella spp. (25%), characterized by different serovars, most frequently Typhimurium (21%), Muenster (11%), and Give (11%). The 13 S. Typhimurium isolates were all associated with enterocolitis characterized by severe damage of the intestine, and only sporadically isolated with another possible causative agent responsible for gastroenteritis, such as Cryptosporidium spp., Rotavirus or Clostridium perfringens. Other Salmonella isolates were mostly isolated from minor intestinal lesions, and often (78% of cases) isolated with other microorganisms, mainly toxinogenic Escherichia coli (35%), Cryptosporidium spp. (20%) and Rotavirus (10%). The S. Typhimurium strains were characterized by phage typing and further genotyped by polymerase chain reaction (PCR) detection of 24 virulence genes. The isolates exhibited nine different phage types and 10 different genetic profiles. Three monophasic S. Typhimurium (B:4,12:i:-) isolates were also found and characterized, displaying three different phage types and three different virulotypes. The molecular characterization was extended to the 7 S. Muenster and 7 S. Give isolates collected, indicating the existence of different virulotypes also within these serovars. Three representative strains of S. Typhimurium were tested in vivo in a mouse model of mixed infection. The most pathogenic strain was characterized by a high number of virulence factors and the presence of the locus agfA, coding for a thin aggregative fimbria. CONCLUSIONS: These results provide evidence that Salmonella is frequently associated with gastroenteritis in water buffalo calves, particularly S. Typhimurium. Moreover, the variety in the number and distribution of different virulence markers among the collected S. Typhimurium strains suggests that within this serovar there are different pathotypes potentially responsible for different clinical syndromes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514206/ doi: 10.1186/1746-6148-8-201 id: cord-009764-m9flptcv author: Bossé, Ynuk title: The Strain on Airway Smooth Muscle During a Deep Inspiration to Total Lung Capacity date: 2019-01-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The deep inspiration (DI) maneuver entices a great deal of interest because of its ability to temporarily ease the flow of air into the lungs. This salutary effect of a DI is proposed to be mediated, at least partially, by momentarily increasing the operating length of airway smooth muscle (ASM). Concerningly, this premise is largely derived from a growing body of in vitro studies investigating the effect of stretching ASM by different magnitudes on its contractility. The relevance of these in vitro findings remains uncertain, as the real range of strains ASM undergoes in vivo during a DI is somewhat elusive. In order to understand the regulation of ASM contractility by a DI and to infer on its putative contribution to the bronchodilator effect of a DI, it is imperative that in vitro studies incorporate levels of strains that are physiologically relevant. This review summarizes the methods that may be used in vivo in humans to estimate the strain experienced by ASM during a DI from functional residual capacity (FRC) to total lung capacity (TLC). The strengths and limitations of each method, as well as the potential confounders, are also discussed. A rough estimated range of ASM strains is provided for the purpose of guiding future in vitro studies that aim at quantifying the regulatory effect of DI on ASM contractility. However, it is emphasized that, owing to the many limitations and confounders, more studies will be needed to reach conclusive statements. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164505/ doi: 10.1115/1.4042309 id: cord-323463-osf6t7cw author: Cercenado, Emilia title: Update on bacterial pathogens: virulence and resistance date: 2008-04-30 words: 15021.0 sentences: 679.0 pages: flesch: 42.0 cache: ./cache/cord-323463-osf6t7cw.txt txt: ./txt/cord-323463-osf6t7cw.txt summary: This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. Although predictions during the 20th century indicated that the incidence of infectious diseases would diminish as a result of improvements in sanitation and by the introduction of many vaccines and antibiotics, at the beginning of the 21st century the rates of infections produced by new pathogens or by reemerging microorganisms possessing new virulence or resistance phenotypes is increasing, threatening the overall human health [1] [2] [3] [4] [5] . It is in this scenario where community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as the most common pathogen isolated from patients with skin and soft-tissue infections attending to the emergency departments in many United States and Australian cities 8, 9 , and at present, its incidence is increasing in other parts of the world 10, 11 . abstract: The present article is an update of the literature on bacterial pathogens. Recognizing the interest and scientific and public health importance of infections produced by bacterial pathogens with new virulence mechanisms and/or new mechanisms of resistance to antimicrobial agents, a multidisciplinary group of Spanish physicians and microbiologists organized a joint session and revised the most important papers produced in the field during 2006. Each article was analyzed and discussed by one of the members of the panel. This paper focus on a variety of diseases that pose major clinical and public health challenges today; and include infections produced by community-acquired methicillin-resistant Staphylococcus aureus and S. aureus small colony variants, infections produced by multiply resistant coagulase-negative staphylococci, pneumococcal infections, human listeriosis, meningococcal disease, Haemophilus influenzae, pertussis, Escherichia coli, ESBL-producing organisms, and infections due to non-fermenters. After a review of the state of the art, papers selected in this field are discussed. url: https://www.sciencedirect.com/science/article/pii/S0213005X0876378X doi: 10.1016/s0213-005x(08)76378-x id: cord-299763-ttb7o8lv author: Choi, Jeong-Won title: Molecular characteristics of a novel strain of canine minute virus associated with hepatitis in a dog date: 2016-06-01 words: 2615.0 sentences: 128.0 pages: flesch: 49.0 cache: ./cache/cord-299763-ttb7o8lv.txt txt: ./txt/cord-299763-ttb7o8lv.txt summary: Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. On analyzing the in situ hybridization images, hepatic cells surrounding the damaged regions and intranuclear inclusion bodies were found positive for MVC nucleic acid (Fig. 1) . However, the NP1 region of the 15D009 strain showed greater nucleotide and amino acid sequence similarity to that of the HM-6 strain (AB158475), which was isolated from a Korean dog in 2004 (99.1 % and 99.4 %, respectively), compared to those of the other MVC strains (mean similarities of 90.9-91.4 % and 93.0 %, respectively) ( Table 1 ). A minute virus of canines (MVC: canine bocavirus) isolated from an elderly dog with severe gastroenteritis, and phylogenetic analysis of MVC strains abstract: A 5-year-old female Yorkshire terrier dog died a few days following hernia and ovariohysterectomy surgeries. Necropsy performed on the dog revealed that the surgeries were not the cause of death; however, degenerative viral hepatitis, showing intranuclear inclusion bodies in hepatic cells, was observed in histopathologic examination. Several diagnostic methods were used to screen for the cause of disease, and minute virus of canines (MVC) was detected in all parenchymal organs, including the liver. Other pathogens that may cause degenerative viral hepatitis were not found. Infection with MVC was confirmed by in situ hybridization, which revealed the presence of MVC nucleic acid in the liver tissue of the dog. Through sequencing and phylogenetic analysis of the nearly complete genome sequence, the strain was found to be distinct from other previously reported MVC strains. These results indicate that this novel MVC strain might be related to degenerative viral hepatitis in dogs. url: https://www.ncbi.nlm.nih.gov/pubmed/27251050/ doi: 10.1007/s00705-016-2895-7 id: cord-271897-9oqzsd70 author: Domanska-Blicharz, Katarzyna title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017 date: 2020-01-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The presence of infectious bronchitis virus (IBV) was identified for the first time in the poultry population in Poland at the end of the 1960s. From this time a few waves of epidemics caused by different IBV variants spread across the country. In order to gain more insight into the molecular epidemiology of IBV in Poland, in the present study the S1 coding region of 34 IBV isolates and nearly whole genome of 10 strains collected over a period of 38 years was characterized. Phylogenetic analysis showed that these strains belonged to five recently established IBV lineages: GI-1, GI-12, GI-13, GI-19 and GI-23. Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. The phylogenetic analyses performed on the genome of ten Polish IBV strains revealed that they cluster into different groups. The Polish GI-1, GI-19 and GI-23 strains cluster with other similar viruses of these lineages, with the exception of the two strains from 1989 and 1997 which are different. It seems that in Poland in the 1980s and 1990s IBV strains with a unique genome backbone circulated in the field, which were then replaced by other strains belonging to other IBV lineages with a genome backbone specific to these lineages. The recombination analysis showed that some Polish strains resulted from a recombination event involving different IBV lineages, most frequently GI-13 and GI-19. url: https://www.ncbi.nlm.nih.gov/pubmed/31917362/ doi: 10.1016/j.meegid.2020.104177 id: cord-002561-7j43yic1 author: Donato, Celeste title: The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses date: 2017-05-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454415/ doi: 10.3390/v9050102 id: cord-012054-bpgb7tgo author: Ferreira, Maria Isabel M. title: Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1 date: 2008-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was able to mineralize 4-FP up to concentrations of 5 mM in batch culture. Stoichiometric release of fluoride ions was observed, suggesting that there is no formation of halogenated dead-end products during 4-FP metabolism. The degradative pathway of 4-FP was investigated using enzyme assays and identification of intermediates by gas chromatography (GC), GC–mass spectrometry (MS), high-performance liquid chromatography, and liquid chromatography–MS. Cell-free extracts of 4-FP-grown cells contained no activity for catechol 1,2-dioxygenase or catechol 2,3-dioxygenase, which indicates that the pathway does not proceed through a catechol intermediate. Cells grown on 4-FP oxidized 4-FP, hydroquinone, and hydroxyquinol but not 4-fluorocatechol. During 4-FP metabolism, hydroquinone accumulated as a product. Hydroquinone could be converted to hydroxyquinol, which was further transformed into maleylacetic acid and β-ketoadipic acid. These results indicate that the biodegradation of 4-FP starts with a 4-FP monooxygenase reaction that yields benzoquinone, which is reduced to hydroquinone and further metabolized via the β-ketoadipic acid pathway. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266783/ doi: 10.1007/s00253-008-1343-3 id: cord-306976-p2521bl4 author: Gao, Mengying title: Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date: 2016-08-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since 2009, strains of the naturally recombinant TW I genotype of infectious bronchitis virus (IBV) have caused considerable damage to the Chinese poultry industry. To better understand the antigenicity and pathogenesis of this genotype, the characteristics of the ck/CH/LDL/140520 strain were compared to those of four commercial IB vaccine strains that are used commonly in China, as well as four attenuated viruses that represent two types of IBV strains, which are believed to have originated in China and are the predominant IBV types circulating in chicken flocks in China and many other parts of the world. The results showed that all eight strains were genetically and serotypically different from the strain ck/CH/LDL/140520. Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age. url: https://doi.org/10.1016/j.vetmic.2016.05.018 doi: 10.1016/j.vetmic.2016.05.018 id: cord-289623-7oc1ykds author: Gendy, Sherif title: Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018 date: 2020-08-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The carriage of both, heavy metal and antibiotic resistance appears to be a common trait in bacterial communities native to long-term contaminated habitats, including the Savannah River Site (SRS). There is widespread soil contamination at the SRS; a United States Department of Energy (DOE) facility with long-term contamination from past industrial and nuclear weapons production activities. To further evaluate the genomic and metabolic traits that underpin metal and antibiotic resistance, a robust mercury (Hg) and uranium (U)-resistant strain- SRS-8-S-2018, was isolated. Minimum inhibitory concentration of this strain revealed resistance to Hg (10 μg/ml) and U (5 mM), the two main heavy metal contaminants at the SRS. Metabolic assessment of strain SRS-8-S-2018 using Biolog metabolic fingerprinting analysis revealed preference for carbohydrate utilization followed by polymers, amino acids, carboxy acids, and esters; this physiological activity diminished when Hg stress was provided at 1 and 3 μg/ml and completely ceased at 5 μg/ml Hg, indicating that continued release of Hg will have negative metabolic impacts to even those microorganisms that possess high resistance ability. Development of antibiotic resistance in strain SRS-8-S-2018 was evaluated at a functional level using phenomics, which confirmed broad resistance against 70.8% of the 48 antibiotics tested. Evolutionary and adaptive traits of strain SRS-8-S-2018 were further assessed using genomics, which revealed the strain to taxonomically affiliate with Serratia marcescens species, possessing a genome size of 5,323,630 bp, 5,261 proteins (CDS), 55 genes for transfer RNA (tRNA), and an average G + C content of 59.48. Comparative genomics with closest taxonomic relatives revealed 360 distinct genes in SRS-8-S-2018, with multiple functions related to both, antibiotic and heavy metal resistance, which likely facilitates the strain’s survival in a metalliferous soil habitat. Comparisons drawn between the environmentally isolated Serratia SRS-8-S-2018 with 31 other strains revealed a closer functional association with medically relevant isolates suggesting that propensity of environmental Serratia isolates in acquiring virulence traits, as a function of long-term exposure to heavy metals, which is facilitating development, recruitment and proliferation of not only metal resistant genes (MRGs) but antibiotic resistant genes (ARGs), which can potentially trigger future bacterial pathogen outbreaks emanating from contaminated environmental habitats. url: https://doi.org/10.3389/fmicb.2020.01923 doi: 10.3389/fmicb.2020.01923 id: cord-000347-gdra8xhj author: Gibbons, Henry S. title: Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant date: 2011-03-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS). RESULTS: Archival strains and two “present day” type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86% identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the “military” isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of “military” isolates on lactate-containing media, and showed that the “military” strains exhibited a hypersporulating phenotype. CONCLUSIONS: Our analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064580/ doi: 10.1371/journal.pone.0017836 id: cord-010187-ymhcfyxx author: Gromeier, Matthias title: Mouse neuropathogenic poliovirus strains cause damage in the central nervous system distinct from poliomyelitis date: 2005-03-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Poliomyelitis as a consequence of poliovirus infection is observed only in primates. Despitea host range restricted to primates, experimental infection of rodents with certain genetically well defined poliovirus strains produces neurological disease. The outcome of infection of mice with mouse-adapted poliovirus strains has been described previously mainly in terms of paralysis and death, and it was generally assumed that these strains produce the same disease syndromes in normal mice and in mice transgenic for the human poliovirus receptor (hPVR-tg mice). We report a comparison of the clinical course and the histopathological features of neurological disease resulting from intracerebral virus inoculation in normal micewith those of murine poliomyelitis in hPVR-tg mice. The consistent pattern of clinical deficits in poliomyelitic transgenic mice contrasted with highly variable neurologic disease that developed in mice infected with different mouse-adapted polioviruses. Histopathological analysis showed a diffuse encephalomyelitis induced by specific poliovirus serotype 2 isolates in normal mice, that affected neuronal cell populations without discrimination, whereas in hPVR-tg animals, damage was restricted to spinal motor neurons. Mouse neurovirulent strains of poliovirus type 2 differed from mouse neurovirulent poliovirus type 1 derivatives in their ability to induce CNS lesions. Our findings indicate that the characteristic clinical appearance and highly specific histopathological features of poliomyelitis are mediated by the hPVR. Our data lead us to conclude that the tissue tropism of mouse-adapted poliovirus strains in normal mice is fundamentally different from that of poliovirus in hPVR-tg mice and primates, and that this is indicative of an as yet unknown mechanism of adsorption and uptake of the virus into cells of the murine CNS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172458/ doi: 10.1016/s0882-4010(05)80002-6 id: cord-355492-0zvqvumc author: Hamm, Ronda L title: Resistance to cyfluthrin and tetrachlorvinphos in the lesser mealworm, Alphitobius diaperinus, collected from the eastern United States date: 2006-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The lesser mealworm, Alphitobius diaperinus (Panzer), is an important pest in poultry facilities. The toxicity of cyfluthrin and tetrachlorvinphos to five strains of the lesser mealworm was compared with the toxicity to a susceptible laboratory strain. Bioassays were carried out with both larvae and adults. For the susceptible strain, cyfluthrin and tetrachlorvinphos had similar toxicity to adults, but cyfluthrin was 5 times more toxic to larvae when compared with tetrachlorvinphos. High levels of resistance to tetrachlorvinphos in two beetle strains were detected in both larvae and adults, although these strains were heterogeneous and still contained susceptible individuals. Resistance to cyfluthrin ranged from 1.7‐ to 9.5‐fold for adults and from 0.5‐ to 29‐fold for larvae at the LC(95). Overall, the patterns of resistance did not mirror the insecticide use patterns reported at these facilities. The implications of these results to management of the lesser mealworms are discussed. Copyright © 2006 Society of Chemical Industry url: https://www.ncbi.nlm.nih.gov/pubmed/16770758/ doi: 10.1002/ps.1230 id: cord-301347-22lt6h40 author: Jarvis, Matthew C. title: Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus date: 2016-01-01 words: 4256.0 sentences: 218.0 pages: flesch: 52.0 cache: ./cache/cord-301347-22lt6h40.txt txt: ./txt/cord-301347-22lt6h40.txt summary: Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. Despite excising a large portion of the genome prior to analysis, the Bayesian trees illustrate two distinct entries of PEDV into the US and characterize the evolution of PEDV compared to other CoVs. Modeling of the pAPN RBD region has revealed that Asian strains have increasing diversity compared to previously developed vaccines, and the variability in both the American and Asian strains needs to be considered for future vaccine development. Phylogenetic analysis of porcine epidemic diarrhea virus (PEDV) field strains in central China based on the ORF3 gene and the main neutralization epitopes Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States 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 abstract: Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n = 126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV. url: https://api.elsevier.com/content/article/pii/S0167587715300416 doi: 10.1016/j.prevetmed.2015.10.020 id: cord-291510-jh2fdks4 author: Jiang, Yi title: Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity date: 2020-02-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious bronchitis (IB) is a highly infectious viral disease responsible for major economic losses in the poultry industry. A reverse genetic vaccine is a safe, rapid, and effective method of achieving IB prevention and control. In this study, we constructed the recombinant strain, rH120-S1/YZ, using a reverse genetic system, based on the backbone of the H120 vaccine strain, with the S1 gene replaced with that of the QX-like nephropathogenic strain, ck/CH/IBYZ/2011, isolated in China. The results of dwarf chicken embryos, growth kinetics, and viral titration in the embryos demonstrated that the biological characteristics of the recombinant virus remained unchanged. Like the rH120-infected group and in contrast to the rIBYZ-infected group, no mortality, clinical signs, or lesions were observed in the lungs or kidneys of young chickens inoculated with rH120-S1/YZ. The viral loads in various tissues, cloacal, and oral swabs was lower in most types of samples, indicating that the rH120-S1/YZ strain was highly safe in chicks. Compared to rH120 vaccination group, when the efficacy of this strain was evaluated against the QX-like IBV strain, better protection, with 100% survival rate and no disease symptom or gross lesion was observed in the chickens vaccinated with rH120-S1/YZ. Increased levels of IBV-specific antibodies were detected in the serum of the rH120-S1/YZ-vaccinated animals 14 days post-vaccination. Collectively, our results suggest that the recombinant strain, rH120-S1/YZ, may represent a promising vaccine candidate against QX-like IBVs. url: https://doi.org/10.1016/j.vaccine.2020.01.001 doi: 10.1016/j.vaccine.2020.01.001 id: cord-022383-pz0htccp author: Kohn, Dennis F. title: Biology and Diseases of Rats date: 2013-11-17 words: 20181.0 sentences: 1195.0 pages: flesch: 50.0 cache: ./cache/cord-022383-pz0htccp.txt txt: ./txt/cord-022383-pz0htccp.txt summary: The severity and prevalence of clinical disease within an infected colony are associated with environmental conditions that induce stress (e.g., experimental manipulation, overcrowding, fluctuations in ambient temperature and humid ity, and copathogens). Salmonellosis, which was once a major cause of disease in laboratory rat and mouse colonies, is rarely reported in either species today. Mycoplasma pulmonis recently has become recognized as an important pathogen in the female genital tract of rats, and thus is being treated here as a distinct disease rather than as a sequella to MRM. Sendai virus commonly infects laboratory rats, but its clinical significance is less than in mice. Infection is usually diagnosed retrospectively in rats, where pulmonary lesions are observed following seroconversion to PVM in the absence of other respiratory pathogens. This disease, which occurs more fre quently in females, has been reported in numerous strains of rats. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155635/ doi: 10.1016/b978-0-12-263620-2.50010-0 id: cord-294509-txk1qic1 author: Li, Zi title: The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets date: 2016-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%–99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/27672502/ doi: 10.7717/peerj.2443 id: cord-355119-sdg9zdc1 author: Lin, Huixing title: Epidemic strain YC2014 of porcine epidemic diarrhea virus could provide piglets against homologous challenge date: 2016-04-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Porcine epidemic diarrhea virus (PEDV) is the main causative agent of porcine epidemic diarrhea (PED). Since December 2010, a large-scale outbreak of diarrhea has been observed in swine farms in China. Accumulated evidence indicates that this large-scale outbreak of diarrhea were caused by highly virulent PEDV variants. METHODS: A PEDV strain, YC2014, was isolated from intestinal samples of suckling piglets with acute diarrhea in 2014. The complete genomic sequence of YC2014 and the nucleotide sequence of S gene were aligned with sequences of published isolates using MEGA 5.1 software. The immune protective efficiency of YC2014 were determined by testing PEDV neutralizing antibodies in sera, the colostrum and the milk on 7th day after farrowing of the immunized sows. The diarrhea symptoms of piglets after challenge were also observed. RESULTS: Phylogenetic analysis of the complete genomic sequence of YC2014 and the nucleotide sequence of S gene demonstrated that the YC2014 PEDV strain was clustered with the PEDV epidemic strains, with >99 % nucleotide identity to these PEDV strains. The S gene sequence of YC2014 shared only 93.9 % ~ 94.4 % identities with classical CV777, DR13 and JS2008 strains, with 15 nucleotide insertion in three sites and three nucleotide deletion in one site. The amino acid (AA) sequence of S gene of YC2014 shared only 92.8 % ~ 93.4 % identities with classical CV777, DR13 and JS2008 strains, with 5 AA insertion in two sites and 1 AA deletion in one site. In the immune protective efficiency tests, the neutralizing antibody titers in sera, the colostrum and the milk on 7th day after farrowing of the inactivated YC2014 PEDV strain immunized group were significantly higher than the inactivated CV777 immunized group and the inactivated DR13 immunized group (P < 0.05). The traditional inactivated PEDV vaccines made from CV777 or DR13 could not protect piglets from YC2014 challenge, while inactivated YC2014 could provide piglets with 100 % protection against YC2014 challenge. CONCLUSIONS: The results showed that, great antigenicity variation had occurred to this YC2014 PEDV strain. The YC2014 PEDV strain could provide piglets against homologous challenge. It is critical for future pathogenic and antigenic studies, as well as for the development of effective preventive and control vaccines against PEDV. url: https://doi.org/10.1186/s12985-016-0529-z doi: 10.1186/s12985-016-0529-z id: cord-279495-zxerb7de author: Liu, Xiaoli title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date: 2012-11-21 words: 5235.0 sentences: 258.0 pages: flesch: 56.0 cache: ./cache/cord-279495-zxerb7de.txt txt: ./txt/cord-279495-zxerb7de.txt summary: Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. The results revealed that strains ck/CH/LNM/091017 and ck/CH/LDL/101212 were closely related to the H120 vaccine, which suggests that they might represent re-isolations of vaccine strains or variants of vaccine strains that have resulted from the accumulated point mutations after several passages in chickens. In contrast, strains ck/CH/LHLJ/07VII and ck/CH/LHLJ/100902 had a close genetic relationship with the pathogenic M41 strain. In addition, molecular markers have been identified that distinguish between field and vaccine (or vaccine-like) Mass-type viruses, which may be able to differentiate between field and vaccine strains for diagnostic purposes. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41- and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. To our knowledge, this is the first time that evidence for the evolution and natural recombination under field conditions between Mass-type pathogenic and vaccinal IBV strains has been documented. These findings provide insights into the emergence and evolution of the Mass-type IB coronaviruses and may help to explain the emergence of Mass-type IBV in chicken flocks all over the world. url: https://api.elsevier.com/content/article/pii/S1567134812003292 doi: 10.1016/j.meegid.2012.09.016 id: cord-296611-ma32oz4o author: Ma, Tianxin title: Novel genotype of infectious bronchitis virus isolated in China date: 2019-01-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recombination events are known to contribute to the emergence of novel infectious bronchitis virus (IBV) genotypes. In this study, we carried out detailed phylogenetic analysis and sequence comparisons based on 74 complete nucleotide sequences of the IBV S1 gene, including strain I0636/16 and 73 representative sequences from each genotype and lineage. The results showed that strain I0636/16 represented a novel genotype, designated as lineage 1 within genotype VII (GVII-1). Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an as-yet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/111119. These results emphasize the importance of limiting exposure to novel IBVs that may serve as a source of genetic material for emerging viruses, as well as the importance of IBV surveillance in chicken flocks. url: https://www.ncbi.nlm.nih.gov/pubmed/30827386/ doi: 10.1016/j.vetmic.2019.01.020 id: cord-003908-wbawzbhz author: Matsushima, Yuki title: Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017 date: 2019-09-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10(−3) and ~2.3 × 10(−3) substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777354/ doi: 10.3389/fmicb.2019.02189 id: cord-301301-ilsenpus author: Mihalov-Kovács, Eszter title: Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission date: 2017-03-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Canine astrovirus RNA was detected in the stools of 17/63 (26.9%) samples, using either a broadly reactive consensus RT-PCR for astroviruses or random RT-PCR coupled with massive deep sequencing. The complete or nearly complete genome sequence of five canine astroviruses was reconstructed that allowed mapping the genome organization and to investigate the genetic diversity of these viruses. The genome was about 6.6 kb in length and contained three open reading frames (ORFs) flanked by a 5′ UTR, and a 3′ UTR plus a poly-A tail. ORF1a and ORF1b overlapped by 43 nucleotides while the ORF2 overlapped by 8 nucleotides with the 3′ end of ORF1b. Upon genome comparison, four strains (HUN/2012/2, HUN/2012/6, HUN/2012/115, and HUN/2012/135) were more related genetically to each other and to UK canine astroviruses (88–96% nt identity), whilst strain HUN/2012/126 was more divergent (75–76% nt identity). In the ORF1b and ORF2, strains HUN/2012/2, HUN/2012/6, and HUN/2012/135 were related genetically to other canine astroviruses identified formerly in Europe and China, whereas strain HUN/2012/126 was related genetically to a divergent canine astrovirus strain, ITA/2010/Zoid. For one canine astrovirus, HUN/2012/8, only a 3.2 kb portion of the genome, at the 3′ end, could be determined. Interestingly, this strain possessed unique genetic signatures (including a longer ORF1b/ORF2 overlap and a longer 3′UTR) and it was divergent in both ORF1b and ORF2 from all other canine astroviruses, with the highest nucleotide sequence identity (68% and 63%, respectively) to a mink astrovirus, thus suggesting a possible event of interspecies transmission. The genetic heterogeneity of canine astroviruses may pose a challenge for the diagnostics and for future prophylaxis strategies. url: https://api.elsevier.com/content/article/pii/S0168170216305731 doi: 10.1016/j.virusres.2016.12.005 id: cord-004116-ckms25na author: Moser, Kara A. title: Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential date: 2020-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions. METHODS: Whole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequences in each strain relative to the reference 3D7 (a clone of NF54) genome. Strains were compared to each other and to a collection of clinical isolates (sequenced as part of this study or from public repositories) from South America, sub-Saharan Africa, and Southeast Asia. RESULTS: While few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains. These variants include SNPs, indels, and small structural variants that fall in regulatory and immunologically important regions, including transcription factors (such as PfAP2-L and PfAP2-G) and pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contributed to diversity in immunologically important regions of the genomes as detected through in silico CD8(+) T cell epitope predictions. Of all heterologous strains, NF135.C10 had the highest number of unique predicted epitope sequences when compared to NF54. Comparison to global clinical isolates revealed that these four strains are representative of their geographic origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently formed subpopulations resistant to artemisinin-based therapies present in the Greater Mekong Sub-region. CONCLUSIONS: These results will assist in the interpretation of vaccine efficacy of whole-organism vaccines against homologous and heterologous CHMI. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-019-0708-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950926/ doi: 10.1186/s13073-019-0708-9 id: cord-004751-4vl0cvyq author: Mostow, S. R. title: The behaviour in vitro of attenuated recombinant influenza viruses date: 1973 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza strains produced by recombination and tested as possible live vaccine candidates were studied in organ cultures of trachea. Two strains which proved to be too virulent in human volunteers regularly caused damage to the ciliated epithelium and viruses grew to high titre. Two strains which proved to be attenuated for volunteers did not cause appreciable damage, although they replicated to low titre in the epithelium. Similar results were obtained with influenza A virus attenuated by passage in the presence of horse sera. The method may be of value for detecting virulent live influenza vaccine candidates without risking severe illness in volunteers. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086870/ doi: 10.1007/bf01556156 id: cord-014461-2ubh9u8r author: Nelson, Oranmiyan W. title: Genome sequences published outside of Standards in Genomic Sciences, July - October 2012 date: 2012-10-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570808/ doi: 10.4056/sigs.3416907 id: cord-353190-7qcoxl81 author: Nicklas, Werner title: Viral Infections of Laboratory Mice date: 2012-05-17 words: 27775.0 sentences: 1482.0 pages: flesch: 39.0 cache: ./cache/cord-353190-7qcoxl81.txt txt: ./txt/cord-353190-7qcoxl81.txt summary: This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler''s murine encephalomyelitis virus. These results are very difficult to summarize because the outcome of experimental infection in laboratory mice depends on various factors such as mouse strain and age, virus strain and passage history [26] , virus dose and route of inoculation [24] . Experimental infection of laboratory mice with MHV-68 is a frequently used model system for the study of human gammaherpesvirus pathogenesis, e.g. of Kaposi''s sarcoma-associated herpesvirus or Epstein-Barr virus (EBV) [62, 63] which are members of the same subfamily. Early descriptions of naturally occurring disease may have been complicated by concurrent infections such as MHV (murine hepatitis virus) or murine rotavirus A (MuRV-A)/epizootic diarrhoea of infant mice (EDIM) virus that contributed to the severity of the lesions especially in liver, pancreas, CNS and intestine. abstract: Viral infections of laboratory mice have considerable impact on research results, and prevention of such infections is therefore of crucial importance. This chapter covers infections of mice with the following viruses: herpesviruses, mousepox virus, murine adenoviruses, polyomaviruses, parvoviruses, lactate dehydrogenase-elevating virus, lymphocytic choriomeningitis virus, mammalian orthoreovirus serotype 3, murine hepatitis virus, murine norovirus, murine pneumonia virus, murine rotavirus, Sendai virus, and Theiler’s murine encephalomyelitis virus. For each virus, there is a description of the agent, epizootiology, clinical symptoms, pathology, methods of diagnosis and control, and its impact on research. url: https://api.elsevier.com/content/article/pii/B9780123820082000192 doi: 10.1016/b978-0-12-382008-2.00019-2 id: cord-010641-hk90qx1k author: Rodrigues, Juliana Falcão title: Strain-specific transcriptional and posttranscriptional regulation of heat-labile toxin expression by enterotoxigenic Escherichia coli date: 2020-02-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Enterotoxigenic Escherichia coli (ETEC) represents one of the most important etiological agents of diarrhea in developing countries and characteristically produces at least one of two enterotoxins: heat-labile toxin (LT) and heat-stable toxin (ST). It has been previously shown that the production and release of LT by human-derived ETEC strains are variable. Although the natural genetic polymorphisms of regulatory sequences of LT-encoding (eltAB) genes may explain the variable production of LT, the knowledge of the transcriptional and posttranscriptional aspects affecting LT expression among ETEC strains is not clear. To further understand the factors affecting LT expression, we evaluated the impact of the natural polymorphism in noncoding regulatory sequences of eltAB among clinically derived ETEC strains. Sequence analyses of seven clinically derived strains and the reference strain H10407 revealed polymorphic sites at both the promoter and upstream regions of the eltAB operon. Operon fusion assays with GFP revealed that specific nucleotide changes in the Pribnow box reduce eltAB transcription. Nonetheless, the total amounts of LT produced by the tested ETEC strains did not strictly correspond to the detected LT-specific mRNA levels. Indeed, the stability of LT varied according to the tested strain, indicating the presence of posttranscriptional mechanisms affecting LT expression. Taken together, our results indicate that the production of LT is a strain-specific process and involves transcriptional and posttranscriptional mechanisms that regulate the final amount of toxin produced and released by specific strains. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42770-020-00231-2) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203263/ doi: 10.1007/s42770-020-00231-2 id: cord-347644-4qenzjiu author: Shorter, John R. title: A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size date: 2019-03-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Reproductive success in the eight founder strains of the Collaborative Cross (CC) was measured using a diallel-mating scheme. Over a 48-month period we generated 4,448 litters, and provided 24,782 weaned pups for use in 16 different published experiments. We identified factors that affect the average litter size in a cross by estimating the overall contribution of parent-of-origin, heterosis, inbred, and epistatic effects using a Bayesian zero-truncated overdispersed Poisson mixed model. The phenotypic variance of litter size has a substantial contribution (82%) from unexplained and environmental sources, but no detectable effect of seasonality. Most of the explained variance was due to additive effects (9.2%) and parental sex (maternal vs. paternal strain; 5.8%), with epistasis accounting for 3.4%. Within the parental effects, the effect of the dam’s strain explained more than the sire’s strain (13.2% vs. 1.8%), and the dam’s strain effects account for 74.2% of total variation explained. Dams from strains C57BL/6J and NOD/ShiLtJ increased the expected litter size by a mean of 1.66 and 1.79 pups, whereas dams from strains WSB/EiJ, PWK/PhJ, and CAST/EiJ reduced expected litter size by a mean of 1.51, 0.81, and 0.90 pups. Finally, there was no strong evidence for strain-specific effects on sex ratio distortion. Overall, these results demonstrate that strains vary substantially in their reproductive ability depending on their genetic background, and that litter size is largely determined by dam’s strain rather than sire’s strain effects, as expected. This analysis adds to our understanding of factors that influence litter size in mammals, and also helps to explain breeding successes and failures in the extinct lines and surviving CC strains. url: https://www.ncbi.nlm.nih.gov/pubmed/30877080/ doi: 10.1534/g3.118.200847 id: cord-269892-bmdpbkni author: Tabares, Paula title: Anti-protease and Immunomodulatory Activities of Bacteria Associated with Caribbean Sponges date: 2011-01-11 words: 5401.0 sentences: 298.0 pages: flesch: 47.0 cache: ./cache/cord-269892-bmdpbkni.txt txt: ./txt/cord-269892-bmdpbkni.txt summary: Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. The first group of sponges (Aplysina fistularis, Plakortis sp., Amphimedon compressa, Aiolochroia crassa, Agelas clathrodes, Agelas cerebrum, Ircinia felix, Scopalina ruetzleri, Erylus formosus, Chondrilla nucula, and Aplysina archeri) was collected by SCUBA diving at depths of 3-20 m in Bahamas in July 2008 (GPS-26°27′3.25″ N, 77°5 4′14.59″ W). In terms of actinomycete diversity, the 79 cultivated strains are represented by 20 different genera namely Microbacterium (21 isolates), Rhodococcus (10), Streptomyces (5), Mycobacterium (6), Micromonospora (5), Knoellia (4), Gordonia (4), Curtobacterium (4), Arthrobacter (4) Salinispora (3), Saccharopolyspora (2), Nocardioides (2), Citromicrobium (2), Sanguibacter (1), Lapillicoccus (1), Kocuria (1), Dietzia (1), Cellulosimicrobium (1) Cellulomonas (1), and Agrococcus (1; Supplementary Table 1) . A family of aeruginosin inhibitors is active against human serine proteases and was isolated from marine sponges and cyanobacterial waterblooms (Ersmark et al. Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes abstract: Marine sponges and their associated bacteria have been proven to be a rich source of novel secondary metabolites with therapeutic usefulness in cancer, infection, and autoimmunity. In this study, 79 strains belonging to 20 genera of the order Actinomycetales and seven strains belonging to two genera of the order Sphingomonadales were cultivated from 18 different Caribbean sponges and identified by 16S rRNA gene sequencing. Seven of these strains are likely to represent novel species. Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. These results highlight the significance of marine sponge-associated bacteria to produce bioactive secondary metabolites with therapeutic potential in the treatment of infectious diseases and disorders of the immune system. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10126-010-9349-0) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s10126-010-9349-0 doi: 10.1007/s10126-010-9349-0 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 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: 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. M gene RT-PCRs showed that 28.36% (57/201) of the samples were positive for CCoV; of the 57 positive samples, CCoV-I and CCoV-II accounted for 15.79% (9/57) and 84.21% (48/57), respectively. A sequence comparison of the partial M gene revealed nucleotide homologies of 88.4%–100% among the 57 CCoV strains, and 88.7%–96.2% identity between the 57 CCoV strains and the Chinese reference strain HF3. The CCoV-I and CCoV-II strains exhibited genetic diversity when compared with reference strains from China and other countries. The 57 CCoV strains exhibited high co-infection rates with canine kobuvirus (CaKV) (33.33%) and canine parvovirus-2 (CPV-2) (31.58%). The CCoV prevalence in diarrheic dogs differed significantly with immunization status, regions, seasons, and ages. Moreover, 28 S genes were amplified from the 57 CCoV-positive samples, including 26 CCoV-IIa strains, one CCoV-IIb strain, and one CCoV-I strain. A sequence comparison of the partial S gene revealed 86.3%–100% nucleotide identity among the 26 CCoV-IIa strains, and 89.6%–92.2% identity between the 26 CCoV-IIa strains and the Chinese reference strain V1. The 26 CCoV-IIa strains showed genetic diversity when compared with reference strains from China and other countries. 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. url: https://doi.org/10.1371/journal.pone.0146975 doi: 10.1371/journal.pone.0146975 id: cord-267671-ys43n672 author: Whary, Mark T. title: Biology and Diseases of Mice date: 2015-07-10 words: 63666.0 sentences: 3678.0 pages: flesch: 40.0 cache: ./cache/cord-267671-ys43n672.txt txt: ./txt/cord-267671-ys43n672.txt summary: Clinical Signs MCMV causes subclinical infection in adult immunocompetent mice, but experimental inoculation of neonates can cause lethal disease due to multisystemic necrosis and inflammation. Diagnosis Because infected mice do not manifest signs or lesions and the virus is very difficult to propagate in cell culture, detection and diagnosis rely on serology and molecular methods. Differential Diagnosis Reovirus infection must be differentiated from other diarrheal diseases of infant mice, including those caused by mouse coronaviruses, EDIM virus, Salmonella spp., or Clostridium piliforme. Epizootiology EDIM virus appears to be infectious only for mice and occurs episodically in mouse colonies, and infection is probably widespread geographically (Livingston and Riley, 2003; Pritchett-Corning LABORATORY ANIMAL MEDICINE et al., 2009) . Sentinel mouse surveillance, using soiled bedding, is an effective strategy for detecting MNV (Manuel et al., 2008) Differential Diagnosis The mild change in fecal consistency associated with MNV in adult mice may mimic rotavirus, coronavirus, Helicobacter spp., Citrobacter rodentium, or other enteric diseases. abstract: Today’s laboratory mouse, Mus musculus, has its origins as the ‘house mouse’ of North America and Europe. Beginning with mice bred by mouse fanciers, laboratory stocks (outbred) derived from M. musculus musculus from eastern Europe and M. m. domesticus from western Europe were developed into inbred strains. Since the mid-1980s, additional strains have been developed from Asian mice (M. m. castaneus from Thailand and M. m. molossinus from Japan) and from M. spretus which originated from the western Mediterranean region. url: https://api.elsevier.com/content/article/pii/B9780124095274000031 doi: 10.1016/b978-0-12-409527-4.00003-1 id: cord-255137-utg8k7qs author: Yinda, Claude Kwe title: Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses date: 2019-01-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae. Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably. IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world’s virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area. url: https://www.ncbi.nlm.nih.gov/pubmed/30674646/ doi: 10.1128/msphere.00585-18 id: cord-288451-npefpo3t author: Yinda, Claude Kwe title: Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis date: 2016-09-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Bats are an important reservoir for zoonotic viruses. To date, only three RVA strains have been reported in bats in Kenya and China. In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. Five (near) complete RVA genomes were obtained. A single RVA strain showed a partial relationship with the Kenyan bat RVA strain, whereas the other strains were completely novel. Only the VP7 and VP4 genes showed significant variability, indicating the occurrence of frequent reassortment events. Comparing these bat RVA strains with currently used human RVA screening primers indicated that most of the novel VP7 and VP4 segments would not be detected in routine epidemiological screening studies. Therefore, novel consensus screening primers were developed and used to screen samples from infants with gastroenteritis living in close proximity with the studied bat population. Although RVA infections were identified in 36% of the infants, there was no evidence of zoonosis. This study identified multiple novel bat RVA strains, but further epidemiological studies in humans will have to assess if these viruses have the potential to cause gastroenteritis in humans. url: https://www.ncbi.nlm.nih.gov/pubmed/27666390/ doi: 10.1038/srep34209 id: cord-255857-y9wjp0aj author: Yuan, Shishan title: Erratum to “Complete genome comparison of porcine reproductive and respiratory syndrome virus parental and attenuated strains” date: 2001-11-05 words: 4283.0 sentences: 235.0 pages: flesch: 56.0 cache: ./cache/cord-255857-y9wjp0aj.txt txt: ./txt/cord-255857-y9wjp0aj.txt summary: Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. However, the cluster of amino acid mutations located near the carboxyl terminal end suggests that the replicase region was altered during passage to result in a more fit virus for replication in cell culture, as evidenced by the in vitro one-step growth curve comparison shown in Fig. 4 . Sequence analysis of strains VR-2332 and RespPRRS indicated that there were 15 nucleotide changes in this region, and all but one of which resulted in amino acid alterations. Attenuation can result from changes in many areas of viral genomes and the 41 nucleotide mutations described include alterations in several key PRRSV regions. abstract: Two full-length porcine reproductive and respiratory syndrome virus (PRRSV) genomes, strain VR-2332 and its cell culture passaged descendent RespPRRS vaccine strain, were compared and analyzed in order to identify possible sites of attenuation. Of the 41 nucleotide changes, 12 resulted in conservative changes and 18 produced non-conservative changes. The results suggest that key amino acids in ORF1 may contribute to the phenotype of RespPRRS, which includes increased growth rate on MA-104 cells and decreased virulence in swine. The results provide a genetic basis for future manipulation of a PRRSV reverse genetics system. url: https://www.ncbi.nlm.nih.gov/pubmed/11551659/ doi: 10.1016/s0168-1702(01)00295-7 id: cord-007890-bie1veti author: nan title: ECC-4 Abstracts date: 2002-04-16 words: 85992.0 sentences: 5665.0 pages: flesch: 50.0 cache: ./cache/cord-007890-bie1veti.txt txt: ./txt/cord-007890-bie1veti.txt summary: Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children''s Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126403/ doi: 10.1016/s0924-8579(02)00033-x id: cord-008777-i2reanan author: nan title: ECB12: 12th European Congess on Biotechnology date: 2005-07-19 words: 151383.0 sentences: 7577.0 pages: flesch: 43.0 cache: ./cache/cord-008777-i2reanan.txt txt: ./txt/cord-008777-i2reanan.txt summary: Mollerup Department of Chemical Engineering, Building 229, DTU, 2800 Lyngby, Denmark A variety of factors that govern the properties of proteins are utilized in the development of chromatographic processes for the recovery of biological products including the binding and release of protons, the non-covalent association with non-polar groups (often hydrophobic interactions), the association of small ions (ion exchange) and the highly specific antigen-antibody interaction (affinity interactions). Such fermenters will be needed in order to meet the increasing pressure on costs for low price commodity type products such as single cell protein or food and technical grade enzymes, and to meet the demands of the new wave of white biotech, in which bio-produced chemicals must be made at prices competitive with those of the traditional chemical industry. The presentation will focus on use of the sensitive sandwich hybridization technology for the quantitative analysis of process relevant marker genes in different kind of microbial cell cultures with a focus on the production of recombinant proteins. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134330/ doi: 10.1016/j.jbiotec.2005.06.005 id: cord-009664-kb9fnbgy author: nan title: Oral presentations date: 2014-12-24 words: 71112.0 sentences: 3948.0 pages: flesch: 47.0 cache: ./cache/cord-009664-kb9fnbgy.txt txt: ./txt/cord-009664-kb9fnbgy.txt summary: Because of the conflicting reports and lack of published data from paediatric patients, we sought to assess possible MIC change over time and to compare results generated by using different methodologies including Etest, agar dilution, and broth microdilution (MicroScan) methods. Recently, in vitro and in vivo studies have shown that NO plays a key role in the eradication of the leishmania parasite Objective: To determine whether a NO donor patch (developed by electrospinning technique) is as effective as meglumine antimoniate in the treatment of CL while causing less adverse events Methods: A double-blind, randomised, placebo-controlled clinical trial was conducted with 178 patients diagnosed with CL in Santander, Colombia, South-America. To follow the development and spread of the resistance among these strains is difficult, as antibiotic susceptibility testing of clinically relevant anaerobes in different routine laboratories in Europe is less and less frequently carried out due to the fact, that clinicians treat many presumed anaerobic infections empirically. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162236/ doi: 10.1111/j.1469-0691.2009.02857.x id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 words: 93588.0 sentences: 5683.0 pages: flesch: 50.0 cache: ./cache/cord-019490-m1cuuehi.txt txt: ./txt/cord-019490-m1cuuehi.txt summary: Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129916/ doi: 10.1111/j.1469-0691.2005.clm_1134_02.x id: cord-022501-9wnmdvg5 author: nan title: P1460 – P1884 date: 2015-12-28 words: 128256.0 sentences: 7808.0 pages: flesch: 51.0 cache: ./cache/cord-022501-9wnmdvg5.txt txt: ./txt/cord-022501-9wnmdvg5.txt summary: Methods: Using published data on (1) the prevalence of MRSA and other bacterial pathogens causing cSSSI in the US, (2) the in-vitro susceptibility rates of commonly used regimens in cSSSI in the US in relation to the most pervasive pathogens identified above, and (3) estimated costs of failure of initial, empiric treatment from a recent study of a large US multi-hospital database, we developed a model to predict the expected clinical and economic impact of increasing prevalence of MRSA. Small outbreaks of VEB-1 ESBL producing Acinetobacter baumannii in Belgian nursing homes and hospitals through cross-border transfer of patients from northern France Methods: From 01/04 to 03/05, all Belgian acute hospitals were invited to report cases of nosocomial infections/colonisations due to MDR Ab isolates presenting a resistance profile similar to the French epidemic strain (resistance to all agents except carbapenems and colistin) and to send such isolates to the reference laboratory for phenotypic confirmation and for genotypic characterization (PCR of VEB-1 and class 1 Integron, PFGE typing). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157935/ doi: 10.1111/j.1470-9465.2006.12_4_1431.x id: cord-023592-w96h4rir author: nan title: Abstracts cont. date: 2015-12-28 words: 67857.0 sentences: 4136.0 pages: flesch: 52.0 cache: ./cache/cord-023592-w96h4rir.txt txt: ./txt/cord-023592-w96h4rir.txt summary: Conclusions: Although the risk of developing more serious gastric lesions increased as the number of virulence factor genes are accumulated in a given Hp strain, we did not find any significant differences or relationship in the cagA, vacA or babA2 status between the Hp isolates from patients with gastritis or peptic ulcer in this study. pneumophila at the serogroup level, it was used in two different outbreaks to demonstrate rapidly the identity of the sequences between strains responsible for severe human infection and those isolated in the hot water reservoir, suggesting a common origin. To determine the antimicrobial resistance in Salmonella and Shigella strains isolated from stool specimens during a 2-year period, from patients admitted to our clinics with a diagnosis of diarrhoea. In our study the susceptibility of 65 bacterial strains isolated in hospital environment (colonising or infecting patients or carried by German cockroaches) to antibiotics and chemical disinfectants was determined. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172567/ doi: 10.1111/j.1469-0691.2004.0902c.x ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel