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M.; Hinz, Andreas; Seaman, Michael S.; Vanzetta, Fabrizia; Fernandez-Rodriguez, Blanca M.; Silacci, Chiara; Pinna, Debora; Jarrossay, David; Balla-Jhagjhoorsingh, Sunita; Willems, Betty; Zekveld, Maria J.; Dreja, Hanna; O'Sullivan, Eithne; Pade, Corinna; Orkin, Chloe; Jeffs, Simon A.; Montefiori, David C.; Davis, David; Weissenhorn, Winfried; McKnight, Áine; Heeney, Jonathan L.; Sallusto, Federica; Sattentau, Quentin J.; Weiss, Robin A.; Lanzavecchia, Antonio title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals date: 2010-01-20 journal: PLoS One DOI: 10.1371/journal.pone.0008805 sha: doc_id: 158 cord_uid: d08buwtu file: cache/cord-000077-d441jam3.json key: cord-000077-d441jam3 authors: Zhang, Hao-Jie; Wang, Yong-Xiang; Wu, Hao; Jin, Dong-Yan; Wen, Yu-Mei; Zheng, Bo-Jian title: The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date: 2009-07-03 journal: PLoS One DOI: 10.1371/journal.pone.0006108 sha: doc_id: 77 cord_uid: d441jam3 file: cache/cord-000638-ss1435el.json key: cord-000638-ss1435el authors: Beq, Stephanie; Rozlan, Sandra; Pelletier, Sandy; Willems, Bernard; Bruneau, Julie; Lelievre, Jean-Daniel; Levy, Yves; Shoukry, Naglaa H.; Cheynier, Rémi title: Altered Thymic Function during Interferon Therapy in HCV-Infected Patients date: 2012-04-16 journal: PLoS One DOI: 10.1371/journal.pone.0034326 sha: doc_id: 638 cord_uid: ss1435el file: cache/cord-000008-3dgjv0x1.json key: cord-000008-3dgjv0x1 authors: Vali, Bahareh; Yue, Feng Yun; Jones, R. Brad; Sheth, Prameet M.; Kaul, Rupert; Betts, Michael R.; Wong, David; Kovacs, Colin; Loutfy, Mona; Common, Andrew; Halpenny, Roberta; Ostrowski, Mario A. title: HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date: 2008-10-20 journal: PLoS One DOI: 10.1371/journal.pone.0003454 sha: doc_id: 8 cord_uid: 3dgjv0x1 file: cache/cord-000736-6f8vyziv.json key: cord-000736-6f8vyziv authors: Pripuzova, Natalia; Wang, Richard; Tsai, Shien; Li, Bingjie; Hung, Guo-Chiuan; Ptak, Roger G.; Lo, Shyh-Ching title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 journal: PLoS One DOI: 10.1371/journal.pone.0043246 sha: doc_id: 736 cord_uid: 6f8vyziv file: cache/cord-000130-dqqcajjd.json key: cord-000130-dqqcajjd authors: Smith?, Robert J; Gordon, Richard title: The OptAIDS project: towards global halting of HIV/AIDS date: 2009-11-18 journal: BMC Public Health DOI: 10.1186/1471-2458-9-s1-s1 sha: doc_id: 130 cord_uid: dqqcajjd file: cache/cord-000849-rrezynbs.json key: cord-000849-rrezynbs authors: Kumar, Rajesh; Andrabi, Raiees; Tiwari, Ashutosh; Prakash, Somi Sankaran; Wig, Naveet; Dutta, Durgashree; Sankhyan, Anurag; Khan, Lubina; Sinha, Subrata; Luthra, Kalpana title: A novel strategy for efficient production of anti-V3 human scFvs against HIV-1 clade C date: 2012-11-15 journal: BMC Biotechnol DOI: 10.1186/1472-6750-12-87 sha: doc_id: 849 cord_uid: rrezynbs file: cache/cord-001532-kz3b01wq.json key: cord-001532-kz3b01wq authors: Gantt, Soren; Gachelet, Eliora; Carlsson, Jacquelyn; Barcy, Serge; Casper, Corey; Lagunoff, Michael title: Nelfinavir Impairs Glycosylation of Herpes Simplex Virus 1 Envelope Proteins and Blocks Virus Maturation date: 2015-01-29 journal: Adv Virol DOI: 10.1155/2015/687162 sha: doc_id: 1532 cord_uid: kz3b01wq file: cache/cord-001228-4eh22ek7.json key: cord-001228-4eh22ek7 authors: Ofori, Leslie O.; Hilimire, Thomas A.; Bennett, Ryan P.; Brown, Nathaniel W.; Smith, Harold C.; Miller, Benjamin L. title: High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity date: 2014-01-05 journal: J Med Chem DOI: 10.1021/jm401438g sha: doc_id: 1228 cord_uid: 4eh22ek7 file: cache/cord-000065-6c3zb3g4.json key: cord-000065-6c3zb3g4 authors: Nguyen, Thu Anh; Oosterhoff, Pauline; Pham, Yen Ngoc; Hardon, Anita; Wright, Pamela title: Health workers' views on quality of prevention of mother-to-child transmission and postnatal care for HIV-infected women and their children date: 2009-05-13 journal: Hum Resour Health DOI: 10.1186/1478-4491-7-39 sha: doc_id: 65 cord_uid: 6c3zb3g4 file: cache/cord-002757-upwe0cpj.json key: cord-002757-upwe0cpj authors: Sullivan, Kathleen E.; Bassiri, Hamid; Bousfiha, Ahmed A.; Costa-Carvalho, Beatriz T.; Freeman, Alexandra F.; Hagin, David; Lau, Yu L.; Lionakis, Michail S.; Moreira, Ileana; Pinto, Jorge A.; de Moraes-Pinto, M. Isabel; Rawat, Amit; Reda, Shereen M.; Reyes, Saul Oswaldo Lugo; Seppänen, Mikko; Tang, Mimi L. K. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 journal: J Clin Immunol DOI: 10.1007/s10875-017-0426-2 sha: doc_id: 2757 cord_uid: upwe0cpj file: cache/cord-000868-vnwpzsu8.json key: cord-000868-vnwpzsu8 authors: Eissmann, Kristin; Mueller, Sebastian; Sticht, Heinrich; Jung, Susan; Zou, Peng; Jiang, Shibo; Gross, Andrea; Eichler, Jutta; Fleckenstein, Bernhard; Reil, Heide title: HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop date: 2013-01-22 journal: PLoS One DOI: 10.1371/journal.pone.0054452 sha: doc_id: 868 cord_uid: vnwpzsu8 file: cache/cord-001079-v01vwu00.json key: cord-001079-v01vwu00 authors: Thoden, J.; Potthoff, A.; Bogner, J. R.; Brockmeyer, N. H.; Esser, S.; Grabmeier-Pfistershammer, K.; Haas, B.; Hahn, K.; Härter, G.; Hartmann, M.; Herzmann, C.; Hutterer, J.; Jordan, A. R.; Lange, C.; Mauss, S.; Meyer-Olson, D.; Mosthaf, F.; Oette, M.; Reuter, S.; Rieger, A.; Rosenkranz, T.; Ruhnke, M.; Schaaf, B.; Schwarze, S.; Stellbrink, H. J.; Stocker, H.; Stoehr, A.; Stoll, M.; Träder, C.; Vogel, M.; Wagner, D.; Wyen, C.; Hoffmann, C. title: Therapy and prophylaxis of opportunistic infections in HIV-infected patients: a guideline by the German and Austrian AIDS societies (DAIG/ÖAG) (AWMF 055/066) date: 2013-09-14 journal: Infection DOI: 10.1007/s15010-013-0504-1 sha: doc_id: 1079 cord_uid: v01vwu00 file: cache/cord-001707-piyo00yg.json key: cord-001707-piyo00yg authors: Murray, Jillian; Cohen, Adam; Walaza, Sibongile; Groome, Michelle; Madhi, Shabir; Variava, Ebrahim; Kahn, Kathleen; Dawood, Halima; Tempia, Stefano; Tshangela, Akhona; Venter, Marietje; Feikin, Daniel; Cohen, Cheryl title: Determining the Provincial and National Burden of Influenza-Associated Severe Acute Respiratory Illness in South Africa Using a Rapid Assessment Methodology date: 2015-07-08 journal: PLoS One DOI: 10.1371/journal.pone.0132078 sha: doc_id: 1707 cord_uid: piyo00yg file: cache/cord-003715-deqiets2.json key: cord-003715-deqiets2 authors: Warren, Cody J.; Meyerson, Nicholas R.; Dirasantha, Obaiah; Feldman, Emily R.; Wilkerson, Gregory K.; Sawyer, Sara L. title: Selective use of primate CD4 receptors by HIV-1 date: 2019-06-10 journal: PLoS Biol DOI: 10.1371/journal.pbio.3000304 sha: doc_id: 3715 cord_uid: deqiets2 file: cache/cord-003764-141u6ax7.json key: cord-003764-141u6ax7 authors: Shrestha, Ashish C.; Wijesundara, Danushka K.; Masavuli, Makutiro G.; Mekonnen, Zelalem A.; Gowans, Eric J.; Grubor-Bauk, Branka title: Cytolytic Perforin as an Adjuvant to Enhance the Immunogenicity of DNA Vaccines date: 2019-04-30 journal: Vaccines (Basel) DOI: 10.3390/vaccines7020038 sha: doc_id: 3764 cord_uid: 141u6ax7 file: cache/cord-004575-b0t6bsya.json key: cord-004575-b0t6bsya authors: Staub, Roger title: Haben HIV-Positive eine besondere Verantwortung?: Ein Diskussionsbeitrag date: 2007-03-27 journal: Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz DOI: 10.1007/s00103-007-0190-1 sha: doc_id: 4575 cord_uid: b0t6bsya file: cache/cord-004827-bnf3mvaf.json key: cord-004827-bnf3mvaf authors: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 journal: Arch Virol DOI: 10.1007/s00705-004-0466-9 sha: doc_id: 4827 cord_uid: bnf3mvaf file: cache/cord-005327-bt7o8yxk.json key: cord-005327-bt7o8yxk authors: Ahn, Insung; Son, Hyeon Seok title: Epidemiological comparisons of codon usage patterns among HIV-1 isolates from Asia, Europe, Africa and the Americas date: 2006-12-01 journal: Exp Mol Med DOI: 10.1038/emm.2006.76 sha: doc_id: 5327 cord_uid: bt7o8yxk file: cache/cord-001972-1zisomq5.json key: cord-001972-1zisomq5 authors: Wang, Xue; Tan, Jiying; Biswas, Santanu; Zhao, Jiangqin; Devadas, Krishnakumar; Ye, Zhiping; Hewlett, Indira title: Pandemic Influenza A (H1N1) Virus Infection Increases Apoptosis and HIV-1 Replication in HIV-1 Infected Jurkat Cells date: 2016-02-02 journal: Viruses DOI: 10.3390/v8020033 sha: doc_id: 1972 cord_uid: 1zisomq5 file: cache/cord-003307-snruk3j2.json key: cord-003307-snruk3j2 authors: Schmidt, Julius J.; Lueck, Catherina; Ziesing, Stefan; Stoll, Matthias; Haller, Hermann; Gottlieb, Jens; Eder, Matthias; Welte, Tobias; Hoeper, Marius M.; Scherag, André; David, Sascha title: Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date: 2018-11-19 journal: Crit Care DOI: 10.1186/s13054-018-2221-8 sha: doc_id: 3307 cord_uid: snruk3j2 file: cache/cord-003895-m1y76ee5.json key: cord-003895-m1y76ee5 authors: Parcesepe, Angela M.; Nash, Denis; Tymejczyk, Olga; Reidy, William; Kulkarni, Sarah Gorrell; Elul, Batya title: Gender, HIV-Related Stigma, and Health-Related Quality of Life Among Adults Enrolling in HIV Care in Tanzania date: 2019-03-30 journal: AIDS Behav DOI: 10.1007/s10461-019-02480-1 sha: doc_id: 3895 cord_uid: m1y76ee5 file: cache/cord-004335-bw3tziup.json key: cord-004335-bw3tziup authors: Perez-Zsolt, Daniel; Martinez-Picado, Javier; Izquierdo-Useros, Nuria title: When Dendritic Cells Go Viral: The Role of Siglec-1 in Host Defense and Dissemination of Enveloped Viruses date: 2019-12-19 journal: Viruses DOI: 10.3390/v12010008 sha: doc_id: 4335 cord_uid: bw3tziup file: cache/cord-004501-guiy89x8.json key: cord-004501-guiy89x8 authors: Cojocaru, Florina-Daniela; Botezat, Doru; Gardikiotis, Ioannis; Uritu, Cristina-Mariana; Dodi, Gianina; Trandafir, Laura; Rezus, Ciprian; Rezus, Elena; Tamba, Bogdan-Ionel; Mihai, Cosmin-Teodor title: Nanomaterials Designed for Antiviral Drug Delivery Transport across Biological Barriers date: 2020-02-18 journal: Pharmaceutics DOI: 10.3390/pharmaceutics12020171 sha: doc_id: 4501 cord_uid: guiy89x8 file: cache/cord-005033-voi9gu0l.json key: cord-005033-voi9gu0l authors: Xuan, Huiyu; Xu, Lida; Li, Lu title: A CA-based epidemic model for HIV/AIDS transmission with heterogeneity date: 2008-06-07 journal: Ann Oper Res DOI: 10.1007/s10479-008-0369-3 sha: doc_id: 5033 cord_uid: voi9gu0l file: cache/cord-006260-ux32zanj.json key: cord-006260-ux32zanj authors: Sarkar, Paul; Gould, Ian M. title: Antimicrobial Agents are Societal Drugs: How Should This Influence Prescribing? date: 2012-09-17 journal: Drugs DOI: 10.2165/00003495-200666070-00001 sha: doc_id: 6260 cord_uid: ux32zanj file: cache/cord-011485-15wtv6bt.json key: cord-011485-15wtv6bt authors: Yang, Wenbo; Yang, Dianlong; Gong, Shisong; Dong, Xiaobing; Liu, Luyao; Yu, Shengda; Zhang, Xiaolei; Ge, Shengxiang; Wang, Dong; Xia, Ningshao; Yu, Duli; Qiu, Xianbo title: An immunoassay cassette with a handheld reader for HIV urine testing in point-of-care diagnostics date: 2020-05-21 journal: Biomed Microdevices DOI: 10.1007/s10544-020-00494-4 sha: doc_id: 11485 cord_uid: 15wtv6bt file: cache/cord-001385-rb5vwolt.json key: cord-001385-rb5vwolt authors: Reuven, Eliran Moshe; Ali, Mohammad; Rotem, Etai; Schwarzter, Roland; Gramatica, Andrea; Futerman, Anthony H.; Shai, Yechiel title: The HIV-1 Envelope Transmembrane Domain Binds TLR2 through a Distinct Dimerization Motif and Inhibits TLR2-Mediated Responses date: 2014-08-14 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004248 sha: doc_id: 1385 cord_uid: rb5vwolt file: cache/cord-004198-h8ch3x14.json key: cord-004198-h8ch3x14 authors: Ebuy, Hiluf; Bekele, Alemayehu; Redae, Getachew title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study date: 2020-01-21 journal: BMC Infect Dis DOI: 10.1186/s12879-020-4790-9 sha: doc_id: 4198 cord_uid: h8ch3x14 file: cache/cord-006716-n371b91w.json key: cord-006716-n371b91w authors: Cone, A. M.; Nadel, S.; Sweeney, B. title: Flumazenil reverses diazepam-induced neonatal apnoea and hypotonia date: 1993 journal: Eur J Pediatr DOI: 10.1007/bf01955914 sha: doc_id: 6716 cord_uid: n371b91w file: cache/cord-002746-qn34eyul.json key: cord-002746-qn34eyul authors: Antzin-Anduetza, Irati; Mahiet, Charlotte; Granger, Luke A.; Odendall, Charlotte; Swanson, Chad M. title: Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication date: 2017-11-09 journal: Retrovirology DOI: 10.1186/s12977-017-0374-1 sha: doc_id: 2746 cord_uid: qn34eyul file: cache/cord-004031-sw60qbbj.json key: cord-004031-sw60qbbj authors: Aylward, Ryan E.; van der Merwe, Elizabeth; Pazi, Sisa; van Niekerk, Minette; Ensor, Jason; Baker, Debbie; Freercks, Robert J. title: Risk factors and outcomes of acute kidney injury in South African critically ill adults: a prospective cohort study date: 2019-12-10 journal: BMC Nephrol DOI: 10.1186/s12882-019-1620-7 sha: doc_id: 4031 cord_uid: sw60qbbj file: cache/cord-004600-5lhnzzvg.json key: cord-004600-5lhnzzvg authors: Dennin, Reinhard H.; Doese, D.; Theobald, W.; Lafrenz, M. title: HIV-Infektion – Grenzen der Präventionskonzepte: Überlegungen zur Verantwortung der Betroffenen, der Politik und der Gesellschaft* date: 2007-03-26 journal: Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz DOI: 10.1007/s00103-007-0212-z sha: doc_id: 4600 cord_uid: 5lhnzzvg file: cache/cord-005335-u04cxiej.json key: cord-005335-u04cxiej authors: Podder, C. 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B.; Strawbridge, E. title: Mathematical Analysis of a Model for Assessing the Impact of Antiretroviral Therapy, Voluntary Testing and Condom Use in Curtailing the Spread of HIV date: 2011-05-05 journal: Differ Equ Dyn Syst DOI: 10.1007/s12591-011-0090-6 sha: doc_id: 5335 cord_uid: u04cxiej file: cache/cord-007237-8y7218oj.json key: cord-007237-8y7218oj authors: Manning, Ashleigh; Willey, Samantha J.; Bell, Jeanne E.; Simmonds, Peter title: Comparison of Tissue Distribution, Persistence, and Molecular Epidemiology of Parvovirus B19 and Novel Human Parvoviruses PARV4 and Human Bocavirus date: 2007-05-01 journal: J Infect Dis DOI: 10.1086/513280 sha: doc_id: 7237 cord_uid: 8y7218oj file: cache/cord-007188-tcq8lnwg.json key: cord-007188-tcq8lnwg authors: Cunningham, Anthony L.; Grohman, Gerhard S.; Harkness, John; Law, Carmela; Marriott, Deborah; Tindall, Brett; Cooper, David A. title: Gastrointestinal Viral Infections in Homosexual Men Who were Symptomatic and Seropositive for Human Immunodeficiency Virus date: 1988-08-17 journal: J Infect Dis DOI: 10.1093/infdis/158.2.386 sha: doc_id: 7188 cord_uid: tcq8lnwg file: cache/cord-004002-b35wm2db.json key: cord-004002-b35wm2db authors: Gaborit, Benjamin Jean; Tessoulin, Benoit; Lavergne, Rose-Anne; Morio, Florent; Sagan, Christine; Canet, Emmanuel; Lecomte, Raphael; Leturnier, Paul; Deschanvres, Colin; Khatchatourian, Lydie; Asseray, Nathalie; Garret, Charlotte; Vourch, Michael; Marest, Delphine; Raffi, François; Boutoille, David; Reignier, Jean title: Outcome and prognostic factors of Pneumocystis jirovecii pneumonia in immunocompromised adults: a prospective observational study date: 2019-11-27 journal: Ann Intensive Care DOI: 10.1186/s13613-019-0604-x sha: doc_id: 4002 cord_uid: b35wm2db file: cache/cord-009388-k3exf8a4.json key: cord-009388-k3exf8a4 authors: Agarwal, Yash; Beatty, Cole; Biradar, Shivkumar; Castronova, Isabella; Ho, Sara; Melody, Kevin; Bility, Moses Turkle title: Moving beyond the mousetrap: current and emerging humanized mouse and rat models for investigating prevention and cure strategies against HIV infection and associated pathologies date: 2020-04-10 journal: Retrovirology DOI: 10.1186/s12977-020-00515-3 sha: doc_id: 9388 cord_uid: k3exf8a4 file: cache/cord-009669-bcdjwpd1.json key: cord-009669-bcdjwpd1 authors: Tsegaye, Theodros Solomon; Pöhlmann, Stefan title: The multiple facets of HIV attachment to dendritic cell lectins date: 2010-09-20 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2010.01519.x sha: doc_id: 9669 cord_uid: bcdjwpd1 file: cache/cord-010001-u0d5jkp1.json key: cord-010001-u0d5jkp1 authors: KOTWAL, GIRISH J.; KACZMAREK, JENNIFER N.; LEIVERS, STEVEN; GHEBREMARIAM, YOHANNES T.; KULKARNI, AMOD P.; BAUER, GABRIELE; DE BEER, CORENA; PREISER, WOLFGANG; MOHAMED, ABDU RAHMAN title: Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date: 2006-01-22 journal: Ann N Y Acad Sci DOI: 10.1196/annals.1352.014 sha: doc_id: 10001 cord_uid: u0d5jkp1 file: cache/cord-010499-yefxrj30.json key: cord-010499-yefxrj30 authors: Yelverton, Elizabeth; Lindsley, Dale; Yamauchi, Phil; Gallant, Jonathan A. title: The function of a ribosomal frameshifting signal from human immunodeficiency virus‐1 in Escherichia coli date: 2006-10-27 journal: Mol Microbiol DOI: 10.1111/j.1365-2958.1994.tb00310.x sha: doc_id: 10499 cord_uid: yefxrj30 file: cache/cord-011457-hqxybv1k.json key: cord-011457-hqxybv1k authors: Kirui, James; Freed, Eric O. title: Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date: 2020-05-19 journal: Retrovirology DOI: 10.1186/s12977-020-00521-5 sha: doc_id: 11457 cord_uid: hqxybv1k file: cache/cord-016255-kkko1xne.json key: cord-016255-kkko1xne authors: van der Meer, J.T.M.; Nouwen, J.L. title: 14 Intravasale infecties en sepsis date: 2011 journal: Microbiologie en infectieziekten DOI: 10.1007/978-90-313-7944-6_14 sha: doc_id: 16255 cord_uid: kkko1xne file: cache/cord-005882-iodfgzjf.json key: cord-005882-iodfgzjf authors: Kaufmann, Stefan H E; McMichael, Andrew J title: Annulling a dangerous liaison: vaccination strategies against AIDS and tuberculosis date: 2005-04-05 journal: Nat Med DOI: 10.1038/nm1221 sha: doc_id: 5882 cord_uid: iodfgzjf file: cache/cord-006381-fsg9x8n7.json key: cord-006381-fsg9x8n7 authors: Howard, O. 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Ayers, Susan; Field, Andy P. title: Posttraumatic growth and adjustment among individuals with cancer or HIV/AIDS: A meta-analysis date: 2010-03-02 journal: Clin Psychol Rev DOI: 10.1016/j.cpr.2010.02.004 sha: doc_id: 268712 cord_uid: rxdw553c file: cache/cord-271970-i35pic5o.json key: cord-271970-i35pic5o authors: Boris, Bonaventure; Antoine, Rebendenne; de Gracia Francisco, Garcia; Marine, Tauziet; Joe, McKellar; Valadão Ana Luiza, Chaves; Valérie, Courgnaud; Eric, Bernard; Laurence, Briant; Nathalie, Gros; Wassila, Djilli; Mary, Arnaud-Arnould; Hugues, Parrinello; Stéphanie, Rialle; Olivier, Moncorgé; Caroline, Goujon title: A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor date: 2020-10-28 journal: bioRxiv DOI: 10.1101/2020.10.28.359356 sha: doc_id: 271970 cord_uid: i35pic5o file: cache/cord-271188-ewlxy5po.json key: cord-271188-ewlxy5po authors: Liu, Wei; Zhang, Shuping; Nekhai, Sergei; Liu, Sijin title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 journal: Curr Clin Microbiol Rep DOI: 10.1007/s40588-020-00140-w sha: doc_id: 271188 cord_uid: ewlxy5po file: cache/cord-271948-iq29xqrn.json key: cord-271948-iq29xqrn authors: Obeng, Billal Musah; 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Sheehy, Susanne; Sargent, Catherine; Democratis, Jane; Abbas, Sarah; Schiefermueller, Jurgen; Angus, Brian J. title: 29 Antiviral drugs date: 2010-12-31 journal: Side Effects of Drugs Annual DOI: 10.1016/s0378-6080(10)32029-0 sha: doc_id: 266294 cord_uid: ua22udlc file: cache/cord-269194-b1wlr3t7.json key: cord-269194-b1wlr3t7 authors: Engstrom-Melnyk, Julia; Rodriguez, Pedro L.; Peraud, Olivier; Hein, Raymond C. title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 journal: Methods in Microbiology DOI: 10.1016/bs.mim.2015.04.005 sha: doc_id: 269194 cord_uid: b1wlr3t7 file: cache/cord-274688-cr1rvy8u.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-274688-cr1rvy8u authors: Jewell, Britta L; Mudimu, Edinah; Stover, John; ten Brink, Debra; Phillips, Andrew N; Smith, Jennifer A; Martin-Hughes, Rowan; Teng, Yu; Glaubius, Robert; Mahiane, Severin Guy; Bansi-Matharu, Loveleen; Taramusi, Isaac; Chagoma, Newton; Morrison, Michelle; Doherty, Meg; Marsh, Kimberly; Bershteyn, Anna; Hallett, Timothy B; Kelly, Sherrie L title: Potential effects of disruption to HIV programmes in sub-Saharan Africa caused by COVID-19: results from multiple mathematical models date: 2020-08-06 journal: Lancet HIV DOI: 10.1016/s2352-3018(20)30211-3 sha: doc_id: 274688 cord_uid: cr1rvy8u file: cache/cord-278831-gwnfcfvk.json key: cord-278831-gwnfcfvk authors: Taniwaki, Sueli Akemi; Figueiredo, Andreza Soriano; Araujo Jr., João Pessoa title: Virus–host interaction in feline immunodeficiency virus (FIV) infection date: 2013-08-02 journal: Comp Immunol Microbiol Infect Dis DOI: 10.1016/j.cimid.2013.07.001 sha: doc_id: 278831 cord_uid: gwnfcfvk file: cache/cord-284128-3obc5k5u.json key: cord-284128-3obc5k5u authors: Ahmed, Ali; Dujaili, Juman; Sandhu, Anisha Kaur; Hashmi, Furqan Khurshid title: Concerns of HIV-positive migrant workers in COVID-19 pandemic: A call for action date: 2020-09-08 journal: Journal of global health DOI: 10.7189/jogh.10.020342 sha: doc_id: 284128 cord_uid: 3obc5k5u file: cache/cord-274019-dao10kx9.json key: cord-274019-dao10kx9 authors: Rife, Brittany D; Mavian, Carla; Chen, Xinguang; Ciccozzi, Massimo; Salemi, Marco; Min, Jae; Prosperi, Mattia CF title: Phylodynamic applications in 21(st) century global infectious disease research date: 2017-05-08 journal: Glob Health Res Policy DOI: 10.1186/s41256-017-0034-y sha: doc_id: 274019 cord_uid: dao10kx9 file: cache/cord-276006-mjjnkqv6.json key: cord-276006-mjjnkqv6 authors: Jarach, Natanel; Dodiuk, Hanna; Kenig, Samuel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 journal: Polymers (Basel) DOI: 10.3390/polym12081727 sha: doc_id: 276006 cord_uid: mjjnkqv6 parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-268901-7cm6m1ol.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-268901-7cm6m1ol authors: Ku, Therese; Lopresti, Natalie; Shirley, Matthew; Mori, Mattia; Marchant, Jan; Heng, Xiao; Botta, Maurizio; Summers, Michael F.; Seley-Radtke, Katherine L. title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date: 2019-07-01 journal: Bioorganic & Medicinal Chemistry DOI: 10.1016/j.bmc.2019.05.019 sha: doc_id: 268901 cord_uid: 7cm6m1ol file: cache/cord-270868-4s3q2i6v.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-270868-4s3q2i6v authors: Collins, Lauren F.; Moran, Caitlin A.; Oliver, Nora T.; Moanna, Abeer; Lahiri, Cecile D.; Colasanti, Jonathan A.; Kelley, Colleen F.; Nguyen, Minh L.; Marconi, Vincent C.; Armstrong, Wendy S.; Ofotokun, Ighovwerha; Sheth, Anandi N. title: Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia date: 2020-10-01 journal: AIDS DOI: 10.1097/qad.0000000000002632 sha: doc_id: 270868 cord_uid: 4s3q2i6v file: cache/cord-275677-hbv49e01.json key: cord-275677-hbv49e01 authors: Ramana, Lakshmi Narashimhan; Anand, Appakkudal R.; Sethuraman, Swaminathan; Krishnan, Uma Maheswari title: Targeting strategies for delivery of anti-HIV drugs date: 2014-10-28 journal: J Control Release DOI: 10.1016/j.jconrel.2014.08.003 sha: doc_id: 275677 cord_uid: hbv49e01 file: cache/cord-278156-zd039ohv.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-278156-zd039ohv authors: Dumas, Fabrice; Preira, Pascal; Salomé, Laurence title: Membrane organization of virus and target cell plays a role in HIV entry date: 2014-09-01 journal: Biochimie DOI: 10.1016/j.biochi.2014.08.015 sha: doc_id: 278156 cord_uid: zd039ohv file: cache/cord-279828-es498qul.json key: cord-279828-es498qul authors: Boulle, Andrew; Davies, Mary-Ann; Hussey, Hannah; Ismail, Muzzammil; Morden, Erna; Vundle, Ziyanda; Zweigenthal, Virginia; Mahomed, Hassan; Paleker, Masudah; Pienaar, David; Tembo, Yamanya; Lawrence, Charlene; Isaacs, Washiefa; Mathema, Hlengani; Allen, Derick; Allie, Taryn; 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Schrueder, Neshaad; Sithole, Nokwanda; Sithole, Sthembiso; Taljaard, Jantjie J; Titus, Gideon; Van Der Merwe, Tian; van Schalkwyk, Marije; Vazi, Luthando; Viljoen, Abraham J; Yazied Chothia, Mogamat; Naidoo, Vanessa; Alan Wallis, Lee; Abbass, Mumtaz; Arendse, Juanita; Armien, Rizqa; Bailey, Rochelle; Bello, Muideen; Carelse, Rachel; Forgus, Sheron; Kalawe, Nosi; Kariem, Saadiq; Kotze, Mariska; Lucas, Jonathan; McClaughlin, Juanita; Murie, Kathleen; Najjaar, Leilah; Petersen, Liesel; Porter, James; Shaw, Melanie; Stapar, Dusica; Williams, Michelle; Aldum, Linda; Berkowitz, Natacha; Girran, Raakhee; Lee, Kevin; Naidoo, Lenny; Neumuller, Caroline; Anderson, Kim; Begg, Kerrin; Boerlage, Lisa; Cornell, Morna; de Waal, Renée; Dudley, Lilian; English, René; Euvrard, Jonathan; Groenewald, Pam; Jacob, Nisha; Jaspan, Heather; Kalk, Emma; Levitt, Naomi; Malaba, Thoko; Nyakato, Patience; Patten, Gabriela; Schneider, Helen; Shung King, Maylene; Tsondai, Priscilla; Van Duuren, James; van Schaik, Nienke; Blumberg, Lucille; Cohen, Cheryl; Govender, Nelesh; Jassat, Waasila; Kufa, Tendesayi; McCarthy, Kerrigan; Morris, Lynn; Hsiao, Nei-yuan; Marais, Ruan; Ambler, Jon; Ngwenya, Olina; Osei-Yeboah, Richard; Johnson, Leigh; Kassanjee, Reshma; Tamuhla, Tsaone title: Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date: 2020-08-29 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1198 sha: doc_id: 279828 cord_uid: es498qul file: cache/cord-284385-ster02o9.json key: cord-284385-ster02o9 authors: Gambichler, Thilo; Reuther, Judith; Scheel, Christina H; Becker, Jürgen Christian title: On the use of immune checkpoint inhibitors in patients with viral infections including COVID-19 date: 2020-07-01 journal: J Immunother Cancer DOI: 10.1136/jitc-2020-001145 sha: doc_id: 284385 cord_uid: ster02o9 file: cache/cord-285151-zynor0b2.json key: cord-285151-zynor0b2 authors: Eisenhut, Michael title: Neopterin in Diagnosis and Monitoring of Infectious Diseases date: 2013-12-08 journal: J Biomark DOI: 10.1155/2013/196432 sha: doc_id: 285151 cord_uid: zynor0b2 file: cache/cord-278876-il7g78w1.json key: cord-278876-il7g78w1 authors: Akkina, Ramesh; Ellerbrok, Heinz; Hall, William; Hasegawa, Hideki; Kawaguchi, Yasushi; Kleanthous, Harold; McSweegan, Edward; Mercer, Natalia; Romanowski, Victor; Sawa, Hirofumi; Vahlne, Anders title: 2016 International meeting of the Global Virus Network date: 2017-03-16 journal: Antiviral Res DOI: 10.1016/j.antiviral.2017.03.005 sha: doc_id: 278876 cord_uid: il7g78w1 file: cache/cord-282063-tkp1tifx.json key: cord-282063-tkp1tifx authors: Saberi, Parya title: Research in the Time of Coronavirus: Continuing Ongoing Studies in the Midst of the COVID-19 Pandemic date: 2020-04-18 journal: AIDS Behav DOI: 10.1007/s10461-020-02868-4 sha: doc_id: 282063 cord_uid: tkp1tifx file: cache/cord-269222-g2ibmo75.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-269222-g2ibmo75 authors: Valenti, Piera; Rosa, Luigi; Capobianco, Daniela; Lepanto, Maria Stefania; Schiavi, Elisa; Cutone, Antimo; Paesano, Rosalba; Mastromarino, Paola title: Role of Lactobacilli and Lactoferrin in the Mucosal Cervicovaginal Defense date: 2018-03-01 journal: Front Immunol DOI: 10.3389/fimmu.2018.00376 sha: doc_id: 269222 cord_uid: g2ibmo75 file: cache/cord-273777-qb0vp9gr.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-273777-qb0vp9gr authors: Happel, Anna-Ursula; Varsani, Arvind; Balle, Christina; Passmore, Jo-Ann; Jaspan, Heather title: The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date: 2020-07-30 journal: Viruses DOI: 10.3390/v12080832 sha: doc_id: 273777 cord_uid: qb0vp9gr file: cache/cord-284523-lknyehsa.json key: cord-284523-lknyehsa authors: da Mata, Élida Cleyse Gomes; Mourão, Caroline Barbosa Farias; Rangel, Marisa; Schwartz, Elisabeth Ferroni title: Antiviral activity of animal venom peptides and related compounds date: 2017-01-06 journal: J Venom Anim Toxins Incl Trop Dis DOI: 10.1186/s40409-016-0089-0 sha: doc_id: 284523 cord_uid: lknyehsa file: cache/cord-285430-o086q2qa.json key: cord-285430-o086q2qa authors: Gribble, Karleen; Mathisen, Roger; Ververs, Mija-tesse; Coutsoudis, Anna title: Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date: 2020-07-25 journal: Int Breastfeed J DOI: 10.1186/s13006-020-00306-8 sha: doc_id: 285430 cord_uid: o086q2qa file: cache/cord-278174-znc99yos.json key: cord-278174-znc99yos authors: Ramsey, Glenn title: Managing recalls and withdrawals of blood components date: 2004-01-31 journal: Transfusion Medicine Reviews DOI: 10.1016/j.tmrv.2003.10.005 sha: doc_id: 278174 cord_uid: znc99yos file: cache/cord-284409-xiyeceib.json key: cord-284409-xiyeceib authors: Prabakaran, Ponraj; Chen, Weizao; Dimitrov, Dimiter S. title: The Antibody Germline/Maturation Hypothesis, Elicitation of Broadly Neutralizing Antibodies Against HIV-1 and Cord Blood IgM Repertoires date: 2014-08-28 journal: Front Immunol DOI: 10.3389/fimmu.2014.00398 sha: doc_id: 284409 cord_uid: xiyeceib file: cache/cord-287754-dh6abx2t.json key: cord-287754-dh6abx2t authors: Akkouh, Ouafae; Ng, Tzi Bun; Singh, Senjam Sunil; Yin, Cuiming; Dan, Xiuli; Chan, Yau Sang; Pan, Wenliang; Cheung, Randy Chi Fai title: Lectins with Anti-HIV Activity: A Review date: 2015-01-06 journal: Molecules DOI: 10.3390/molecules20010648 sha: doc_id: 287754 cord_uid: dh6abx2t file: cache/cord-288440-w7g2agaf.json key: cord-288440-w7g2agaf authors: Jia, Rui; Ding, Shilei; Pan, Qinghua; Liu, Shan-Lu; Qiao, Wentao; Liang, Chen title: The C-Terminal Sequence of IFITM1 Regulates Its Anti-HIV-1 Activity date: 2015-03-04 journal: PLoS One DOI: 10.1371/journal.pone.0118794 sha: doc_id: 288440 cord_uid: w7g2agaf file: cache/cord-282675-s4zmffj3.json key: cord-282675-s4zmffj3 authors: Sagaon-Teyssier, Luis; Kamissoko, Aliou; Yattassaye, Adam; Diallo, Fodié; Rojas Castro, Daniela; Delabre, Rosemary; Pouradier, Fabrice; Maradan, Gwenaëlle; Bourrelly, Michel; Cissé, Mamadou; Vidal, Laurent; Dembélé Keïta, Bintou; Spire, Bruno title: Assessment of mental health outcomes and associated factors among workers in community-based HIV care centers in the early stage of the COVID-19 outbreak in Mali date: 2020-10-15 journal: Health Policy Open DOI: 10.1016/j.hpopen.2020.100017 sha: doc_id: 282675 cord_uid: s4zmffj3 file: cache/cord-273324-xhpv783y.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-273324-xhpv783y authors: Land, Kevin J.; Boeras, Debrah I.; Chen, Xiang-Sheng; Ramsay, Andrew R.; Peeling, Rosanna W. title: REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: 2018-12-13 journal: Nat Microbiol DOI: 10.1038/s41564-018-0295-3 sha: doc_id: 273324 cord_uid: xhpv783y file: cache/cord-291534-c6cjxq07.json key: cord-291534-c6cjxq07 authors: Gwyer Findlay, Emily; Currie, Silke M.; Davidson, Donald J. title: Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date: 2013-05-07 journal: BioDrugs DOI: 10.1007/s40259-013-0039-0 sha: doc_id: 291534 cord_uid: c6cjxq07 file: cache/cord-287286-4l963z2q.json key: cord-287286-4l963z2q authors: Green, Victoria A.; Munshi, Saif U.; Marakalala, Mohlopheni J.; Mourão, Marina M. title: Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date: 2010-07-28 journal: IUBMB Life DOI: 10.1002/iub.364 sha: doc_id: 287286 cord_uid: 4l963z2q file: cache/cord-288982-63ddlh20.json key: cord-288982-63ddlh20 authors: Peeling, Rosanna W. title: Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date: 2015-11-09 journal: Int Health DOI: 10.1093/inthealth/ihv062 sha: doc_id: 288982 cord_uid: 63ddlh20 file: cache/cord-283346-0v4b6do2.json key: cord-283346-0v4b6do2 authors: Ansari, Abdul Wahid; Bhatnagar, Nupur; Dittrich-Breiholz, Oliver; Kracht, Michael; Schmidt, Reinhold E.; Heiken, Hans title: Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals date: 2006-08-17 journal: Int Immunol DOI: 10.1093/intimm/dxl078 sha: doc_id: 283346 cord_uid: 0v4b6do2 file: cache/cord-286194-2emwfx89.json key: cord-286194-2emwfx89 authors: Mirzaei, Hossein; McFarland, Willi; Karamouzian, Mohammad; Sharifi, Hamid title: COVID-19 Among People Living with HIV: A Systematic Review date: 2020-07-30 journal: AIDS Behav DOI: 10.1007/s10461-020-02983-2 sha: doc_id: 286194 cord_uid: 2emwfx89 file: cache/cord-292286-ygomb3oi.json key: cord-292286-ygomb3oi authors: Zakaryan, Hovakim; Arabyan, Erik; Oo, Adrian; Zandi, Keivan title: Flavonoids: promising natural compounds against viral infections date: 2017-05-25 journal: Arch Virol DOI: 10.1007/s00705-017-3417-y sha: doc_id: 292286 cord_uid: ygomb3oi file: cache/cord-277818-8w15dz20.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-277818-8w15dz20 authors: Jaichenco, Andre L.; Lima, Luciana Cavalcanti title: Infectious Disease Considerations for the Operating Room date: 2018-02-09 journal: A Practice of Anesthesia for Infants and Children DOI: 10.1016/b978-0-323-42974-0.00050-1 sha: doc_id: 277818 cord_uid: 8w15dz20 file: cache/cord-286352-uftl1mx5.json key: cord-286352-uftl1mx5 authors: Baril, Martin; Dulude, Dominic; Steinberg, Sergey V; Brakier-Gingras, Léa title: The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot date: 2003-08-15 journal: Journal of Molecular Biology DOI: 10.1016/s0022-2836(03)00784-8 sha: doc_id: 286352 cord_uid: uftl1mx5 file: cache/cord-287018-g4y5kjju.json key: cord-287018-g4y5kjju authors: Konstantinova, P; de Vries, W; Haasnoot, J; ter Brake, O; de Haan, P; Berkhout, B title: Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA date: 2006-05-18 journal: Gene Ther DOI: 10.1038/sj.gt.3302786 sha: doc_id: 287018 cord_uid: g4y5kjju file: cache/cord-287337-2ljbsia2.json key: cord-287337-2ljbsia2 authors: Ludwig, Christine; Wagner, Ralf title: Virus-like particles—universal molecular toolboxes date: 2008-01-04 journal: Curr Opin Biotechnol DOI: 10.1016/j.copbio.2007.10.013 sha: doc_id: 287337 cord_uid: 2ljbsia2 file: cache/cord-287853-cob7ur35.json key: cord-287853-cob7ur35 authors: Sharma, Vaneet Kumar; Sharma, Ity; Glick, James title: The expanding role of mass spectrometry in the field of vaccine development date: 2018-05-31 journal: Mass Spectrom Rev DOI: 10.1002/mas.21571 sha: doc_id: 287853 cord_uid: cob7ur35 file: cache/cord-269759-1n1oo6wc.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-269759-1n1oo6wc authors: Villamil-Gómez, Wilmer E.; Sánchez, Álvaro; Gelis, Libardo; Silvera, Luz Alba; Barbosa, Juliana; Otero-Nader, Octavio; Bonilla-Salgado, Carlos David; Rodríguez-Morales, Alfonso J. title: Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia date: 2020-02-06 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2020.101573 sha: doc_id: 269759 cord_uid: 1n1oo6wc file: cache/cord-286574-t9z2ynt5.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-286574-t9z2ynt5 authors: nan title: Speaker presentations date: 2017-09-30 journal: International Journal of Antimicrobial Agents DOI: 10.1016/s0924-8579(17)30340-0 sha: doc_id: 286574 cord_uid: t9z2ynt5 file: cache/cord-289274-3g67f8sw.json key: cord-289274-3g67f8sw authors: Tosoni, Elena; Frasson, Ilaria; Scalabrin, Matteo; Perrone, Rosalba; Butovskaya, Elena; Nadai, Matteo; Palù, Giorgio; Fabris, Dan; Richter, Sara N. title: Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription date: 2015-10-15 journal: Nucleic Acids Res DOI: 10.1093/nar/gkv897 sha: doc_id: 289274 cord_uid: 3g67f8sw file: cache/cord-285443-9y2kkmby.json key: cord-285443-9y2kkmby authors: Pessi, Antonello title: Cholesterol‐conjugated peptide antivirals: a path to a rapid response to emerging viral diseases date: 2014-10-20 journal: J Pept Sci DOI: 10.1002/psc.2706 sha: doc_id: 285443 cord_uid: 9y2kkmby file: cache/cord-285603-f4572w5m.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-285603-f4572w5m authors: Ortega, Joseph T.; Serrano, Maria Luisa; Jastrzebska, Beata title: Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date: 2020-06-24 journal: Biomolecules DOI: 10.3390/biom10060954 sha: doc_id: 285603 cord_uid: f4572w5m file: cache/cord-264225-vzcfeh7t.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-264225-vzcfeh7t authors: Talbert-Slagle, Kristina; Atkins, Katherine E.; Yan, Koon-Kiu; Khurana, Ekta; Gerstein, Mark; Bradley, Elizabeth H.; Berg, David; Galvani, Alison P.; Townsend, Jeffrey P. title: Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body date: 2014-05-08 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004092 sha: doc_id: 264225 cord_uid: vzcfeh7t file: cache/cord-274663-zyzgk2z3.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-274663-zyzgk2z3 authors: Chang, Stewart T.; Sova, Pavel; Peng, Xinxia; Weiss, Jeffrey; Law, G. Lynn; Palermo, Robert E.; Katze, Michael G. title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line date: 2011-09-20 journal: mBio DOI: 10.1128/mbio.00134-11 sha: doc_id: 274663 cord_uid: zyzgk2z3 file: cache/cord-277417-f71jwdzj.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-277417-f71jwdzj authors: Geoghegan, Jemma L.; Holmes, Edward C. title: The phylogenomics of evolving virus virulence date: 2018-10-10 journal: Nat Rev Genet DOI: 10.1038/s41576-018-0055-5 sha: doc_id: 277417 cord_uid: f71jwdzj file: cache/cord-278456-gsv6dh36.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-278456-gsv6dh36 authors: Qureshi, Abid; Kaur, Gazaldeep; Kumar, Manoj title: AVCpred: an integrated web server for prediction and design of antiviral compounds date: 2016-09-09 journal: Chem Biol Drug Des DOI: 10.1111/cbdd.12834 sha: doc_id: 278456 cord_uid: gsv6dh36 file: cache/cord-286711-nr6vnl9h.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-286711-nr6vnl9h authors: nan title: Other viruses causing gastroenteritis date: 2003-12-31 journal: Perspectives in Medical Virology DOI: 10.1016/s0168-7069(03)09037-2 sha: doc_id: 286711 cord_uid: nr6vnl9h file: cache/cord-291063-de7v4e5s.json key: cord-291063-de7v4e5s authors: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 journal: J Biomed Biotechnol DOI: 10.1155/2009/419539 sha: doc_id: 291063 cord_uid: de7v4e5s file: cache/cord-292830-gcfx1095.json key: cord-292830-gcfx1095 authors: Ianevski, Aleksandr; Zusinaite, Eva; Kuivanen, Suvi; Strand, Mårten; Lysvand, Hilde; Teppor, Mona; Kakkola, Laura; Paavilainen, Henrik; Laajala, Mira; Kallio-Kokko, Hannimari; Valkonen, Miia; Kantele, Anu; Telling, Kaidi; Lutsar, Irja; Letjuka, Pille; Metelitsa, Natalja; Oksenych, Valentyn; Bjørås, Magnar; Nordbø, Svein Arne; Dumpis, Uga; Vitkauskiene, Astra; Öhrmalm, Christina; Bondeson, Kåre; Bergqvist, Anders; Aittokallio, Tero; Cox, Rebecca J.; Evander, Magnus; Hukkanen, Veijo; Marjomaki, Varpu; Julkunen, Ilkka; Vapalahti, Olli; Tenson, Tanel; Merits, Andres; Kainov, Denis title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 journal: Antiviral Res DOI: 10.1016/j.antiviral.2018.04.016 sha: doc_id: 292830 cord_uid: gcfx1095 file: cache/cord-281367-qm5a5c4b.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-281367-qm5a5c4b authors: Des Jarlais, Don C; Johnston, Patrick; Friedmann, Patricia; Kling, Ryan; Liu, Wei; Ngu, Doan; Chen, Yi; Hoang, Tran V; Donghua, Meng; Van, Ly K; Tung, Nguyen D; Binh, Kieu T; Hammett, Theodore M title: Patterns of HIV prevalence among injecting drug users in the cross-border area of Lang Son Province, Vietnam, and Ning Ming County, Guangxi Province, China date: 2005-08-24 journal: BMC Public Health DOI: 10.1186/1471-2458-5-89 sha: doc_id: 281367 cord_uid: qm5a5c4b file: cache/cord-281941-97t45w73.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-281941-97t45w73 authors: Zhou, Daijun; Mei, Qiang; Li, Jintao; He, Haiyang title: Cyclophilin A and viral infections date: 2012-08-10 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2012.07.024 sha: doc_id: 281941 cord_uid: 97t45w73 file: cache/cord-283127-jetmocvk.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-283127-jetmocvk authors: Wang, Denong; Tang, Jin; Tang, Jiulai; Wang, Lai-Xi title: Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date: 2015-03-12 journal: Molecules DOI: 10.3390/molecules20034610 sha: doc_id: 283127 cord_uid: jetmocvk file: cache/cord-284608-ba7wq52t.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-284608-ba7wq52t authors: Sias, Catia; Salichos, Leonidas; Lapa, Daniele; Del Nonno, Franca; Baiocchini, Andrea; Capobianchi, Maria Rosaria; Garbuglia, Anna Rosa title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 journal: Virol J DOI: 10.1186/s12985-019-1132-x sha: doc_id: 284608 cord_uid: ba7wq52t file: cache/cord-285898-rtqkvf63.json key: cord-285898-rtqkvf63 authors: Padberg, Stephanie title: Anti-infective Agents date: 2014-09-29 journal: Drugs During Pregnancy and Lactation DOI: 10.1016/b978-0-12-408078-2.00007-x sha: doc_id: 285898 cord_uid: rtqkvf63 file: cache/cord-292521-tpb12dkq.json key: cord-292521-tpb12dkq authors: Howard, John; Thompson, Thomas Z.; MacArthur, Rodger D.; Rojiani, Amyn M.; White, Joseph title: Widely Disseminated Cryptococcosis Manifesting in a Previously Undiagnosed Human Immunodeficiency Virus (HIV)-Positive 18-Year-Old date: 2020-10-12 journal: Am J Case Rep DOI: 10.12659/ajcr.924410 sha: doc_id: 292521 cord_uid: tpb12dkq file: cache/cord-295062-8rl4kswe.json key: cord-295062-8rl4kswe authors: Marsh, Mark; Helenius, Ari title: Virus Entry: Open Sesame date: 2006-02-24 journal: Cell DOI: 10.1016/j.cell.2006.02.007 sha: doc_id: 295062 cord_uid: 8rl4kswe file: cache/cord-295494-wal0gtrs.json key: cord-295494-wal0gtrs authors: Limeres Posse, Jacobo; Diz Dios, Pedro; Scully, Crispian title: Infection Transmission by Saliva and the Paradoxical Protective Role of Saliva date: 2017-07-31 journal: Saliva Protection and Transmissible Diseases DOI: 10.1016/b978-0-12-813681-2.00001-9 sha: doc_id: 295494 cord_uid: wal0gtrs file: cache/cord-297257-lzybfwc2.json key: cord-297257-lzybfwc2 authors: Savarino, Andrea; Shytaj, Iart Luca title: Chloroquine and beyond: exploring anti-rheumatic drugs to reduce immune hyperactivation in HIV/AIDS date: 2015-06-18 journal: Retrovirology DOI: 10.1186/s12977-015-0178-0 sha: doc_id: 297257 cord_uid: lzybfwc2 file: cache/cord-297530-7zbvgvk8.json key: cord-297530-7zbvgvk8 authors: Kühnert, Denise; Wu, Chieh-Hsi; Drummond, Alexei J. title: Phylogenetic and epidemic modeling of rapidly evolving infectious diseases date: 2011-08-31 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2011.08.005 sha: doc_id: 297530 cord_uid: 7zbvgvk8 file: cache/cord-297303-cpajrgba.json key: cord-297303-cpajrgba authors: Nguyen, Annie L.; Christensen, Christopher; Taylor, Jeff; Brown, Brandon title: Leaning on Community-Based Participatory Research to Respond During COVID-19 date: 2020-05-14 journal: AIDS Behav DOI: 10.1007/s10461-020-02922-1 sha: doc_id: 297303 cord_uid: cpajrgba file: cache/cord-298033-kzdp9edn.json key: cord-298033-kzdp9edn authors: Domingo, Esteban title: Quasispecies dynamics in disease prevention and control date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00008-8 sha: doc_id: 298033 cord_uid: kzdp9edn file: cache/cord-299762-qr6kbwuo.json key: cord-299762-qr6kbwuo authors: Fok, Jelle Anthony; Mayer, Clemens title: Genetic code expansion strategies for vaccine development date: 2020-06-30 journal: Chembiochem DOI: 10.1002/cbic.202000343 sha: doc_id: 299762 cord_uid: qr6kbwuo file: cache/cord-285505-8norumv6.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-285505-8norumv6 authors: Vere Hodge, R. Anthony title: Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA date: 2014-09-16 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.08.009 sha: doc_id: 285505 cord_uid: 8norumv6 file: cache/cord-287949-243xlmep.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-287949-243xlmep authors: Onovo, A. A.; Atobatele, A.; Kalaiwo, A.; Obanubi, C.; James, E.; Gado, P.; Odezugo, G.; Magaji, D.; Ogundehin, D.; Russell, M. title: Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis date: 2020-05-02 journal: nan DOI: 10.1101/2020.04.27.20082057 sha: doc_id: 287949 cord_uid: 243xlmep file: cache/cord-292546-un0blb3w.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-292546-un0blb3w authors: Dandachi, Dima; Geiger, Grant; Montgomery, Mary W; Karmen-Tuohy, Savannah; Golzy, Mojgan; Antar, Annukka A R; Llibre, Josep M; Camazine, Maraya; Díaz-De Santiago, Alberto; Carlucci, Philip M; Zacharioudakis, Ioannis M; Rahimian, Joseph; Wanjalla, Celestine N; Slim, Jihad; Arinze, Folasade; Kratz, Ann Marie Porreca; Jones, Joyce L; Patel, Shital M; Kitchell, Ellen; Francis, Adero; Ray, Manoj; Koren, David E; Baddley, John W; Hill, Brannon; Sax, Paul E; Chow, Jeremy title: Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date: 2020-09-09 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1339 sha: doc_id: 292546 cord_uid: un0blb3w file: cache/cord-293653-u2qrxq6t.json key: cord-293653-u2qrxq6t authors: Watashi, Koichi; Shimotohno, Kunitada title: Cyclophilin and Viruses: Cyclophilin as a Cofactor for Viral Infection and Possible Anti-Viral Target date: 2007-02-05 journal: Drug Target Insights DOI: nan sha: doc_id: 293653 cord_uid: u2qrxq6t file: cache/cord-295290-hs5ntlok.json key: cord-295290-hs5ntlok authors: Atlan, H.; Gersten, M. J.; Salk, P. L.; Salk, J. title: Mechanisms of autoimmunity and AIDS: prospects for therapeutic intervention date: 1994-12-31 journal: Research in Immunology DOI: 10.1016/s0923-2494(94)80181-9 sha: doc_id: 295290 cord_uid: hs5ntlok file: cache/cord-297135-mg2qs3b6.json key: cord-297135-mg2qs3b6 authors: Smith, Kumi; Bartlett, Nicholas; Wang, Ning title: A harm reduction paradox: Comparing China's policies on needle and syringe exchange and methadone maintenance date: 2012-07-31 journal: International Journal of Drug Policy DOI: 10.1016/j.drugpo.2011.09.010 sha: doc_id: 297135 cord_uid: mg2qs3b6 file: cache/cord-300793-tuq8z6gm.json key: cord-300793-tuq8z6gm authors: Weiss, Robin A; McMichael, Anthony J title: Social and environmental risk factors in the emergence of infectious diseases date: 2004 journal: Nat Med DOI: 10.1038/nm1150 sha: doc_id: 300793 cord_uid: tuq8z6gm file: cache/cord-270399-yfko8mpc.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-270399-yfko8mpc authors: Foster, Allison; Khan, Zohaib; Siddiqui, Aisha; Singh, Sukhdev; Atere, Muhammed; Nfonoyim, Jay M title: It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date: 2020-10-15 journal: SAGE Open Med Case Rep DOI: 10.1177/2050313x20965423 sha: doc_id: 270399 cord_uid: yfko8mpc file: cache/cord-286219-qcx5ehnh.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-286219-qcx5ehnh authors: Calistri, Arianna; Munegato, Denis; Carli, Ilaria; Parolin, Cristina; Palù, Giorgio title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 journal: Cells DOI: 10.3390/cells3020386 sha: doc_id: 286219 cord_uid: qcx5ehnh file: cache/cord-286719-1xjmlwqr.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-286719-1xjmlwqr authors: Draz, Mohamed Shehata; Shafiee, Hadi title: Applications of gold nanoparticles in virus detection date: 2018-02-15 journal: Theranostics DOI: 10.7150/thno.23856 sha: doc_id: 286719 cord_uid: 1xjmlwqr file: cache/cord-287348-00yaxpkp.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-287348-00yaxpkp authors: Martinez, Maria Jose Abad; Olmo, Luis Miguel Bedoya Del; Benito, Paulina Bermejo title: Antiviral Activities of Polysaccharides from Natural Sources date: 2005-12-31 journal: Studies in Natural Products Chemistry DOI: 10.1016/s1572-5995(05)80038-9 sha: doc_id: 287348 cord_uid: 00yaxpkp file: cache/cord-293857-o8rlqsq5.json key: cord-293857-o8rlqsq5 authors: Ghosh, Arun K.; Brindisi, Margherita title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 journal: J Med Chem DOI: 10.1021/jm501371s sha: doc_id: 293857 cord_uid: o8rlqsq5 file: cache/cord-296309-i1mpov7k.json key: cord-296309-i1mpov7k authors: Houldcroft, Charlotte J.; Beale, Mathew A.; Breuer, Judith title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro.2016.182 sha: doc_id: 296309 cord_uid: i1mpov7k file: cache/cord-301449-5okb7wf2.json key: cord-301449-5okb7wf2 authors: Nixon, Douglas F. title: Comments on “coinfection of SARS‐CoV‐2 and HIV in a patient in Wuhan city, China” date: 2020-04-08 journal: J Med Virol DOI: 10.1002/jmv.25821 sha: doc_id: 301449 cord_uid: 5okb7wf2 file: cache/cord-289443-46w52de3.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-289443-46w52de3 authors: Sironi, Manuela; Cagliani, Rachele; Forni, Diego; Clerici, Mario title: Evolutionary insights into host–pathogen interactions from mammalian sequence data date: 2015-03-18 journal: Nat Rev Genet DOI: 10.1038/nrg3905 sha: doc_id: 289443 cord_uid: 46w52de3 file: cache/cord-291577-nf80kih2.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-291577-nf80kih2 authors: Baluku, Joseph Baruch; Mwebaza, Shem; Ingabire, Gloria; Nsereko, Chris; Muwanga, Moses title: HIV and SARS‐CoV‐2 co‐infection: A case report from Uganda date: 2020-05-21 journal: J Med Virol DOI: 10.1002/jmv.26044 sha: doc_id: 291577 cord_uid: nf80kih2 file: cache/cord-292740-b4cdj96q.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-292740-b4cdj96q authors: Wahid, Braira; Ali, Amjad; Idrees, Muhammad; Rafique, Shazia title: Immunotherapeutic strategies for sexually transmitted viral infections: HIV, HSV and HPV date: 2016-08-03 journal: Cell Immunol DOI: 10.1016/j.cellimm.2016.08.001 sha: doc_id: 292740 cord_uid: b4cdj96q file: cache/cord-293379-c4qdmkw5.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-293379-c4qdmkw5 authors: Weiss, Robin A title: HIV and AIDS: looking ahead date: 2003 journal: Nat Med DOI: 10.1038/nm0703-887 sha: doc_id: 293379 cord_uid: c4qdmkw5 file: cache/cord-299754-tgexahwd.json key: cord-299754-tgexahwd authors: van Tol, Sarah; Hage, Adam; Giraldo, Maria Isabel; Bharaj, Preeti; Rajsbaum, Ricardo title: The TRIMendous Role of TRIMs in Virus–Host Interactions date: 2017-08-22 journal: Vaccines (Basel) DOI: 10.3390/vaccines5030023 sha: doc_id: 299754 cord_uid: tgexahwd file: cache/cord-301506-q2a5aogo.json key: cord-301506-q2a5aogo authors: Sun, Xinhua; Lu, Fan; Wu, Zunyou; Poundstone, Katharine; Zeng, Gang; Xu, Peng; Zhang, Dapeng; Liu, Kangmai; Liau, Adrian title: Evolution of information-driven HIV/AIDS policies in China date: 2010-12-24 journal: Int J Epidemiol DOI: 10.1093/ije/dyq217 sha: doc_id: 301506 cord_uid: q2a5aogo file: cache/cord-297612-swc2pitd.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-297612-swc2pitd authors: Nosyk, Bohdan; Armstrong, Wendy S; del Rio, Carlos title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US date: 2020-04-27 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa501 sha: doc_id: 297612 cord_uid: swc2pitd file: cache/cord-300522-okbupw61.json key: cord-300522-okbupw61 authors: Sansone, Clementina; Brunet, Christophe; Noonan, Douglas M.; Albini, Adriana title: Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date: 2020-05-07 journal: Antioxidants (Basel) DOI: 10.3390/antiox9050392 sha: doc_id: 300522 cord_uid: okbupw61 file: cache/cord-300642-c7adeis1.json key: cord-300642-c7adeis1 authors: Lai, Andrew SH; Lai, Kar Neng title: Viral nephropathy date: 2006 journal: Nat Clin Pract Nephrol DOI: 10.1038/ncpneph0166 sha: doc_id: 300642 cord_uid: c7adeis1 file: cache/cord-302082-aaokc182.json key: cord-302082-aaokc182 authors: Stanberry, Lawrence R.; Strugnell, Richard title: Vaccines of the future date: 2011-08-31 journal: Perspectives in Vaccinology DOI: 10.1016/j.pervac.2011.05.006 sha: doc_id: 302082 cord_uid: aaokc182 file: cache/cord-302321-6x7hyald.json key: cord-302321-6x7hyald authors: Qiao, Shan; Li, Zhenlong; Weissman, Sharon; Li, Xiaoming; Olatosi, Bankole; Davis, Christal; Mansaray, Ali B. title: Disparity in HIV Service Interruption in the Outbreak of COVID-19 in South Carolina date: 2020-08-27 journal: AIDS Behav DOI: 10.1007/s10461-020-03013-x sha: doc_id: 302321 cord_uid: 6x7hyald file: cache/cord-302784-jkjdglns.json key: cord-302784-jkjdglns authors: Alotaibi, Badriah; Bieh, Kingsley; Yassin, Yara; Mushi, Abdulaziz; Maashi, Fuad; Awam, Amnah; Mohamed, Gamal; Hassan, Amir; Yezli, Saber title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study date: 2019-07-13 journal: Travel Med Infect Dis DOI: 10.1016/j.tmaid.2019.07.007 sha: doc_id: 302784 cord_uid: jkjdglns file: cache/cord-297125-la20vi9j.json key: cord-297125-la20vi9j authors: Brower, Jennifer L. title: The Threat and Response to Infectious Diseases (Revised) date: 2016-08-01 journal: Microb Ecol DOI: 10.1007/s00248-016-0806-9 sha: doc_id: 297125 cord_uid: la20vi9j file: cache/cord-300968-dtaasxk1.json key: cord-300968-dtaasxk1 authors: Kliger, Yossef; Levanon, Erez Y.; Gerber, Doron title: From genome to antivirals: SARS as a test tube date: 2005-03-01 journal: Drug Discovery Today DOI: 10.1016/s1359-6446(04)03320-3 sha: doc_id: 300968 cord_uid: dtaasxk1 file: cache/cord-301349-m4nr3pqx.json key: cord-301349-m4nr3pqx authors: Mirza, Muhammad Usman; Saadabadi, Atefeh; Vanmeert, Michiel; Salo-Ahen, Outi M.H.; Abdullah, Iskandar; Claes, Sandra; De Jonghe, Steven; Schols, Dominique; Ahmad, Sarfraz; Froeyen, Matheus title: Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore‐based virtual screening approach date: 2020-09-02 journal: Eur J Pharm Sci DOI: 10.1016/j.ejps.2020.105537 sha: doc_id: 301349 cord_uid: m4nr3pqx file: cache/cord-301704-mb2oylqb.json key: cord-301704-mb2oylqb authors: Eapen, Paul; Cates, Jennifer; Mundell, Rich; Palmer, Kenneth E.; Fuqua, Joshua L. title: In Preparation for Outdoor Pharming: Griffithsin Can Be Expressed in Nicotiana excelsiana and Retains Activity After Storage as Silage date: 2020-03-18 journal: Front Bioeng Biotechnol DOI: 10.3389/fbioe.2020.00199 sha: doc_id: 301704 cord_uid: mb2oylqb file: cache/cord-302928-nnly9ju8.json key: cord-302928-nnly9ju8 authors: Adachi, Akio title: Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date: 2020-03-18 journal: Front Microbiol DOI: 10.3389/fmicb.2020.00431 sha: doc_id: 302928 cord_uid: nnly9ju8 file: cache/cord-303165-ikepr2p2.json key: cord-303165-ikepr2p2 authors: Tulchinsky, Theodore H.; Varavikova, Elena A. title: Expanding the Concept of Public Health date: 2014-10-10 journal: The New Public Health DOI: 10.1016/b978-0-12-415766-8.00002-1 sha: doc_id: 303165 cord_uid: ikepr2p2 file: cache/cord-295099-ghc85pf5.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-295099-ghc85pf5 authors: Sun, Zehua; Yan, Lixin; Tang, Jiansong; Qian, Qian; Lenberg, Jerica; Zhu, Dandan; Liu, Wan; Wu, Kao; Wang, Yilin; Lu, Shiqiang title: Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies date: 2018-01-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.10.011 sha: doc_id: 295099 cord_uid: ghc85pf5 file: cache/cord-302530-pp6bl941.json key: cord-302530-pp6bl941 authors: Gale, Paul title: How virus size and attachment parameters affect the temperature sensitivity of virus binding to host cells: Predictions of a thermodynamic model for arboviruses and HIV date: 2020-03-12 journal: Microb Risk Anal DOI: 10.1016/j.mran.2020.100104 sha: doc_id: 302530 cord_uid: pp6bl941 file: cache/cord-294366-swwz4kzd.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-294366-swwz4kzd authors: Bramwell, Vincent W.; Perrie, Yvonne title: The rational design of vaccines date: 2005-11-15 journal: Drug Discov Today DOI: 10.1016/s1359-6446(05)03600-7 sha: doc_id: 294366 cord_uid: swwz4kzd file: cache/cord-302403-kahi8cbc.json key: cord-302403-kahi8cbc authors: Miller, Robert F.; Lipman, Marc C.I. title: Pulmonary Infections date: 2009-05-15 journal: Clinical Respiratory Medicine DOI: 10.1016/b978-032304825-5.10034-0 sha: doc_id: 302403 cord_uid: kahi8cbc file: cache/cord-302854-buzyani0.json key: cord-302854-buzyani0 authors: Prabakaran, Ponraj; Zhu, Zhongyu; Chen, Weizao; Gong, Rui; Feng, Yang; Streaker, Emily; Dimitrov, Dimiter S. title: Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing date: 2012-08-02 journal: Front Microbiol DOI: 10.3389/fmicb.2012.00277 sha: doc_id: 302854 cord_uid: buzyani0 file: cache/cord-303189-ktl4jw8v.json key: cord-303189-ktl4jw8v authors: Coccia, Eliana M.; Battistini, Angela title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 journal: Seminars in Immunology DOI: 10.1016/j.smim.2015.03.005 sha: doc_id: 303189 cord_uid: ktl4jw8v file: cache/cord-303208-4bui0ioe.json key: cord-303208-4bui0ioe authors: Jarlais, Don C Des; Arasteh, Kamyar; Gwadz, Marya title: Increasing HIV prevention and care for injecting drug users date: 2010-02-26 journal: Lancet DOI: 10.1016/s0140-6736(10)60314-5 sha: doc_id: 303208 cord_uid: 4bui0ioe file: cache/cord-303408-coesfldm.json key: cord-303408-coesfldm authors: Konstantinova, Pavlina; ter Brake, Olivier; Haasnoot, Joost; de Haan, Peter; Berkhout, Ben title: Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome date: 2007-03-01 journal: Retrovirology DOI: 10.1186/1742-4690-4-15 sha: doc_id: 303408 cord_uid: coesfldm file: cache/cord-304157-u0mlee6u.json key: cord-304157-u0mlee6u authors: Nyasulu, Juliet; Pandya, Himani title: The effects of coronavirus disease 2019 pandemic on the South African health system: A call to maintain essential health services date: 2020-07-22 journal: Afr J Prim Health Care Fam Med DOI: 10.4102/phcfm.v12i1.2480 sha: doc_id: 304157 cord_uid: u0mlee6u file: cache/cord-304873-ppb9k3zu.json key: cord-304873-ppb9k3zu authors: Kang, Hunseung title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 date: 1998-04-01 journal: Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression DOI: 10.1016/s0167-4781(98)00004-9 sha: doc_id: 304873 cord_uid: ppb9k3zu file: cache/cord-304188-1nm1tbig.json key: cord-304188-1nm1tbig authors: Moody, M. Anthony title: Modulation of HIV-1 immunity by adjuvants date: 2014-04-10 journal: Curr Opin HIV AIDS DOI: 10.1097/coh.0000000000000052 sha: doc_id: 304188 cord_uid: 1nm1tbig file: cache/cord-304214-66nxk4e8.json key: cord-304214-66nxk4e8 authors: Sanders, John W.; Ponzio, Todd A. title: Vectored immunoprophylaxis: an emerging adjunct to traditional vaccination date: 2017-02-10 journal: Trop Dis Travel Med Vaccines DOI: 10.1186/s40794-017-0046-0 sha: doc_id: 304214 cord_uid: 66nxk4e8 file: cache/cord-304794-z2kx314h.json key: cord-304794-z2kx314h authors: Métifiot, Mathieu; Amrane, Samir; Litvak, Simon; Andreola, Marie-Line title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 journal: Nucleic Acids Res DOI: 10.1093/nar/gku999 sha: doc_id: 304794 cord_uid: z2kx314h file: cache/cord-304427-r7jt95ko.json key: cord-304427-r7jt95ko authors: Pasquato, A.; Dettin, M.; Basak, A.; Gambaretto, R.; Tonin, L.; Seidah, N.G.; Di Bello, C. title: Heparin enhances the furin cleavage of HIV-1 gp160 peptides date: 2007-12-22 journal: FEBS Lett DOI: 10.1016/j.febslet.2007.11.050 sha: doc_id: 304427 cord_uid: r7jt95ko file: cache/cord-305195-e41yfo89.json key: cord-305195-e41yfo89 authors: Rainwater-Lovett, Kaitlin; Rodriguez-Barraquer, Isabel; Moss, William J. title: Viral Epidemiology: Tracking Viruses with Smartphones and Social Media date: 2016-02-12 journal: Viral Pathogenesis DOI: 10.1016/b978-0-12-800964-2.00018-5 sha: doc_id: 305195 cord_uid: e41yfo89 file: cache/cord-304748-ddwawfv2.json key: cord-304748-ddwawfv2 authors: Mendelsohn, Andrea S.; Ritchwood, Tiarney title: COVID-19 and Antiretroviral Therapies: South Africa’s Charge Towards 90–90–90 in the Midst of a Second Pandemic date: 2020-04-30 journal: AIDS Behav DOI: 10.1007/s10461-020-02898-y sha: doc_id: 304748 cord_uid: ddwawfv2 file: cache/cord-304816-7gg6pxnt.json key: cord-304816-7gg6pxnt authors: Li, Wei; Ma, Qiang; Wang, Xiao; Tang, Min; Lin, Jie; Xiao, Bin title: Letter to the Editor: The characteristics of two patients co‐infected with SARS‐CoV‐2 and HIV in Wuhan, China date: 2020-06-10 journal: J Med Virol DOI: 10.1002/jmv.26155 sha: doc_id: 304816 cord_uid: 7gg6pxnt file: cache/cord-305602-yzc4bosn.json key: cord-305602-yzc4bosn authors: Llano, Manuel; Peña-Hernandez, Mario A. title: Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date: 2018-12-31 journal: Advances in Protein Chemistry and Structural Biology DOI: 10.1016/bs.apcsb.2017.11.001 sha: doc_id: 305602 cord_uid: yzc4bosn file: cache/cord-305394-wwabxlgr.json key: cord-305394-wwabxlgr authors: Venter, W D Francois; Nel, Jeremy title: COVID-19: First data from Africa date: 2020-08-31 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1293 sha: doc_id: 305394 cord_uid: wwabxlgr file: cache/cord-305039-grsv06j7.json key: cord-305039-grsv06j7 authors: Flego, Michela; Ascione, Alessandro; Cianfriglia, Maurizio; Vella, Stefano title: Clinical development of monoclonal antibody-based drugs in HIV and HCV diseases date: 2013-01-04 journal: BMC Med DOI: 10.1186/1741-7015-11-4 sha: doc_id: 305039 cord_uid: grsv06j7 file: cache/cord-306050-y8i8759c.json key: cord-306050-y8i8759c authors: García, Juan Ignacio; Meléndez, Johanna; Álvarez, Rosa; Mejía-Chew, Carlos; Kelley, Holden V.; Sidiki, Sabeen; Castillo, Alejandra; Mazariegos, Claudia; López-Téllez, Cesar; Forno, Diana; Ayala, Nancy; Balada-Llasat, Joan-Miquel; Mejía-Villatoro, Carlos Rodolfo; Wang, Shu-Hua; Torrelles, Jordi B.; Ikeda, Janet title: Accuracy of the tuberculosis point-of-care Alere determine lipoarabinomannan antigen diagnostic test using α-mannosidase treated and untreated urine in a cohort of people living with HIV in Guatemala date: 2020-10-19 journal: AIDS Res Ther DOI: 10.1186/s12981-020-00318-8 sha: doc_id: 306050 cord_uid: y8i8759c file: cache/cord-306315-vt2e0crh.json key: cord-306315-vt2e0crh authors: Elabbadi, Alexandre; Pichon, Jérémie; Visseaux, Benoit; Schnuriger, Aurélie; Bouadma, Lila; Philippot, Quentin; Patrier, Juliette; Labbé, Vincent; Ruckly, Stéphane; Fartoukh, Muriel; Timsit, Jean-François; Voiriot, Guillaume title: Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study) date: 2020-09-14 journal: Ann Intensive Care DOI: 10.1186/s13613-020-00738-9 sha: doc_id: 306315 cord_uid: vt2e0crh file: cache/cord-305085-bv7udg9k.json key: cord-305085-bv7udg9k authors: Lawrence, Robert M. title: Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date: 2011-12-31 journal: Breastfeeding DOI: 10.1016/b978-1-4377-0788-5.10013-6 sha: doc_id: 305085 cord_uid: bv7udg9k file: cache/cord-307817-2vy28i4m.json key: cord-307817-2vy28i4m authors: Lou, Zhiyong; Sun, Yuna; Rao, Zihe title: Current progress in antiviral strategies date: 2014-01-14 journal: Trends Pharmacol Sci DOI: 10.1016/j.tips.2013.11.006 sha: doc_id: 307817 cord_uid: 2vy28i4m file: cache/cord-015324-y44sfr0c.json key: cord-015324-y44sfr0c authors: nan title: Scientific Programme date: 2007-09-01 journal: Pediatr Nephrol DOI: 10.1007/s00467-007-0558-3 sha: doc_id: 15324 cord_uid: y44sfr0c file: cache/cord-309489-ubf55eux.json key: cord-309489-ubf55eux authors: Carvalho, John J. title: OUR COMMON ENEMY: COMBATTING THE WORLD'S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date: 2009-02-19 journal: Zygon DOI: 10.1111/j.1467-9744.2009.00985.x sha: doc_id: 309489 cord_uid: ubf55eux file: cache/cord-309900-4nln90jn.json key: cord-309900-4nln90jn authors: Doornekamp, Laura; Stegers-Jager, Karen M.; Vlek, Odette M.; Klop, Tanja; Goeijenbier, Marco; van Gorp, Eric C. M. title: Experience with a Multinational, Secondary School Education Module with a Focus on Prevention of Virus Infections date: 2017-07-12 journal: Am J Trop Med Hyg DOI: 10.4269/ajtmh.16-0661 sha: doc_id: 309900 cord_uid: 4nln90jn file: cache/cord-311559-vkb7a4cm.json key: cord-311559-vkb7a4cm authors: Kanwugu, Osman N.; Adadi, Parise title: HIV/SARS‐CoV‐2 coinfection: A global perspective date: 2020-07-28 journal: J Med Virol DOI: 10.1002/jmv.26321 sha: doc_id: 311559 cord_uid: vkb7a4cm file: cache/cord-306701-hs9cfdsu.json key: cord-306701-hs9cfdsu authors: Gona, Philimon N.; Gona, Clara M.; Ballout, Suha; Rao, Sowmya R.; Kimokoti, Ruth; Mapoma, Chabila C.; Mokdad, Ali H. title: Burden and changes in HIV/AIDS morbidity and mortality in Southern Africa Development Community Countries, 1990–2017 date: 2020-06-05 journal: BMC Public Health DOI: 10.1186/s12889-020-08988-9 sha: doc_id: 306701 cord_uid: hs9cfdsu file: cache/cord-312167-d16ylykc.json key: cord-312167-d16ylykc authors: Lazzarin, Serena Marita; Cannizzaro, Miryam; Russo, Tommaso; Sangalli, Francesca; Callea, Marcella; Colombo, Bruno; Moiola, Lucia; Filippi, Massimo title: Successful treatment of HIV-associated tumefactive demyelinating lesions with corticosteroids and cyclophosphamide: a case report date: 2020-11-03 journal: J Neurol DOI: 10.1007/s00415-020-10296-6 sha: doc_id: 312167 cord_uid: d16ylykc file: cache/cord-310430-7eww1oet.json key: cord-310430-7eww1oet authors: Singh, Ram Sarup; Thakur, Shivani Rani; Bansal, Parveen title: Algal lectins as promising biomolecules for biomedical research date: 2013-07-16 journal: Crit Rev Microbiol DOI: 10.3109/1040841x.2013.798780 sha: doc_id: 310430 cord_uid: 7eww1oet file: cache/cord-310931-5165078t.json key: cord-310931-5165078t authors: Oppong, Joseph R. title: Globalization of Communicable Diseases date: 2019-12-04 journal: International Encyclopedia of Human Geography DOI: 10.1016/b978-0-08-102295-5.10438-x sha: doc_id: 310931 cord_uid: 5165078t file: cache/cord-312194-1jiaghrb.json key: cord-312194-1jiaghrb authors: Brondani, M.; Donnelly, L. title: The HIV and SARS-CoV-2 Parallel in Dentistry from the Perspectives of the Oral Health Care Team date: 2020-09-18 journal: JDR Clin Trans Res DOI: 10.1177/2380084420961089 sha: doc_id: 312194 cord_uid: 1jiaghrb file: cache/cord-306266-8qdrshz3.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-306266-8qdrshz3 authors: Scully, Crispian title: Respiratory medicine date: 2014-06-25 journal: Scully's Medical Problems in Dentistry DOI: 10.1016/b978-0-7020-5401-3.00015-1 sha: doc_id: 306266 cord_uid: 8qdrshz3 file: cache/cord-311366-uodq4foi.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-311366-uodq4foi authors: Sanyal, Anwesha; Shen, Chengli; Ding, Ming; Reinhart, Todd A.; Chen, Yue; Sankapal, Soni; Gupta, Phalguni title: Neisseria gonorrhoeae uses cellular proteins CXCL10 and IL8 to enhance HIV‐1 transmission across cervical mucosa date: 2019-04-11 journal: Am J Reprod Immunol DOI: 10.1111/aji.13111 sha: doc_id: 311366 cord_uid: uodq4foi file: cache/cord-311679-m6poosn3.json key: cord-311679-m6poosn3 authors: Santos, Glenn-Milo; Ackerman, Benjamin; Rao, Amrita; Wallach, Sara; Ayala, George; Lamontage, Erik; Garner, Alex; Holloway, Ian W.; Arreola, Sonya; Silenzio, Vince; Strömdahl, Susanne; Yu, Louis; Strong, Carol; Adamson, Tyler; Yakusik, Anna; Doan, Tran Thu; Huang, Poyao; Cerasuolo, Damiano; Bishop, Amie; Noori, Teymur; Pharris, Anastasia; Aung, Max; Dara, Masoud; Chung, Ssu Yu; Hanley, Marguerite; Baral, Stefan; Beyrer, Chris; Howell, Sean title: Economic, Mental Health, HIV Prevention and HIV Treatment Impacts of COVID-19 and the COVID-19 Response on a Global Sample of Cisgender Gay Men and Other Men Who Have Sex with Men date: 2020-07-11 journal: AIDS Behav DOI: 10.1007/s10461-020-02969-0 sha: doc_id: 311679 cord_uid: m6poosn3 file: cache/cord-031907-ilhr3iu5.json key: cord-031907-ilhr3iu5 authors: nan title: ISEV2020 Abstract Book date: 2020-07-15 journal: nan DOI: 10.1080/20013078.2020.1784511 sha: doc_id: 31907 cord_uid: ilhr3iu5 file: cache/cord-304251-dohglrm1.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-304251-dohglrm1 authors: Scully, C; Samaranayake, LP title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 journal: Oral Dis DOI: 10.1111/odi.12356 sha: doc_id: 304251 cord_uid: dohglrm1 file: cache/cord-313729-mydyc68y.json key: cord-313729-mydyc68y authors: McDiarmid, Melissa A. title: Hazards of the Health Care Sector: Looking Beyond Infectious Disease date: 2014-11-25 journal: Ann Glob Health DOI: 10.1016/j.aogh.2014.08.001 sha: doc_id: 313729 cord_uid: mydyc68y file: cache/cord-312513-mad9xkz8.json key: cord-312513-mad9xkz8 authors: Iordanou, Stelios; Koukios, Dimitris; Matsentidou, Chrystalla‐Timiliotou; Markoulaki, Despina; Raftopoulos, Vasilios title: Severe SARS‐CoV‐2 pneumonia in a 58‐year‐old patient with HIV: a clinical case report from the Republic of Cyprus date: 2020-05-25 journal: J Med Virol DOI: 10.1002/jmv.26053 sha: doc_id: 312513 cord_uid: mad9xkz8 file: cache/cord-306111-wn1gxhk9.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-306111-wn1gxhk9 authors: Dommett, R. M.; Klein, N; Turner, M. W. title: Mannose‐binding lectin in innate immunity: past, present and future date: 2006-09-01 journal: Tissue Antigens DOI: 10.1111/j.1399-0039.2006.00649.x sha: doc_id: 306111 cord_uid: wn1gxhk9 parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-306972-alyyju5x.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-306972-alyyju5x authors: James, Peter Bai; Wardle, Jonathan; Steel, Amie; Adams, Jon title: An assessment of Ebola-related stigma and its association with informal healthcare utilisation among Ebola survivors in Sierra Leone: a cross-sectional study date: 2020-02-05 journal: BMC Public Health DOI: 10.1186/s12889-020-8279-7 sha: doc_id: 306972 cord_uid: alyyju5x file: cache/cord-310867-78cx3o29.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-310867-78cx3o29 authors: Mo, Phoenix K. H.; Ng, Charlson T. Y. title: Stigmatization among people living with HIV in Hong Kong: A qualitative study date: 2017-02-14 journal: Health Expect DOI: 10.1111/hex.12535 sha: doc_id: 310867 cord_uid: 78cx3o29 file: cache/cord-308916-6p2qutc5.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-308916-6p2qutc5 authors: le Roux, David M.; Zar, Heather J. title: Community-acquired pneumonia in children — a changing spectrum of disease date: 2017-09-21 journal: Pediatr Radiol DOI: 10.1007/s00247-017-3827-8 sha: doc_id: 308916 cord_uid: 6p2qutc5 file: cache/cord-312332-rwmuucsp.json key: cord-312332-rwmuucsp authors: Dicker, Kate; Järvelin, Aino I.; Garcia-Moreno, Manuel; Castello, Alfredo title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.08.002 sha: doc_id: 312332 cord_uid: rwmuucsp file: cache/cord-313617-hh7lccet.json key: cord-313617-hh7lccet authors: Sigel, Keith; Swartz, Talia; Golden, Eddye; Paranjpe, Ishan; Somani, Sulaiman; Richter, Felix; De Freitas, Jessica K; Miotto, Riccardo; Zhao, Shan; Polak, Paz; Mutetwa, Tinaye; Factor, Stephanie; Mehandru, Saurabh; Mullen, Michael; Cossarini, Francesca; Bottinger, Erwin; Fayad, Zahi; Merad, Miriam; Gnjatic, Sacha; Aberg, Judith; Charney, Alexander; Nadkarni, Girish; Glicksberg, Benjamin S title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date: 2020-06-28 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa880 sha: doc_id: 313617 cord_uid: hh7lccet file: cache/cord-317213-vhprfb1o.json key: cord-317213-vhprfb1o authors: Tram, Dai Thien Nhan; Wang, Hao; Sugiarto, Sigit; Li, Tao; Ang, Wee Han; Lee, Chengkuo; Pastorin, Giorgia title: Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases date: 2016-09-26 journal: Biotechnol Adv DOI: 10.1016/j.biotechadv.2016.09.003 sha: doc_id: 317213 cord_uid: vhprfb1o file: cache/cord-318570-wj7r6953.json key: cord-318570-wj7r6953 authors: Xiao, Yinzong; Thompson, Alexander J.; Howell, Jessica title: Point-of-Care Tests for Hepatitis B: An Overview date: 2020-10-02 journal: Cells DOI: 10.3390/cells9102233 sha: doc_id: 318570 cord_uid: wj7r6953 file: cache/cord-314528-5yq95giq.json key: cord-314528-5yq95giq authors: Hirayama, Makoto; Shibata, Hiromi; Imamura, Koji; Sakaguchi, Takemasa; Hori, Kanji title: High-Mannose Specific Lectin and Its Recombinants from a Carrageenophyta Kappaphycus alvarezii Represent a Potent Anti-HIV Activity Through High-Affinity Binding to the Viral Envelope Glycoprotein gp120 date: 2015-12-12 journal: Mar Biotechnol (NY) DOI: 10.1007/s10126-015-9684-2 sha: doc_id: 314528 cord_uid: 5yq95giq file: cache/cord-010092-uftc8inx.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-010092-uftc8inx authors: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 journal: Vox Sang DOI: 10.1111/vox.12792 sha: doc_id: 10092 cord_uid: uftc8inx file: cache/cord-314098-1i6c0l3e.json key: cord-314098-1i6c0l3e authors: Hayward, Joshua A; Tachedjian, Mary; Cui, Jie; Cheng, Adam Z; Johnson, Adam; Baker, Michelle L; Harris, Reuben S; Wang, Lin-Fa; Tachedjian, Gilda title: Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity date: 2018-03-29 journal: Mol Biol Evol DOI: 10.1093/molbev/msy048 sha: doc_id: 314098 cord_uid: 1i6c0l3e file: cache/cord-316273-vo6j8zb0.json key: cord-316273-vo6j8zb0 authors: Cosset, François-Loic; Lavillette, Dimitri title: Cell Entry of Enveloped Viruses date: 2011-02-08 journal: Adv Genet DOI: 10.1016/b978-0-12-380860-8.00004-5 sha: doc_id: 316273 cord_uid: vo6j8zb0 file: cache/cord-314331-7k0oym5i.json key: cord-314331-7k0oym5i authors: Menza, Timothy W.; Garai, Jillian; Ferrer, Joshua; Hecht, Jen title: Rapid Uptake of Home-Based HIV Self-testing During Social Distancing for SARS-CoV2 Infection in Oregon date: 2020-06-27 journal: AIDS Behav DOI: 10.1007/s10461-020-02959-2 sha: doc_id: 314331 cord_uid: 7k0oym5i file: cache/cord-314560-rswa5zdn.json key: cord-314560-rswa5zdn authors: Manjunath, N.; Kumar, Priti; Lee, Sang Kyung; Shankar, Premlata title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 journal: Trends Immunol DOI: 10.1016/j.it.2006.05.006 sha: doc_id: 314560 cord_uid: rswa5zdn file: cache/cord-316789-nb4437qs.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-316789-nb4437qs authors: Omel’yanchuk, L. V.; Yudina, O. S. title: Drosophila melanogaster as a model for studying the function of animal viral proteins date: 2011-07-16 journal: Russ J Genet DOI: 10.1134/s1022795411040090 sha: doc_id: 316789 cord_uid: nb4437qs file: cache/cord-314753-xflhxb13.json key: cord-314753-xflhxb13 authors: Manso, Carmen F.; Bibby, David F.; Mbisa, Jean L. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 journal: Sci Rep DOI: 10.1038/s41598-017-02239-5 sha: doc_id: 314753 cord_uid: xflhxb13 file: cache/cord-317037-1qydcc5e.json key: cord-317037-1qydcc5e authors: Kumar, Asit; Kodidela, Sunitha; Tadrous, Erene; Cory, Theodore James; Walker, Crystal Martin; Smith, Amber Marie; Mukherjee, Ahona; Kumar, Santosh title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 journal: Viruses DOI: 10.3390/v12080887 sha: doc_id: 317037 cord_uid: 1qydcc5e file: cache/cord-318272-spt0oea0.json key: cord-318272-spt0oea0 authors: Bhardwaj, Prateek; Bhatia, Eshant; Sharma, Shivam; Ahamad, Nadim; Banerjee, Rinti title: Advancements in prophylactic and therapeutic nanovaccines date: 2020-04-05 journal: Acta Biomater DOI: 10.1016/j.actbio.2020.03.020 sha: doc_id: 318272 cord_uid: spt0oea0 file: cache/cord-315918-12rbbe8c.json key: cord-315918-12rbbe8c authors: Mukherjee, Pulok K. title: Antiviral Evaluation of Herbal Drugs date: 2019-06-21 journal: Quality Control and Evaluation of Herbal Drugs DOI: 10.1016/b978-0-12-813374-3.00016-8 sha: doc_id: 315918 cord_uid: 12rbbe8c file: cache/cord-317277-rr9zue4l.json key: cord-317277-rr9zue4l authors: Cifuentes-Munoz, Nicolas; El Najjar, Farah; Dutch, Rebecca Ellis title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2020.09.002 sha: doc_id: 317277 cord_uid: rr9zue4l file: cache/cord-317990-61is0hgm.json key: cord-317990-61is0hgm authors: Quinn, Katherine G. title: Applying the Popular Opinion Leader Intervention for HIV to COVID-19 date: 2020-06-25 journal: AIDS Behav DOI: 10.1007/s10461-020-02954-7 sha: doc_id: 317990 cord_uid: 61is0hgm file: cache/cord-318587-ewvnkdr2.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-318587-ewvnkdr2 authors: Steeds, Kimberley; Hall, Yper; Slack, Gillian S.; Longet, Stephanie; Strecker, Thomas; Fehling, Sarah Katharina; Wright, Edward; Bore, Joseph Akoi; Koundouno, Fara Raymond; Konde, Mandy Kader; Hewson, Roger; Hiscox, Julian A.; Pollakis, Georgios; Carroll, Miles W. title: Pseudotyping of VSV with Ebola virus glycoprotein is superior to HIV-1 for the assessment of neutralising antibodies date: 2020-08-31 journal: Sci Rep DOI: 10.1038/s41598-020-71225-1 sha: doc_id: 318587 cord_uid: ewvnkdr2 file: cache/cord-316534-ep7ezoko.json key: cord-316534-ep7ezoko authors: Gamble, Lena J; Matthews, Qiana L title: Current progress in the development of a prophylactic vaccine for HIV-1 date: 2010-12-22 journal: Drug Des Devel Ther DOI: 10.2147/dddt.s6959 sha: doc_id: 316534 cord_uid: ep7ezoko file: cache/cord-315687-stgj6olw.json key: cord-315687-stgj6olw authors: Demma, LJ; Vanderford, TH; Logsdon, JM; Feinberg, MB; Staprans, SI title: Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host date: 2006-03-20 journal: Retrovirology DOI: 10.1186/1742-4690-3-19 sha: doc_id: 315687 cord_uid: stgj6olw file: cache/cord-309515-0pxl0sta.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-309515-0pxl0sta authors: Blanco, Jose L; Ambrosioni, Juan; Garcia, Felipe; Martínez, Esteban; Soriano, Alex; Mallolas, Josep; Miro, Jose M title: COVID-19 in patients with HIV: clinical case series date: 2020-04-15 journal: Lancet HIV DOI: 10.1016/s2352-3018(20)30111-9 sha: doc_id: 309515 cord_uid: 0pxl0sta file: cache/cord-319354-jbain7n6.json key: cord-319354-jbain7n6 authors: Gondim, Ana C. S.; Roberta da Silva, Suzete; Mathys, Leen; Noppen, Sam; Liekens, Sandra; Holanda Sampaio, Alexandre; Nagano, Celso S.; Renata Costa Rocha, Cintia; Nascimento, Kyria S.; Cavada, Benildo S.; Sadler, Peter J.; Balzarini, Jan title: Potent antiviral activity of carbohydrate-specific algal and leguminous lectins from the Brazilian biodiversity date: 2019-01-14 journal: Medchemcomm DOI: 10.1039/c8md00508g sha: doc_id: 319354 cord_uid: jbain7n6 file: cache/cord-318363-1mv5j4w2.json key: cord-318363-1mv5j4w2 authors: Zvolensky, Michael J.; Garey, Lorra; Rogers, Andrew H.; Schmidt, Norman B.; Vujanovic, Anka A.; Storch, Eric A.; Buckner, Julia D.; Paulus, Daniel J.; Alfano, Candice; Smits, Jasper A.J.; O'Cleirigh, Conall title: Psychological, addictive, and health behavior implications of the COVID-19 pandemic date: 2020-08-27 journal: Behav Res Ther DOI: 10.1016/j.brat.2020.103715 sha: doc_id: 318363 cord_uid: 1mv5j4w2 file: cache/cord-320116-63yvpuqx.json key: cord-320116-63yvpuqx authors: Bancroft, Tara; DeBuysscher, Blair L.; Weidle, Connor; Schwartz, Allison; Wall, Abigail; Gray, Matthew D.; Feng, Junli; Steach, Holly R.; Fitzpatrick, Kristin S.; Gewe, Mesfin M.; Skog, Patrick D.; Doyle-Cooper, Colleen; Ota, Takayuki; Strong, Roland K.; Nemazee, David; Pancera, Marie; Stamatatos, Leonidas; McGuire, Andrew T.; Taylor, Justin J. title: Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes date: 2019-10-07 journal: J Exp Med DOI: 10.1084/jem.20190164 sha: doc_id: 320116 cord_uid: 63yvpuqx file: cache/cord-320156-xs936r6u.json key: cord-320156-xs936r6u authors: Nunes, Marta C.; Kuschner, Zachary; Rabede, Zelda; Cutland, Clare L.; Madimabe, Richard; Kuwanda, Locadiah; Klugman, Keith P.; Adrian, Peter V.; Madhi, Shabir A. title: Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children date: 2014-10-28 journal: J Clin Virol DOI: 10.1016/j.jcv.2014.10.013 sha: doc_id: 320156 cord_uid: xs936r6u file: cache/cord-321773-5fw9abzl.json key: cord-321773-5fw9abzl authors: Cheng, Wenyu; Chen, Guohua; Jia, Huaijie; He, Xiaobing; Jing, Zhizhong title: DDX5 RNA Helicases: Emerging Roles in Viral Infection date: 2018-04-09 journal: Int J Mol Sci DOI: 10.3390/ijms19041122 sha: doc_id: 321773 cord_uid: 5fw9abzl file: cache/cord-322256-mv9ll0h4.json key: cord-322256-mv9ll0h4 authors: Edelman, E. Jennifer; Aoun-Barakat, Lydia; Villanueva, Merceditas; Friedland, Gerald title: Confronting Another Pandemic: Lessons from HIV can Inform Our COVID-19 Response date: 2020-05-12 journal: AIDS Behav DOI: 10.1007/s10461-020-02908-z sha: doc_id: 322256 cord_uid: mv9ll0h4 file: cache/cord-319609-y0gdjn64.json key: cord-319609-y0gdjn64 authors: Van Duyne, Rachel; Guendel, Irene; Kehn-Hall, Kylene; Easley, Rebecca; Klase, Zachary; Liu, Chenglong; Young, Mary; Kashanchi, Fatah title: The identification of unique serum proteins of HIV-1 latently infected long-term non-progressor patients date: 2010-07-06 journal: AIDS Res Ther DOI: 10.1186/1742-6405-7-21 sha: doc_id: 319609 cord_uid: y0gdjn64 file: cache/cord-317533-xpfqdeqv.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-317533-xpfqdeqv authors: Smuts, Heidi title: Human coronavirus NL63 infections in infants hospitalised with acute respiratory tract infections in South Africa date: 2008-07-24 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2008.00049.x sha: doc_id: 317533 cord_uid: xpfqdeqv file: cache/cord-317988-1buh1wm0.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-317988-1buh1wm0 authors: Kalichman, Seth C.; Eaton, Lisa A.; Berman, Marcie; Kalichman, Moira O.; Katner, Harold; Sam, Soya S.; Caliendo, Angela M. title: Intersecting Pandemics: Impact of SARS-CoV-2 (COVID-19) Protective Behaviors on People Living With HIV, Atlanta, Georgia date: 2020-06-05 journal: J Acquir Immune Defic Syndr DOI: 10.1097/qai.0000000000002414 sha: doc_id: 317988 cord_uid: 1buh1wm0 file: cache/cord-322503-fynprt6f.json key: cord-322503-fynprt6f authors: Thakur, Aarzoo; Tan, Shawn Pei Feng; Chan, James Chun Yip title: Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date: 2020-08-07 journal: Clin Pharmacol Ther DOI: 10.1002/cpt.2014 sha: doc_id: 322503 cord_uid: fynprt6f file: cache/cord-320832-q1oojklw.json key: cord-320832-q1oojklw authors: Hanum, Nadia; Cambiano, Valentina; Sewell, Janey; Phillips, Andrew N; Rodger, Alison J; Speakman, Andrew; Nwokolo, Nneka; Asboe, David; Gilson, Richard; Clarke, Amanda; Miltz, Ada R; Collins, Simon; Lampe, Fiona C title: Use of HIV pre-exposure prophylaxis among men who have sex with men in England: data from the AURAH2 prospective study date: 2020-09-01 journal: Lancet Public Health DOI: 10.1016/s2468-2667(20)30186-9 sha: doc_id: 320832 cord_uid: q1oojklw file: cache/cord-324034-6cmztvyf.json key: cord-324034-6cmztvyf authors: Ashare, Rebecca L; Bernstein, Steven L; Schnoll, Robert; Gross, Robert; Catz, Sheryl L; Cioe, Patricia; Crothers, Kristina; Hitsman, Brian; Marhefka, Stephanie L; McClure, Jennifer B; Pacek, Lauren R; Vidrine, Damon J; Vilardaga, Roger; Kaufman, Annette; Edelman, E Jennifer title: The United States National Cancer Institute’s Coordinated Research Effort on Tobacco Use as a Major Cause of Morbidity and Mortality among People with HIV date: 2020-08-17 journal: Nicotine Tob Res DOI: 10.1093/ntr/ntaa155 sha: doc_id: 324034 cord_uid: 6cmztvyf file: cache/cord-324829-0nz0qioh.json key: cord-324829-0nz0qioh authors: Carabineiro, Sónia Alexandra Correia title: Applications of Gold Nanoparticles in Nanomedicine: Recent Advances in Vaccines † date: 2017-05-22 journal: Molecules DOI: 10.3390/molecules22050857 sha: doc_id: 324829 cord_uid: 0nz0qioh file: cache/cord-319043-hczwgf6o.json key: cord-319043-hczwgf6o authors: Ashkenazi, Avraham; Viard, Mathias; Unger, Linor; Blumenthal, Robert; Shai, Yechiel title: Sphingopeptides: dihydrosphingosine-based fusion inhibitors against wild-type and enfuvirtide-resistant HIV-1 date: 2012-08-07 journal: The FASEB Journal DOI: 10.1096/fj.12-215111 sha: doc_id: 319043 cord_uid: hczwgf6o file: cache/cord-322915-zrjx31ev.json key: cord-322915-zrjx31ev authors: Demain, Arnold L; Sanchez, Sergio title: Microbial drug discovery: 80 years of progress date: 2009-01-09 journal: J Antibiot (Tokyo) DOI: 10.1038/ja.2008.16 sha: doc_id: 322915 cord_uid: zrjx31ev file: cache/cord-318591-ssnlfjap.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-318591-ssnlfjap authors: Pecego, AC; Amâncio, RT; Costa, DM; Bozza, FA; Siqueira, MM; Oliveira, ML; Cerbino-Neto, J; Japiassu, A title: Etiology, clinical, and epidemiological characteristics of severe respiratory infection in people living with HIV date: 2020-01-22 journal: Int J STD AIDS DOI: 10.1177/0956462419882587 sha: doc_id: 318591 cord_uid: ssnlfjap file: cache/cord-319002-xmsfkaoc.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-319002-xmsfkaoc authors: Brown, James; 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Varavikova, Elena A. title: 4 Communicable Diseases date: 2000-12-31 journal: The New Public Health DOI: 10.1016/b978-012703350-1/50006-1 sha: doc_id: 325300 cord_uid: wawui0fd file: cache/cord-324056-cvvyf3cb.json key: cord-324056-cvvyf3cb authors: Kelley, Patrick W. title: Global Health: Governance and Policy Development date: 2011-06-30 journal: Infectious Disease Clinics of North America DOI: 10.1016/j.idc.2011.02.014 sha: doc_id: 324056 cord_uid: cvvyf3cb file: cache/cord-324690-82qsirnk.json key: cord-324690-82qsirnk authors: Dieffenbach, Carl W; Fauci, Anthony S title: The search for an HIV vaccine, the journey continues date: 2020-05-16 journal: J Int AIDS Soc DOI: 10.1002/jia2.25506 sha: doc_id: 324690 cord_uid: 82qsirnk file: cache/cord-319263-g49jma8n.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-319263-g49jma8n authors: Marziali, Megan E.; Card, Kiffer G.; McLinden, Taylor; Wang, Lu; Trigg, Jason; Hogg, Robert S. title: Physical Distancing in COVID-19 May Exacerbate Experiences of Social Isolation among People Living with HIV date: 2020-04-23 journal: AIDS Behav DOI: 10.1007/s10461-020-02872-8 sha: doc_id: 319263 cord_uid: g49jma8n file: cache/cord-326642-kc85pev4.json key: cord-326642-kc85pev4 authors: Cohen, Adam L.; Sahr, Philip K.; Treurnicht, Florette; Walaza, Sibongile; Groome, Michelle J.; Kahn, Kathleen; Dawood, Halima; Variava, Ebrahim; Tempia, Stefano; Pretorius, Marthi; Moyes, Jocelyn; Olorunju, Steven A. S.; Malope-Kgokong, Babatyi; Kuonza, Lazarus; Wolter, Nicole; von Gottberg, Anne; Madhi, Shabir A.; Venter, Marietjie; Cohen, Cheryl title: Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 date: 2015-09-19 journal: Open Forum Infect Dis DOI: 10.1093/ofid/ofv139 sha: doc_id: 326642 cord_uid: kc85pev4 file: cache/cord-323261-1of5ertf.json key: cord-323261-1of5ertf authors: Lo, Catherine Yuk-ping title: Securitizing HIV/AIDS: a game changer in state-societal relations in China? date: 2018-05-16 journal: Global Health DOI: 10.1186/s12992-018-0364-7 sha: doc_id: 323261 cord_uid: 1of5ertf file: cache/cord-325936-rwxg187r.json key: cord-325936-rwxg187r authors: Eyal, Nir; Halkitis, Perry N. title: AIDS Activism and Coronavirus Vaccine Challenge Trials date: 2020-06-26 journal: AIDS Behav DOI: 10.1007/s10461-020-02953-8 sha: doc_id: 325936 cord_uid: rwxg187r file: cache/cord-328287-3qgzulgj.json key: cord-328287-3qgzulgj authors: Moni, Mohammad Ali; Liò, Pietro title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 journal: BMC Bioinformatics DOI: 10.1186/1471-2105-15-333 sha: doc_id: 328287 cord_uid: 3qgzulgj file: cache/cord-327461-ohgkgvry.json key: cord-327461-ohgkgvry authors: Lu, Ying; Ni, Yuxin; Li, Xiaofeng; He, Xi; Huang, Shanzi; Zhou, Yi; Dai, Wencan; Wu, Dan; Tucker, Joseph D.; Shen, Guangquan; Sha, Yongjie; Jiang, Hongbo; Huang, Liqun; Tang, Weiming title: Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial date: 2020-06-12 journal: BMC Public Health DOI: 10.1186/s12889-020-09048-y sha: doc_id: 327461 cord_uid: ohgkgvry parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-330581-g5r2b043.json key: cord-330581-g5r2b043 authors: Marini, Elena; Tiberio, Laura; Caracciolo, Sonia; Tosti, Giorgio; Guzman, Carlos A.; Schiaffonati, Luisa; Fiorentini, Simona; Caruso, Arnaldo title: HIV‐1 matrix protein p17 binds to monocytes and selectively stimulates MCP‐1 secretion: role of transcriptional factor AP‐1 date: 2007-10-26 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2007.01073.x sha: doc_id: 330581 cord_uid: g5r2b043 file: cache/cord-327135-4c2flue4.json key: cord-327135-4c2flue4 authors: Chinnaswamy, S title: Gene–disease association with human IFNL locus polymorphisms extends beyond hepatitis C virus infections date: 2016-06-09 journal: Genes Immun DOI: 10.1038/gene.2016.24 sha: doc_id: 327135 cord_uid: 4c2flue4 file: cache/cord-330698-9t24jo8s.json key: cord-330698-9t24jo8s authors: Wurdinger, Thomas; Gatson, NaTosha N.; Balaj, Leonora; Kaur, Balveen; Breakefield, Xandra O.; Pegtel, D. Michiel title: Extracellular Vesicles and Their Convergence with Viral Pathways date: 2012-07-25 journal: Adv Virol DOI: 10.1155/2012/767694 sha: doc_id: 330698 cord_uid: 9t24jo8s file: cache/cord-326744-eled2tgo.json key: cord-326744-eled2tgo authors: Millett, Gregorio A.; Honermann, Brian; Jones, Austin; Lankiewicz, Elise; Sherwood, Jennifer; Blumenthal, Susan; Sayas, Asal title: White Counties Stand Apart: The Primacy of Residential Segregation in COVID-19 and HIV Diagnoses date: 2020-10-01 journal: AIDS Patient Care STDS DOI: 10.1089/apc.2020.0155 sha: doc_id: 326744 cord_uid: eled2tgo file: cache/cord-330465-16j5vm7h.json key: cord-330465-16j5vm7h authors: Marciniec, Krzysztof; Chrobak, Elwira; Dąbrowska, Aleksandra; Bębenek, Ewa; Kadela-Tomanek, Monika; Pęcak, Paweł; Boryczka, Stanisław title: Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date: 2020-08-05 journal: Biomolecules DOI: 10.3390/biom10081148 sha: doc_id: 330465 cord_uid: 16j5vm7h file: cache/cord-331673-xv1tcugl.json key: cord-331673-xv1tcugl authors: Reina, Giacomo; Peng, Shiyuan; Jacquemin, Lucas; Andrade, Andrés Felipe; Bianco, Alberto title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 journal: ACS Nano DOI: 10.1021/acsnano.0c04117 sha: doc_id: 331673 cord_uid: xv1tcugl file: cache/cord-329361-0mpbau1b.json key: cord-329361-0mpbau1b authors: Bennasser, Yamina; Yeung, Man Lung; Jeang, Kuan-Teh title: RNAi Therapy for HIV Infection: Principles and Practicalities date: 2012-08-16 journal: BioDrugs DOI: 10.2165/00063030-200721010-00003 sha: doc_id: 329361 cord_uid: 0mpbau1b file: cache/cord-329223-f84gjxm1.json key: cord-329223-f84gjxm1 authors: Kouokam, Joseph Calvin; Huskens, Dana; Schols, Dominique; Johannemann, Andrew; Riedell, Shonna K.; Walter, Wendye; Walker, Janice M.; Matoba, Nobuyuki; O'Keefe, Barry R.; Palmer, Kenneth E. title: Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date: 2011-08-02 journal: PLoS One DOI: 10.1371/journal.pone.0022635 sha: doc_id: 329223 cord_uid: f84gjxm1 file: cache/cord-332569-af8oq2d6.json key: cord-332569-af8oq2d6 authors: Friedman, Henry; Ator, Nancy; Haigwood, Nancy; Newsome, William; Allan, James S.; Golos, Thaddeus G.; Kordower, Jeff H.; Shade, Robert E.; Goldberg, Michael E.; Bailey, Matthew R.; Bianchi, Paul title: The Critical Role of Nonhuman Primates in Medical Research date: 2017-08-23 journal: Pathog Immun DOI: 10.20411/pai.v2i3.186 sha: doc_id: 332569 cord_uid: af8oq2d6 file: cache/cord-329890-wg23sa1u.json key: cord-329890-wg23sa1u authors: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 journal: Health Policy DOI: 10.1016/j.healthpol.2006.03.002 sha: doc_id: 329890 cord_uid: wg23sa1u file: cache/cord-330970-6kkqoh7f.json key: cord-330970-6kkqoh7f authors: Weiss, Robin A title: Apes, lice and prehistory date: 2009-02-10 journal: J Biol DOI: 10.1186/jbiol114 sha: doc_id: 330970 cord_uid: 6kkqoh7f file: cache/cord-332610-t99l3zii.json key: cord-332610-t99l3zii authors: Mayer, J.D. title: Emerging Diseases: Overview date: 2008-08-26 journal: International Encyclopedia of Public Health DOI: 10.1016/b978-012373960-5.00453-6 sha: doc_id: 332610 cord_uid: t99l3zii file: cache/cord-333405-ji58jbct.json key: cord-333405-ji58jbct authors: Morens, David M.; Folkers, Gregory K.; Fauci, Anthony S. title: The challenge of emerging and re-emerging infectious diseases date: 2004-07-08 journal: Nature DOI: 10.1038/nature02759 sha: doc_id: 333405 cord_uid: ji58jbct file: cache/cord-333730-qsx0m68e.json key: cord-333730-qsx0m68e authors: Tsai, Y. C.; Tsai, T. F. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 journal: Ther Adv Musculoskelet Dis DOI: 10.1177/1759720x20947296 sha: doc_id: 333730 cord_uid: qsx0m68e file: cache/cord-332588-k4tghibp.json key: cord-332588-k4tghibp authors: D’Alessandro, Sarah; Scaccabarozzi, Diletta; Signorini, Lucia; Perego, Federica; Ilboudo, Denise P.; Ferrante, Pasquale; Delbue, Serena title: The Use of Antimalarial Drugs against Viral Infection date: 2020-01-08 journal: Microorganisms DOI: 10.3390/microorganisms8010085 sha: doc_id: 332588 cord_uid: k4tghibp file: cache/cord-331879-w7008uyy.json key: cord-331879-w7008uyy authors: Iversen, Jenny; Sabin, Keith; Chang, Judy; Morgan Thomas, Ruth; Prestage, Garrett; Strathdee, Steffanie A; Maher, Lisa title: COVID‐19, HIV and key populations: cross‐cutting issues and the need for population‐specific responses date: 2020-10-01 journal: J Int AIDS Soc DOI: 10.1002/jia2.25632 sha: doc_id: 331879 cord_uid: w7008uyy file: cache/cord-329396-cl28bjnd.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-329396-cl28bjnd authors: Carrico, Adam W.; Horvath, Keith J.; Grov, Christian; Moskowitz, Judith T.; Pahwa, Savita; Pallikkuth, Suresh; Hirshfield, Sabina title: Double Jeopardy: Methamphetamine Use and HIV as Risk Factors for COVID-19 date: 2020-04-07 journal: AIDS Behav DOI: 10.1007/s10461-020-02854-w sha: doc_id: 329396 cord_uid: cl28bjnd file: cache/cord-332396-nattdect.json key: cord-332396-nattdect authors: Ejima, K.; Koizumi, Y.; Yamamoto, N.; Rosenberg, M.; Ludema, C.; Bento, A. I.; Yoneoka, D.; Ichikawa, S.; Mizushima, D.; Iwami, S. title: HIV testing by public health centers and municipalities, and new HIV cases during the COVID-19 pandemic in Japan date: 2020-10-18 journal: nan DOI: 10.1101/2020.10.16.20213959 sha: doc_id: 332396 cord_uid: nattdect file: cache/cord-330800-s91zfzfi.json key: cord-330800-s91zfzfi authors: Reta, Daniel Hussien; Tessema, Tesfaye Sisay; Ashenef, Addis Simachew; Desta, Adey Feleke; Labisso, Wajana Lako; Gizaw, Solomon Tebeje; Abay, Solomon Mequanente; Melka, Daniel Seifu; Reta, Fisseha Alemu title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 journal: Int J Microbiol DOI: 10.1155/2020/8832728 sha: doc_id: 330800 cord_uid: s91zfzfi file: cache/cord-338594-wft7yy6j.json key: cord-338594-wft7yy6j authors: Winkler, Michael; Gärtner, Sabine; Wrensch, Florian; Krawczak, Michael; Sauermann, Ulrike; Pöhlmann, Stefan title: Rhesus macaque IFITM3 gene polymorphisms and SIV infection date: 2017-03-03 journal: PLoS One DOI: 10.1371/journal.pone.0172847 sha: doc_id: 338594 cord_uid: wft7yy6j file: cache/cord-331289-02411gfv.json key: cord-331289-02411gfv authors: Di Minno, Giovanni; Perno, Carlo Federico; Tiede, Andreas; Navarro, David; Canaro, Mariana; Güertler, Lutz; Ironside, James W. title: Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date: 2015-07-20 journal: Blood Rev DOI: 10.1016/j.blre.2015.07.004 sha: doc_id: 331289 cord_uid: 02411gfv file: cache/cord-334104-mphz1aye.json key: cord-334104-mphz1aye authors: Apisarnthanarak, Anucha; Mundy, Linda M. title: Etiology of Community-Acquired Pneumonia date: 2005-03-28 journal: Clin Chest Med DOI: 10.1016/j.ccm.2004.10.016 sha: doc_id: 334104 cord_uid: mphz1aye file: cache/cord-334855-s0ci3r8w.json key: cord-334855-s0ci3r8w authors: Andersen, Petter I.; Krpina, Klara; Ianevski, Aleksandr; Shtaida, Nastassia; Jo, Eunji; Yang, Jaewon; Koit, Sandra; Tenson, Tanel; Hukkanen, Veijo; Anthonsen, Marit W.; Bjoras, Magnar; Evander, Magnus; Windisch, Marc P.; Zusinaite, Eva; Kainov, Denis E. title: Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date: 2019-10-18 journal: Viruses DOI: 10.3390/v11100964 sha: doc_id: 334855 cord_uid: s0ci3r8w file: cache/cord-338438-q5fis2v8.json key: cord-338438-q5fis2v8 authors: Young, Sean D.; Schneider, John title: Clinical Care, Research, and Telehealth Services in the Era of Social Distancing to Mitigate COVID-19 date: 2020-05-21 journal: AIDS Behav DOI: 10.1007/s10461-020-02924-z sha: doc_id: 338438 cord_uid: q5fis2v8 file: cache/cord-332093-iluqwwxs.json key: cord-332093-iluqwwxs authors: Lessler, Justin; Cummings, Derek A. T. title: Mechanistic Models of Infectious Disease and Their Impact on Public Health date: 2016-02-17 journal: American Journal of Epidemiology DOI: 10.1093/aje/kww021 sha: doc_id: 332093 cord_uid: iluqwwxs file: cache/cord-338804-nreqluol.json key: cord-338804-nreqluol authors: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.00079-9 sha: doc_id: 338804 cord_uid: nreqluol file: cache/cord-330852-n7j0c4ne.json key: cord-330852-n7j0c4ne authors: Fischer, Wolfgang B.; Wang, Yi-Ting; Schindler, Christina; Chen, Chin-Pei title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 journal: Int Rev Cell Mol Biol DOI: 10.1016/b978-0-12-394305-7.00006-9 sha: doc_id: 330852 cord_uid: n7j0c4ne file: cache/cord-337720-kmwft059.json key: cord-337720-kmwft059 authors: Closson, Kalysha; Lee, Melanie; Gibbs, Andrew; Kaida, Angela title: When Home is Not a Safe Place: Impacts of Social Distancing Directives on Women Living with HIV date: 2020-06-02 journal: AIDS Behav DOI: 10.1007/s10461-020-02941-y sha: doc_id: 337720 cord_uid: kmwft059 file: cache/cord-337315-qv8ycdhe.json key: cord-337315-qv8ycdhe authors: Miller, Maureen; Hagan, Emily title: Integrated biological–behavioural surveillance in pandemic-threat warning systems date: 2017-01-01 journal: Bull World Health Organ DOI: 10.2471/blt.16.175984 sha: doc_id: 337315 cord_uid: qv8ycdhe file: cache/cord-337897-hkvll3xh.json key: cord-337897-hkvll3xh authors: Yang, Zheng Rong title: Peptide Bioinformatics- Peptide Classification Using Peptide Machines date: 2009 journal: Artificial Neural Networks DOI: 10.1007/978-1-60327-101-1_9 sha: doc_id: 337897 cord_uid: hkvll3xh file: cache/cord-334454-cqaado3u.json key: cord-334454-cqaado3u authors: Leal, Rodolfo Oliveira; Gil, Solange title: The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives date: 2016-10-27 journal: Vet Sci DOI: 10.3390/vetsci3040032 sha: doc_id: 334454 cord_uid: cqaado3u file: cache/cord-339341-c2o42b5j.json key: cord-339341-c2o42b5j authors: Matibag, Gino C.; Igarashi, Manabu; La Porte, Ron E.; Tamashiro, Hiko title: Advocacy, promotion and e-learning: Supercourse for zoonosis date: 2005-09-01 journal: Environmental Health and Preventive Medicine DOI: 10.1007/bf02897702 sha: doc_id: 339341 cord_uid: c2o42b5j file: cache/cord-326725-0jgw083h.json key: cord-326725-0jgw083h authors: Klamroth, Robert; Gröner, Albrecht; Simon, Toby L. title: Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date: 2013-09-30 journal: Transfusion DOI: 10.1111/trf.12423 sha: doc_id: 326725 cord_uid: 0jgw083h file: cache/cord-333622-0ddutmdd.json key: cord-333622-0ddutmdd authors: Dyer, Wayne B; Zaunders, John J; Yuan, Fang Fang; Wang, Bin; Learmont, Jennifer C; Geczy, Andrew F; Saksena, Nitin K; McPhee, Dale A; Gorry, Paul R; Sullivan, John S title: Mechanisms of HIV non-progression; robust and sustained CD4+ T-cell proliferative responses to p24 antigen correlate with control of viraemia and lack of disease progression after long-term transfusion-acquired HIV-1 infection date: 2008-12-11 journal: Retrovirology DOI: 10.1186/1742-4690-5-112 sha: doc_id: 333622 cord_uid: 0ddutmdd file: cache/cord-337458-dc90ecfe.json key: cord-337458-dc90ecfe authors: Markwalter, Christine F.; Kantor, Andrew G.; Moore, Carson P.; Richardson, Kelly A.; Wright, David W. title: Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date: 2018-12-04 journal: Chem Rev DOI: 10.1021/acs.chemrev.8b00136 sha: doc_id: 337458 cord_uid: dc90ecfe file: cache/cord-338654-ma9ayu80.json key: cord-338654-ma9ayu80 authors: Eaton, Lisa A.; Kalichman, Seth C. title: Social and behavioral health responses to COVID-19: lessons learned from four decades of an HIV pandemic date: 2020-04-25 journal: J Behav Med DOI: 10.1007/s10865-020-00157-y sha: doc_id: 338654 cord_uid: ma9ayu80 file: cache/cord-333655-lylt7qld.json key: cord-333655-lylt7qld authors: Van Breedam, Wander; Pöhlmann, Stefan; Favoreel, Herman W.; de Groot, Raoul J.; Nauwynck, Hans J. title: Bitter‐sweet symphony: glycan–lectin interactions in virus biology date: 2013-12-06 journal: FEMS Microbiol Rev DOI: 10.1111/1574-6976.12052 sha: doc_id: 333655 cord_uid: lylt7qld file: cache/cord-334010-gxu0refq.json key: cord-334010-gxu0refq authors: Banerjee, Nilotpal; Mukhopadhyay, Sumi title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 journal: VirusDisease DOI: 10.1007/s13337-015-0293-5 sha: doc_id: 334010 cord_uid: gxu0refq file: cache/cord-340703-vtuy806l.json key: cord-340703-vtuy806l authors: Cascio, Antonio; Colomba, Claudia; Di Carlo, Paola; Serra, Nicola; Lo Re, Giuseppe; Gambino, Angelo; Lo Casto, Antonio; Guglielmi, Giuseppe; Veronese, Nicola; Lagalla, Roberto; Sergi, Consolato title: Low bone mineral density in HIV-positive young Italians and migrants date: 2020-09-03 journal: PLoS One DOI: 10.1371/journal.pone.0237984 sha: doc_id: 340703 cord_uid: vtuy806l file: cache/cord-334133-61om170g.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334133-61om170g authors: Hollier, Mark J.; Dimmock, Nigel J. title: The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date: 2005-07-05 journal: Virology DOI: 10.1016/j.virol.2005.04.015 sha: doc_id: 334133 cord_uid: 61om170g file: cache/cord-340489-yo3cp5vs.json key: cord-340489-yo3cp5vs authors: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 journal: Innere Medizin DOI: 10.1016/b978-3-437-42831-9.10013-0 sha: doc_id: 340489 cord_uid: yo3cp5vs file: cache/cord-340619-3tjquzx8.json key: cord-340619-3tjquzx8 authors: Menghua, Wu; Xin, Zheng; Jianwei, Liu; Yu, Zhang; Qinwei, Yao title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date: 2020-07-23 journal: AIDS Res Ther DOI: 10.1186/s12981-020-00301-3 sha: doc_id: 340619 cord_uid: 3tjquzx8 file: cache/cord-340389-0fybiybv.json key: cord-340389-0fybiybv authors: Fahrioglu, Umut; Ergoren, Mahmut Cerkez; Mocan, Gamze title: CCR5-Δ32 gene variant frequency in the Turkish Cypriot population date: 2020-07-31 journal: Braz J Microbiol DOI: 10.1007/s42770-020-00352-8 sha: doc_id: 340389 cord_uid: 0fybiybv file: cache/cord-341304-jdvzpvdx.json key: cord-341304-jdvzpvdx authors: Pata, Rama Kanth; Ahmady, Abolfazl; Kiani, Roudabeh title: Human Immunodeficiency Virus: A Dark Cloud With Silver Lining During the COVID-19 Pandemic date: 2020-07-20 journal: Cureus DOI: 10.7759/cureus.9302 sha: doc_id: 341304 cord_uid: jdvzpvdx file: cache/cord-341503-3cvtoc2j.json key: cord-341503-3cvtoc2j authors: Jaiswal, J.; LoSchiavo, C.; Perlman, D. C. title: Disinformation, Misinformation and Inequality-Driven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism date: 2020-05-21 journal: AIDS Behav DOI: 10.1007/s10461-020-02925-y sha: doc_id: 341503 cord_uid: 3cvtoc2j file: cache/cord-329482-haenltxn.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-329482-haenltxn authors: Small, Eusebius; Sharma, Bonita B.; Nikolova, Silviya Pavlova title: Covid-19 and Gender in LMICs: Potential Lessons from HIV Pandemic date: 2020-05-25 journal: AIDS Behav DOI: 10.1007/s10461-020-02932-z sha: doc_id: 329482 cord_uid: haenltxn file: cache/cord-344084-z4t2wkgk.json key: cord-344084-z4t2wkgk authors: Ellwanger, Joel Henrique; Kulmann-Leal, Bruna; Kaminski, Valéria de Lima; Rodrigues, Andressa Gonçalves; de Souza Bragatte, Marcelo Alves; Chies, José Artur Bogo title: Beyond HIV infection: neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases date: 2020-05-30 journal: Virus Res DOI: 10.1016/j.virusres.2020.198040 sha: doc_id: 344084 cord_uid: z4t2wkgk file: cache/cord-340879-gu91cact.json key: cord-340879-gu91cact authors: Li, Miao; Liu, Qin; Cui, Yajuan; Li, Dong; Wang, Hexiang; Ng, Tzi Bun title: Isolation and Characterization of a Phaseolus vulgaris Trypsin Inhibitor with Antiproliferative Activity on Leukemia and Lymphoma Cells date: 2017-01-23 journal: Molecules DOI: 10.3390/molecules22010187 sha: doc_id: 340879 cord_uid: gu91cact file: cache/cord-341323-mw352rr1.json key: cord-341323-mw352rr1 authors: Logie, Carmen H title: Lessons learned from HIV can inform our approach to COVID‐19 stigma date: 2020-05-04 journal: J Int AIDS Soc DOI: 10.1002/jia2.25504 sha: doc_id: 341323 cord_uid: mw352rr1 file: cache/cord-340763-cxnu9g8y.json key: cord-340763-cxnu9g8y authors: Grimm, Sebastian K.; Battles, Michael B.; Ackerman, Margaret E. title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date: 2015-02-17 journal: PLoS One DOI: 10.1371/journal.pone.0117227 sha: doc_id: 340763 cord_uid: cxnu9g8y file: cache/cord-346557-s6c7d70y.json key: cord-346557-s6c7d70y authors: Brennan, David J.; Card, Kiffer G.; Collict, David; Jollimore, Jody; Lachowsky, Nathan J. title: How Might Social Distancing Impact Gay, Bisexual, Queer, Trans and Two-Spirit Men in Canada? date: 2020-04-30 journal: AIDS Behav DOI: 10.1007/s10461-020-02891-5 sha: doc_id: 346557 cord_uid: s6c7d70y file: cache/cord-339879-92esdjy9.json key: cord-339879-92esdjy9 authors: Delhalle, Sylvie; Schmit, Jean-Claude; Chevigné, Andy title: Phages and HIV-1: From Display to Interplay date: 2012-04-13 journal: Int J Mol Sci DOI: 10.3390/ijms13044727 sha: doc_id: 339879 cord_uid: 92esdjy9 file: cache/cord-342719-bdxb45us.json key: cord-342719-bdxb45us authors: Yamamoto, Shinya; Saito, Makoto; Nagai, Etsuko; Toriuchi, Keiko; Nagai, Hiroyuki; Yotsuyanagi, Hiroshi; Nakagama, Yu; Kido, Yasutoshi; Adachi, Eisuke title: Antibody Response to SARS-CoV-2 in people living with HIV date: 2020-10-02 journal: J Microbiol Immunol Infect DOI: 10.1016/j.jmii.2020.09.005 sha: doc_id: 342719 cord_uid: bdxb45us file: cache/cord-345771-3v2avxiv.json key: cord-345771-3v2avxiv authors: Traub, Ariana Moriah; Ifafore-Calfee, Temitayo; Phelps, Benjamin Ryan title: Multimonth Dispensing of Antiretroviral Therapy Protects the Most Vulnerable From 2 Pandemics at Once date: 2020-06-30 journal: Glob Health Sci Pract DOI: 10.9745/ghsp-d-20-00160 sha: doc_id: 345771 cord_uid: 3v2avxiv file: cache/cord-340777-d1vwjqk6.json key: cord-340777-d1vwjqk6 authors: O’Byrne, Patrick; Orser, Lauren; Vandyk, Amanda title: Immediate PrEP after PEP: Results from an Observational Nurse-Led PEP2PrEP Study date: 2020-08-28 journal: J Int Assoc Provid AIDS Care DOI: 10.1177/2325958220939763 sha: doc_id: 340777 cord_uid: d1vwjqk6 file: cache/cord-339796-gccnvh0z.json key: cord-339796-gccnvh0z authors: Zhang, Si Min; Jejcic, Alenka; Tam, James P.; Vahlne, Anders title: Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date: 2015-07-31 journal: PLoS One DOI: 10.1371/journal.pone.0134851 sha: doc_id: 339796 cord_uid: gccnvh0z file: cache/cord-341097-c96hm610.json key: cord-341097-c96hm610 authors: Mayer, Craig S.; Williams, Nick; Huser, Vojtech title: Analysis of data dictionary formats of HIV clinical trials date: 2020-10-05 journal: PLoS One DOI: 10.1371/journal.pone.0240047 sha: doc_id: 341097 cord_uid: c96hm610 file: cache/cord-341298-mqpovrms.json key: cord-341298-mqpovrms authors: Morse, S.A.; Meyer, R.F. title: Viruses and Bioterrorism date: 2016-10-31 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.11007-6 sha: doc_id: 341298 cord_uid: mqpovrms file: cache/cord-342936-43u7afl3.json key: cord-342936-43u7afl3 authors: Balzarini, Jan title: Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date: 2007 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro1707 sha: doc_id: 342936 cord_uid: 43u7afl3 file: cache/cord-337659-x4oywbrj.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-337659-x4oywbrj authors: Wilson, Brenda A. title: Global biosecurity in a complex, dynamic world date: 2008-07-31 journal: Complexity DOI: 10.1002/cplx.20246 sha: doc_id: 337659 cord_uid: x4oywbrj file: cache/cord-346424-gfccstoz.json key: cord-346424-gfccstoz authors: Friedrich, Brian M; Murray, James L; Li, Guangyu; Sheng, Jinsong; Hodge, Thomas W; Rubin, Donald H; O'Brien, William A; Ferguson, Monique R title: A Functional Role for ADAM10 in Human Immunodeficiency Virus Type-1 Replication date: 2011-05-11 journal: Retrovirology DOI: 10.1186/1742-4690-8-32 sha: doc_id: 346424 cord_uid: gfccstoz file: cache/cord-343470-w215pzdc.json key: cord-343470-w215pzdc authors: Tsai, Kevin; Cullen, Bryan R. title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 journal: Nat Rev Microbiol DOI: 10.1038/s41579-020-0382-3 sha: doc_id: 343470 cord_uid: w215pzdc file: cache/cord-349104-p0egfpx9.json key: cord-349104-p0egfpx9 authors: Modi, Anita R.; Koval, Christine E.; Taege, Alan J.; Modaresi Esfeh, Jamak; Eghtesad, Bijan; Narayanan Menon, K. V.; Quintini, Cristiano; Miller, Charles title: Coronavirus disease 2019 in an orthotopic liver transplant recipient living with human immunodeficiency virus date: 2020-06-17 journal: Transpl Infect Dis DOI: 10.1111/tid.13351 sha: doc_id: 349104 cord_uid: p0egfpx9 file: cache/cord-351004-h6fde7vm.json key: cord-351004-h6fde7vm authors: Gudipati, Smitha; Brar, Indira; Murray, Shannon; McKinnon, John E.; Yared, Nicholas; Markowitz, Norman title: Descriptive Analysis of Patients Living With HIV Affected by COVID-19 date: 2020-07-13 journal: J Acquir Immune Defic Syndr DOI: 10.1097/qai.0000000000002450 sha: doc_id: 351004 cord_uid: h6fde7vm file: cache/cord-341838-lkz8ro90.json key: cord-341838-lkz8ro90 authors: Gervasoni, Cristina; Meraviglia, Paola; Riva, Agostino; Giacomelli, Andrea; Oreni, Letizia; Minisci, Davide; Atzori, Chiara; Ridolfo, Annalisa; Cattaneo, Dario title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa579 sha: doc_id: 341838 cord_uid: lkz8ro90 file: cache/cord-338572-5ifc2lx6.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-338572-5ifc2lx6 authors: Nagarakanti, Sandhya R.; Okoh, Alexis K; Grinberg, Sagy; Bishburg, Eliahu title: Clinical outcomes of patients with COVID‐19 and HIV coinfection date: 2020-09-19 journal: J Med Virol DOI: 10.1002/jmv.26533 sha: doc_id: 338572 cord_uid: 5ifc2lx6 file: cache/cord-351740-779g8tr1.json key: cord-351740-779g8tr1 authors: Khaba, Moshawa Calvin; Ngale, Tshepo Cletus; Madala, Nomandla title: COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date: 2020-09-25 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.09.1435 sha: doc_id: 351740 cord_uid: 779g8tr1 file: cache/cord-342076-3a6aky7i.json key: cord-342076-3a6aky7i authors: Zhang, Lei; Fung Chow, Eric Pui; Zhang, Jun; Jing, Jun; Wilson, David P title: Describing the Chinese HIV Surveillance System and the Influences of Political Structures and Social Stigma date: 2012-09-07 journal: Open AIDS J DOI: 10.2174/1874613601206010163 sha: doc_id: 342076 cord_uid: 3a6aky7i file: cache/cord-346314-o9fjpqaj.json key: cord-346314-o9fjpqaj authors: Jarboui, Mohamed Ali; Bidoia, Carlo; Woods, Elena; Roe, Barbara; Wynne, Kieran; Elia, Giuliano; Hall, William W.; Gautier, Virginie W. title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 journal: PLoS One DOI: 10.1371/journal.pone.0048702 sha: doc_id: 346314 cord_uid: o9fjpqaj file: cache/cord-353895-tgn1kk07.json key: cord-353895-tgn1kk07 authors: Kavanagh, Matthew M; Katz, Ingrid T; Holmes, Charles B title: Reckoning with mortality: global health, HIV, and the politics of data date: 2020-07-03 journal: Lancet DOI: 10.1016/s0140-6736(20)31046-1 sha: doc_id: 353895 cord_uid: tgn1kk07 file: cache/cord-350540-s6is9ndm.json key: cord-350540-s6is9ndm authors: Pinto, Rogério M.; Park, Sunggeun title: COVID-19 Pandemic Disrupts HIV Continuum of Care and Prevention: Implications for Research and Practice Concerning Community-Based Organizations and Frontline Providers date: 2020-04-28 journal: AIDS Behav DOI: 10.1007/s10461-020-02893-3 sha: doc_id: 350540 cord_uid: s6is9ndm file: cache/cord-341155-3d64mso0.json key: cord-341155-3d64mso0 authors: Slots, Jørgen; Slots, Henrik title: Bacterial and viral pathogens in saliva: disease relationship and infectious risk date: 2010-12-07 journal: Periodontol 2000 DOI: 10.1111/j.1600-0757.2010.00361.x sha: doc_id: 341155 cord_uid: 3d64mso0 file: cache/cord-345342-04tvuj9f.json key: cord-345342-04tvuj9f authors: Kumar, Rebecca N.; Tanna, Sajal D.; Shetty, Aneesha A.; Stosor, Valentina title: COVID‐19 in an HIV‐positive Kidney Transplant Recipient date: 2020-05-26 journal: Transpl Infect Dis DOI: 10.1111/tid.13338 sha: doc_id: 345342 cord_uid: 04tvuj9f file: cache/cord-354374-rtgjjglc.json key: cord-354374-rtgjjglc authors: C.G. Pollok, Richard; J.G. Farthing, Michael title: Enteric viruses in HIV-related diarrhoea date: 2000-12-01 journal: Mol Med Today DOI: 10.1016/s1357-4310(00)01816-5 sha: doc_id: 354374 cord_uid: rtgjjglc file: cache/cord-347356-uc9dqhyq.json key: cord-347356-uc9dqhyq authors: Cooper, TJ; Woodward, BL; Alom, S; Harky, A title: Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date: 2020-07-15 journal: HIV Med DOI: 10.1111/hiv.12911 sha: doc_id: 347356 cord_uid: uc9dqhyq file: cache/cord-349790-dezauioa.json key: cord-349790-dezauioa authors: Johnson, Stephanie; Parker, Michael title: Ethical challenges in pathogen sequencing: a systematic scoping review date: 2020-06-03 journal: Wellcome Open Res DOI: 10.12688/wellcomeopenres.15806.1 sha: doc_id: 349790 cord_uid: dezauioa file: cache/cord-350221-8u6q3wfa.json key: cord-350221-8u6q3wfa authors: Yang, Sung-Tae; Kreutzberger, Alex J. B.; Kiessling, Volker; Ganser-Pornillos, Barbie K.; White, Judith M.; Tamm, Lukas K. title: HIV virions sense plasma membrane heterogeneity for cell entry date: 2017-06-28 journal: Sci Adv DOI: 10.1126/sciadv.1700338 sha: doc_id: 350221 cord_uid: 8u6q3wfa file: cache/cord-355475-kdubhh73.json key: cord-355475-kdubhh73 authors: Patton, Lauren L. title: Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date: 2020-11-05 journal: Oral Surg Oral Med Oral Pathol Oral Radiol DOI: 10.1016/j.oooo.2020.10.022 sha: doc_id: 355475 cord_uid: kdubhh73 file: cache/cord-354050-kcn67stj.json key: cord-354050-kcn67stj authors: Shi, Guoli; Schwartz, Olivier; Compton, Alex A. title: More than meets the I: the diverse antiviral and cellular functions of interferon-induced transmembrane proteins date: 2017-11-21 journal: Retrovirology DOI: 10.1186/s12977-017-0377-y sha: doc_id: 354050 cord_uid: kcn67stj file: cache/cord-354972-nc496v6s.json key: cord-354972-nc496v6s authors: Margolin, Emmanuel; Burgers, Wendy A.; Sturrock, Edward D.; Mendelson, Marc; Chapman, Rosamund; Douglass, Nicola; Williamson, Anna-Lise; Rybicki, Edward P. title: Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date: 2020-09-10 journal: Nat Rev Microbiol DOI: 10.1038/s41579-020-00441-3 sha: doc_id: 354972 cord_uid: nc496v6s file: cache/cord-346153-9162w7il.json key: cord-346153-9162w7il authors: Openshaw, P J title: Crossing barriers: infections of the lung and the gut date: 2008-12-24 journal: Mucosal Immunol DOI: 10.1038/mi.2008.79 sha: doc_id: 346153 cord_uid: 9162w7il file: cache/cord-353012-rxhi8wd2.json key: cord-353012-rxhi8wd2 authors: Zhou, Nan; Pan, Ting; Zhang, Junsong; Li, Qianwen; Zhang, Xue; Bai, Chuan; Huang, Feng; Peng, Tao; Zhang, Jianhua; Liu, Chao; Tao, Liang; Zhang, Hui title: Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date: 2016-03-07 journal: Journal of Biological Chemistry DOI: 10.1074/jbc.m116.716100 sha: doc_id: 353012 cord_uid: rxhi8wd2 file: cache/cord-349358-leicos9j.json key: cord-349358-leicos9j authors: Ketzinel‐Gilad, Mali; Shaul, Yosef; Galun, Eithan title: RNA interference for antiviral therapy date: 2006-06-16 journal: J Gene Med DOI: 10.1002/jgm.929 sha: doc_id: 349358 cord_uid: leicos9j file: cache/cord-348409-oxjd263z.json key: cord-348409-oxjd263z authors: Stern, Zachariah; Stylianou, Dora C.; Kostrikis, Leondios G. title: The development of inovirus-associated vector vaccines using phage-display technologies date: 2019-09-08 journal: Expert Rev Vaccines DOI: 10.1080/14760584.2019.1651649 sha: doc_id: 348409 cord_uid: oxjd263z file: cache/cord-350443-ca5avyjf.json key: cord-350443-ca5avyjf authors: Zhang, Lei; Wilson, David P. title: Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date: 2012-02-16 journal: PLoS One DOI: 10.1371/journal.pone.0031076 sha: doc_id: 350443 cord_uid: ca5avyjf file: cache/cord-354790-xx6imhzb.json key: cord-354790-xx6imhzb authors: Lambour, Jennifer; Naranjo-Gomez, Mar; Piechaczyk, Marc; Pelegrin, Mireia title: Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play date: 2016-08-17 journal: Emerg Microbes Infect DOI: 10.1038/emi.2016.97 sha: doc_id: 354790 cord_uid: xx6imhzb file: cache/cord-355439-eqtk51q3.json key: cord-355439-eqtk51q3 authors: Lesko, Catherine R; Bengtson, Angela M title: HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date: 2020-07-22 journal: Am J Epidemiol DOI: 10.1093/aje/kwaa158 sha: doc_id: 355439 cord_uid: eqtk51q3 file: cache/cord-354974-bh2expef.json key: cord-354974-bh2expef authors: Peterson, Ingrid; Bar-Zeev, Naor; Kennedy, Neil; Ho, Antonia; Newberry, Laura; SanJoaquin, Miguel A.; Menyere, Mavis; Alaerts, Maaike; Mapurisa, Gugulethu; Chilombe, Moses; Mambule, Ivan; Lalloo, David G.; Anderson, Suzanne T.; Katangwe, Thembi; Cunliffe, Nigel; Nagelkerke, Nico; McMorrow, Meredith; Widdowson, Marc-Allain; French, Neil; Everett, Dean; Heyderman, Robert S. title: Respiratory Virus–Associated Severe Acute Respiratory Illness and Viral Clustering in Malawian Children in a Setting With a High Prevalence of HIV Infection, Malaria, and Malnutrition date: 2016-09-13 journal: Journal of Infectious Diseases DOI: 10.1093/infdis/jiw426 sha: doc_id: 354974 cord_uid: bh2expef file: cache/cord-347992-coby2m6e.json key: cord-347992-coby2m6e authors: Marton, Soledad; Reyes-Darias, José A.; Sánchez-Luque, Francisco J.; Romero-López, Cristina; Berzal-Herranz, Alfredo title: In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules date: 2010-06-28 journal: Molecules DOI: 10.3390/molecules15074610 sha: doc_id: 347992 cord_uid: coby2m6e file: cache/cord-354029-mp5r82g4.json key: cord-354029-mp5r82g4 authors: Earp, L. J.; Delos, S. E.; Park, H. E.; White, J. M. title: The Many Mechanisms of Viral Membrane Fusion Proteins date: 2005 journal: Membrane Trafficking in Viral Replication DOI: 10.1007/3-540-26764-6_2 sha: doc_id: 354029 cord_uid: mp5r82g4 file: cache/cord-355541-5sctqkwr.json key: cord-355541-5sctqkwr authors: Alcamí, José; Joseph Munné, Joan; Muñoz-Fernández, María Ángeles; Esteban, Mariano title: Current situation in the development of a preventive HIV vaccine date: 2005-07-31 journal: Enfermedades Infecciosas y Microbiología Clínica DOI: 10.1016/s0213-005x(05)75157-0 sha: doc_id: 355541 cord_uid: 5sctqkwr file: cache/cord-355318-qm79gz8w.json key: cord-355318-qm79gz8w authors: Smit, Albertus J.; Fitchett, Jennifer M.; Engelbrecht, Francois A.; Scholes, Robert J.; Dzhivhuho, Godfrey; Sweijd, Neville A. title: Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date: 2020-08-05 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165634 sha: doc_id: 355318 cord_uid: qm79gz8w file: cache/cord-347710-ff64y6ef.json key: cord-347710-ff64y6ef authors: Wan, Qianya; Song, Dan; Li, Huangcan; He, Ming-liang title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00233-4 sha: doc_id: 347710 cord_uid: ff64y6ef file: cache/cord-350569-dtxtjtfo.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-350569-dtxtjtfo authors: Kasoka, Kasoka title: Autonomy in HIV testing: a call for a rethink of personal autonomy in the HIV response in sub-Saharan Africa date: 2020-06-13 journal: Med Health Care Philos DOI: 10.1007/s11019-020-09959-y sha: doc_id: 350569 cord_uid: dtxtjtfo file: cache/cord-350571-6tapkjb6.json key: cord-350571-6tapkjb6 authors: nan title: 45th ESCP-NSF international symposium on clinical pharmacy: clinical pharmacy tackling inequalities and access to health care. Oslo, Norway, 5–7 October 2016 date: 2017-01-10 journal: Int J Clin Pharm DOI: 10.1007/s11096-016-0404-4 sha: doc_id: 350571 cord_uid: 6tapkjb6 file: cache/cord-010119-t1x9gknd.json key: cord-010119-t1x9gknd authors: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 journal: Transfusion DOI: 10.1111/trf.14286 sha: doc_id: 10119 cord_uid: t1x9gknd Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-hiv-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47204 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: 47346 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: 47420 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: 47598 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: 47597 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: 47569 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: 47797 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: 47381 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === 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: 47861 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === 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: 47789 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: 47833 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: 48071 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: 48250 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: 48366 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: 48498 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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: 46885 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: 48061 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: 48796 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === 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: 49055 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: 49401 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: 49542 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: 47694 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50132 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48777 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: 50430 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49058 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.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: 48199 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: 51880 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50241 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: 51389 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: 51570 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: 52389 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50971 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: 51137 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: 51286 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: 51984 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51209 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: 51612 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: 51768 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: 51878 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: 53050 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /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: 51915 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: 50295 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: 52680 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /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: 53649 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: 53392 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 54846 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: 54153 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-000130-dqqcajjd author: Smith?, Robert J title: The OptAIDS project: towards global halting of HIV/AIDS date: 2009-11-18 pages: extension: .txt txt: ./txt/cord-000130-dqqcajjd.txt cache: ./cache/cord-000130-dqqcajjd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000130-dqqcajjd.txt' === file2bib.sh === id: cord-004575-b0t6bsya author: Staub, Roger title: Haben HIV-Positive eine besondere Verantwortung?: Ein Diskussionsbeitrag date: 2007-03-27 pages: extension: .txt txt: ./txt/cord-004575-b0t6bsya.txt cache: ./cache/cord-004575-b0t6bsya.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004575-b0t6bsya.txt' === file2bib.sh === id: cord-004600-5lhnzzvg author: Dennin, Reinhard H. title: HIV-Infektion – Grenzen der Präventionskonzepte: Überlegungen zur Verantwortung der Betroffenen, der Politik und der Gesellschaft* date: 2007-03-26 pages: extension: .txt txt: ./txt/cord-004600-5lhnzzvg.txt cache: ./cache/cord-004600-5lhnzzvg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004600-5lhnzzvg.txt' === file2bib.sh === id: cord-010001-u0d5jkp1 author: KOTWAL, GIRISH J. title: Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date: 2006-01-22 pages: extension: .txt txt: ./txt/cord-010001-u0d5jkp1.txt cache: ./cache/cord-010001-u0d5jkp1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010001-u0d5jkp1.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-006716-n371b91w author: Cone, A. M. title: Flumazenil reverses diazepam-induced neonatal apnoea and hypotonia date: 1993 pages: extension: .txt txt: ./txt/cord-006716-n371b91w.txt cache: ./cache/cord-006716-n371b91w.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006716-n371b91w.txt' /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: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: 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: 54936 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 90. 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: 55696 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 53638 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: 52851 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55246 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/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: 57948 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.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/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/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-015936-4fwkf8fn author: nan title: SUBJECT INDEX, volumes 123-130 date: 2005-11-04 pages: extension: .txt txt: ./txt/cord-015936-4fwkf8fn.txt cache: ./cache/cord-015936-4fwkf8fn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-015936-4fwkf8fn.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === 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: 55899 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.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: 50499 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: 57675 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 56748 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: 55530 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55472 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === 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: 55199 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55903 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: 56039 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: 57697 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: 58357 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: 58373 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55707 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. 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: 55372 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.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/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.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/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-000077-d441jam3 author: Zhang, Hao-Jie title: The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date: 2009-07-03 pages: extension: .txt txt: ./txt/cord-000077-d441jam3.txt cache: ./cache/cord-000077-d441jam3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000077-d441jam3.txt' === file2bib.sh === id: cord-001972-1zisomq5 author: Wang, Xue title: Pandemic Influenza A (H1N1) Virus Infection Increases Apoptosis and HIV-1 Replication in HIV-1 Infected Jurkat Cells date: 2016-02-02 pages: extension: .txt txt: ./txt/cord-001972-1zisomq5.txt cache: ./cache/cord-001972-1zisomq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001972-1zisomq5.txt' === file2bib.sh === id: cord-003307-snruk3j2 author: Schmidt, Julius J. title: Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date: 2018-11-19 pages: extension: .txt txt: ./txt/cord-003307-snruk3j2.txt cache: ./cache/cord-003307-snruk3j2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003307-snruk3j2.txt' === file2bib.sh === id: cord-009669-bcdjwpd1 author: Tsegaye, Theodros Solomon title: The multiple facets of HIV attachment to dendritic cell lectins date: 2010-09-20 pages: extension: .txt txt: ./txt/cord-009669-bcdjwpd1.txt cache: ./cache/cord-009669-bcdjwpd1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009669-bcdjwpd1.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 57195 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: 57358 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: 60487 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: 62292 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /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/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-000008-3dgjv0x1 author: Vali, Bahareh title: HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date: 2008-10-20 pages: extension: .txt txt: ./txt/cord-000008-3dgjv0x1.txt cache: ./cache/cord-000008-3dgjv0x1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000008-3dgjv0x1.txt' /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: 61563 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: 55455 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: 59592 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: 60694 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: 60986 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. 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: 53964 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: 61691 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-009891-gqrhbhbn author: Rassool, G. Hussein title: Current issues and forthcoming events date: 2003-09-03 pages: extension: .txt txt: ./txt/cord-009891-gqrhbhbn.txt cache: ./cache/cord-009891-gqrhbhbn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009891-gqrhbhbn.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-005033-voi9gu0l author: Xuan, Huiyu title: A CA-based epidemic model for HIV/AIDS transmission with heterogeneity date: 2008-06-07 pages: extension: .txt txt: ./txt/cord-005033-voi9gu0l.txt cache: ./cache/cord-005033-voi9gu0l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-005033-voi9gu0l.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-005585-lc3fqhb0 author: Barbier, François title: Etiologies and outcome of acute respiratory failure in HIV-infected patients date: 2009-07-03 pages: extension: .txt txt: ./txt/cord-005585-lc3fqhb0.txt cache: ./cache/cord-005585-lc3fqhb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-005585-lc3fqhb0.txt' === file2bib.sh === id: cord-018440-qugmnolo author: nan title: When a Diagnosis Is Reportable date: 2008 pages: extension: .txt txt: ./txt/cord-018440-qugmnolo.txt cache: ./cache/cord-018440-qugmnolo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018440-qugmnolo.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 56071 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: 52601 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62017 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: 47737 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-010499-yefxrj30 author: Yelverton, Elizabeth title: The function of a ribosomal frameshifting signal from human immunodeficiency virus‐1 in Escherichia coli date: 2006-10-27 pages: extension: .txt txt: ./txt/cord-010499-yefxrj30.txt cache: ./cache/cord-010499-yefxrj30.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010499-yefxrj30.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 86. 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: 63496 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-004247-lagv3tp7 author: Hooft van Huijsduijnen, Rob title: Reassessing therapeutic antibodies for neglected and tropical diseases date: 2020-01-30 pages: extension: .txt txt: ./txt/cord-004247-lagv3tp7.txt cache: ./cache/cord-004247-lagv3tp7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-004247-lagv3tp7.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-020101-5rib7pe8 author: nan title: Cumulative Author Index for 2008 date: 2008-11-17 pages: extension: .txt txt: ./txt/cord-020101-5rib7pe8.txt cache: ./cache/cord-020101-5rib7pe8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020101-5rib7pe8.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-015376-z739ifu5 author: Savarino, Andrea title: Potential therapies for coronaviruses date: 2006-08-31 pages: extension: .txt txt: ./txt/cord-015376-z739ifu5.txt cache: ./cache/cord-015376-z739ifu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015376-z739ifu5.txt' === file2bib.sh === id: cord-013336-42thiglv author: Wang, Cheng title: Correlates of HIV self-testing among female sex workers in China: implications for expanding HIV screening date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-013336-42thiglv.txt cache: ./cache/cord-013336-42thiglv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-013336-42thiglv.txt' === file2bib.sh === id: cord-001385-rb5vwolt author: Reuven, Eliran Moshe title: The HIV-1 Envelope Transmembrane Domain Binds TLR2 through a Distinct Dimerization Motif and Inhibits TLR2-Mediated Responses date: 2014-08-14 pages: extension: .txt txt: ./txt/cord-001385-rb5vwolt.txt cache: ./cache/cord-001385-rb5vwolt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001385-rb5vwolt.txt' === file2bib.sh === id: cord-011457-hqxybv1k author: Kirui, James title: Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date: 2020-05-19 pages: extension: .txt txt: ./txt/cord-011457-hqxybv1k.txt cache: ./cache/cord-011457-hqxybv1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-011457-hqxybv1k.txt' === file2bib.sh === id: cord-010845-pakh49dy author: Isiguzo, Godsent title: Diagnosis and Management of Tuberculous Pericarditis: What Is New? date: 2020-01-15 pages: extension: .txt txt: ./txt/cord-010845-pakh49dy.txt cache: ./cache/cord-010845-pakh49dy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-010845-pakh49dy.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 63947 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /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: 59319 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: 60900 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. 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 parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-015958-68dmza13 author: Ceccherini-Nelli, Luca title: Globalizzazione in medicina: l’emergenza HIV date: 2007 pages: extension: .txt txt: ./txt/cord-015958-68dmza13.txt cache: ./cache/cord-015958-68dmza13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015958-68dmza13.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 84. 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: 66019 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 88. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 65603 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 83. 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: 66185 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 86. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 82. 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: 65649 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 86. 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 parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-004986-en7taikk author: Nagy, Nathalie title: Infections gastro-intestinales chez le patient immunocompromis date: 2002 pages: extension: .txt txt: ./txt/cord-004986-en7taikk.txt cache: ./cache/cord-004986-en7taikk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004986-en7taikk.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-018137-rmtyrbg0 author: Saad, Farouk Tijjani title: Global Stability Analysis of HIV+ Model date: 2018-12-29 pages: extension: .txt txt: ./txt/cord-018137-rmtyrbg0.txt cache: ./cache/cord-018137-rmtyrbg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018137-rmtyrbg0.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 82. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-013442-kjfk7hq6 author: Muñoz-Laboy, Miguel title: “En la Lucha”: Strategies to Improve HIV Care for Puerto Ricans with Opioids Use Disorders date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-013442-kjfk7hq6.txt cache: ./cache/cord-013442-kjfk7hq6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013442-kjfk7hq6.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 88. 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: 64809 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 89. 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/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 85. 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 /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === 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: 67453 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 65306 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 84. 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 parallel: Warning: No more processes: Decreasing number of running jobs to 88. 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: 58806 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: 65540 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: 67264 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: 67414 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === 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: 67276 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-010689-d2qn1doq author: Chehardoli, Gholamabbas title: Synthetic strategies, SAR studies, and computer modeling of indole 2 and 3-carboxamides as the strong enzyme inhibitors: a review date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-010689-d2qn1doq.txt cache: ./cache/cord-010689-d2qn1doq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-010689-d2qn1doq.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 78. 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: 67778 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: 67539 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: 68464 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 87. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 82. 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 === file2bib.sh === id: cord-011903-zqt6vu6d author: Duby, Zoe title: “As a Young Pregnant Girl… The Challenges You Face”: Exploring the Intersection Between Mental Health and Sexual and Reproductive Health Amongst Adolescent Girls and Young Women in South Africa date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-011903-zqt6vu6d.txt cache: ./cache/cord-011903-zqt6vu6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011903-zqt6vu6d.txt' === file2bib.sh === id: cord-003715-deqiets2 author: Warren, Cody J. title: Selective use of primate CD4 receptors by HIV-1 date: 2019-06-10 pages: extension: .txt txt: ./txt/cord-003715-deqiets2.txt cache: ./cache/cord-003715-deqiets2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003715-deqiets2.txt' === file2bib.sh === id: cord-017719-8lfn6mih author: Böhles, Hansjosef title: Infestationen und Infektionen bei Migranten – Die wichtigsten Erkrankungen date: 2018-02-09 pages: extension: .txt txt: ./txt/cord-017719-8lfn6mih.txt cache: ./cache/cord-017719-8lfn6mih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017719-8lfn6mih.txt' === file2bib.sh === id: cord-000868-vnwpzsu8 author: Eissmann, Kristin title: HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop date: 2013-01-22 pages: extension: .txt txt: ./txt/cord-000868-vnwpzsu8.txt cache: ./cache/cord-000868-vnwpzsu8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000868-vnwpzsu8.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-017782-dtveihrj author: Fong, I. W. title: Litigations for HIV Related Complications date: 2010-11-30 pages: extension: .txt txt: ./txt/cord-017782-dtveihrj.txt cache: ./cache/cord-017782-dtveihrj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017782-dtveihrj.txt' /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.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: 68407 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === 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: 66026 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: 67901 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: 68228 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: 68318 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: 69007 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: 69608 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /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: 53881 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-017439-0c6ohmmg author: Hughes-Oliver, Jacqueline M. title: Pooling Experiments for Blood Screening and Drug Discovery date: 2006 pages: extension: .txt txt: ./txt/cord-017439-0c6ohmmg.txt cache: ./cache/cord-017439-0c6ohmmg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017439-0c6ohmmg.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 58788 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-018040-k0h5ejjt author: Ilyinskii, P. title: Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date: 2009 pages: extension: .txt txt: ./txt/cord-018040-k0h5ejjt.txt cache: ./cache/cord-018040-k0h5ejjt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018040-k0h5ejjt.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /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: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-018646-fqy82sm6 author: Huremović, Damir title: Brief History of Pandemics (Pandemics Throughout History) date: 2019-05-16 pages: extension: .txt txt: ./txt/cord-018646-fqy82sm6.txt cache: ./cache/cord-018646-fqy82sm6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018646-fqy82sm6.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 70448 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: 68011 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 81. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 77. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === 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: 68194 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 86. 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 /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 71138 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /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: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === 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: 70470 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 71574 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: 70215 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-016041-427mbaqc author: Hengge, Ulrich R. title: Gentherapie date: 2008 pages: extension: .txt txt: ./txt/cord-016041-427mbaqc.txt cache: ./cache/cord-016041-427mbaqc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016041-427mbaqc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 71715 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: 70176 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: 71111 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: 71407 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable parallel: Warning: No more processes: Decreasing number of running jobs to 81. 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: 70465 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 76. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 85. 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 === file2bib.sh === id: cord-034714-6e37yylk author: Alleg, Manel title: Progressive multifocal leukoencephalopathy: MRI findings in HIV-infected patients are closer to rituximab- than natalizumab-associated PML date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-034714-6e37yylk.txt cache: ./cache/cord-034714-6e37yylk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-034714-6e37yylk.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-018864-c1r2n17o author: Pöhlmann, Stefan title: Attachment of human immunodeficiency virus to cells and its inhibition date: 2007 pages: extension: .txt txt: ./txt/cord-018864-c1r2n17o.txt cache: ./cache/cord-018864-c1r2n17o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018864-c1r2n17o.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-027659-rxbo7b0e author: Bates, Imelda title: Blood Transfusion date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-027659-rxbo7b0e.txt cache: ./cache/cord-027659-rxbo7b0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027659-rxbo7b0e.txt' === file2bib.sh === id: cord-256477-dftt5m6i author: Feller, John M. title: Potential Ebola prophylaxis date: 2015-07-01 pages: extension: .txt txt: ./txt/cord-256477-dftt5m6i.txt cache: ./cache/cord-256477-dftt5m6i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256477-dftt5m6i.txt' /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-026112-58sa5z03 author: Dehghani-Dehej, Farzaneh title: Prevalence of HCV and/or HBV coinfection in Iranian HIV-infected patients date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-026112-58sa5z03.txt cache: ./cache/cord-026112-58sa5z03.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026112-58sa5z03.txt' === file2bib.sh === id: cord-022168-qautse9a author: Liu, Li title: Clinical Use of DNA Vaccines date: 2017-07-25 pages: extension: .txt txt: ./txt/cord-022168-qautse9a.txt cache: ./cache/cord-022168-qautse9a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022168-qautse9a.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 71403 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: 73874 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: 74155 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-032438-cpoalxyd author: Nachega, Jean B title: The where, when, and how of community-based versus clinic-based ART delivery in South Africa and Uganda date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-032438-cpoalxyd.txt cache: ./cache/cord-032438-cpoalxyd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032438-cpoalxyd.txt' === file2bib.sh === id: cord-027678-k64whepc author: Chan, Kai Man title: Pneumonia date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-027678-k64whepc.txt cache: ./cache/cord-027678-k64whepc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-027678-k64whepc.txt' === file2bib.sh === id: cord-254951-anfkuigj author: Pierre, Gashema title: Attendance to HIV Antiretroviral Collection Clinic Appointments During COVID-19 Lockdown. A Single Center Study in Kigali, Rwanda date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-254951-anfkuigj.txt cache: ./cache/cord-254951-anfkuigj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254951-anfkuigj.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 72412 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: 72945 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: 73850 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-254187-dcdc6sqi author: Kimball, AM title: “What, me worry?” Businesses and AIDS at Davos date: 2005-04-05 pages: extension: .txt txt: ./txt/cord-254187-dcdc6sqi.txt cache: ./cache/cord-254187-dcdc6sqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254187-dcdc6sqi.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 73934 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: 74095 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: 74578 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: 75175 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 80. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-021872-rhi7hi9m author: Wilkes, Rebecca P. title: Update on Antiviral Therapies date: 2015-12-04 pages: extension: .txt txt: ./txt/cord-021872-rhi7hi9m.txt cache: ./cache/cord-021872-rhi7hi9m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021872-rhi7hi9m.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 75. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 90. 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: 74706 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: 75633 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: 76133 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: 73834 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: 76346 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: 75528 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: 75061 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: 75212 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 79. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-103350-jj9pc4a6 author: Tang, Pingtao title: An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-103350-jj9pc4a6.txt cache: ./cache/cord-103350-jj9pc4a6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-103350-jj9pc4a6.txt' === file2bib.sh === id: cord-033558-lcgo1tiy author: Schmiedel, Stefan title: Infektionen, Impfungen, Reisemedizin date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-033558-lcgo1tiy.txt cache: ./cache/cord-033558-lcgo1tiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-033558-lcgo1tiy.txt' === file2bib.sh === id: cord-259503-dkfrk71a author: Smith, Sarah E. title: Sherlock Genomes — viral investigator date: 2013-02-15 pages: extension: .txt txt: ./txt/cord-259503-dkfrk71a.txt cache: ./cache/cord-259503-dkfrk71a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259503-dkfrk71a.txt' /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-022535-08hqmwlg author: Schmiedel, Stefan title: Infektionen, Impfungen, Reisemedizin date: 2013-06-26 pages: extension: .txt txt: ./txt/cord-022535-08hqmwlg.txt cache: ./cache/cord-022535-08hqmwlg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022535-08hqmwlg.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.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: No child processes === file2bib.sh === id: cord-029416-738t6rk1 author: Mandal, Sandip title: The potential impact of preventive therapy against tuberculosis in the WHO South-East Asian Region: a modelling approach date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-029416-738t6rk1.txt cache: ./cache/cord-029416-738t6rk1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-029416-738t6rk1.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 89. 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: 74755 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 78. 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: 75750 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 74. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 79. 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: 77805 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-030427-fn9pfqts author: Huang, Feifei title: Acculturation, HIV-Related Stigma, Stress, and Patient-Healthcare Provider Relationships Among HIV-Infected Asian Americans: A Path Analysis date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-030427-fn9pfqts.txt cache: ./cache/cord-030427-fn9pfqts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-030427-fn9pfqts.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 78367 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes === file2bib.sh === id: cord-256459-6h358si5 author: Sharpstone, D title: Gastrointestinal manifestations of HIV infection date: 1996-08-10 pages: extension: .txt txt: ./txt/cord-256459-6h358si5.txt cache: ./cache/cord-256459-6h358si5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256459-6h358si5.txt' /data-disk/reader-compute/reader-cord/bin/cordent2carrel.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/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-255075-6azu6k3h author: Zhuang, Jianjian title: Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-255075-6azu6k3h.txt cache: ./cache/cord-255075-6azu6k3h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255075-6azu6k3h.txt' === file2bib.sh === id: cord-027242-7qq82j2f author: Chrissafidou, Angeliki title: Infektionen, Impfungen, Reisemedizin date: 2008-12-11 pages: extension: .txt txt: ./txt/cord-027242-7qq82j2f.txt cache: ./cache/cord-027242-7qq82j2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027242-7qq82j2f.txt' === file2bib.sh === id: cord-022141-yxttl3gh author: Siegel, Frederic R. title: Progressive Adaptation: The Key to Sustaining a Growing Global Population date: 2014-08-23 pages: extension: .txt txt: ./txt/cord-022141-yxttl3gh.txt cache: ./cache/cord-022141-yxttl3gh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022141-yxttl3gh.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 70161 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: 69558 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: 78356 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: 77919 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: 77831 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: 75965 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: 79325 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-256324-w3bejmy5 author: Hamada, Yoshio title: New directions for protease inhibitors directed drug discovery date: 2016-07-22 pages: extension: .txt txt: ./txt/cord-256324-w3bejmy5.txt cache: ./cache/cord-256324-w3bejmy5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256324-w3bejmy5.txt' === file2bib.sh === id: cord-020494-d5sreohg author: Schmutzhard, E. title: Entzündliche Erkrankungen date: 2006 pages: extension: .txt txt: ./txt/cord-020494-d5sreohg.txt cache: ./cache/cord-020494-d5sreohg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-020494-d5sreohg.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-023884-etkhrgxp author: Meremikwu, Martin title: Malaria in Women and Children date: 2009-05-18 pages: extension: .txt txt: ./txt/cord-023884-etkhrgxp.txt cache: ./cache/cord-023884-etkhrgxp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023884-etkhrgxp.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 82067 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: 82166 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: 82876 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 88. 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: 81884 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: 82856 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: 83041 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: 83419 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: 83254 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-260191-0u0pu0br author: Haas, W. title: „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date: 2004-05-29 pages: extension: .txt txt: ./txt/cord-260191-0u0pu0br.txt cache: ./cache/cord-260191-0u0pu0br.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260191-0u0pu0br.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 87. 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: 83178 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: 82926 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: 83282 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-260604-lz1qd69t author: Singh, Ramendra K. title: Synthesis, structure–activity relationship and antiviral activity of 3′-N,N-dimethylamino-2′,3′-dideoxythymidine and its prodrugs date: 2010-09-30 pages: extension: .txt txt: ./txt/cord-260604-lz1qd69t.txt cache: ./cache/cord-260604-lz1qd69t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-260604-lz1qd69t.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 83403 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-048467-1dus0u4m author: Civaner, Murat title: Can "presumed consent" justify the duty to treat infectious diseases? An analysis date: 2008-03-06 pages: extension: .txt txt: ./txt/cord-048467-1dus0u4m.txt cache: ./cache/cord-048467-1dus0u4m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-048467-1dus0u4m.txt' === file2bib.sh === id: cord-263452-y2ral8nx author: Watanabe, Yasunori title: Site-specific glycan analysis of the SARS-CoV-2 spike date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-263452-y2ral8nx.txt cache: ./cache/cord-263452-y2ral8nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263452-y2ral8nx.txt' === file2bib.sh === id: cord-254190-bxfne94u author: Tu, Wenwei title: Application of Humanized Mice in Immunological Research date: 2015-07-07 pages: extension: .txt txt: ./txt/cord-254190-bxfne94u.txt cache: ./cache/cord-254190-bxfne94u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254190-bxfne94u.txt' === file2bib.sh === id: cord-257217-f9sdt7ax author: Nunes, Marta C. title: Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date: 2014-02-03 pages: extension: .txt txt: ./txt/cord-257217-f9sdt7ax.txt cache: ./cache/cord-257217-f9sdt7ax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257217-f9sdt7ax.txt' === file2bib.sh === id: cord-264050-6zpw6itb author: Pirofski, Liise-anne title: Immune-Mediated Damage Completes the Parabola: Cryptococcus neoformans Pathogenesis Can Reflect the Outcome of a Weak or Strong Immune Response date: 2017-12-12 pages: extension: .txt txt: ./txt/cord-264050-6zpw6itb.txt cache: ./cache/cord-264050-6zpw6itb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264050-6zpw6itb.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 86. 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: 83783 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: 83762 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: 83187 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-259131-36udb7uc author: Hunegnaw, Ruth title: Alveolar Macrophage Dysfunction and Increased PD-1 Expression During Chronic SIV Infection of Rhesus Macaques date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-259131-36udb7uc.txt cache: ./cache/cord-259131-36udb7uc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-259131-36udb7uc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 84167 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: 84189 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: 83334 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: 84600 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: 81794 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: 84837 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-261382-cyty5noi author: Goffinet, Christine title: Cellular Antiviral Factors that Target Particle Infectivity of HIV-1 date: 2016-05-17 pages: extension: .txt txt: ./txt/cord-261382-cyty5noi.txt cache: ./cache/cord-261382-cyty5noi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-261382-cyty5noi.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85349 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-260496-s2ba7uy3 author: Moncany, Maurice L.J. title: Identification of conserved lentiviral sequences as landmarks of genomic flexibility date: 2006-08-08 pages: extension: .txt txt: ./txt/cord-260496-s2ba7uy3.txt cache: ./cache/cord-260496-s2ba7uy3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260496-s2ba7uy3.txt' === file2bib.sh === id: cord-262752-bwofzbwa author: Li, Qianqian title: Current status on the development of pseudoviruses for enveloped viruses date: 2017-12-07 pages: extension: .txt txt: ./txt/cord-262752-bwofzbwa.txt cache: ./cache/cord-262752-bwofzbwa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-262752-bwofzbwa.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 85374 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: 82781 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: 85372 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: 86014 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: 85061 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: 85398 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: 85063 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: 85375 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: 83173 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-022521-r72jtoso author: Miller, Tracie L. title: Gastrointestinal Complications of Secondary Immunodeficiency Syndromes date: 2010-12-27 pages: extension: .txt txt: ./txt/cord-022521-r72jtoso.txt cache: ./cache/cord-022521-r72jtoso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022521-r72jtoso.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 86378 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: 86680 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: 86868 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: 76037 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-018721-othar2uv author: Schwab, Stefan title: Infektionen date: 2012-03-17 pages: extension: .txt txt: ./txt/cord-018721-othar2uv.txt cache: ./cache/cord-018721-othar2uv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018721-othar2uv.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81411 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: 87283 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: 87013 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: 87022 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: 86677 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: 85799 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-274688-cr1rvy8u author: Jewell, Britta L title: Potential effects of disruption to HIV programmes in sub-Saharan Africa caused by COVID-19: results from multiple mathematical models date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-274688-cr1rvy8u.txt cache: ./cache/cord-274688-cr1rvy8u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274688-cr1rvy8u.txt' === file2bib.sh === id: cord-271948-iq29xqrn author: Obeng, Billal Musah title: Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-271948-iq29xqrn.txt cache: ./cache/cord-271948-iq29xqrn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271948-iq29xqrn.txt' === file2bib.sh === id: cord-271188-ewlxy5po author: Liu, Wei title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-271188-ewlxy5po.txt cache: ./cache/cord-271188-ewlxy5po.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271188-ewlxy5po.txt' === file2bib.sh === id: cord-254194-962vynwk author: Galdiero, Stefania title: Silver Nanoparticles as Potential Antiviral Agents date: 2011-10-24 pages: extension: .txt txt: ./txt/cord-254194-962vynwk.txt cache: ./cache/cord-254194-962vynwk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-254194-962vynwk.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87016 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: 88309 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: 87500 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: 87991 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-270868-4s3q2i6v author: Collins, Lauren F. title: Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-270868-4s3q2i6v.txt cache: ./cache/cord-270868-4s3q2i6v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270868-4s3q2i6v.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88946 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: 87634 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: 87981 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: 88045 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: 87978 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-270726-w59fu9c9 author: Dikman, Andrew E. title: Human Immunodeficiency Virus-Associated Diarrhea: Still an Issue in the Era of Antiretroviral Therapy date: 2015-03-14 pages: extension: .txt txt: ./txt/cord-270726-w59fu9c9.txt cache: ./cache/cord-270726-w59fu9c9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-270726-w59fu9c9.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 89286 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-269759-1n1oo6wc author: Villamil-Gómez, Wilmer E. title: Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia date: 2020-02-06 pages: extension: .txt txt: ./txt/cord-269759-1n1oo6wc.txt cache: ./cache/cord-269759-1n1oo6wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269759-1n1oo6wc.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 87238 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: 88896 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-276870-gxtvlji7 author: Bobrowski, Tesia title: Learning from history: do not flatten the curve of antiviral research! date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-276870-gxtvlji7.txt cache: ./cache/cord-276870-gxtvlji7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276870-gxtvlji7.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88210 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: 89643 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-279849-zzkliu76 author: DaPalma, T. title: A systematic approach to virus–virus interactions date: 2010-01-20 pages: extension: .txt txt: ./txt/cord-279849-zzkliu76.txt cache: ./cache/cord-279849-zzkliu76.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-279849-zzkliu76.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88713 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: 89639 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: 90938 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: 90301 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: 90957 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: 87287 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: 89112 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: 90973 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: 90942 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-271241-w1q46y63 author: Ruggiero, Emanuela title: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-271241-w1q46y63.txt cache: ./cache/cord-271241-w1q46y63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271241-w1q46y63.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88899 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-272051-arz8r204 author: Federico, Maurizio title: HIV-protease inhibitors block the replication of both vesicular stomatitis and influenza viruses at an early post-entry replication step date: 2011-08-15 pages: extension: .txt txt: ./txt/cord-272051-arz8r204.txt cache: ./cache/cord-272051-arz8r204.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272051-arz8r204.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 91787 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-259846-oxbmtend author: Naik, Parvaiz Ahmad title: Global dynamics of a fractional order model for the transmission of HIV epidemic with optimal control date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-259846-oxbmtend.txt cache: ./cache/cord-259846-oxbmtend.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-259846-oxbmtend.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 93964 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: 92290 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: 92642 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: 93892 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: 94183 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: 91530 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: 94789 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: 93866 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-288982-63ddlh20 author: Peeling, Rosanna W. title: Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date: 2015-11-09 pages: extension: .txt txt: ./txt/cord-288982-63ddlh20.txt cache: ./cache/cord-288982-63ddlh20.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288982-63ddlh20.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 85. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === id: cord-297303-cpajrgba author: Nguyen, Annie L. title: Leaning on Community-Based Participatory Research to Respond During COVID-19 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-297303-cpajrgba.txt cache: ./cache/cord-297303-cpajrgba.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297303-cpajrgba.txt' === file2bib.sh === id: cord-287754-dh6abx2t author: Akkouh, Ouafae title: Lectins with Anti-HIV Activity: A Review date: 2015-01-06 pages: extension: .txt txt: ./txt/cord-287754-dh6abx2t.txt cache: ./cache/cord-287754-dh6abx2t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287754-dh6abx2t.txt' === file2bib.sh === id: cord-275859-ix8du1er author: Mouzakis, Kathryn D. title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date: 2012-12-15 pages: extension: .txt txt: ./txt/cord-275859-ix8du1er.txt cache: ./cache/cord-275859-ix8du1er.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-275859-ix8du1er.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 94602 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-268901-7cm6m1ol author: Ku, Therese title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date: 2019-07-01 pages: extension: .txt txt: ./txt/cord-268901-7cm6m1ol.txt cache: ./cache/cord-268901-7cm6m1ol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268901-7cm6m1ol.txt' === file2bib.sh === id: cord-265699-0socw0hp author: Ortega, Miguel Ángel title: Dendrimers and Dendritic Materials: From Laboratory to Medical Practice in Infectious Diseases date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-265699-0socw0hp.txt cache: ./cache/cord-265699-0socw0hp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265699-0socw0hp.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 94691 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: 94785 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: 94205 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-263438-9ra94uda author: Snowden, Frank M. title: Emerging and reemerging diseases: a historical perspective date: 2008-09-19 pages: extension: .txt txt: ./txt/cord-263438-9ra94uda.txt cache: ./cache/cord-263438-9ra94uda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-263438-9ra94uda.txt' === file2bib.sh === id: cord-268712-rxdw553c author: Sawyer, Alexandra title: Posttraumatic growth and adjustment among individuals with cancer or HIV/AIDS: A meta-analysis date: 2010-03-02 pages: extension: .txt txt: ./txt/cord-268712-rxdw553c.txt cache: ./cache/cord-268712-rxdw553c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268712-rxdw553c.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 88744 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: 95151 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-281941-97t45w73 author: Zhou, Daijun title: Cyclophilin A and viral infections date: 2012-08-10 pages: extension: .txt txt: ./txt/cord-281941-97t45w73.txt cache: ./cache/cord-281941-97t45w73.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281941-97t45w73.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95893 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-285603-f4572w5m author: Ortega, Joseph T. title: Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-285603-f4572w5m.txt cache: ./cache/cord-285603-f4572w5m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-285603-f4572w5m.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95930 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: 95897 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: 60513 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-287286-4l963z2q author: Green, Victoria A. title: Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date: 2010-07-28 pages: extension: .txt txt: ./txt/cord-287286-4l963z2q.txt cache: ./cache/cord-287286-4l963z2q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-287286-4l963z2q.txt' === file2bib.sh === id: cord-292546-un0blb3w author: Dandachi, Dima title: Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-292546-un0blb3w.txt cache: ./cache/cord-292546-un0blb3w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-292546-un0blb3w.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95887 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: 95884 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: 96507 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: 89601 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-014608-g3p19coe author: nan title: Pneumococcal colonization and carriage date: 2014-12-01 pages: extension: .txt txt: ./txt/cord-014608-g3p19coe.txt cache: ./cache/cord-014608-g3p19coe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-014608-g3p19coe.txt' === file2bib.sh === id: cord-269222-g2ibmo75 author: Valenti, Piera title: Role of Lactobacilli and Lactoferrin in the Mucosal Cervicovaginal Defense date: 2018-03-01 pages: extension: .txt txt: ./txt/cord-269222-g2ibmo75.txt cache: ./cache/cord-269222-g2ibmo75.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-269222-g2ibmo75.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 96640 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: 96223 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: 96606 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: 96366 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-287949-243xlmep author: Onovo, A. A. title: Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-287949-243xlmep.txt cache: ./cache/cord-287949-243xlmep.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287949-243xlmep.txt' === file2bib.sh === id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 pages: extension: .txt txt: ./txt/cord-284608-ba7wq52t.txt cache: ./cache/cord-284608-ba7wq52t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284608-ba7wq52t.txt' === file2bib.sh === id: cord-304816-7gg6pxnt author: Li, Wei title: Letter to the Editor: The characteristics of two patients co‐infected with SARS‐CoV‐2 and HIV in Wuhan, China date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-304816-7gg6pxnt.txt cache: ./cache/cord-304816-7gg6pxnt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304816-7gg6pxnt.txt' === file2bib.sh === id: cord-293653-u2qrxq6t author: Watashi, Koichi title: Cyclophilin and Viruses: Cyclophilin as a Cofactor for Viral Infection and Possible Anti-Viral Target date: 2007-02-05 pages: extension: .txt txt: ./txt/cord-293653-u2qrxq6t.txt cache: ./cache/cord-293653-u2qrxq6t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293653-u2qrxq6t.txt' === file2bib.sh === id: cord-297135-mg2qs3b6 author: Smith, Kumi title: A harm reduction paradox: Comparing China's policies on needle and syringe exchange and methadone maintenance date: 2012-07-31 pages: extension: .txt txt: ./txt/cord-297135-mg2qs3b6.txt cache: ./cache/cord-297135-mg2qs3b6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297135-mg2qs3b6.txt' === file2bib.sh === id: cord-277818-8w15dz20 author: Jaichenco, Andre L. title: Infectious Disease Considerations for the Operating Room date: 2018-02-09 pages: extension: .txt txt: ./txt/cord-277818-8w15dz20.txt cache: ./cache/cord-277818-8w15dz20.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-277818-8w15dz20.txt' === file2bib.sh === id: cord-266294-ua22udlc author: Koch, Oliver title: 29 Antiviral drugs date: 2010-12-31 pages: extension: .txt txt: ./txt/cord-266294-ua22udlc.txt cache: ./cache/cord-266294-ua22udlc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-266294-ua22udlc.txt' === file2bib.sh === id: cord-304427-r7jt95ko author: Pasquato, A. title: Heparin enhances the furin cleavage of HIV-1 gp160 peptides date: 2007-12-22 pages: extension: .txt txt: ./txt/cord-304427-r7jt95ko.txt cache: ./cache/cord-304427-r7jt95ko.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304427-r7jt95ko.txt' === file2bib.sh === id: cord-295062-8rl4kswe author: Marsh, Mark title: Virus Entry: Open Sesame date: 2006-02-24 pages: extension: .txt txt: ./txt/cord-295062-8rl4kswe.txt cache: ./cache/cord-295062-8rl4kswe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-295062-8rl4kswe.txt' === file2bib.sh === id: cord-294366-swwz4kzd author: Bramwell, Vincent W. title: The rational design of vaccines date: 2005-11-15 pages: extension: .txt txt: ./txt/cord-294366-swwz4kzd.txt cache: ./cache/cord-294366-swwz4kzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294366-swwz4kzd.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-304214-66nxk4e8 author: Sanders, John W. title: Vectored immunoprophylaxis: an emerging adjunct to traditional vaccination date: 2017-02-10 pages: extension: .txt txt: ./txt/cord-304214-66nxk4e8.txt cache: ./cache/cord-304214-66nxk4e8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304214-66nxk4e8.txt' === file2bib.sh === id: cord-300968-dtaasxk1 author: Kliger, Yossef title: From genome to antivirals: SARS as a test tube date: 2005-03-01 pages: extension: .txt txt: ./txt/cord-300968-dtaasxk1.txt cache: ./cache/cord-300968-dtaasxk1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300968-dtaasxk1.txt' === file2bib.sh === id: cord-304188-1nm1tbig author: Moody, M. Anthony title: Modulation of HIV-1 immunity by adjuvants date: 2014-04-10 pages: extension: .txt txt: ./txt/cord-304188-1nm1tbig.txt cache: ./cache/cord-304188-1nm1tbig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304188-1nm1tbig.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1736 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: 1203 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: 98297 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-313617-hh7lccet author: Sigel, Keith title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-313617-hh7lccet.txt cache: ./cache/cord-313617-hh7lccet.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313617-hh7lccet.txt' === file2bib.sh === id: cord-302082-aaokc182 author: Stanberry, Lawrence R. title: Vaccines of the future date: 2011-08-31 pages: extension: .txt txt: ./txt/cord-302082-aaokc182.txt cache: ./cache/cord-302082-aaokc182.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-302082-aaokc182.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1671 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: 2300 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: 98288 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: 2426 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: 1752 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-306050-y8i8759c author: García, Juan Ignacio title: Accuracy of the tuberculosis point-of-care Alere determine lipoarabinomannan antigen diagnostic test using α-mannosidase treated and untreated urine in a cohort of people living with HIV in Guatemala date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-306050-y8i8759c.txt cache: ./cache/cord-306050-y8i8759c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306050-y8i8759c.txt' === file2bib.sh === id: cord-295290-hs5ntlok author: Atlan, H. title: Mechanisms of autoimmunity and AIDS: prospects for therapeutic intervention date: 1994-12-31 pages: extension: .txt txt: ./txt/cord-295290-hs5ntlok.txt cache: ./cache/cord-295290-hs5ntlok.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295290-hs5ntlok.txt' === file2bib.sh === id: cord-295099-ghc85pf5 author: Sun, Zehua title: Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies date: 2018-01-02 pages: extension: .txt txt: ./txt/cord-295099-ghc85pf5.txt cache: ./cache/cord-295099-ghc85pf5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295099-ghc85pf5.txt' === file2bib.sh === id: cord-309489-ubf55eux author: Carvalho, John J. title: OUR COMMON ENEMY: COMBATTING THE WORLD'S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date: 2009-02-19 pages: extension: .txt txt: ./txt/cord-309489-ubf55eux.txt cache: ./cache/cord-309489-ubf55eux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309489-ubf55eux.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-313729-mydyc68y author: McDiarmid, Melissa A. title: Hazards of the Health Care Sector: Looking Beyond Infectious Disease date: 2014-11-25 pages: extension: .txt txt: ./txt/cord-313729-mydyc68y.txt cache: ./cache/cord-313729-mydyc68y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313729-mydyc68y.txt' === file2bib.sh === id: cord-314331-7k0oym5i author: Menza, Timothy W. title: Rapid Uptake of Home-Based HIV Self-testing During Social Distancing for SARS-CoV2 Infection in Oregon date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-314331-7k0oym5i.txt cache: ./cache/cord-314331-7k0oym5i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314331-7k0oym5i.txt' === file2bib.sh === id: cord-309515-0pxl0sta author: Blanco, Jose L title: COVID-19 in patients with HIV: clinical case series date: 2020-04-15 pages: extension: .txt txt: ./txt/cord-309515-0pxl0sta.txt cache: ./cache/cord-309515-0pxl0sta.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309515-0pxl0sta.txt' === file2bib.sh === id: cord-317990-61is0hgm author: Quinn, Katherine G. title: Applying the Popular Opinion Leader Intervention for HIV to COVID-19 date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-317990-61is0hgm.txt cache: ./cache/cord-317990-61is0hgm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317990-61is0hgm.txt' === file2bib.sh === id: cord-292740-b4cdj96q author: Wahid, Braira title: Immunotherapeutic strategies for sexually transmitted viral infections: HIV, HSV and HPV date: 2016-08-03 pages: extension: .txt txt: ./txt/cord-292740-b4cdj96q.txt cache: ./cache/cord-292740-b4cdj96q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292740-b4cdj96q.txt' === file2bib.sh === id: cord-316789-nb4437qs author: Omel’yanchuk, L. V. title: Drosophila melanogaster as a model for studying the function of animal viral proteins date: 2011-07-16 pages: extension: .txt txt: ./txt/cord-316789-nb4437qs.txt cache: ./cache/cord-316789-nb4437qs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316789-nb4437qs.txt' === file2bib.sh === id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 pages: extension: .txt txt: ./txt/cord-307817-2vy28i4m.txt cache: ./cache/cord-307817-2vy28i4m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307817-2vy28i4m.txt' === file2bib.sh === id: cord-314560-rswa5zdn author: Manjunath, N. title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 pages: extension: .txt txt: ./txt/cord-314560-rswa5zdn.txt cache: ./cache/cord-314560-rswa5zdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-314560-rswa5zdn.txt' === file2bib.sh === id: cord-308916-6p2qutc5 author: le Roux, David M. title: Community-acquired pneumonia in children — a changing spectrum of disease date: 2017-09-21 pages: extension: .txt txt: ./txt/cord-308916-6p2qutc5.txt cache: ./cache/cord-308916-6p2qutc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308916-6p2qutc5.txt' === file2bib.sh === id: cord-016690-3gsq724l author: Li, Hongjun title: HIV/AIDS Related Respiratory Diseases date: 2013-09-30 pages: extension: .txt txt: ./txt/cord-016690-3gsq724l.txt cache: ./cache/cord-016690-3gsq724l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-016690-3gsq724l.txt' === file2bib.sh === id: cord-306701-hs9cfdsu author: Gona, Philimon N. title: Burden and changes in HIV/AIDS morbidity and mortality in Southern Africa Development Community Countries, 1990–2017 date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-306701-hs9cfdsu.txt cache: ./cache/cord-306701-hs9cfdsu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306701-hs9cfdsu.txt' === file2bib.sh === id: cord-314753-xflhxb13 author: Manso, Carmen F. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 pages: extension: .txt txt: ./txt/cord-314753-xflhxb13.txt cache: ./cache/cord-314753-xflhxb13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314753-xflhxb13.txt' === file2bib.sh === id: cord-322256-mv9ll0h4 author: Edelman, E. Jennifer title: Confronting Another Pandemic: Lessons from HIV can Inform Our COVID-19 Response date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-322256-mv9ll0h4.txt cache: ./cache/cord-322256-mv9ll0h4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322256-mv9ll0h4.txt' === file2bib.sh === id: cord-318587-ewvnkdr2 author: Steeds, Kimberley title: Pseudotyping of VSV with Ebola virus glycoprotein is superior to HIV-1 for the assessment of neutralising antibodies date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-318587-ewvnkdr2.txt cache: ./cache/cord-318587-ewvnkdr2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318587-ewvnkdr2.txt' === file2bib.sh === id: cord-317533-xpfqdeqv author: Smuts, Heidi title: Human coronavirus NL63 infections in infants hospitalised with acute respiratory tract infections in South Africa date: 2008-07-24 pages: extension: .txt txt: ./txt/cord-317533-xpfqdeqv.txt cache: ./cache/cord-317533-xpfqdeqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317533-xpfqdeqv.txt' === file2bib.sh === id: cord-322503-fynprt6f author: Thakur, Aarzoo title: Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-322503-fynprt6f.txt cache: ./cache/cord-322503-fynprt6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322503-fynprt6f.txt' === file2bib.sh === id: cord-319354-jbain7n6 author: Gondim, Ana C. S. title: Potent antiviral activity of carbohydrate-specific algal and leguminous lectins from the Brazilian biodiversity date: 2019-01-14 pages: extension: .txt txt: ./txt/cord-319354-jbain7n6.txt cache: ./cache/cord-319354-jbain7n6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-319354-jbain7n6.txt' === file2bib.sh === id: cord-318570-wj7r6953 author: Xiao, Yinzong title: Point-of-Care Tests for Hepatitis B: An Overview date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-318570-wj7r6953.txt cache: ./cache/cord-318570-wj7r6953.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318570-wj7r6953.txt' === file2bib.sh === id: cord-304794-z2kx314h author: Métifiot, Mathieu title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 pages: extension: .txt txt: ./txt/cord-304794-z2kx314h.txt cache: ./cache/cord-304794-z2kx314h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304794-z2kx314h.txt' === file2bib.sh === id: cord-310430-7eww1oet author: Singh, Ram Sarup title: Algal lectins as promising biomolecules for biomedical research date: 2013-07-16 pages: extension: .txt txt: ./txt/cord-310430-7eww1oet.txt cache: ./cache/cord-310430-7eww1oet.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310430-7eww1oet.txt' === file2bib.sh === id: cord-023168-cd7adns8 author: Thachil, Jecko title: Haematological Diseases in the Tropics date: 2013-10-21 pages: extension: .txt txt: ./txt/cord-023168-cd7adns8.txt cache: ./cache/cord-023168-cd7adns8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023168-cd7adns8.txt' === file2bib.sh === id: cord-320156-xs936r6u author: Nunes, Marta C. title: Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children date: 2014-10-28 pages: extension: .txt txt: ./txt/cord-320156-xs936r6u.txt cache: ./cache/cord-320156-xs936r6u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320156-xs936r6u.txt' === file2bib.sh === id: cord-305039-grsv06j7 author: Flego, Michela title: Clinical development of monoclonal antibody-based drugs in HIV and HCV diseases date: 2013-01-04 pages: extension: .txt txt: ./txt/cord-305039-grsv06j7.txt cache: ./cache/cord-305039-grsv06j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305039-grsv06j7.txt' === file2bib.sh === id: cord-304251-dohglrm1 author: Scully, C title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 pages: extension: .txt txt: ./txt/cord-304251-dohglrm1.txt cache: ./cache/cord-304251-dohglrm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-304251-dohglrm1.txt' === file2bib.sh === id: cord-327324-4c4a4bfz author: Wilkinson, Robert J title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-327324-4c4a4bfz.txt cache: ./cache/cord-327324-4c4a4bfz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327324-4c4a4bfz.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-314098-1i6c0l3e author: Hayward, Joshua A title: Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-314098-1i6c0l3e.txt cache: ./cache/cord-314098-1i6c0l3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314098-1i6c0l3e.txt' === file2bib.sh === id: cord-317988-1buh1wm0 author: Kalichman, Seth C. title: Intersecting Pandemics: Impact of SARS-CoV-2 (COVID-19) Protective Behaviors on People Living With HIV, Atlanta, Georgia date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-317988-1buh1wm0.txt cache: ./cache/cord-317988-1buh1wm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317988-1buh1wm0.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 6890 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: 6744 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: 3761 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-302530-pp6bl941 author: Gale, Paul title: How virus size and attachment parameters affect the temperature sensitivity of virus binding to host cells: Predictions of a thermodynamic model for arboviruses and HIV date: 2020-03-12 pages: extension: .txt txt: ./txt/cord-302530-pp6bl941.txt cache: ./cache/cord-302530-pp6bl941.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302530-pp6bl941.txt' === file2bib.sh === id: cord-314528-5yq95giq author: Hirayama, Makoto title: High-Mannose Specific Lectin and Its Recombinants from a Carrageenophyta Kappaphycus alvarezii Represent a Potent Anti-HIV Activity Through High-Affinity Binding to the Viral Envelope Glycoprotein gp120 date: 2015-12-12 pages: extension: .txt txt: ./txt/cord-314528-5yq95giq.txt cache: ./cache/cord-314528-5yq95giq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-314528-5yq95giq.txt' === file2bib.sh === id: cord-306111-wn1gxhk9 author: Dommett, R. M. title: Mannose‐binding lectin in innate immunity: past, present and future date: 2006-09-01 pages: extension: .txt txt: ./txt/cord-306111-wn1gxhk9.txt cache: ./cache/cord-306111-wn1gxhk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-306111-wn1gxhk9.txt' === file2bib.sh === id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-312332-rwmuucsp.txt cache: ./cache/cord-312332-rwmuucsp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-312332-rwmuucsp.txt' === file2bib.sh === id: cord-321773-5fw9abzl author: Cheng, Wenyu title: DDX5 RNA Helicases: Emerging Roles in Viral Infection date: 2018-04-09 pages: extension: .txt txt: ./txt/cord-321773-5fw9abzl.txt cache: ./cache/cord-321773-5fw9abzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321773-5fw9abzl.txt' === file2bib.sh === id: cord-315687-stgj6olw author: Demma, LJ title: Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host date: 2006-03-20 pages: extension: .txt txt: ./txt/cord-315687-stgj6olw.txt cache: ./cache/cord-315687-stgj6olw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-315687-stgj6olw.txt' === file2bib.sh === id: cord-319043-hczwgf6o author: Ashkenazi, Avraham title: Sphingopeptides: dihydrosphingosine-based fusion inhibitors against wild-type and enfuvirtide-resistant HIV-1 date: 2012-08-07 pages: extension: .txt txt: ./txt/cord-319043-hczwgf6o.txt cache: ./cache/cord-319043-hczwgf6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319043-hczwgf6o.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9151 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: 8813 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-325936-rwxg187r author: Eyal, Nir title: AIDS Activism and Coronavirus Vaccine Challenge Trials date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-325936-rwxg187r.txt cache: ./cache/cord-325936-rwxg187r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325936-rwxg187r.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9596 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: 9991 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-324690-82qsirnk author: Dieffenbach, Carl W title: The search for an HIV vaccine, the journey continues date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-324690-82qsirnk.txt cache: ./cache/cord-324690-82qsirnk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324690-82qsirnk.txt' === file2bib.sh === id: cord-322581-v96k4yxg author: Mockiene, Vida title: Nurses' willingness to take care of people living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) — does a teaching intervention make a difference? date: 2011-08-31 pages: extension: .txt txt: ./txt/cord-322581-v96k4yxg.txt cache: ./cache/cord-322581-v96k4yxg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-322581-v96k4yxg.txt' === file2bib.sh === id: cord-309242-ilsupfl8 author: Schuchat, Anne title: Global health and the US Centers for Disease Control and Prevention date: 2014-07-02 pages: extension: .txt txt: ./txt/cord-309242-ilsupfl8.txt cache: ./cache/cord-309242-ilsupfl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309242-ilsupfl8.txt' === file2bib.sh === id: cord-319002-xmsfkaoc author: Brown, James title: Community-Acquired Pneumonia in HIV-Infected Individuals date: 2014-02-22 pages: extension: .txt txt: ./txt/cord-319002-xmsfkaoc.txt cache: ./cache/cord-319002-xmsfkaoc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319002-xmsfkaoc.txt' === file2bib.sh === id: cord-306266-8qdrshz3 author: Scully, Crispian title: Respiratory medicine date: 2014-06-25 pages: extension: .txt txt: ./txt/cord-306266-8qdrshz3.txt cache: ./cache/cord-306266-8qdrshz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306266-8qdrshz3.txt' === file2bib.sh === id: cord-317213-vhprfb1o author: Tram, Dai Thien Nhan title: Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases date: 2016-09-26 pages: extension: .txt txt: ./txt/cord-317213-vhprfb1o.txt cache: ./cache/cord-317213-vhprfb1o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317213-vhprfb1o.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5762 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-326642-kc85pev4 author: Cohen, Adam L. title: Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 date: 2015-09-19 pages: extension: .txt txt: ./txt/cord-326642-kc85pev4.txt cache: ./cache/cord-326642-kc85pev4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326642-kc85pev4.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-319263-g49jma8n author: Marziali, Megan E. title: Physical Distancing in COVID-19 May Exacerbate Experiences of Social Isolation among People Living with HIV date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-319263-g49jma8n.txt cache: ./cache/cord-319263-g49jma8n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-319263-g49jma8n.txt' === file2bib.sh === id: cord-015372-76xvzvdg author: nan title: National scientific medical meeting 1996 abstracts date: 1996 pages: extension: .txt txt: ./txt/cord-015372-76xvzvdg.txt cache: ./cache/cord-015372-76xvzvdg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015372-76xvzvdg.txt' === file2bib.sh === id: cord-329361-0mpbau1b author: Bennasser, Yamina title: RNAi Therapy for HIV Infection: Principles and Practicalities date: 2012-08-16 pages: extension: .txt txt: ./txt/cord-329361-0mpbau1b.txt cache: ./cache/cord-329361-0mpbau1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329361-0mpbau1b.txt' === file2bib.sh === id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-317037-1qydcc5e.txt cache: ./cache/cord-317037-1qydcc5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317037-1qydcc5e.txt' === file2bib.sh === id: cord-326744-eled2tgo author: Millett, Gregorio A. title: White Counties Stand Apart: The Primacy of Residential Segregation in COVID-19 and HIV Diagnoses date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-326744-eled2tgo.txt cache: ./cache/cord-326744-eled2tgo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326744-eled2tgo.txt' === file2bib.sh === id: cord-327461-ohgkgvry author: Lu, Ying title: Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-327461-ohgkgvry.txt cache: ./cache/cord-327461-ohgkgvry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327461-ohgkgvry.txt' === file2bib.sh === id: cord-326558-6tss9ydx author: Chen, Jiao title: A binning tool to reconstruct viral haplotypes from assembled contigs date: 2019-11-04 pages: extension: .txt txt: ./txt/cord-326558-6tss9ydx.txt cache: ./cache/cord-326558-6tss9ydx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326558-6tss9ydx.txt' === file2bib.sh === id: cord-320116-63yvpuqx author: Bancroft, Tara title: Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes date: 2019-10-07 pages: extension: .txt txt: ./txt/cord-320116-63yvpuqx.txt cache: ./cache/cord-320116-63yvpuqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320116-63yvpuqx.txt' === file2bib.sh === id: cord-303189-ktl4jw8v author: Coccia, Eliana M. title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 pages: extension: .txt txt: ./txt/cord-303189-ktl4jw8v.txt cache: ./cache/cord-303189-ktl4jw8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303189-ktl4jw8v.txt' === file2bib.sh === id: cord-329396-cl28bjnd author: Carrico, Adam W. title: Double Jeopardy: Methamphetamine Use and HIV as Risk Factors for COVID-19 date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-329396-cl28bjnd.txt cache: ./cache/cord-329396-cl28bjnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329396-cl28bjnd.txt' === file2bib.sh === id: cord-324056-cvvyf3cb author: Kelley, Patrick W. title: Global Health: Governance and Policy Development date: 2011-06-30 pages: extension: .txt txt: ./txt/cord-324056-cvvyf3cb.txt cache: ./cache/cord-324056-cvvyf3cb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324056-cvvyf3cb.txt' === file2bib.sh === id: cord-293857-o8rlqsq5 author: Ghosh, Arun K. title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 pages: extension: .txt txt: ./txt/cord-293857-o8rlqsq5.txt cache: ./cache/cord-293857-o8rlqsq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-293857-o8rlqsq5.txt' === file2bib.sh === id: cord-338438-q5fis2v8 author: Young, Sean D. title: Clinical Care, Research, and Telehealth Services in the Era of Social Distancing to Mitigate COVID-19 date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-338438-q5fis2v8.txt cache: ./cache/cord-338438-q5fis2v8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338438-q5fis2v8.txt' === file2bib.sh === id: cord-324137-nau83mjv author: Saranathan, Nandhini title: G-Quadruplexes: More Than Just a Kink in Microbial Genomes date: 2018-09-14 pages: extension: .txt txt: ./txt/cord-324137-nau83mjv.txt cache: ./cache/cord-324137-nau83mjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324137-nau83mjv.txt' === file2bib.sh === id: cord-337720-kmwft059 author: Closson, Kalysha title: When Home is Not a Safe Place: Impacts of Social Distancing Directives on Women Living with HIV date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-337720-kmwft059.txt cache: ./cache/cord-337720-kmwft059.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337720-kmwft059.txt' === file2bib.sh === id: cord-333730-qsx0m68e author: Tsai, Y. C. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-333730-qsx0m68e.txt cache: ./cache/cord-333730-qsx0m68e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-333730-qsx0m68e.txt' === file2bib.sh === id: cord-331879-w7008uyy author: Iversen, Jenny title: COVID‐19, HIV and key populations: cross‐cutting issues and the need for population‐specific responses date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-331879-w7008uyy.txt cache: ./cache/cord-331879-w7008uyy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331879-w7008uyy.txt' === file2bib.sh === id: cord-330465-16j5vm7h author: Marciniec, Krzysztof title: Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-330465-16j5vm7h.txt cache: ./cache/cord-330465-16j5vm7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330465-16j5vm7h.txt' === file2bib.sh === id: cord-317277-rr9zue4l author: Cifuentes-Munoz, Nicolas title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-317277-rr9zue4l.txt cache: ./cache/cord-317277-rr9zue4l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-317277-rr9zue4l.txt' === file2bib.sh === id: cord-318272-spt0oea0 author: Bhardwaj, Prateek title: Advancements in prophylactic and therapeutic nanovaccines date: 2020-04-05 pages: extension: .txt txt: ./txt/cord-318272-spt0oea0.txt cache: ./cache/cord-318272-spt0oea0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-318272-spt0oea0.txt' === file2bib.sh === id: cord-330698-9t24jo8s author: Wurdinger, Thomas title: Extracellular Vesicles and Their Convergence with Viral Pathways date: 2012-07-25 pages: extension: .txt txt: ./txt/cord-330698-9t24jo8s.txt cache: ./cache/cord-330698-9t24jo8s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330698-9t24jo8s.txt' === file2bib.sh === id: cord-319116-2ts6zpdb author: Ruggiero, Emanuela title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-319116-2ts6zpdb.txt cache: ./cache/cord-319116-2ts6zpdb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319116-2ts6zpdb.txt' === file2bib.sh === id: cord-316904-g7dli0a8 author: Chang, Hernan R. title: Role of cytokines in AIDS wasting date: 1998-12-31 pages: extension: .txt txt: ./txt/cord-316904-g7dli0a8.txt cache: ./cache/cord-316904-g7dli0a8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316904-g7dli0a8.txt' === file2bib.sh === id: cord-330581-g5r2b043 author: Marini, Elena title: HIV‐1 matrix protein p17 binds to monocytes and selectively stimulates MCP‐1 secretion: role of transcriptional factor AP‐1 date: 2007-10-26 pages: extension: .txt txt: ./txt/cord-330581-g5r2b043.txt cache: ./cache/cord-330581-g5r2b043.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-330581-g5r2b043.txt' === file2bib.sh === id: cord-338594-wft7yy6j author: Winkler, Michael title: Rhesus macaque IFITM3 gene polymorphisms and SIV infection date: 2017-03-03 pages: extension: .txt txt: ./txt/cord-338594-wft7yy6j.txt cache: ./cache/cord-338594-wft7yy6j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338594-wft7yy6j.txt' === file2bib.sh === id: cord-334855-s0ci3r8w author: Andersen, Petter I. title: Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date: 2019-10-18 pages: extension: .txt txt: ./txt/cord-334855-s0ci3r8w.txt cache: ./cache/cord-334855-s0ci3r8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-334855-s0ci3r8w.txt' === file2bib.sh === id: cord-027860-s97hdhh6 author: Zeimet, Anthony title: Infectious Diseases date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-027860-s97hdhh6.txt cache: ./cache/cord-027860-s97hdhh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-027860-s97hdhh6.txt' === file2bib.sh === id: cord-328287-3qgzulgj author: Moni, Mohammad Ali title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 pages: extension: .txt txt: ./txt/cord-328287-3qgzulgj.txt cache: ./cache/cord-328287-3qgzulgj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328287-3qgzulgj.txt' === file2bib.sh === id: cord-302403-kahi8cbc author: Miller, Robert F. title: Pulmonary Infections date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-302403-kahi8cbc.txt cache: ./cache/cord-302403-kahi8cbc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302403-kahi8cbc.txt' === file2bib.sh === id: cord-333405-ji58jbct author: Morens, David M. title: The challenge of emerging and re-emerging infectious diseases date: 2004-07-08 pages: extension: .txt txt: ./txt/cord-333405-ji58jbct.txt cache: ./cache/cord-333405-ji58jbct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333405-ji58jbct.txt' === file2bib.sh === id: cord-340619-3tjquzx8 author: Menghua, Wu title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-340619-3tjquzx8.txt cache: ./cache/cord-340619-3tjquzx8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340619-3tjquzx8.txt' === file2bib.sh === id: cord-322915-zrjx31ev author: Demain, Arnold L title: Microbial drug discovery: 80 years of progress date: 2009-01-09 pages: extension: .txt txt: ./txt/cord-322915-zrjx31ev.txt cache: ./cache/cord-322915-zrjx31ev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322915-zrjx31ev.txt' === file2bib.sh === id: cord-342719-bdxb45us author: Yamamoto, Shinya title: Antibody Response to SARS-CoV-2 in people living with HIV date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-342719-bdxb45us.txt cache: ./cache/cord-342719-bdxb45us.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342719-bdxb45us.txt' === file2bib.sh === id: cord-341503-3cvtoc2j author: Jaiswal, J. title: Disinformation, Misinformation and Inequality-Driven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism date: 2020-05-21 pages: extension: .txt txt: ./txt/cord-341503-3cvtoc2j.txt cache: ./cache/cord-341503-3cvtoc2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341503-3cvtoc2j.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 12111 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: 14268 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-327135-4c2flue4 author: Chinnaswamy, S title: Gene–disease association with human IFNL locus polymorphisms extends beyond hepatitis C virus infections date: 2016-06-09 pages: extension: .txt txt: ./txt/cord-327135-4c2flue4.txt cache: ./cache/cord-327135-4c2flue4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-327135-4c2flue4.txt' === file2bib.sh === id: cord-323261-1of5ertf author: Lo, Catherine Yuk-ping title: Securitizing HIV/AIDS: a game changer in state-societal relations in China? date: 2018-05-16 pages: extension: .txt txt: ./txt/cord-323261-1of5ertf.txt cache: ./cache/cord-323261-1of5ertf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323261-1of5ertf.txt' === file2bib.sh === id: cord-337315-qv8ycdhe author: Miller, Maureen title: Integrated biological–behavioural surveillance in pandemic-threat warning systems date: 2017-01-01 pages: extension: .txt txt: ./txt/cord-337315-qv8ycdhe.txt cache: ./cache/cord-337315-qv8ycdhe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337315-qv8ycdhe.txt' === file2bib.sh === id: cord-329482-haenltxn author: Small, Eusebius title: Covid-19 and Gender in LMICs: Potential Lessons from HIV Pandemic date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-329482-haenltxn.txt cache: ./cache/cord-329482-haenltxn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329482-haenltxn.txt' === file2bib.sh === id: cord-341304-jdvzpvdx author: Pata, Rama Kanth title: Human Immunodeficiency Virus: A Dark Cloud With Silver Lining During the COVID-19 Pandemic date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-341304-jdvzpvdx.txt cache: ./cache/cord-341304-jdvzpvdx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341304-jdvzpvdx.txt' === file2bib.sh === id: cord-338654-ma9ayu80 author: Eaton, Lisa A. title: Social and behavioral health responses to COVID-19: lessons learned from four decades of an HIV pandemic date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-338654-ma9ayu80.txt cache: ./cache/cord-338654-ma9ayu80.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338654-ma9ayu80.txt' === file2bib.sh === id: cord-334454-cqaado3u author: Leal, Rodolfo Oliveira title: The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives date: 2016-10-27 pages: extension: .txt txt: ./txt/cord-334454-cqaado3u.txt cache: ./cache/cord-334454-cqaado3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334454-cqaado3u.txt' === file2bib.sh === id: cord-341323-mw352rr1 author: Logie, Carmen H title: Lessons learned from HIV can inform our approach to COVID‐19 stigma date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-341323-mw352rr1.txt cache: ./cache/cord-341323-mw352rr1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341323-mw352rr1.txt' === file2bib.sh === id: cord-346557-s6c7d70y author: Brennan, David J. title: How Might Social Distancing Impact Gay, Bisexual, Queer, Trans and Two-Spirit Men in Canada? date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-346557-s6c7d70y.txt cache: ./cache/cord-346557-s6c7d70y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346557-s6c7d70y.txt' === file2bib.sh === id: cord-331289-02411gfv author: Di Minno, Giovanni title: Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date: 2015-07-20 pages: extension: .txt txt: ./txt/cord-331289-02411gfv.txt cache: ./cache/cord-331289-02411gfv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331289-02411gfv.txt' === file2bib.sh === id: cord-329223-f84gjxm1 author: Kouokam, Joseph Calvin title: Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date: 2011-08-02 pages: extension: .txt txt: ./txt/cord-329223-f84gjxm1.txt cache: ./cache/cord-329223-f84gjxm1.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329223-f84gjxm1.txt' === file2bib.sh === id: cord-338804-nreqluol author: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-338804-nreqluol.txt cache: ./cache/cord-338804-nreqluol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-338804-nreqluol.txt' === file2bib.sh === id: cord-340389-0fybiybv author: Fahrioglu, Umut title: CCR5-Δ32 gene variant frequency in the Turkish Cypriot population date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-340389-0fybiybv.txt cache: ./cache/cord-340389-0fybiybv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340389-0fybiybv.txt' === file2bib.sh === id: cord-337897-hkvll3xh author: Yang, Zheng Rong title: Peptide Bioinformatics- Peptide Classification Using Peptide Machines date: 2009 pages: extension: .txt txt: ./txt/cord-337897-hkvll3xh.txt cache: ./cache/cord-337897-hkvll3xh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337897-hkvll3xh.txt' === file2bib.sh === id: cord-333622-0ddutmdd author: Dyer, Wayne B title: Mechanisms of HIV non-progression; robust and sustained CD4+ T-cell proliferative responses to p24 antigen correlate with control of viraemia and lack of disease progression after long-term transfusion-acquired HIV-1 infection date: 2008-12-11 pages: extension: .txt txt: ./txt/cord-333622-0ddutmdd.txt cache: ./cache/cord-333622-0ddutmdd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-333622-0ddutmdd.txt' === file2bib.sh === id: cord-340879-gu91cact author: Li, Miao title: Isolation and Characterization of a Phaseolus vulgaris Trypsin Inhibitor with Antiproliferative Activity on Leukemia and Lymphoma Cells date: 2017-01-23 pages: extension: .txt txt: ./txt/cord-340879-gu91cact.txt cache: ./cache/cord-340879-gu91cact.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340879-gu91cact.txt' === file2bib.sh === id: cord-340703-vtuy806l author: Cascio, Antonio title: Low bone mineral density in HIV-positive young Italians and migrants date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-340703-vtuy806l.txt cache: ./cache/cord-340703-vtuy806l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340703-vtuy806l.txt' === file2bib.sh === id: cord-326725-0jgw083h author: Klamroth, Robert title: Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date: 2013-09-30 pages: extension: .txt txt: ./txt/cord-326725-0jgw083h.txt cache: ./cache/cord-326725-0jgw083h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326725-0jgw083h.txt' === file2bib.sh === id: cord-332610-t99l3zii author: Mayer, J.D. title: Emerging Diseases: Overview date: 2008-08-26 pages: extension: .txt txt: ./txt/cord-332610-t99l3zii.txt cache: ./cache/cord-332610-t99l3zii.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332610-t99l3zii.txt' === file2bib.sh === id: cord-345771-3v2avxiv author: Traub, Ariana Moriah title: Multimonth Dispensing of Antiretroviral Therapy Protects the Most Vulnerable From 2 Pandemics at Once date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-345771-3v2avxiv.txt cache: ./cache/cord-345771-3v2avxiv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345771-3v2avxiv.txt' === file2bib.sh === id: cord-318363-1mv5j4w2 author: Zvolensky, Michael J. title: Psychological, addictive, and health behavior implications of the COVID-19 pandemic date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-318363-1mv5j4w2.txt cache: ./cache/cord-318363-1mv5j4w2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318363-1mv5j4w2.txt' === file2bib.sh === id: cord-339341-c2o42b5j author: Matibag, Gino C. title: Advocacy, promotion and e-learning: Supercourse for zoonosis date: 2005-09-01 pages: extension: .txt txt: ./txt/cord-339341-c2o42b5j.txt cache: ./cache/cord-339341-c2o42b5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339341-c2o42b5j.txt' === file2bib.sh === id: cord-329890-wg23sa1u author: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 pages: extension: .txt txt: ./txt/cord-329890-wg23sa1u.txt cache: ./cache/cord-329890-wg23sa1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329890-wg23sa1u.txt' === file2bib.sh === id: cord-349104-p0egfpx9 author: Modi, Anita R. title: Coronavirus disease 2019 in an orthotopic liver transplant recipient living with human immunodeficiency virus date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-349104-p0egfpx9.txt cache: ./cache/cord-349104-p0egfpx9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349104-p0egfpx9.txt' === file2bib.sh === id: cord-285898-rtqkvf63 author: Padberg, Stephanie title: Anti-infective Agents date: 2014-09-29 pages: extension: .txt txt: ./txt/cord-285898-rtqkvf63.txt cache: ./cache/cord-285898-rtqkvf63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-285898-rtqkvf63.txt' === file2bib.sh === id: cord-338572-5ifc2lx6 author: Nagarakanti, Sandhya R. title: Clinical outcomes of patients with COVID‐19 and HIV coinfection date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-338572-5ifc2lx6.txt cache: ./cache/cord-338572-5ifc2lx6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338572-5ifc2lx6.txt' === file2bib.sh === id: cord-341838-lkz8ro90 author: Gervasoni, Cristina title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-341838-lkz8ro90.txt cache: ./cache/cord-341838-lkz8ro90.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341838-lkz8ro90.txt' === file2bib.sh === id: cord-351004-h6fde7vm author: Gudipati, Smitha title: Descriptive Analysis of Patients Living With HIV Affected by COVID-19 date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-351004-h6fde7vm.txt cache: ./cache/cord-351004-h6fde7vm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351004-h6fde7vm.txt' === file2bib.sh === id: cord-334010-gxu0refq author: Banerjee, Nilotpal title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 pages: extension: .txt txt: ./txt/cord-334010-gxu0refq.txt cache: ./cache/cord-334010-gxu0refq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-334010-gxu0refq.txt' === file2bib.sh === id: cord-334133-61om170g author: Hollier, Mark J. title: The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date: 2005-07-05 pages: extension: .txt txt: ./txt/cord-334133-61om170g.txt cache: ./cache/cord-334133-61om170g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-334133-61om170g.txt' === file2bib.sh === id: cord-351740-779g8tr1 author: Khaba, Moshawa Calvin title: COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-351740-779g8tr1.txt cache: ./cache/cord-351740-779g8tr1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351740-779g8tr1.txt' === file2bib.sh === id: cord-340777-d1vwjqk6 author: O’Byrne, Patrick title: Immediate PrEP after PEP: Results from an Observational Nurse-Led PEP2PrEP Study date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-340777-d1vwjqk6.txt cache: ./cache/cord-340777-d1vwjqk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340777-d1vwjqk6.txt' === file2bib.sh === id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-330800-s91zfzfi.txt cache: ./cache/cord-330800-s91zfzfi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330800-s91zfzfi.txt' === file2bib.sh === id: cord-353895-tgn1kk07 author: Kavanagh, Matthew M title: Reckoning with mortality: global health, HIV, and the politics of data date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-353895-tgn1kk07.txt cache: ./cache/cord-353895-tgn1kk07.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353895-tgn1kk07.txt' === file2bib.sh === id: cord-340763-cxnu9g8y author: Grimm, Sebastian K. title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date: 2015-02-17 pages: extension: .txt txt: ./txt/cord-340763-cxnu9g8y.txt cache: ./cache/cord-340763-cxnu9g8y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-340763-cxnu9g8y.txt' === file2bib.sh === id: cord-350540-s6is9ndm author: Pinto, Rogério M. title: COVID-19 Pandemic Disrupts HIV Continuum of Care and Prevention: Implications for Research and Practice Concerning Community-Based Organizations and Frontline Providers date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-350540-s6is9ndm.txt cache: ./cache/cord-350540-s6is9ndm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350540-s6is9ndm.txt' === file2bib.sh === id: cord-345342-04tvuj9f author: Kumar, Rebecca N. title: COVID‐19 in an HIV‐positive Kidney Transplant Recipient date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-345342-04tvuj9f.txt cache: ./cache/cord-345342-04tvuj9f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345342-04tvuj9f.txt' === file2bib.sh === id: cord-341298-mqpovrms author: Morse, S.A. title: Viruses and Bioterrorism date: 2016-10-31 pages: extension: .txt txt: ./txt/cord-341298-mqpovrms.txt cache: ./cache/cord-341298-mqpovrms.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341298-mqpovrms.txt' === file2bib.sh === id: cord-341097-c96hm610 author: Mayer, Craig S. title: Analysis of data dictionary formats of HIV clinical trials date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-341097-c96hm610.txt cache: ./cache/cord-341097-c96hm610.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341097-c96hm610.txt' === file2bib.sh === id: cord-355475-kdubhh73 author: Patton, Lauren L. title: Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-355475-kdubhh73.txt cache: ./cache/cord-355475-kdubhh73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355475-kdubhh73.txt' === file2bib.sh === id: cord-346153-9162w7il author: Openshaw, P J title: Crossing barriers: infections of the lung and the gut date: 2008-12-24 pages: extension: .txt txt: ./txt/cord-346153-9162w7il.txt cache: ./cache/cord-346153-9162w7il.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346153-9162w7il.txt' === file2bib.sh === id: cord-316273-vo6j8zb0 author: Cosset, François-Loic title: Cell Entry of Enveloped Viruses date: 2011-02-08 pages: extension: .txt txt: ./txt/cord-316273-vo6j8zb0.txt cache: ./cache/cord-316273-vo6j8zb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-316273-vo6j8zb0.txt' === file2bib.sh === id: cord-354374-rtgjjglc author: C.G. Pollok, Richard title: Enteric viruses in HIV-related diarrhoea date: 2000-12-01 pages: extension: .txt txt: ./txt/cord-354374-rtgjjglc.txt cache: ./cache/cord-354374-rtgjjglc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354374-rtgjjglc.txt' === file2bib.sh === id: cord-339796-gccnvh0z author: Zhang, Si Min title: Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date: 2015-07-31 pages: extension: .txt txt: ./txt/cord-339796-gccnvh0z.txt cache: ./cache/cord-339796-gccnvh0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-339796-gccnvh0z.txt' === file2bib.sh === id: cord-346424-gfccstoz author: Friedrich, Brian M title: A Functional Role for ADAM10 in Human Immunodeficiency Virus Type-1 Replication date: 2011-05-11 pages: extension: .txt txt: ./txt/cord-346424-gfccstoz.txt cache: ./cache/cord-346424-gfccstoz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-346424-gfccstoz.txt' === file2bib.sh === id: cord-355439-eqtk51q3 author: Lesko, Catherine R title: HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-355439-eqtk51q3.txt cache: ./cache/cord-355439-eqtk51q3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355439-eqtk51q3.txt' === file2bib.sh === id: cord-347356-uc9dqhyq author: Cooper, TJ title: Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-347356-uc9dqhyq.txt cache: ./cache/cord-347356-uc9dqhyq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347356-uc9dqhyq.txt' === file2bib.sh === id: cord-337659-x4oywbrj author: Wilson, Brenda A. title: Global biosecurity in a complex, dynamic world date: 2008-07-31 pages: extension: .txt txt: ./txt/cord-337659-x4oywbrj.txt cache: ./cache/cord-337659-x4oywbrj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337659-x4oywbrj.txt' === file2bib.sh === id: cord-349790-dezauioa author: Johnson, Stephanie title: Ethical challenges in pathogen sequencing: a systematic scoping review date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-349790-dezauioa.txt cache: ./cache/cord-349790-dezauioa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349790-dezauioa.txt' === file2bib.sh === id: cord-348409-oxjd263z author: Stern, Zachariah title: The development of inovirus-associated vector vaccines using phage-display technologies date: 2019-09-08 pages: extension: .txt txt: ./txt/cord-348409-oxjd263z.txt cache: ./cache/cord-348409-oxjd263z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348409-oxjd263z.txt' === file2bib.sh === id: cord-353012-rxhi8wd2 author: Zhou, Nan title: Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date: 2016-03-07 pages: extension: .txt txt: ./txt/cord-353012-rxhi8wd2.txt cache: ./cache/cord-353012-rxhi8wd2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353012-rxhi8wd2.txt' === file2bib.sh === id: cord-354974-bh2expef author: Peterson, Ingrid title: Respiratory Virus–Associated Severe Acute Respiratory Illness and Viral Clustering in Malawian Children in a Setting With a High Prevalence of HIV Infection, Malaria, and Malnutrition date: 2016-09-13 pages: extension: .txt txt: ./txt/cord-354974-bh2expef.txt cache: ./cache/cord-354974-bh2expef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354974-bh2expef.txt' === file2bib.sh === id: cord-342936-43u7afl3 author: Balzarini, Jan title: Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date: 2007 pages: extension: .txt txt: ./txt/cord-342936-43u7afl3.txt cache: ./cache/cord-342936-43u7afl3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-342936-43u7afl3.txt' === file2bib.sh === id: cord-350221-8u6q3wfa author: Yang, Sung-Tae title: HIV virions sense plasma membrane heterogeneity for cell entry date: 2017-06-28 pages: extension: .txt txt: ./txt/cord-350221-8u6q3wfa.txt cache: ./cache/cord-350221-8u6q3wfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350221-8u6q3wfa.txt' === file2bib.sh === id: cord-343470-w215pzdc author: Tsai, Kevin title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-343470-w215pzdc.txt cache: ./cache/cord-343470-w215pzdc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-343470-w215pzdc.txt' === file2bib.sh === id: cord-346314-o9fjpqaj author: Jarboui, Mohamed Ali title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 pages: extension: .txt txt: ./txt/cord-346314-o9fjpqaj.txt cache: ./cache/cord-346314-o9fjpqaj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346314-o9fjpqaj.txt' === file2bib.sh === id: cord-354050-kcn67stj author: Shi, Guoli title: More than meets the I: the diverse antiviral and cellular functions of interferon-induced transmembrane proteins date: 2017-11-21 pages: extension: .txt txt: ./txt/cord-354050-kcn67stj.txt cache: ./cache/cord-354050-kcn67stj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354050-kcn67stj.txt' === file2bib.sh === id: cord-354790-xx6imhzb author: Lambour, Jennifer title: Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play date: 2016-08-17 pages: extension: .txt txt: ./txt/cord-354790-xx6imhzb.txt cache: ./cache/cord-354790-xx6imhzb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354790-xx6imhzb.txt' === file2bib.sh === id: cord-341155-3d64mso0 author: Slots, Jørgen title: Bacterial and viral pathogens in saliva: disease relationship and infectious risk date: 2010-12-07 pages: extension: .txt txt: ./txt/cord-341155-3d64mso0.txt cache: ./cache/cord-341155-3d64mso0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341155-3d64mso0.txt' === file2bib.sh === id: cord-350443-ca5avyjf author: Zhang, Lei title: Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date: 2012-02-16 pages: extension: .txt txt: ./txt/cord-350443-ca5avyjf.txt cache: ./cache/cord-350443-ca5avyjf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350443-ca5avyjf.txt' === file2bib.sh === id: cord-355541-5sctqkwr author: Alcamí, José title: Current situation in the development of a preventive HIV vaccine date: 2005-07-31 pages: extension: .txt txt: ./txt/cord-355541-5sctqkwr.txt cache: ./cache/cord-355541-5sctqkwr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355541-5sctqkwr.txt' === file2bib.sh === id: cord-303165-ikepr2p2 author: Tulchinsky, Theodore H. title: Expanding the Concept of Public Health date: 2014-10-10 pages: extension: .txt txt: ./txt/cord-303165-ikepr2p2.txt cache: ./cache/cord-303165-ikepr2p2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-303165-ikepr2p2.txt' === file2bib.sh === id: cord-354972-nc496v6s author: Margolin, Emmanuel title: Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-354972-nc496v6s.txt cache: ./cache/cord-354972-nc496v6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354972-nc496v6s.txt' === file2bib.sh === id: cord-347992-coby2m6e author: Marton, Soledad title: In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules date: 2010-06-28 pages: extension: .txt txt: ./txt/cord-347992-coby2m6e.txt cache: ./cache/cord-347992-coby2m6e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347992-coby2m6e.txt' === file2bib.sh === id: cord-333655-lylt7qld author: Van Breedam, Wander title: Bitter‐sweet symphony: glycan–lectin interactions in virus biology date: 2013-12-06 pages: extension: .txt txt: ./txt/cord-333655-lylt7qld.txt cache: ./cache/cord-333655-lylt7qld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333655-lylt7qld.txt' === file2bib.sh === id: cord-264408-vk4lt83x author: Ruiz, Sara I. title: Animal Models of Human Viral Diseases date: 2017-06-23 pages: extension: .txt txt: ./txt/cord-264408-vk4lt83x.txt cache: ./cache/cord-264408-vk4lt83x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-264408-vk4lt83x.txt' === file2bib.sh === id: cord-350569-dtxtjtfo author: Kasoka, Kasoka title: Autonomy in HIV testing: a call for a rethink of personal autonomy in the HIV response in sub-Saharan Africa date: 2020-06-13 pages: extension: .txt txt: ./txt/cord-350569-dtxtjtfo.txt cache: ./cache/cord-350569-dtxtjtfo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-350569-dtxtjtfo.txt' === file2bib.sh === id: cord-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 pages: extension: .txt txt: ./txt/cord-349358-leicos9j.txt cache: ./cache/cord-349358-leicos9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349358-leicos9j.txt' === file2bib.sh === id: cord-020010-q58x6xb0 author: nan title: 19th ICAR Abstracts: date: 2006-03-13 pages: extension: .txt txt: ./txt/cord-020010-q58x6xb0.txt cache: ./cache/cord-020010-q58x6xb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-020010-q58x6xb0.txt' === file2bib.sh === id: cord-330852-n7j0c4ne author: Fischer, Wolfgang B. title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 pages: extension: .txt txt: ./txt/cord-330852-n7j0c4ne.txt cache: ./cache/cord-330852-n7j0c4ne.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330852-n7j0c4ne.txt' === file2bib.sh === id: cord-354029-mp5r82g4 author: Earp, L. J. title: The Many Mechanisms of Viral Membrane Fusion Proteins date: 2005 pages: extension: .txt txt: ./txt/cord-354029-mp5r82g4.txt cache: ./cache/cord-354029-mp5r82g4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354029-mp5r82g4.txt' === file2bib.sh === id: cord-355318-qm79gz8w author: Smit, Albertus J. title: Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-355318-qm79gz8w.txt cache: ./cache/cord-355318-qm79gz8w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-355318-qm79gz8w.txt' === file2bib.sh === id: cord-339879-92esdjy9 author: Delhalle, Sylvie title: Phages and HIV-1: From Display to Interplay date: 2012-04-13 pages: extension: .txt txt: ./txt/cord-339879-92esdjy9.txt cache: ./cache/cord-339879-92esdjy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-339879-92esdjy9.txt' === file2bib.sh === id: cord-325300-wawui0fd author: Tulchinsky, Theodore H. title: 4 Communicable Diseases date: 2000-12-31 pages: extension: .txt txt: ./txt/cord-325300-wawui0fd.txt cache: ./cache/cord-325300-wawui0fd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325300-wawui0fd.txt' === file2bib.sh === id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 pages: extension: .txt txt: ./txt/cord-340489-yo3cp5vs.txt cache: ./cache/cord-340489-yo3cp5vs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-340489-yo3cp5vs.txt' === file2bib.sh === id: cord-305085-bv7udg9k author: Lawrence, Robert M. title: Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date: 2011-12-31 pages: extension: .txt txt: ./txt/cord-305085-bv7udg9k.txt cache: ./cache/cord-305085-bv7udg9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-305085-bv7udg9k.txt' === file2bib.sh === id: cord-337458-dc90ecfe author: Markwalter, Christine F. title: Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date: 2018-12-04 pages: extension: .txt txt: ./txt/cord-337458-dc90ecfe.txt cache: ./cache/cord-337458-dc90ecfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337458-dc90ecfe.txt' === file2bib.sh === id: cord-023017-k6edtg58 author: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 pages: extension: .txt txt: ./txt/cord-023017-k6edtg58.txt cache: ./cache/cord-023017-k6edtg58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023017-k6edtg58.txt' === file2bib.sh === id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-347710-ff64y6ef.txt cache: ./cache/cord-347710-ff64y6ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-347710-ff64y6ef.txt' === file2bib.sh === id: cord-002774-tpqsjjet author: nan title: Section II: Poster Sessions date: 2017-12-01 pages: extension: .txt txt: ./txt/cord-002774-tpqsjjet.txt cache: ./cache/cord-002774-tpqsjjet.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-002774-tpqsjjet.txt' === file2bib.sh === 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 10 resourceName b'cord-007890-bie1veti.txt' === file2bib.sh === id: cord-019347-tj3ye1mx author: nan title: ABSTRACT BOOK date: 2010-02-19 pages: extension: .txt txt: ./txt/cord-019347-tj3ye1mx.txt cache: ./cache/cord-019347-tj3ye1mx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-019347-tj3ye1mx.txt' === file2bib.sh === id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023346-8sqbqjm1.txt cache: ./cache/cord-023346-8sqbqjm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023346-8sqbqjm1.txt' === file2bib.sh === id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023354-f2ciho6o.txt cache: ./cache/cord-023354-f2ciho6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 19 resourceName b'cord-023354-f2ciho6o.txt' === file2bib.sh === id: cord-350571-6tapkjb6 author: nan title: 45th ESCP-NSF international symposium on clinical pharmacy: clinical pharmacy tackling inequalities and access to health care. Oslo, Norway, 5–7 October 2016 date: 2017-01-10 pages: extension: .txt txt: ./txt/cord-350571-6tapkjb6.txt cache: ./cache/cord-350571-6tapkjb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-350571-6tapkjb6.txt' === file2bib.sh === id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023364-ut56gczm.txt cache: ./cache/cord-023364-ut56gczm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023364-ut56gczm.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-022633-fr55uod6 author: nan title: SAEM Abstracts, Plenary Session date: 2012-04-26 pages: extension: .txt txt: ./txt/cord-022633-fr55uod6.txt cache: ./cache/cord-022633-fr55uod6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022633-fr55uod6.txt' === file2bib.sh === id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 pages: extension: .txt txt: ./txt/cord-022888-dnsdg04n.txt cache: ./cache/cord-022888-dnsdg04n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-022888-dnsdg04n.txt' === file2bib.sh === id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-031907-ilhr3iu5.txt cache: ./cache/cord-031907-ilhr3iu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 16 resourceName b'cord-031907-ilhr3iu5.txt' === file2bib.sh === id: cord-015324-y44sfr0c author: nan title: Scientific Programme date: 2007-09-01 pages: extension: .txt txt: ./txt/cord-015324-y44sfr0c.txt cache: ./cache/cord-015324-y44sfr0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 13 resourceName b'cord-015324-y44sfr0c.txt' === file2bib.sh === id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 pages: extension: .txt txt: ./txt/cord-010092-uftc8inx.txt cache: ./cache/cord-010092-uftc8inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-010092-uftc8inx.txt' === file2bib.sh === id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 pages: extension: .txt txt: ./txt/cord-010119-t1x9gknd.txt cache: ./cache/cord-010119-t1x9gknd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-010119-t1x9gknd.txt' Que is empty; done keyword-hiv-cord === reduce.pl bib === === reduce.pl bib === id = cord-000077-d441jam3 author = Zhang, Hao-Jie title = The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date = 2009-07-03 pages = extension = .txt mime = text/plain words = 5426 sentences = 267 flesch = 54 summary = Reverse transcriptase (RT) of human immunodeficiency virus (HIV)-1 plays a key role in initiating viral replication and is an important target for developing anti-HIV drugs. Our native gel analysis indicated that the mutations at 271 and 274 amino acids might cause conformational changes, leading to the formation of higher order oligomers instead of dimers, resulting in increased protein instability and susceptibility to viral protease. As shown in Fig. 3A , similar levels of Pr160 gag-pol , Gag protein (Pr55 Gag ) and capsid protein p24 (CA p24) were found in cells transfected with the wild type or mutant constructs, indicating that the expression and stability of RT precursor protein were not affected by the mutations. To study if the RTs in the viral particles of Y271A and I274A mutants were degraded by proteolysis that made them undetectable, pseudoviruses of wild type and mutants were generated in the presence or absence of indinavir, a highly specific inhibitor of HIV-1 protease. cache = ./cache/cord-000077-d441jam3.txt txt = ./txt/cord-000077-d441jam3.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-000008-3dgjv0x1 author = Vali, Bahareh title = HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date = 2008-10-20 pages = extension = .txt mime = text/plain words = 5253 sentences = 236 flesch = 47 summary = In response to stimulation with HIV peptide pool, untreated co-infected individuals showed significantly higher frequencies of intra-hepatic CD4 + T-cells producing IFN-c, compared to HCV mono-infected [0.1660.05% vs 0.0260.01%, p,0.05], and HAART-treated co-infected individuals [0.1660.05% vs 0.0360.05%, p,0.05] (Figure 2a ). Therapy naïve co-infected subjects had greater IFN-c producing CD8 + T-cells in response to HIV peptides compared to HCV mono-infected individuals [1.3960.37% vs 0.0260.0%, p,0.05], and HAART was associated with a significant reduction in the frequencies of these cells [1.3960.37% vs 0.3060.26%, p,0.05] (figure 2b). The tetramer cytokine response pattern was shown to be different in the liver compared to blood of the same individual, with diminished intra-hepatic tetramer-specific IFN-c responses and an increase in both CD107a and TNF-a responses, with the majority of SL9 tetramer positive cells expressing these two markers. Therapy naïve co-infected individuals demonstrated a higher frequency of intra-hepatic CD8 + T-cells that produce TNF-a in response to both HCV and HIV antigen stimulation compared to HCV mono-infected individuals. cache = ./cache/cord-000008-3dgjv0x1.txt txt = ./txt/cord-000008-3dgjv0x1.txt === reduce.pl bib === id = cord-000130-dqqcajjd author = Smith?, Robert J title = The OptAIDS project: towards global halting of HIV/AIDS date = 2009-11-18 pages = extension = .txt mime = text/plain words = 2383 sentences = 146 flesch = 54 summary = The OptAIDS workshop was the first of its kind: a scientific meeting held simultaneously in both a real world location and also Second Life ® http://secondlife.com, a virtual landscape that allows real-time communication. Spending our way out of the epidemic Theme 1 comprises an introduction and overview of mathematical modeling [22] , as well as a history of AIDS in Africa and its effects on human development [23] . Theme 4 examines in-host modeling -a crucial element in tackling the disease, often overlooked by epidemiologists -by proposing new methods for evaluating the efficacy of antiretroviral treatment [31] and examining antioxidant supplementation as HIV therapy, with a focus on injecting drug users [32] . Finally, Theme 6 examines the question at the core of the OptAIDS project: spending our way out of the AIDS epidemic [6] . Predicting and preventing measles epidemics in New Zealand: application of a mathematical model Halting HIV/AIDS with avatars and havatars: a virtual world approach to modelling epidemics cache = ./cache/cord-000130-dqqcajjd.txt txt = ./txt/cord-000130-dqqcajjd.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004575-b0t6bsya author = Staub, Roger title = Haben HIV-Positive eine besondere Verantwortung?: Ein Diskussionsbeitrag date = 2007-03-27 pages = extension = .txt mime = text/plain words = 1953 sentences = 233 flesch = 62 summary = Von HIV-infizierten Menschen sollten wir erwarten, dass sie den geliebten Partner, die geliebte Partnerin nicht gefährden bei sexuellen Begegnungen, die im Rahmen einer aktuellen oder erhofften zukünftigen Beziehung stattfinden. Auch von einer HIV-positiven Prostituierten oder von einem HIV-positiven Homosexuellen bei einem One-Night-Stand ist nicht zu erwarten, dass sie Verantwortung für den Schutz des anderen übernehmen. Lässt sich eine HIV-positive Person auf eine so geartete Beziehung ein, kann die Liebe nach dem Verlobungstest nur weiter gedeihen, wenn der HIV-positive oder ungetestete Partner von Anfang an seine Verantwortung wahrgenommen und für konsequenten Schutz gesorgt hat. Wenn wir es schaffen, auch von einer HIV-positiven Prostituierten nicht zu erwarten, dass sie auf das Angebot eines Freiers verzichten muss, der für "ohne" gar mehr bezahlen will, dann können wir auch mit Freiern deutlich kommunizieren und sie zum "immer mit" motivieren. cache = ./cache/cord-004575-b0t6bsya.txt txt = ./txt/cord-004575-b0t6bsya.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-000868-vnwpzsu8 author = Eissmann, Kristin title = HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop date = 2013-01-22 pages = extension = .txt mime = text/plain words = 9072 sentences = 425 flesch = 51 summary = Performing a virus-cell fusion assay and temperature-arrested HIV-infection kinetics, we provide evidence that the HIV-inhibitory E2 peptides interfere with late HIV-1 entry steps after the engagement of gp120 with CD4 receptor and coreceptor. Using synthetic peptides presenting different regions of E2, we recently demonstrated that this interference with HIV-1 entry can be ascribed to the N-terminal part of the GBV-C E2 protein ranging from residue 29 to 72 (according to GenBank accession no. The Effect of GBV-C E2 Peptides Arises After gp120/CD4 and gp120/coreceptor engagement To find out whether early or late steps of HIV-1 entry are affected by the E2 peptides, the E2 peptide activity was determined before and after gp120/CD4 engagement using the Vpr-b-lactamase (Vpr-BlaM) enzyme-based virus-cell fusion assay under standard (pre-CD4 binding) and temperature-arrested state (TAS; post-CD4 binding) conditions, respectively. cache = ./cache/cord-000868-vnwpzsu8.txt txt = ./txt/cord-000868-vnwpzsu8.txt === reduce.pl bib === === reduce.pl bib === id = cord-003715-deqiets2 author = Warren, Cody J. title = Selective use of primate CD4 receptors by HIV-1 date = 2019-06-10 pages = extension = .txt mime = text/plain words = 9529 sentences = 457 flesch = 55 summary = We next tested HIV-1 pseudotyped with Envs from four macrophage-tropic viruses [31, [64] [65] [66] [67] [68] [69] [70] [71] [72] for their ability to infect cells bearing primate CD4 receptors ( Fig 3B) . (A, B) Cells stably expressing various primate CD4 receptors (x-axis), along with human CCR5, were infected with Q23ΔEnv-GFP pseudotyped with (A) early HIV-1 Envelopes (Envs) or (B) Envs from common macrophagetropic HIV-1 isolates. Collectively, these data suggest that most early HIV-1 isolates from the blood, which have lower affinity for human CD4 compared to macrophage-tropic viruses, do not bind well to chimpanzee and macaque CD4. In this study, we have shown that Envs from over 30 early and chronic HIV-1 isolates from human blood (mother-infant pairs, etc.) all demonstrate selective entry via only some primate CD4 receptors. (B) Dog thymocytes (Cf2Th cells) stably expressing human CCR5 and the indicated rhesus macaque CD4 alleles (x-axis) were infected with HIV-1 (Q23ΔEnv-GFP) bearing a subtype A (BG505) or subtype C (CAP210.2.00.E8) Envelope (Env). cache = ./cache/cord-003715-deqiets2.txt txt = ./txt/cord-003715-deqiets2.txt === reduce.pl bib === === reduce.pl bib === id = cord-001972-1zisomq5 author = Wang, Xue title = Pandemic Influenza A (H1N1) Virus Infection Increases Apoptosis and HIV-1 Replication in HIV-1 Infected Jurkat Cells date = 2016-02-02 pages = extension = .txt mime = text/plain words = 3921 sentences = 197 flesch = 46 summary = These data indicate that HIV-1 replication can be activated by pH1N1 virus in HIV-1-infected cells resulting in induction of cell death through apoptotic pathways. Cells treated with pH1N1 had higher level of NF-kB phosphorylation and increased protein expression of NFAT and AP-1 ( Figure 3B ) relative to HIV-1 infection alone, suggesting pH1N1 infection can activate host transcription factors required for HIV-1 replication in Jurkat cells. These data indicate that pandemic influenza A (H1N1) infection can increase accumulation of CD4 protein and induce T cell signaling and activate host transcription factors required for HIV-1 replication. In conclusion, our results demonstrate that pandemic influenza A (H1N1) virus infection can induce cell death through apoptotic signaling pathways and promote HIV-1 replication through the MAPK and TCR-related signaling pathways in HIV-1-infected Jurkat cells. Pandemic influenza A (H1N1) virus infection is also able to reactivate HIV-1 replication from its state of latent infection through activating apoptosis and TCR-signaling pathways. cache = ./cache/cord-001972-1zisomq5.txt txt = ./txt/cord-001972-1zisomq5.txt === reduce.pl bib === id = cord-005033-voi9gu0l author = Xuan, Huiyu title = A CA-based epidemic model for HIV/AIDS transmission with heterogeneity date = 2008-06-07 pages = extension = .txt mime = text/plain words = 6567 sentences = 395 flesch = 57 summary = In this paper, we develop an extended CA simulation model to study the dynamical behaviors of HIV/AIDS transmission. Additional, we divide the post-infection process of AIDS disease into several sub-stages in order to facilitate the study of the dynamics in different development stages of epidemics. Higher population density, higher mobility, higher number of infection source, and greater neighborhood are more likely to result in high levels of infections and in persistence. Ahmed and Agiza (1998) develop a CA model that takes into consideration the latency and incubation period of epidemics and allow each individual (agent) to have distinctive susceptibility. We also define four types of agents that are characterized by different infectivity (and susceptibility) and various forms of neighborhood to represent four types of people in real life. To capture this, we extend classical CA models by allowing each agent to have its own attributes such as mobility, infectivity, resistibility (susceptibility) 2 and different extent of neighborhood. cache = ./cache/cord-005033-voi9gu0l.txt txt = ./txt/cord-005033-voi9gu0l.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-003307-snruk3j2 author = Schmidt, Julius J. title = Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date = 2018-11-19 pages = extension = .txt mime = text/plain words = 4068 sentences = 239 flesch = 51 summary = BACKGROUND: Despite modern intensive care with standardized strategies against acute respiratory distress syndrome (ARDS), Pneumocystis pneumonia (PcP) remains a life-threatening disease with a high mortality rate. Based on the high burden of PcP and the likelihood of unfavorable outcome particularly in non-HIV-positive patients, chemoprophylaxis with trimethoprim-sulfame thoxazole (TMP-SMX) is recommended in high-risk populations [13] . We here report comprehensive epidemiological, clinical, laboratory, therapeutic and outcome data on 240 cases of PcP, including a high percentage of non-HIV-positive patients, in a tertiary care center over the last 17 years. For every patient, clinical data on demographic characteristics, underlying disease, status of immune competence, treatment regimens of immunosuppression, PcP therapy regimen and mortality, were gathered in the study database. Outcomes and prognostic factors of non-HIV patients with pneumocystis jirovecii pneumonia and pulmonary CMV co-infection: a retrospective cohort study cache = ./cache/cord-003307-snruk3j2.txt txt = ./txt/cord-003307-snruk3j2.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-006716-n371b91w author = Cone, A. M. title = Flumazenil reverses diazepam-induced neonatal apnoea and hypotonia date = 1993 pages = extension = .txt mime = text/plain words = 1621 sentences = 90 flesch = 59 summary = These strategies are required in some European countries where the large proportion of intravenous drug user (IVDU) women of child-bearing age leads to increasing numbers of perinatally infected children [2] . These mechanisms have been already identified [1] and, as in others' data [1] , a prior unharmed experience seems to be a factor influencing reproductive decision; (2) HIV-1 testing in pregnancy is mostly useful for sexually infected women often unconscious of their condition. Sir: We describe a case in which flumazenil, a specific benzodiazepine antagonist, reversed diazepam-induced neonatal apnoea and hypotonia. Diazepam levels were not measured, but in view of the prolonged half-life of this drug, it was likely that the infant would remain susceptible to its effects after cessation of the flumazenil infusion. Complement activation and the prognostic value of C3 a in patients at risk of the adult respiratory distress syndrome cache = ./cache/cord-006716-n371b91w.txt txt = ./txt/cord-006716-n371b91w.txt === reduce.pl bib === === reduce.pl bib === id = cord-001385-rb5vwolt author = Reuven, Eliran Moshe title = The HIV-1 Envelope Transmembrane Domain Binds TLR2 through a Distinct Dimerization Motif and Inhibits TLR2-Mediated Responses date = 2014-08-14 pages = extension = .txt mime = text/plain words = 6147 sentences = 318 flesch = 51 summary = Figure 1A and B show that 20 minutes after addition of LTA to RAW cells that were pre-incubated with the gp41 TMD peptide, there was a significant decrease in ERK1,2 phosphorylation compared to nontreated cells, indicating less receptor activation. We next measured the expression levels of NFkB downstream genes; Tumor Necrosis Factor a (TNFa), a hallmark cytokine of TLR activation, and Monocyte Chemotactic Protein 1 (MCP-1), a major chemokine mainly secreted by macrophages [22] , in order to ensure that the inhibitive effect on ERK1,2 phosphorylation is a result of inhibition of TLR2 signaling. IL-6 is an additional target gene of TLR2 but it is transcribed via a different transcription factor complex than TNFa. Cells were pre-incubated with ENV TMD peptides for two hours prior to LTA activation. In order to confirm this hypothesis we utilized the ectopic expression of HIV-1 ENV-YFP chimeric protein in RAW 264.7 cells, which mimics the HIV-1 infection of macrophages, and tested their responsiveness to LTA by measuring TNFa secretion. cache = ./cache/cord-001385-rb5vwolt.txt txt = ./txt/cord-001385-rb5vwolt.txt === reduce.pl bib === id = cord-004600-5lhnzzvg author = Dennin, Reinhard H. title = HIV-Infektion – Grenzen der Präventionskonzepte: Überlegungen zur Verantwortung der Betroffenen, der Politik und der Gesellschaft* date = 2007-03-26 pages = extension = .txt mime = text/plain words = 2694 sentences = 329 flesch = 50 summary = Die HIV-Epidemie ist bestimmt durch ein komplexes Zusammenwirken von personengebundener Transmission, über eine Dekade langer, klinisch asymptomatischer Zeit bis zur Manifestation der Krankheit, bei permanenter Infektiosität. Die individuelle intime Sphäre des Sexualverhaltens ist durch unsere gesellschaftliche Verhaltensnormen geschützt; somit kann die HIV-Infektion als personengebundene Transmission nicht wie andere Infektionen, die den community acquired infections zugerechnet werden, z. Angewandt auf die Präventionskonzepte gegen die Ausbreitung von HIV war damit ein Vertrauens-und Erwartungsvorschuss für bereits von der HIV-Infektion betroffene wie noch HIV-naive Mitmenschen verbunden, sich den an die kognitive Ebene richtenden rationalen Präventionsbotschaften entsprechend zu verhalten, d. Die Argumente von Vertretern der wesentlich auf Konzepten der NPH basierenden HIV-Präventionskampagnen, diese hätten wesentlich zu den "geringen" Zuwachsraten an HIV-Infizierten in Deutschland und -wegen der europäischen Abstimmung -auch in Europa beigetragen, sind nach der derzeitigen Datenlage weder zu widerlegen noch zu belegen, da ein anderes Modell der Prävention nicht eingeführt wurde. cache = ./cache/cord-004600-5lhnzzvg.txt txt = ./txt/cord-004600-5lhnzzvg.txt === reduce.pl bib === id = cord-009669-bcdjwpd1 author = Tsegaye, Theodros Solomon title = The multiple facets of HIV attachment to dendritic cell lectins date = 2010-09-20 pages = extension = .txt mime = text/plain words = 4852 sentences = 199 flesch = 40 summary = Trans-infection was reported to depend on DC-SIGNmediated binding and cellular uptake of HIV into dendritic cells (Geijtenbeek et al., 2000; Kwon et al., 2002) , followed by intracellular transport of virions to sites of dendritic cell-T cell contact, termed infectious synapses (McDonald et al., 2003) (Fig. 1) . Finally, signalling via TLR8 and DC-SIGN was required for NFkB-dependent recruitment of the transcription factor pTEF-b to the viral promoter, and thus for the generation of full-length HIV transcripts in dendritic cells -a prerequisite for productive infection (Gringhuis et al., 2010) (Fig. 2) . Dendritic cell-mediated trans-enhancement of human immunodeficiency virus type 1 infectivity is independent of DC-SIGN The C-type lectin surface receptor DCIR acts as a new attachment factor for HIV-1 in dendritic cells and contributes to trans-and cis-infection pathways Functionally distinct transmission of human immunodeficiency virus type 1 mediated by immature and mature dendritic cells cache = ./cache/cord-009669-bcdjwpd1.txt txt = ./txt/cord-009669-bcdjwpd1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-010001-u0d5jkp1 author = KOTWAL, GIRISH J. title = Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date = 2006-01-22 pages = extension = .txt mime = text/plain words = 2608 sentences = 123 flesch = 51 summary = With a well-established infrastructure and the methodology to cultivate and to titer viruses accurately 6 to evaluate antiviral effects, it was possible to show that indeed a small volume of the plant extract termed Secomet-V was able to inactivate approximately 1 million virus particles of the attenuated recombinant vaccinia virus vGK5 7 in 1 minute consistently and reproducibly. Secomet-V, an extract of an African plant also found elsewhere in Asia, has been found to have potent antiviral activity against a poxvirus (vaccinia virus), rendering about 1 million particles noninfectious in 1 min with a 50th of a milliliter in in vitro assays (FIG. HIV-infected cells treated with plant extract showed no significant effect on the viral levels (TABLE 1) . There was no difference in the effectiveness of the plant extract in rendering vaccinia virus noninfectious whether it was autoclaved or not, suggesting that the bioactive agent is most likely but not necessarily a heat-stable compound and not a small peptide. cache = ./cache/cord-010001-u0d5jkp1.txt txt = ./txt/cord-010001-u0d5jkp1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-010499-yefxrj30 author = Yelverton, Elizabeth title = The function of a ribosomal frameshifting signal from human immunodeficiency virus‐1 in Escherichia coli date = 2006-10-27 pages = extension = .txt mime = text/plain words = 5883 sentences = 330 flesch = 60 summary = Ribosomal frameshifting in both rightward and leftward directions has also been shown to occur at certain 'hungry' codons whose cognate aminoacyi-tRNAs are in short supply (Gallant and Foley, 1980; Weiss and Gailant, 1983; 1986; Gallant et ai, 1985; Kurland and Gallant, 1986) . Not all hungry codons are equally prone to shift: in a survey of 21 frameshift mutations of the rllB gene of phage T4, Weiss and Gallant (1986) found that oniy a minority were phenotypicaily suppressible when challenged by limitation for any of several aminoacyl-tRNAs. The context njies governing ribosome frameshifting at hungry sites are under investigation, and have been defined in a few cases (Weiss et al., 1988; Gallant and Lindsiey, 1992; Peter et ai. coli the rate of ribosomal frameshifting on that sequence can be increased by limitation for leucine, the amino acid encoded at the frameshift site. cache = ./cache/cord-010499-yefxrj30.txt txt = ./txt/cord-010499-yefxrj30.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-011457-hqxybv1k author = Kirui, James title = Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date = 2020-05-19 pages = extension = .txt mime = text/plain words = 5612 sentences = 249 flesch = 46 summary = To enable simple and highly sensitive measurement of virus release from transfected cells, we generated HIV-1 reporter viruses in which Nanoluciferase (NanoLuc) was inserted between the MA and CA domains of Gag (Gag-iNanoLuc). We generated viruses using the pNL4-3 Gag-iNanoLuc vector complemented with different ratios of the WT HIV-1 molecular clone pNL4-3 and tested their infectivity by measuring the HIV-1 Tat-driven firefly luciferase activity in TZM-bl cells. These results demonstrate that the Gag-iNanoLuc vector provides a highly sensitive and quantitative tool for measuring the effects of Gag mutations, host cell restriction factors, and small-molecule inhibitors on HIV-1 particle assembly and release. The Gag-NanoLuc fusion protein is expressed in the cell and released at similar levels to WT Gag, thereby enabling simple yet highly sensitive quantification of viral gene expression and virus particle production by measurement of the NanoLuc reporter protein bioluminescent activity in the cell lysates and supernatants. cache = ./cache/cord-011457-hqxybv1k.txt txt = ./txt/cord-011457-hqxybv1k.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-013442-kjfk7hq6 author = Muñoz-Laboy, Miguel title = “En la Lucha”: Strategies to Improve HIV Care for Puerto Ricans with Opioids Use Disorders date = 2020-10-30 pages = extension = .txt mime = text/plain words = 7646 sentences = 386 flesch = 52 summary = Based on more than two decades of organizational experiences since the onset of the HIV epidemic in Philadelphia, and the review of the scientific literature in HIV care continuum outcomes, the leadership of both organizations and the intervention designers decided to establish Clínica Bienestar as guided by three principles: (1) Colocation of services for transnational groups to increase utilization of HIV services by minimizing unnecessary navigation through complex health care systems (primary care services, HIV services, substance use disorder treatment) while decreasing duplicative costs to achieve similar health outcomes [27] . (2) HIV diagnosis and trajectory to engagement in care at Clínica Bienestar Philadelphia; (3) Substance use trajectory into current treatment and recovery; (4) Mapping of kinship and community support systems; (5) Services received for the past 24 months at Clínica Bienestar. cache = ./cache/cord-013442-kjfk7hq6.txt txt = ./txt/cord-013442-kjfk7hq6.txt === reduce.pl bib === id = cord-005585-lc3fqhb0 author = Barbier, François title = Etiologies and outcome of acute respiratory failure in HIV-infected patients date = 2009-07-03 pages = extension = .txt mime = text/plain words = 4236 sentences = 209 flesch = 45 summary = OBJECTIVE: To assess the etiologies and outcome of acute respiratory failure (ARF) in HIV-infected patients over the first decade of combination antiretroviral therapy (ART) use. Acute respiratory failure (ARF) is the leading reason for intensive care unit (ICU) admission in HIV-infected patients, with bacterial pneumonia and Pneumocystis jirovecii pneumonia (PCP) accounting for most cases [1] [2] [3] [4] [5] [6] [7] [8] . Significant results HIV human immunodeficiency syndrome, ICU intensive care unit, PCP Pneumocystis jirovecii pneumonia, IRIS immune restorationinduced syndrome, ARF acute respiratory failure, COPD chronic obstructive pulmonary disease, AIDS acquired immunodeficiency syndrome a Clinically documented bacterial pneumonia was defined as an appropriate history and response to empiric antimicrobial therapy with focal pneumonia on chest X-ray, and either septic shock or predominantly neutrophils on BAL fluid examination, without documented bacterial pathogen b Including co-infection with Haemophilus influenzae (n = 1) and Staphylococcus aureus (n = 1) c Including co-infection with Streptococcus pneumonia (n = 1) and S. cache = ./cache/cord-005585-lc3fqhb0.txt txt = ./txt/cord-005585-lc3fqhb0.txt === reduce.pl bib === id = cord-004247-lagv3tp7 author = Hooft van Huijsduijnen, Rob title = Reassessing therapeutic antibodies for neglected and tropical diseases date = 2020-01-30 pages = extension = .txt mime = text/plain words = 6756 sentences = 314 flesch = 42 summary = This mAb was protective in an in vitro, antigen-dependent, cellular cytotoxicity assay with rat macrophages or eosinophils and also in vivo during the early phase of infection Second, beyond the cell-surface proteins, schistosomes also express a large number of glycans as part of their glycoprotein and glycolipid repertoire, and an antibody response against those glycans is mounted by the infected host [80] . In addition to antibodies that directly target and inhibit the fungal pathogen, mAbs can be directed to checkpoints that control the host immune response. In addition to highlighting the potential of mAbs as therapeutics, these studies have demonstrated the diversity of inhibitory actions that mAbs can perform on cryptococcal cells, which can include opsonization and increased phagocytosis, inhibition of fungal growth, capsular polysaccharide release and biofilm formation, antibody-mediated target cleavage, and augmentation of the host response [104] [105] [106] [107] . cache = ./cache/cord-004247-lagv3tp7.txt txt = ./txt/cord-004247-lagv3tp7.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-014608-g3p19coe author = nan title = Pneumococcal colonization and carriage date = 2014-12-01 pages = extension = .txt mime = text/plain words = 21648 sentences = 1365 flesch = 50 summary = Background and Aims: Data on the nasopharyngeal carriage prevalence of Streptococcus pneumoniae across age groups are important to help predict the impact of introducing pneumococcal conjugate vaccines (PCVs) into routine vaccination programmes, given their important indirect effect. Methods: Nasopharyngeal swabs were collected from well children 3 months to 5Y of age from Karachi, Pakistan as part of a pneumococcal carriage study to evaluate PCV-10 impact. Methods: To determine pneumococcal colonization, we recruited a convenience sample of residents of all ages from 8 rural villages and children aged <5 years at 2 urban pediatric clinics annually during 2008-2012; we determined their PCV13 vaccination status and obtained nasopharyngeal swab specimens. No conflict of interest ISPPD-9 / pneumonia 2014 Mar 9-13;3:1-286 Background: Using nasopharyngeal carriage as a marker of vaccine impact, pneumococcal colonisation and its relation to invasive disease and demographic attributes were examined in children, their parents, and older adults in the UK following the introduction of PCV7 and prior to PCV13. cache = ./cache/cord-014608-g3p19coe.txt txt = ./txt/cord-014608-g3p19coe.txt === reduce.pl bib === === reduce.pl bib === id = cord-004986-en7taikk author = Nagy, Nathalie title = Infections gastro-intestinales chez le patient immunocompromis date = 2002 pages = extension = .txt mime = text/plain words = 6147 sentences = 672 flesch = 58 summary = Dans 44 h 68 % des patients sida prEsentant une entEropathie due ~un ou plusieurs agents pathogEnes concomitant, des symptEmes gastro-intestinaux sont retrouvEs. Le diagnostic d'infections opportunistes est en gEnEral base sur une combinaison de culture de selles, examen direct des selles ~ la recherche d'ceufs ou de larves, et d'une biopsie endoscopique. L'infection herpEtique semble 6tre plus frEquente chez le patient HIV que chez les autres patients immunodEprimEs. Dans une importante Etude prospective r6alisEe sur 100 patients HIV pr6sentant une cesophagite her-pEtique, le virus HSV n'a 6tE identifi6 que darts 5 % des cas alors que la prevalence du virus CMV atteignait 50 % [4] . Les infections ~ Campylobacter ont 6t6 identifi6es dans approximativement 11% des coprocultures des patients sida, qu'ils souffrent ou non de diarrh6es ; ces patients, pr6sentant une incidence d'infection, sont 39 fois plus importants que dans la population g6n6rale. Cependant une colonisation m6me par des agents non pathog6nes peut 8tre responsable d'affections s6vhres chez les patients immunocompromis [6] . cache = ./cache/cord-004986-en7taikk.txt txt = ./txt/cord-004986-en7taikk.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-015958-68dmza13 author = Ceccherini-Nelli, Luca title = Globalizzazione in medicina: l’emergenza HIV date = 2007 pages = extension = .txt mime = text/plain words = 5163 sentences = 529 flesch = 59 summary = L'ottimismo generato dalle migliori condizioni di vita (cibo e acqua più sani, migliori sistemi di raccolta rifiuti e di discarica, nuove conoscenze nella biologia e nella medicina capaci di consentire lo sviluppo e l'uso diffuso di vaccini, la produzione di antinfettivi e di antiparassitari più sicuri ed efficaci) che avevano portato nel mondo occidentale all'allungamento dell'aspettativa di vita da una media di 46,5 anni nel 1950 a 65 anni nel 2002 (51 anni per i redditi bassi, 78 per gli alti), negli anni Ottanta si era già esaurito per l'emergenza di agenti infettivi "nuovi" (non riconosciuti prima) e per la riemergenza di altri già noti, a causa sia di fattori determinati dall'agente infettante stesso, quali l'acquisizione della capacità di salto di specie o la formazione di varianti farmacoresistenti, che di fattori determinati dall'ospite, quali: 1) manovre invasive iatrogene responsabili di infezioni ospedaliere; 2) cambiamenti climatici capaci di favorire il diffondersi di parassiti vettori di infezione e alterazioni degli ecosistemi (con prevalenza incontrollata di predatori o di prede); 3) esplosione demografica con ripercussioni importanti sulle tecnologie industriali di produzione alimentare, sullo sviluppo economico-urbanistico tumultuoso, sulle migrazioni di rifugiati; 4) promiscuità sessuale e turismo sessuale; 5) tossicodipendenza, e infine 6) spostamenti delle persone e delle merci che sono sempre stati fonte di diffusione degli agenti infettivi, ma che avevano raggiunto livelli di quantità e frequenza impensabili precedentemente [1] (vedi anche i Capitoli pubblicati altrove in questo volume). cache = ./cache/cord-015958-68dmza13.txt txt = ./txt/cord-015958-68dmza13.txt === reduce.pl bib === id = cord-009891-gqrhbhbn author = Rassool, G. Hussein title = Current issues and forthcoming events date = 2003-09-03 pages = extension = .txt mime = text/plain words = 3466 sentences = 168 flesch = 49 summary = The Centers for Disease Control and Prevention (CDC), USA, reports that 'transmission to health care workers appears to have occurred after close contact with symptomatic individuals (e.g. persons with fever or respiratory symptoms) before recommended infection control precautions for SARS were implemented (i.e. unprotected exposures).' There is also a possibility that the causative agent can remain viable for extended periods of time after drying on environmental surfaces. Preliminary results of a large-scale trial of a candidate AIDS vaccine announced by the US-based biotechnology company VaxGen suggest that it is possible to protect some individuals from HIV infection. The result is that poor diagnosis of pain in cancer patients remains a significant problem, with many physicians finding it difficult to differentiate between the various pain types; and, many underestimating its severity. Poor diagnosis, poor assessment, the choice of less appropriate treatments, plus patients and physicians fears about controlled drugs such as morphine all contribute to under treatment of cancer pain. cache = ./cache/cord-009891-gqrhbhbn.txt txt = ./txt/cord-009891-gqrhbhbn.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-015376-z739ifu5 author = Savarino, Andrea title = Potential therapies for coronaviruses date = 2006-08-31 pages = extension = .txt mime = text/plain words = 6361 sentences = 313 flesch = 48 summary = These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. cache = ./cache/cord-015376-z739ifu5.txt txt = ./txt/cord-015376-z739ifu5.txt === reduce.pl bib === id = cord-011903-zqt6vu6d author = Duby, Zoe title = “As a Young Pregnant Girl… The Challenges You Face”: Exploring the Intersection Between Mental Health and Sexual and Reproductive Health Amongst Adolescent Girls and Young Women in South Africa date = 2020-07-18 pages = extension = .txt mime = text/plain words = 7227 sentences = 295 flesch = 47 summary = Poor mental health, including depressive disorders and stress, contributes significantly to the burden of disease in South Africa, and other parts of sub-Saharan Africa, and is also associated with negative sexual and reproductive health (SRH) outcomes for women, such as 'unintended' or early pregnancy, and increased risk behaviours for HIV [1] [2] [3] . In the accounts of AGYW, poor mental health, including depression and suicidal risk were linked to sexual/ romantic relationship challenges, early pregnancy and child-bearing, parenting responsibilities, experiences of violence/abuse, HIV status, and lack of emotional support. Building on previous research that has found associations between depressive symptoms and psychological distress related to pregnancy, combined with a lack of social support amongst South African women [16] , our findings provide rich descriptive data on the lived reality of the interconnected psychosocial risks including stress, emotional isolation, feelings of depression and suicidal ideation, with 'unintended' pregnancy and HIV that AGYW in South Africa face, from their own perspectives. cache = ./cache/cord-011903-zqt6vu6d.txt txt = ./txt/cord-011903-zqt6vu6d.txt === reduce.pl bib === === reduce.pl bib === id = cord-015372-76xvzvdg author = nan title = National scientific medical meeting 1996 abstracts date = 1996 pages = extension = .txt mime = text/plain words = 36596 sentences = 2204 flesch = 53 summary = One, two and five-year survival rates were examined; age at diagnosis and lesion type were extremely significant factors in relation to patient outcome. Patients' age, sex, risk group, CDC stage, CD4 count, indication for therapy, complication rate and response to treatment are described. Fifty-eight patients (34 male, 24 female) ranging in age from 15 to 65 years (Mean + SD = 28.4 + 10.8) were included in the study. Among these 48 patients (mean age 68.0+12.7), after controlling for age and for the duration and continuity of subsequent antipsychotic treatment, increasing duration of initially untreated psychosis was associated with greater severity of negative symptoms (p<0.005) and with lower scores on the MMSE (p<0.05) but not with executive dysfunction on the EXIT (p=0.3). Conclusion Although not a population based study, care of IDDM in Ireland is almost totally hospital clinic based Cigarette smoking is identified as the major problem to be addressed Patients with diabetes meltitus (DM) are at a higher risk of developing vascular complications, including coronary artery disease (CAD). cache = ./cache/cord-015372-76xvzvdg.txt txt = ./txt/cord-015372-76xvzvdg.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-010689-d2qn1doq author = Chehardoli, Gholamabbas title = Synthetic strategies, SAR studies, and computer modeling of indole 2 and 3-carboxamides as the strong enzyme inhibitors: a review date = 2020-05-12 pages = extension = .txt mime = text/plain words = 6179 sentences = 348 flesch = 42 summary = In this review, synthetic strategies of indole 2 and 3-carboxamide derivatives, the type, and mode of interaction of these derivatives against HLGP, HIV-1, renin enzyme, and structure–activity studies of these compounds were investigated. Based on our experiences on synthesis of various heterocycle compounds, such as: quinoxalines [15] , epoxides [16] , urazoles [17, 18] , pyrazolone [19] , benzoxazine [20] and especially the synthesis of 3H-indoles [21] , in this paper, we wish to present a comprehensive review about the synthesis, structure-activity relationship studies and computer modeling of indole 2 and 3-carboxamides as potent inhibitors of various enzymes. According to the results of docking calculations, the presences of indole ring and carboxamide moiety have a decisive role in the inhibitory activity of these compounds. According to the research conducted up to 2008, the presence of carboxamide moiety in the indole derivatives is essential for their inhibitory activity against HLGP. cache = ./cache/cord-010689-d2qn1doq.txt txt = ./txt/cord-010689-d2qn1doq.txt === reduce.pl bib === id = cord-017439-0c6ohmmg author = Hughes-Oliver, Jacqueline M. title = Pooling Experiments for Blood Screening and Drug Discovery date = 2006 pages = extension = .txt mime = text/plain words = 7874 sentences = 461 flesch = 51 summary = Today, pooling experiments are driven by the potential cost savings and precision gains that can result, and they are making a substantial impact on blood screening and drug discovery. A general review of pooling experiments is given here, with additional details and discussion of issues and methods for two important application areas, namely, blood testing and drug discovery. Recognizing that developing countries can ill-afford the cost of 100% one-at-a-time screening, WHO issued recommendations for testing for HIV antibody on serum pools (WHO, 1991) in areas where seroprevalence is less than 2%. Since the late 1980s, statistical contributions to pooling for blood testing have focused on the following aspects: assessing changes in sensitivity and specificity due to pooling, designing pooling strategies to accommodate both cheap initial screens and gold-standard confirmatory screens, and estimation of covariate-dependent prevalences. On the information and accuracy of pooled testing in estimating prevalence of a rare disease: Application to HIV screening cache = ./cache/cord-017439-0c6ohmmg.txt txt = ./txt/cord-017439-0c6ohmmg.txt === reduce.pl bib === === reduce.pl bib === id = cord-010845-pakh49dy author = Isiguzo, Godsent title = Diagnosis and Management of Tuberculous Pericarditis: What Is New? date = 2020-01-15 pages = extension = .txt mime = text/plain words = 4108 sentences = 176 flesch = 37 summary = The statement is particularly true for tuberculous pericarditis (TBP), where lack of understanding of this severe form of extra-pulmonary tuberculosis (EPTB) has hampered discovery and translation of cost-effective, rapid diagnostic tests and host-directed therapies able to prevent its debilitating complications and associated mortality. Finally, recent reports suggest that among both HIV-infected and HIVuninfected patients with culture-positive pericardial fluid, Mtb bacillary loads are as high as 3.91 log 10 CFU/mL (range 0.5-8.96), with bacillary loads over 5.53 log 10 CFU/mL being significantly associated with mortality [18] . Diagnostic accuracy of quantitative PCR (Xpert MTB/RIF) for tuberculous pericarditis compared to adenosine deaminase and unstimulated interferon-γ in a high burden setting: a prospective study Diagnostic accuracy of quantitative PCR (Xpert MTB/RIF) for tuberculous pericarditis compared to adenosine deaminase and unstimulated interferon-gamma in a high burden setting: a prospective study cache = ./cache/cord-010845-pakh49dy.txt txt = ./txt/cord-010845-pakh49dy.txt === reduce.pl bib === id = cord-015936-4fwkf8fn author = nan title = SUBJECT INDEX, volumes 123-130 date = 2005-11-04 pages = extension = .txt mime = text/plain words = 69 sentences = 10 flesch = 78 summary = key: cord-015936-4fwkf8fn authors: nan title: SUBJECT INDEX, volumes 123-130 date: 2005-11-04 journal: J Virol Methods DOI: 10.1016/s0166-0934(05)00346-0 sha: doc_id: 15936 cord_uid: 4fwkf8fn nan HIV; 2 LTR circles; New marker (125) 11 HIV antigen/antibody combined assay; HIV; Serology; HIV-1 p24 antigen assay (127) (127) (128) (128) 67 Yeast expression; Pichia pastoris; SARS-CoV; N protein (130) 83 enzyme analysis; Flaviviruses; RT-PCR cache = ./cache/cord-015936-4fwkf8fn.txt txt = ./txt/cord-015936-4fwkf8fn.txt === reduce.pl bib === === reduce.pl bib === id = cord-016041-427mbaqc author = Hengge, Ulrich R. title = Gentherapie date = 2008 pages = extension = .txt mime = text/plain words = 7287 sentences = 824 flesch = 46 summary = Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (>Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (>Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. Neue Verfahren des Vektor-Targetings sowie interessante Techniken wie Elektroporation und hydrodynamische Injektion konnten die Transgenexpression in vivo verbessern, indem eine verbesserte Verteilung der Plasmid-DNA im Zielorgan erreicht wurde (Wolff u. Bei einer weiteren Zytokin-Gentherapie wurde Melanompatienten intratumoral ein Canarypox-Virus-Vektor injiziert, der das IL-12-Gen exprimierte, und zur T-Zell-Akkumulation in injizierten Melanomen führte (Triozzi et al. Es ist jedoch schwierig, einen Zusammenhang zwischen Tumorregression und der Existenz einer durch die Vakzinierung induzierten zytotoxischen T-Zell-Antwort unzweifelhaft festzustellen, da nicht alle Patienten mit zellulären Immunantworten auf den Tumor eine Regression desselben zeigen. Ein Paradebeispiel hierfür ist das p53-Protein, das erst nach einem aufgetretenen DNA-Schaden den Zellzyklus blockiert und die Zellen der Apoptose unterwirft (Roth 2006) . cache = ./cache/cord-016041-427mbaqc.txt txt = ./txt/cord-016041-427mbaqc.txt === reduce.pl bib === === reduce.pl bib === id = cord-016690-3gsq724l author = Li, Hongjun title = HIV/AIDS Related Respiratory Diseases date = 2013-09-30 pages = extension = .txt mime = text/plain words = 26772 sentences = 1583 flesch = 46 summary = Its difference from the clinical manifestations of non-HIV infected patients is as the following: (1) More common pulmonary infi ltration with multiple involvements and rare cavities; (2) Higher incidence of dissemination (87-96 %) commonly along with blood fl ow and higher incidence of extrapulmonary tuberculosis (60-70 %); (3) More common lymph node tuberculosis, such as hilar, mediastinal and extrapleural lymphadenectasis; (4) Lower positive rate of tuberculin test (PPD); (5) More patients with no expectoration, with sputum smear for acid-fast bacilli staining is negative; (6) Higher incidence of resistant strains, high recurrence rate, and higher mortality (Table 17 .1 ). Based on the course of the disease, the diagnostic imaging demonstrations of Rhodococcus equi pulmonary infection can be divided into early stage, showing round liked fl aky blurry shadows surrounding unilateral hilum that has blurry boundary; middle stage (parenchymal change), showing central sphere liked high density shadow surrounding unilateral hilum, in parenchymal changes and with clear boundary; advanced stage (necrosis) showing secondary cavity of the pulmonary mass, possibly with hydropneumothorax and pleurisy. cache = ./cache/cord-016690-3gsq724l.txt txt = ./txt/cord-016690-3gsq724l.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-013336-42thiglv author = Wang, Cheng title = Correlates of HIV self-testing among female sex workers in China: implications for expanding HIV screening date = 2020-10-22 pages = extension = .txt mime = text/plain words = 3641 sentences = 191 flesch = 52 summary = However, there have been few studies examining HIV self-testing among female sex workers in countries outside of sub-Saharan Africa, including China [16] [17] [18] . We partnered with eight local female sex workers community-based organizations (CBO) in those eight cities with experience of conducting female sex workers outreach programs including condom promotion, sexual health education, HIV and syphilis rapid testing and counseling, and linkage to care (accompaniment to clinical services for infected individuals). Since the World Health Organization released guidelines recommending HIV self-testing among under-served and high-risk populations in 2016 [25] , many studies in the sub-Saharan Africa have shown that HIV self-testing has a good acceptability and feasibility for female sex workers [12, 14, 15, 26] . Studies have suggested that adding HIV self-testing to existing community-based testing and counseling services among female sex workers is acceptable, cost-effective and efficient to improve linkage to care [15, 26, 27] . cache = ./cache/cord-013336-42thiglv.txt txt = ./txt/cord-013336-42thiglv.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002774-tpqsjjet author = nan title = Section II: Poster Sessions date = 2017-12-01 pages = extension = .txt mime = text/plain words = 83515 sentences = 5162 flesch = 54 summary = Results: The CHIP Framework The CHIP framework aims to improve the health and wellness of the urban communities served by St. Josephs Health Centre through four intersecting pillars: • Raising Community Voices provides an infrastructure and process that supports community stakeholder input into health care service planning, decision-making, and delivery by the hospital and across the continuum of care; • Sharing Reciprocal Capacity promotes healthy communities through the sharing of our intellectual and physical capacity with our community partners; • Cultivating Integration Initiatives facilitates vertical, horizontal, and intersectoral integration initiatives in support of community-identified needs and gaps; and • Facilitating Healthy Exchange develops best practices in community integration through community-based research, and facilitates community voice in informing public policy. cache = ./cache/cord-002774-tpqsjjet.txt txt = ./txt/cord-002774-tpqsjjet.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017719-8lfn6mih author = Böhles, Hansjosef title = Infestationen und Infektionen bei Migranten – Die wichtigsten Erkrankungen date = 2018-02-09 pages = extension = .txt mime = text/plain words = 4646 sentences = 743 flesch = 56 summary = Unter den Migranten aus dem subsaharischen Afrika ist auf das Vorliegen von HIV-Infektionen zu achten. Die Hautveränderungen über den Gängen sind u.U. leicht erhaben und zeigen eine "kommaförmige" Rötung. Es bilden sich dabei stark juckende Pusteln an Handflächen und Fußsohlen aus, die als Skabies verkannt werden können. Sie ist eine in typischer Weise mit Armut assoziierte Erkrankung, die in der Gesamtbevölkerung eine Prävalenz von ca. Die Behandlung der Larva migrans ist somit eine "off-label"-Therapie. Ca. 2 Wochen nach der Infestation kann sich eine pulmonale Askariasis manifestieren, die als Löffler-Syndrom bezeichnet wird. Die Malariaserologie spielt in der Akutdiagnostik keine Rolle und kann nur zum retrospektiven Nachweis einer stattgefundenen Erkrankung benutzt werden. 2015 ) 5 Bei jüngeren Kindern präsentiert sich die Erkrankung häufig nicht mit der klassischen Trias aus Husten, Gewichtsverlust und subfebrilen Temperaturen (Marais et al. Jahre bis Jahrzehnte nach der Erkrankung kann sich ein "Postpoliosyndrom" mit Zunahme von Schwäche und Atrophie entwickeln. cache = ./cache/cord-017719-8lfn6mih.txt txt = ./txt/cord-017719-8lfn6mih.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-017782-dtveihrj author = Fong, I. W. title = Litigations for HIV Related Complications date = 2010-11-30 pages = extension = .txt mime = text/plain words = 6292 sentences = 332 flesch = 54 summary = Specific charges were: (1) the GP should have repeated the HIV serology to confirm that the plaintiff was HIV infected, (2) the defendant was negligent in starting treatment for HIV infection without proof of disease, (3) the physician lacked knowledge of HIV infection and should have referred the patient to a specialist or HIV clinic, (4) treatment of toxic medications were given for several years without any clear indication, and (5) the GP did not adequately inform the patient on the pros and cons of therapy, nor explain the potential toxicities and side-effects. Although the CD4 + T lymphocyte quantitative count is a very useful and standard test to monitor patients for progression of HIV disease or response to therapy, it can be low in many conditions. Long-term non-progression or elite controllers represent <5% of HIV-infected subjects who maintain relatively normal CD4 + cell count and very low or immeasurable viral load for 8 years to decades without therapy. cache = ./cache/cord-017782-dtveihrj.txt txt = ./txt/cord-017782-dtveihrj.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 === id = cord-018040-k0h5ejjt author = Ilyinskii, P. title = Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date = 2009 pages = extension = .txt mime = text/plain words = 6930 sentences = 309 flesch = 41 summary = Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. The size of these vectors is generally within 10-1000 nm and it is a specific mechanism by which our immune system recognizes such particles that underlies their adjuvant potencies (in addition, many carriers protect proteins/NA from rapid degradation in vivo and release them into the organism during prolonged periods of time, which also results in higher immunogenicity). Several VLPbased vaccines have been licensed for general use, many of them against HBV, which are composed of HBV surface antigen (HBsAg), which is a main component of currently used protein-based, alum adjuvant-potentiated vaccine. cache = ./cache/cord-018040-k0h5ejjt.txt txt = ./txt/cord-018040-k0h5ejjt.txt === reduce.pl bib === id = cord-018137-rmtyrbg0 author = Saad, Farouk Tijjani title = Global Stability Analysis of HIV+ Model date = 2018-12-29 pages = extension = .txt mime = text/plain words = 2932 sentences = 168 flesch = 57 summary = Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio [Formula: see text] was also calculated by the use of next generation matrix. Efforts to improve the use of antiretroviral treatment in some part of the world were still not enough to reduce a significant number of deaths, the HIV/AIDS epidemic claimed 3.1 million lives in 2005, of which about 570000 were children (UNAIDS/WHO [8] ). We shall study the global stabilities of both disease free and endemic equilibria by the use of Lyapunov function. Here we use the real data obtained from MOH, in which there were a total of 13646 HIV-1 positive reported cases in the year 2016, in the year 2016 to study and predict the dynamics of HIV in Turkey using our model. Stability analysis of an HIV/Aids epidemic model with treatment Stability analysis of an HIV/AIDS epidemic model with screening Global analysis of an HIV/AIDS epidemic model cache = ./cache/cord-018137-rmtyrbg0.txt txt = ./txt/cord-018137-rmtyrbg0.txt === reduce.pl bib === id = cord-018440-qugmnolo author = nan title = When a Diagnosis Is Reportable date = 2008 pages = extension = .txt mime = text/plain words = 2202 sentences = 113 flesch = 57 summary = In many states, once the HHS is notified of a reportable disease such as confirmed HIV infection, a health investigator representing that state's HHS will become The Law involved in the case. If a patient has not personally notified their partners of their risk for HIV infection, the investigator may then contact all divulged sexual partners for the need to pursue testing and potential treatment for HIV. Anyone who has sexual relations with or engages in other risk behaviors with Scott is at risk for contracting HIV and syphilis, and protecting the health and welfare of those contact persons takes precedent over maintaining Scott's confidentiality. Once Scott's diagnosis is reported, he will meet with a health investigator who will record the names of his contacts and notify them of their exposure to syphilis and HIV. Scott should be informed that his diagnosis will be reported to the public health department and that he will be asked to meet with an investigator and give the names of his sexual contacts. cache = ./cache/cord-018440-qugmnolo.txt txt = ./txt/cord-018440-qugmnolo.txt === reduce.pl bib === id = cord-018646-fqy82sm6 author = Huremović, Damir title = Brief History of Pandemics (Pandemics Throughout History) date = 2019-05-16 pages = extension = .txt mime = text/plain words = 6864 sentences = 333 flesch = 56 summary = Starting with religious texts, which heavily reference plagues, this chapter establishes the fundamentals for our understanding of the scope, social, medical, and psychological impact that some pandemics effected on civilization, including the Black Death (a plague outbreak from the fourteenth century), the Spanish Flu of 1918, and the more recent outbreaks in the twenty-first century, including SARS, Ebola, and Zika. This includes the unexamined ways pandemic outbreaks might have shaped the specialty of psychiatry; psychoanalysis was gaining recognition as an established treatment within medical community at the time the last great pandemic was making global rounds a century ago. Stemming from Doric Greek word plaga (strike, blow), the word plague is a polyseme, used interchangeably to describe a particular, virulent contagious febrile disease caused by Yersinia pestis, as a general term for any epidemic disease causing a high rate of mortality, or more widely, as a metaphor for any sudden outbreak of a disastrous evil or affliction [4] . cache = ./cache/cord-018646-fqy82sm6.txt txt = ./txt/cord-018646-fqy82sm6.txt === reduce.pl bib === id = cord-018721-othar2uv author = Schwab, Stefan title = Infektionen date = 2012-03-17 pages = extension = .txt mime = text/plain words = 13415 sentences = 1662 flesch = 40 summary = Zusammenfassend kann aufgrund der zur Verfügung stehenden Daten die Gabe von Dexamethason bei erwachsenen Patienten mit Verdacht auf eine bakterielle Meningitis (d. Für Entwicklungsländer mit eingeschränkter medizinischer Versorgung und einem hohen Anteil HIV-positiver Patienten konnte keine Wirksamkeit für Dexamethason bei der bakteriellen Meningitis nachgewiesen werden [32] , [33] , [34] . HIV-positive Patienten mit intrakraniellen Tuberkulomen können im Rahmen des "immune reconstitution syndrome" (IRIS) eine durchaus dramatische klinisch neurologische Verschlechterung erfahren, mit Zunahme der neurologi-z Diagnostik Die Untersuchung des Liquor cerebrospinalis ist für die Diagnose einer chronischen Meningitis unverzichtbar, der Liquor ist typischerweise klar, bei deutlich erhöhtem Eiweiß auch xanthochrom wirkend. Da bei der Pathogenese dieser Enzephalitis auch Autoimmunmechanismen eine wichtige Rolle spielen, scheint unter einer kombinierten Th erapie mit Aciclovir und Dexamethason die Rate von Patienten mit schlechtem Outcome geringer zu sein als unter alleiniger Th erapie mit Aciclovir [158] . cache = ./cache/cord-018721-othar2uv.txt txt = ./txt/cord-018721-othar2uv.txt === reduce.pl bib === id = cord-020101-5rib7pe8 author = nan title = Cumulative Author Index for 2008 date = 2008-11-17 pages = extension = .txt mime = text/plain words = 2140 sentences = 126 flesch = 29 summary = Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors cache = ./cache/cord-020101-5rib7pe8.txt txt = ./txt/cord-020101-5rib7pe8.txt === reduce.pl bib === === reduce.pl bib === id = cord-020010-q58x6xb0 author = nan title = 19th ICAR Abstracts: date = 2006-03-13 pages = extension = .txt mime = text/plain words = 46663 sentences = 2181 flesch = 44 summary = In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. cache = ./cache/cord-020010-q58x6xb0.txt txt = ./txt/cord-020010-q58x6xb0.txt === reduce.pl bib === id = cord-021872-rhi7hi9m author = Wilkes, Rebecca P. title = Update on Antiviral Therapies date = 2015-12-04 pages = extension = .txt mime = text/plain words = 9933 sentences = 524 flesch = 47 summary = Topical antiviral therapy has been mainly used for herpetic ocular disease, but studies have evaluated a systemic antiviral compound (famciclovir) for treatment of multiple clinical syndromes associated with FHV-1 infections. 7 A related drug, (R)-9-(2-phosphonylmethoxypropyl)-2,6diaminopurine (PMPDAP), has been shown previously to be a potent inhibitor of FIV replication in cell culture and has reduced the viral load in three of four cats experimentally infected with FIV when treated at 20 mg/kg SC three times per week for 6 weeks. 1 A prodrug of acyclovir, valacyclovir, was developed for increased bioavailability in humans, but use for FHV-1 treatment in experimentally infected cats induced fatal renal and hepatic necrosis and bone marrow suppression, and did not reduce viral shedding or clinical disease severity. 20 Even though this study did not mimic how cats with natural infection would be treated, results from a clinical case study suggested this drug is likely effective for treatment of clinical cases, though it was not blinded and placebo controlled. cache = ./cache/cord-021872-rhi7hi9m.txt txt = ./txt/cord-021872-rhi7hi9m.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-018864-c1r2n17o author = Pöhlmann, Stefan title = Attachment of human immunodeficiency virus to cells and its inhibition date = 2007 pages = extension = .txt mime = text/plain words = 5827 sentences = 238 flesch = 38 summary = In fact, the determinant role played by dendritic cells (DCs) in HIV-1 transmission might rely on specific interactions between gp120 and C-type lectins, of which the DC-specific intercellular adhesion molecule-3 (ICAM-3) grabbing nonintegrin (DC-SIGN) and DC-SIGNR (for DC-SIGN-related) are the best studied [10, 11]. In addition to its own virus-encoded envelope glycoproteins, the virus incorporates many different cellular proteins normally found on the cell surface (reviewed in [12] [13] [14] [15] The process of incorporation of host cell membrane proteins was found to be conserved among all tested HIV-1 subtypes and strains that were expanded in natural cellular reservoirs, such as mitogen-activated peripheral blood lymphocytes and human lymphoid tissue cultured ex vivo [27] [28] [29] [30] [31] [32] . Statin compounds reduce human immunodeficiency virus type 1 replication by preventing the interaction between virion-associated host intercellular adhesion molecule 1 and its natural cell surface ligand LFA-1 A dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN)-related protein is highly expressed on human liver sinusoidal endothelial cells and promotes HIV-1 infection cache = ./cache/cord-018864-c1r2n17o.txt txt = ./txt/cord-018864-c1r2n17o.txt === reduce.pl bib === id = cord-020494-d5sreohg author = Schmutzhard, E. title = Entzündliche Erkrankungen date = 2006 pages = extension = .txt mime = text/plain words = 9279 sentences = 1352 flesch = 45 summary = Die antibiotische Therapie der bakteriellen Meningitis wird von den epidemiologischen Gegebenheiten, insbesondere dem Alter des Patienten, der regionalen Resistenzsituation der jeweiligen Erreger und von evtl. ⊡ Tabelle 32.4 zeigt die wahrscheinlichsten Erreger in den entsprechenden Altersgruppen und gibt das antibiotische Regime, das sofort nach der Diagnose einer eitrigen Meningitis verabreicht werden soll, an. Die klinische Symptomatik und der klinisch-neurologische Verlauf bei einem Patienten mit einem/mehreren Hirnabszessen kann von mild über protrahiert bis zu fulminant sein. Bei begründetem Verdacht auf einen Hirnabszess ist eine Lumbalpunktion kontraindiziert, da der diagnostische Wert der Liquoruntersuchung nur sehr gering ist und die LP die Gefahr einer Einklemmung mit sich bringt. Ein Subduralempyem sollte bei jedem Patienten mit Meningismus und fokalem neurologischem Defizit vermutet werden, insbesondere, wenn sich die Klinik sehr rasch verschlechtert und auf eine Hirnhemi sphäre beschränkt ist. Diese anamnestischen Angaben sind aber keine obligatorische Voraussetzung für die Diagnose einer Neuroborreliose, da das Frühstadium klinisch stumm verlaufen kann und der Zeckenstich vom Patienten nicht immer bemerkt wird. cache = ./cache/cord-020494-d5sreohg.txt txt = ./txt/cord-020494-d5sreohg.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-022535-08hqmwlg author = Schmiedel, Stefan title = Infektionen, Impfungen, Reisemedizin date = 2013-06-26 pages = extension = .txt mime = text/plain words = 6075 sentences = 1245 flesch = 50 summary = • Kinder > 1 J.: Zuwarten bei Fieber bis 3 d, so weit kein klarer Lokalbefund vorliegt und der AZ es erlaubt, rein symptomatische Ther. Facharztüberweisung oder Klinikeinweisung bei reduziertem AZ, bei hohem Fieber und Vorliegen eines Immundefekts (HIV-Inf., immunsuppressive Ther., Z.n. Splenektomie), sowie bei Fortbestehen des Fiebers über 1 Wo. hinaus. Die Immunisierung durch Impfungen ist eine der wichtigsten und wirksamsten Maßnahmen zum Schutz vor Infektionskrankheiten. • Nach Auftreten von KO bei einer Impfung besteht bis zur Klärung der Ursachen eine KI für denselben Impfstoff. • Bei 2 Tetanus-Impfungen in der Vorgeschichte und wenn die Verletzung nicht länger als 24 h zurückliegt, nur Impfung und kein Tetanus-Immunglobulin. Durch Impfung bleiben später der Stress und die Kosten des Varizellen-Immunglobulins bei Varizellen-Exposition von seroneg. Impfbefreiungszeugnis Falls obligatorische Impfungen bei Reisenden kontraindiziert sind, muss ein Impfbefreiungszeugnis mit Unterschrift des Arztes und einem Beglaubigungsstempel mitgeführt werden; je nach Reiseland in englischer oder französischer Sprache und evtl cache = ./cache/cord-022535-08hqmwlg.txt txt = ./txt/cord-022535-08hqmwlg.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 === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-022141-yxttl3gh author = Siegel, Frederic R. title = Progressive Adaptation: The Key to Sustaining a Growing Global Population date = 2014-08-23 pages = extension = .txt mime = text/plain words = 11114 sentences = 489 flesch = 52 summary = Adaptation by the global community as a unit is vital to cope with the effects of increasing populations, global warming/climate change, the chemical, biological, and physical impacts on life-sustaining ecosystems, and competition for life sustaining and economically important natural resources. The chronic malnutrition that about 1 billion people suffered from in 2013 is likely to grow in number in some regions due to global warming/climate change because humans cannot adapt to less food if they are already at subsistence rations. As the global population increases and more people in developing and less developed nations have more disposable income, there will be a growing draw on natural resources other than water and food to service their industrial, agricultural, and manufacturing needs and wants. The effects of higher temperatures from global warming and climate change included what has been discussed in previous chapters of this book: heat, drought, sea level rise, coastal zones, typhoons, flooding, river runoff, water availability, ecosystem shifts, crop yields, fishing, aquaculture, livestock, health and poverty, and tourism. cache = ./cache/cord-022141-yxttl3gh.txt txt = ./txt/cord-022141-yxttl3gh.txt === reduce.pl bib === id = cord-022521-r72jtoso author = Miller, Tracie L. title = Gastrointestinal Complications of Secondary Immunodeficiency Syndromes date = 2010-12-27 pages = extension = .txt mime = text/plain words = 13694 sentences = 812 flesch = 36 summary = However, in the United States and other developed countries, severe malnutrition and new cases of perinatal HIV-1 disease are rare because of relatively high standards of living and effective highly active antiretroviral therapies (HAART) given to pregnant HIV-infected women that prevent transmission of HIV to the infants. Examination of both acute simian immunodeficiency virus (SIV) and HIV infection have documented reduced CD4 cell levels in GALT prior to a detectable reduction in T cells of the peripheral blood, highlighting the gastrointestinal tract's role and susceptibility. Previous studies have shown that activated mucosal T cells play a role in the pathogenesis of enteropathy in the human small intestine 37 and can affect the morphology of the villi and crypts in a manner similar to that seen in patients with HIV-1 infection. Immune restoration disease after the treatment of immunodeficient HIV-infected patients with highly active antiretroviral therapy cache = ./cache/cord-022521-r72jtoso.txt txt = ./txt/cord-022521-r72jtoso.txt === reduce.pl bib === id = cord-022168-qautse9a author = Liu, Li title = Clinical Use of DNA Vaccines date = 2017-07-25 pages = extension = .txt mime = text/plain words = 7120 sentences = 321 flesch = 38 summary = Specifically, the strategies that allow DNA vaccines to overcome antigenic diversity for viral infection and break immune tolerance for cancer therapy are explored. To overcome these obstacles, several approaches focusing on augmenting DNA uptake, maximizing protein expression, and enhancing antigen immunogenicity have been developed and tested in clinical trials. Therefore, one key element to improve DNA vaccine efficacy is to formulate a vaccine with an immunogenic cancer antigen so that it can prime T cells for immune responses. To date, the most successful and encouraging outcomes of using DNA vaccine in the clinical setting were obtained from treatment of malignant diseases where the etiological agent is of foreign viral origin, such as the human papillomavirus (HPV), as these viral agents can readily induce a strong immune response against cancerous cells harboring viral antigens. cache = ./cache/cord-022168-qautse9a.txt txt = ./txt/cord-022168-qautse9a.txt === reduce.pl bib === === reduce.pl bib === id = cord-023017-k6edtg58 author = nan title = AASLD Abstracts (pp. 282A–382A) date = 2006-02-10 pages = extension = .txt mime = text/plain words = 65796 sentences = 3553 flesch = 51 summary = 14/55 (25%) patients in AC who did not discontinue by week 24 received ribavirin dose reduction in comparison to 31/108 ( The clinical outcome in response to combination therapy for treatment of chronic hepatitis C virus (HCV) infection appears to be different for Caucasian versus African American patients. Over the period of combination therapy, most patients in which serum virus titers were reduced to non detectable levels had significant increases in T cell responses to HCV proteins. CHRONIC Background: Recent large prospective trials demonstrated that the combination therapy of interferon (1FN)-alphalribavirin significantly increased the ratio of a sustained virological response in patients with chronic hepatitis C in comparison with IFN monotherapy, especially in patients with high HCV-RNA titer and genotype lb. Results: Patients with chronic HCV infection showed higher MxA gene expression levels than healthy controls, indicating that hepatitis C virus induces IFN production. cache = ./cache/cord-023017-k6edtg58.txt txt = ./txt/cord-023017-k6edtg58.txt === reduce.pl bib === id = cord-023168-cd7adns8 author = Thachil, Jecko title = Haematological Diseases in the Tropics date = 2013-10-21 pages = extension = .txt mime = text/plain words = 30224 sentences = 1724 flesch = 44 summary = The most useful laboratory measure of iron status Low value is diagnostic in the presence of anaemia Very high values (>100 µg/L) usually exclude iron deficiency' Being an acute-phase protein, it increases in inflammatory conditions, and certain malignancies, making it unreliable Also increased in tissue damage especially of the liver Levels are falsely decreased in vitamin C deficiency and hypothyroidism Erythrocyte zinc protoporphyrin An intermediate in haem biosynthesis and elevated concentrations indicate interrupted haem synthesis due to iron deficiency when zinc is incorporated in place of iron Can be measured on a drop of blood with a portable haematofluorometer Small sample size makes it very useful as a screening test in field surveys, particularly in children, and pregnant women where inflammatory states may not co-exist Red cells should be washed before measurement (serum bilirubin and fluorescent compounds like some drugs can give falsely high values) although not often done Lead poisoning can give falsely high values Rarely acute myeloid leukaemia and sideroblastic anaemia give slightly high values Useful in that it is not increased in thalassaemias WHO recommends normal level >70 µmol/mol haem Iron studies Serum iron concentration represents the iron entering and leaving the circulation. cache = ./cache/cord-023168-cd7adns8.txt txt = ./txt/cord-023168-cd7adns8.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-027678-k64whepc author = Chan, Kai Man title = Pneumonia date = 2020-06-22 pages = extension = .txt mime = text/plain words = 6626 sentences = 414 flesch = 40 summary = The differential diagnosis and the likely causative organisms can be narrowed by using epidemiological clues, the most important of which are whether the pneumonia is community-acquired or healthcare-associated and whether the patient is immunocompromised. An acute infection of the pulmonary parenchyma that is associated with at least some symptoms of acute infection, accompanied by an acute infiltrate on a chest radiograph (CXR), or auscultatory findings consistent with pneumonia (e.g. altered breath sounds, localised crackles) in a patient not hospitalised or residing in a long-term care facility for ≥14 days prior to the onset of symptoms. Diagnosis may be difficult: the clinical features of pneumonia are non-specific and many non-infectious conditions (e.g. atelectasis, pulmonary embolus, aspiration, heart Table 36 .2 Procedure for obtaining microbiological samples using bronchoscopy and protected specimen brushing and/or bronchoalveolar lavage 35, 49 Infection control cache = ./cache/cord-027678-k64whepc.txt txt = ./txt/cord-027678-k64whepc.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-033558-lcgo1tiy author = Schmiedel, Stefan title = Infektionen, Impfungen, Reisemedizin date = 2020-10-09 pages = extension = .txt mime = text/plain words = 5008 sentences = 1080 flesch = 52 summary = 9 HIV und AIDS 524 9.9.1 Epidemiologie und Übertragungswege 524 9.9.2 Labordiagnostik 524 9.9.3 Stadieneinteilung und Verlauf 527 9.9.4 Diagnostik bei HIV-Positiven 529 9.9.5 Häufige Krankheitsbilder bei AIDS 529 9.9.6 Therapie 534 9.9.7 Medikamente bei HIV-Patienten 539 9.9.8 Vorgehen bei Kontakt mit HIVkontaminiertem Material und Postexpositionsprophylaxe (PEP) 542 9.9.9 Präexpositionsprophylaxe (PREP) 543 9.10 Reisemedizin 544 9.10.1 Allgemeines 544 9.10.2 Allgemeine Empfehlungen zur Reisefähigkeit 544 9.10.3 Empfehlungen für Schwangere 549 9.10.4 Empfehlungen für ältere Menschen 550 9.10.5 Empfehlungen für Kinder und Säuglinge 551 9.10.6 Empfehlungen für chronisch Kranke 553 9.10.7 Reisevorbereitungen/ Prophylaxen 555 9.10.8 Reiseimpfungen u. Die Immunisierung durch Impfungen ist eine der wichtigsten u. B. Hühnereiweiß, ▶ 9.2.4) • Nach Auftreten von KO bei einer Impfung besteht bis zur Klärung der Ursachen eine KI für denselben Impfstoff • Es gibt keine unzulässig großen Abstände zwischen Impfungen. Bei Impfungen, die nur bis zu einem bestimmten Alter empfohlen werden, sollen keine weiteren Dosen verabreicht werden, wenn Pat. dieses Alter überschritten hat. Impfung gegen Influenza in der Klinik • Grad 3: Pat. mit Sofortreaktion nach Verzehr von Hühnereiweiß mit Urtikaria, Laryngo-/Bronchospasmus, RR-Abfall. cache = ./cache/cord-033558-lcgo1tiy.txt txt = ./txt/cord-033558-lcgo1tiy.txt === reduce.pl bib === id = cord-027659-rxbo7b0e author = Bates, Imelda title = Blood Transfusion date = 2020-06-22 pages = extension = .txt mime = text/plain words = 4169 sentences = 211 flesch = 49 summary = Hospital-based transfusion services place an enormous burden on laboratory resources and on the families of patients because they are responsible for fi nding suitable blood donors. 2 In wealthy countries with nationally or regionally centralized transfusion services, blood donor recruitment, and screening and processing of donated blood, are carried out in purpose-built centres which are separate from the hospitals where the blood is transfused. Infections with organisms that are common in tropical countries, such as HIV-1 and -2, hepatitis A, B, C and D, cytomegalovirus, syphilis, lyme borreliosis, malaria, babesiosis, American trypanosomiasis (Chagas' disease) and toxoplasmosis, can all be acquired through blood transfusions. Further research to assess the risks and benefi ts of screening blood for malaria is needed, particularly in relation to pregnant women and patients with HIV infection. cache = ./cache/cord-027659-rxbo7b0e.txt txt = ./txt/cord-027659-rxbo7b0e.txt === reduce.pl bib === === reduce.pl bib === id = cord-034714-6e37yylk author = Alleg, Manel title = Progressive multifocal leukoencephalopathy: MRI findings in HIV-infected patients are closer to rituximab- than natalizumab-associated PML date = 2020-11-06 pages = extension = .txt mime = text/plain words = 3746 sentences = 170 flesch = 37 summary = title: Progressive multifocal leukoencephalopathy: MRI findings in HIV-infected patients are closer to rituximabthan natalizumab-associated PML OBJECTIVES: To compare brain MRI findings in progressive multifocal leukoencephalopathy (PML) associated to rituximab and natalizumab treatments and HIV infection. Inclusion criteria were (1) a "definite" PML diagnosis according to the American Academy of Neurology criteria [19] including clinical and imaging-compatible features and detection of JCV DNA in the cerebrospinal fluid or in brain tissue by polymerase chain reaction (PCR) or immunohistochemistry; (2) HIV-infected patients or patients treated with immunomodulatory or immunosuppressive drugs such as natalizumab or rituximab, possibly in association with other drugs and whatever the initial illness; and (3) consent was provided for in the hospital's charter. This study aims to describe the MRI characteristics of PML associated with rituximab and natalizumab and in HIV infection while comparing imaging findings with the level of immunosuppression. cache = ./cache/cord-034714-6e37yylk.txt txt = ./txt/cord-034714-6e37yylk.txt === reduce.pl bib === id = cord-026112-58sa5z03 author = Dehghani-Dehej, Farzaneh title = Prevalence of HCV and/or HBV coinfection in Iranian HIV-infected patients date = 2020-04-24 pages = extension = .txt mime = text/plain words = 4005 sentences = 198 flesch = 47 summary = This study aimed to investigate molecular epidemiology of HBV and HCV coinfection in Iranian HIV-infected individuals. Materials & methods: In this cross-sectional study, serological markers of HBV and HCV infection (hepatitis B surface antigen [HBsAg], hepatitis B e-antigen [HBeAg], hepatitis B e-antibody [HBeAb] and hepatitis B core antibody [HBcAb]) and anti-HCV antibodies [anti-HCV Abs] were tested in 198 Iranian HIV-infected patients. HIV/HBV-coinfected people have a higher rate of progression to liver fibrosis, cirrhosis, HCC, less clearance of HBsAg and occult HBV infections (OBI) are more frequent in these patients [13] . The aim for this study is to investigate the prevalence of HCV and/or HBV coinfection in Iranian HIV-infected individuals. According to a previous study, prevalence of cirrhosis in HIV/HBV/HCV triple-infected patients was higher than HIV/HBV-or HIV/HCV-coinfected individuals [57] . cache = ./cache/cord-026112-58sa5z03.txt txt = ./txt/cord-026112-58sa5z03.txt === reduce.pl bib === id = cord-023884-etkhrgxp author = Meremikwu, Martin title = Malaria in Women and Children date = 2009-05-18 pages = extension = .txt mime = text/plain words = 8513 sentences = 412 flesch = 46 summary = falciparum infections (often in persons who have no immunity to malaria or whose immunity has decreased) are complicated by serious organ failures or abnormalities in the patient's blood or metabolism, resulting in cerebral malaria, with abnormal behavior, impairment of consciousness, seizures, coma, or other neurologic abnormalities, severe anemia due to hemolysis (destruction of the red blood cells), hemoglobinuria (hemoglobin in the urine) due to hemolysis, pulmonary edema (fluid buildup in the lungs) or acute respiratory distress syndrome (ARDS), which may occur even after the parasite counts have decreased in response to treatment, abnormalities in blood coagulation and thrombocytopenia (decrease in blood platelets), cardiovascular collapse, shock, acute kidney failure, hyperparasitemia, where more than 5% of the red blood cells are infected by malaria parasites, metabolic acidosis (excessive acidity in the blood and tissue fluids), often in association with hypoglycemia (low blood glucose). A review of studies in areas of sub-Saharan Africa with high and stable malaria transmission shows that HIV-1 infection and clinically diagnosed AIDS increased the incidence of malaria 1.2-fold and 2fold, respectively (Korenromp et al. Achieving high coverage of insecticide-treated bed nets (ITNs) use and prompt access to treatment with artemisininbased combination treatments (ACTs) would contribute to the reduction in the morbidity and Source: WHO-AFRO (2004) mortality attributable to HIV co-infection with malaria in high transmission areas. cache = ./cache/cord-023884-etkhrgxp.txt txt = ./txt/cord-023884-etkhrgxp.txt === reduce.pl bib === === reduce.pl bib === id = cord-027242-7qq82j2f author = Chrissafidou, Angeliki title = Infektionen, Impfungen, Reisemedizin date = 2008-12-11 pages = extension = .txt mime = text/plain words = 6531 sentences = 1335 flesch = 55 summary = 9 HIV und AIDS 543 9.9.1 Epidemiologie und Ü bertragungswege 543 9.9.2 Labordiagnostik 546 9.9.3 Stadieneinteilung und Verlauf 548 9.9.4 Diagnostik bei HIV-Positiven 548 9.9.5 Hä ufige Krankheitsbilder bei AIDS 554 9.9.6 Therapie 560 9.9.7 Medikamente bei HIV-Patienten 564 9.9.8 Vorgehen bei Kontakt mit HIVkontaminiertem Material und Postexpositionsprophylaxe (PEP) 567 9.10 Reisemedizin 567 9.10.1 Allgemeine Empfehlungen zur Reisefä higkeit 572 9.10.2 Empfehlungen fü r Schwangere 573 9.10.3 Empfehlungen fü r ä ltere Menschen 574 9.10.4 Empfehlungen fü r Kinder und Sä uglinge 575 9.10.5 Empfehlungen fü r chronisch Kranke 577 9.10.6 Reisevorbereitungen/Prophylaxen 580 9.10.7 Reiseimpfungen und Chemoprophylaxe 587 9.10.8 Gesundheitsrisiken auf Reisen 596 9.10.9 Screening nach Reiseende 597 9.11 Infektionsschutzgesetz 9.1 Die Immunisierung durch Impfungen ist eine der wichtigsten und wirksamsten Maßnahmen zum Schutz vor Infektionskrankheiten. Aktive Immunisierung: Der Organismus wird mit Antigenen von Krankheitserregern konfrontiert und muss selbst eine Immunität ausbilden. Totimpfstoffe: Abgetö tete Krankheitserreger oder aufbereitete Antigene; keine Impfinfektion mö glich, deshalb auch bei Pat. mit Immundefekten applizierbar. cache = ./cache/cord-027242-7qq82j2f.txt txt = ./txt/cord-027242-7qq82j2f.txt === reduce.pl bib === === reduce.pl bib === id = cord-029416-738t6rk1 author = Mandal, Sandip title = The potential impact of preventive therapy against tuberculosis in the WHO South-East Asian Region: a modelling approach date = 2020-07-20 pages = extension = .txt mime = text/plain words = 5177 sentences = 255 flesch = 43 summary = The 2018 World Health Organization (WHO) guidelines on eligibility for preventive therapy to treat latent TB infection (LTBI) include people living with human immunodeficiency virus (PLHIV), household contacts of TB patients including children, and those with clinical conditions including silicosis, dialysis, transplantation, etc. Relative to both scenarios, for each country in the region, we projected TB cases and deaths averted between 2020 and 2030, by full uptake of preventive therapy, defined as comprehensive coverage amongst eligible populations as per WHO guidelines, and assuming outcomes consistent with clinical trials. In the absence of a widely deployable test to identify who would benefit most from preventive therapy, World Health Organization (WHO) guidelines identify high-risk groups for eligibility: for example, those with human immunodeficiency virus (HIV) coinfection [10] and, in the most recently updated guidelines, all household contacts of diagnosed TB cases and those with clinical conditions including silicosis, those on anti-TNF treatment, and other country-specific groups [11] . cache = ./cache/cord-029416-738t6rk1.txt txt = ./txt/cord-029416-738t6rk1.txt === reduce.pl bib === === reduce.pl bib === id = cord-103350-jj9pc4a6 author = Tang, Pingtao title = An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy date = 2020-05-08 pages = extension = .txt mime = text/plain words = 4041 sentences = 204 flesch = 46 summary = rAd-Tat and LacZ control vectors (2 × 109) were expressed in the kidney of newborn wild type and HIV-transgenic (Tg26) FVB/N mice without significant proteinuria (n = 5 8 per group). Results HIV-Tat induced the expression of HIV-1 genes (env) and heparin binding growth factors in the kidney of HIV-Tg26 mice, and precipitated HIVAN in the first month of life. Summary statement We developed a new inducible mouse model system of childhood HIV-associated nephropathy, and demonstrated that HIV-Tat plays a critical role in this renal disease acting in synergy with other HIV-1 genes and heparin binding cytokines. Therefore, we carried out this study to determine whether the HIV-1 trans-activator (Tat) gene precipitates HIVAN in young mice, and define whether this approach could be used to generate an inducible mouse model system of childhood HIVAN. Our study showed that the activation and basic binding domains of Tat are sufficient to induce the renal expression of HIV-genes and precipitate HIVAN in young mice. cache = ./cache/cord-103350-jj9pc4a6.txt txt = ./txt/cord-103350-jj9pc4a6.txt === reduce.pl bib === === reduce.pl bib === id = cord-027860-s97hdhh6 author = Zeimet, Anthony title = Infectious Diseases date = 2020-06-22 pages = extension = .txt mime = text/plain words = 28925 sentences = 1728 flesch = 45 summary = Although common upper respiratory bacterial pathogens, such as Moraxella (Branhamella) catarrhalis, Streptococcus pneumoniae, and Haemophilus influenzae, may be isolated from patients with acute bronchitis, their relevance is questionable because these bacteria can be present in the respiratory tract of healthy individuals. In the treatment of Bordetella pertussis, early administration of a macrolide antibiotic and patient isolation will likely decrease coughing paroxysms and limit spread of disease (Braman, 2006) (SOR: A). Risk factors for Pseudomonas infection include severe structural lung disease (e.g., bronchiectasis) and recent antibiotic therapy, health care-associated exposures or stay in hospital (especially in the ICU). Patients who present with severe infection or whose infection is progressing despite empiric antibiotic therapy should be treated more aggressively; the treatment strategy should be based on results of appropriate Gram stain, culture, and drug susceptibility analysis. For suspected MRSA skin infections, oral treatment options include trimethoprim-sulfamethoxazole, clindamycin, and doxycycline of purulent material when performing incision and drainage in the event that the patient fails to improve and antibiotic coverage becomes necessary. cache = ./cache/cord-027860-s97hdhh6.txt txt = ./txt/cord-027860-s97hdhh6.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-030427-fn9pfqts author = Huang, Feifei title = Acculturation, HIV-Related Stigma, Stress, and Patient-Healthcare Provider Relationships Among HIV-Infected Asian Americans: A Path Analysis date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3439 sentences = 162 flesch = 42 summary = title: Acculturation, HIV-Related Stigma, Stress, and Patient-Healthcare Provider Relationships Among HIV-Infected Asian Americans: A Path Analysis A bias-corrected factor score path analysis was performed to examine the proposed model of relations among acculturation, stigma, stress, and patient-HCP relationships. A convenience sample of 69 HIV-positive Asian Americans in San Francisco, Los Angeles, and New York City were recruited and collect data were collected on demographics, HIV-related stigma, stress, and patient-HCP relationships. Similar to other people living with HIV/AIDS (PLWHA), HIV-infected Asian Americans may also suffer from HIV-related stigma and stress, which in turn influences their patient-healthcare provider (HCP) relationships [4, 5] . The present study showed that acculturation is beneficial for patient-HCP relationships to the extent that it decreases perceived stigma and stress in Asian American PLWHA. In this paper, we examined the associations among acculturation, HIV-related stigma, stress, and patient-HCP relationships among Asian American PLWHA. cache = ./cache/cord-030427-fn9pfqts.txt txt = ./txt/cord-030427-fn9pfqts.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-254190-bxfne94u author = Tu, Wenwei title = Application of Humanized Mice in Immunological Research date = 2015-07-07 pages = extension = .txt mime = text/plain words = 6246 sentences = 254 flesch = 34 summary = On the contrary, humanized mice established by peripheral blood cells provide a ready platform for studying the functions of mature immune cells but the length of window appropriate for research is still limited by chronic GVHD and ongoing reduced engraftment. Distinct from their T cell companion, reconstitution of functional B lymphocytes is generally poor in humanized mice and needed to improve in the future although their primary repertoire were principally unaltered by the differences between mouse and human stromal environments [ 53 ] and their ability to produce antigen-specifi c antibody was partly developed [ 54 ] . In above three studies, investigators planted solid grafts into immunodefi cient mice before reconstitution of human immune system and induced rejection by infusion of mature human cells. Humanized immune system (HIS) mice as a tool to study human NK cell development Humanized mice as a model to study human hematopoietic stem cell transplantation cache = ./cache/cord-254190-bxfne94u.txt txt = ./txt/cord-254190-bxfne94u.txt === reduce.pl bib === id = cord-032438-cpoalxyd author = Nachega, Jean B title = The where, when, and how of community-based versus clinic-based ART delivery in South Africa and Uganda date = 2020-09-21 pages = extension = .txt mime = text/plain words = 1286 sentences = 59 flesch = 40 summary = In this issue of The Lancet Global Health, Ruanne Barnabas and colleagues report results of the Delivery Optimization of Antiretroviral Therapy (DO-ART) study, a multicentre, randomised trial comparing community-based ART initiation, monitoring, and resupply with use of a hybrid approach (ART initiation at the clinic with community monitoring and resupply), and with standard clinicbased ART delivery among individuals from South Africa and Uganda with detectable HIV viral load. 7 However, most communitybased differentiated service delivery models for ART delivery have been developed for patients who are already stable on ART, and the most important contribution of the study by Barnabas and colleagues is that community-based, same-day ART initiation in individuals with elevated viral load was safe and resulted in improved viral suppression after 12 months, particularly among men. Community-based antiretroviral therapy versus standard clinic-based services for HIV in South Africa and Uganda (DO ART): a randomised trial cache = ./cache/cord-032438-cpoalxyd.txt txt = ./txt/cord-032438-cpoalxyd.txt === reduce.pl bib === === reduce.pl bib === id = cord-019347-tj3ye1mx author = nan title = ABSTRACT BOOK date = 2010-02-19 pages = extension = .txt mime = text/plain words = 107926 sentences = 6940 flesch = 53 summary = Method:Case Report:A 15y/o w/f athlete presented with a two month history of recurrent hives and angioedema which she associated with ingestion of Halloween candy .One week before evaluation she had hives with Coconut as well.Her history was othewise unremarkable except for recurrent UTI'S, annual sinusitis, pneumonia in 1998 as well as migraines.She denied sexual activity.Her physical exam was normal.Results:An evaluation for autoimmune disease revealed normal ESR, ANA, DSDNA, mono and hepatitis serology as well as lyme titers however her CH50 was low17u/ml(normal 26-58U/ml)and evaluation of complement revealed c4 14mg/dl(normal 16-47mg//dl)and c2 <1.3mg/dl(normal 1.6-3.5mg/dl)with normal c3, c5-c9.Her father had nor-malc4 but c2 was 1.4mg/dl (normal 1.6-3.5mg/dl)Her sister had c2 of 1.5mg/dl and normal c4 and her mother had normal c2 and c4.Her workup included positive prick skin test to ragweed, ash and grass and she was started on Rhinocort and Clarinex seasonally.She has been followed for one year with resolution of hives and is asymptomatic.Her diagnosis had been confirmed by a pediatric rheumatologist.Conclusion;We present an atypical case of C2 complement deficiency in an currently asymptomatic individual. cache = ./cache/cord-019347-tj3ye1mx.txt txt = ./txt/cord-019347-tj3ye1mx.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-256324-w3bejmy5 author = Hamada, Yoshio title = New directions for protease inhibitors directed drug discovery date = 2016-07-22 pages = extension = .txt mime = text/plain words = 5066 sentences = 292 flesch = 55 summary = 23 Most b-secretase inhibitors possess a transition state analogue at the P 1 position and are designed based on the amino acid sequence of Swedish mutant APP, which has a double mutation around the b-site (at the K670N and M671L residues). Many inhibitors with an aromatic ring at the P 1 position were subsequently reported; for example, a research group at Merck Sharp and Dohme (MSD) reported the potent inhibitors 50 63, 64 Although 18 was designed based on peptidomimetic inhibitors by using the SBDD approach, it is notable because it forms a unique cyclic structure at the P 1 position where the hydroxyl and amino groups on the cyclic sulfone ring of 18 appear to interact with two Asp residues at the active site of b-secretase as well as acting as a transition state analogue. cache = ./cache/cord-256324-w3bejmy5.txt txt = ./txt/cord-256324-w3bejmy5.txt === reduce.pl bib === id = cord-256459-6h358si5 author = Sharpstone, D title = Gastrointestinal manifestations of HIV infection date = 1996-08-10 pages = extension = .txt mime = text/plain words = 3644 sentences = 201 flesch = 36 summary = Mucosal biopsy: Although diagnosis by stool analysis alone has been suggested by Johanson and Sonnenberg, 32 this study may have overestimated the value of symptomatic treatment and ignored the possibility that cytomegalovirus infection sometimes responds to therapy. Analysis of six stool samples and histological examination of small and large bowel biopsy speicmens detect more than 90% of infectious causes of diarrhoea in HIV-seropositive individuals. Since diagnosis of cytomegalovirus enteritis is improving, patients with milder symptoms are being detected and the quality of life with treatment-anti-CMV agents have to be given intravenously and have considerable toxicitymay not be enhanced compared with no therapy. The other origin of abdominal pain unique to HIV-seropositive patients is an AIDS-related sclerosing cholangitis caused by various opportunists including Microsporidia, CMV, and Cryptosporidia. Effects of zidovudine treatment on the small intestinal mucosa in patients infected with the human immunodeficiency virus Atrovaquone is effective treatment for the symptoms of gastrointestinal microsporidiosis in HIV-1 infected patients cache = ./cache/cord-256459-6h358si5.txt txt = ./txt/cord-256459-6h358si5.txt === reduce.pl bib === id = cord-048467-1dus0u4m author = Civaner, Murat title = Can "presumed consent" justify the duty to treat infectious diseases? An analysis date = 2008-03-06 pages = extension = .txt mime = text/plain words = 7746 sentences = 303 flesch = 51 summary = The purpose of this study was to investigate the opinions and beliefs held by both physicians and dentists regarding the occupational risks of infectious diseases, and to analyze the argument that the notion of "presumed consent" on the part of professionals may be grounds for supporting the duty to treat. CONCLUSION: If we use the presumed consent argument to establish the duty of the HCW to provide care, we are confronted with problems ranging over the difficulty of choosing a profession autonomously, the constant level of uncertainty present in the medical profession, the near-impossibility of being able to evaluate retrospectively whether every individual was informed, and the seemingly inescapable problem that this practice would legitimize, and perhaps even foster, discrimination against patients with certain diseases. In order to carry out this analysis, the opinions and beliefs of physicians and dentists regarding the occupational risks of infectious diseases were investigated; and, by extension, the argument that the notion of "presumed consent" may be grounds for supporting the HCWs' duty to treat was also analyzed. cache = ./cache/cord-048467-1dus0u4m.txt txt = ./txt/cord-048467-1dus0u4m.txt === reduce.pl bib === id = cord-254187-dcdc6sqi author = Kimball, AM title = “What, me worry?” Businesses and AIDS at Davos date = 2005-04-05 pages = extension = .txt mime = text/plain words = 1836 sentences = 103 flesch = 57 summary = At the Davos Summit in February, 2005, the World Economic Forum released its current survey on businesses and HIV/AIDS. In Asia, the prospective new epicentre of the epidemic, the efforts of the Thailand Business Coalition on AIDS and the Tata Group in India highlight roles business can play: prevention and education for workers; workplace programmes to prevent discrimination; and public-private collaboration and funding for effective programmes. 5 The most recent survey of the World Economic Forum's Global Health Initiative 6 shows that awareness by business that AIDS will affect operations and profits reflects the level of efforts to combat the disease. 6 The Global Health Initiative worked with several South African firms to organise case studies, which vividly illustrate the imperatives and benefits for companies offering antiretrovirals to their employees. A role for business in HIV/AIDS in Asia cache = ./cache/cord-254187-dcdc6sqi.txt txt = ./txt/cord-254187-dcdc6sqi.txt === reduce.pl bib === id = cord-254951-anfkuigj author = Pierre, Gashema title = Attendance to HIV Antiretroviral Collection Clinic Appointments During COVID-19 Lockdown. A Single Center Study in Kigali, Rwanda date = 2020-06-25 pages = extension = .txt mime = text/plain words = 1213 sentences = 66 flesch = 57 summary = According to The Joint United Nations Programme on HIV and AIDS (UNAIDS) and the World Health Organization (WHO), a 6-month disruption of antiretroviral therapy (ART) during the COVID-19 pandemic in sub-Saharan Africa will increase HIV-related death rate by more than half a million [8] . Given the recent total lockdown in Rwanda, this note presents findings from a study aimed to assess attendance to ART collection clinic appointments in the period 21 March to 30 April 2020 in Kigali, Rwanda. Less than half (48%) had attended scheduled ART collection clinic appointments during the lockdown period of 21 March to 30 April 2020. There was an association between place of residence and attendance status (p = 0.040), 50% staying within Kigali attended scheduled ART collection clinic appointments during the lockdown period compared to 35% among those living outside Kigali. cache = ./cache/cord-254951-anfkuigj.txt txt = ./txt/cord-254951-anfkuigj.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-259131-36udb7uc author = Hunegnaw, Ruth title = Alveolar Macrophage Dysfunction and Increased PD-1 Expression During Chronic SIV Infection of Rhesus Macaques date = 2019-07-03 pages = extension = .txt mime = text/plain words = 7426 sentences = 376 flesch = 46 summary = AM expression of proinflammatory cytokines TNF-α, IL-6, IL-1β, and chemokine RANTES drastically increased 2-wpi compared to AMs of naïve macaques (p < 0.0001 for all), but dropped significantly with progression to chronic infection. AM expression of proinflammatory cytokines TNF-α, IL-6, IL-1β, and chemokine RANTES drastically increased 2-wpi compared to AMs of naïve macaques (p < 0.0001 for all), but dropped significantly with progression to chronic infection. In addition, the low proinflammatory cytokine response in chronic infection was not associated with an increase in IL-10-expressing AMs. To investigate AM activation, BAL cells obtained from naïve and acute and chronically infected macaques at weeks 2, 4, 8, 12, and 20 wpi, were incubated with native gp120 from R5 tropic SIV or LPS for 6 h, and intracellular expression of MIP-1β and IL-6 was assessed (Figures 3A,B) . Decreased Fc receptor expression on innate immune cells is associated with impaired antibody-mediated cellular phagocytic activity in chronically HIV-1 infected individuals cache = ./cache/cord-259131-36udb7uc.txt txt = ./txt/cord-259131-36udb7uc.txt === reduce.pl bib === id = cord-256477-dftt5m6i author = Feller, John M. title = Potential Ebola prophylaxis date = 2015-07-01 pages = extension = .txt mime = text/plain words = 604 sentences = 43 flesch = 53 summary = The hypothesis that CQ might afford Ebola prophylaxis comes from our own work showing hydroxychloroquine (HCQ) induces apoptosis (programmed cell death) in peripheral blood mononuclear cells. 4, 5 A randomised controlled trial (RCT) in 13 ART-naïve patients found CQ was associated with decreased memory CD8 T-cell activation, CD4 and CD8 T-cell proliferation and lipopolysaccharide levels compared with baseline, but there were no changes in plasma HIV RNA. 6 However, another RCT of HCQ in ART-naïve patients demonstrated no change in T-cell activation and proliferation, an increase in HIV RNA and a decrease in CD4 T-cell counts. Ebola infects dendritic cells, which display signals of infection on their surfaces to activate T lymphocytes that destroy other infected cells before the virus replicates further. Reduction of immune activation with chloroquine therapy during chronic HIV infection Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial cache = ./cache/cord-256477-dftt5m6i.txt txt = ./txt/cord-256477-dftt5m6i.txt === reduce.pl bib === === reduce.pl bib === id = cord-254194-962vynwk author = Galdiero, Stefania title = Silver Nanoparticles as Potential Antiviral Agents date = 2011-10-24 pages = extension = .txt mime = text/plain words = 10034 sentences = 447 flesch = 38 summary = Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. Theoretically, any metal could be analysed for antiviral activity, however, little effort has been done to determine the interactions of metal nanoparticles with viruses, and only recently some studies have emerged showing that metal nanoparticles can be effective antiviral agents against HIV-1 [37] [38] [39] [40] , hepatitis B virus [41] , respiratory syncytial virus [42] , herpes simplex virus type 1 [43, 44] , monkeypox virus [45] , influenza virus [46] and Tacaribe virus [47] . cache = ./cache/cord-254194-962vynwk.txt txt = ./txt/cord-254194-962vynwk.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-259503-dkfrk71a author = Smith, Sarah E. title = Sherlock Genomes — viral investigator date = 2013-02-15 pages = extension = .txt mime = text/plain words = 806 sentences = 54 flesch = 56 summary = Deep sequencing technologies and stateof-the-art bioinformatics techniques have revolutionized the way that RNA viruses, a notoriously variable group of pathogens, can be identified and characterized. By using de novo assembly of short reads, the authors showed that this method could generate full genomes for viruses within all four major HIV-1 genetic groups. Even when almost nothing is known about the agent of a viral infection, deep sequencing technologies can identify a pathogen and produce the full genome, fast. When SARS-CoV began infecting people in 2002, it took a large team to generate a full genome by capillary sequencing. 2 used random priming to amplify viral RNA isolated from the Saudi Arabian patient, and then deep-sequenced the genome. Knowing the sequence of the whole genome enabled the authors to further characterize this new virus, named human CoV (HCoV)-EMC2012. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes cache = ./cache/cord-259503-dkfrk71a.txt txt = ./txt/cord-259503-dkfrk71a.txt === reduce.pl bib === id = cord-255075-6azu6k3h author = Zhuang, Jianjian title = Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date = 2020-05-12 pages = extension = .txt mime = text/plain words = 3141 sentences = 230 flesch = 49 summary = Multiplexed efficient on-chip sample preparation 613 and sensitive amplification-free detection of Ebola virus A bead-based 689 immunofluorescence-assay on a microfluidic dielectrophoresis platform for rapid dengue virus 690 detection Fast and Parallel Detection of Four Ebola Virus Species on a Microfluidic-Chip-Based Portable 770 An integrated self-driven microfluidic device for rapid 781 detection of the influenza A (H1N1) virus by reverse transcription loop-mediated isothermal 782 amplification Paper-based RNA detection and 785 multiplexed analysis for Ebola virus diagnostics Multiplex microfluidic paper-based 805 immunoassay for the diagnosis of hepatitis C virus infection Simultaneous and automated detection of influenza A virus hemagglutinin H7 and H9 based on 965 magnetism and size mediated microfluidic chip A 1026 point of care platform based on microfluidic chip for nucleic acid extraction in less than 1 minute D: Schematic of a 1149 paper-based chip for the detection of HIV developed by Li et al. cache = ./cache/cord-255075-6azu6k3h.txt txt = ./txt/cord-255075-6azu6k3h.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-257217-f9sdt7ax author = Nunes, Marta C. title = Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date = 2014-02-03 pages = extension = .txt mime = text/plain words = 4629 sentences = 215 flesch = 43 summary = We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and –KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI). METHODS: Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and –uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and influenza A/B. The aim of this study was to identify the prevalence of hBoV, hRV, WUPyV, KIPyV, CoV-OC43, CoV-NL63, CoV-HKU1 and CoV-229E among HIV-infected and -uninfected children who were hospitalized for LRTI using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Very few viral aetiology studies have been conducted in Africa: in a Mozambican study of virus-associated acute respiratory infections (ARI) in infants with an estimated 3-5% HIV prevalence, the most frequently detected viruses were hRV (26%), influenza (15%) and adenovirus (14%) [27] . cache = ./cache/cord-257217-f9sdt7ax.txt txt = ./txt/cord-257217-f9sdt7ax.txt === reduce.pl bib === id = cord-260496-s2ba7uy3 author = Moncany, Maurice L.J. title = Identification of conserved lentiviral sequences as landmarks of genomic flexibility date = 2006-08-08 pages = extension = .txt mime = text/plain words = 5991 sentences = 296 flesch = 51 summary = Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). Immunodeficiency lentiviral genomes correspond to 171 human viruses (155 HIV-1s and 16 HIV-2s), 33 simian viruses (3 CPZ, 9 AGM, 8 Macaque, 2 Mandrill, 10 Sooty Mangabey, 1 Sykes' monkey viruses) and 33 non-primate mammal viruses (2 bovine, 2 caprine, 11 equine, 9 feline, 3 ovine and 6 ovine/caprine viruses). From the particular organization of the HIV-1 and HIV-2 ( Fig. 1) , AGM and macaque (Fig. 2) , CPZ, feline, equine and D-particle-forming viruses (Fig. 3) and that of sooty mangabey, mandrill and other non-primate lentiviruses (supplementary data), it appears that a given CLS occupied on the viral genome a specific position that was roughly conserved in the different viral families. cache = ./cache/cord-260496-s2ba7uy3.txt txt = ./txt/cord-260496-s2ba7uy3.txt === reduce.pl bib === === reduce.pl bib === id = cord-261382-cyty5noi author = Goffinet, Christine title = Cellular Antiviral Factors that Target Particle Infectivity of HIV-1 date = 2016-05-17 pages = extension = .txt mime = text/plain words = 4084 sentences = 177 flesch = 35 summary = Whereas well-established restriction factors interfere with early post-entry steps and release of HIV-1, recent research has revealed a diverse set of proteins that reduce the infectious quality of released particles using individual, to date poorly understood modes of action. Alternatively, alteration of the virus membrane fluidity, restriction of the accessibility of the HIV-1 Env glycoprotein to the HIV-1 receptor/coreceptor complex by steric hindrance through an incorporated protein or inhibition of the maturation-induced clustering of HIV-1 Env trimers could represent mechanisms of cellular defense that target particle infectivity. Since it shares mRNA upregulation in CD4+ T-cells of HIV-1 infected individuals [11] and type I IFN-induced expression [10, 12, 13] with established restriction factors of HIV-1, it was included in a functional screen of candidate ISGs for antiviral activity (Goffinet, unpublished data). Additional family members, including IFITM5, whose expression is restricted to osteoblasts [22] , and 10 additional, recently discovered human ifitm genes [21] probably do not contribute to inhibition of HIV-1 infection or haven't yet been tested for antiviral activity, respectively. cache = ./cache/cord-261382-cyty5noi.txt txt = ./txt/cord-261382-cyty5noi.txt === reduce.pl bib === === reduce.pl bib === id = cord-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130043 sentences = 7330 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023346-8sqbqjm1.txt txt = ./txt/cord-023346-8sqbqjm1.txt === reduce.pl bib === id = cord-260191-0u0pu0br author = Haas, W. title = „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date = 2004-05-29 pages = extension = .txt mime = text/plain words = 2431 sentences = 335 flesch = 51 summary = Abstract Some emerging infectious diseases have recently become endemic in Germany.Others remain confined to specific regions in the world.Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms.Several of these emerging infections will be explained.HIV is an example for an imported pathogen which has become endemic in Germany.SARS and avian influenza are zoonoses with the potential to spread from person to person.Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain.Outbreaks of dengue fever in endemic areas are reflected in increased infec-gehäuften Erkrankungen bei Rückkehrern wieder.West-Nil-Virus-Erkrankungen kommen derzeit nur als importierte Erkrankungen in Deutschland vor.Wichtig ist,diese Erkrankungen frühzeitig in die differenzialdiagnostischen Überlegungen des Klinikers einzubeziehen,um die erforderlichen Maßnahmen zur Diagnostik,Therapie und zum Infektionsschutz rechtzeitig einleiten zu können.Dies erfordert ein gutes Zusammenspiel mit dem Labor und dem öffentlichen Gesundheitsdienst. cache = ./cache/cord-260191-0u0pu0br.txt txt = ./txt/cord-260191-0u0pu0br.txt === reduce.pl bib === === reduce.pl bib === id = cord-260604-lz1qd69t author = Singh, Ramendra K. title = Synthesis, structure–activity relationship and antiviral activity of 3′-N,N-dimethylamino-2′,3′-dideoxythymidine and its prodrugs date = 2010-09-30 pages = extension = .txt mime = text/plain words = 3096 sentences = 170 flesch = 58 summary = Molecular docking studies with HIV-1 RT using DS 2.5 and pymol softwares have shown marked differences in the interaction patterns between the lead compound 4 and AZT. The lead molecule, DMAT, was designed keeping AZT, an approved NRTI drug against HIV/AIDS, in mind, where azido group has been replaced by dimethylamino function, Fig. 1 . Compounds 4 and 5 have showed similar values of CC 50 and EC 50 against all viruses studied and thus no activity was observed, while 5 0 -L-phenylalanyl derivative 6, having free amino function was potentially active at an EC 50 of 0.03 mM against VSV in HeLa and HEL cell cultures. The fact that the lead molecule DMAT (and its prodrugs) being a dideoxynucleoside and having structural features similar to AZT, did not show any activity against HIV and rather proved toxic, prompted us to study its interaction with HIV-1 RT. cache = ./cache/cord-260604-lz1qd69t.txt txt = ./txt/cord-260604-lz1qd69t.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-262752-bwofzbwa author = Li, Qianqian title = Current status on the development of pseudoviruses for enveloped viruses date = 2017-12-07 pages = extension = .txt mime = text/plain words = 3268 sentences = 179 flesch = 37 summary = Early work by Witte and colleagues showed that when they used VSV to infect the cells in which MLV is packaged, they were able to harvest pseudovirus for use in neutralization antibody assays. Development of in vitro and in vivo rabies virus neutralization assays based on a high-titer pseudovirus system Development of a pseudotyped-lentiviral-vector-based neutralization assay for chikungunya virus infection Second generation of pseudotype-based serum neutralization assay for Nipah virus antibodies: sensitive and high-throughput analysis utilizing secreted alkaline phosphatase Use of vesicular stomatitis virus pseudotypes bearing Hantaan or Seoul virus envelope proteins in a rapid and safe neutralization test A neutralization test for specific detection of Nipah virus antibodies using pseudotyped vesicular stomatitis virus expressing green fluorescent protein Truncation of the human immunodeficiency virus-type-2 envelope glycoprotein allows efficient pseudotyping of murine leukemia virus retroviral vector particles Cholesterol supplementation during production increases the infectivity of retroviral and Lentiviral vectors pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) cache = ./cache/cord-262752-bwofzbwa.txt txt = ./txt/cord-262752-bwofzbwa.txt === reduce.pl bib === id = cord-264050-6zpw6itb author = Pirofski, Liise-anne title = Immune-Mediated Damage Completes the Parabola: Cryptococcus neoformans Pathogenesis Can Reflect the Outcome of a Weak or Strong Immune Response date = 2017-12-12 pages = extension = .txt mime = text/plain words = 2752 sentences = 121 flesch = 36 summary = The demonstration that host-mediated damage can drive cryptococcal disease provides proof of concept that the parabola put forth in the damage-response framework has the flexibility to depict complex and changing outcomes of host-microbe interaction. However, the emergence of Cryptococcus gattii in apparently healthy persons in the Pacific Northwest (7) and the unexpected appearance of immune reconstitution inflammatory syndrome (IRIS)-associated cryptococcosis in patients with HIV/AIDS after initiation of antiretroviral therapy (ART) (8, 9) revealed that the host immune response itself can contribute to the pathogenesis of cryptococcosis. The emergence of IRIS-associated cryptococcosis in the setting of ART initiation provided clear evidence that host damage in patients with cryptococcal disease may be driven by inflammation (12) . Chemokine levels and chemokine receptor expression in the blood and the cerebrospinal fluid of HIV-infected patients with cryptococcal meningitis and cryptococcosis-associated immune reconstitution inflammatory syndrome cache = ./cache/cord-264050-6zpw6itb.txt txt = ./txt/cord-264050-6zpw6itb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-263438-9ra94uda author = Snowden, Frank M. title = Emerging and reemerging diseases: a historical perspective date = 2008-09-19 pages = extension = .txt mime = text/plain words = 14393 sentences = 608 flesch = 47 summary = Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. In 1996, in addition, President Bill Clinton (28) issued a fact sheet entitled 'Addressing the Threat of Emerging Infectious Diseases' in which he declared them 'one of the most significant health and security challenges facing the global community.' There were also highly visible hearings on emerging infections in the US Congress (29) . The Rand Corporation intelligence report The Global Threat of New and Reemerging Infectious Diseases: Reconciling U.S. National Security and Public Health Policy (53) had two leading themes. cache = ./cache/cord-263438-9ra94uda.txt txt = ./txt/cord-263438-9ra94uda.txt === reduce.pl bib === id = cord-259846-oxbmtend author = Naik, Parvaiz Ahmad title = Global dynamics of a fractional order model for the transmission of HIV epidemic with optimal control date = 2020-06-18 pages = extension = .txt mime = text/plain words = 8469 sentences = 533 flesch = 53 summary = Furthermore, for the fractional optimal control problem associated with the control strategies such as condom use for exposed class, treatment for aware infectives, awareness about disease among unaware infectives and behavioral change for susceptibles, we formulated a fractional optimality condition for the proposed model. We incorporate into the model time dependent controls such as condom use for exposed individuals, treatment for infected female sex workers, awareness about the disease among unaware infectives and behavioral change for susceptibles in order to reduce the risk of the spread of HIV/AIDS disease. In order to justify our theoretical findings, we introduced in this section some numerical experiments obtained for different instances of fractional power κ for the HIV epidemic model without control (9) and with control (24) along with adjoint variable systems and the control strategies. We present the numerical results for the model (9) when all control measures are absent and also to examine the role of fractional order κ on the HIV disease spread. cache = ./cache/cord-259846-oxbmtend.txt txt = ./txt/cord-259846-oxbmtend.txt === reduce.pl bib === id = cord-022633-fr55uod6 author = nan title = SAEM Abstracts, Plenary Session date = 2012-04-26 pages = extension = .txt mime = text/plain words = 147405 sentences = 8927 flesch = 54 summary = Staff satisfaction was evaluated through pre/ post-shift and study surveys; administrative data (physician initial assessment (PIA), length of stay (LOS), patients leaving without being seen (LWBS) and against medical advice [LAMA] ) were collected from an electronic, real-time ED information system. Communication Background: The link between extended shift lengths, sleepiness, and occupational injury or illness has been shown, in other health care populations, to be an important and preventable public health concern but heretofore has not been fully described in emergency medical services (EMS Objectives: To assess the effect of an ED-based computer screening and referral intervention for IPV victims and to determine what characteristics resulted in a positive change in their safety. Objectives: Using data from longitudinal surveys by the American Board of Emergency Medicine, the primary objective of this study was to evaluate if resident self-assessments of performance in required competencies improve over the course of graduate medical training and in the years following. cache = ./cache/cord-022633-fr55uod6.txt txt = ./txt/cord-022633-fr55uod6.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-264408-vk4lt83x author = Ruiz, Sara I. title = Animal Models of Human Viral Diseases date = 2017-06-23 pages = extension = .txt mime = text/plain words = 34464 sentences = 1865 flesch = 47 summary = Well-developed animal models are necessary to understand disease progression, pathogenesis, and immunologic responses to viral infections in humans. NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus are monitored for the extent of viral shedding; however, no clinical disease is observed in these models. Intracerebral and IN routes of infection resulted in a fatal disease that was highly dependent on dose while intradermal (ID) and subQ inoculations caused only 50% fatality in mice regardless of the amount of virus (liu et al., 1970) . Ferrets infected with Hendra or Nipah virus display the same clinical disease as seen in the hamster model and human cases (Bossart et al., 2009; Pallister et al., 2011) . Characterization studies with IFNAr −/− mice challenged with different routes (IP, IN, IM, and subQ) showed that CCHFV causes acute disease with high viral loads, pathology in liver and lymphoid tissues, increased proinflammatory response, severe thrombocytopenia, coagulopathy, and death, all of which are characteristics of human disease . cache = ./cache/cord-264408-vk4lt83x.txt txt = ./txt/cord-264408-vk4lt83x.txt === reduce.pl bib === === reduce.pl bib === id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130046 sentences = 7333 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023354-f2ciho6o.txt txt = ./txt/cord-023354-f2ciho6o.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-263452-y2ral8nx author = Watanabe, Yasunori title = Site-specific glycan analysis of the SARS-CoV-2 spike date = 2020-05-04 pages = extension = .txt mime = text/plain words = 2073 sentences = 121 flesch = 50 summary = To resolve the site-specific glycosylation of SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo-electron microscopy (cryo-EM) structure, albeit without glycan processing blockade using kifunensine (4). The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, as observed on SARS-CoV-1 S (10, 13), HIV-1 Env (27) , influenza HA (28, 29) , and LASV GPC (24). For example, one of the most densely glycosylated viral spike proteins is HIV-1 Env, which exhibits ~60% oligomannose-type glycans (21, 34) . This suggests that SARS-CoV-2 S protein is less densely glycosylated and that the glycans form less of a shield compared with other viral glycoproteins including HIV-1 Env and LASV GPC, which may be beneficial for the elicitation of neutralizing antibodies. SARS-CoV-2 spike site-specific N-linked glycan analysis cache = ./cache/cord-263452-y2ral8nx.txt txt = ./txt/cord-263452-y2ral8nx.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130049 sentences = 7334 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023364-ut56gczm.txt txt = ./txt/cord-023364-ut56gczm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-270726-w59fu9c9 author = Dikman, Andrew E. title = Human Immunodeficiency Virus-Associated Diarrhea: Still an Issue in the Era of Antiretroviral Therapy date = 2015-03-14 pages = extension = .txt mime = text/plain words = 5191 sentences = 279 flesch = 43 summary = The etiology of noninfectious diarrhea in patients with HIV is multifactorial and includes ART-associated diarrhea and gastrointestinal damage related to HIV infection (i.e., HIV enteropathy). A basic algorithm for the diagnosis of diarrhea in patients with HIV includes physical examination, a review of medical history, assessment of HIV viral load and CD4+ T cell count, stool microbiologic assessment, and endoscopic evaluation, if needed. In addition, these agents can be associated with treatment-limiting adverse events (AEs), such as drug–drug interactions with ART regimens, abuse liability, and additional gastrointestinal AEs. Currently, crofelemer, an antisecretory agent, is the only therapy approved in the USA for the symptomatic relief of noninfectious diarrhea in patients with HIV on ART. While infection has historically been the major cause of diarrhea in patients with HIV, with the widespread use of ART therapy, noninfectious diarrhea has become a burden in this population. cache = ./cache/cord-270726-w59fu9c9.txt txt = ./txt/cord-270726-w59fu9c9.txt === reduce.pl bib === id = cord-265699-0socw0hp author = Ortega, Miguel Ángel title = Dendrimers and Dendritic Materials: From Laboratory to Medical Practice in Infectious Diseases date = 2020-09-14 pages = extension = .txt mime = text/plain words = 11148 sentences = 591 flesch = 41 summary = This review provides the reader a general overview about the uses of dendrimers and dendritic materials in the treatment, prevention, and diagnosis of highly prevalent infectious diseases, and their advantages compared to traditional approaches. Key commercial successes include the Stratus CS Acute Care Diagnostic System (Siemens Healthcare GmbH, Erlangen, Germany), for emergency diagnosis of cardiovascular infarctions; VivaGel ® products (Starpharma, Melbourne, Australia), for the prevention and treatment of sexually transmitted infections (STIs); Targeted DEP ® and Priostar ® (Starpharma), for the delivery of anticancer drugs and agrochemical products, respectively; or SpheriCal (Polymer Factory, Stockholm, Sweden), as mass spectrometry standards [59] . Key commercial successes include the Stratus CS Acute Care Diagnostic System (Siemens Healthcare GmbH, Erlangen, Germany), for emergency diagnosis of cardiovascular infarctions; VivaGel ® products (Starpharma, Melbourne, Australia), for the prevention and treatment of sexually transmitted infections (STIs); Targeted DEP ® and Priostar ® (Starpharma), for the delivery of anticancer drugs and agrochemical products, respectively; or SpheriCal (Polymer Factory, Stockholm, Sweden), as mass spectrometry standards [59] . cache = ./cache/cord-265699-0socw0hp.txt txt = ./txt/cord-265699-0socw0hp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-279849-zzkliu76 author = DaPalma, T. title = A systematic approach to virus–virus interactions date = 2010-01-20 pages = extension = .txt mime = text/plain words = 8230 sentences = 366 flesch = 36 summary = Therefore, in this review we identify known and potential types of virus-virus interactions (VVIs) and organize them into three categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) a subset of indirect interactions called immunological interactions, unique to organisms equipped with an adaptive immune system. One of the first helper-dependent viruses described was bacteriophage P4, a bacteria-infecting virus that is able to replicate its own genome, but requires the presence of a coinfecting bacteriophage, such as P2, to provide capsid components and cell lysis (Shore et al., 1978; Six and Klug, 1973) . While direct binding and activation of viral transactivating proteins to heterologous viral promoters has been documented, more common are reports of viral infections inducing increased expression or activation of cellular transcription factors, which then act on promoters of coinfecting viruses. Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection cache = ./cache/cord-279849-zzkliu76.txt txt = ./txt/cord-279849-zzkliu76.txt === reduce.pl bib === id = cord-271241-w1q46y63 author = Ruggiero, Emanuela title = Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date = 2020-05-18 pages = extension = .txt mime = text/plain words = 8912 sentences = 495 flesch = 45 summary = Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. 1 In the past few decades, pharmaceutical and biotechnological advance has succeeded in developing new therapeutics for the management of different viral diseases: for example, anti-retroviral therapy against the human immunodeficiency virus (HIV), or the pan-genotypic direct-acting antiviral drugs used for hepatitis C (HCV) management. In addition, such PQSs are highly conserved, despite the high recombination rates that characterize viruses, suggesting a crucial role for G4s in viral evolution and replication, and corroborating their targeting as a valid pharmacological approach for antiviral therapy. cache = ./cache/cord-271241-w1q46y63.txt txt = ./txt/cord-271241-w1q46y63.txt === reduce.pl bib === id = cord-272051-arz8r204 author = Federico, Maurizio title = HIV-protease inhibitors block the replication of both vesicular stomatitis and influenza viruses at an early post-entry replication step date = 2011-08-15 pages = extension = .txt mime = text/plain words = 6772 sentences = 320 flesch = 49 summary = Since the replication of many virus species requires the activity of host cell proteases, investigating the effects of PIs on the life cycle of viruses other than HIV would be of interest. Considering that PIs are well tolerated drugs in vivo, and that many relevant human pathogens belong to the family of RNA viruses infecting cells through an endocytic pathway, this finding would open the way towards a broader therapeutic use of PIs. HIV virions emerging from cells treated with PIs remain immature viral particles as a consequence of the block of Gag polyprotein cleavage. Cells were treated overnight with the PI doses most effective against VSV and/or influenza virus replication, then labeled with LysoSensor Green DND-189 for 30 min in the presence of PIs, and finally analyzed by FACS. cache = ./cache/cord-272051-arz8r204.txt txt = ./txt/cord-272051-arz8r204.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-268712-rxdw553c author = Sawyer, Alexandra title = Posttraumatic growth and adjustment among individuals with cancer or HIV/AIDS: A meta-analysis date = 2010-03-02 pages = extension = .txt mime = text/plain words = 8820 sentences = 475 flesch = 46 summary = Consequently, this meta-analysis explored the relationship between posttraumatic growth and psychological and physical wellbeing in adults diagnosed with cancer or HIV/AIDS and examined potential moderators of these relationships. As such the aim of the current paper is to present a meta-analysis of the existing literature that will aim to objectively summarize PTG and its relation to adjustment in individuals living with a life threatening illness (cancer or HIV/ AIDS) and to examine potential moderators of this relationship. Primarily it is concerned with estimating the overall effect size of the relationship between PTG following a life threatening illness (cancer or HIV/AIDS) and various indicators of adjustment. This meta-analytic review summarized the findings from 38 studies examining the association between PTG following cancer or HIV/AIDS and positive psychological adjustment, negative psychological adjustment, and subjective physical health. cache = ./cache/cord-268712-rxdw553c.txt txt = ./txt/cord-268712-rxdw553c.txt === reduce.pl bib === === reduce.pl bib === id = cord-271188-ewlxy5po author = Liu, Wei title = Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date = 2020-04-20 pages = extension = .txt mime = text/plain words = 4237 sentences = 245 flesch = 42 summary = Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 cache = ./cache/cord-271188-ewlxy5po.txt txt = ./txt/cord-271188-ewlxy5po.txt === reduce.pl bib === id = cord-271948-iq29xqrn author = Obeng, Billal Musah title = Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana date = 2020-07-24 pages = extension = .txt mime = text/plain words = 3572 sentences = 203 flesch = 56 summary = title: Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana BACKGROUND: Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana. This study found major drug resistance mutations, E138A and K65R that respectively confer high level resistance to NNRTIs and NRTIs. Although, CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. The data obtained is useful for the selection of drugs for ART initiation to maximize therapeutic outcomes in drug-naïve HIV-1 patients in Ghana. cache = ./cache/cord-271948-iq29xqrn.txt txt = ./txt/cord-271948-iq29xqrn.txt === reduce.pl bib === id = cord-276870-gxtvlji7 author = Bobrowski, Tesia title = Learning from history: do not flatten the curve of antiviral research! date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5089 sentences = 219 flesch = 49 summary = Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. However, despite many experimental and clinical studies, no effective drugs or treatments have emerged to treat the previous six epidemics of bird flu, SARS, swine flu, MERS, Ebola, and Zika as well as, thus far, COVID-19. We evaluated the number of publications (in both peer-reviewed journals and ArXiv preprint servers) and the number of clinical trials performed over the course of the epidemic to estimate the engagement and success of the scientific community in response to the seven major outbreaks of the past two decades: bird flu, SARS, swine flu, MERS, Ebola, Zika, and COVID-19. cache = ./cache/cord-276870-gxtvlji7.txt txt = ./txt/cord-276870-gxtvlji7.txt === reduce.pl bib === id = cord-275859-ix8du1er author = Mouzakis, Kathryn D. title = HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date = 2012-12-15 pages = extension = .txt mime = text/plain words = 6721 sentences = 322 flesch = 50 summary = In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Here, we investigate the role of the HIV-1 RNA structure in frameshifting, focusing on elucidating the relationships between frameshift efficiency and (i) the downstream RNA stem-loop thermodynamic stability, (ii) spacer length and (iii) surrounding genomic secondary structure. Our data further indicate that the base pairs important for frameshifting are located at a distance of 8 nt from the slippery site, which corresponds to the length of the spacer and is consistent with a structural model of the ribosome paused at the frameshift site. Instead, we observe a strong correlation (R 2 = 0.88) between frameshift efficiency and local stability of the first 3 bp at the base of the stem-loop using a one-phase exponential decay function ( Figure 3C and Supplementary Table S3 ). cache = ./cache/cord-275859-ix8du1er.txt txt = ./txt/cord-275859-ix8du1er.txt === reduce.pl bib === === reduce.pl bib === id = cord-266294-ua22udlc author = Koch, Oliver title = 29 Antiviral drugs date = 2010-12-31 pages = extension = .txt mime = text/plain words = 10777 sentences = 526 flesch = 47 summary = Metabolism The hemochromatosis gene polymorphism HFE 187C> G and possibly mitochondrial haplogroup J gave relative protection against lipoatrophy during antiretroviral drug therapy in a trial in which 96 patients were randomized to didanosine þ stavudine or zidovudine þ lamivudine, combined with efavirenz and/ or nelfinavir in AIDS Clinical Trials Group (ACTG) 384 sub-study A5005s (20 C ). Gastrointestinal In a retrospective obser vational study of highly active antiretroviral therapy (HAART), 27 of 50 patients who took indinavir in combination with zidovudine and lamivudine developed nausea and were significantly more likely to stop taking the treatment than those who were taking zidovudine þ lamivudine þ tenofovir (24 c ). cache = ./cache/cord-266294-ua22udlc.txt txt = ./txt/cord-266294-ua22udlc.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 pages = extension = .txt mime = text/plain words = 188640 sentences = 9313 flesch = 45 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. cache = ./cache/cord-022888-dnsdg04n.txt txt = ./txt/cord-022888-dnsdg04n.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-274688-cr1rvy8u author = Jewell, Britta L title = Potential effects of disruption to HIV programmes in sub-Saharan Africa caused by COVID-19: results from multiple mathematical models date = 2020-08-06 pages = extension = .txt mime = text/plain words = 1865 sentences = 90 flesch = 48 summary = METHODS: In this modelling study, we used five well described models of HIV epidemics (Goals, Optima HIV, HIV Synthesis, an Imperial College London model, and Epidemiological MODeling software [EMOD]) to estimate the effect of various potential disruptions to HIV prevention, testing, and treatment services on HIV-related deaths and new infections in sub-Saharan Africa lasting 6 months over 1 year from April 1, 2020. FINDINGS: A 6-month interruption of supply of antiretroviral therapy (ART) drugs across 50% of the population of people living with HIV who are on treatment would be expected to lead to a 1·63 times (median across models; range 1·39–1·87) increase in HIV-related deaths over a 1-year period compared with no disruption. The HIV-related death rate for people living with HIV who were on ART, but who stopped treatment due to potential disruption on the antiretroviral (ARV) drug supply as a result of the COVID-19 pandemic was modeled to represent findings from the SMART Study (1). cache = ./cache/cord-274688-cr1rvy8u.txt txt = ./txt/cord-274688-cr1rvy8u.txt === reduce.pl bib === === reduce.pl bib === id = cord-268901-7cm6m1ol author = Ku, Therese title = Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date = 2019-07-01 pages = extension = .txt mime = text/plain words = 7766 sentences = 507 flesch = 67 summary = title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. cache = ./cache/cord-268901-7cm6m1ol.txt txt = ./txt/cord-268901-7cm6m1ol.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-270868-4s3q2i6v author = Collins, Lauren F. title = Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia date = 2020-10-01 pages = extension = .txt mime = text/plain words = 2170 sentences = 119 flesch = 48 summary = title: Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia BACKGROUND: There are limited data describing the presenting characteristics and outcomes among US persons with HIV (PWH) requiring hospitalization for coronavirus disease 2019 (COVID-19). CONCLUSION: The multisite series in the Southern United States provides characteristics and early outcomes of hospitalized PWH with COVID-19. To understand how COVID-19 may affect persons with HIV (PWH) in the Southern United States, a prematurely aging population with a high comorbidity burden [3, 4] , we analyzed cases among hospitalized PWH in Atlanta, Georgia. The prevalence and burden of non-AIDS comorbidities among women living with or at-risk for HIV infection in the United States Presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with COVID-19 in the New York City area Characteristics and clinical outcomes of adult patients hospitalized with COVID-19 -Georgia cache = ./cache/cord-270868-4s3q2i6v.txt txt = ./txt/cord-270868-4s3q2i6v.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-269222-g2ibmo75 author = Valenti, Piera title = Role of Lactobacilli and Lactoferrin in the Mucosal Cervicovaginal Defense date = 2018-03-01 pages = extension = .txt mime = text/plain words = 9642 sentences = 449 flesch = 28 summary = Lactoferrin is strongly increased in lower genital tract mucosal fluid of women affected by Neisseria gonorrheae, Chlamydia trachomatis, and Trichomonas vaginalis infections promoting both innate and adaptive immune responses. Lactoferrin is strongly increased in lower genital tract mucosal fluid of women affected by Neisseria gonorrheae, Chlamydia trachomatis, and Trichomonas vaginalis infections promoting both innate and adaptive immune responses. Lactobacilli exert their protective effects by several mechanisms: (i) microbial competition for the nutrients and for adherence to the vaginal epithelium; (ii) reduction of the vaginal pH by the production of organic acids, especially lactic acid, through the degradation of glycogen released by vaginal cells thus exerting selective antimicrobial activity against non-resident microbiota; (iii) production of antimicrobial substances, such as bacteriocins and hydrogen peroxide (H2O2) able to suppress the growth of several microorganisms; and (iv) modulation of the local immune system (16) . cache = ./cache/cord-269222-g2ibmo75.txt txt = ./txt/cord-269222-g2ibmo75.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-287754-dh6abx2t author = Akkouh, Ouafae title = Lectins with Anti-HIV Activity: A Review date = 2015-01-06 pages = extension = .txt mime = text/plain words = 6947 sentences = 380 flesch = 45 summary = Examples of lectins that exhibit antiviral activity and bind high-mannose carbohydrates are jacalin [25] , concanavalin A [26] , Urtica diocia agglutinin [27] , Myrianthus holstii lectin, P. The mannose-specific plant lectins Hippeastrum hybrid agglutinin, Galanthus nivalis agglutinin, Narcissus pseudonarcissus agglutinin; Cymbidium agglutinin; cyanovirin-N; and N-acetylglucosamine specific Urtica dioica agglutinin efficiently abrogate dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN)-directed HIV-1 capture and subsequent transmission to T lymphocytes [55] . The nematode (Laxus oneistus) Ca 2+ -dependent C-type lectin Mermaid, a structural homologue of DC-SIGN devoid of cytotoxicity, shares the glycan specificity with DC-SIGN, interacts with high mannose structures on gp120 and prevents HIV-1 binding to DC-SIGN on DCs. Mermaid inhibits DC-SIGN-mediated HIV-1 transmission from DC to T cells. Discovery of cyanovirin-N, a novel human immunodeficiency virus-inactivating protein that binds viral surface envelope glycoprotein gp120: Potential applications to microbicide development The high mannose-type glycan binding lectin actinohivin: Dimerization greatly improves anti-HIV activity cache = ./cache/cord-287754-dh6abx2t.txt txt = ./txt/cord-287754-dh6abx2t.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-287286-4l963z2q author = Green, Victoria A. title = Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date = 2010-07-28 pages = extension = .txt mime = text/plain words = 7368 sentences = 363 flesch = 43 summary = The main themes of discussion at the summer school were: 1) why viral infection can lead to cancer; 2) how a greater understanding of the mechanisms underpinning human immunodeficiency virus (HIV) propagation can inform new antiviral strategies; 3) the abilities of viruses to evade the immune system and the obstacles to the development of effective vaccines; and, 4) the potential afforded by viruses as research tools. The import of the host, including an ability to regulate viral gene expression in different tissues and to mount an effective immune response, is becoming increasingly apparent in determining the molecular basis of HPV-associated tumor progression. Advantages CoVs possess over other viruses as expression vectors include: 1) the possibility of spike protein manipulation, to engineer virus tropism (88, 89) ; 2) the replication of the RNA genome in the cytoplasm, side-stepping potential problems associated with integration (90); 3) the existence of nonpathogenic strains that infect a wide range of species of health and economic importance; 4) the ability to carry large genomes (27-30 kb) , which could favor the introduction of extensive foreign genes (91); and 5) the availability of cDNA clones derived from infectious strains (92, 93) . cache = ./cache/cord-287286-4l963z2q.txt txt = ./txt/cord-287286-4l963z2q.txt === reduce.pl bib === id = cord-288982-63ddlh20 author = Peeling, Rosanna W. title = Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date = 2015-11-09 pages = extension = .txt mime = text/plain words = 4391 sentences = 216 flesch = 44 summary = Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. In the last decade, rapid point-of-care (POC) diagnostic tests fulfilling the ASSURED criteria (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable) have become commercially available and are widely used for infectious diseases such as malaria, HIV and syphilis. cache = ./cache/cord-288982-63ddlh20.txt txt = ./txt/cord-288982-63ddlh20.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 === id = cord-277818-8w15dz20 author = Jaichenco, Andre L. title = Infectious Disease Considerations for the Operating Room date = 2018-02-09 pages = extension = .txt mime = text/plain words = 9728 sentences = 528 flesch = 39 summary = Hand hygiene is a well-known and effective solution to the problem of bacterial transmission within and across patients and is considered the most important and cost-effective individual intervention in the prevention of health care–associated infections in children and health care providers Compliance with the current "5 moments" World Health Organization guidelines could make a major inroad into reducing provider hand and workspace contamination. These findings have clinical implications for the risk of colonization and subsequent HCIs-for example, SSIs. This calls attention to the need to develop and enforce strict hand hygiene guidelines for personnel who are providing anesthesia care, but more importantly the need to increase compliance with environmental disinfection of the OR (between cases and terminal cleaning), and to study further the directions of the spread of pathogens in the OR and anesthesia work areas. cache = ./cache/cord-277818-8w15dz20.txt txt = ./txt/cord-277818-8w15dz20.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-269759-1n1oo6wc author = Villamil-Gómez, Wilmer E. title = Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia date = 2020-02-06 pages = extension = .txt mime = text/plain words = 836 sentences = 55 flesch = 50 summary = title: Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia We would like to discuss the relevance of other respiratory viruses, including other CoV different to MERS-CoV, the Severe Acute Respiratory Syndrome CoV (SARS-CoV) and the 2019 novel CoV (2019nCoV) [2] in relation to a case of coinfection between HCoV-229E, respiratory syncytial virus (RSV) and HIV we had in Colombia. There is a lack of reported cases of a human coronavirus infection in HIV infected patients from Colombia and South America, confirmed by RT-PCR. HCoV-229E causes common cold but occasionally it can be associated with more severe respiratory infections in children [3, 4] , elderly and persons with underlying illness [3, 5] , which would be the case of HIV infection, as seen in this report [4, 6] . In Colombia, the unique previous reference to coronaviruses was the identification of avian infectious bronchitis virus strains (an avian coronavirus, genus Gammacoronavirus) in Antioquia [8] , a department close to Sucre, where our patient was diagnosed. cache = ./cache/cord-269759-1n1oo6wc.txt txt = ./txt/cord-269759-1n1oo6wc.txt === reduce.pl bib === === reduce.pl bib === id = cord-285603-f4572w5m author = Ortega, Joseph T. title = Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date = 2020-06-24 pages = extension = .txt mime = text/plain words = 5994 sentences = 348 flesch = 47 summary = In order to gain a deeper understanding if the pharmacokinetic parameters of the SARS-CoV2 protease inhibitors could be related to positive outcomes in the therapy, we analyzed the ADME parameters of famotidine and compared with several known antiviral drugs such as ribavirin, lopinavir, and nafamostat, which were evaluated against SARS-CoV2. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Altogether, in this study, we showed that famotidine could be used as an antiviral agent against SARS-CoV2, targeting proteases involved in the virus replication, mostly the main protease, as well as the viral PLpro and human host Tmprss2. cache = ./cache/cord-285603-f4572w5m.txt txt = ./txt/cord-285603-f4572w5m.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 === id = cord-284608-ba7wq52t author = Sias, Catia title = Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date = 2019-03-04 pages = extension = .txt mime = text/plain words = 5645 sentences = 281 flesch = 55 summary = title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . cache = ./cache/cord-284608-ba7wq52t.txt txt = ./txt/cord-284608-ba7wq52t.txt === reduce.pl bib === id = cord-295062-8rl4kswe author = Marsh, Mark title = Virus Entry: Open Sesame date = 2006-02-24 pages = extension = .txt mime = text/plain words = 8504 sentences = 401 flesch = 42 summary = Virus Particles as Devices for Targeted Gene Transfer A viral particle is composed of nucleic acids (RNA or DNA), protein, and, in the case of enveloped viruses, membrane lipids. Viruses use signaling activities to induce changes in the cell that promote viral entry and early cytoplasmic events, as well as to optimize later processes in the replication cycle. Like cholera toxin, these viruses bind to the sugar moiety of gangliosides and enter cells via caveolar/raft pathways that are dependent on cholesterol ( Figures 2D and 2E ) and the activation of tyrosine-kinase signaling cascades (Anderson et al., 1996; Pelkmans et al., 2001; Smith et al., 2003a; Stang et al., 1997; Tsai et al., 2003) . Nevertheless, in the majority of cases, the transfer of viral genomes from cell to cell appears to occur through the formation of virus particles that are released from infected cells and use the mechanisms described above to enter new uninfected hosts. cache = ./cache/cord-295062-8rl4kswe.txt txt = ./txt/cord-295062-8rl4kswe.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-281941-97t45w73 author = Zhou, Daijun title = Cyclophilin A and viral infections date = 2012-08-10 pages = extension = .txt mime = text/plain words = 3410 sentences = 184 flesch = 43 summary = A number of reports have demonstrated that CyPA plays a critical role in the successful replication of viruses such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), etc. Thus, CyPA plays a suppressive role in the development of CD4 + T cell responses through its interaction with Itk. In recent years many studies showed that CyPA was involved in the pathogenesis of viral infection [8] , cardiovascular disease [9] and cancer [10] . The viral protein R (Vpr) of HIV-1 is the major virion-associated accessory protein that affects a number of biological functions in the retroviral life cycle, including promotion of the transport of the pre-integration complex into the nucleus and the induction of G2 host cell cycle arrest [20] . Cyclophilin A regulates HIV-1 infectivity, as demonstrated by gene targeting in human T cells Critical role of cyclophilin A and its prolyl-peptidyl isomerase activity in the structure and function of the hepatitis C virus replication complex cache = ./cache/cord-281941-97t45w73.txt txt = ./txt/cord-281941-97t45w73.txt === reduce.pl bib === id = cord-285898-rtqkvf63 author = Padberg, Stephanie title = Anti-infective Agents date = 2014-09-29 pages = extension = .txt mime = text/plain words = 23992 sentences = 1446 flesch = 42 summary = In the case of clarithromycin, there was some 2.6 Anti-infective Agents 2 Pregnancy initial concern as animal experiments demonstrated teratogenic effects, and for instance, in some studies cardiovascular defects were induced in rats. In a prospective cohort study with 949 women who were exposed to a fluorquinolone during the first trimester, neither the rate of major birth defects, nor the risk of spontaneous abortion were increased compared to a control group (Padberg 2014) . Danish cohort studies based on a prescription register also could not find an increased risk of birth defects after first trimester exposure in several thousand pregnant women (Nørgaard 2008 , Sørensen 1999 ). Data from the Antiretroviral Pregnancy Registry (2013) with 27 birth defects in 905 cases, indicate a malformation rate of 3.0% after exposure during the first trimester, similarly as seen in the general population of the USA. Three birth defects were observed among 141 pregnant women with first trimester exposures reported to the Antiretroviral Pregnancy Registry (2013). cache = ./cache/cord-285898-rtqkvf63.txt txt = ./txt/cord-285898-rtqkvf63.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-297303-cpajrgba author = Nguyen, Annie L. title = Leaning on Community-Based Participatory Research to Respond During COVID-19 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1175 sentences = 54 flesch = 53 summary = Located in Palm Springs, California (a popular retirement community in the Coachella Valley with the highest proportion of people aging with HIV in the United States), we have been working over the past five years to prepare stakeholders to conduct innovative and local research. Since the committee is responsive to current needs, they shifted their efforts to COVID-19 with the idea to conduct a needs and post-traumatic stress disorder (PTSD) assessment survey of older adults living with HIV in the Coachella Valley. In the implementation phase of the study, we reached out to local service-based groups in the Coachella Valley known to assist older adults living with HIV and distributed recruitment emails to their members through their mailing lists. Our next step is to provide data in real-time to local service based groups in the Coachella Valley, so organizations can respond to the emergent needs of older adults living with HIV. cache = ./cache/cord-297303-cpajrgba.txt txt = ./txt/cord-297303-cpajrgba.txt === reduce.pl bib === === reduce.pl bib === id = cord-292546-un0blb3w author = Dandachi, Dima title = Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date = 2020-09-09 pages = extension = .txt mime = text/plain words = 3438 sentences = 274 flesch = 57 summary = BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. [12] [13] [14] [15] Some of these studies reported that PWH with COVID-19 had similar clinical characteristics and comparable risk of severe disease to the general population. Study variables included patient demographics, HIV-associated variables, underlying medical problems, COVID-19 clinical presentation as reported by patients, laboratory values, treatment, and clinical outcomes. In a multivariable analysis, older age, lower CD4 count, chronic lung disease, hypertension, and high comorbidity burden were significantly associated with severe outcomes (Table 4) . As reported in multiple other studies in people without HIV, we found that age, chronic lung disease, and comorbidity burden were associated with increased rates of severe outcomes. In addition, among HIV-specific factors, we found that a lower CD4 count (< 200 cells/mm3) was associated with poor outcomes, including higher hospitalization rates, lower ICU-free survival, and overall survival. cache = ./cache/cord-292546-un0blb3w.txt txt = ./txt/cord-292546-un0blb3w.txt === reduce.pl bib === id = cord-287949-243xlmep author = Onovo, A. A. title = Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis date = 2020-05-02 pages = extension = .txt mime = text/plain words = 4908 sentences = 233 flesch = 51 summary = Explanatory or independent variables in the model included total population, GDP per capita, percentage of population with access to electricity, percentage of population with access to basic drinking water, incidence of malaria (per 1,000 population at risk), percentage of men and women aged 15 and over who currently smoke any tobacco product, Diarrhea treatment (percent of children under 5 receiving oral rehydration and continued feeding), percentage of infants who received third-dose of pneumococcal conjugate-based vaccine (PCV), incidence of tuberculosis (per 100,000 people), percent out-of-pocket expenditure, life expectancy at birth, Health Systems Performance Index, estimated incidence rate (new HIV infection per 1,000 uninfected population, children aged 0-14 years), estimated incidence rate (new HIV infection per 1,000 uninfected population, adolescents aged 10-19 years), HIV prevalence among people aged 15-49 years, transmission classification of COVID-19 disease (1=imported, 2=local transmission), income group (1=High Income, 2=Low income, 3=Lower middle income, 4=Upper middle income), Geocoordinates of SSA countries (latitude and longitude), and Time (days) between the first and last reported coronavirus cases. cache = ./cache/cord-287949-243xlmep.txt txt = ./txt/cord-287949-243xlmep.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-295290-hs5ntlok author = Atlan, H. title = Mechanisms of autoimmunity and AIDS: prospects for therapeutic intervention date = 1994-12-31 pages = extension = .txt mime = text/plain words = 9832 sentences = 424 flesch = 38 summary = Based on this hypothesis, a T-cell vaccination procedure against effector T cells responsible for autoimmunopathic activity in HIV-seropositive patients is proposed, similar to the one known from experimental study of autoimmunity and presently being tested in human autoimmune diseases. These include cross-reactive recognition of self-MHC and a secondary antiidiotypic response to CD4, to be found in the first large set of references mentioned above, elimination of infected T4 cells by virus-specific, HLArestricted cytotoxic lymphocytes (Shearer, 1986; Zinkernagel, 1988) , elimination of uninfected T4 cells by immune responses directed against HIV (Klatzmann and Gluckman, 1986; Salk, 1987; Lyerly et al., 1987; Lanzavecchia et al., 1988; Lanzavecchia, 1989 ; Siliciano et al., 1988 ; Israel-Biet et al., 1990 ; Morrow et al., 1991) and/or T4 cell antigens (Stricker et al., 1987; Martinez-A. Autoimmunopathic destruction of T4 cells might thus result, in this case, from the destabilization of a self-tolerance-maintaining regulatory network by immune responses to HIV components with homologies to antigens normally present on T4 cells. cache = ./cache/cord-295290-hs5ntlok.txt txt = ./txt/cord-295290-hs5ntlok.txt === reduce.pl bib === id = cord-297135-mg2qs3b6 author = Smith, Kumi title = A harm reduction paradox: Comparing China's policies on needle and syringe exchange and methadone maintenance date = 2012-07-31 pages = extension = .txt mime = text/plain words = 5305 sentences = 207 flesch = 42 summary = Abstract Background China has launched methadone maintenance treatment (MMT) and needle and syringe exchange programmes (NSEP) as part of the country's HIV prevention strategy amongst injection drug users. The State Council AIDS Working Committee, an interagency committee formed to streamline the government's AIDS policy, created an opportunity for a rare partnership between the Ministries of Health and Public Security and this resulted in experimentation with progressive strategies including needle and syringe exchange programmes (NSEP) and methadone maintenance treatment (MMT) (State Council, People's Republic of China, 2001 China, , 2006a . A key distinction is the international attention garnered by MMT in the form of publications, recognition from international drug policy groups-Director Zunyou Wu of the Chinese National Centre for AIDS/STD Control & Prevention (NCAIDS) was awarded the International Harm Reduction Association's Rolleston Award for significant contributions to the field (IHRD, 2008)-and study tours by health experts from Russia, Vietnam, and Malaysia (Malinowska-Sempruch & Bartlett, 2006) . cache = ./cache/cord-297135-mg2qs3b6.txt txt = ./txt/cord-297135-mg2qs3b6.txt === reduce.pl bib === id = cord-293653-u2qrxq6t author = Watashi, Koichi title = Cyclophilin and Viruses: Cyclophilin as a Cofactor for Viral Infection and Possible Anti-Viral Target date = 2007-02-05 pages = extension = .txt mime = text/plain words = 4891 sentences = 304 flesch = 46 summary = In addition to these cellular events, a number of reports demonstrated that CyP plays a critical role in the life cycle of viruses, especially human immunodeficiency virus (HIV) and hepatitis C virus (HCV). The action of PPIases leads to changes in protein conformation (Takahashi, 1999) , but the binding of CsA and FK506 to CyP and FKBP, respectively, inhibits the activity of these enzymes (Fischer et al. The CsA/CyP or FK506/FKBP complex, subsequently interacts with and inhibits calcineurin (CN), a phosphatase involved in the activation of the transcription factor NF-AT. Members of the CyP family play roles in a variety of cellular processes including the immune response, transcription, mitochondrial function, cell death, and chemotaxis, as described below. However, the best-characterized role identified for CyPA is not in normal cellular physiology, but rather as co-factor during the human immunodefi ciency virus-1 (HIV-1) viral life cycle (See below). cache = ./cache/cord-293653-u2qrxq6t.txt txt = ./txt/cord-293653-u2qrxq6t.txt === reduce.pl bib === === reduce.pl bib === id = cord-293857-o8rlqsq5 author = Ghosh, Arun K. title = Organic Carbamates in Drug Design and Medicinal Chemistry date = 2015-01-07 pages = extension = .txt mime = text/plain words = 18165 sentences = 1121 flesch = 41 summary = Also, we will outline successful designs of organic carbamates, including a variety of cyclic ether-derived carbamates, as suitable amide bond surrogates leading to a wide range of novel organic carbamates as potent HIV-1 protease, βsecretase, serine protease, and cysteine protease inhibitors. 172−174 A number of FDA-approved HIV protease inhibitor drugs contain an important carbamate functionality. 179, 230 Further development of carbamate-derived novel HIV-1 protease inhibitors is shown in Figure 12 . This backbone binding strategy to combat drug resistance led to the development of a series of very potent carbamate-derived protease inhibitors. Carbamate derivative 281 (Figure 24 ), a diphenyl phosphonate ester containing a Cbz group and bearing a single amino acid side chain, showed very good inhibitory activity against human plasma kallikrein, useful for the treatment of hereditary angioedema. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation cache = ./cache/cord-293857-o8rlqsq5.txt txt = ./txt/cord-293857-o8rlqsq5.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-292740-b4cdj96q author = Wahid, Braira title = Immunotherapeutic strategies for sexually transmitted viral infections: HIV, HSV and HPV date = 2016-08-03 pages = extension = .txt mime = text/plain words = 10099 sentences = 516 flesch = 34 summary = Within initial three months of infection, high concentration of antibodies is developed against different viral proteins in HIV-1 infected patients and recent studies unfolded that antibodies, CD8+ T cell activity, and CD4+ helper responses lead to control of HIV virus. Replication defective recombinant adenovirus 5 vector with HIV-1 clade B nef/gag/pol inserts was the first T-cell vaccine that underwent clinical efficacy trials and exhibited significant increase in CD8+ T cell but these CD8+ immune responses targeted the variable but not the conserved regions of virus. Immunomodulators include both immunosuppressive and immunostimulatory agents that trigger secretion of cytokines from macrophages (IL-12, IFN-12, TNF-a) leading to increased Th1 response, antibody production in response to improved antigen presentation by dendritic cells, and cell-mediated immunity which is being used clinically to cure viral infections like herpes simplex virus, human papillomavirus and cancerous lesions in immunocompromised individuals [136] . cache = ./cache/cord-292740-b4cdj96q.txt txt = ./txt/cord-292740-b4cdj96q.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-302082-aaokc182 author = Stanberry, Lawrence R. title = Vaccines of the future date = 2011-08-31 pages = extension = .txt mime = text/plain words = 7736 sentences = 348 flesch = 37 summary = To address these challenges researchers are exploring many avenues: novel adjuvants are being developed that enhance the immune response elicited by a vaccine while maintaining high levels of tolerability; methods of protective antigen identification are iterated with every success; vaccine storage and transport systems are improving (including optimising the cold chain and developing temperature-stable vaccines); and new and potentially more convenient methods of vaccine administration are being pursued. One approach to addressing the weak immunogenicity of the antigen has been to link it to a potent Toll-like receptor adjuvant such as flagellin, an approach developed by VaxInnate Inc. During primary infection of a single individual with HIV, mutations in surface proteins of the virus lead to selection of a 'cloud' of antigenic variants that can evade the cell-mediated immune responses complicating the development of broadly effective vaccines. cache = ./cache/cord-302082-aaokc182.txt txt = ./txt/cord-302082-aaokc182.txt === reduce.pl bib === === reduce.pl bib === id = cord-300968-dtaasxk1 author = Kliger, Yossef title = From genome to antivirals: SARS as a test tube date = 2005-03-01 pages = extension = .txt mime = text/plain words = 5104 sentences = 272 flesch = 46 summary = Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. This strategy seems promising in developing anti-viral therapeutic peptides to other viruses that possess type 1 viral fusion proteins [e.g. measles virus and respiratory syncytial virus (RSV)], which share some structural motifs with HIV. Similar to HIV, binding of the viral spike glycoprotein to some receptor(s) on host cells is the first step in SARS-CoV infection. HIV entry involves the binding of the viral envelope glycoproteins (comprising gp120 and gp41, which are the homologous of SARS-CoV S1 and S2, respectively) to CD4 on the host cell plasma membrane. Following the rule: formation of the 6-helix bundle of the fusion core from severe acute respiratory syndrome coronavirus spike protein and identification of potent peptide inhibitors Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoproteinmediated viral entry Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeatderived peptides cache = ./cache/cord-300968-dtaasxk1.txt txt = ./txt/cord-300968-dtaasxk1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-303165-ikepr2p2 author = Tulchinsky, Theodore H. title = Expanding the Concept of Public Health date = 2014-10-10 pages = extension = .txt mime = text/plain words = 33919 sentences = 1389 flesch = 41 summary = It also demands special attention through health promotion activities of all kinds at national and local societal levels to provide access for groups with special risks and needs to medical and community health care with the currently available and newly developing knowledge and technologies. 5. Environmental, biological, occupational, social, and economic factors that endanger health and human life, addressing: (a) physical and mental illness, diseases and infirmity, trauma and injuries (b) local and global sanitation and environmental ecology (c) healthful nutrition and food security including availability, quality, safety, access, and affordability of food products (d) disasters, natural and human-made, including war, terrorism, and genocide (e) population groups at special risk and with specific health needs. It acts to improve health and social welfare, and to reduce specific determinants of diseases and risk factors that adversely affect the health, well-being, and productive capacities of an individual or society, setting targets based on the size of the problem but also the feasibility of successful intervention, in a cost-effective way. cache = ./cache/cord-303165-ikepr2p2.txt txt = ./txt/cord-303165-ikepr2p2.txt === reduce.pl bib === === reduce.pl bib === id = cord-302530-pp6bl941 author = Gale, Paul title = How virus size and attachment parameters affect the temperature sensitivity of virus binding to host cells: Predictions of a thermodynamic model for arboviruses and HIV date = 2020-03-12 pages = extension = .txt mime = text/plain words = 14797 sentences = 905 flesch = 66 summary = These are:-1 The predicted effect of the magnitude of ΔC p on the temperature dependence of Dengue virus (DENV) transmission by Aedes albopictus; 2 The predicted effect of the magnitude of ΔC p on the temperature peak observed for the specific binding of Western equine encephalitis virus (WEEV) to susceptible Culex tarsalis brush border fragments (BBFs); 3 A large negative ΔC p for a protein:protein GP/Cr system as represented by HIV gp120:CD4 diminishes host cell binding at human body temperature; 4 A large virus diameter as for the HIV virion diminishes host cell binding at the higher temperature of the human body through the large negative ΔS a_immob ; 5 Non-specific attachment factors may partially overcome the unfavourable ΔS a_immob and hence enhance specific HIV binding through Env:CD4 interactions at human body temperature; and 6 Increasing the number, n, of GP/Cr contacts with temperature to reproduce the data of Frey et al. cache = ./cache/cord-302530-pp6bl941.txt txt = ./txt/cord-302530-pp6bl941.txt === reduce.pl bib === id = cord-295099-ghc85pf5 author = Sun, Zehua title = Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies date = 2018-01-02 pages = extension = .txt mime = text/plain words = 7441 sentences = 366 flesch = 39 summary = Antibody responses to neutralize human immunodeficiency virus-1 (HIV-1) are mediated by direct binding to viral spikes, which are trimers composed of glycoproteins gp120 and gp41 (Pincus et al., 2017a; Pincus et al., 2017b; Blair et al., 2007; Morris et al., 2000; Micoli et al., 2000; Pegu et al., 2017; Haynes and Mascola, 2017; Liao et al., 2004; Brodine et al., 2003; Ward and Wilson, 2017; Debnath et al., 1994; Moore et al., 1993) . M43 and m44 are HIV-1 cross-reactive human monoclonal antibodies isolated from a recombinant phage display library by competitive antigen panning (Zhang et al., 2012; Zhang et al., 2008; Zhang et al., 2006; Zhang et al., 2004a; Zhang et al., 2004b) . HIV-1 specific antibodies isolated by display techniques are less potent than those isolated by micro neutralization or single B cell sorting and cloning. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries cache = ./cache/cord-295099-ghc85pf5.txt txt = ./txt/cord-295099-ghc85pf5.txt === reduce.pl bib === id = cord-302403-kahi8cbc author = Miller, Robert F. title = Pulmonary Infections date = 2009-05-15 pages = extension = .txt mime = text/plain words = 18163 sentences = 918 flesch = 43 summary = Before HAART, defined as a combination of medications that usually includes at least three potent anti-HIV agents, treatment largely consisted of specific opportunistic infection management and less effective antiretroviral therapy. In many parts of the world, the main causes of death in patients with HIV infection include bacterial pneumonia, tuberculosis, and PCP. Recent work has shown chronic obstructive pulmonary disease (COPD) and lung cancer occur more frequently among HIV-infected individuals compared with the general population. In addition to pulmonary tuberculosis, extrapulmonary disease occurs in a high proportion of HIV-infected individuals with low CD4 lymphocyte counts (<150 cells/mL). Hence, some centers advocate use of empirical therapy for HIV-infected patients who are seen with symptoms and chest radiographic and blood gas abnormalities typical of mild PCP, without the need for bronchoscopy. On the basis of current evidence, patients with CD4 counts >200 cells/mL have a low risk of HIV disease progression or death during 6 months of treatment for tuberculosis. cache = ./cache/cord-302403-kahi8cbc.txt txt = ./txt/cord-302403-kahi8cbc.txt === reduce.pl bib === id = cord-294366-swwz4kzd author = Bramwell, Vincent W. title = The rational design of vaccines date = 2005-11-15 pages = extension = .txt mime = text/plain words = 4880 sentences = 200 flesch = 31 summary = By definition of perceived need, we are most acutely aware of the requirement of effective vaccines against infectious agents, pathogens ancient, re-emergent and new, yet the opportunities for manipulation of immune responses offer potential in the prevention and treatment of a far larger diversity of diseases. For example, the level of protection required in a population (herd immunity) will be different and this could allow theoretical flexibility in vaccine efficacy.The application of molecular biology techniques can be crucial in the identification of new candidate antigens and subsequent determination of vaccine efficacy using adjuvants can feed knowledge back to correlates of protection in terms of immunological markers.This knowledge can then be used in choice of appropriate adjuvants and formulation.The key implication projected by this schematic is that for the greatest challenges in vaccine development the cyclical generation of knowledge provides a strong role for rational design. cache = ./cache/cord-294366-swwz4kzd.txt txt = ./txt/cord-294366-swwz4kzd.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-303189-ktl4jw8v author = Coccia, Eliana M. title = Early IFN type I response: Learning from microbial evasion strategies date = 2015-03-31 pages = extension = .txt mime = text/plain words = 15202 sentences = 738 flesch = 40 summary = Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. In these cells, the HCV-induced miR-21 has been recently reported to be involved in evasion of IFN-I production and stimulation of HCV replication, upon suppression of MyD88 and IRAK1 expression, that is required for the TLR7-mediated sensing of the virus [100] . Amongst RNA viruses that, as HCV, can establish a persistent infection, HIV-1, a lentivirus from the Retroviridae family, represents a paradigm for its ability to prevent or circumvent the innate immune response mediated by IFN-I. Overall, viruses as HCV and HIV-1 have evolved nifty strategies to dampen the host innate response in cells where a productive infection may take place, while they induce infection-independent mechanisms in non-permissive cells to facilitate the viral life cycle and promote a chronic inflammation. cache = ./cache/cord-303189-ktl4jw8v.txt txt = ./txt/cord-303189-ktl4jw8v.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-304188-1nm1tbig author = Moody, M. Anthony title = Modulation of HIV-1 immunity by adjuvants date = 2014-04-10 pages = extension = .txt mime = text/plain words = 5154 sentences = 249 flesch = 43 summary = Although no vaccine formulation has yet succeeded in eliciting broad neutralizing antibodies against HIV-1, the ability of adjuvants to direct the immune response to immunogens suggests they will be critically important in any successful HIV-1 vaccine. This is accomplished in one of two ways -through the incorporation of active compounds in a vaccine formulation (e.g., formulating a protein immunogen in a liposome containing a TLR4 agonist) or by incorporating elements in the vaccine that result in the production of immune stimulants (e.g., addition of plasmids expressing cytokines in a DNA vaccine regimen). [12] reported in 1993 on another group of chimpanzees immunized with formaldehyde-inactivated HIV-1 adjuvanted with alum, Freund's incomplete adjuvant (an oil-in-water emulsion), or with a zinc hydroxide/lecithin-based adjuvant; in this study, antibody titers were best with the lecithin-based adjuvant, although proliferation and antibodydependent cell-mediated cytotoxicity (ADCC) responses were similar between lecithin and alum arms. cache = ./cache/cord-304188-1nm1tbig.txt txt = ./txt/cord-304188-1nm1tbig.txt === reduce.pl bib === id = cord-304794-z2kx314h author = Métifiot, Mathieu title = G-quadruplexes in viruses: function and potential therapeutic applications date = 2014-11-10 pages = extension = .txt mime = text/plain words = 9102 sentences = 490 flesch = 47 summary = Conversely, a G-quadruplex or G4 is formed by nucleic acid sequences (DNA or RNA) containing G-tracts or Gblocks (adjacent runs of guanines) and composed of various numbers of guanines. Short RNA templates from the central region of the HIV-1 genome contain G-rich sequences near the central polypurine tract (cPPT) at the 3 end of the pol gene (IN coding sequence); this is a region where one of the two primers used for synthesizing the (−) strand DNA is produced during reverse transcription. In addition, one could imagine alternative therapeutic strategies focused on targeting RNA structures within viral ORFs to interfere with the virus cycle as well as to promote antigen presentation and to stimulate the host immune response. Topology of a DNA G-quadruplex structure formed in the HIV-1 promoter: a potential target for anti-HIV drug development U3 Region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence cache = ./cache/cord-304794-z2kx314h.txt txt = ./txt/cord-304794-z2kx314h.txt === reduce.pl bib === === reduce.pl bib === id = cord-304427-r7jt95ko author = Pasquato, A. title = Heparin enhances the furin cleavage of HIV-1 gp160 peptides date = 2007-12-22 pages = extension = .txt mime = text/plain words = 3356 sentences = 176 flesch = 54 summary = The 18mer, 41mer, and 51mer were synthesized on a semi-automatic synthesizer (Applied Biosystems, Mod. 431A) using a Rink amide MBHA resin Abbreviations: HIV-1, human immunodeficiency virus type 1; GAGs, glycosaminoglycans; CD, circular dichroism; AIDS, acquired immunodeficiency syndrome; RP-HPLC, reverse phase high performance liquid chromatography; PC, proprotein convertase; BTMD, before trans membrane domain; MS, mass spectrometry; AMC, 7-amino-4methyl-coumarin; MCA, 7-amido-4-methylcoumarin; TFE, trifluoroethanol; SDS, sodium dodecyl sulfate; Tris-HCl, Tris-(hydroxymethyl) aminomethane-HCl; DMSO, dimethyl sulfoxide; HF, hydrofluoric acid; cmk, chloromethylketone; PBS, phosphate buffer saline (NovaBiochem, La Jolla, 0.48 mmol/g, 0.25 mmol), Boc chemistry and HBTU/HOBt activation. Similarly, peptides derived from the cleavage site of the human respiratory syncytial virus (RSV) fusion glycoprotein bind heparin and cellular GAGs [26] . Heparin was shown to strongly interact with the 41mer and 51mer peptides, inducing conformational changes, thereby exposing site1 for cleavage. cache = ./cache/cord-304427-r7jt95ko.txt txt = ./txt/cord-304427-r7jt95ko.txt === reduce.pl bib === === reduce.pl bib === id = cord-304214-66nxk4e8 author = Sanders, John W. title = Vectored immunoprophylaxis: an emerging adjunct to traditional vaccination date = 2017-02-10 pages = extension = .txt mime = text/plain words = 3742 sentences = 173 flesch = 36 summary = Rather than passively transfering pre-formed antibodies, VIP is a process in which genes encoding previously characterized neutralizing antibodies are vectored into non-hematopoietic cells which then secrete the monoclonal antibodes encoded by those genes [1] (See Fig. 1 .) This vectored delivery and production of specified antibodies allows for protection without generating a standard immune response and results in endogenous antibody production that has the potential to be sustained [9] . Saunders, et al., used an rAAV serotype 8 vector to produce a full length IgG of a simianized form of the broadly neutralizing antibody VRC07 in macaques which was protective against simian-human immunodeficiency virus (SHIV) infection 5.5 weeks after treatment [24] . Using HIV-1-infected humanized mice, Horwitz, et al., demonstrated that following initial treatment with anti-retroviral therapy (ART), a single injection of adeno-associated virus directing expression of broadly neutralizing antibody 10-1074, produced durable viremic control after the ART was stopped [26] . cache = ./cache/cord-304214-66nxk4e8.txt txt = ./txt/cord-304214-66nxk4e8.txt === reduce.pl bib === id = cord-304816-7gg6pxnt author = Li, Wei title = Letter to the Editor: The characteristics of two patients co‐infected with SARS‐CoV‐2 and HIV in Wuhan, China date = 2020-06-10 pages = extension = .txt mime = text/plain words = 1000 sentences = 69 flesch = 57 summary = In the present study, we reported two young male COVID-19 patients co-infected with HIV and analyzed the clinical and laboratory features of them. It will provide clues for the diagnosis and treatment of COVID-19 patients co-infected with HIV. The laboratory test results showed that the protein synthesis by hepatocytes like TP or ALB were decreased and the hepatocellular enzymes ALT or AST were significantly increased, the absolute count of lymphocytes was lower than the normal reference value. We reported two cases of COVID-19 patients co-infected with HIV. Although there is a lack of epidemiological investigation on whether HIV patients are susceptible to COVID-19, the above cases presented the following distinctive clinical course and manifestations. Co-infection of SARS-CoV-2 and HIV in a patient in Wuhan city COVID-19 in a patient with HIV infection Clinical features and outcome of HIV/SARS-CoV-2 co-infected patients in the Bronx cache = ./cache/cord-304816-7gg6pxnt.txt txt = ./txt/cord-304816-7gg6pxnt.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-305039-grsv06j7 author = Flego, Michela title = Clinical development of monoclonal antibody-based drugs in HIV and HCV diseases date = 2013-01-04 pages = extension = .txt mime = text/plain words = 10985 sentences = 476 flesch = 37 summary = As for HIV, mAbs directed against spike viral proteins, as well as against host receptors, may act at an early stage of infection by preventing the binding of the virus on the cell surface. In some chronic viral infections, virus-specific immune cells may persist in a 'non-functional' state, because of an imbalance of immunoregulatory signals involving multiple inhibitory and activating receptors, triggered by soluble factors and/or cell surface ligands. Therapeutic approaches using specific mAbs to block host immunosuppressive molecules (antagonism) or to trigger activating receptors (agonism) may be a valid strategy to restore immune cell function and treat various chronic viral infections. In a proof-of-concept passive immunization trial with humans, it has been demonstrated that a cocktail of the three broadly neutralizing mAbs -2G12, 4E10 and 2F5was able to delay viral rebound in patients whose infections were fully suppressed by antiretroviral treatment before administration of the antibodies [76] . cache = ./cache/cord-305039-grsv06j7.txt txt = ./txt/cord-305039-grsv06j7.txt === reduce.pl bib === id = cord-306050-y8i8759c author = García, Juan Ignacio title = Accuracy of the tuberculosis point-of-care Alere determine lipoarabinomannan antigen diagnostic test using α-mannosidase treated and untreated urine in a cohort of people living with HIV in Guatemala date = 2020-10-19 pages = extension = .txt mime = text/plain words = 5288 sentences = 263 flesch = 48 summary = title: Accuracy of the tuberculosis point-of-care Alere determine lipoarabinomannan antigen diagnostic test using α-mannosidase treated and untreated urine in a cohort of people living with HIV in Guatemala The aim of the study is to evaluate the performance of the lipoarabinomannan antigen test (LAM-test) with and without α-mannosidase pre-treated urine in a cohort of PLWH in primary care clinics in Guatemala. A composite reference standard of either a positive Mycobacterium tuberculosis complex culture and/or GeneXpert(®) MTB/RIF (Xpert, Cepheid, Sunnyvale, CA, USA) results was used in the LAM-test diagnostic accuracy studies. We also determined if a 30 min α-mannosidase pre-treatment of urine using an enzyme that removes the mannose caps of LAM could improve the sensitivity of the LAM-test as we have shown in the laboratory settings [14] , and further correlated LAM-test results with TB incidence, mortality rates, and risk factors in our cohort of PLWH. cache = ./cache/cord-306050-y8i8759c.txt txt = ./txt/cord-306050-y8i8759c.txt === reduce.pl bib === === reduce.pl bib === id = cord-305085-bv7udg9k author = Lawrence, Robert M. title = Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date = 2011-12-31 pages = extension = .txt mime = text/plain words = 45849 sentences = 2358 flesch = 45 summary = Postnatal exposure of susceptible infants to CMV, including premature infants without passively acquired maternal antibodies against CMV, infants born to CMV-seronegative mothers, and immunodeficient infants, can cause significant clinical illness (pneumonitis, hepatitis, thrombocytopenia).* In one study of premature infants followed up to 12 months, Vochem et al 430 found CMV transmission in 17 of 29 infants (59%) exposed to CMV virolactia and breastfed compared with no infants infected of 27 exposed to breast milk without CMV. 38, 104, 121 Laboratory reports demonstrate the presence of cell-free virus and cell-associated virus in breast milk as well as various immunologic factors that could block or limit infection.* A dose-response relationship has been observed, correlating the HIV viral load in human milk as well as a mother' s plasma viral load with an increased transmission risk for the breastfed infant. 76 No case of transmission of yellow fever virus from an infected mother to her infant via breastfeeding or breast milk has been reported. cache = ./cache/cord-305085-bv7udg9k.txt txt = ./txt/cord-305085-bv7udg9k.txt === reduce.pl bib === id = cord-307817-2vy28i4m author = Lou, Zhiyong title = Current progress in antiviral strategies date = 2014-01-14 pages = extension = .txt mime = text/plain words = 7555 sentences = 343 flesch = 36 summary = The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. cache = ./cache/cord-307817-2vy28i4m.txt txt = ./txt/cord-307817-2vy28i4m.txt === reduce.pl bib === id = cord-015324-y44sfr0c author = nan title = Scientific Programme date = 2007-09-01 pages = extension = .txt mime = text/plain words = 197618 sentences = 12774 flesch = 53 summary = In order to further validate this approach, we performed a prospective randomized open-label multicenter trial in 41 low-risk pediatric renal transplant recipients (12 f, 29 m; mean age 10.1 yrs; range, 3.4 to 17.8) on CsA (target trough level 100-200 ng/ml), MMF (1200 mg/m 2 per day) and methylprednisolone (3) (4) mg/m 2 per day), who were randomly assigned >1 year posttransplant to continue steroids or to withdraw over a period of 3 months. We evaluated MMF in 15 children with LN, 11 F/4 M, mean age: 12.4±3.9 yrs, proteinuria >3 g/day, decreased C3 and increased anti-dsDNA serum levels, normal renal function. Patients and methods: 91 children and adolescents (60 male, 31 female, mean age at transplantation 9.7±5.2 years) with stable renal function and observation period exceeding 6 months were included. cache = ./cache/cord-015324-y44sfr0c.txt txt = ./txt/cord-015324-y44sfr0c.txt === reduce.pl bib === id = cord-309489-ubf55eux author = Carvalho, John J. title = OUR COMMON ENEMY: COMBATTING THE WORLD'S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date = 2009-02-19 pages = extension = .txt mime = text/plain words = 5291 sentences = 231 flesch = 44 summary = Of the emerging viruses, five have particular importance for what scientists and world leaders can learn concerning their impact on geopolitical stability, human rights, and equity health care for the underprivileged in both developed and developing nations. For example, in Latin America, population growth and uncontrolled migration from the countryside to the cities have resulted in poor housing conditions, inappropriate disposal of waste, and lack of adequate food, clean water and health care-all of which are concurrent with an increase in infected mosquitoes carrying different versions of dengue virus (Torres and Castro 2007) . Continuing with these themes, it is clear that the geographical expansion of three viruses (HIV, dengue, and rotavirus), the increase in frequency of the infectious diseases they cause, and the relationship between these viruses and geopolitical stability, human rights, and equity health care for developing nations are problems of great concern promoted not only by biological and technological factors but also by social, religious, and cultural ones. cache = ./cache/cord-309489-ubf55eux.txt txt = ./txt/cord-309489-ubf55eux.txt === reduce.pl bib === === reduce.pl bib === id = cord-306701-hs9cfdsu author = Gona, Philimon N. title = Burden and changes in HIV/AIDS morbidity and mortality in Southern Africa Development Community Countries, 1990–2017 date = 2020-06-05 pages = extension = .txt mime = text/plain words = 6030 sentences = 278 flesch = 50 summary = We conducted a descriptive epidemiological analysis of HIV/AIDS burden for the 16 SADC countries using secondary data from the Global Burden of Diseases, Injuries and Risk Factor (GBD) Study. We assessed morbidity and mortality in the 16 SADC countries using a descriptive epidemiological analysis of HIV/AIDS burden based on secondary data from GBD study in 1990, 2005, 2010 , and 2017. The GBD study estimates country-specific incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to diseases such as HIV/AIDS. To facilitate comparison of HIV/AIDS outcomes of morbidity and mortality across countries, time, age-groups, and sex, the Institute for Health Metrics and Evaluation (IHME) improved previously established metrics like prevalence and incidence. The five leading countries with the proportion deaths attributable to HIV/AIDS in 2017 were Botswana, South Africa, Lesotho, eSwatini, and Mozambique, also had the highest age-standardized mortality, YLL, YLD rates. cache = ./cache/cord-306701-hs9cfdsu.txt txt = ./txt/cord-306701-hs9cfdsu.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-310430-7eww1oet author = Singh, Ram Sarup title = Algal lectins as promising biomolecules for biomedical research date = 2013-07-16 pages = extension = .txt mime = text/plain words = 6079 sentences = 347 flesch = 45 summary = In general, marine algal lectins are monomeric, low molecular weight proteins, exhibiting high content of acidic amino acids, with isoelectric point (pI) in the range of 4-6, do not require metal ions for their biological activities and most of them show specificity for glycoproteins than monosaccharides Rogers & Hori, 1993; Shiomi et al., 1981) . They concluded that marine algal agglutinins are most sensitive to protease treated sheep erythrocytes followed by native rabbit and sheep erythrocytes, but not to human and chicken red blood cells. Lectins from cyanobacteria and other marine macro-algae are specific for high-mannose which makes them promising candidates for the prevention of transmission of various enveloped viruses such as human immunodeficiency virus (HIV), influenza virus, hepatitis C virus (HCV), Ebola virus and severe acute respiratory syndrome coronavirus (SARS-CoV) (Ziolkowska & Wlodawer, 2006) . Antinociceptive and anti-inflammatory effects of a mucin-binding agglutinin isolated from the red marine alga Hypnea cervicornis cache = ./cache/cord-310430-7eww1oet.txt txt = ./txt/cord-310430-7eww1oet.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-306266-8qdrshz3 author = Scully, Crispian title = Respiratory medicine date = 2014-06-25 pages = extension = .txt mime = text/plain words = 13246 sentences = 698 flesch = 42 summary = Other factors that have been studied include: ■ air pollution -There is an association between air pollution and aggravation of existing asthma ■ allergen avoidance -There is no consistent evidence of benefit ■ breast-feeding -There is evidence of a protective effect in relation to early asthma ■ electrolytes -There is no consistent evidence of benefit ■ fish oils and fatty acid -There is no consistent evidence of benefit ■ house dust mites -Measures to reduce the numbers of house dust mites do not affect asthma severity ■ immunotherapy -Allergenspecific immunotherapy is beneficial in allergic asthma ■ microbial exposure -There is insufficient evidence to indicate that the use of probiotics in pregnancy reduces the incidence of childhood asthma ■ modified milk formulae -There is no consistent evidence of benefit pets -There are no controlled trials on the benefits of removing pets from the home ■ tobacco -Exposure to cigarette smoke adversely affects quality of life, lung function, need for rescue medications and longterm control with inhaled steroids. cache = ./cache/cord-306266-8qdrshz3.txt txt = ./txt/cord-306266-8qdrshz3.txt === reduce.pl bib === === reduce.pl bib === id = cord-031907-ilhr3iu5 author = nan title = ISEV2020 Abstract Book date = 2020-07-15 pages = extension = .txt mime = text/plain words = 200999 sentences = 11528 flesch = 44 summary = L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. cache = ./cache/cord-031907-ilhr3iu5.txt txt = ./txt/cord-031907-ilhr3iu5.txt === reduce.pl bib === === reduce.pl bib === id = cord-304251-dohglrm1 author = Scully, C title = Emerging and changing viral diseases in the new millennium date = 2015-08-06 pages = extension = .txt mime = text/plain words = 6254 sentences = 322 flesch = 47 summary = Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. cache = ./cache/cord-304251-dohglrm1.txt txt = ./txt/cord-304251-dohglrm1.txt === reduce.pl bib === === reduce.pl bib === id = cord-306111-wn1gxhk9 author = Dommett, R. M. title = Mannose‐binding lectin in innate immunity: past, present and future date = 2006-09-01 pages = extension = .txt mime = text/plain words = 9061 sentences = 436 flesch = 43 summary = Third MBL mutation in codon 52 (variant D) described (52) 1995 Polymorphisms found in promoter region of MBL gene (55) 1997 Second MASP found to activate complement (20) MBL mutations are an important risk factor for infections in children (132) 1998 Reconstitution of opsonizing activity by infusion of purified MBL into MBL-deficient humans (112) 1999 Truncated form of MASP-2 -MAp19 (21) 2000 Complement-activating complex of ficolins and MASP (133) MBL shown to bind to clinically relevant organisms (15) Structural aspects of MBL cache = ./cache/cord-306111-wn1gxhk9.txt txt = ./txt/cord-306111-wn1gxhk9.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-317213-vhprfb1o author = Tram, Dai Thien Nhan title = Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases date = 2016-09-26 pages = extension = .txt mime = text/plain words = 11575 sentences = 794 flesch = 48 summary = This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases. • no tagging is required • about two orders of magnitude more sensitive than some common colorimetric techniques • selectivity down to the level of single-base mismatch • quantitative signal intensity varied with the length of target RNA sequence (Nam et al., 2004) Analyte: nucleotide sequence indicative of anthrax lethal factor Sample size: 30 μl Assay time: 3-4 h Detection range: 500 zM-5 fM Performance: cache = ./cache/cord-317213-vhprfb1o.txt txt = ./txt/cord-317213-vhprfb1o.txt === reduce.pl bib === id = cord-313617-hh7lccet author = Sigel, Keith title = Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date = 2020-06-28 pages = extension = .txt mime = text/plain words = 2565 sentences = 190 flesch = 56 summary = We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. We then compared differences in time to death to assess disease trajectory for hospitalized patients by HIV status by fitting unadjusted cumulative incidence function curves with hospital discharge as a competing risk. [7] To compare cumulative incidence of death by HIV status accounting for potential confounding factors we then fit a multivariable survival model using Fine-Grey competing risk methods, including demographics, COVID-19 severity, comorbid conditions and laboratory values that differed by HIV status. cache = ./cache/cord-313617-hh7lccet.txt txt = ./txt/cord-313617-hh7lccet.txt === reduce.pl bib === id = cord-308916-6p2qutc5 author = le Roux, David M. title = Community-acquired pneumonia in children — a changing spectrum of disease date = 2017-09-21 pages = extension = .txt mime = text/plain words = 4936 sentences = 213 flesch = 33 summary = New conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae have contributed to decreases in radiologic, clinical and complicated pneumonia cases and have reduced hospitalization and mortality. In a review of four randomized controlled trials and two case-control studies of Haemophilus influenzae type B conjugate vaccination in high-burden communities, the vaccination was associated with an 18% decrease in radiologic pneumonia [13] . However, given the high mortality from pneumonia in low-and middle-income countries, the lack of easy access to care, and the high prevalence of risk factors for severe disease, revised World Health Organization pneumonia guidelines still recommend antibiotic treatment for all children who meet the WHO pneumonia case definitions [80] . Effectiveness of heptavalent pneumococcal conjugate vaccine in children younger than 5 years of age for prevention of pneumonia: updated analysis using World Health Organization standardized interpretation of chest radiographs cache = ./cache/cord-308916-6p2qutc5.txt txt = ./txt/cord-308916-6p2qutc5.txt === reduce.pl bib === id = cord-312332-rwmuucsp author = Dicker, Kate title = The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date = 2020-09-10 pages = extension = .txt mime = text/plain words = 9235 sentences = 480 flesch = 45 summary = title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the 'knowns' and 'unknowns' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . cache = ./cache/cord-312332-rwmuucsp.txt txt = ./txt/cord-312332-rwmuucsp.txt === reduce.pl bib === id = cord-313729-mydyc68y author = McDiarmid, Melissa A. title = Hazards of the Health Care Sector: Looking Beyond Infectious Disease date = 2014-11-25 pages = extension = .txt mime = text/plain words = 2949 sentences = 156 flesch = 47 summary = BACKGROUND: Possessing every hazard class, the health care sector poses significant health threats to its workforce in both high-resource settings and lowand middle-income countries (LMICs). 5 Although preventing exposure to infectious agents and musculoskeletal injuries resulting from patient lifting have been the primary focus of employee safety programs, the chemical hazards in health care have been more slowly recognized. 10 Bloodborne pathogens, which include viruses capable of causing hepatitis or HIV infections continue to threaten health workers in both high-resource areas and in LMICs. 17 In developing countries, 40% to 65% of hepatitis B (HBV) and C virus (HCV) infections in health care workers were attributed to percutaneous occupational exposure. 29 The basic occupational health approach to minimizing exposure to any workplace hazard uses a combination of protective industrial hygiene control methods that are applied in a specified order or hierarchy. cache = ./cache/cord-313729-mydyc68y.txt txt = ./txt/cord-313729-mydyc68y.txt === reduce.pl bib === id = cord-318570-wj7r6953 author = Xiao, Yinzong title = Point-of-Care Tests for Hepatitis B: An Overview date = 2020-10-02 pages = extension = .txt mime = text/plain words = 8331 sentences = 350 flesch = 40 summary = If active infection is confirmed, subsequent blood tests are performed to determine the stage of disease and need for treatment, including a hepatitis B virus (HBV) polymerase chain reaction (PCR)-based quantitative DNA level or viral load, a hepatitis B eAg and eAb assay and liver function tests to determine whether an elevated aminotransferase (ALT) indicative of liver inflammation or other signs of impaired liver function are present. POCs usually require small amounts of body fluids (for example, a finger-prick blood sample or oral swab), short turn-around time, and are generally easy to use with minimal required training and therefore can be provided to people in a variety of community and outreach settings by a broad range of trained workers [22] and are scalable to rapidly reach large populations as has been seen with the highly successful Egyptian national hepatitis C screening program [23] . cache = ./cache/cord-318570-wj7r6953.txt txt = ./txt/cord-318570-wj7r6953.txt === reduce.pl bib === id = cord-010092-uftc8inx author = nan title = Abstract of 29th Regional Congress of the ISBT date = 2019-06-07 pages = extension = .txt mime = text/plain words = 233304 sentences = 13171 flesch = 54 summary = Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. cache = ./cache/cord-010092-uftc8inx.txt txt = ./txt/cord-010092-uftc8inx.txt === reduce.pl bib === id = cord-314528-5yq95giq author = Hirayama, Makoto title = High-Mannose Specific Lectin and Its Recombinants from a Carrageenophyta Kappaphycus alvarezii Represent a Potent Anti-HIV Activity Through High-Affinity Binding to the Viral Envelope Glycoprotein gp120 date = 2015-12-12 pages = extension = .txt mime = text/plain words = 8228 sentences = 437 flesch = 56 summary = title: High-Mannose Specific Lectin and Its Recombinants from a Carrageenophyta Kappaphycus alvarezii Represent a Potent Anti-HIV Activity Through High-Affinity Binding to the Viral Envelope Glycoprotein gp120 We previously reported that a high-mannose binding lectin KAA-2 from the red alga Kappaphycus alvarezii, which is an economically important species and widely cultivated as a source of carrageenans, had a potent anti-influenza virus activity. They consisted of four internal tandem-repeated domains, which are conserved in high-mannose specific lectins from lower organisms, including a cyanobacterium Oscillatoria agardhii and a red alga Eucheuma serra. alvarezii preferentially recognized high-mannose-type oligosaccharides bearing an exposed α1-3 Man at the nonreducing end in D2 arm and inhibited infection of various influenza virus strains with EC 50 s of low nanomolar levels through direct binding to the viral envelope hemagglutinin protein, which has several high-mannose N-glycans (Sato et al. cache = ./cache/cord-314528-5yq95giq.txt txt = ./txt/cord-314528-5yq95giq.txt === reduce.pl bib === id = cord-316273-vo6j8zb0 author = Cosset, François-Loic title = Cell Entry of Enveloped Viruses date = 2011-02-08 pages = extension = .txt mime = text/plain words = 23421 sentences = 1013 flesch = 40 summary = On the one hand, they acquired a domain to bind to a specific cellular protein, named "receptor." On the other hand, they developed in a different manner, according to the genus of the virus, a function of fusion that allows the destabilization of the membrane and the opening of a pore through which the genetic material will enter the cell. Thus, we need to distinguish cell surface molecules such as heparan sulfate proteoglycans, DC-SIGN, or integrins that can enhance infections by concentrating retroviruses onto cells (Bounou et al., 2002; Geijtenbeek et al., 2000; Jinno-Oue et al., 2001; Mondor et al., 1998; Pohlmann et al., 2001; Saphire et al., 2001) from authentic receptors that induce conformational changes in EnvGP that are a prerequisite for fusion of the viral and cellular membranes. cache = ./cache/cord-316273-vo6j8zb0.txt txt = ./txt/cord-316273-vo6j8zb0.txt === reduce.pl bib === id = cord-314331-7k0oym5i author = Menza, Timothy W. title = Rapid Uptake of Home-Based HIV Self-testing During Social Distancing for SARS-CoV2 Infection in Oregon date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2378 sentences = 112 flesch = 57 summary = We implemented a pilot home HIV self-testing program one week after a stay-home order for SARS-CoV2 was enacted in Oregon. In addition, 77% of MSM who use apps wanted social or sexual networking apps to add a feature that would allow them to order an HIV home test from the app. We implemented a pilot home-based HIV testing program to increase access to HIV testing separate from the SARS-CoV2 pandemic; however, its launch coincided with rising SARS-CoV2 cases and the stay-home order in Oregon. One-third of program participants had never tested before, a proportion greater than that found in a prior survey of MSM who use apps and in a trial of home HIV self-testing [9, 10] . Based on the feedback provided by participants, home self-testing appears to ameliorate several barriers to accessing an HIV test. Finally, home HIV testing allowed participants to test without risking exposure to SARS-CoV2 infection in a healthcare setting. cache = ./cache/cord-314331-7k0oym5i.txt txt = ./txt/cord-314331-7k0oym5i.txt === reduce.pl bib === id = cord-314560-rswa5zdn author = Manjunath, N. title = Interfering antiviral immunity: application, subversion, hope? date = 2006-06-06 pages = extension = .txt mime = text/plain words = 5875 sentences = 352 flesch = 48 summary = RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. However, in recent years, a new type of genomic immunity mediated by RNA interference (RNAi) has emerged and has sparked intense interest as a potential treatment strategy for a variety of diseases, including viral infections, cancer and degenerative diseases [1] [2] [3] [4] . In RNAi, long double-stranded (ds) RNA generated during viral infection is cleaved by an enzyme termed Dicer into short, 21-23 nucleotide (nt) dsRNA molecules termed small interfering (si)RNAs that mediate sequence-specific gene silencing [5, 6] . A landmark development in the field occurred with the discovery that the introduction of 21-nt-long synthetic RNA resembling the Dicer-processed siRNA into mammalian cells induces sequence-specific gene silencing without evoking the interferon response [10] . cache = ./cache/cord-314560-rswa5zdn.txt txt = ./txt/cord-314560-rswa5zdn.txt === reduce.pl bib === id = cord-316789-nb4437qs author = Omel’yanchuk, L. V. title = Drosophila melanogaster as a model for studying the function of animal viral proteins date = 2011-07-16 pages = extension = .txt mime = text/plain words = 3481 sentences = 174 flesch = 52 summary = Studies in which Drosophila melanogaster individuals carrying transgenes of animal viruses were used to analyze the action of animal viral proteins on the cell are reviewed. At the same time, it is commonly known that in addition to these proteins serving the structural function viral genomes contain genes responsible for finer aspects of interaction with host cells: cell proliferation (in fact, isolation of oncogenes was made on the basis of this property) and cell apoptosis. Drosophila was successfully used to study viral genes and proteins inhibiting programmed death (apoptosis) of host cells. The authors of the work [19] cloned the HIV tat gene in the pCasPeR vector containing the hs promoter capable of heat shock activation of transgene expression in all tissues. cache = ./cache/cord-316789-nb4437qs.txt txt = ./txt/cord-316789-nb4437qs.txt === reduce.pl bib === id = cord-314753-xflhxb13 author = Manso, Carmen F. title = Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date = 2017-06-23 pages = extension = .txt mime = text/plain words = 6333 sentences = 296 flesch = 48 summary = The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration. cache = ./cache/cord-314753-xflhxb13.txt txt = ./txt/cord-314753-xflhxb13.txt === reduce.pl bib === id = cord-314098-1i6c0l3e author = Hayward, Joshua A title = Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity date = 2018-03-29 pages = extension = .txt mime = text/plain words = 6805 sentences = 379 flesch = 50 summary = Several bat APOBEC3 proteins are antiviral as demonstrated by restriction of retroviral infectivity using HIV-1 as a model, and recombinant A3Z1 subtypes possess strong DNA deaminase activity. In this study, pteropid A3 loci were generated through the step-wise extension of cDNA-mapped gene scaffolds followed by remapping of sequence read archives, supported experimentally by an A3 expression analysis of bat spleen tissue. The antiviral activity of bat A3 proteins was determined by assessing the capacity of representatives of each bat A3 subtype to restrict HIV-1 infectivity in target cells. doi:10.1093/molbev/msy048 MBE Ancient Bat Retroviruses Were Hypermutated by APOBEC3 A3 activity results in C to U lesions in the negative (cDNA) strand, which lead to positive (genomic) strand G to A mutations in endogenous retroviruses (ERVs) within host genomes (Perez-Caballero et al. cache = ./cache/cord-314098-1i6c0l3e.txt txt = ./txt/cord-314098-1i6c0l3e.txt === reduce.pl bib === id = cord-318272-spt0oea0 author = Bhardwaj, Prateek title = Advancements in prophylactic and therapeutic nanovaccines date = 2020-04-05 pages = extension = .txt mime = text/plain words = 14561 sentences = 732 flesch = 32 summary = 'Nanovaccines' have been explored to elicit a strong immune response with the advantages of nano-sized range, high antigen loading, enhanced immunogenicity, controlled antigen presentation, more retention in lymph nodes and promote patient compliance by a lower frequency of dosing. The role of different nanovaccines in activating various arms of immunity with an intent to abate the use of frequent booster doses as vaccines for tuberculosis, malaria, HIV (human immunodeficiency virus), influenza, and cancer are discussed. Polyanhydride-based nanoparticles encapsulating F1-V antigen when administered intranasally induced an immune response that persisted for 23 weeks and elicited a high anti-F1-V IgG1 antibody response post-vaccination and conferred long-lived protective immunity against Yersinia pestis infections compared to recombinant F1-V antigen [47] . Another interesting strategy for developing personalized biomimetic cancer nanovaccines is the use of cancer cell membrane coated virus for increased adjuvanticity, infectivity and oncolytic activities to generate a strong anti-tumor immune response. cache = ./cache/cord-318272-spt0oea0.txt txt = ./txt/cord-318272-spt0oea0.txt === reduce.pl bib === id = cord-317037-1qydcc5e author = Kumar, Asit title = Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date = 2020-08-13 pages = extension = .txt mime = text/plain words = 9406 sentences = 511 flesch = 37 summary = Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. cache = ./cache/cord-317037-1qydcc5e.txt txt = ./txt/cord-317037-1qydcc5e.txt === reduce.pl bib === id = cord-317277-rr9zue4l author = Cifuentes-Munoz, Nicolas title = Viral cell-to-cell spread: Conventional and non-conventional ways date = 2020-09-29 pages = extension = .txt mime = text/plain words = 13085 sentences = 638 flesch = 45 summary = Cell-free viral particles can be released into the extracellular space through different mechanisms, such as: (a) cell lysis induced by viral proteins, as is the case for many non-enveloped viruses such as reoviruses, rotaviruses, adenoviruses and picornaviruses (Giorda and Hebert, 2013; Hu et al., 2012; Nieva et al., 2012) ; (b) by budding directly from the plasma membrane, where virions acquire their envelope, as is the case of human immunodeficiency virus (HIV-1), influenza, paramyxoviruses, and pneumoviruses (Lorizate and Krausslich, 2011; Votteler and Sundquist, 2013; Weissenhorn et al., 2013) ; (c) by exocytosis of intracellularly assembled viral particles, as is the case for bunyaviruses, flaviviruses and coronaviruses (Cifuentes-Munoz et al., 2014; Lorizate and Krausslich, 2011) . An interesting observation made for alphaviruses is that the filopodia-like extensions are not able to transfer cytosolic or plasma membrane components, suggesting they are not openended connections like TNTs. Instead, viral particles are hypothesized to bud into a protected space at the filopodial tip and then rapidly enter the target cell, preventing access of neutralizing antibodies. cache = ./cache/cord-317277-rr9zue4l.txt txt = ./txt/cord-317277-rr9zue4l.txt === reduce.pl bib === id = cord-318587-ewvnkdr2 author = Steeds, Kimberley title = Pseudotyping of VSV with Ebola virus glycoprotein is superior to HIV-1 for the assessment of neutralising antibodies date = 2020-08-31 pages = extension = .txt mime = text/plain words = 4973 sentences = 244 flesch = 46 summary = We evaluated the suitability of EBOV GP pseudotyped human immunodeficiency virus type 1 (HIV-1) and vesicular stomatitis virus (VSV) to measure the neutralising ability of plasma from EVD survivors, when compared to results from a live EBOV neutralisation assay. The aim of this study was to assess the suitability of EBOV GP pseudotyped HIV-1 and VSV systems to measure neutralisation by EVD survivor plasma, in comparison with results from a live EBOV neutralisation assay. To determine the optimal pseudotyped virus input to use in the HIV-and VSV-based assays, neutralisation of different amounts of the EBOV GP pseudotyped viruses by plasma from a Guinean EVD survivor donor or human anti-EBOV GP mAb KZ52 was assessed. When IC 50 values of EBOV GP pseudotyped HIV-1 neutralisation of the 30 EVD survivor and 10 negative plasma samples were compared with GMT values for the live EBOV neutralisation assay, a positive correlation (r s = 0.54) was determined using the nonparametric Spearman correlation coefficient (Fig. 5a) and this was statistically significant (p = 0.0004). cache = ./cache/cord-318587-ewvnkdr2.txt txt = ./txt/cord-318587-ewvnkdr2.txt === reduce.pl bib === id = cord-317990-61is0hgm author = Quinn, Katherine G. title = Applying the Popular Opinion Leader Intervention for HIV to COVID-19 date = 2020-06-25 pages = extension = .txt mime = text/plain words = 2198 sentences = 104 flesch = 41 summary = have recently noted, the spread of medical mistrust and public health misinformation evident in the current COVID-19 pandemic mirrors long-standing challenges in the HIV epidemic [1] . Accordingly, we can take lessons learned from the HIV epidemic about the spread of public health information and its effects on behavior change apply them to the current pandemic. This Note focuses on social networks and the popular opinion leader model, which may be key in disseminating trusted information about COVID-19 in a rapidly changing public health landscape. Yet, engaging trusted community leaders and social influencers to disseminate accurate public health information may help overcome these challenges to address inequities reduce COVID-19 stigma, and strengthen norms that contribute to sustained behavior change (e.g. social distancing, mask wearing, hand washing). Aligned with social distancing guidelines for COVID-19 prevention, we are using online social networks as an efficient and effective way to disseminate accurate information and influence community norms and behaviors [36] . cache = ./cache/cord-317990-61is0hgm.txt txt = ./txt/cord-317990-61is0hgm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-315687-stgj6olw author = Demma, LJ title = Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host date = 2006-03-20 pages = extension = .txt mime = text/plain words = 6439 sentences = 322 flesch = 46 summary = To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time. Although phylogenetic analyses of SIV sequences reveal considerable viral genetic diversity between different infected individuals [19] , the magnitude of intra-animal viral diversity, the substrate for selection in cross-species transmission events, has not been studied. The pre-existence of viral env variants in naturally infected SMs that are capable of replicating to high levels in a new host species pointed to the importance of SIVsm diversity in the reservoir host in enabling cross-species transmission. Here we describe extraordinarily high intra-host SIVsm env V1V2 diversity in naturally infected SMs, maintained by its high replication rate and positive selection most likely mediated by antibody responses. The similar levels of viral variation may also indicate that selective forces acting on env V1V2 are comparable in both SIVsm-infected natural mangabey reservoir hosts and in HIV-infected humans. cache = ./cache/cord-315687-stgj6olw.txt txt = ./txt/cord-315687-stgj6olw.txt === reduce.pl bib === id = cord-309515-0pxl0sta author = Blanco, Jose L title = COVID-19 in patients with HIV: clinical case series date = 2020-04-15 pages = extension = .txt mime = text/plain words = 1009 sentences = 71 flesch = 58 summary = 3 Here we describe, to our knowledge, the first single-centre experience of COVID-19 in patients infected with HIV-1, including clinical characteristics, antiviral and antiretroviral treatment, and outcomes. We explained to patients treated with ART that we were making a transitional change in their regimen on the basis of the fact that HIV protease inhibitors might have activity against the have sex with men (MSM). Additionally, Janssen reported on March 18, 2020, that darunavir was ineffective against SARS-CoV-2 due to low affinity to coronavirus protease. Fourth, we did not give our patients remdesivir, the most active in-vitro and in-vivo antiviral drug against coronavirus to date, 5 and is currently only available through clinical trials or for compassionate use. By generating information such as we present here, the management and prognosis of patients co-infected with HIV and SARS-CoV-2 might be improved. Co-infection of SARS-CoV-2 and HIV in a patient in Wuhan city cache = ./cache/cord-309515-0pxl0sta.txt txt = ./txt/cord-309515-0pxl0sta.txt === reduce.pl bib === id = cord-319354-jbain7n6 author = Gondim, Ana C. S. title = Potent antiviral activity of carbohydrate-specific algal and leguminous lectins from the Brazilian biodiversity date = 2019-01-14 pages = extension = .txt mime = text/plain words = 4052 sentences = 201 flesch = 52 summary = For example, lectins from Bryothamnion triquetrum (BTL) and Bryothamnion seaforthii (BSL) have been used to differentiate human colon carcinoma cell variants, 10 while the algal (cyanobacterial) lectin cyanovirin-N (CV-N) shows not only potent antiviral activity against HIV-1 and HIV-2, but also against influenza virus and Ebola virus. Given the potent anti-HIV activity of several lectins, and their pronounced effect on syncytium formation in SupT1-HUT-78/HIV-1 co-cultures, the binding of the lectins to the HIV-1 envelope glycoproteins gp120 and gp41 and the cellular CD4 receptor was investigated by surface plasmon resonance (SPR) technology. The leguminous lectins (DLasiL, DSclerL, ConBr, ConM) appeared to show higher binding to the three glycoproteins than the algal (SfL, HML) lectins (Table S1 †) . Thus, these and other lectins might act as antiviral compounds efficiently preventing viral entry into the host cells, which generally occurs through specific interactions of the lectins with glycans exposed on the gp120 (and gp41) glycoproteins (in the case of HIV) of the virus surface. cache = ./cache/cord-319354-jbain7n6.txt txt = ./txt/cord-319354-jbain7n6.txt === reduce.pl bib === id = cord-318363-1mv5j4w2 author = Zvolensky, Michael J. title = Psychological, addictive, and health behavior implications of the COVID-19 pandemic date = 2020-08-27 pages = extension = .txt mime = text/plain words = 15836 sentences = 701 flesch = 39 summary = Additional risk factors for the development or exacerbation of PTSD symptoms include a prior history of trauma or mental health disturbances, depressed or anxious mood, significant concurrent life stressors (e.g., financial problems, job loss, relationship stress), low social connectedness or support, sleep disturbance, substance use, and emotional numbing or detachment (Colvonen, Straus, Acheson, & Gehrman, 2019; Cusack et al., 2019; Germain, McKeon, & Campbell, 2017; Hancock & Bryant, 2018; Shalev et al., 2019; Steenkamp et al., 2017; Vujanovic & Back, 2019) . That is, a specific type of individual difference factor like anxiety sensitivity is linked to a particular type of problem (e.g., anxiety disorder, worsening of a chronic respiratory illness, severity of hazardous drinking) via a specified mediating process (e.g., smoking, sleep disruption) in the context of certain moderating variables (e.g., higher levels of COVID-19 stress burden). cache = ./cache/cord-318363-1mv5j4w2.txt txt = ./txt/cord-318363-1mv5j4w2.txt === reduce.pl bib === id = cord-320116-63yvpuqx author = Bancroft, Tara title = Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes date = 2019-10-07 pages = extension = .txt mime = text/plain words = 11866 sentences = 656 flesch = 55 summary = Immunization with a multimerized version of this anti-idiotype induced the proliferation of transgenic murine B cells expressing the iglb12 heavy chain in vivo, despite the presence of deletion and anergy within this population. Using anti-idiotypes specific for the inferred germline version of b12 (iglb12) as baits for single B cell sorting, we identified a subset of human germline BCRs using V H 1-3 with some heavy chain CDRH3 similarity to iglb12. Identification of iglb12-like BCRs using anti-iglb12 idiotypes We next assessed whether the anti-iglb12 idiotypes could be used to identify B cells expressing iglb12-like BCRs from within the polyclonal human B cell repertoire of HIV-uninfected individuals using single B cell sorting followed by RT-PCR amplification and sequencing of heavy and light chain genes. To our knowledge, this study represents the first time antiidiotypes have been used to identify and analyze naive B cells expressing BCRs with similarities to the inferred germline sequence of a broadly neutralizing HIV-1-specific antibody. cache = ./cache/cord-320116-63yvpuqx.txt txt = ./txt/cord-320116-63yvpuqx.txt === reduce.pl bib === id = cord-320156-xs936r6u author = Nunes, Marta C. title = Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children date = 2014-10-28 pages = extension = .txt mime = text/plain words = 3682 sentences = 186 flesch = 44 summary = OBJECTIVES: To determine the prevalence and clinical manifestations of WUPyV and KIPyV-associated lower respiratory tract infections (LRTIs) hospitalization in HIV-infected and -uninfected children; and probe the role of pneumococcal co-infection. Co-infections with other respiratory-viruses were detected in 65.5% of WUPyV-positive LRTIs and in 75.0% of KIPyV-positive LRTIs. Among HIV-uninfected children, there was a lower incidence of hospitalization for clinical pneumonia episodes in which KIPyV (80%; 95% CI: 41, 93) and WUPyV (49%; 95% CI: 9, 71) were identified among PCV9-recipients compared to placebo-recipients. The aim of this study was to determine the burden and clinical features of WUPyV and KIPyV infections in HIV-infected and HIV-uninfected children hospitalized for LRTIs. Furthermore, as an exploratory analysis we used the design of a RCT of a 9-valent PCV (PCV9) to probe whether pneumococcal co-infection may contribute to hospitalization for PyV-associated pneumonia. cache = ./cache/cord-320156-xs936r6u.txt txt = ./txt/cord-320156-xs936r6u.txt === reduce.pl bib === id = cord-321773-5fw9abzl author = Cheng, Wenyu title = DDX5 RNA Helicases: Emerging Roles in Viral Infection date = 2018-04-09 pages = extension = .txt mime = text/plain words = 6739 sentences = 370 flesch = 48 summary = Given the crucial roles of DDX5 in RNA biology, several RNA viruses were found to interact with the protein to promote viral replication (Table 1) , including severe acute respiratory syndrome (SARS) coronavirus (CoV) [16] , human immunodeficiency virus 1 (HIV-1) [17] , hepatitis C virus (HCV) [18] , Japanese encephalitis virus (JEV) [19] , porcine reproductive and respiratory syndrome virus (PRRSV) [20] , and influenza virus [21] . There are several studies that focus on specific inhibitors or drugs of the host DEAD-box helicase to inhibit virus replication or treat cancers [65] [66] [67] , but it remains to be determined whether small molecular inhibitors of the interaction between DDX5 and Rev can be found. The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3 UTR The DEAD-box RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro cache = ./cache/cord-321773-5fw9abzl.txt txt = ./txt/cord-321773-5fw9abzl.txt === reduce.pl bib === id = cord-322256-mv9ll0h4 author = Edelman, E. Jennifer title = Confronting Another Pandemic: Lessons from HIV can Inform Our COVID-19 Response date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1747 sentences = 73 flesch = 40 summary = We reflect on how this relates to (1) testing, including contact tracing; (2) health system redesign; (3) telehealth; (4) health disparities; (5) political denial, with inadequate and uncoordinated governmental response; (6) occupational exposure; and (7) complex reactions among healthcare providers. Experiences with HIV and partner services has taught us the critical role of public health collaboration to promote contact tracing to ensure that individuals who have been exposed to an infectious disease receive appropriate counseling, testing, and treatment [2] . The differences in routes of transmission render COVID-19 many fold more dangerous than HIV in the health care setting and mandates the need for ensuring adequate PPE for healthcare workers and others providing care for individuals exposed by aerosols and contact with patients with COVID-19 and cannot be overstated. cache = ./cache/cord-322256-mv9ll0h4.txt txt = ./txt/cord-322256-mv9ll0h4.txt === reduce.pl bib === === reduce.pl bib === id = cord-317533-xpfqdeqv author = Smuts, Heidi title = Human coronavirus NL63 infections in infants hospitalised with acute respiratory tract infections in South Africa date = 2008-07-24 pages = extension = .txt mime = text/plain words = 2374 sentences = 137 flesch = 52 summary = Objective To determine the role of HCoV‐NL63 in infants and young children hospitalised with acute respiratory tract infections (ARI) in Cape Town, South Africa. A number of respiratory viruses including influenza viruses, respiratory syncytial virus (RSV), parainfluenza viruses, adenovirus and the recently described human metapneumovirus (hMPV) play an important role in acute respiratory tract infections (ARI) in children. In the South African setting, where the prevalence of HIV is high, all infant respiratory samples are routinely screened for CMV as in our setting this virus is a major cause of pneumonia in HIV-infected children. In conclusion these findings suggest that although HCoV-NL63 is circulating in the community it plays a minor role in severe respiratory tract infections in young children who require hospitalisation. A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalised with respiratory tract infections in Belgium Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children cache = ./cache/cord-317533-xpfqdeqv.txt txt = ./txt/cord-317533-xpfqdeqv.txt === reduce.pl bib === id = cord-317988-1buh1wm0 author = Kalichman, Seth C. title = Intersecting Pandemics: Impact of SARS-CoV-2 (COVID-19) Protective Behaviors on People Living With HIV, Atlanta, Georgia date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4040 sentences = 216 flesch = 47 summary = At follow-up, in the first month of responding to COVID-19, engaging in more social distancing behaviors was related to difficulty accessing food and medications and increased cancelation of health care appointments, both by self and providers. These results suggest social responses to COVID-19 adversely impacted the health care of people living with HIV, supporting continued monitoring to determine the long-term effects of co-occurring HIV and COVID-19 pandemics. 15 High prevalence of substance use and co-occurring underlying health conditions have the potential to amplify the severity of COVID-19 in people living with HIV. 43 Although people with HIV will recognize their increased risks due to an immune suppressive condition, the added burden of smoking and other substance use, as well as underlying conditions common to HIV infection, have not been included in Centers for Disease Control and Prevention reports of severe case outcomes and have not been included in public health messaging. cache = ./cache/cord-317988-1buh1wm0.txt txt = ./txt/cord-317988-1buh1wm0.txt === reduce.pl bib === id = cord-322503-fynprt6f author = Thakur, Aarzoo title = Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date = 2020-08-07 pages = extension = .txt mime = text/plain words = 3527 sentences = 210 flesch = 48 summary = Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. To address this possibility, we utilized physiologically-based pharmacokinetic (PBPK) modeling to simulate the unbound lung concentration of lopinavir achieved by 400/100 mg twice daily dose of lopinavir/ritonavir in both Caucasians and Chinese populations. 14, 15 Therefore, we derived unbound EC 50 (EC 50,unbound ) values against SARS-CoV-2 from various literature reports and compared it against the predicted C u,lung values to determine if clinically used doses of 400/100 mg twice a day would reach efficacious lung concentrations in Caucasian and Chinese populations. The impact of protein binding on PK/PD assessments were then assessed by comparing the predicted total and unbound lung concentrations of 400/100 mg twice daily lopinavir/ritonavir with EC 50 and EC 50,unbound values of lopinavir against SARS-CoV-2 respectively. cache = ./cache/cord-322503-fynprt6f.txt txt = ./txt/cord-322503-fynprt6f.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-319043-hczwgf6o author = Ashkenazi, Avraham title = Sphingopeptides: dihydrosphingosine-based fusion inhibitors against wild-type and enfuvirtide-resistant HIV-1 date = 2012-08-07 pages = extension = .txt mime = text/plain words = 5676 sentences = 309 flesch = 50 summary = We hypothesized that by minimizing the affinity of the peptides to the viral fusion site (using short fragments from the core); we would mainly identify the contribution of the conjugated lipid moiety to antiviral activity. This exclusive inhibitory activity of sphinganine-based peptides (sphingopeptides) was further observed in a wider spectrum of viral entry systems, consisting of different HIV strains (wildtype HXB2 and LAI) and different target cells (TZM-bl reporter cells and Jurkat T cells), as well as in cell-cell fusion assay (Fig. 2) . Thus, we hypothesized that its dihydrosphingosine (sphinganine) backbone may penetrate into the site of membrane fusion mediated by the HIV Env. To investigate this, we conjugated sphinganine as well as other lipids to short, otherwise inert, peptides from the HIV-1 Env core and their antiviral activities were investigated in several types of HIV-1 infection assays. cache = ./cache/cord-319043-hczwgf6o.txt txt = ./txt/cord-319043-hczwgf6o.txt === reduce.pl bib === id = cord-322915-zrjx31ev author = Demain, Arnold L title = Microbial drug discovery: 80 years of progress date = 2009-01-09 pages = extension = .txt mime = text/plain words = 11246 sentences = 688 flesch = 40 summary = Evidence of the importance of natural products in the discovery of leads for the development of drugs for the treatment of human diseases is provided by the fact that close to half of the best selling pharmaceuticals in 1991 were either natural products or their derivatives. In addition to the antibiotic-resistance problem, new families of anti-infective compounds are needed to enter the marketplace at regular intervals to tackle the new diseases caused by evolving pathogens. 28 Among the novel class of antimicrobial agents used in treating resistance to Gram-positive infections, we can also mention the cyclic lipopeptide antibiotic daptomycin produced by Streptomyces roseosporus. 44 Other applications include antitumor drugs, enzyme inhibitors, gastrointestinal motor stimulator agents, hypocholesterolemic drugs, ruminant growth stimulants, insecticides, herbicides, coccidiostats, antiparasitics vs coccidia, helminths and other pharmacological activities. Considering that animal health research and the development of new anti-infective product discovery have decreased, the discovery of new antibiotics has decreased over the past 15 years, with few new drug approvals. cache = ./cache/cord-322915-zrjx31ev.txt txt = ./txt/cord-322915-zrjx31ev.txt === reduce.pl bib === === reduce.pl bib === id = cord-319002-xmsfkaoc author = Brown, James title = Community-Acquired Pneumonia in HIV-Infected Individuals date = 2014-02-22 pages = extension = .txt mime = text/plain words = 5661 sentences = 228 flesch = 35 summary = Studies in populations other than in Europe and the US have confirmed the importance of bacterial pneumonia in HIV-infected individuals, with recent work in Taiwan showing this to be the most common respiratory complication of HIV infection in those with CD4 counts above 200 cells/μL [9] . This may be due to the high levels of immunocompromise in this population despite the availability of ART, although an increase in invasive pneumococcal disease was found amongst women in that study, suggesting that general uptake of the childhood pneumococcal conjugate vaccination (PCV; which now forms part of the childhood immunization schedule in South Africa) may be particularly effective at reducing rates of invasive pneumococcal disease amongst HIV-infected adults in this community. Several interventions can be made that have been shown to reduce this risk; these include: the use of ART and achievement of an undetectable plasma HIV load, smoking cessation, and the uptake of the pneumococcal and influenza immunizations, which international guidelines recommend for HIV-infected individuals. cache = ./cache/cord-319002-xmsfkaoc.txt txt = ./txt/cord-319002-xmsfkaoc.txt === reduce.pl bib === === reduce.pl bib === id = cord-322581-v96k4yxg author = Mockiene, Vida title = Nurses' willingness to take care of people living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) — does a teaching intervention make a difference? date = 2011-08-31 pages = extension = .txt mime = text/plain words = 4347 sentences = 219 flesch = 56 summary = Summary The aim of this study is to describe the impact of an education intervention programme on nurses' willingness to care for HIV-positive people in Lithuania. The MEDLINE, Cochrane Library, ERIC databases, and Lithuanian AIDS Centre were searched for relevant English-language citations between 2000 and 2010 using the following search terms: education intervention, HIV, Lithuania, nurse, and willingness to take care. The aim of the study is to explore the impact of an intervention programme on nurses' willingness to take care of HIV-positive people in Lithuania. The aim of this study was to ascertain what kind of impact the intervention has on nurses' willingness to take care of HIV-positive people or those with AIDS in Lithuania. cache = ./cache/cord-322581-v96k4yxg.txt txt = ./txt/cord-322581-v96k4yxg.txt === reduce.pl bib === id = cord-327324-4c4a4bfz author = Wilkinson, Robert J title = Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date = 2020-06-13 pages = extension = .txt mime = text/plain words = 872 sentences = 61 flesch = 43 summary = title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Active tuberculosis has a transcriptomic signature dominated by a neutrophil-driven type 1 and 2 interferoninducible gene profile. The exaggerated inflammation that characterizes HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is triggered by Toll-like receptor and inflammasome signalling [14] . Male sex and diabetes have been identified in virtually every study as risk factors for severe COVID-19 infection, associated in the largest study to date with an adjusted hazard ratio for in-hospital death of 1.99 (male sex) and 1.50 for controlled (HbA1c < 58 mmol/mol) and 2.36 for uncontrolled DM [18] . Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is characterized by Toll-like receptor and inflammasome signalling Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis cache = ./cache/cord-327324-4c4a4bfz.txt txt = ./txt/cord-327324-4c4a4bfz.txt === reduce.pl bib === id = cord-319116-2ts6zpdb author = Ruggiero, Emanuela title = G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date = 2018-04-20 pages = extension = .txt mime = text/plain words = 9124 sentences = 410 flesch = 42 summary = Since the number of reports describing the presence of G4s in virus genomes has boomed in the past 2 years and treatment with several G4 ligands has shown potentially interesting therapeutic activity, we here aim at presenting, organizing and discussing an up-to-date close-up of the literature on G4s in viruses and the classes of molecules that have shown antiviral activity by viral G4 targeting. The research of G4s in the HIV-1 genome has been quite productive, concerning not only the two RNA viral genome copies, but also the integrated proviral genome, specifically For each virus the following information is shown: virion structure and dimension, genome size and organization; schematic representation of the G4 (red dots) location in the viral genomes or in the mRNA and G4 binding proteins; number of G4s assessed through bioinformatics analysis, according to the corresponding references; G4 ligands reported to date to display antiviral effect and corresponding references. cache = ./cache/cord-319116-2ts6zpdb.txt txt = ./txt/cord-319116-2ts6zpdb.txt === reduce.pl bib === id = cord-324137-nau83mjv author = Saranathan, Nandhini title = G-Quadruplexes: More Than Just a Kink in Microbial Genomes date = 2018-09-14 pages = extension = .txt mime = text/plain words = 6722 sentences = 379 flesch = 42 summary = Several reports convincingly demonstrate antimicrobial activity of quadruplex-binding ligands against clinically challenging pathogens, including HIV-1, HCV, Ebola virus, Plasmodium falciparum, and Mycobacterium tuberculosis. An earlier study reports that, following concatemeric replication of HHV-1, the cleavage of unit length genomes and their encapsidation is achieved by the binding of virus proteins to a DNA secondary structure formed by a DNA packaging sequence (pac-1) [50] . G4s have been shown to inhibit the transcription or translation of structural and nonstructural proteins in viruses, deleteriously affecting the virus loads and their pathogenicity; the stabilization of these quadruplexes with ligands has been investigated as a potential mechanism for targeting viruses. Negative regulation of virus transcription, translation or replication by quadruplex motifs in virus genomes forms the basis of using G4-binding ligands as antiviral agents. G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions cache = ./cache/cord-324137-nau83mjv.txt txt = ./txt/cord-324137-nau83mjv.txt === reduce.pl bib === id = cord-316904-g7dli0a8 author = Chang, Hernan R. title = Role of cytokines in AIDS wasting date = 1998-12-31 pages = extension = .txt mime = text/plain words = 8300 sentences = 433 flesch = 40 summary = Indeed, although wasting is not universally observed in AIDS patients, the wasting syndrome in a human immunodeficiency virus (HIV)-seropositive individual is generally utilized to establish the diagnosis of AIDS 1 and is defined by a decrease in body mass greater than 10% in the absence of concomitant opportunistic infections, malignancies, and other identifiable causes of weight loss. 33 It is against this background presentation of the interacting factors contributing to malnutrition and functional impairment in HIVinfected patients-namely anorexia, malabsorption, hypermetabolism, lethargy, and impaired fat and protein metabolism-that the role of cytokines in the AIDS wasting syndrome is discussed in the following sections. In addition to their pleiotropic actions on many body systems, they could potentially contribute to the wasting and cachexia of AIDS by their ability to induce anorexia, alter energy expenditure, increase muscle proteolysis and net protein breakdown, and initiate various abnormalities of lipid metabolism. cache = ./cache/cord-316904-g7dli0a8.txt txt = ./txt/cord-316904-g7dli0a8.txt === reduce.pl bib === id = cord-325300-wawui0fd author = Tulchinsky, Theodore H. title = 4 Communicable Diseases date = 2000-12-31 pages = extension = .txt mime = text/plain words = 31276 sentences = 1672 flesch = 47 summary = No less important are organized programs to promote self protection, case finding, and effective treatment of infections to stop their spread to other susceptible persons (e.g., HIV, sexually transmitted diseases, tuberculosis, malaria). Very great progress has been made in infectious disease control by clinical, public health, and societal means since 1900 in the industrialized countries and since the 1970s in the developing world. The WHO in 1998 has declared hepatitis prevention as a major public health crisis, with an estimated 170 million persons infected worldwide (1996) , stressing that this "silent epidemic" is being neglected and that screening of blood products is vital to reduce transmission of this disease as for HIu HCV is a major cause of chronic cirrhosis and liver cancer. Varicella vaccine is now recommended for routine immunization at age 12-18 months in the United States, with catch-up for children up to age 13 years and for occupationally exposed persons in health or child care settings. cache = ./cache/cord-325300-wawui0fd.txt txt = ./txt/cord-325300-wawui0fd.txt === reduce.pl bib === id = cord-326558-6tss9ydx author = Chen, Jiao title = A binning tool to reconstruct viral haplotypes from assembled contigs date = 2019-11-04 pages = extension = .txt mime = text/plain words = 6709 sentences = 429 flesch = 54 summary = CONCLUSIONS: In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. These methods usually estimate the bin number by aligning metagenomic data to a pre-established marker gene database, and then assign assembled contigs to different bins using sequence composition information and read coverage levels. We evaluate the haplotype number estimation and clustering performance of VirBin on both simulated and mock HIV quasispecies sequencing data. It uses bowtie2 to map reads to a set of universal genes and infers the within-species strains abundances by Fig. 3 The recall and precision of contig binning results by MaxBin. X-axis represents each haplotype, in decreasing order of relative abundance. Although abundance-based clustering has been used for contig binning from multiple samples [15, 19] , existing tools are not designed Fig. 7 The pipeline of VirBin to tackle key challenges of distinguishing contigs of different haplotypes. cache = ./cache/cord-326558-6tss9ydx.txt txt = ./txt/cord-326558-6tss9ydx.txt === reduce.pl bib === === reduce.pl bib === id = cord-309242-ilsupfl8 author = Schuchat, Anne title = Global health and the US Centers for Disease Control and Prevention date = 2014-07-02 pages = extension = .txt mime = text/plain words = 2886 sentences = 161 flesch = 50 summary = CDC staff work with peers in Ministries of Health and other host country entities to implement eff ective national programmes in HIV care and treatment, tuberculosis-HIV integration, maternal and child health, HIV prevention, and HIV counselling and testing. President Obama announced in December, 2011, ambitious new targets for priority evidence-based interventions that were to be realised in just 2 years' time: PEPFAR, in 2013, was committed to directly support 6 million patients receiving treatment, an increase of 50% over the previous target; provision of therapy to 1·5 million pregnant women to prevent vertical infection of HIV; and to cumulatively reach 4·7 million men with voluntary medical male circumcisions. 5 CDC implemented an innovative approach to prevent mother-to-child transmission of HIV in Malawi by working with the Ministry of Health and local partners. cache = ./cache/cord-309242-ilsupfl8.txt txt = ./txt/cord-309242-ilsupfl8.txt === reduce.pl bib === id = cord-324690-82qsirnk author = Dieffenbach, Carl W title = The search for an HIV vaccine, the journey continues date = 2020-05-16 pages = extension = .txt mime = text/plain words = 1469 sentences = 73 flesch = 51 summary = Over the past decade, three different vaccine approaches have been implemented, possible correlates of protection identified, and two have moved through clinical evaluation to advanced clinical trials. Analysis of the correlates of protection seen in the non-human primate studies point to qualitatively different responses than those observed in RV144, and the trials are evaluating in silico designed immunogens to present the most globally conserved HIV sequences to trigger quantitatively superior CD8 + T cell responses [8, 9] . The Antibody Mediated Protection (AMP) trials are currently evaluating VRC01, the CD4 binding site targeted bNAb, to determine the ability of this single antibody to prevent HIV infection in women in Southern Africa and MSM and transgender persons in the Americas [13] . The authors thank the trial participants, community members, activists and researchers who have so willingly participated in the challenging work of HIV vaccine discovery and development. cache = ./cache/cord-324690-82qsirnk.txt txt = ./txt/cord-324690-82qsirnk.txt === reduce.pl bib === id = cord-324056-cvvyf3cb author = Kelley, Patrick W. title = Global Health: Governance and Policy Development date = 2011-06-30 pages = extension = .txt mime = text/plain words = 5948 sentences = 334 flesch = 48 summary = Owing to the increasing recognition that health is fundamental to the broader UN goals of fostering the international rule of law, global security, economic development, social progress, human rights, and world peace, health issues have now taken a more prominent place than they had in the United Nation's first 50 years. GAVI also supports innovative financing Box 3 The goals and targets of the US government global health initiative HIV/AIDS: The US President's Emergency Plan for AIDS Relief will: (1) support the prevention of more than 12 million new HIV infections; (2) provide direct support for more than 4 million people on treatment; and (3) support care for more than 12 million people, including 5 million orphans and vulnerable children. Reflecting the emergence of the new era in global health governance, in 1998 the Rockefeller Foundation established an initiative to create innovative new public-private partnerships, including the Medicines for Malaria Venture, the Global Alliance for TB Drug Development, and the International Partnership on Microbicides. cache = ./cache/cord-324056-cvvyf3cb.txt txt = ./txt/cord-324056-cvvyf3cb.txt === reduce.pl bib === id = cord-326642-kc85pev4 author = Cohen, Adam L. title = Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 date = 2015-09-19 pages = extension = .txt mime = text/plain words = 4060 sentences = 176 flesch = 48 summary = title: Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 After adjusting for age, HIV serostatus, and respiratory viral coinfection, the attributable fraction for PIV was 65.6% (95% CI [confidence interval], 47.1–77.7); PIV contributed to SARI among HIV-infected and -uninfected children <5 years of age and among individuals infected with PIV types 1 and 3. Parainfluenza virus causes substantial severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV. In this study, we aimed to describe the epidemiological and clinical characteristics of HIV-infected and -uninfected children and adults hospitalized with PIV-associated pneumonia in South Africa. Parainfluenza virus is associated with a significant amount of severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV. cache = ./cache/cord-326642-kc85pev4.txt txt = ./txt/cord-326642-kc85pev4.txt === reduce.pl bib === id = cord-323261-1of5ertf author = Lo, Catherine Yuk-ping title = Securitizing HIV/AIDS: a game changer in state-societal relations in China? date = 2018-05-16 pages = extension = .txt mime = text/plain words = 9433 sentences = 400 flesch = 46 summary = Considering the low priority of health policies since the economic reform, the limitation of the "third sector" activity permitted in authoritarian China, together with the political sensitivity of the HIV/AIDS problem in the country, this article aims to explain the proliferation of HIV/AIDS-focused NGOs in China with the usage of the securitization framework in the field of international relations (IR). Based on the discourse analysis of the official documents and newspaper articles, it is argued that Chinese national leaders followed suit the international move (i.e. UNSC Resolution 1308) to securitize HIV/AIDS in the country, framing HIV/ AIDS as a threat with social, political, economic, and security implications. Along with the weakening of international securitization efforts and the rise of Chinese government's involvement in managing NGOs in the post-Global Fund era, the continuous proliferation of NGOs is further complicated by the fragmented nature of HIV/AIDS-focused civil society groups in China. cache = ./cache/cord-323261-1of5ertf.txt txt = ./txt/cord-323261-1of5ertf.txt === reduce.pl bib === id = cord-325936-rwxg187r author = Eyal, Nir title = AIDS Activism and Coronavirus Vaccine Challenge Trials date = 2020-06-26 pages = extension = .txt mime = text/plain words = 2220 sentences = 115 flesch = 51 summary = To minimize risk to participants, live SARS-CoV-2 vaccine challenge trials would need to recruit participants who, in the-likely-event of infection, would remain at relatively low fatality risk. Shortly after HIV sterilizing cure trials transplanted allogenic stem cell in participants, with well over a thousand times the fatal risk of SARS-Cov-2 infection in healthy young participants [17, 18] , AIDS activist David Evans interviewed the participants of these risky trials and concluded, "We should recognize their great capacity to understand the risks they may confront as research participants and, after a careful ethical and scientific review, respect the motivations of those who decide that the benefits of knowing that their contributions may help others outweighs the risks" [19] . That is not the case for COVID-19, which means that adequately communicating about and assessing potential risks and benefits of participating in a challenge study and ensuring appropriate informed consent may be impossible. cache = ./cache/cord-325936-rwxg187r.txt txt = ./txt/cord-325936-rwxg187r.txt === reduce.pl bib === id = cord-328287-3qgzulgj author = Moni, Mohammad Ali title = Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date = 2014-10-24 pages = extension = .txt mime = text/plain words = 10643 sentences = 547 flesch = 43 summary = Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). To observe the association of SARS and HIV infections with other 7 important diseases (chronic heart failure, kidney disorders, breast cancer, parkinson, osteoporosis, type 1 and type 2 diabetes), we have collected mRNA microarray raw data associated with each disease from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) accession numbers are GSE9006, GSE9128, GSE15072, GSE7158, GSE8977 and GSE7621 [59] . cache = ./cache/cord-328287-3qgzulgj.txt txt = ./txt/cord-328287-3qgzulgj.txt === reduce.pl bib === id = cord-327461-ohgkgvry author = Lu, Ying title = Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial date = 2020-06-12 pages = extension = .txt mime = text/plain words = 4420 sentences = 221 flesch = 47 summary = title: Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial Digital network-based secondary distribution is considered as an effective model to enhance HIV self-testing (HIVST) among key populations. We describe a three-arm randomized controlled trial to examine the effect of monetary incentives and peer referral in promoting digital network-based secondary distribution of HIVST among MSM in China. Our trial aims to enable more Chinese MSM to receive HIV self-testing, reach more first-time HIV testing alters, and identify more people with an HIV-positive (reactive) result by implementing the photo-verified HIV self-testing method under different scenarios, i.e., standard secondary distribution, secondary distribution with monetary incentives and secondary distribution with monetary incentives plus peer-referral links. Hypothesis 2: Compared with standard secondary distribution, secondary distribution with monetary incentives plus peer referral will promote index MSM to distribute more HIVST kits to people within their social network. cache = ./cache/cord-327461-ohgkgvry.txt txt = ./txt/cord-327461-ohgkgvry.txt === reduce.pl bib === id = cord-330581-g5r2b043 author = Marini, Elena title = HIV‐1 matrix protein p17 binds to monocytes and selectively stimulates MCP‐1 secretion: role of transcriptional factor AP‐1 date = 2007-10-26 pages = extension = .txt mime = text/plain words = 8241 sentences = 419 flesch = 52 summary = C. AP-1 protein family profiling for DNA-binding activity of an ELISA-based transcription factor assay kit using nuclear extracts (4 mg per sample) from human monocytes cultured for 1 h in the presence or absence of p17-and AP-1-specific oligonucleotides immobilized to a 96-well plate. Due to the large number of primary monocytes required for the analysis of transcription factor DNA-binding activity in protein nuclear extracts, we further investigated the involvement of AP-1 transcription factor in p17-induced MCP-1 transcriptional events using the monocytic cell line THP-1, which constitutively expresses p17Rs on its surface (data not shown). Among these, the HIV-1 matrix protein p17 has been recently identified as a critical determinant in AIDS pathogenesis as it binds to a cellular receptor expressed on immune cells and enhances viral replication and infectivity (De Francesco et al., 1998) , through a combination of different effector functions (De Francesco et al., 2002; Vitale et al., 2003) . cache = ./cache/cord-330581-g5r2b043.txt txt = ./txt/cord-330581-g5r2b043.txt === reduce.pl bib === id = cord-330698-9t24jo8s author = Wurdinger, Thomas title = Extracellular Vesicles and Their Convergence with Viral Pathways date = 2012-07-25 pages = extension = .txt mime = text/plain words = 7445 sentences = 365 flesch = 39 summary = Finally, endogenous retrovirus and retrotransposon elements deposited in our genomes millions of years ago can be released from cells within microvesicles, suggestive of a viral origin of the microvesicle system or perhaps of an evolutionary conserved system of virus-vesicle codependence. Microvesicles released by infected cells contain specific components of the cell and the virus, many of which facilitate the ability of virions to persist in a hostile antiviral immune environment [44, 55, 56, 58] . During HSV-1 infection the release of microvesicles, formerly known as L-particles containing viral tegument proteins and glycoproteins, can prime surrounding cells for productive infection and reduce immune rejection [48] [49] [50] . In the case of the human CMV, microvesicles released by infected cells present the C-type lectin family molecule expressed on dendritic cells-used in capture and internalization of pathogens-in complex with the CMV glycoprotein B. Also, the convergence of these pathways may explain the observations of virus-like particles, which can be exosomes or shed microvesicles containing viral proteins or nucleic acids. cache = ./cache/cord-330698-9t24jo8s.txt txt = ./txt/cord-330698-9t24jo8s.txt === reduce.pl bib === id = cord-319263-g49jma8n author = Marziali, Megan E. title = Physical Distancing in COVID-19 May Exacerbate Experiences of Social Isolation among People Living with HIV date = 2020-04-23 pages = extension = .txt mime = text/plain words = 1289 sentences = 75 flesch = 48 summary = title: Physical Distancing in COVID-19 May Exacerbate Experiences of Social Isolation among People Living with HIV We have discussed that people living with HIV (PLHIV) are at greater risk of experiencing social isolation [13] . Therefore, due to the various shelter-in-place and physical distancing measures, it is likely that this disease is resulting in more social isolation, and in greater severity, than previously experienced among PLHIV. Among participants with poor self-rated physical health, of whom 42% are living with HIV, 87% experienced loneliness. This study provides further support for the notion that social isolation and loneliness can have a tangible impact on the health of an individual. Therefore, it is necessary to also focus on evaluating mental health of PLHIV, during and after the COVID-19 control measures, to better understand and address loneliness in this population. cache = ./cache/cord-319263-g49jma8n.txt txt = ./txt/cord-319263-g49jma8n.txt === reduce.pl bib === id = cord-327135-4c2flue4 author = Chinnaswamy, S title = Gene–disease association with human IFNL locus polymorphisms extends beyond hepatitis C virus infections date = 2016-06-09 pages = extension = .txt mime = text/plain words = 9813 sentences = 499 flesch = 48 summary = Interferon (IFN) lambda (IFN-λ or type III IFN) gene polymorphisms were discovered in the year 2009 to have a strong association with spontaneous and treatment-induced clearance of hepatitis C virus (HCV) infection in human hosts. Three independent groups conducted genome-wide association studies (GWASs) involving treatment response to chronic hepatitis C virus (HCV) infections, in three different geographical regions of the world, and reported that single-nucleotide polymorphisms (SNPs) in the IFNL locus (Figure 1 ), had strong association with treatment-induced HCV clearance irrespective of ethnicity and geographical location of the hosts. 49 In stark contrast, a dominant model of inheritance (of the non-beneficial IFNL SNP minor allele) has consistently given the best explanation on the observed phenotypes in association studies with both spontaneous clearance and IFN-based treatment response in chronic HCV infections. cache = ./cache/cord-327135-4c2flue4.txt txt = ./txt/cord-327135-4c2flue4.txt === reduce.pl bib === id = cord-326744-eled2tgo author = Millett, Gregorio A. title = White Counties Stand Apart: The Primacy of Residential Segregation in COVID-19 and HIV Diagnoses date = 2020-10-01 pages = extension = .txt mime = text/plain words = 3228 sentences = 178 flesch = 54 summary = 28 Attributing racial disparities to underlying conditions implicitly blames communities of color for COVID-19 disparities due to poor health decisions; but there is ample literature showing how social determinants contribute to worse health outcomes in communities of color, 29 including well-cited HIV research studies of youth, gay men, and PWID, which show that HIV disparities persist in black communities despite similar or fewer behavioral risks than whites. A CDC demonstration project that scaled up HIV testing efforts in black and Latino communities in the District of Columbia dramatically reduced the proportion of concurrent AIDS diagnoses at first positive test; 46 and encouraging data from a recent study 35 show shifts in COVID-19 testing from wealthier and white neighborhoods to poorer and more diverse neighborhoods in cities initially hit by the COVID-19 pandemic. cache = ./cache/cord-326744-eled2tgo.txt txt = ./txt/cord-326744-eled2tgo.txt === reduce.pl bib === === reduce.pl bib === id = cord-330465-16j5vm7h author = Marciniec, Krzysztof title = Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date = 2020-08-05 pages = extension = .txt mime = text/plain words = 6908 sentences = 396 flesch = 48 summary = The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. In order to check the potential toxic properties of the compounds 3-5, docking study of phosphate betulin derivatives to cellular proteins was carried out. According to the results of docking (Table S1 ) obtained from AutoDock Vina, four potential SARS-CoV-2 inhibitors (BVM, betulinic acid, and compounds 4 and 6) were selected based on a lower negative dock energy value. cache = ./cache/cord-330465-16j5vm7h.txt txt = ./txt/cord-330465-16j5vm7h.txt === reduce.pl bib === id = cord-329361-0mpbau1b author = Bennasser, Yamina title = RNAi Therapy for HIV Infection: Principles and Practicalities date = 2012-08-16 pages = extension = .txt mime = text/plain words = 2645 sentences = 200 flesch = 56 summary = Inside eukaryotic cells, small RNA duplexes, called small interfering RNAs (siRNAs), activate a conserved RNA interference (RNAi) pathway which leads to specific degradation of complementary target mRNAs through base-pairing recognition. The practical use of RNAi therapy for HIV infection will depend on overcoming several challenges, including the ability to establish long-term expression of siRNA without off-target effects and the capacity to counteract mutant escape viruses. [4] Hence, in plants and Drosophila, when a cell they have sequence specificity for silencing mRNAs, these small is infected by a virus, an RNAi response is triggered by the foreign RNAs potentially represent a future class of antiviral drugs. [42] silencing of viral RNA and transient suppression of HIV replicaobserved that an siRNA targeted to nef rapidly elicited the emertion over a period of 3 to 4 days in single round infection of gence of siRNA-resistant viruses with point mutations in the nef cultured cells have been achieved. cache = ./cache/cord-329361-0mpbau1b.txt txt = ./txt/cord-329361-0mpbau1b.txt === reduce.pl bib === id = cord-329223-f84gjxm1 author = Kouokam, Joseph Calvin title = Investigation of Griffithsin's Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date = 2011-08-02 pages = extension = .txt mime = text/plain words = 8837 sentences = 382 flesch = 47 summary = In contrast to several other antiviral lectins however, GRFT treatment induces only minimal changes in secretion of inflammatory cytokines and chemokines by epithelial cells or human PBMC, has no measureable effect on cell viability and does not significantly upregulate markers of T-cell activation. When freshly-isolated PBMC were pre-incubated for 24 hrs with GRFT at various concentrations, washed and then infected with HIV-1 R5 strain BaL (without adding new compound), GRFT inhibited viral replication for 9 days of cell culture (Fig. 2) . In addition, the numbers of CD4 2 /CD25 + cells were elevated when PBMC were cultured in presence of PHA or ConA compared to their PBS and GRFT counterpart (Fig. 6 , left panel and data not shown). The heat map shown in Fig. 9A indicates that cells exposed for 24 hours to GRFT Lec-(1 and 8 mM), and low concentrations of GRFT (0.1 mM ) and CV-N (0.05 mM) showed comparable gene expression profiles to those that were incubated in presence of PBS alone. cache = ./cache/cord-329223-f84gjxm1.txt txt = ./txt/cord-329223-f84gjxm1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-329890-wg23sa1u author = Quah, Stella R. title = Public image and governance of epidemics: Comparing HIV/AIDS and SARS date = 2007-02-28 pages = extension = .txt mime = text/plain words = 9734 sentences = 423 flesch = 49 summary = Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people's lifestyles and approaches to the control and prevention of epidemics. The second assumption is that in contrast to SARS, the overall negative public 'image' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people's perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. The second assumption to be explored here is that in contrast to SARS, the overall negative social 'image' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people's perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. cache = ./cache/cord-329890-wg23sa1u.txt txt = ./txt/cord-329890-wg23sa1u.txt === reduce.pl bib === id = cord-332610-t99l3zii author = Mayer, J.D. title = Emerging Diseases: Overview date = 2008-08-26 pages = extension = .txt mime = text/plain words = 9596 sentences = 469 flesch = 52 summary = The potential for new diseases to emerge in the United States was there, and it took just a few years until this happened, catching the medical and public health communities by surprise. The issue at the time was whether legionnaires disease and toxic shock syndrome were anomalies, whether the assumption of the conquest of infectious diseases had clearly been erroneous, or whether these two outbreaks were harbingers of a new stage in 'epidemiologic history'a historical period during which emerging infections would become common and would catch the attention of the public, the public health community, the medical community, and government agencies. Severe acute respiratory syndrome (SARS) proved to be of great import in both the public awareness of emerging infectious diseases and in the testing and real-time construction of both domestic and international systems of public health surveillance and response. cache = ./cache/cord-332610-t99l3zii.txt txt = ./txt/cord-332610-t99l3zii.txt === reduce.pl bib === id = cord-333405-ji58jbct author = Morens, David M. title = The challenge of emerging and re-emerging infectious diseases date = 2004-07-08 pages = extension = .txt mime = text/plain words = 6421 sentences = 315 flesch = 41 summary = Of the 'newly emerging' and 're-emerging/resurging' diseases that have followed the appearance of AIDS (Fig. 1) , some have been minor curiosities, such as the 2003 cases of monkeypox imported into the United States 4 , whereas others, such as severe acute respiratory syndrome (SARS), which emerged in the same year 5 , have had a worldwide impact. The impact of both new and re-emerging infectious diseases on human populations is affected by the rate and degree to which they spread across geographical areas, depending on the movement of human hosts or of the vectors or reservoirs of infections. Immune deficiency associated with AIDS, and with chemotherapy for cancer, immune-mediated diseases and transplantation, has contributed to an enormous global increase in the numbers of immunosuppressed people over the past few decades (probably more than 1% of the world's population), setting the stage for the re-emergence of many opportunistic infections. cache = ./cache/cord-333405-ji58jbct.txt txt = ./txt/cord-333405-ji58jbct.txt === reduce.pl bib === id = cord-333730-qsx0m68e author = Tsai, Y. C. title = Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4920 sentences = 297 flesch = 35 summary = However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial cache = ./cache/cord-333730-qsx0m68e.txt txt = ./txt/cord-333730-qsx0m68e.txt === reduce.pl bib === === reduce.pl bib === id = cord-331879-w7008uyy author = Iversen, Jenny title = COVID‐19, HIV and key populations: cross‐cutting issues and the need for population‐specific responses date = 2020-10-01 pages = extension = .txt mime = text/plain words = 3688 sentences = 143 flesch = 36 summary = However, the conditions faced by specific populations vary according to social, structural and environmental factors, including stigma and discrimination, criminalization, social and economic safety nets and the local epidemiology of HIV and COVID‐19, which determine risk of exposure and vulnerability to adverse health outcomes, as well as the ability to comply with measures such as physical distancing. Significant heterogeneity in the COVID‐19 pandemic, the underlying HIV epidemic and the ability of key populations to protect themselves means that people who inject drugs and sex workers face particular challenges, including indirect impacts as a result of police targeting, loss of income and sometimes both. Global networks, including the International Network of People who use Drugs (INPUD), the Global Network of Sex Work Projects (NSWP), the Global Network of People Living with HIV (GNP+) and MPact Global Action for Gay Men's Health and Rights have issued statements calling for urgent action to protect their communities and to address population-specific needs for prevention, care and treatment [9,18-20]. cache = ./cache/cord-331879-w7008uyy.txt txt = ./txt/cord-331879-w7008uyy.txt === reduce.pl bib === === reduce.pl bib === id = cord-329396-cl28bjnd author = Carrico, Adam W. title = Double Jeopardy: Methamphetamine Use and HIV as Risk Factors for COVID-19 date = 2020-04-07 pages = extension = .txt mime = text/plain words = 2317 sentences = 109 flesch = 40 summary = In our prior bio-behavioral research conducted with MSM with treated HIV infection who use meth, those who provided a urine sample that was reactive for stimulants (i.e., meth or cocaine) displayed differential expression of genes and 2-directional perturbation of pathways relevant to systemic immune activation and inflammation [25] . The clinical relevance of these findings is supported by the fact that markers of systemic immune activation and inflammation are implicated in multiple, chronic medical conditions such as cardiovascular disease in people living with HIV, which have been identified as key risk factors for COVID-19 progression [28, 29] . Smoking is a prevalent mode of administration for meth and crack-cocaine that could enhance local immune dysregulation in the lungs and modify the expression of ACE-2 receptors to increase vulnerability to SARS-CoV-2 infection and COVID-19 progression. Further clinical research is needed to characterize the psychiatric consequences of the COVID-19 pandemic and test novel mHealth approaches to improve adherence to social distancing guidelines in MSM who use meth and other stimulants. cache = ./cache/cord-329396-cl28bjnd.txt txt = ./txt/cord-329396-cl28bjnd.txt === reduce.pl bib === id = cord-330800-s91zfzfi author = Reta, Daniel Hussien title = Molecular and Immunological Diagnostic Techniques of Medical Viruses date = 2020-09-04 pages = extension = .txt mime = text/plain words = 10548 sentences = 574 flesch = 43 summary = e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. cache = ./cache/cord-330800-s91zfzfi.txt txt = ./txt/cord-330800-s91zfzfi.txt === reduce.pl bib === id = cord-338594-wft7yy6j author = Winkler, Michael title = Rhesus macaque IFITM3 gene polymorphisms and SIV infection date = 2017-03-03 pages = extension = .txt mime = text/plain words = 4633 sentences = 277 flesch = 48 summary = In particular, polymorphisms of the human IFITM3 gene have been shown to affect disease severity and progression in influenza A virus (FLUAV) and human immunodeficiency virus (HIV) infection, respectively. Employing previously characterized samples from two cohorts of SIV-infected rhesus macaques, we investigated the relationship between these rhIFITM3 polymorphisms and both AIDS-free survival time and virus load. Polymorphisms in several immune-relevant gene loci such as MHC or KIR are associated with the transmission and course of disease in SIV infected rhesus macaques and HIV-1 infected humans [36, 37] . Immune-related IFITM proteins have been established as important antiviral effectors of the interferon response, and a polymorphism in the human IFITM3 gene has been found to be associated with disease severity and progression in FLUAV and HIV-1 infection [27, 33] . Notably, all polymorphism in the coding region were silent and strong evidence for an association of rhIFITM3 polymorphisms with disease progression and viral load in SIV infected animals was not obtained. cache = ./cache/cord-338594-wft7yy6j.txt txt = ./txt/cord-338594-wft7yy6j.txt === reduce.pl bib === id = cord-331289-02411gfv author = Di Minno, Giovanni title = Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date = 2015-07-20 pages = extension = .txt mime = text/plain words = 8171 sentences = 395 flesch = 43 summary = In general, clinicians assess the level of risk associated with the use of blood/ plasma-derived products by evaluating factors such as patient characteristics (e.g. age, immune status, geographical location, lifestyle) and the nature of the pathogen (e.g. physical characteristics, level of virulence, chronicity of infection, prevalence). Current donor selection and screening practices have improved our ability to detect or reduce the presence of pathogens in blood/plasma-derived products; for example, the residual risk of transfusion-transmitted infection (TTI) with HIV/HBV/HCV has fallen to near or less than 1 per million transfused units [14, 15] . Since TTV is often detected in healthy individuals and is not associated with any particular disease, routine screening for this virus is not considered to be necessary; even a test with excellent sensitivity/specificity would not contribute to increase the level of safety of blood/plasma-derived products with regard to TTV. cache = ./cache/cord-331289-02411gfv.txt txt = ./txt/cord-331289-02411gfv.txt === reduce.pl bib === === reduce.pl bib === id = cord-334855-s0ci3r8w author = Andersen, Petter I. title = Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date = 2019-10-18 pages = extension = .txt mime = text/plain words = 4274 sentences = 272 flesch = 48 summary = Here, we identified novel activities of obatoclax and emetine against herpes simplex virus type 2 (HSV-2), echovirus 1 (EV1), human metapneumovirus (HMPV) and Rift Valley fever virus (RVFV) in cell cultures. The expected response of the emetine-obatoclax drug combination on the viability of FLUAV-and mock-infected RPE cells was calculated using Bliss reference model [29] . After the initial screening, we identified four compounds (obatoclax, emetine, niclosamide and ganciclovir) that at none-cytotoxic concentrations rescued cells from virus-mediated death (Figure 2A) . Table S1 : Compounds, their suppliers and catalogue numbers; Table S2 : Developmental status of broad-spectrum antivirals used in the study; Table S3 : Human viruses and associated diseases; Figure S1 : The expected response of the emetine-obatoclax drug combination on the viability of FLUAV-and mock-infected RPE cells, as measured with the CTG assay using the Bliss reference model; Figure S2 cache = ./cache/cord-334855-s0ci3r8w.txt txt = ./txt/cord-334855-s0ci3r8w.txt === reduce.pl bib === id = cord-338438-q5fis2v8 author = Young, Sean D. title = Clinical Care, Research, and Telehealth Services in the Era of Social Distancing to Mitigate COVID-19 date = 2020-05-21 pages = extension = .txt mime = text/plain words = 1442 sentences = 63 flesch = 40 summary = In this Note, we describe considerations for integrating technologies, such as telemedicine; social media, mobile applications (apps), and chatbots; and biosensors/wearables into clinical HIV care delivery and research, as well as case examples of current uses of these technologies in adapting to the changing clinical and research needs among populations at risk for and/living with HIV as a result of the COVID-19 pandemic. Social media, chatbots, and mobile apps have been studied across a number of clinical and public health settings, including patient outreach, screening and monitoring; intervention delivery; remote vital sign assessment; as well for providing treatment recommendations and retaining patients in care. COVID-19 will continue to impact the way that technologies are integrated into HIV clinical care and research long after the removal of social distancing policies, making it important to begin investing in the knowledge, infrastructure, and implementation of these technologies now to be prepared for the future. cache = ./cache/cord-338438-q5fis2v8.txt txt = ./txt/cord-338438-q5fis2v8.txt === reduce.pl bib === === reduce.pl bib === id = cord-338804-nreqluol author = Heise, M.T. title = Viral Pathogenesis date = 2014-11-28 pages = extension = .txt mime = text/plain words = 6413 sentences = 232 flesch = 35 summary = Viral interactions with these receptors can have a significant impact upon several aspects of viral pathogenesis, including determining the cell or tissue tropism of a virus or even whether a virus can efficiently infect and cause disease in a specific host species. Therefore, viruses that are defective in their ability to antagonize the host type I interferon system are often unable to replicate and spread efficiently within the host, illustrating the importance of viral immune evasion strategies in determining whether a virus will be pathogenic ( Figure 2) . (b) If the virus effectively interferes with the type I interferon response, interferon will be prevented from inducing a robust antiviral state within the host, and the virus is able to replicate to higher levels, will spread more efficiently, and may cause more severe disease. Therefore, like other aspects of viral pathogenesis, a complex series of virus-host interactions determines whether infection with cancer associated viruses ultimately results in disease development. cache = ./cache/cord-338804-nreqluol.txt txt = ./txt/cord-338804-nreqluol.txt === reduce.pl bib === id = cord-330852-n7j0c4ne author = Fischer, Wolfgang B. title = Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date = 2012-02-23 pages = extension = .txt mime = text/plain words = 23680 sentences = 1178 flesch = 53 summary = By adding data from functional studies like Cys scanning and electrophysiological measurements as mentioned as well as computational modeling data (Sansom and Kerr, 1993; Sansom et al., 1997; Zhong et al., 1998) , an approximate structural model of the tetrameric assembly of the TMDs of M2 with the histidines and tryptophans as important pore lining residues has been generated. Amiloride derivatives block ion channel activity and enhancement of virus-like particle budding caused by HIV-1 protein Vpu Backbone structure of the amantadine-blocked trans-membrane domain M2 protein channel from influenza A virus Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1 Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 cache = ./cache/cord-330852-n7j0c4ne.txt txt = ./txt/cord-330852-n7j0c4ne.txt === reduce.pl bib === id = cord-337720-kmwft059 author = Closson, Kalysha title = When Home is Not a Safe Place: Impacts of Social Distancing Directives on Women Living with HIV date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1741 sentences = 84 flesch = 48 summary = As HIV care, research participation, and workplace settings are being transitioned to virtual and telephone-based methods, women living with HIV experiencing violence are less able to connect to critical social and protective networks [18] . As such, necessary social distancing measures have the potential to impact the rates and consequences of IPV, increasing social isolation and mental health concerns, which taken together can hinder women living with HIV's access to, and use of, HIV treatment and violence support, further than they already experience [9, 17] . As social distancing measures limit access to supports, such as family, friends, and health care provides, that help women living with HIV cope with experiences of violence and histories of trauma, research is needed to understand the unique ways in which women living with HIV have developed resilience and coping strategies during COVID-19 restrictions and how these can be best supported. cache = ./cache/cord-337720-kmwft059.txt txt = ./txt/cord-337720-kmwft059.txt === reduce.pl bib === id = cord-337897-hkvll3xh author = Yang, Zheng Rong title = Peptide Bioinformatics- Peptide Classification Using Peptide Machines date = 2009 pages = extension = .txt mime = text/plain words = 7631 sentences = 495 flesch = 54 summary = The earlier work was to investigate a set of experimentally determined (synthesized) functional peptides to find some conserved amino acids, referred In protease cleavage site prediction, we commonly use peptides with a fixed length. The bio-basis function method has been successfully applied to various peptide classification tasks, for instance, the prediction of trypsin cleavage sites [ 9 ] , the prediction of HIV cleavage sites [ 10 ] , the prediction of hepatitis C virus protease cleavage sites [ 16 ] , the prediction of the disorder segments in proteins [ 7 , 17 ] , the prediction of protein phosphorylation sites [ 18 , 19 ] , the prediction of the O-linkage sites in glycoproteins [ 20 ] , the prediction of signal peptides [ 21 ] , the prediction of factor Xa protease cleavage sites [ 22 ] , the analysis of mutation patterns of HIV-1 Fig. 9 . cache = ./cache/cord-337897-hkvll3xh.txt txt = ./txt/cord-337897-hkvll3xh.txt === reduce.pl bib === id = cord-337315-qv8ycdhe author = Miller, Maureen title = Integrated biological–behavioural surveillance in pandemic-threat warning systems date = 2017-01-01 pages = extension = .txt mime = text/plain words = 4629 sentences = 267 flesch = 40 summary = 13 Similar surveillance could help identify behavioural risk factors and high-risk subgroups for zoonotic infections such as Ebola -potentially before diseases of pandemic potential are identified in clinical settings or major outbreaks occur in communities. When designed according to Strengthening the Reporting of Observational Studies in Epidemiology criteria, integrated surveillance requires that both behavioural risk factors -i.e. exposure variables -and disease-indicator outcome variables be measured in behavioural surveys. 22 In the development of pandemic-threat warning systems, integrated biological-behavioural surveillance can be tightly focused on specific viral families in the high-risk population subgroups that live in identified hotspots and are environmentally or occupationally exposed to animals. The remainder of this article presents an overview of issues relevant to the design of rigorous behavioural surveys to assess the spillover of emerging zoonotic disease and the associated transmission risk factors, which is the first step in designing effective integrated surveillance. cache = ./cache/cord-337315-qv8ycdhe.txt txt = ./txt/cord-337315-qv8ycdhe.txt === reduce.pl bib === id = cord-339341-c2o42b5j author = Matibag, Gino C. title = Advocacy, promotion and e-learning: Supercourse for zoonosis date = 2005-09-01 pages = extension = .txt mime = text/plain words = 5855 sentences = 317 flesch = 44 summary = This paper discusses the history of emerging infectious diseases, risk communication and perception, and the Supercourse lectures as means to strengthen the concepts and definition of risk management and global governance of zoonosis. The overall goal of the "Supercourse for Zoonosis" is to show the most recent development in the knowledge of SARS and other zoonotic diseases such as avian influenza and bovine spongiform encephalopathy (BSE), inter alia, which have significant global impact not only on health but also on the economy. The specific objectives of "Supercourse for Zoonosis" are to develop a set of educational materials for the control of zoonotic diseases, to disseminate them effectively via the Internet, to facilitate their use in the prevention and control of the diseases, and to promote human health while minimizing their economic impact. cache = ./cache/cord-339341-c2o42b5j.txt txt = ./txt/cord-339341-c2o42b5j.txt === reduce.pl bib === id = cord-334454-cqaado3u author = Leal, Rodolfo Oliveira title = The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives date = 2016-10-27 pages = extension = .txt mime = text/plain words = 4320 sentences = 201 flesch = 41 summary = title: The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives More than summarizing the main conclusions about rFeIFN-ω in cats, this review emphasizes the immune-modulation properties of IFN therapy, opening new perspectives for its use in retroviral infections. Firstly, the effect of rFeIFN-ω licensed protocol in cats living in an animal shelter was evaluated, assessing clinical improvement and monitoring concurrent viral excretion (namely herpesvirus, calicivirus, and coronavirus) [26] . Following the same methodology of previous studies, the clinical improvement, concurrent viral excretion, APP profiles, and different hematology and biochemistry parameters in FIV-infected cats treated with the oral protocol were assessed. Only one study had previously reported that the licensed protocol does not change viremia or proviral load in treated FIV-infected cats, suggesting that this compound may not act on acquired immunity [17] . cache = ./cache/cord-334454-cqaado3u.txt txt = ./txt/cord-334454-cqaado3u.txt === reduce.pl bib === id = cord-326725-0jgw083h author = Klamroth, Robert title = Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date = 2013-09-30 pages = extension = .txt mime = text/plain words = 5972 sentences = 303 flesch = 41 summary = These measures include selection of donors, screening of donations and plasma pools for markers of infection with known viruses, and a manufacturing process with a high capacity to inactivate and/or remove viruses by selected steps validated for their virus reduction capacity. [7] [8] [9] Although screening for viral markers by serology and virus nucleic acid by nucleic acid testing (NAT) ensures that nearly all plasma units entering production are free of HBV, HCV, and HIV, inactivation and removal steps are necessary to reduce any viruses that may enter the plasma pool during a "window period" before markers can be detected. 46 Although B19V was reduced by dry heat in validation studies, the reduction factor may not be sufficient for complete inactivation of the virus load in the final product; asymptomatic B19V infection was detected in a patient who received FVIII concentrate treated at 80°C for 72 hours. cache = ./cache/cord-326725-0jgw083h.txt txt = ./txt/cord-326725-0jgw083h.txt === reduce.pl bib === id = cord-333622-0ddutmdd author = Dyer, Wayne B title = Mechanisms of HIV non-progression; robust and sustained CD4+ T-cell proliferative responses to p24 antigen correlate with control of viraemia and lack of disease progression after long-term transfusion-acquired HIV-1 infection date = 2008-12-11 pages = extension = .txt mime = text/plain words = 5615 sentences = 243 flesch = 44 summary = title: Mechanisms of HIV non-progression; robust and sustained CD4+ T-cell proliferative responses to p24 antigen correlate with control of viraemia and lack of disease progression after long-term transfusion-acquired HIV-1 infection Early studies on this cohort of TAHIV patients led to the identification of the Sydney Blood Bank Cohort (SBBC) of long-term survivors [8] , and that an attenuated nef-deleted strain of HIV-1, transmitted from a single donor resulted in slow to non-progression in these individuals [9] . In addition to the well described host genetic factors which may prolong non-progression [7] , recent studies have suggested an influence from innate immune mechanisms, including polymorphisms that decrease TLR function thereby reducing immune activation upon exposure to infections diseases [18] , or the FcγRIIA polymorphism (R/R) which is strongly associated with progressive HIV disease as a result of impaired elimination of HIV immune complexes [19] . cache = ./cache/cord-333622-0ddutmdd.txt txt = ./txt/cord-333622-0ddutmdd.txt === reduce.pl bib === id = cord-337458-dc90ecfe author = Markwalter, Christine F. title = Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date = 2018-12-04 pages = extension = .txt mime = text/plain words = 40568 sentences = 2391 flesch = 40 summary = In this review, we define the components of a diagnostic to include: (1) the target biomarker, an endogenous indicator of a disease state, which is most often a pathogen or host protein, carbohydrate, or nucleic acid sequence, (2) sample preparation, which allows for biomarker isolation, purification, and/or concentration from complex biological matrices, (3) molecular recognition elements, which specifically capture and detect the target biomarker, (4) signal generation and amplification, and (5) instrumentation for signal read-out. 113, 114 In subsequent studies, the group developed and optimized a hand-held, easy-to-use device 85, 115 (Figure 8A ) in which HRP2-bound, IMAC-functionalized magnetic beads were directly transferred to the sample pad of commercial malaria lateral flow assays. If combined with one of the sample preparation strategies discussed previously (section 3) or integrated with paper or another field-ready substrate, this Ir(III)-based detection strategy could produce a robust and sensitive assay that is applicable in low-resource diagnostic settings. cache = ./cache/cord-337458-dc90ecfe.txt txt = ./txt/cord-337458-dc90ecfe.txt === reduce.pl bib === id = cord-333655-lylt7qld author = Van Breedam, Wander title = Bitter‐sweet symphony: glycan–lectin interactions in virus biology date = 2013-12-06 pages = extension = .txt mime = text/plain words = 18667 sentences = 875 flesch = 42 summary = In sum, it appears that the dimeric lectin galectin-1 can enhance HIV-1 infection efficiency by cross-linking viral and host cell glycans and thereby promoting firmer adhesion of the virus to the target cell surface and facilitating virus-receptor interactions (Ouellet et al., 2005; Mercier et al., 2008; St-Pierre et al., 2011; Sato et al., 2012) . As has been shown for IAV, acquisition or deletion of glycosylation sites may affect crucial steps in the viral infection/replication process (e.g. receptor binding, fusion, release of newly formed virions) (Ohuchi et al., 1997; Wagner et al., 2000; Tsuchiya et al., 2002; Kim & Park, 2012) , alter the capacity of the virus to avoid induction of/recognition by virus-specific antibodies (glycan shielding) Wei et al., 2010; Wanzeck et al., 2011; Kim & Park, 2012; Job et al., 2013; Sun et al., 2013) , and modulate viral interaction with various immune system lectins (Reading et al., 2007; Vigerust et al., 2007; Reading et al., 2009; Tate et al., 2011a, b) . cache = ./cache/cord-333655-lylt7qld.txt txt = ./txt/cord-333655-lylt7qld.txt === reduce.pl bib === id = cord-338654-ma9ayu80 author = Eaton, Lisa A. title = Social and behavioral health responses to COVID-19: lessons learned from four decades of an HIV pandemic date = 2020-04-25 pages = extension = .txt mime = text/plain words = 3425 sentences = 160 flesch = 39 summary = The current state of COVID-19 disease transmission has left our public health approaches to be heavily dependent on social and behavioral change strategies to halt transmissions. We focus on multiple levels of intervention including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. We focus on multiple levels of intervention including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. The model has multiple foci, including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. Interventions to address stigma have been developed that target individuals, health care workers, communities, and social figures, which will likely find new purpose in COVID-19 (Andersson et al., 2020; Rao et al., 2019; Stangl et al., 2013) . cache = ./cache/cord-338654-ma9ayu80.txt txt = ./txt/cord-338654-ma9ayu80.txt === reduce.pl bib === id = cord-334010-gxu0refq author = Banerjee, Nilotpal title = Viral glycoproteins: biological role and application in diagnosis date = 2016-01-18 pages = extension = .txt mime = text/plain words = 6657 sentences = 406 flesch = 46 summary = The sema-domain is the [18, 43] Fusion with host cell membrane Sialic Acid and attachment [43] 3-5 million cases Worldwide [78, 105] SARS-CoV Spike(S) glycoprotein [25, 115] Membrane fusion [115] 8422 within the duration of 1st November 2002 to 7th August 2003 occurring worldwide [113, 114] Hepatitis C virus E1 and E2 [55, 98] Binding to Host receptor and Conformational change necessary for membrane fusion [98] 130 to 150 million people globally [103, 106] Human immunodeficiency virus 1 gp120, gp160, gp41 [16] Intracellular transport [16] 35 million globally up to 2013 [83, 104, 108, 112] Zaire Ebola virus Spike Protein Gp1-Gp2 [64] Primary Host cell activation [64] up to 28th June 2015 total 27,550 cases [107, 110, 111] Dengue virus E (dimer) [64] Host cell fusion and attachment [64] WHO reported recently that there are 390 million dengue infections per year globally [109] . cache = ./cache/cord-334010-gxu0refq.txt txt = ./txt/cord-334010-gxu0refq.txt === reduce.pl bib === id = cord-340703-vtuy806l author = Cascio, Antonio title = Low bone mineral density in HIV-positive young Italians and migrants date = 2020-09-03 pages = extension = .txt mime = text/plain words = 4488 sentences = 230 flesch = 55 summary = We aimed to evaluate the bone mineral density (BMD) in naïve antiretroviral (ARV) treated HIV positive patients comparing native Italian group (ItG) to a Migrants group (MiG) upon arrival in Italy. Lumbar site low BMD is an initial condition of bone loss in HIV young patients, especially in female migrants. Our study aims to emphasize the burden of bone health in naïve ARV HIV positive patients and compare the bone density of the native Italian population group (ItG) with that of HIV Migrants (MiG) upon arrival in Italy. Finally, in Table 3 , we report the logistic regression analysis between Low BMD variable (dichotomous) and the independent variables: Gender (dichotomous), BMI (continuous), Hydroxy-Vitamin D (continuous), CD4 (continuous), and Previous Fractures (dichotomous) for the total sample, ItG, and MiG. Our previous reports [13, 14] on the prevalence of Low-BMD in HIV mono-infected patients who underwent ARV therapy showed higher percentage rates of osteopenia (44.9%) and osteoporosis (20.9%) than an agerelated healthy Italian population (18%) [16] . cache = ./cache/cord-340703-vtuy806l.txt txt = ./txt/cord-340703-vtuy806l.txt === reduce.pl bib === id = cord-334133-61om170g author = Hollier, Mark J. title = The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date = 2005-07-05 pages = extension = .txt mime = text/plain words = 8424 sentences = 437 flesch = 57 summary = For example, the GL envelope protein of equine arteritis virus is proposed to have 1 or 3 MSDs (Snijder and Meulenberg, 1998) , the M protein of transmissible gastroenteritis coronavirus and equine arteritis virus, and the S antigen of hepatitis B virus are proposed to have three or four MSDs (Prange and Streeck, 1995; Risco et al., 1995; Snijder and Meulenberg, 1998) , and the herpes simplex virus glycoprotein B (Pellett et al., 1985) , and the Epstein -Barr virus 58 kDa latent protein Hennessy et al., 1984) both have multiple MSDs. Based on an analysis of their sequence and structure, we propose that the gp41 transmembrane region and C-terminal tail of all HIV-1 clades A to D can exist in two conformations, with either 1 MSD (the conventional structure) or with 3 MSDs. We suggest that these are, respectively, the majority and minority forms of intracellular Env. In the 3-MSD form, MSD 1 and MSD 2 are separated by a highly conserved beta turn, while the MSD 2 and MSD 3 support an unstructured hydrophilic loop/minor ectodomain of 41 residues that in clade B strains is highly antibody-reactive and involved in fusion. cache = ./cache/cord-334133-61om170g.txt txt = ./txt/cord-334133-61om170g.txt === reduce.pl bib === id = cord-340489-yo3cp5vs author = nan title = KAPITEL 13 Infektionskrankheiten date = 2008-12-31 pages = extension = .txt mime = text/plain words = 26536 sentences = 3917 flesch = 45 summary = Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. cache = ./cache/cord-340489-yo3cp5vs.txt txt = ./txt/cord-340489-yo3cp5vs.txt === reduce.pl bib === id = cord-340619-3tjquzx8 author = Menghua, Wu title = Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date = 2020-07-23 pages = extension = .txt mime = text/plain words = 1601 sentences = 119 flesch = 63 summary = title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. Here we reported a case of HIV and SARS-CoV-2 coinfection who had a prolonged viral shedding duration about 28 days. [11] reported a patient with kidney transplantation who had a prolonged viral shedding duration for 63 days. This is the first report of a patient co-infected with HIV and SARS-CoV-2 who showed a prolonged viral shedding duration. The lymphocyte count of our case was also less than 2.0 × 10 9 /L, which might be a co-factor for the prolonged viral shedding duration. Viral shedding prolongation in a kidney transplant patient with COVID-19 pneumonia cache = ./cache/cord-340619-3tjquzx8.txt txt = ./txt/cord-340619-3tjquzx8.txt === reduce.pl bib === id = cord-340389-0fybiybv author = Fahrioglu, Umut title = CCR5-Δ32 gene variant frequency in the Turkish Cypriot population date = 2020-07-31 pages = extension = .txt mime = text/plain words = 3532 sentences = 202 flesch = 57 summary = In the current study, we aimed to determine the CCR5-Δ32 allele frequency in the Turkish Cypriot population with 326 subjects, 141 men (43.1%) and 185 (56.9%) women. In the current study, we aimed to determine the CCR5-Δ32 allele frequency in the Turkish Cypriot population. As the results of our study suggest, most of the Turkish Cypriot population is at greater risk of HIV infection and faster disease progression due to a very low frequency of the Δ32 allele. By keeping the greater risk in mind and using studies like ours, a dialog with health authorities must begin in order to develop a more structured and up-to-date strategy for testing and preventing HIV with the hopes of eliminating HIV/AIDS from the Turkish Cypriot population. Frequencies of 32 base pair deletion of the (Delta 32) allele of the CCR5 HIV-1 co-receptor gene in Caucasians: a comparative analysis cache = ./cache/cord-340389-0fybiybv.txt txt = ./txt/cord-340389-0fybiybv.txt === reduce.pl bib === id = cord-341503-3cvtoc2j author = Jaiswal, J. title = Disinformation, Misinformation and Inequality-Driven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism date = 2020-05-21 pages = extension = .txt mime = text/plain words = 2551 sentences = 146 flesch = 39 summary = Much of the evidence needed to fully inform clinical and public health responses is not yet available, making COVID-19 uniquely vulnerable to a proliferation of disinformation, misinformation, and medical mistrust, including what are often called "conspiracy beliefs" [6, 7] . The purpose of this commentary is to suggest that understanding the etiologies of disinformation, misinformation, and medical mistrust must be an important component of the public health response to COVID-19. It is vital to consider how people, as individuals and as members of groups, experience and interpret social and economic inequality, and how those experiences affect their trust in or mistrust of evidence-based public health messaging, as well as their readiness to accept any promulgated misinformation or disinformation [64] . Public health and medical professionals have a responsibility to communicate science in an effective, accurate and accessible manner, without bias-and with the understanding that structural racism and other forms of oppression are root causes of inequality-driven mistrust. cache = ./cache/cord-341503-3cvtoc2j.txt txt = ./txt/cord-341503-3cvtoc2j.txt === reduce.pl bib === id = cord-341304-jdvzpvdx author = Pata, Rama Kanth title = Human Immunodeficiency Virus: A Dark Cloud With Silver Lining During the COVID-19 Pandemic date = 2020-07-20 pages = extension = .txt mime = text/plain words = 1871 sentences = 105 flesch = 53 summary = In December 2019, China reported a cluster of pneumonia patients infected by a new virus from the coronavirus family called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus quickly spread around the world and infected millions of people, and the World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020. On March 22, 2020, a 67-year-old female with a past medical history of asthma, coronary artery disease (status post-coronary artery bypass graft two years ago), hypertension, hyperlipidemia, and HIV on antiretroviral medications [bictegrav/emtricit/tenofov ala (Biktarvy® 50-200-25 mg tablet, Gilead Sciences, Foster City, CA) and darunavir/cobicistat (Prezcobix® 800 mg-150 mg tablet, Janssen Pharmaceutica, Beerse, Belgium)] was brought in by emergency medical services (EMS) for progressively worsening shortening of breath associated with weakness and two episodes of watery non-bloody diarrhea for one day. showed clinical improvement in the first case of COVID-19 in the United States after the use of remdesivir [8] . cache = ./cache/cord-341304-jdvzpvdx.txt txt = ./txt/cord-341304-jdvzpvdx.txt === reduce.pl bib === id = cord-329482-haenltxn author = Small, Eusebius title = Covid-19 and Gender in LMICs: Potential Lessons from HIV Pandemic date = 2020-05-25 pages = extension = .txt mime = text/plain words = 1581 sentences = 96 flesch = 53 summary = According to the World Bank, almost 24 million fewer people will escape poverty in East Asia and the Pacific because of the financial impact of COVID-19 in 2020 [9] . Among the LMICs in sub-Saharan Africa, COVID-19 could push these countries farther into a spiral of poverty, ravaging their already tenuous health systems [2, 5] . During the HIV outbreak, a significant limited reproductive health care and family planning services were available to women. According to the United Nations, an unrelated crisis impacting women worldwide are the spikes in domestic violence due to COVID-19 lockdowns [7] . Additionally, women who are transgender and are living with HIV are disproportionately impacted by intimate partner violence [24] , stay at home COVID-19 orders could exacerbate their wellbeing. A pandemic of the poor: social disadvantage and the U.S. HIV epidemic Gender-Based Violence Increases Risk of HIV/AIDS for Women in Sub-Saharan Africa -Population Reference Bureau cache = ./cache/cord-329482-haenltxn.txt txt = ./txt/cord-329482-haenltxn.txt === reduce.pl bib === === reduce.pl bib === id = cord-340879-gu91cact author = Li, Miao title = Isolation and Characterization of a Phaseolus vulgaris Trypsin Inhibitor with Antiproliferative Activity on Leukemia and Lymphoma Cells date = 2017-01-23 pages = extension = .txt mime = text/plain words = 4150 sentences = 228 flesch = 48 summary = title: Isolation and Characterization of a Phaseolus vulgaris Trypsin Inhibitor with Antiproliferative Activity on Leukemia and Lymphoma Cells The intent of the present study was to isolate a trypsin inhibitor from the gold bean and to test it for inhibitory action on tumor cells, viral enzymes, and fungal growth. Gold bean trypsin inhibitor is also devoid of any inhibitory effect on HIV-1 integrase and SARS coronavirus proteinase. Gold bean trypsin inhibitor is also devoid of any inhibitory effect on HIV-1 integrase and SARS coronavirus proteinase. A lectin, an antifungal protein and a trypsin inhibitor can be isolated from the gold bean [24, 25] . A homodimeric sporamin-type trypsin inhibitor with antiproliferative, hiv reverse transcriptase-inhibitory and antifungal activities from wampee (clausena lansium) seeds The isolation of two proteins, glycoprotein i and a trypsin inhibitor, from the seeds of kidney bean (Phaseolus vulgaris) cache = ./cache/cord-340879-gu91cact.txt txt = ./txt/cord-340879-gu91cact.txt === reduce.pl bib === id = cord-341323-mw352rr1 author = Logie, Carmen H title = Lessons learned from HIV can inform our approach to COVID‐19 stigma date = 2020-05-04 pages = extension = .txt mime = text/plain words = 1560 sentences = 100 flesch = 50 summary = We are moving away from siloed stigma research on individual health conditions (e.g. HIV, mental health), social identities (e.g. race, sexual orientation) and practices (e.g., sex work, drug use) [15] . Intersecting stigmasuch as racism and povertyinteract with HIV-related stigma to harm health engagement and outcomes [16, 17] and may present analogous barriers to COVID-19 testing and treatment [14] . There are complex associations between HIV-related stigma and age, whereby older persons living with HIV may experience reduced health effects of stigma [21, 22] . The contact approach involves people who have experienced the stigma being targeted (e.g. persons living with HIV, persons experiencing COVID-19 stigma) delivering the intervention to provide a face to the pandemic that in turn can foster empathy and reduce othering [26, 27] . Creating space for stories of COVID-19 that reveal stigma and solidarity, of front-line healthcare workers' experiences, and of people living in quarantine, can reduce fear and spark empathy by helping us to see ourselves and our communities reflected in the pandemic [28] . cache = ./cache/cord-341323-mw352rr1.txt txt = ./txt/cord-341323-mw352rr1.txt === reduce.pl bib === id = cord-340763-cxnu9g8y author = Grimm, Sebastian K. title = Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date = 2015-02-17 pages = extension = .txt mime = text/plain words = 7822 sentences = 341 flesch = 45 summary = title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies Because the intrinsic instability and complexity of this trimeric glycoprotein has greatly impeded the development of immunogens that properly represent the structure of native envelope, this platform addresses an essential need for methodologies with the capacity to rapidly engineer HIV spike proteins towards improved homogeneity, stability, and presentation of neutralizing epitopes. The rationally designed d-SOSIP variant and a mutant with disrupted CD4 binding site (CD4bs)-specific Ab binding (d-SOSIP D368R) were displayed as Aga2 fusion proteins on yeast ( Fig. 2A ), and compared for display level and binding to a panel of HIV bnAbs together with the well-characterized and folded YU2 gp120 core [47] and an unrelated viral envelope protein (E2) derived from Hepatitis C virus (HCV E2) as positive and negative controls Fig. 2) . cache = ./cache/cord-340763-cxnu9g8y.txt txt = ./txt/cord-340763-cxnu9g8y.txt === reduce.pl bib === id = cord-346557-s6c7d70y author = Brennan, David J. title = How Might Social Distancing Impact Gay, Bisexual, Queer, Trans and Two-Spirit Men in Canada? date = 2020-04-30 pages = extension = .txt mime = text/plain words = 1803 sentences = 92 flesch = 53 summary = Given that social distancing measures may yet last for several months [20] , and potentially even longer for older and immune-compromised GBQT2+ [21] , it is important to take this opportunity to study the impact of social distancing on marginalized populations-particularly if COVID-19 We recruited participants using promotional materials in French and English shared by various partner organizations across the country through newsletters, listservs, and social media platforms (e.g., Facebook, Instagram, Twitter). The eligibility criteria restricted participation to individuals who identified as men or another gender other than women (e.g., non-binary, genderqueer, agender; inclusive of trans men and Two-Spirit people); identified as gay, bisexual, queer, asexual, or other non-heterosexual identity (inclusive of Two-Spirit) and/or have reported having had sex with another man in the last 5 years; were at least 15 years of age; lived in Canada; provided informed consent; completed a questionnaire in either French or English; and did not already participate in this study cycle. cache = ./cache/cord-346557-s6c7d70y.txt txt = ./txt/cord-346557-s6c7d70y.txt === reduce.pl bib === id = cord-339879-92esdjy9 author = Delhalle, Sylvie title = Phages and HIV-1: From Display to Interplay date = 2012-04-13 pages = extension = .txt mime = text/plain words = 21838 sentences = 978 flesch = 44 summary = The BNtAb IgG1 b12 was the first neutralizing MAb selected from a phage-displayed Fab (antibody fragment composed of one constant and one variable domain of the heavy (CH1 and VH) and the light (CL and VL) chains linked together) library derived from an HIV-1-infected donor (See section 3.1.1.1.1.) [41] . At the end of the second round, selected phages displaying longer inserts of 40 to 50 AA corresponding to the N-and C-terminal regions of Gag were identified, revealing the presence of two distinct antigenic regions in Gag. This study demonstrated that gene-fragment phage display could be used to identify epitopes targeted by polyclonal Abs. Although they occur at a very low frequency in humans, antibodies targeting host proteins involved in HIV-1 infection have been reported in immunized animals. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries cache = ./cache/cord-339879-92esdjy9.txt txt = ./txt/cord-339879-92esdjy9.txt === reduce.pl bib === id = cord-342719-bdxb45us author = Yamamoto, Shinya title = Antibody Response to SARS-CoV-2 in people living with HIV date = 2020-10-02 pages = extension = .txt mime = text/plain words = 408 sentences = 39 flesch = 62 summary = All five patients received consecutive serological test, and four of five patients had seroconversion by one month after the symptom onset, which were similar to non-HIV-infected patients. 1 Ample studies have demonstrated that PLWH generally show poor serological response to other viruses or viral antigens such as hepatitis B vaccine, 2 especially for PLWH with a high HIV viral load and decreased CD4+ T-cell. 2 One previous report described that an untreated HIV case had seroconversion of SARS-CoV-2 two months after symptoms appeared. ART occurred similarly to that in COVID-19 patients without HIV infection. Absence of seroconversion, as was observed in our Case 2, has been reported particularly in mild 1 or asymptomatic patients. 5 We highlighted that seroconversion of SARS-CoV-2 was similar between well-controlled PLWH and patients without HIV. One case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a low CD4(+) T-cell count Antibody Responses to SARS-CoV-2 at 8 weeks postinfection in asymptomatic patients. cache = ./cache/cord-342719-bdxb45us.txt txt = ./txt/cord-342719-bdxb45us.txt === reduce.pl bib === id = cord-345771-3v2avxiv author = Traub, Ariana Moriah title = Multimonth Dispensing of Antiretroviral Therapy Protects the Most Vulnerable From 2 Pandemics at Once date = 2020-06-30 pages = extension = .txt mime = text/plain words = 703 sentences = 44 flesch = 56 summary = We encourage governments in countries that have a high prevalence of people living with HIV to implement multimonth dispensing of antiretroviral therapy to safeguard both patients with HIV and health care workers from coronavirus disease 2019. 2,3 However, as with other infectious diseases, it is expected that PLHIV who are not virally suppressed and/or on antiretroviral therapy (ART) might be at an increased risk of COVID-19 infection, severe disease, and poor health outcomes. Thus, policy makers-including the U.S. President's Emergency Plan for AIDS Relief-are encouraging countries to provide PLHIV with a multimonth supply of ART as a key strategy to safeguard PLHIV and health care workers involved in providing HIV services. As a key strategy to safeguard patients and health care workers providing HIV services, MMD also reduces clinic visits, improves viral suppression, encourages social distancing, and potentially saves patients from the dual threat of SARS-CoV-2 and HIV. cache = ./cache/cord-345771-3v2avxiv.txt txt = ./txt/cord-345771-3v2avxiv.txt === reduce.pl bib === id = cord-340777-d1vwjqk6 author = O’Byrne, Patrick title = Immediate PrEP after PEP: Results from an Observational Nurse-Led PEP2PrEP Study date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4855 sentences = 229 flesch = 55 summary = 3 This last point has led some guidelines to suggest that PEP use more than once warrants preexposure prophylaxis (PrEP), which is the use antiretroviral medications before a potential HIV exposure to prevent seroconversion. 4, 5 To inform this decision and address high seroconversion rates among PEP patients, we began offering PEP2PrEP to patients who (1) initiated PEP at our sexually transmitted infection (STI) testing clinic, (2) reported good adherence to the PEP, and (3) had no serologic or physical evidence of HIV infection. Extracted data focused on demographics (age, gender, income), sexual and drug use practices (sex practices, gender of partners, substance use), mental health (depression, anxiety, using the patient health questionnaire 9 [PHQ9], and generalized anxiety 7 scale [GAD7], respectively), reason for PEP use and follow-up details (practices that warranted PEP, symptoms, test results), and information on PrEP visits (attendance, symptoms, results). cache = ./cache/cord-340777-d1vwjqk6.txt txt = ./txt/cord-340777-d1vwjqk6.txt === reduce.pl bib === id = cord-339796-gccnvh0z author = Zhang, Si Min title = Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date = 2015-07-31 pages = extension = .txt mime = text/plain words = 9073 sentences = 403 flesch = 45 summary = The MPER in the human immunodeficiency virus type I (HIV-1) envelope protein (Env) interacts with the lipid bilayers through a cluster of tryptophan (Trp) residues and a C-terminal cholesterol-interacting motif. We found that elimination of the membrane-active elements in MPER peptides, namely, penta Trp→alanine (Ala) substitutions and the disruption of the C-terminal cholesterol-interacting motif through deletion inhibited the anti-viral effect against the pseudotyped HIV-1. The secondary structure study revealed that the penta-Trp→Ala substitutions also increased the helical content in the MPER sequence, which prompted us to study the biological relevance of such mutations in pre-fusion Env. We observed that Ala mutations of Trp664, Trp668 and Trp670 in MPER moderately lowered the intracellular and intraviral contents of Env while significantly elevating the content of another viral structural protein, p55/Gag and its derivative p24/capsid. Here we describe the roles of the Trp residues in the membrane-active MPER sequence in anti-HIV fusion inhibitor design and a surprising role in the biosynthesis of viral structural proteins. cache = ./cache/cord-339796-gccnvh0z.txt txt = ./txt/cord-339796-gccnvh0z.txt === reduce.pl bib === id = cord-341097-c96hm610 author = Mayer, Craig S. title = Analysis of data dictionary formats of HIV clinical trials date = 2020-10-05 pages = extension = .txt mime = text/plain words = 6899 sentences = 366 flesch = 57 summary = To facilitate aggregation across studies, we defined three types of data dictionary (data element, forms, and permissible values) and created a simple information model for each type. The presented study is limited to data dictionary analysis, although the motivation is to later analyze a large body of past HIV data elements to inform data-driven consensus on CDEs. This study is part of a larger research project titled 'Identification of Research Common Data Elements in HIV/AIDS using data science methods' [12] . We use the term Forms Data Dictionary (or forms dictionary in shorter form) to refer to a data dictionary that provides a full list of titles and descriptions of all Case Report Forms (CRFs) used in the study (or other relevant metadata for data element grouping). Use of categorical data elements in research is extremely common and, as stated earlier, most studies would be expected to provide a permissible value dictionary. cache = ./cache/cord-341097-c96hm610.txt txt = ./txt/cord-341097-c96hm610.txt === reduce.pl bib === id = cord-341298-mqpovrms author = Morse, S.A. title = Viruses and Bioterrorism date = 2016-10-31 pages = extension = .txt mime = text/plain words = 4787 sentences = 224 flesch = 44 summary = Requirements for an ideal biological warfare agent may include: availability; ease of production; stability after production; a susceptible population (human or animal); absence of specific treatment; ability to incapacitate or kill the host; appropriate particle size in aerosols so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims; ability to be disseminated via food or water; and, the availability of a vaccine to protect certain groups. Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs incapacitating (eg, VEE) or lethal infections (EEE case fatality rates range from 50 to 75%) (Sidwell and Smee, 2003) . An Australian research group (Jackson et al., 2001) was investigating virally vectored immunocontraceptive vaccines based on ectromelia virus, the causative agent of the disease termed mousepox. cache = ./cache/cord-341298-mqpovrms.txt txt = ./txt/cord-341298-mqpovrms.txt === reduce.pl bib === id = cord-342936-43u7afl3 author = Balzarini, Jan title = Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date = 2007 pages = extension = .txt mime = text/plain words = 11304 sentences = 534 flesch = 44 summary = Perhaps more importantly, such carbohydrate-binding agents (CBAs) may force the virus to delete at least part of its glycan shield to escape drug pressure 5 ; this might result in the initiation of an immune response against uncovered immunogenic envelope epitopes. Although such a mechanism may be efficient for a first-line inactivation of HIV, CBA-exposed HIV strains may decrease the efficiency of LCs to eliminate HIV, but at the same time may compromise the ability of the virus to be efficiently transmitted by DCs. The interactions of several CBAs have been extensively investigated, including: the prokaryotic CV-N and actinohivin; a variety of plant lectins, including Hippeastrum hybrid agglutinin (HHA) and UDA; the non-peptidic low-molecular-weight antibiotic PRM-A; and the monoclonal antibody 2G12 with the HIV-envelope gp120 and/or several glycan structures. cache = ./cache/cord-342936-43u7afl3.txt txt = ./txt/cord-342936-43u7afl3.txt === reduce.pl bib === id = cord-337659-x4oywbrj author = Wilson, Brenda A. title = Global biosecurity in a complex, dynamic world date = 2008-07-31 pages = extension = .txt mime = text/plain words = 10626 sentences = 469 flesch = 45 summary = Although one might argue that the principal difference in the infectious disease threat today versus say 10, 25, or 50 years ago is bioterrorism, the resources spend on preparing for a bioterror attack is viewed by most scientists as grossly exorbitant [6] , particularly considering the small numbers of individuals who have been or could be affected by this type of attack and considering the relatively low medical relevance or prevalence of the diseases caused by the limited number of highpriority bioterror bioagents, the socalled ''category A select agents.'' And, while admittedly the preparedness and surveillance measures put in place for one has certainly helped to protect against the other (the improved global response to and curtailment of SARS coming after the anthrax bioterrorist attacks is a prime example of this), most scientists feel that the limited resources available from an already overburdened system should instead be used for studying and preparing against the looming and potentially more devastating infectious disease threats from natural or accidental exposure [7] , which could affect millions of people and animals and could have huge health and economic consequences. cache = ./cache/cord-337659-x4oywbrj.txt txt = ./txt/cord-337659-x4oywbrj.txt === reduce.pl bib === id = cord-346424-gfccstoz author = Friedrich, Brian M title = A Functional Role for ADAM10 in Human Immunodeficiency Virus Type-1 Replication date = 2011-05-11 pages = extension = .txt mime = text/plain words = 6319 sentences = 330 flesch = 46 summary = RESULTS: Silencing ADAM10 expression with small interfering RNA (siRNA) 48 hours before infection significantly inhibited HIV-1 replication in primary human monocyte-derived macrophages and in CD4(+ )cell lines. In studies reported herein, it was found that transfecting cells with ADAM10 small interfering RNA (siRNA) dramatically inhibited replication of X4 and R5 HIV-1 strains, both in primary human monocyte-derived macrophages and in CD4 + cell lines. Figure 1A shows that ADAM10 silencing effectively inhibited R5-tropic HIV-1 replication when human monocyte-derived macrophages were transfected with siRNAs 48 h prior to infection. To determine whether ADAM10 is required for entry or HIV-1 reverse transcription, small non-genomic DNA was isolated from control-and ADAM10 siRNA-transfected macrophages at 48 h post-infection for quantification by real-time PCR. To determine the effect of silencing cellular genes on HIV-1 replication, TZM-bl cells or primary human macrophages were transfected with siRNA SMARTpools for 48 h prior to infection. cache = ./cache/cord-346424-gfccstoz.txt txt = ./txt/cord-346424-gfccstoz.txt === reduce.pl bib === id = cord-349104-p0egfpx9 author = Modi, Anita R. title = Coronavirus disease 2019 in an orthotopic liver transplant recipient living with human immunodeficiency virus date = 2020-06-17 pages = extension = .txt mime = text/plain words = 1207 sentences = 76 flesch = 38 summary = Yet immunocompromised status alone, in the absence of other comorbidities, may not necessarily predict severe illness presentations and poorer clinical outcomes as indicated by recent reports of COVID‐19‐infected solid organ transplant recipients and people living with human immunodeficiency virus (HIV). Yet immunocompromised status alone, in the absence of other comorbidities, may not necessarily predict severe illness presentations and poorer clinical outcomes as indicated by recent reports of COVID-19-infected solid organ transplant recipients and people living with human immunodeficiency virus (HIV). COVID-19, HIV, hydroxychloroquine, immunocompromised, orthotopic liver transplantation Solid organ transplant recipients living with HIV uniquely demonstrate features of both immune suppression and immune activation, as evidenced by the increased rates of allograft rejection in such patients. We hope to contribute to the literature of COVID-19 in immunocompromised patients by describing an orthotopic liver transplant (OLT) recipient with well-controlled HIV who experienced a mild flu-like illness attributed to SARS-CoV-2. cache = ./cache/cord-349104-p0egfpx9.txt txt = ./txt/cord-349104-p0egfpx9.txt === reduce.pl bib === id = cord-343470-w215pzdc author = Tsai, Kevin title = Epigenetic and epitranscriptomic regulation of viral replication date = 2020-06-12 pages = extension = .txt mime = text/plain words = 9761 sentences = 452 flesch = 41 summary = Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. First, the viral protein VP16, which is packaged into the tegument layer of incoming virions, recruits host proteins, including host-cell factor 1 (HCF-1) and octamer-binding factor (Oct-1), in order to form a complex that recruits the histone demethylases lysine-specific demethylase 1 (LSD1) and Jumonji domain 2 (JMJD2) family members as a means to remove repressive H3K9 marks from viral immediate early promoters 42 Upon entry into the cell nucleus, the DNA of many viruses initiates the replication process adjacent to subnuclear structures called pro-myelocytic leukaemia nuclear bodies (PML-NBs). cache = ./cache/cord-343470-w215pzdc.txt txt = ./txt/cord-343470-w215pzdc.txt === reduce.pl bib === id = cord-351004-h6fde7vm author = Gudipati, Smitha title = Descriptive Analysis of Patients Living With HIV Affected by COVID-19 date = 2020-07-13 pages = extension = .txt mime = text/plain words = 2472 sentences = 151 flesch = 54 summary = METHODS: This is a case series that included 14 PLWH with laboratory-confirmed COVID-19 infection who were evaluated at Henry Ford Hospital in Detroit, Michigan, between March 20, 2020, and April 30, 2020. CONCLUSION: Although the clinical spectrum of COVID-19 among PLWH cannot be fully ascertained by this report, it adds to the data that suggest that HIV-positive patients with SARS-CoV-2 infection are not at a greater risk of severe disease or death as compared to HIV-negative patients. This is a case series that included 14 PLWH who were evaluated in the Henry Ford Hospital (HFH) emergency department for laboratory-confirmed COVID-19 infection, between March 20, 2020, and April 30, 2020. Our case series, the current published literature on HIV and SARS-CoV-2, and the published data from HFH on COVID-19 patients without known HIV supports the theory that there is not an excess morbidity and mortality among PLWH affected by COVID-19 compared with the general public. cache = ./cache/cord-351004-h6fde7vm.txt txt = ./txt/cord-351004-h6fde7vm.txt === reduce.pl bib === id = cord-341838-lkz8ro90 author = Gervasoni, Cristina title = Clinical features and outcomes of HIV patients with coronavirus disease 2019 date = 2020-05-14 pages = extension = .txt mime = text/plain words = 1794 sentences = 117 flesch = 59 summary = The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. cache = ./cache/cord-341838-lkz8ro90.txt txt = ./txt/cord-341838-lkz8ro90.txt === reduce.pl bib === id = cord-338572-5ifc2lx6 author = Nagarakanti, Sandhya R. title = Clinical outcomes of patients with COVID‐19 and HIV coinfection date = 2020-09-19 pages = extension = .txt mime = text/plain words = 1598 sentences = 103 flesch = 55 summary = We present the clinical outcomes of HIV patients hospitalized for COVID‐19 in a matched comparison with historical controls. Data on baseline clinical characteristics and hospital course was documented and compared with that of a matched control group of COVID‐19 patients who had no history of HIV. CONCLUSIONS: In our cohort of HIV infected patients hospitalized for COVID‐19, there was no difference in mortality, ICU admission and the need for mechanical ventilation when compared to a matched control of COVID ‐19 patients with HIV. We evaluated their clinical outcomes and compared them to that of a well-matched control group of patients with no HIV. These data points included HIV-associated characteristics such as most recent CD4+ T cells, CD4/CD8 ratio, ( obtained by flow cytometry Clinical outcomes of hospitalized patients were compared to that of a propensity matched cohort of COVID-19 patients who had no history of HIV infection. cache = ./cache/cord-338572-5ifc2lx6.txt txt = ./txt/cord-338572-5ifc2lx6.txt === reduce.pl bib === id = cord-351740-779g8tr1 author = Khaba, Moshawa Calvin title = COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date = 2020-09-25 pages = extension = .txt mime = text/plain words = 1830 sentences = 126 flesch = 55 summary = We report the first autopsy case of HIV-infected individual with COVID-19 as the cause of death. The first confirmed case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was reported in China in December 2019. To the best of our knowledge, this manuscript represents the first published report of an autopsy performed on an HIV infected patient with cause of death attributed to COVID-19. The final cause of death was SARS-CoV-2 (COVID-19) infection in HIV infected patient. In accord to what is already published, the lung findings on the index patient showed early phase of diffuse alveolar damage with associated microthrombi which is seen in COVID-19. Whilst HIV infected people on treatment with normal CD4 count and low viral load may not be at a high risk of serious illness, the presence of other chronic conditions may increase their overall risk (7) The fact that SARS-CoV-2 can cause transient immune deficiency, it denotes that HIV and COVID-19 interaction may have adverse immunological and clinical outcomes. cache = ./cache/cord-351740-779g8tr1.txt txt = ./txt/cord-351740-779g8tr1.txt === reduce.pl bib === === reduce.pl bib === id = cord-346314-o9fjpqaj author = Jarboui, Mohamed Ali title = Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date = 2012-11-15 pages = extension = .txt mime = text/plain words = 10004 sentences = 521 flesch = 36 summary = Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. Following the detailed annotation of the quantitative abundance changes in the nucleolar protein composition upon Tat expression, we focussed on the Tat-affected cellular complexes and signalling pathways associated with ribosome biogenesis, spliceosome, molecular chaperones, DNA replication and repair and metabolism and discuss their potential involvement in HIV-1 pathogenesis. In this study, we investigated the quantitative changes in the nucleolar proteome of Jurkat T cells constitutively expressing HIV-1 Tat (86aa) versus their Tat-negative counterpart, using stable isotope labelling with amino acids in cell culture (SILAC) technology, followed by ESI tandem mass spectrometry and implemented the experimental approach described in Figure 1A . cache = ./cache/cord-346314-o9fjpqaj.txt txt = ./txt/cord-346314-o9fjpqaj.txt === reduce.pl bib === id = cord-353895-tgn1kk07 author = Kavanagh, Matthew M title = Reckoning with mortality: global health, HIV, and the politics of data date = 2020-07-03 pages = extension = .txt mime = text/plain words = 1848 sentences = 94 flesch = 46 summary = Studies in South Africa, Kenya, Zambia, and the Democratic Republic of the Congo have shown that most patients with HIV admitted to hospital have already been on antiretroviral therapy (often for years) but they either stop treatment or are on a treatment regimen that is not effectively suppressing the virus. In South Africa, in particular, tracking the mortality of young people using systems at the local level helped monitor the effectiveness of HIV programmes. 20 Hopefully, this step will improve patient outcomes by incentivising effective interventions for advanced HIV disease and support for people who have stopped treatment to re-enter care. 17 Third, we can move towards a variety of outcomeoriented global health programmes beyond HIV, for which measures of success move from the number of patients receiving services to explicit reductions in mortality rates. cache = ./cache/cord-353895-tgn1kk07.txt txt = ./txt/cord-353895-tgn1kk07.txt === reduce.pl bib === id = cord-350540-s6is9ndm author = Pinto, Rogério M. title = COVID-19 Pandemic Disrupts HIV Continuum of Care and Prevention: Implications for Research and Practice Concerning Community-Based Organizations and Frontline Providers date = 2020-04-28 pages = extension = .txt mime = text/plain words = 2028 sentences = 100 flesch = 49 summary = title: COVID-19 Pandemic Disrupts HIV Continuum of Care and Prevention: Implications for Research and Practice Concerning Community-Based Organizations and Frontline Providers Community-based organizations (CBOs) employ frontline service providers-social workers, health educators, navigators-to help (1) individuals of unknown HIV status access testing; (2) those at high-risk for HIV but who test negative to access physicians who can prescribe PrEP; Nonetheless, community-engaged research suggests that, prior to the COVID-19 pandemic, these frontline providers had not been consistent in how often or in how they linked clients to care continuum services. Providers having day-to-day interactions with clients in primary care, outpatient, and prevention settings are poised to help PLWH and vulnerable individuals overcome HIV-related stigma, PrEP stigma, inadequate health insurance, and can help improve HIV testing rates [20] [21] [22] [23] [24] [25] . cache = ./cache/cord-350540-s6is9ndm.txt txt = ./txt/cord-350540-s6is9ndm.txt === reduce.pl bib === id = cord-341155-3d64mso0 author = Slots, Jørgen title = Bacterial and viral pathogens in saliva: disease relationship and infectious risk date = 2010-12-07 pages = extension = .txt mime = text/plain words = 9332 sentences = 447 flesch = 36 summary = Human viruses are also frequent inhabitants of the human mouth, and their presence in saliva may be caused by the direct transfer of saliva from infected individuals, a bloodborne infection of the salivary glands, infection of the oral mucosa, or serumal exudates from diseased periodontal sites. Caries risk is assessed by the levels of mutans streptococci and lactobacilli in stimulated saliva (94, 96) , and salivary transmission of cariogenic bacteria frequently occurs from the mother to her child (92, 100) . As high quantities of salivary Epstein-Barr virus DNA can be recovered from fully edentulous patients (155) , the occurrence of the virus in saliva may not be a reliable indicator of its subgingival level or of the periodontitis disease status. Taken together, the saliva of HIV-infected persons is a risk factor for the transmission of several virulent herpesvirus species, and patients receiving HAART cannot be assumed to be less infectious for herpesviruses than individuals not receiving HAART. cache = ./cache/cord-341155-3d64mso0.txt txt = ./txt/cord-341155-3d64mso0.txt === reduce.pl bib === id = cord-345342-04tvuj9f author = Kumar, Rebecca N. title = COVID‐19 in an HIV‐positive Kidney Transplant Recipient date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1451 sentences = 93 flesch = 50 summary = This case describes the clinical course of a symptomatic kidney transplant recipient with HIV who tested positive for SARS-CoV-2. A 50-year-old HIV+ (CD4 395 cells/µL, CD4% 28%, HIV RNA < 20 copies/mL) African-American male with deceased donor kidney transplantation 14 months earlier for end-stage renal disease secondary to HIV-associated nephropathy (HIVAN)/focal segmental glomerulosclerosis (FSGS) presented to the Emergency Department (ED) complaining of fevers for two days, with temperatures to 101°F, chills, nasal congestion, and mild cough. All rights reserved There have been reported cases of COVID-19 in HIV-infected patients and cases of COVID-19 in transplant recipients [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . However, this case is the first detailed report of an HIVpositive kidney transplant recipient who developed and recovered from COVID-19. Case Report: A Kidney Transplant Patient with Mild COVID-19 Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? cache = ./cache/cord-345342-04tvuj9f.txt txt = ./txt/cord-345342-04tvuj9f.txt === reduce.pl bib === id = cord-354374-rtgjjglc author = C.G. Pollok, Richard title = Enteric viruses in HIV-related diarrhoea date = 2000-12-01 pages = extension = .txt mime = text/plain words = 3488 sentences = 191 flesch = 37 summary = Colonic CMV infection can occur in association with infection elsewhere in the GI tract including the oesophagus, which usually results in dysphagia and odynophagia, and the pancreatico-biliary tree, which results from AIDS-related cholangiopathy or pancreatitis and manifests as pain in the upper abdomen. However, with the exception of cytomegalovirus (CMV) and human herpes simplex virus (HSV), which are established aetiological agents of disease in the GI tract in patients with HIV, the role of other enteric viruses remains controversial. Between 44% and 82% of HIV patients with chronic diarrhoea have a pathogen that is readily identifiable using a well-established diagnostic protocol that includes stool culture, microscopy and histological examination of biopsies obtained by endoscopy of the upper and lower GI tract [1] [2] [3] [4] . • What role do non-CMV enteric viruses, particularly adenovirus, have in HIV-related diarrhoea? cache = ./cache/cord-354374-rtgjjglc.txt txt = ./txt/cord-354374-rtgjjglc.txt === reduce.pl bib === id = cord-347356-uc9dqhyq author = Cooper, TJ title = Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date = 2020-07-15 pages = extension = .txt mime = text/plain words = 3949 sentences = 228 flesch = 54 summary = OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The aim of this systematic review was to identify studies that discuss PLHIV who have been infected with SARS-CoV-2 and that report whether coinfection results in a greater risk of adverse outcomes and, furthermore, whether controlled HIV infection vs. A comprehensive literature search was carried out in Global Health, SCOPUS, Medline and EMBASE to identify articles that discussed HIV-positive patients and the clinical implications of HIV infection in COVID-19 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines [13] . [21] , also highlighted a case study of a HIV patient with SARS-CoV2 co-infection, diagnosis of viral pneumonia was made on clinical examination and chest CT findings. cache = ./cache/cord-347356-uc9dqhyq.txt txt = ./txt/cord-347356-uc9dqhyq.txt === reduce.pl bib === id = cord-349790-dezauioa author = Johnson, Stephanie title = Ethical challenges in pathogen sequencing: a systematic scoping review date = 2020-06-03 pages = extension = .txt mime = text/plain words = 6222 sentences = 273 flesch = 41 summary = Methods: We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. Implementation science research may also inform best practices for discussing the meaning and limitations of sequence data and cluster membership with community members and help to identify acceptable and evidence-based approaches that impose the least risk to persons within specific contexts. Many noted that there are important reasons to ensure that the public and individuals understand the uses of data collected as part of a sequencing studies, and the potential risks. cache = ./cache/cord-349790-dezauioa.txt txt = ./txt/cord-349790-dezauioa.txt === reduce.pl bib === id = cord-350221-8u6q3wfa author = Yang, Sung-Tae title = HIV virions sense plasma membrane heterogeneity for cell entry date = 2017-06-28 pages = extension = .txt mime = text/plain words = 7788 sentences = 413 flesch = 55 summary = We used giant plasma membrane vesicles (GPMVs) derived from HeLa cells that stably express the CD4 receptor and CCR5 co-receptor (CD4 + /CCR5 + ), investigated the lateral partitioning of both receptors in these membranes, and imaged the preferred regions of HIV binding and fusion at the single-particle level (Fig. 1A) . Recognition of Lo/Ld membrane boundaries by HIV Next, we examined whether and how HIV envelope (Env) particles interact with GPMVs. Murine leukemia viruses (MLVs) pseudotyped with HIV gp120/gp41 and fluorescently labeled with mKO-Gag were incubated with CD4 + /CCR5 + GPMVs. We visualized bound particles by epifluorescence microscopy and found that they migrate along The preparation of large-scale phase-separated GPMVs facilitates the study of the lateral distribution of CD4 and CCR5 and the role of ordered lipid domains in HIV entry. cache = ./cache/cord-350221-8u6q3wfa.txt txt = ./txt/cord-350221-8u6q3wfa.txt === reduce.pl bib === id = cord-355475-kdubhh73 author = Patton, Lauren L. title = Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date = 2020-11-05 pages = extension = .txt mime = text/plain words = 2161 sentences = 104 flesch = 45 summary = An early survey in May and June 2020 of practicing dentists in private practice and public health settings in the United States (U.S.), a short 2 months after the first COVID-19 wave and national shortages of personal protective equipment caused offices to move to emergency only dental care, showed that 99.7% of offices had implemented enhanced infection control procedures. While hope for a COVID-19 vaccine to quell transmission is widespread, we must not lose sight of the fact that diverse vaccine development technologies and novel drug discovery efforts made today will benefit our response to the next pandemic. 14 When the diversity of oral mucosal and salivary gland disorders were observed in HIV/AIDS patients, international collaborative groups such as the European Community We learned from HIV disease management that the antiretroviral drugs can have acute and long-term toxicities including ulcers, xerostomia/parotid lipomatosis, taste disturbances, perioral paresthesia, erythema multiforme and facial fat wasting. cache = ./cache/cord-355475-kdubhh73.txt txt = ./txt/cord-355475-kdubhh73.txt === reduce.pl bib === id = cord-354972-nc496v6s author = Margolin, Emmanuel title = Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date = 2020-09-10 pages = extension = .txt mime = text/plain words = 10919 sentences = 464 flesch = 37 summary = As of 8 August 2020, there have been over 1.2 million confirmed cases of COVID-19 in Africa, with 29,833 deaths reported (Africa CDC) There is concern that the pandemic may pose an even greater risk to countries in Africa owing to their weak health-care infrastructure, large burden of co-infections, including HIV-1 and tuberculosis, and ongoing outbreaks of emerging and re-emerging infections such as Ebola virus (Democratic Republic of Congo) and Lassa haemorrhagic fever (Nigeria) that will divert much-needed resources away from the fight against COVID-19 (ref. Given the optimistic development timeline of 12-18 months before any vaccines could be available for widespread use, it is clear that these efforts will not Box 1 | Potential impact of climate on SArS-coV-2 dissemination the comparatively low incidence of coronavirus disease-2019 (COviD19) in africa has raised the possibility that climate could influence the spread of severe acute respiratory syndrome coronavirus 2 (sars-Cov-2). cache = ./cache/cord-354972-nc496v6s.txt txt = ./txt/cord-354972-nc496v6s.txt === reduce.pl bib === id = cord-354050-kcn67stj author = Shi, Guoli title = More than meets the I: the diverse antiviral and cellular functions of interferon-induced transmembrane proteins date = 2017-11-21 pages = extension = .txt mime = text/plain words = 6846 sentences = 313 flesch = 36 summary = Most of what we know about the antiviral activities of IFITM proteins results from work using IAV and vesicular stomatitis virus (VSV), which perform pH-dependent fusion reactions in endosomes to gain access to the cell interior [22] . As the primary determinant for virus-cell attachment and the subsequent fusion reaction, the viral envelope glycoprotein (Env) was suspected to play an important role in whether or not HIV-1 and related lentiviruses are subject to inhibition by IFITM proteins. In addition to restricting virus entry, recent findings indicate that IFITM proteins perform antiviral functions impacting late stages of the HIV-1 life cycle. This antiviral activity is enhanced upon expression of an IFITM3 mutant that is defective for endocytosis, indicating that restriction of HIV-1 virion infectivity is performed at the plasma membrane [5] . Nonetheless, the recent identification of Env variants that are resistant to the IFITM3-mediated restriction of virion infectivity confirms this viral protein as an important determinant. cache = ./cache/cord-354050-kcn67stj.txt txt = ./txt/cord-354050-kcn67stj.txt === reduce.pl bib === id = cord-353012-rxhi8wd2 author = Zhou, Nan title = Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date = 2016-03-07 pages = extension = .txt mime = text/plain words = 6412 sentences = 334 flesch = 53 summary = Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Considering that the inhibitory dose of teicoplanin on the activity of cathepsin L is higher than that required for Ebola virus infection inhibition, a cell viability assay was performed to confirm that the inhibitory effect is not due to cytotoxicity (Fig. 6C) . Ebola trVLP system (28) , which can simulate the life cycle of wild-type Ebola viruses to a large extent, was applied to investigate whether teicoplanin and its glycopeptide antibiotic homologs dalbavancin, oritavancin, telavancin, and vancomycin can also inhibit the entry of Ebola trVLPs. Accordingly, the p4cis plasmid encoding Renilla luciferase, VP40, GP, and VP24 was transfected into HEK293T cells along with plasmids expressing T7 RNA polymerase, NP, VP35, VP30, and L viral proteins to produce Ebola trVLPs (Fig. 7A) . cache = ./cache/cord-353012-rxhi8wd2.txt txt = ./txt/cord-353012-rxhi8wd2.txt === reduce.pl bib === id = cord-346153-9162w7il author = Openshaw, P J title = Crossing barriers: infections of the lung and the gut date = 2008-12-24 pages = extension = .txt mime = text/plain words = 1716 sentences = 90 flesch = 43 summary = Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. However, the coronavirus copy number in some studies showed an increase between day 5 and day 10, so that maximal infectivity followed the fever, 7 leading perhaps to a false sense of security amongst those caring for SARS patients. e reason for these interactions are incompletely understood, but intriguing recent study show that in uenza and respiratory syndrome virus are both capable of causing a persistent inhibition of the innate response to bacterial superinfection, and therefore to increased bacterial replication and disease. Highly pathogenic strains of in uenza also cause intense systemic symptoms, sometimes associated with gastrointestinal disease. Microbial translocation is a cause of systemic immune activation in chronic HIV infection cache = ./cache/cord-346153-9162w7il.txt txt = ./txt/cord-346153-9162w7il.txt === reduce.pl bib === id = cord-349358-leicos9j author = Ketzinel‐Gilad, Mali title = RNA interference for antiviral therapy date = 2006-06-16 pages = extension = .txt mime = text/plain words = 12734 sentences = 684 flesch = 44 summary = During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. cache = ./cache/cord-349358-leicos9j.txt txt = ./txt/cord-349358-leicos9j.txt === reduce.pl bib === id = cord-348409-oxjd263z author = Stern, Zachariah title = The development of inovirus-associated vector vaccines using phage-display technologies date = 2019-09-08 pages = extension = .txt mime = text/plain words = 6043 sentences = 315 flesch = 41 summary = Areas covered: The architectural traits of filamentous viruses and their derivatives, IAVs, facilitate the display of specific antigenic peptides which induce antibody production to prevent or curtail infection. The creation of Random Peptide Libraries (RPL), where random oligopeptides are fused to major capsid proteins (gp3 or gp8) and displayed on individual inovirus clones creating a random variety of IAVs which can be used for vaccine design via epitope mapping using monoclonal or polyclonal antibodies. Through this breakthrough technology which was the subject matter of the Nobel Prize in Chemistry 2018 (see 'Expert Commentary' below), inovriuses displaying oligopeptides mimicking antigens (or specific epitopes of an antigen) can be used to vaccinate hosts thus inducing the desired antibody production. Unlike previous studies, which used a single specific peptide fused to a inovirus, four different antigenic peptides were displayed by inoviruses in a cocktail of recombinant IAVs. The induction of a cellular response completely vaccinated 1/3 of the pigs in the study and reduced the number of cysticerci in all other pigs [61] . cache = ./cache/cord-348409-oxjd263z.txt txt = ./txt/cord-348409-oxjd263z.txt === reduce.pl bib === id = cord-350443-ca5avyjf author = Zhang, Lei title = Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date = 2012-02-16 pages = extension = .txt mime = text/plain words = 7958 sentences = 383 flesch = 49 summary = This study reviews trends in notifiable infectious diseases in China, in their historical context, discusses the current epidemiological state of these infections and their implications for disease surveillance and public health interventions. The total number of diagnosed and death cases were estimated by multiplying morbidity and mortality rates by the overall Chinese population in the study years. In 2008, the three most frequently reported disease types included viral hepatitis (38.3%), bacterial infections (33.3%) and STIs and HIV (9.8%), which account for 5.4, 4.8 and 1.4 million diagnosed cases respectively during the period 2005-2008 (Table 1) . Second, the rapid rise in the number of notified cases of STIs, especially HIV infection, and viral hepatitis in China is associated with growth of the sex industry, increasingly frequent risky sexual behaviours and an increasing number of sexual partners in the general Chinese population. cache = ./cache/cord-350443-ca5avyjf.txt txt = ./txt/cord-350443-ca5avyjf.txt === reduce.pl bib === id = cord-354790-xx6imhzb author = Lambour, Jennifer title = Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play date = 2016-08-17 pages = extension = .txt mime = text/plain words = 6499 sentences = 324 flesch = 33 summary = 31 In addition to controlling the viral propagation by these mechanisms, the opsonization of viral particles and/or infected cells by therapeutic antiviral mAbs of the IgG type leads to the formation of immune complexes (ICs) recognizable by the FcγRs expressed on antigen-presenting cells (APCs) such as DCs. This can potentially affect the endogenous antiviral adaptive immune response of passive immunotherapy-treated individuals. Moreover, as the in vivo activity of anti-HIV-1 bNAbs, including viral load control, was recently shown to crucially depend on Fc effector functions, 53,54 an important issue is identifying that Fc-FcγRs interactions are involved in the induction of vaccinelike effects by antiviral mAbs. To understand the mechanisms underlying the enhancement of antiviral responses by ICs, several in vitro studies have addressed whether antibody-mediated viral uptake by DCs could lead to stronger activation of these cells and the development of stronger virus-specific CD4 + and CD8 + T-cell responses in an Fc-dependent manner. cache = ./cache/cord-354790-xx6imhzb.txt txt = ./txt/cord-354790-xx6imhzb.txt === reduce.pl bib === id = cord-355439-eqtk51q3 author = Lesko, Catherine R title = HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date = 2020-07-22 pages = extension = .txt mime = text/plain words = 3288 sentences = 154 flesch = 46 summary = Surveillance data, such as those available from South Africa or Wuhan, will provide the most complete picture of COVID-19 risk among PLWH (e.g., by not restricting to PLWH who are in care and who are more likely to have wellcontrolled HIV disease); however clinical data, such as those from Madrid, may provide the most depth (e.g., by allowing examination of the role of comorbidities, medications, and COVID-19 treatments) as long as potential selection bias is considered. Despite some good telehealth outcomes for some PLWH, telehealth has the potential to exacerbate disparities in care for people with lower socio-economic status: lack of necessary technology and services, technology literacy, and safe, confidential surroundings to participate fully in telehealth may be barriers to engagement in care (32 distancing restrictions if they need to go outside their homes to access alcohol or other drugs, or critically, medication assisted treatments (such as methadone or buprenorphine). cache = ./cache/cord-355439-eqtk51q3.txt txt = ./txt/cord-355439-eqtk51q3.txt === reduce.pl bib === id = cord-354974-bh2expef author = Peterson, Ingrid title = Respiratory Virus–Associated Severe Acute Respiratory Illness and Viral Clustering in Malawian Children in a Setting With a High Prevalence of HIV Infection, Malaria, and Malnutrition date = 2016-09-13 pages = extension = .txt mime = text/plain words = 3863 sentences = 192 flesch = 45 summary = BACKGROUND: We used data from 4 years of pediatric severe acute respiratory illness (SARI) sentinel surveillance in Blantyre, Malawi, to identify factors associated with clinical severity and coviral clustering. A total of 605 SARI cases (26.8%) had warning signs, which were positively associated with HIV infection (adjusted risk ratio [aRR], 2.4; 95% confidence interval [CI], 1.4–3.9), respiratory syncytial virus infection (aRR, 1.9; 95% CI, 1.3–3.0) and rainy season (aRR, 2.4; 95% CI, 1.6–3.8). In the context of a low-income population with multiple drivers of immune compromise (eg, human immunodeficiency virus [HIV] infection, malnutrition, and malaria) [11] , we conducted active surveillance at a large urban teaching hospital in Malawi to estimate the incidence of childhood SARI and explore the association of SARI clinical severity with HIV infection and clustering of respiratory viral coinfection. After adjustment for age, sex, and HIV status, rainy season recruitment was significantly associated with SARI with warning signs in influenza virus-positive patients with SARI (aRR, 3.42; 95% CI, 1.37-8.53; analysis not shown). cache = ./cache/cord-354974-bh2expef.txt txt = ./txt/cord-354974-bh2expef.txt === reduce.pl bib === id = cord-347992-coby2m6e author = Marton, Soledad title = In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules date = 2010-06-28 pages = extension = .txt mime = text/plain words = 10035 sentences = 535 flesch = 45 summary = Although ribozymes and DNAzymes have been extensively assayed as potential therapeutic agents, and different clinical trials have already tested their efficiency against various diseases [49] [50] [51] [52] , very few reports have described the direct application of in vitro selection strategies in the development of potentially therapeutic catalytic nucleic acids. Molecular studies have shown that this aptamer binds to the cell surface protein nucleolin and inhibits the activity of NF-KB, a ubiquitous transcription factor, through intracellular complex formation [108] . In a different approach, SELEX has been performed with the E2F1 protein to find in vitro selected RNA aptamers that bind to and inhibit E2F activity. Astier-Gi's group described the characterization of two DNA aptamers (27v and 127v) that specifically bind to hepatitis C virus (HCV) RNA polymerase (NS5B), inhibiting its activity in vitro [146] . In vitro selection procedures for identifying DNA and RNA aptamers targeted to nucleic acids and proteins cache = ./cache/cord-347992-coby2m6e.txt txt = ./txt/cord-347992-coby2m6e.txt === reduce.pl bib === id = cord-354029-mp5r82g4 author = Earp, L. J. title = The Many Mechanisms of Viral Membrane Fusion Proteins date = 2005 pages = extension = .txt mime = text/plain words = 12130 sentences = 702 flesch = 50 summary = Despite their differences, common principles for how fusion proteins function are emerging: In response to an activating trigger, the metastable fusion protein converts to an extended, in some cases rodlike structure, which inserts into the target membrane via its fusion peptide. Although several viral fusion proteins, such as influenza hemagglutinin (HA) and the human immunodeficiency virus (HIV) envelope glycoprotein (Env), have emerged as paradigms, it is important to realize that there are many distinguishing features among viral fusion proteins (Table 1 ). We now review a lipid rearrangement model and focus on the roles of different regions of viral fusion proteins in choreographing the structural changes that the membranes undergo throughout the fusion cascade (Fig. 3) . Cellular membrane-binding ability of the C-terminal cytoplasmic domain of human immunodeficiency virus type 1 envelope transmembrane protein gp41 Role of the N-terminal peptides of viral envelope proteins in membrane fusion cache = ./cache/cord-354029-mp5r82g4.txt txt = ./txt/cord-354029-mp5r82g4.txt === reduce.pl bib === id = cord-355541-5sctqkwr author = Alcamí, José title = Current situation in the development of a preventive HIV vaccine date = 2005-07-31 pages = extension = .txt mime = text/plain words = 7258 sentences = 310 flesch = 39 summary = This review analyses the major challenges in developing an aids vaccine, in particular the mechanisms involved in viral escape from the immune response, and summarizes the results obtained with the different prototypes of therapeutic and preventive vaccines. In order to develop a vaccine, it is necessary to know the genes of the pathogen involved in the induction of a specific immune response, and to use experimental models to test the efficacy of the virus. The most conclusive experimental data on the role of the cellular response in the control of viral replication come from studies in which selective depletion of CD8 lymphocytes in macaques infected with SIV leads to a huge increase in viremia and accelerated evolution to aids 22 . These types of preparation have failed as preventive vaccines in animal models, since they have not achieved protective immunity, probably due to the fact that the humoral response induced against HIV proteins is erratic and of reduced potency. cache = ./cache/cord-355541-5sctqkwr.txt txt = ./txt/cord-355541-5sctqkwr.txt === reduce.pl bib === id = cord-355318-qm79gz8w author = Smit, Albertus J. title = Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date = 2020-08-05 pages = extension = .txt mime = text/plain words = 15419 sentences = 706 flesch = 41 summary = Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Thus, if climate factors do play a role in COVID-19 infection rates, the concurrence of transition of southern hemisphere countries to their winter season with the mid-stages of the disease transmission trajectory is of concern, especially with respect to containment policy and health system resource allocation. Environmental variables considered in preprint and peer-reviewed publications as modulators of SARS-CoV-2 transmission rates include mean, minimum and/or maximum daily temperature, and diurnal temperature range; an undefined 'humidity' variable, relative humidity, specific humidity and absolute humidity; dew point temperature; rainfall; wind speed or wind power; air pressure; some metric of solar or UV radiation; and 'air quality' (Supplementary Tables S1 and S2 ). The general prevalence of climatologically-coupled seasonal signals and environmental variable modulation seen in the majority of other viral respiratory diseases creates the expectation for a similar effect on SARS-CoV-2 and in COVID-19 epidemiology. cache = ./cache/cord-355318-qm79gz8w.txt txt = ./txt/cord-355318-qm79gz8w.txt === reduce.pl bib === id = cord-347710-ff64y6ef author = Wan, Qianya title = Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date = 2020-07-13 pages = extension = .txt mime = text/plain words = 36567 sentences = 2487 flesch = 46 summary = hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. cache = ./cache/cord-347710-ff64y6ef.txt txt = ./txt/cord-347710-ff64y6ef.txt === reduce.pl bib === id = cord-010119-t1x9gknd author = nan title = Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date = 2017-09-04 pages = extension = .txt mime = text/plain words = 230193 sentences = 13234 flesch = 55 summary = Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). cache = ./cache/cord-010119-t1x9gknd.txt txt = ./txt/cord-010119-t1x9gknd.txt === reduce.pl bib === id = cord-350569-dtxtjtfo author = Kasoka, Kasoka title = Autonomy in HIV testing: a call for a rethink of personal autonomy in the HIV response in sub-Saharan Africa date = 2020-06-13 pages = extension = .txt mime = text/plain words = 13925 sentences = 639 flesch = 51 summary = In most SSA countries the ethic or value of personal autonomy or self-determination is promoted as primary in HIV testing decision-making. Without rethinking the value of autonomy in HIV testing decision-making, the article cautions that attainment of the Sustainable Development Goal (SDG) 3 and the UNAIDS fast-track strategy that explicitly call to end the epidemic by 2030 will not be feasible for SSA. 9 My article interrogates the personal autonomy arguments and reaches a conclusion that the philosophy surrounding the value is problematic, as well as, it is silent on the ethics of the actual implications of an autonomous decision in HIV testing (Selemogo 2010) . HIV testing ethics, in particular informed consent requirements that are now premised on personal autonomy, should reflect a human being who is unique and yet a creature of the inescapable inculcating environment that makes her the 'I That Is We'. cache = ./cache/cord-350569-dtxtjtfo.txt txt = ./txt/cord-350569-dtxtjtfo.txt === reduce.pl bib === id = cord-350571-6tapkjb6 author = nan title = 45th ESCP-NSF international symposium on clinical pharmacy: clinical pharmacy tackling inequalities and access to health care. Oslo, Norway, 5–7 October 2016 date = 2017-01-10 pages = extension = .txt mime = text/plain words = 106013 sentences = 6203 flesch = 48 summary = Possible solutions might be to use shared communication tools like Internet based communication programs and to introduce the patient as a participant at the IMRs. Please specify your abstract type: Research abstract Background and objective: International good pharmacy practice guidelines describe how pharmacists should counsel the patients about their medicines, offer additional services where needed, and intervene at drug related problems. Please specify your abstract type: Descriptive abstract (for projects) Background and objective: In order to improve the medication reconciliation and to implement training programs for the medical team in an associated to general hospital nursing (ASNH) home we measured the discrepancies between pharmacy registered treatments (PRT) and medical prescriptions (MP), and we analysed potentially inappropriate prescriptions according to ''American Geriatrics Society 2015 Beers Criteria'' and ''STOPP-START 2014 criteria. cache = ./cache/cord-350571-6tapkjb6.txt txt = ./txt/cord-350571-6tapkjb6.txt ===== Reducing email addresses cord-004575-b0t6bsya cord-009891-gqrhbhbn cord-020010-q58x6xb0 cord-027242-7qq82j2f cord-261382-cyty5noi cord-260422-z22t57ju cord-271188-ewlxy5po cord-283346-0v4b6do2 cord-304873-ppb9k3zu cord-306315-vt2e0crh cord-326558-6tss9ydx cord-331673-xv1tcugl cord-325300-wawui0fd cord-329890-wg23sa1u cord-337720-kmwft059 cord-342076-3a6aky7i Creating transaction Updating adr 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table Building ./etc/reader.txt cord-022633-fr55uod6 cord-015324-y44sfr0c cord-350571-6tapkjb6 cord-339879-92esdjy9 cord-316534-ep7ezoko cord-022521-r72jtoso number of items: 549 sum of words: 4,110,563 average size in words: 14,322 average readability score: 46 nouns: patients; virus; cells; infection; cell; blood; study; disease; results; treatment; protein; health; data; viruses; risk; use; infections; expression; time; type; studies; analysis; activity; group; therapy; methods; proteins; response; children; years; system; cases; levels; transfusion; antibodies; patient; care; number; drug; host; diseases; donors; control; vaccine; antibody; replication; role; population; plasma; gene verbs: used; showed; included; increasing; associated; based; infected; found; compared; reported; developed; binding; identified; induced; follow; provided; reduced; cause; required; suggested; performed; treated; determine; related; led; die; tested; occurred; observed; detected; result; demonstrated; containing; expressed; inhibited; gave; makes; mediating; involve; evaluating; received; improve; presented; indicated; known; targeting; described; obtained; producing; derived adjectives: viral; human; high; clinical; specific; immune; anti; positive; different; new; antiviral; non; significant; low; first; important; many; higher; negative; severe; infectious; respiratory; several; acute; effective; common; chronic; renal; cellular; similar; single; primary; early; major; potential; small; available; molecular; large; multiple; lower; medical; bacterial; recent; normal; possible; active; present; public; therapeutic adverbs: also; however; well; significantly; respectively; therefore; highly; even; often; previously; recently; still; especially; usually; less; currently; particularly; now; directly; furthermore; prior; moreover; approximately; first; mainly; generally; together; potentially; frequently; commonly; specifically; later; finally; rather; clinically; yet; relatively; interestingly; almost; least; rapidly; much; already; indeed; alone; far; similarly; widely; additionally; successfully pronouns: we; it; their; our; its; they; i; them; he; his; her; she; us; your; itself; you; one; themselves; my; me; him; ha3; himself; ourselves; s; herself; oneself; myself; ifitm3; mg; iga1; yourself; m19fc; esat-6; p210bcr; mrnas; 's; isgf3; em; ours; ns3/4a; netmhcpan4.0; igg1; ifitms; theirs; p24ag; nr-818; imagej; hers; trim21 proper nouns: HIV; HIV-1; RNA; AIDS; T; HCV; CD4; C; SARS; der; B; Health; PCR; HBV; Fig; IFN; China; mg; A; COVID-19; Africa; DNA; RBC; TB; ED; •; von; United; University; M; mit; HLA; II; CMV; bei; CCR5; CD8; Summary; D; DC; gp120; Ebola; eine; G; States; Table; RT; und; Study; CoV-2 keywords: hiv; hiv-1; virus; rna; aids; cell; sars; hcv; infection; covid-19; cd4; patient; dna; disease; study; hbv; pcr; viral; health; protein; vaccine; africa; die; cmv; result; der; ifn; human; hla; antibody; united; method; group; china; art; antiviral; und; test; drug; child; ccr5; university; research; hospital; ebola; blood; treatment; states; response; immune one topic; one dimension: hiv file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808385/ titles(s): Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals three topics; one dimension: patients; hiv; der file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159364/, https://doi.org/10.1016/b978-0-12-380860-8.00004-5, https://api.elsevier.com/content/article/pii/B9783437428319100130 titles(s): SAEM Abstracts, Plenary Session | Cell Entry of Enveloped Viruses | KAPITEL 13 Infektionskrankheiten five topics; three dimensions: virus hiv cells; blood patients results; patients infection hiv; hiv health aids; der evs die file(s): https://doi.org/10.1016/b978-0-12-380860-8.00004-5, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087899/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140236/, https://api.elsevier.com/content/article/pii/B9783437428319100130 titles(s): Cell Entry of Enveloped Viruses | EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS | Infections gastro-intestinales chez le patient immunocompromis | Is universal access to antiretroviral drugs an emerging international norm? | KAPITEL 13 Infektionskrankheiten Type: cord title: keyword-hiv-cord date: 2021-05-25 time: 00:10 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:hiv ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-034269-gqy61g8l author: Abayneh, Kinfe title: Clients’ Satisfaction with Services for Prevention of Mother-to-Child Transmission of HIV in Public Health Facilities in Diredawa City, Eastern Ethiopia date: 2020-10-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Ethiopia has a very high burden of HIV infection among children, contracted from their mothers, and nearly two-thirds of pregnant women do not receive prevention of mother-to-child transmission (PMTCT) services. Ensuring clients’ satisfaction with PMTCT services is one of the bases to scale up service utilization and mitigate MTCT of HIV. However, in Ethiopia, particularly in the study area, evidence related to clients’ satisfaction with PMTCT services is scanty. METHODS: A facility-based cross-sectional study was conducted among women attending antenatal care in Diredawa city. Systematic random sampling was used to select 517 study participants. Interviewer-administered structured and pretested questionnaires were used to collect data. Statistical significance was regarded as P≤0.05 with a 95% CI. RESULTS: Client satisfaction with PMTCT services was 82.2% (95% CI 66.4%–94.3). Receiving the service from a hospital (AOR 2.34; 95% CI 1.5, 3.98), no formal education (AOR 2.53, 95% CI 1.52–4.2), primary education (AOR 2.17 95% CI 1.17–4.04), receiving pre- and post-HIV test counseling from the same provider (AOR 4.93, 95% CI 2.98–7.17), gestational age above first trimester (AOR 1.74, 95% CI 1.12–2.71), and waiting time ≤15 minutes (AOR 2.31, 95% CI 1.28–4.16) were positively associated with client satisfaction with PMTCT services. CONCLUSION: Client satisfaction with PMTCT services is relatively high. Receiving the service from a hospital, no formal education or only primary education, gestational age above first trimester, getting pre- and post-HIV test counseling from the same provider, and waiting time ≤15 minutes to receive services were factors associated with client satisfaction. A greater number of skilled PMTCT-service providers would improve service quality and hasten its delivery. Furthermore, providing mentoring and supportive supervision of health centers with PMTCT programs and keeping the same provider in posttest counseling is also mandatory. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585811/ doi: 10.2147/hiv.s264854 id: cord-021382-10omkpwl author: Abdul-Khaliq, Catherine title: Development of a United Kingdom National External Quality Assessment Scheme (UK NEQAS) for HIV point of care testing date: 2011-03-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The use of HIV point of care tests (POCTs) is increasing rapidly in both laboratory and other settings. These tests are often performed by non-laboratory trained staff. At the present time there are no external quality assessment (EQA) providers in the UK offering proficiency testing schemes for HIV point of care testing. The aim of this study is to develop such an EQA scheme. Firstly, a selection of the most widely used POCTs was selected and their performance assessed using existing HIV-positive serology EQA specimens. All assays produced the correct results however intensity of results observed for the same specimen differed greatly between POCT devices. In addition the effect of various sub-groups of HIV-1 serum samples on the HIV POCT assays was investigated and no difference between the results on the POCTs was observed. Ultimately four serum specimens, two HIV-1 and one HIV-2 positive, one HIV negative, were chosen and sent to NHS laboratories and sexual health clinics for testing as part of a pilot EQA scheme for HIV POCT. Results were excellent with 97% of participants reporting correct results (n= 20). The study highlighted a lack of awareness of EQA particularly in non-laboratory settings, although recommendations (ISO 22870:2006) are in place for the users of such devices. In conclusion, the need for EQA for providers of point of care testing is an integral part of ensuring reliability of results and quality of care for the patient. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149475/ doi: 10.1093/biohorizons/hzr004 id: cord-302928-nnly9ju8 author: Adachi, Akio title: Grand Challenge in Human/Animal Virology: Unseen, Smallest Replicative Entities Shape the Whole Globe date: 2020-03-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32256480/ doi: 10.3389/fmicb.2020.00431 id: cord-009388-k3exf8a4 author: Agarwal, Yash title: Moving beyond the mousetrap: current and emerging humanized mouse and rat models for investigating prevention and cure strategies against HIV infection and associated pathologies date: 2020-04-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The development of safe and effective combination antiretroviral therapies for human immunodeficiency virus (HIV) infection over the past several decades has significantly reduced HIV-associated morbidity and mortality. Additionally, antiretroviral drugs have provided an effective means of protection against HIV transmission. Despite these advances, significant limitations exist; namely, the inability to eliminate HIV reservoirs, the inability to reverse lymphoid tissues damage, and the lack of an effective vaccine for preventing HIV transmission. Evaluation of the safety and efficacy of therapeutics and vaccines for eliminating HIV reservoirs and preventing HIV transmission requires robust in vivo models. Since HIV is a human-specific pathogen, that targets hematopoietic lineage cells and lymphoid tissues, in vivo animal models for HIV-host interactions require incorporation of human hematopoietic lineage cells and lymphoid tissues. In this review, we will discuss the construction of mouse models with human lymphoid tissues and/or hematopoietic lineage cells, termed, human immune system (HIS)-humanized mice. These HIS-humanized mouse models can support the development of functional human innate and adaptive immune cells, along with primary (thymus) and secondary (spleen) lymphoid tissues. We will discuss applications of HIS-humanized mouse models in evaluating the safety and efficacy of therapeutics against HIV reservoirs and associated immunopathology, and delineate the human immune response elicited by candidate HIV vaccines. In addition to focusing on how these HIS-humanized mouse models have already furthered our understanding of HIV and contributed to HIV therapeutics development, we discuss how emerging HIS-humanized rat models could address the limitations of HIS-mouse models. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149862/ doi: 10.1186/s12977-020-00515-3 id: cord-284128-3obc5k5u author: Ahmed, Ali title: Concerns of HIV-positive migrant workers in COVID-19 pandemic: A call for action date: 2020-09-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33110542/ doi: 10.7189/jogh.10.020342 id: cord-005327-bt7o8yxk author: Ahn, Insung title: Epidemiological comparisons of codon usage patterns among HIV-1 isolates from Asia, Europe, Africa and the Americas date: 2006-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: To investigate the genomic properties of HIV-1, we collected 3,081 sequences from the HIV Sequence Database. The sequences were categorized according to sampling region, country, year, subtype, gene name, and sequence and were saved in a database constructed for this study. The relative synonymous codon usage (RSCU) values of matrix, capsid, and gp120 and gp41 genes were calculated using correspondence analysis. The synonymous codon usage patterns based on the geographical regions of African countries showed broad distributions; when all the other regions, including Asia, Europe, and the Americas, were taken into account, the Asian countries tended to be divided into two groups. The sequences were clustered into nine non-CRF subtypes. Among these, subtype C showed the most distinct codon usage pattern. To determine why the codon usage patterns in Asian countries were divided into two groups for four target genes, the sequences of the isolates from the Asian countries were analyzed. As a result, the synonymous codon usage patterns among Asian countries were divided into two groups, the southern Asian countries and the other Asian countries, with subtype 01_AE being the most dominant subtype in southern Asia. In summary, the synonymous codon usage patterns among the individual HIV-1 subtypes reflect genetic variations, and this bioinformatics technique may be useful in conjunction with phylogenetic methods for predicting the evolutionary patterns of pandemic viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090625/ doi: 10.1038/emm.2006.76 id: cord-278876-il7g78w1 author: Akkina, Ramesh title: 2016 International meeting of the Global Virus Network date: 2017-03-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The Global Virus Network (GVN) was established in 2011 in order to strengthen research and responses to current viral causes of human disease and to prepare against new viral pandemic threats. There are now 38 GVN Centers of Excellence and 6 Affiliate laboratories in 24 countries. GVN scientists meet annually to learn about each other's current research, address collaborative priorities and plan future programs. The 2016 meeting was held from October 23–25 in Hokkaido, Japan, in partnership with the Japanese Society for Virology, the National Institute of Infectious Diseases of Japan and the Research Center for Zoonosis Control of Hokkaido University. This report highlights the accomplishments of GVN researchers in many priority areas of medical virology, including the current Zika epidemic, infections by human papillomavirus, influenza, Ebola, Lassa, dengue, HIV, hepatitis C, and chikungunya viruses, and the development of improved diagnostics and new vaccines. url: https://doi.org/10.1016/j.antiviral.2017.03.005 doi: 10.1016/j.antiviral.2017.03.005 id: cord-287754-dh6abx2t author: Akkouh, Ouafae title: Lectins with Anti-HIV Activity: A Review date: 2015-01-06 words: 6947.0 sentences: 380.0 pages: flesch: 45.0 cache: ./cache/cord-287754-dh6abx2t.txt txt: ./txt/cord-287754-dh6abx2t.txt summary: Examples of lectins that exhibit antiviral activity and bind high-mannose carbohydrates are jacalin [25] , concanavalin A [26] , Urtica diocia agglutinin [27] , Myrianthus holstii lectin, P. The mannose-specific plant lectins Hippeastrum hybrid agglutinin, Galanthus nivalis agglutinin, Narcissus pseudonarcissus agglutinin; Cymbidium agglutinin; cyanovirin-N; and N-acetylglucosamine specific Urtica dioica agglutinin efficiently abrogate dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN)-directed HIV-1 capture and subsequent transmission to T lymphocytes [55] . The nematode (Laxus oneistus) Ca 2+ -dependent C-type lectin Mermaid, a structural homologue of DC-SIGN devoid of cytotoxicity, shares the glycan specificity with DC-SIGN, interacts with high mannose structures on gp120 and prevents HIV-1 binding to DC-SIGN on DCs. Mermaid inhibits DC-SIGN-mediated HIV-1 transmission from DC to T cells. Discovery of cyanovirin-N, a novel human immunodeficiency virus-inactivating protein that binds viral surface envelope glycoprotein gp120: Potential applications to microbicide development The high mannose-type glycan binding lectin actinohivin: Dimerization greatly improves anti-HIV activity abstract: Lectins including flowering plant lectins, algal lectins, cyanobacterial lectins, actinomycete lectin, worm lectins, and the nonpeptidic lectin mimics pradimicins and benanomicins, exhibit anti-HIV activity. The anti-HIV plant lectins include Artocarpus heterophyllus (jacalin) lectin, concanavalin A, Galanthus nivalis (snowdrop) agglutinin-related lectins, Musa acuminata (banana) lectin, Myrianthus holstii lectin, Narcissus pseudonarcissus lectin, and Urtica diocia agglutinin. The anti-HIV algal lectins comprise Boodlea coacta lectin, Griffithsin, Oscillatoria agardhii agglutinin. The anti-HIV cyanobacterial lectins are cyanovirin-N, scytovirin, Microcystis viridis lectin, and microvirin. Actinohivin is an anti-HIV actinomycete lectin. The anti-HIV worm lectins include Chaetopterus variopedatus polychaete marine worm lectin, Serpula vermicularis sea worm lectin, and C-type lectin Mermaid from nematode (Laxus oneistus). The anti-HIV nonpeptidic lectin mimics comprise pradimicins and benanomicins. Their anti-HIV mechanisms are discussed. url: https://doi.org/10.3390/molecules20010648 doi: 10.3390/molecules20010648 id: cord-355541-5sctqkwr author: Alcamí, José title: Current situation in the development of a preventive HIV vaccine date: 2005-07-31 words: 7258.0 sentences: 310.0 pages: flesch: 39.0 cache: ./cache/cord-355541-5sctqkwr.txt txt: ./txt/cord-355541-5sctqkwr.txt summary: This review analyses the major challenges in developing an aids vaccine, in particular the mechanisms involved in viral escape from the immune response, and summarizes the results obtained with the different prototypes of therapeutic and preventive vaccines. In order to develop a vaccine, it is necessary to know the genes of the pathogen involved in the induction of a specific immune response, and to use experimental models to test the efficacy of the virus. The most conclusive experimental data on the role of the cellular response in the control of viral replication come from studies in which selective depletion of CD8 lymphocytes in macaques infected with SIV leads to a huge increase in viremia and accelerated evolution to aids 22 . These types of preparation have failed as preventive vaccines in animal models, since they have not achieved protective immunity, probably due to the fact that the humoral response induced against HIV proteins is erratic and of reduced potency. abstract: The uncontrolled progression of the aids epidemic has made the development of an efficacious human immunodeficiency virus (HIV) vaccine a major objective of scientific research. No effective preventive vaccine against HIV is currently available and sterilizing immunity has not yet been achieved in animal models. This review analyses the major challenges in developing an aids vaccine, in particular the mechanisms involved in viral escape from the immune response, and summarizes the results obtained with the different prototypes of therapeutic and preventive vaccines. Finally, social, economic and healthcare aspects of research into HIV vaccines and current controversies regarding the development of clinical trials are discussed. url: https://api.elsevier.com/content/article/pii/S0213005X05751570 doi: 10.1016/s0213-005x(05)75157-0 id: cord-034714-6e37yylk author: Alleg, Manel title: Progressive multifocal leukoencephalopathy: MRI findings in HIV-infected patients are closer to rituximab- than natalizumab-associated PML date: 2020-11-06 words: 3746.0 sentences: 170.0 pages: flesch: 37.0 cache: ./cache/cord-034714-6e37yylk.txt txt: ./txt/cord-034714-6e37yylk.txt summary: title: Progressive multifocal leukoencephalopathy: MRI findings in HIV-infected patients are closer to rituximabthan natalizumab-associated PML OBJECTIVES: To compare brain MRI findings in progressive multifocal leukoencephalopathy (PML) associated to rituximab and natalizumab treatments and HIV infection. Inclusion criteria were (1) a "definite" PML diagnosis according to the American Academy of Neurology criteria [19] including clinical and imaging-compatible features and detection of JCV DNA in the cerebrospinal fluid or in brain tissue by polymerase chain reaction (PCR) or immunohistochemistry; (2) HIV-infected patients or patients treated with immunomodulatory or immunosuppressive drugs such as natalizumab or rituximab, possibly in association with other drugs and whatever the initial illness; and (3) consent was provided for in the hospital''s charter. This study aims to describe the MRI characteristics of PML associated with rituximab and natalizumab and in HIV infection while comparing imaging findings with the level of immunosuppression. abstract: OBJECTIVES: To compare brain MRI findings in progressive multifocal leukoencephalopathy (PML) associated to rituximab and natalizumab treatments and HIV infection. MATERIALS AND METHODS: In this retrospective, multicentric study, we analyzed brain MRI exams from 72 patients diagnosed with definite PML: 32 after natalizumab treatment, 20 after rituximab treatment, and 20 HIV patients. We compared T2- or FLAIR-weighted images, diffusion-weighted images, T2*-weighted images, and contrast enhancement features, as well as lesion distribution, especially gray matter involvement. RESULTS: The three PML entities affect U-fibers associated with low signal intensities on T2*-weighted sequences. Natalizumab-associated PML showed a punctuate microcystic appearance in or in the vicinity of the main PML lesions, a potential involvement of the cortex, and contrast enhancement. HIV and rituximab-associated PML showed only mild contrast enhancement, punctuate appearance, and cortical involvement. The CD4/CD8 ratio showed a trend to be higher in the natalizumab group, possibly mirroring a more efficient immune response. CONCLUSION: Imaging features of rituximab-associated PML are different from those of natalizumab-associated PML and are closer to those observed in HIV-associated PML. KEY POINTS: • Nowadays, PML is emerging as a complication of new effective therapies based on monoclonal antibodies. • Natalizumab-associated PML shows more inflammatory signs, a perivascular distribution “the milky way,” and more cortex involvement than rituximab- and HIV-associated PML. • MRI differences are probably related to higher levels of immunosuppression in HIV patients and those under rituximab therapy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7644389/ doi: 10.1007/s00330-020-07362-y id: cord-302784-jkjdglns author: Alotaibi, Badriah title: Management of hospitalized drug sensitive pulmonary tuberculosis patients during the Hajj mass gathering: A cross sectional study date: 2019-07-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: To document the management of drug-sensitive TB patients during the Hajj and assess compliance with the Saudi TB management guidelines. METHOD: The study was conducted in hospitals in Makkah during the 2016 and 2017 Hajj seasons. Structured questionnaire was used to collect data on relevant indices on TB management and a scoring system was developed to assess compliance with guidelines. RESULTS: Data was collected from 31 TB cases, 65.4% (17/26) were Saudi residents. Sputum culture was the only diagnostic test applied in 67.7% (21/31) of patients. Most (96.8%, 30/31) confirmed TB cases were isolated, but only 12.9% (4/28) were tested for HIV and merely 37% (10/27) received the recommended four 1st-line anti-TB drugs. Guideline compliance scores were highest for infection prevention and control and surveillance (9.6/10) and identifying TB suspects (7.2/10). The least scores were obtained for treating TB (5.0/10) and diagnosing TB (3.0/10). CONCLUSIONS: Healthcare providers training and supervision are paramount to improve their knowledge and skill and ensure their compliance with existing TB management guidelines. However, there may be a need for the introduction of an international policy/guideline for TB control and management during mass gatherings such as the Hajj to guide providers’ choices and facilitate monitoring. url: https://doi.org/10.1016/j.tmaid.2019.07.007 doi: 10.1016/j.tmaid.2019.07.007 id: cord-334855-s0ci3r8w author: Andersen, Petter I. title: Novel Antiviral Activities of Obatoclax, Emetine, Niclosamide, Brequinar, and Homoharringtonine date: 2019-10-18 words: 4274.0 sentences: 272.0 pages: flesch: 48.0 cache: ./cache/cord-334855-s0ci3r8w.txt txt: ./txt/cord-334855-s0ci3r8w.txt summary: Here, we identified novel activities of obatoclax and emetine against herpes simplex virus type 2 (HSV-2), echovirus 1 (EV1), human metapneumovirus (HMPV) and Rift Valley fever virus (RVFV) in cell cultures. The expected response of the emetine-obatoclax drug combination on the viability of FLUAV-and mock-infected RPE cells was calculated using Bliss reference model [29] . After the initial screening, we identified four compounds (obatoclax, emetine, niclosamide and ganciclovir) that at none-cytotoxic concentrations rescued cells from virus-mediated death (Figure 2A) . Table S1 : Compounds, their suppliers and catalogue numbers; Table S2 : Developmental status of broad-spectrum antivirals used in the study; Table S3 : Human viruses and associated diseases; Figure S1 : The expected response of the emetine-obatoclax drug combination on the viability of FLUAV-and mock-infected RPE cells, as measured with the CTG assay using the Bliss reference model; Figure S2 abstract: Viruses are the major causes of acute and chronic infectious diseases in the world. According to the World Health Organization, there is an urgent need for better control of viral diseases. Repurposing existing antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we identified novel activities of obatoclax and emetine against herpes simplex virus type 2 (HSV-2), echovirus 1 (EV1), human metapneumovirus (HMPV) and Rift Valley fever virus (RVFV) in cell cultures. Moreover, we demonstrated novel activities of emetine against influenza A virus (FLUAV), niclosamide against HSV-2, brequinar against human immunodeficiency virus 1 (HIV-1), and homoharringtonine against EV1. Our findings may expand the spectrum of indications of these safe-in-man agents and reinforce the arsenal of available antiviral therapeutics pending the results of further in vitro and in vivo tests. url: https://doi.org/10.3390/v11100964 doi: 10.3390/v11100964 id: cord-016718-cxn1ewfw author: Anderson, Virginia title: Performing Interventions: The Politics and Theatre of China’s AIDS Crisis in the Early Twenty-First Century date: 2017-11-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Theatrical productions attest to a radical shift in Chinese governmental policy and public awareness of the AIDS epidemic at the dawn of the twenty-first century; state-subsidised theatre worked directly with the government to contain the transmission of HIV. Produced by two of the country’s most elite cultural institutions, the Shanghai Dramatic Arts Center and the Beijing People’s Art Theatre respectively, The Dying Kiss (Shengsi Zhiwen) in 2003 and Student Zhao Ping (Zhao Ping Tongxue) in 2005 represented a sea change in the political response to the epidemic while documenting public perceptions towards people living with HIV and AIDS in China. Marking policy change, they reflect experiences that capture a society transitioning from denial to confrontation at the dawn of the twenty-first century. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121085/ doi: 10.1007/978-3-319-70317-6_9 id: cord-104491-uu2rbtem author: Andiman, Warren A. title: Where Have All the “AIDS Babies” Gone? A Historical Memoir of the Pediatric AIDS Epidemic in New Haven and its Eventual Eradication date: 2020-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: S.L. was one of our first HIV-positive babies. He was born at Yale-New Haven Hospital (YNHH) in 1982. His mother was a sex worker who also injected drugs. He died at 3½ years following multiple episodes of opportunistic infection and metastatic lymphoma. In the years between 1986 and 1990, 163 HIV-positive mothers gave birth at YNHH. The mother-to-child transmission (MTCT) rate was 20 percent. Women represented 8 percent of all HIV cases in the US compared with 29 percent in New Haven. We had a six times greater proportion of children living with HIV. The mean number of HIV-exposed babies rose annually from 26 (1985-87) to 37 (1988-90). Our first team of caregivers comprised a nurse practitioner, a social worker, and me. We were, in time, joined by a growing number of colleagues. Enlightened and generous hospital administrators provided us with outpatient space and the promise of continued funding to support additional staff and in 1987, an independent Pediatric AIDS Care Program. We implemented the proven MTCT prevention guidelines articulated in the Pediatric AIDS Clinical Trials Group (PACTG) protocol 076 and by 1995, the MTCT rate at YNHH fell to 9 percent. Since 1996, the MTCT rate at YNHH has been zero percent. Combination antiretroviral therapy, cART, made its debut in the mid-1990s; five classes of drugs with multiple agents in each were licensed between 2003 and 2013. We designed individual treatment plans for each child and gradually entered an era when our clinic was populated with healthier long-term survivors. Our Program flourished, based on a multidisciplinary approach which honored interprofessional collaboration. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513449/ doi: nan id: cord-283346-0v4b6do2 author: Ansari, Abdul Wahid title: Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals date: 2006-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Several cytokines and chemokines including chemokine (C-C motif) ligand-2 (CCL2) are induced in HIV-1 infection. However, the impact of HIV-1 viremia on CCL2 regulation is largely unknown. We utilized a DNA oligonucleotide microarray covering 110 inflammatory genes. Five genes were induced by at least 2-fold in PBMCs of HIV-1 viremic (>100.000 RNA copies ml(−1)) as compared with aviremic (<50 RNA copies ml(−1)) individuals. These genes were CCL2, CXC chemokine ligand-10, IFN-γ, GTP-cyclohydrolase-1 and C-C chemokine receptor-1. In addition to microarray data verification by real-time PCR, analysis of independent patient samples revealed a similar expression pattern. CCL2 was the most strongly regulated gene at mRNA level and its serum concentration was significantly elevated in viremic compared with aviremic and HIV-1 seronegative controls, indicating a positive correlation between viremia and CCL2. Flow cytometric studies demonstrated a higher percentage of CCL2-expressing CD14+ monocytes in viremic compared with aviremic individuals. These results suggest a highly restricted modulation of host inflammatory gene response by HIV. Genes up-regulated in the viremic state, in particular CCL2, presumably serve as potential enhancing factors in HIV-1 replication, represented by high viral load in HIV-1 viremic patients. Inhibition of increased CCL2 production could provide a new therapeutic intervention in HIV-1 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/16916890/ doi: 10.1093/intimm/dxl078 id: cord-002746-qn34eyul author: Antzin-Anduetza, Irati title: Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication date: 2017-11-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) structural protein Gag is necessary and sufficient to form viral particles. In addition to encoding the amino acid sequence for Gag, the underlying RNA sequence could encode cis-acting elements or nucleotide biases that are necessary for viral replication. Furthermore, RNA sequences that inhibit viral replication could be suppressed in gag. However, the functional relevance of RNA elements and nucleotide biases that promote or repress HIV-1 replication remain poorly understood. RESULTS: To characterize if the RNA sequence in gag controls HIV-1 replication, the matrix (MA) region was codon modified, allowing the RNA sequence to be altered without affecting the protein sequence. Codon modification of nucleotides (nt) 22-261 or 22-378 in gag inhibited viral replication by decreasing genomic RNA (gRNA) abundance, gRNA stability, Gag expression, virion production and infectivity. Comparing the effect of these point mutations to deletions of the same region revealed that the mutations inhibited infectious virus production while the deletions did not. This demonstrated that codon modification introduced inhibitory sequences. There is a much lower than expected frequency of CpG dinucleotides in HIV-1 and codon modification introduced a substantial increase in CpG abundance. To determine if they are necessary for inhibition of HIV-1 replication, codons introducing CpG dinucleotides were mutated back to the wild type codon, which restored efficient Gag expression and infectious virion production. To determine if they are sufficient to inhibit viral replication, CpG dinucleotides were inserted into gag in the absence of other changes. The increased CpG dinucleotide content decreased HIV-1 infectivity and viral replication. CONCLUSIONS: The HIV-1 RNA sequence contains low abundance of CpG dinucleotides. Increasing the abundance of CpG dinucleotides inhibits multiple steps of the viral life cycle, providing a functional explanation for why CpG dinucleotides are suppressed in HIV-1. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12977-017-0374-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679385/ doi: 10.1186/s12977-017-0374-1 id: cord-334104-mphz1aye author: Apisarnthanarak, Anucha title: Etiology of Community-Acquired Pneumonia date: 2005-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Community-acquired pneumonia (CAP) is a serious lower respiratory tract infection associated with significant morbidity and mortality that is characterized by disputes over diagnostic evaluations and therapeutic decisions. With the widespread use of broad-spectrum antimicrobial agents and the increasing number of immunocompromised hosts, the etiology and the drug resistance patterns of pathogens responsible for CAP have changed. Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis remain the leading causes of CAP in immunocompetent patients. Opportunistic infections with organisms such as Pneumocystis jiroveci and Mycobacterium tuberculosis and other opportunistic fungal pneumonias should also be considered in the differential diagnosis of CAP in immunocompromised patients. This article examines the current peer-reviewed literature on etiology, risk factors, and outcomes of patients with CAP. url: https://api.elsevier.com/content/article/pii/S0272523104001042 doi: 10.1016/j.ccm.2004.10.016 id: cord-008530-yni0poh9 author: Asensio, Valerie C. title: Chemokines and viral diseases of the central nervous system date: 2004-01-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter discusses chemokines and their receptors in the evolution of viral infectious diseases of the central nervous system (CNS). Infection of the human CNS with many different viruses or infection of the rodent CNS induces vigorous host-inflammatory responses with recruitment of large numbers of leukocytes, particularly T lymphocytes and macrophages. Chemokines coordinate trafficking of peripheral blood leukocytes by stimulating their chemotaxis, adhesion, extravasation, and other effector functions. In view of these properties, research efforts have turned increasingly to the possible involvement of chemokines in regulating both peripheral tissue and CNS leukocyte migration during viral infection. The biological effects of chemokines are mediated via their interaction with receptors belonging to the family of seven transmembrane (7TM)-spanning, G-protein coupled receptors (GPCRs). In the normal mammalian CNS, the number of leukocytes present in the brain is scant. However, these cells are attracted to, and accumulate in, a variety of pathologic states, many involving viral infection. Although leukocyte migration into local tissue compartments, such as the CNS, is a multifactorial process, it has become clear that chemokines are pivotal components of this process, providing a necessary chemotactic signal for leukocyte recruitment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131585/ doi: 10.1016/s0065-3527(01)56006-6 id: cord-324034-6cmztvyf author: Ashare, Rebecca L title: The United States National Cancer Institute’s Coordinated Research Effort on Tobacco Use as a Major Cause of Morbidity and Mortality among People with HIV date: 2020-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The use of antiretroviral therapy (ART) for people with HIV (PWH) has improved life expectancy. However, PWH now lose more life-years to tobacco use than to HIV infection. Unfortunately, PWH smoke at higher rates and have more difficulty maintaining abstinence than the general population, compounding their risk for chronic disease. In this Commentary, we describe a United States National Cancer Institute (NCI)-led initiative to address the relative lack of research focused on developing, testing, and implementing smoking cessation interventions for PWH. This initiative supports seven clinical trials designed to systematically test and/or develop and test adaptations of evidence-based smoking cessation interventions for PWH (e.g., combination of behavioral and pharmacological). We summarize each project, including setting/recruitment sites, inclusion/exclusion criteria, interventions being tested, and outcomes. This initiative provides critical opportunities for collaboration and data harmonization across projects. The knowledge gained will inform strategies to assist PWH to promote and maintain abstinence, and ensure that these efforts are adaptable and scalable, thereby addressing one of the major threats to the health of PWH. Reducing smoking behavior may be particularly important during the COVID-19 pandemic given that smokers who become infected with SARS-CoV-2 may be at risk for more severe disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32803251/ doi: 10.1093/ntr/ntaa155 id: cord-319043-hczwgf6o author: Ashkenazi, Avraham title: Sphingopeptides: dihydrosphingosine-based fusion inhibitors against wild-type and enfuvirtide-resistant HIV-1 date: 2012-08-07 words: 5676.0 sentences: 309.0 pages: flesch: 50.0 cache: ./cache/cord-319043-hczwgf6o.txt txt: ./txt/cord-319043-hczwgf6o.txt summary: We hypothesized that by minimizing the affinity of the peptides to the viral fusion site (using short fragments from the core); we would mainly identify the contribution of the conjugated lipid moiety to antiviral activity. This exclusive inhibitory activity of sphinganine-based peptides (sphingopeptides) was further observed in a wider spectrum of viral entry systems, consisting of different HIV strains (wildtype HXB2 and LAI) and different target cells (TZM-bl reporter cells and Jurkat T cells), as well as in cell-cell fusion assay (Fig. 2) . Thus, we hypothesized that its dihydrosphingosine (sphinganine) backbone may penetrate into the site of membrane fusion mediated by the HIV Env. To investigate this, we conjugated sphinganine as well as other lipids to short, otherwise inert, peptides from the HIV-1 Env core and their antiviral activities were investigated in several types of HIV-1 infection assays. abstract: Understanding the structural organization of lipids in the cell and viral membranes is essential for elucidating mechanisms of viral fusion that lead to entry of enveloped viruses into their host cells. The HIV lipidome shows a remarkable enrichment in dihydrosphingomyelin, an unusual sphingolipid formed by a dihydrosphingosine backbone. Here we investigated the ability of dihydrosphingosine to incorporate into the site of membrane fusion mediated by the HIV envelope (Env) protein. Dihydrosphingosine as well as cholesterol, fatty acid, and tocopherol was conjugated to highly conserved, short HIV-1 Env-derived peptides with no antiviral activity otherwise. We showed that dihydrosphingosine exclusively endowed nanomolar antiviral activity to the peptides (IC(50) as low as 120 nM) in HIV-1 infection on TZM-bl cells and on Jurkat T cells, as well as in the cell-cell fusion assay. These sphingopeptides were active against enfuvirtide-resistant and wild-type CXCR4 and CCR5 tropic HIV strains. The anti-HIV activity was determined by both the peptides and their dihydrosphingosine conjugate. Moreover, their mode of action involved accumulation in the cells and viruses and binding to membranes enriched in sphingomyelin and cholesterol. The data suggest that sphingopeptides are recruited to the HIV membrane fusion site and provide a general concept in developing inhibitors of sphingolipid-mediated biological systems.—Ashkenazi, A., Viard, M., Unger, L., Blumenthal, R., Shai, Y. Sphingopeptides: dihydrosphingosine-based fusion inhibitors against wild-type and enfuvirtide-resistant HIV-1. url: https://www.ncbi.nlm.nih.gov/pubmed/22872679/ doi: 10.1096/fj.12-215111 id: cord-295290-hs5ntlok author: Atlan, H. title: Mechanisms of autoimmunity and AIDS: prospects for therapeutic intervention date: 1994-12-31 words: 9832.0 sentences: 424.0 pages: flesch: 38.0 cache: ./cache/cord-295290-hs5ntlok.txt txt: ./txt/cord-295290-hs5ntlok.txt summary: Based on this hypothesis, a T-cell vaccination procedure against effector T cells responsible for autoimmunopathic activity in HIV-seropositive patients is proposed, similar to the one known from experimental study of autoimmunity and presently being tested in human autoimmune diseases. These include cross-reactive recognition of self-MHC and a secondary antiidiotypic response to CD4, to be found in the first large set of references mentioned above, elimination of infected T4 cells by virus-specific, HLArestricted cytotoxic lymphocytes (Shearer, 1986; Zinkernagel, 1988) , elimination of uninfected T4 cells by immune responses directed against HIV (Klatzmann and Gluckman, 1986; Salk, 1987; Lyerly et al., 1987; Lanzavecchia et al., 1988; Lanzavecchia, 1989 ; Siliciano et al., 1988 ; Israel-Biet et al., 1990 ; Morrow et al., 1991) and/or T4 cell antigens (Stricker et al., 1987; Martinez-A. Autoimmunopathic destruction of T4 cells might thus result, in this case, from the destabilization of a self-tolerance-maintaining regulatory network by immune responses to HIV components with homologies to antigens normally present on T4 cells. abstract: Summary The network theory of autoimmunity is presented with recent experimental data relevant to the understanding of the pathogenesis of AIDS. Schematically, effector T cells specific for self-antigens exist normally, but their activity is modulated and prevented by networks of regulatory T cells. As a result of mimicry between molecular components of microorganisms and self-antigens, autoimmune disease can be triggered by specific foreign pathogens which alter the state of activity of the network from suppression to activation. Conversely, by a procedure known as T-cell vaccination, autologous effector T cells re-injected after in vitro stimulation and attenuation may alter the state of the network from an activation to a suppression. Numerous observations are reviewed that support the concept of autoimmune activity in the destruction of non-infected T4 cells. Such activity is presumed to be triggered by an antigen of viral origin, the most likely, but not the only one, being the envelope protein gp120. Based on this hypothesis, a T-cell vaccination procedure against effector T cells responsible for autoimmunopathic activity in HIV-seropositive patients is proposed, similar to the one known from experimental study of autoimmunity and presently being tested in human autoimmune diseases. Its purpose would be to prevent T-cell loss and the onset of immunodeficiency disease in HIV-seropositive patients. Apart from its potential therapeutic value, this procedure will have use as a therapeutic test from which insight will be gained about the immunopathogenesis of AIDS. url: https://www.ncbi.nlm.nih.gov/pubmed/7991942/ doi: 10.1016/s0923-2494(94)80181-9 id: cord-032504-tmohg1mj author: Auld, Sara C. title: HIV and the tuberculosis “set point”: how HIV impairs alveolar macrophage responses to tuberculosis and sets the stage for progressive disease date: 2020-09-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: As HIV has fueled a global resurgence of tuberculosis over the last several decades, there is a growing awareness that HIV-mediated impairments in both innate and adaptive immunity contribute to the heightened risk of tuberculosis in people with HIV. Since early immune responses to Mycobacterium tuberculosis (Mtb) set the stage for subsequent control or progression to active tuberculosis disease, early host–pathogen interactions following Mtb infection can be thought of as establishing a mycobacterial “set point,” which we define as the mycobacterial burden at the point of adaptive immune activation. This early immune response is impaired in the context of HIV coinfection, allowing for a higher mycobacterial set point and greater likelihood of progression to active disease with greater bacterial burden. Alveolar macrophages, as the first cells to encounter Mtb in the lungs, play a critical role in containing Mtb growth and establishing the mycobacterial set point. However, a number of key macrophage functions, ranging from pathogen recognition and uptake to phagocytosis and microbial killing, are blunted in HIV coinfection. To date, research evaluating the effects of HIV on the alveolar macrophage response to Mtb has been relatively limited, particularly with regard to the critical early events that help to dictate the mycobacterial set point. A greater understanding of alveolar macrophage functions impacted by HIV coinfection will improve our understanding of protective immunity to Mtb and may reveal novel pathways amenable to intervention to improve both early immune control of Mtb and clinical outcomes for the millions of people worldwide infected with HIV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509826/ doi: 10.1186/s12977-020-00540-2 id: cord-004031-sw60qbbj author: Aylward, Ryan E. title: Risk factors and outcomes of acute kidney injury in South African critically ill adults: a prospective cohort study date: 2019-12-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: There is a marked paucity of data concerning AKI in Sub-Saharan Africa, where there is a substantial burden of trauma and HIV. METHODS: Prospective data was collected on all patients admitted to a multi-disciplinary ICU in South Africa during 2017. Development of AKI (before or during ICU admission) was recorded and renal recovery 90 days after ICU discharge was determined. RESULTS: Of 849 admissions, the mean age was 42.5 years and mean SAPS 3 score was 48.1. Comorbidities included hypertension (30.5%), HIV (32.6%), diabetes (13.3%), CKD (7.8%) and active tuberculosis (6.2%). The most common reason for admission was trauma (26%). AKI developed in 497 (58.5%). Male gender, illness severity, length of stay, vasopressor drugs and sepsis were independently associated with AKI. AKI was associated with a higher in-hospital mortality rate of 31.8% vs 7.23% in those without AKI. Age, active tuberculosis, higher SAPS 3 score, mechanical ventilation, vasopressor support and sepsis were associated with an increased adjusted odds ratio for death. HIV was not independently associated with AKI or hospital mortality. CKD developed in 14 of 110 (12.7%) patients with stage 3 AKI; none were dialysis-dependent. CONCLUSIONS: In this large prospective multidisciplinary ICU cohort of younger patients, AKI was common, often associated with trauma in addition to traditional risk factors and was associated with good functional renal recovery at 90 days in most survivors. Although the HIV prevalence was high and associated with higher mortality, this was related to the severity of illness and not to HIV status per se. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902455/ doi: 10.1186/s12882-019-1620-7 id: cord-291577-nf80kih2 author: Baluku, Joseph Baruch title: HIV and SARS‐CoV‐2 co‐infection: A case report from Uganda date: 2020-05-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: There are no reports of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and HIV co‐infection from sub‐Saharan Africa where 70% of people living with HIV are found. We report a case of HIV/SARS‐CoV‐2 co‐infection from Uganda. A 34 year old HIV‐positive female on antiretroviral therapy (tenofovir disoproxil fumarate, lamivudine and efavirenz) for 5 years, tested positive for SARS‐CoV‐2, the causative agent for coronavirus disease 19 (COVID‐19). She was asymptomatic at presentation but subsequently developed headache, chest pain, diarrhoea, anorexia and fatigue on day 3 of isolation without cough, fever or shortness of breath. Her CD4 count was 965 cells/mm(3), the HIV viral load was undetectable (<1,000 cells/mm(3)) and other laboratory work up was normal. She was successfully managed with hydroxychloroquine and broad spectrum antibiotics, and was discharged after 24 days. This case demonstrates an atypical clinical presentation of COVID – 19 in an HIV infected patient without other co‐morbidity. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26044 doi: 10.1002/jmv.26044 id: cord-342936-43u7afl3 author: Balzarini, Jan title: Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy date: 2007 words: 11304.0 sentences: 534.0 pages: flesch: 44.0 cache: ./cache/cord-342936-43u7afl3.txt txt: ./txt/cord-342936-43u7afl3.txt summary: Perhaps more importantly, such carbohydrate-binding agents (CBAs) may force the virus to delete at least part of its glycan shield to escape drug pressure 5 ; this might result in the initiation of an immune response against uncovered immunogenic envelope epitopes. Although such a mechanism may be efficient for a first-line inactivation of HIV, CBA-exposed HIV strains may decrease the efficiency of LCs to eliminate HIV, but at the same time may compromise the ability of the virus to be efficiently transmitted by DCs. The interactions of several CBAs have been extensively investigated, including: the prokaryotic CV-N and actinohivin; a variety of plant lectins, including Hippeastrum hybrid agglutinin (HHA) and UDA; the non-peptidic low-molecular-weight antibiotic PRM-A; and the monoclonal antibody 2G12 with the HIV-envelope gp120 and/or several glycan structures. abstract: Several chronic viral infections (such as HIV and hepatitis C virus) are highly prevalent and are a serious health risk. The adaptation of animal viruses to the human host, as recently exemplified by influenza viruses and the severe acute respiratory syndrome coronavirus, is also a continuous threat. There is a high demand, therefore, for new antiviral lead compounds and novel therapeutic concepts. In this Review, an original therapeutic concept for suppressing enveloped viruses is presented that is based on a specific interaction of carbohydrate-binding agents (CBAs) with the glycans present on viral-envelope glycoproteins. This approach may also be extended to other pathogens, including parasites, bacteria and fungi. url: https://www.ncbi.nlm.nih.gov/pubmed/17632570/ doi: 10.1038/nrmicro1707 id: cord-320116-63yvpuqx author: Bancroft, Tara title: Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes date: 2019-10-07 words: 11866.0 sentences: 656.0 pages: flesch: 55.0 cache: ./cache/cord-320116-63yvpuqx.txt txt: ./txt/cord-320116-63yvpuqx.txt summary: Immunization with a multimerized version of this anti-idiotype induced the proliferation of transgenic murine B cells expressing the iglb12 heavy chain in vivo, despite the presence of deletion and anergy within this population. Using anti-idiotypes specific for the inferred germline version of b12 (iglb12) as baits for single B cell sorting, we identified a subset of human germline BCRs using V H 1-3 with some heavy chain CDRH3 similarity to iglb12. Identification of iglb12-like BCRs using anti-iglb12 idiotypes We next assessed whether the anti-iglb12 idiotypes could be used to identify B cells expressing iglb12-like BCRs from within the polyclonal human B cell repertoire of HIV-uninfected individuals using single B cell sorting followed by RT-PCR amplification and sequencing of heavy and light chain genes. To our knowledge, this study represents the first time antiidiotypes have been used to identify and analyze naive B cells expressing BCRs with similarities to the inferred germline sequence of a broadly neutralizing HIV-1-specific antibody. abstract: Many tested vaccines fail to provide protection against disease despite the induction of antibodies that bind the pathogen of interest. In light of this, there is much interest in rationally designed subunit vaccines that direct the antibody response to protective epitopes. Here, we produced a panel of anti-idiotype antibodies able to specifically recognize the inferred germline version of the human immunodeficiency virus 1 (HIV-1) broadly neutralizing antibody b12 (iglb12). We determined the crystal structure of two anti-idiotypes in complex with iglb12 and used these anti-idiotypes to identify rare naive human B cells expressing B cell receptors with similarity to iglb12. Immunization with a multimerized version of this anti-idiotype induced the proliferation of transgenic murine B cells expressing the iglb12 heavy chain in vivo, despite the presence of deletion and anergy within this population. Together, our data indicate that anti-idiotypes are a valuable tool for the study and induction of potentially protective antibodies. url: https://www.ncbi.nlm.nih.gov/pubmed/31345930/ doi: 10.1084/jem.20190164 id: cord-334010-gxu0refq author: Banerjee, Nilotpal title: Viral glycoproteins: biological role and application in diagnosis date: 2016-01-18 words: 6657.0 sentences: 406.0 pages: flesch: 46.0 cache: ./cache/cord-334010-gxu0refq.txt txt: ./txt/cord-334010-gxu0refq.txt summary: The sema-domain is the [18, 43] Fusion with host cell membrane Sialic Acid and attachment [43] 3-5 million cases Worldwide [78, 105] SARS-CoV Spike(S) glycoprotein [25, 115] Membrane fusion [115] 8422 within the duration of 1st November 2002 to 7th August 2003 occurring worldwide [113, 114] Hepatitis C virus E1 and E2 [55, 98] Binding to Host receptor and Conformational change necessary for membrane fusion [98] 130 to 150 million people globally [103, 106] Human immunodeficiency virus 1 gp120, gp160, gp41 [16] Intracellular transport [16] 35 million globally up to 2013 [83, 104, 108, 112] Zaire Ebola virus Spike Protein Gp1-Gp2 [64] Primary Host cell activation [64] up to 28th June 2015 total 27,550 cases [107, 110, 111] Dengue virus E (dimer) [64] Host cell fusion and attachment [64] WHO reported recently that there are 390 million dengue infections per year globally [109] . abstract: The viruses that infect humans cause a huge global disease burden and produce immense challenge towards healthcare system. Glycoproteins are one of the major components of human pathogenic viruses. They have been demonstrated to have important role(s) in infection and immunity. Concomitantly high titres of antibodies against these antigenic viral glycoproteins have paved the way for development of novel diagnostics. Availability of appropriate biomarkers is necessary for advance diagnosis of infectious diseases especially in case of outbreaks. As human mobilization has increased manifold nowadays, dissemination of infectious agents became quicker that paves the need of rapid diagnostic system. In case of viral infection it is an emergency as virus spreads and mutates very fast. This review encircles the vast arena of viral glycoproteins, their importance in health and disease and their diagnostic applications. url: https://www.ncbi.nlm.nih.gov/pubmed/26925438/ doi: 10.1007/s13337-015-0293-5 id: cord-016313-n4ewq0pt author: Baranyi, Lajos title: Advances in Lentiviral Vector-based Cell Therapy with Mesenchymal Stem Cells date: 2012-09-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The field of possible application of mesenchymal stem cells in medicine and research expanded tremendously with the advent of improved Lentiviral-vectors capable of inserting stable copies of genes of interest and expressing proteins or biologically active RNA species ad libitum, performing delicate gene editing or active gene silencing or serving as advanced drug delivery systems utilized in ex vivo cell therapy. The combination of these two fields has created a number of new areas of research in the landscape of modern medicine which are now extensively studied and discussed here. These areas include tissue engineering, tissue repair, wound healing and tissue implants, anticancer therapies, angiogenesis, myocardial infarction and repair as well as understanding and treating acute lung damage and injury. In addition, genetically modified, tagged MSCs are being intensively deployed in research and therapeutic attempts of the various ailments of the central nervous system including Parkinson’s disease, Alzheimer’s disease, various phases of acute ischemia and trauma. The emergence of new and important data for type II diabetes research is being followed with treatment suggestions and studies of senescence to find novel applications for genetically engineered MSCs. We find in ­general that genetically modified MSCs are at the cusp of breaking through from basic research into the next phase of clinical trials. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120558/ doi: 10.1007/978-1-62703-200-1_14 id: cord-005585-lc3fqhb0 author: Barbier, François title: Etiologies and outcome of acute respiratory failure in HIV-infected patients date: 2009-07-03 words: 4236.0 sentences: 209.0 pages: flesch: 45.0 cache: ./cache/cord-005585-lc3fqhb0.txt txt: ./txt/cord-005585-lc3fqhb0.txt summary: OBJECTIVE: To assess the etiologies and outcome of acute respiratory failure (ARF) in HIV-infected patients over the first decade of combination antiretroviral therapy (ART) use. Acute respiratory failure (ARF) is the leading reason for intensive care unit (ICU) admission in HIV-infected patients, with bacterial pneumonia and Pneumocystis jirovecii pneumonia (PCP) accounting for most cases [1] [2] [3] [4] [5] [6] [7] [8] . Significant results HIV human immunodeficiency syndrome, ICU intensive care unit, PCP Pneumocystis jirovecii pneumonia, IRIS immune restorationinduced syndrome, ARF acute respiratory failure, COPD chronic obstructive pulmonary disease, AIDS acquired immunodeficiency syndrome a Clinically documented bacterial pneumonia was defined as an appropriate history and response to empiric antimicrobial therapy with focal pneumonia on chest X-ray, and either septic shock or predominantly neutrophils on BAL fluid examination, without documented bacterial pathogen b Including co-infection with Haemophilus influenzae (n = 1) and Staphylococcus aureus (n = 1) c Including co-infection with Streptococcus pneumonia (n = 1) and S. abstract: OBJECTIVE: To assess the etiologies and outcome of acute respiratory failure (ARF) in HIV-infected patients over the first decade of combination antiretroviral therapy (ART) use. METHODS: Retrospective study of all HIV-infected patients (n = 147) admitted to a single intensive care unit (ICU) for ARF between 1996 and 2006. RESULTS: ARF revealed the diagnosis of HIV infection in 43 (29.2%) patients. Causes of ARF were bacterial pneumonia (n = 74), Pneumocystis jirovecii pneumonia (PCP, n = 52), other opportunistic infections (n = 19), and noninfectious pulmonary disease (n = 33); the distribution of causes did not change over the 10-year study period. Two or more causes were identified in 33 patients. The 43 patients on ART more frequently had bacterial pneumonia and less frequently had opportunistic infections (P = 0.02). Noninvasive ventilation was needed in 49 patients and endotracheal intubation in 42. Hospital mortality was 19.7%. Factors independently associated with mortality were mechanical ventilation [odds ratio (OR) = 8.48, P < 0.0001], vasopressor use (OR, 4.48; P = 0.03), time from hospital admission to ICU admission (OR, 1.05 per day; P = 0.01), and number of causes (OR, 3.19; P = 0.02). HIV-related variables (CD4 count, viral load, and ART) were not associated with mortality. CONCLUSION: Bacterial pneumonia and PCP remain the leading causes of ARF in HIV-infected patients in the ART era. Hospital survival has improved, and depends on the extent of organ dysfunction rather than on HIV-related characteristics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094937/ doi: 10.1007/s00134-009-1559-4 id: cord-286352-uftl1mx5 author: Baril, Martin title: The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot date: 2003-08-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Human immunodeficiency virus type 1 (HIV-1) requires a programmed −1 ribosomal frameshift to produce Gag–Pol, the precursor of its enzymatic activities. This frameshift occurs at a slippery sequence on the viral messenger RNA and is stimulated by a specific structure, downstream of the shift site. While in group M, the most abundant HIV-1 group, the frameshift stimulatory signal is an extended bulged stem-loop, we show here, using a combination of mutagenesis and probing studies, that it is a pseudoknot in group O. The mutagenesis and probing studies coupled to an in silico analysis show that group O pseudoknot is a hairpin-type pseudoknot with two coaxially stacked stems of eight base-pairs (stem 1 and stem 2), connected by single-stranded loops of 2nt (loop 1) and 20nt (loop 2). Mutations impairing formation of stem 1 or stem 2 of the pseudoknot reduce frameshift efficiency, whereas compensatory changes that allow re-formation of these stems restore the frameshift efficiency to near wild-type level. The difference between the frameshift stimulatory signal of group O and group M supports the hypothesis that these groups originate from a different monkey to human transmission. url: https://www.sciencedirect.com/science/article/pii/S0022283603007848 doi: 10.1016/s0022-2836(03)00784-8 id: cord-256786-7gca01lr author: Bartilotti‐Matos, F title: Pearls and Pitfalls: two contrasting HIV diagnoses in the COVID‐19 era and the case for screening date: 2020-08-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The risk of coronavirus disease 2019 (COVID‐19) for people living with HIV (PLWH) is poorly understood. The vast majority of reported cases of COVID‐19/HIV co‐infection consists of those with an established HIV diagnosis who are on anti‐retroviral therapy (ART). Better knowledge of the effects of COVID19 on HIV patients who are ART naïve is required. Two cases of previously undiagnosed HIV presenting to secondary care with respiratory symptoms are detailed in this series, with a view to extrapolate lessons on blood borne virus (BBV) screening in the COVID‐19 era. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32790222/ doi: 10.1002/jmv.26428 id: cord-027659-rxbo7b0e author: Bates, Imelda title: Blood Transfusion date: 2020-06-22 words: 4169.0 sentences: 211.0 pages: flesch: 49.0 cache: ./cache/cord-027659-rxbo7b0e.txt txt: ./txt/cord-027659-rxbo7b0e.txt summary: Hospital-based transfusion services place an enormous burden on laboratory resources and on the families of patients because they are responsible for fi nding suitable blood donors. 2 In wealthy countries with nationally or regionally centralized transfusion services, blood donor recruitment, and screening and processing of donated blood, are carried out in purpose-built centres which are separate from the hospitals where the blood is transfused. Infections with organisms that are common in tropical countries, such as HIV-1 and -2, hepatitis A, B, C and D, cytomegalovirus, syphilis, lyme borreliosis, malaria, babesiosis, American trypanosomiasis (Chagas'' disease) and toxoplasmosis, can all be acquired through blood transfusions. Further research to assess the risks and benefi ts of screening blood for malaria is needed, particularly in relation to pregnant women and patients with HIV infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310926/ doi: 10.1016/b978-1-4160-4470-3.50018-5 id: cord-005833-fizh495d author: Baumschlager, D. title: Emotionale Befindlichkeit, kognitive Leistungsfähigkeit und Lebensqualität bei HIV-Patienten: Ergebnisse einer explorativen Untersuchung date: 2010-09-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Due to the change of HIV disease from an acute life-threatening disease to a chronic infection, it is more psychosocial rather than therapeutic aspects that have become of interest in scientific investigations. The purpose of this exploratory study was to evaluate emotional distress, health-related quality of life (HRQoL) and cognitive performance. The diagnosis of HIV was considered a life event that may lead to post-traumatic stress syndrome. METHOD: We recruited 37 HIV-positive outpatients and assessed the frequency of depressive (BDI) and post-traumatic stress symptoms (PTSS) due to the diagnosis of HIV (IES), HRQoL (SF-36) and cognitive performance (SKT). Further, the new diagnostic concept of adjustment disorder as a stress response syndrome according to Maercker was considered. RESULTS: Of the 37 Patients, 67.6% (n=25) of the sample had a post-traumatic stress syndrome. The HIV-related PTSS was considered adjustment disorder using the concept proposed by Maercker. Fourteen patients (37.8%) suffered from a depressive syndrome, and 27% (n=10) showed cognitive deficits (minimal: n=8; mild: n=1; moderate: n =1). HIV-positive patients with PTSS had significantly unfavourable values in the SF-36 domains general health (p=0.003), vitality (p=0.007), social functioning (p=0.000), role-emotional (p=0.016) and mental health (p=0.000). CONCLUSION: HIV-infected patients may face a major risk of HIV-related PTSS in the sense of adjustment disorder according to Maercker, depression and cognitive dysfunction. The presence of emotional distress is associated with impairments in quality of life. We therefore suggest an early and comprehensive bio-psycho-social assessment and therapy of HIV-infected patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095816/ doi: 10.1007/s00115-010-3124-3 id: cord-253426-s57wuzyg author: Benkovic, Scott title: 4 Cases: HIV and SARS‐CoV‐2 Co‐infection in patients from Long Island, New York date: 2020-05-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Originating from Wuhan, China, the novel coronavirus 2019 (SARS‐CoV‐2) has been spreading worldwide since the end of 2019. The most common features of these patients include fever, cough, myalgia or fatigue [1]. As of April 16, 2020 the CDC has reported 605,390 cases and 24,582 deaths in the United States. The illness continues to spread through the world infecting people with various different comorbid conditions. Presented here are four cases which represent some of the first cases of HIV and SARS‐CoV‐2 coinfection in Long Island, New York. These HIV infected patients were compliant with their HIV medication regimen and had robust CD4 T cell counts. The clinical severity ranged from mild to requiring hospitalization. Three of the four patients had fever and two had cough. One patient presented with diarrhea, the incidence rate of diarrhea in SARS‐CoV‐2 infection range from 2% to 50% of cases [4]. One patient had anosmia and aguesia, in a study by Moein et al, the 98% of SARS‐CoV‐2 infected patient experienced some smell dysfunction [5]. One patient required hospitalization however this patient was also infected with influenza A. These cases suggest that uncomplicated cases of SARS‐CoV‐2 in an HIV infected patient can be managed with self‐isolation at home. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32427361/ doi: 10.1002/jmv.26029 id: cord-329361-0mpbau1b author: Bennasser, Yamina title: RNAi Therapy for HIV Infection: Principles and Practicalities date: 2012-08-16 words: 2645.0 sentences: 200.0 pages: flesch: 56.0 cache: ./cache/cord-329361-0mpbau1b.txt txt: ./txt/cord-329361-0mpbau1b.txt summary: Inside eukaryotic cells, small RNA duplexes, called small interfering RNAs (siRNAs), activate a conserved RNA interference (RNAi) pathway which leads to specific degradation of complementary target mRNAs through base-pairing recognition. The practical use of RNAi therapy for HIV infection will depend on overcoming several challenges, including the ability to establish long-term expression of siRNA without off-target effects and the capacity to counteract mutant escape viruses. [4] Hence, in plants and Drosophila, when a cell they have sequence specificity for silencing mRNAs, these small is infected by a virus, an RNAi response is triggered by the foreign RNAs potentially represent a future class of antiviral drugs. [42] silencing of viral RNA and transient suppression of HIV replicaobserved that an siRNA targeted to nef rapidly elicited the emertion over a period of 3 to 4 days in single round infection of gence of siRNA-resistant viruses with point mutations in the nef cultured cells have been achieved. abstract: Inside eukaryotic cells, small RNA duplexes, called small interfering RNAs (siRNAs), activate a conserved RNA interference (RNAi) pathway which leads to specific degradation of complementary target mRNAs through base-pairing recognition. As with other viruses, studies have shown that replication of the HIV-1 in cultured cells can be targeted and inhibited by synthetic siRNAs. The relative ease of siRNA design and the versatility of RNAi to target a broad spectrum of mRNAs have led to the promise that drug discovery in the RNAi pathway could be effective against pathogens. This review discusses the current experimental principles that guide the application of RNAi against HIV and describes challenges and limitations that need to be surmounted in order for siRNAs to become practical antiviral drugs. The practical use of RNAi therapy for HIV infection will depend on overcoming several challenges, including the ability to establish long-term expression of siRNA without off-target effects and the capacity to counteract mutant escape viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17263586/ doi: 10.2165/00063030-200721010-00003 id: cord-000638-ss1435el author: Beq, Stephanie title: Altered Thymic Function during Interferon Therapy in HCV-Infected Patients date: 2012-04-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Interferon alpha (IFNα) therapy, despite good efficacy in curing HCV infection, leads to major side effects, in particular inducement of a strong peripheral T-cell lymphocytopenia. We here analyze the early consequences of IFNα therapy on both thymic function and peripheral T-cell homeostasis in patients in the acute or chronic phase of HCV-infection as well as in HIV/HCV co-infected patients. The evolution of T-cell subsets and T-cell homeostasis were estimated by flow cytometry while thymic function was measured through quantification of T-cell receptor excision circles (TREC) and estimation of intrathymic precursor T-cell proliferation during the first four months following the initiation of IFNα therapy. Beginning with the first month of therapy, a profound lymphocytopenia was observed for all T-cell subsets, including naïve T-cells and recent thymic emigrants (RTE), associated with inhibition of intrathymic precursor T-cell proliferation. Interleukin (IL)-7 plasma concentration rapidly dropped while lymphocytopenia progressed. This was neither a consequence of higher consumption of the cytokine nor due to its neutralization by soluble CD127. Decrease in IL-7 plasma concentration under IFNα therapy correlated with the decline in HCV viral load, thymic activity and RTE concentration in blood. These data demonstrate that IFNα-based therapy rapidly impacts on thymopoiesis and, consequently, perturbs T-cell homeostasis. Such a side effect might be detrimental for the continuation of IFNα therapy and may lead to an increased level of infectious risk, in particular in HIV/HCV co-infected patients. Altogether, this study suggests the therapeutic potential of IL-7 in the maintenance of peripheral T-cell homeostasis in IFNα-treated patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328332/ doi: 10.1371/journal.pone.0034326 id: cord-318272-spt0oea0 author: Bhardwaj, Prateek title: Advancements in prophylactic and therapeutic nanovaccines date: 2020-04-05 words: 14561.0 sentences: 732.0 pages: flesch: 32.0 cache: ./cache/cord-318272-spt0oea0.txt txt: ./txt/cord-318272-spt0oea0.txt summary: ''Nanovaccines'' have been explored to elicit a strong immune response with the advantages of nano-sized range, high antigen loading, enhanced immunogenicity, controlled antigen presentation, more retention in lymph nodes and promote patient compliance by a lower frequency of dosing. The role of different nanovaccines in activating various arms of immunity with an intent to abate the use of frequent booster doses as vaccines for tuberculosis, malaria, HIV (human immunodeficiency virus), influenza, and cancer are discussed. Polyanhydride-based nanoparticles encapsulating F1-V antigen when administered intranasally induced an immune response that persisted for 23 weeks and elicited a high anti-F1-V IgG1 antibody response post-vaccination and conferred long-lived protective immunity against Yersinia pestis infections compared to recombinant F1-V antigen [47] . Another interesting strategy for developing personalized biomimetic cancer nanovaccines is the use of cancer cell membrane coated virus for increased adjuvanticity, infectivity and oncolytic activities to generate a strong anti-tumor immune response. abstract: Vaccines activate suitable immune responses to fight against diseases but can possess limitations such as compromised efficacy and immunogenic responses, poor stability, and requirement of adherence to multiple doses. ‘Nanovaccines’ have been explored to elicit a strong immune response with the advantages of nano-sized range, high antigen loading, enhanced immunogenicity, controlled antigen presentation, more retention in lymph nodes and promote patient compliance by a lower frequency of dosing. Various types of nanoparticles with diverse pathogenic or foreign antigens can help to overcome immunotolerance and alleviate the need of booster doses as required with conventional vaccines. Nanovaccines have the potential to induce both cell-mediated and antibody-mediated immunity and can render long-lasting immunogenic memory. With such properties, nanovaccines have shown high potential for the prevention of infectious diseases such as acquired immunodeficiency syndrome (AIDS), malaria, tuberculosis, influenza, and cancer. Their therapeutic potential has also been explored in the treatment of cancer. The various kinds of nanomaterials used for vaccine development and their effects on immune system activation have been discussed with special relevance to their implications in various pathological conditions. STATEMENT OF SIGNIFICANCE: Interaction of nanoparticles with the immune system has opened multiple avenues to combat a variety of infectious and non-infectious pathological conditions. Limitations of conventional vaccines have paved the path for nanomedicine associated benefits with a hope of producing effective nanovaccines. This review highlights the role of different types of nanovaccines and the role of nanoparticles in modulating the immune response of vaccines. The applications of nanovaccines in infectious and non-infectious diseases like malaria, tuberculosis, AIDS, influenza, and cancers have been discussed. It will help the readers develop an understanding of mechanisms of immune activation by nanovaccines and design appropriate strategies for novel nanovaccines. url: https://www.sciencedirect.com/science/article/pii/S1742706120301616 doi: 10.1016/j.actbio.2020.03.020 id: cord-309515-0pxl0sta author: Blanco, Jose L title: COVID-19 in patients with HIV: clinical case series date: 2020-04-15 words: 1009.0 sentences: 71.0 pages: flesch: 58.0 cache: ./cache/cord-309515-0pxl0sta.txt txt: ./txt/cord-309515-0pxl0sta.txt summary: 3 Here we describe, to our knowledge, the first single-centre experience of COVID-19 in patients infected with HIV-1, including clinical characteristics, antiviral and antiretroviral treatment, and outcomes. We explained to patients treated with ART that we were making a transitional change in their regimen on the basis of the fact that HIV protease inhibitors might have activity against the have sex with men (MSM). Additionally, Janssen reported on March 18, 2020, that darunavir was ineffective against SARS-CoV-2 due to low affinity to coronavirus protease. Fourth, we did not give our patients remdesivir, the most active in-vitro and in-vivo antiviral drug against coronavirus to date, 5 and is currently only available through clinical trials or for compassionate use. By generating information such as we present here, the management and prognosis of patients co-infected with HIV and SARS-CoV-2 might be improved. Co-infection of SARS-CoV-2 and HIV in a patient in Wuhan city abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32304642/ doi: 10.1016/s2352-3018(20)30111-9 id: cord-276870-gxtvlji7 author: Bobrowski, Tesia title: Learning from history: do not flatten the curve of antiviral research! date: 2020-07-15 words: 5089.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-276870-gxtvlji7.txt txt: ./txt/cord-276870-gxtvlji7.txt summary: Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. However, despite many experimental and clinical studies, no effective drugs or treatments have emerged to treat the previous six epidemics of bird flu, SARS, swine flu, MERS, Ebola, and Zika as well as, thus far, COVID-19. We evaluated the number of publications (in both peer-reviewed journals and ArXiv preprint servers) and the number of clinical trials performed over the course of the epidemic to estimate the engagement and success of the scientific community in response to the seven major outbreaks of the past two decades: bird flu, SARS, swine flu, MERS, Ebola, Zika, and COVID-19. abstract: Here, we explore the dynamics of the response of the scientific community to several epidemics, including Coronavirus 2019 (COVID-19), as assessed by the numbers of clinical trials, publications, and level of research funding over time. All six prior epidemics studied [bird flu, severe acute respiratory syndrome (SARS), swine flu, Middle East Respiratory Syndrome (MERS), Ebola, and Zika] were characterized by an initial spike of research response that flattened shortly thereafter. Unfortunately, no antiviral medications have been discovered to date as treatments for any of these diseases. By contrast, the HIV/AIDS pandemic has garnered consistent research investment since it began and resulted in drugs being developed within 7 years of its start date, with many more to follow. We argue that, to develop effective treatments for COVID-19 and be prepared for future epidemics, long-term, consistent investment in antiviral research is needed. url: https://doi.org/10.1016/j.drudis.2020.07.008 doi: 10.1016/j.drudis.2020.07.008 id: cord-025628-9611eglg author: Bonagura, Vincent Robert title: Infections that cause secondary immune deficiency date: 2020-05-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Discriminating between patients with microbial infections that cause secondary immune effects from those with the same infection who have primary immune deficiency disease can be difficult. There are many microbes that temporarily “stun” innate and/or adaptive immunity during a primary infection. The common result of temporary inhibition, or permanent depletion of host immunity during some primary infections is the development of superinfections of other microbes that cause significant morbidity, and on occasion, mortality. In addition, microbes that cause persistent infection, such as the human immune deficiency virus, deplete effective immunity over time and can also lead to secondary infections with other microbes ultimately leading to death if not appropriately treated. In some cases, such as influenza virus infection, mortality can be dramatic due in large part to acquired secondary bacterial infections. Many microbes manipulate host immunity and thereby inhibit the ability of patients to combat secondary microbial infections. The overall survival of patients primarily infected with some viruses, parasites, or bacteria, is closely linked to the ability of secondary infections to take advantage of the immune modulation induced by the primary infection. Herein we discuss some of the secondary immune defects caused by select viruses (measles, influenza, HIV1, HTLV), parasites, (leishmania, malaria), and bacteria (Bordetella pertussis). Furthermore, the genetic susceptibility of a given host to become infected, or develop severe disease, also determines whether an infected individual who becomes infected with a secondary microbe survives. Future studies are needed to explore not only the immunomodulation caused by select microbes, but also the repertoire of immune responses expressed by infected individuals in order to predict clinical outcomes of these infections. Thus, understanding the delicate balance that exists between “immune altering” microbes that suppress immune responses during primary infections leading to severe secondary infections versus those infections found in patients with inborn errors of innate or adaptive immunity, is essential in predicting the clinical outcome and the appropriate treatment for these two different patient populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7258708/ doi: 10.1016/b978-0-12-816768-7.00049-1 id: cord-271970-i35pic5o author: Boris, Bonaventure title: A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor date: 2020-10-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Genome-wide CRISPR/Cas9 knock-out genetic screens are powerful approaches to unravel new regulators of viral infections. With the aim of identifying new cellular inhibitors of HIV-1, we have developed a strategy in which we took advantage of the ability of type 1 interferon (IFN) to potently inhibit HIV-1 infection, in order to create a cellular environment hostile to viral replication. This approach led to the identification of the DEAD-box RNA helicase DDX42 as an intrinsic inhibitor of HIV-1. Depletion of endogenous DDX42 using siRNA or CRISPR/Cas9 knock-out increased HIV-1 infection, both in model cell lines and in physiological targets of HIV-1, primary CD4+ T cells and monocyte-derived macrophages (MDMs), and irrespectively of the IFN treatment. Similarly, the overexpression of a dominant-negative mutant of DDX42 positively impacted HIV-1 infection, whereas wild-type DDX42 overexpression potently inhibited HIV-1 infection. The positive impact of endogenous DDX42 depletion on HIV-1 infection was directly correlated to an increase in viral DNA accumulation. Interestingly, proximity ligation assays showed that DDX42, which can be mainly found in the nucleus but is also present in the cytoplasm, was in the close vicinity of HIV-1 Capsid during infection of primary monocyte-derived macrophages. Moreover, we show that DDX42 is also able to substantially decrease infection with other retroviruses and retrotransposition of long interspersed elements-1 (LINE-1). Finally, we reveal that DDX42 potently inhibits other pathogenic viruses, including Chikungunya virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). url: https://doi.org/10.1101/2020.10.28.359356 doi: 10.1101/2020.10.28.359356 id: cord-279828-es498qul author: Boulle, Andrew title: Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa date: 2020-08-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Risk factors for COVID-19 death in sub-Saharan Africa and the effects of HIV and tuberculosis on COVID-19 outcomes are unknown. METHODS: We conducted a population cohort study using linked data from adults attending public sector health facilities in the Western Cape, South Africa. We used Cox-proportional hazards models adjusted for age, sex, location and comorbidities to examine the association between HIV, tuberculosis and COVID-19 death from 1 March-9 June 2020 among (i) public sector “active patients” (≥1 visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. We calculated the standardized mortality ratio (SMR) for COVID-19 comparing HIV positive vs. negative adults using modelled population estimates. RESULTS: Among 3,460,932 patients (16% HIV positive), 22,308 were diagnosed with COVID-19, of whom 625 died. COVID-19 death was associated with male sex, increasing age, diabetes, hypertension and chronic kidney disease. HIV was associated with COVID-19 mortality (adjusted hazard ratio [aHR] 2.14; 95% confidence interval [CI] 1.70-2.70), with similar risks across strata of viral load and immunosuppression. Current and previous tuberculosis were associated with COVID-19 death (aHR [95%CI] 2.70 [1.81-4.04] and 1.51 [1.18-1.93] respectively). The SMR for COVID-19 death associated with HIV was 2.39 (95%CI 1.96-2.86); population attributable fraction 8.5% (95%CI 6.1-11.1). CONCLUSION: While our findings may over-estimate HIV- and tuberculosis-associated COVID-19 mortality risks due to residual confounding, both HIV and current tuberculosis were independently associated with increased COVID-19 mortality. The associations between age, sex and other comorbidities and COVID-19 mortality were similar to other settings. url: https://www.ncbi.nlm.nih.gov/pubmed/32860699/ doi: 10.1093/cid/ciaa1198 id: cord-294366-swwz4kzd author: Bramwell, Vincent W. title: The rational design of vaccines date: 2005-11-15 words: 4880.0 sentences: 200.0 pages: flesch: 31.0 cache: ./cache/cord-294366-swwz4kzd.txt txt: ./txt/cord-294366-swwz4kzd.txt summary: By definition of perceived need, we are most acutely aware of the requirement of effective vaccines against infectious agents, pathogens ancient, re-emergent and new, yet the opportunities for manipulation of immune responses offer potential in the prevention and treatment of a far larger diversity of diseases. For example, the level of protection required in a population (herd immunity) will be different and this could allow theoretical flexibility in vaccine efficacy.The application of molecular biology techniques can be crucial in the identification of new candidate antigens and subsequent determination of vaccine efficacy using adjuvants can feed knowledge back to correlates of protection in terms of immunological markers.This knowledge can then be used in choice of appropriate adjuvants and formulation.The key implication projected by this schematic is that for the greatest challenges in vaccine development the cyclical generation of knowledge provides a strong role for rational design. abstract: This review provides an insight into the various opportunities for vaccine intervention, analysis of strategies for vaccine development, vaccine ability to modulate immune responses and resultant rational vaccine design. In addition, wider aspects are considered, such as biotechnological advances, advances in immunological understanding and host–pathogen interactions. The key question addressed here is, with all our research and understanding, have we reached a new echelon in vaccine development, that of rational design? url: https://www.ncbi.nlm.nih.gov/pubmed/16257375/ doi: 10.1016/s1359-6446(05)03600-7 id: cord-346557-s6c7d70y author: Brennan, David J. title: How Might Social Distancing Impact Gay, Bisexual, Queer, Trans and Two-Spirit Men in Canada? date: 2020-04-30 words: 1803.0 sentences: 92.0 pages: flesch: 53.0 cache: ./cache/cord-346557-s6c7d70y.txt txt: ./txt/cord-346557-s6c7d70y.txt summary: Given that social distancing measures may yet last for several months [20] , and potentially even longer for older and immune-compromised GBQT2+ [21] , it is important to take this opportunity to study the impact of social distancing on marginalized populations-particularly if COVID-19 We recruited participants using promotional materials in French and English shared by various partner organizations across the country through newsletters, listservs, and social media platforms (e.g., Facebook, Instagram, Twitter). The eligibility criteria restricted participation to individuals who identified as men or another gender other than women (e.g., non-binary, genderqueer, agender; inclusive of trans men and Two-Spirit people); identified as gay, bisexual, queer, asexual, or other non-heterosexual identity (inclusive of Two-Spirit) and/or have reported having had sex with another man in the last 5 years; were at least 15 years of age; lived in Canada; provided informed consent; completed a questionnaire in either French or English; and did not already participate in this study cycle. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32356033/ doi: 10.1007/s10461-020-02891-5 id: cord-312194-1jiaghrb author: Brondani, M. title: The HIV and SARS-CoV-2 Parallel in Dentistry from the Perspectives of the Oral Health Care Team date: 2020-09-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: The aim of this study was to unravel the professional and social consequences of COVID-19 as compared with the AIDS pandemic according to oral health care providers, staff, and administrators. METHODS: An exploratory qualitative inquiry via at-a-distance, semistructured interviews engaged a purposefully recruited sample of oral health care team workers in British Columbia. Interviews took place between April 20 and May 15, 2020; they were audio recorded, transcribed verbatim, and deidentified for interactive thematic analysis. An inductive process of coding was used to identify themes, subthemes, and categories of information. RESULTS: Forty-five interviews were conducted with 18 dentists, 12 dental hygienists, 6 certified dental assistants, and 9 administrators; 22 were females. Interviews each lasted an average of 48 min. After the transcripts were coded, 3 subthemes emerged: 1) personal protective equipment and universal precautions as commonsense approaches to care during both pandemics; 2) an (un)collapsed world in terms of global lockdowns; and 3) social unrest in terms of the potential for stigma and discrimination caused by both pandemics. These subthemes made up the COVID-19–AIDS parallel theme. CONCLUSION: This study explored the extent to which the current COVID-19 pandemic is leading to professional and social consequences when a parallel is drawn with the AIDS pandemic. This is the first qualitative study that identifies the potential social unrest of the pandemic from the perspective of oral health care providers and administrators. Future studies should include other providers across Canada, as well the patients receiving oral health care during this pandemic. KNOWLEDGE TRANSFER STATEMENT: The COVID-19 pandemic has unraveled potential societal implications in a parallel to the HIV/AIDS era from the perspectives of oral health care providers and their staff. Such implications are changing the way that oral health care is delivered; it may also be leading to social unrest in the form of stigma and discrimination. This study discusses some of these implications from the perspective of oral health care providers and administrators. url: https://www.ncbi.nlm.nih.gov/pubmed/32942933/ doi: 10.1177/2380084420961089 id: cord-297125-la20vi9j author: Brower, Jennifer L. title: The Threat and Response to Infectious Diseases (Revised) date: 2016-08-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The threat from microorganisms is complex, and the approaches for reducing the challenges the world is facing are also multifaceted, but a combination approach including several simple steps can make a difference and reduce morbidity and mortality and the economic cost of fighting infectious diseases. This paper discusses the continually evolving infectious disease landscape, contributing factors in the rise of the threat, reasons for optimism, and the policies, technologies, actions, and institutions that might be harnessed to further reduce the dangers introduced by pathogens. It builds upon and updates the work of other authors that have recognized the dangers of emerging and re-emerging pathogens and have explored and documented potential solutions. url: https://www.ncbi.nlm.nih.gov/pubmed/27480226/ doi: 10.1007/s00248-016-0806-9 id: cord-319002-xmsfkaoc author: Brown, James title: Community-Acquired Pneumonia in HIV-Infected Individuals date: 2014-02-22 words: 5661.0 sentences: 228.0 pages: flesch: 35.0 cache: ./cache/cord-319002-xmsfkaoc.txt txt: ./txt/cord-319002-xmsfkaoc.txt summary: Studies in populations other than in Europe and the US have confirmed the importance of bacterial pneumonia in HIV-infected individuals, with recent work in Taiwan showing this to be the most common respiratory complication of HIV infection in those with CD4 counts above 200 cells/μL [9] . This may be due to the high levels of immunocompromise in this population despite the availability of ART, although an increase in invasive pneumococcal disease was found amongst women in that study, suggesting that general uptake of the childhood pneumococcal conjugate vaccination (PCV; which now forms part of the childhood immunization schedule in South Africa) may be particularly effective at reducing rates of invasive pneumococcal disease amongst HIV-infected adults in this community. Several interventions can be made that have been shown to reduce this risk; these include: the use of ART and achievement of an undetectable plasma HIV load, smoking cessation, and the uptake of the pneumococcal and influenza immunizations, which international guidelines recommend for HIV-infected individuals. abstract: Community-acquired pneumonia continues to be an important complication of HIV infection. Rates of pneumonia decrease with the use of antiretroviral therapy but continue to be higher than in HIV uninfected individuals. Risk factors for pneumonia include low blood CD4+ count, unsuppressed plasma HIV load, smoking, injection drug use and renal impairment. Immunization against Streptococcus pneumoniae and smoking cessation can reduce this risk. It is unclear whether newly reported viral respiratory pathogens (such as the Middle East respiratory syndrome coronavirus, will be more of a problem in HIV-infected individuals than the general population. url: https://doi.org/10.1007/s11908-014-0397-x doi: 10.1007/s11908-014-0397-x id: cord-004395-erqmbi2b author: Bugembe, Daniel Lule title: Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort date: 2020-02-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Identifying immunogens that induce HIV-1-specific immune responses is a lengthy process that can benefit from computational methods, which predict T-cell epitopes for various HLA types. METHODS: We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. To provide a benchmark we compared the predictions for NetMHCpan4.0 to MHCflurry1.2.0 and NetCTL1.2. RESULTS: NetMHCpan4.0 performed best correctly predicting 88 of the 93 experimentally mapped epitopes for a set length of 9-mer and matched HLA class I alleles. Receiver Operator Characteristic (ROC) analysis gave an area under the curve (AUC) of 0.928. Setting NetMHCpan4.0 to predict 11-14mer length did not improve the prediction (37–79 of 93 peptides) with an inverse correlation between the number of predictions and length set. Late time point peptides were significantly stronger binders than early peptides (Wilcoxon signed rank test: p = 0.0000005). MHCflurry1.2.0 similarly predicted all but 2 of the peptides that NetMHCpan4.0 predicted and NetCTL1.2 predicted only 14 of the 93 experimental peptides. CONCLUSION: NetMHCpan4.0 class I epitope predictions covered 95% of the epitope responses identified in six HIV-1 infected individuals, and would have reduced the number of experimental confirmatory tests by > 80%. Algorithmic epitope prediction in conjunction with HLA allele frequency information can cost-effectively assist immunogen design through minimizing the experimental effort. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036183/ doi: 10.1186/s12879-020-4876-4 id: cord-017719-8lfn6mih author: Böhles, Hansjosef title: Infestationen und Infektionen bei Migranten – Die wichtigsten Erkrankungen date: 2018-02-09 words: 4646.0 sentences: 743.0 pages: flesch: 56.0 cache: ./cache/cord-017719-8lfn6mih.txt txt: ./txt/cord-017719-8lfn6mih.txt summary: Unter den Migranten aus dem subsaharischen Afrika ist auf das Vorliegen von HIV-Infektionen zu achten. Die Hautveränderungen über den Gängen sind u.U. leicht erhaben und zeigen eine "kommaförmige" Rötung. Es bilden sich dabei stark juckende Pusteln an Handflächen und Fußsohlen aus, die als Skabies verkannt werden können. Sie ist eine in typischer Weise mit Armut assoziierte Erkrankung, die in der Gesamtbevölkerung eine Prävalenz von ca. Die Behandlung der Larva migrans ist somit eine "off-label"-Therapie. Ca. 2 Wochen nach der Infestation kann sich eine pulmonale Askariasis manifestieren, die als Löffler-Syndrom bezeichnet wird. Die Malariaserologie spielt in der Akutdiagnostik keine Rolle und kann nur zum retrospektiven Nachweis einer stattgefundenen Erkrankung benutzt werden. 2015 ) 5 Bei jüngeren Kindern präsentiert sich die Erkrankung häufig nicht mit der klassischen Trias aus Husten, Gewichtsverlust und subfebrilen Temperaturen (Marais et al. Jahre bis Jahrzehnte nach der Erkrankung kann sich ein "Postpoliosyndrom" mit Zunahme von Schwäche und Atrophie entwickeln. abstract: Skabies (Krätze) ist bei Migranten sehr häufig. Über den Gängen der Krätzmilbe ist die Haut entzündlich verändert. An Händen und Füssen sind die Veränderungen vor allem in den interdigitalen Räumen erkennbar. Kopfläuse nehmen als Problem zu. Sie sind nur am menschlichen Kopf überlebensfähig. Flohstiche entstehen auch an bedeckten Körperstellen. An der Stichstelle entwickelt sich eine stark juckende Quaddel mit einer zentralen Blutung. Die Bettwanze sticht in der Nacht und saugt Blut. Stiche sind typischerweise longitudinal angeordnet. Unter den Parasiten haben Würmer eine große Bedeutung. Bei Kindern in Deutschland kommen Madenwürmer (Oxyuren) am häufigsten vor. Wurmeier werden anal, perianal und auch vaginal abgelegt und führen zu einem starken nächtlichen analen Pruritus. Unter den Infektionen hat die Tuberkulose bei Migranten eine höhere Prävalenz als in Deutschland gewohnt. Unter den Migranten aus dem subsaharischen Afrika ist auf das Vorliegen von HIV-Infektionen zu achten. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122363/ doi: 10.1007/978-3-662-56035-8_10 id: cord-354374-rtgjjglc author: C.G. Pollok, Richard title: Enteric viruses in HIV-related diarrhoea date: 2000-12-01 words: 3488.0 sentences: 191.0 pages: flesch: 37.0 cache: ./cache/cord-354374-rtgjjglc.txt txt: ./txt/cord-354374-rtgjjglc.txt summary: Colonic CMV infection can occur in association with infection elsewhere in the GI tract including the oesophagus, which usually results in dysphagia and odynophagia, and the pancreatico-biliary tree, which results from AIDS-related cholangiopathy or pancreatitis and manifests as pain in the upper abdomen. However, with the exception of cytomegalovirus (CMV) and human herpes simplex virus (HSV), which are established aetiological agents of disease in the GI tract in patients with HIV, the role of other enteric viruses remains controversial. Between 44% and 82% of HIV patients with chronic diarrhoea have a pathogen that is readily identifiable using a well-established diagnostic protocol that includes stool culture, microscopy and histological examination of biopsies obtained by endoscopy of the upper and lower GI tract [1] [2] [3] [4] . • What role do non-CMV enteric viruses, particularly adenovirus, have in HIV-related diarrhoea? abstract: HIV-related diarrhoea is an important cause of morbidity and mortality in HIV infection. Cytomegalovirus is a well-established cause of diarrhoea, but the role of other enteric viruses is less clear and will be discussed here. The clinical manifestations, disease mechanisms, diagnostic techniques and current treatments for the management of these infections are reviewed. url: https://api.elsevier.com/content/article/pii/S1357431000018165 doi: 10.1016/s1357-4310(00)01816-5 id: cord-286219-qcx5ehnh author: Calistri, Arianna title: The Ubiquitin-Conjugating System: Multiple Roles in Viral Replication and Infection date: 2014-05-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Through the combined action of ubiquitinating and deubiquitinating enzymes, conjugation of ubiquitin to a target protein acts as a reversible post-translational modification functionally similar to phosphorylation. Indeed, ubiquitination is more and more recognized as a central process for the fine regulation of many cellular pathways. Due to their nature as obligate intracellular parasites, viruses rely on the most conserved host cell machineries for their own replication. Thus, it is not surprising that members from almost every viral family are challenged by ubiquitin mediated mechanisms in different steps of their life cycle and have evolved in order to by-pass or exploit the cellular ubiquitin conjugating system to maximize their chance to establish a successful infection. In this review we will present several examples of the complex interplay that links viruses and the ubiquitin conjugation machinery, with a special focus on the mechanisms evolved by the human immunodeficiency virus to escape from cellular restriction factors and to exit from infected cells. url: https://doi.org/10.3390/cells3020386 doi: 10.3390/cells3020386 id: cord-324829-0nz0qioh author: Carabineiro, Sónia Alexandra Correia title: Applications of Gold Nanoparticles in Nanomedicine: Recent Advances in Vaccines † date: 2017-05-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Nowadays, gold is used in (nano-)medicine, usually in the form of nanoparticles, due to the solid proofs given of its therapeutic effects on several diseases. Gold also plays an important role in the vaccine field as an adjuvant and a carrier, reducing toxicity, enhancing immunogenic activity, and providing stability in storage. An even brighter golden future is expected for gold applications in this area. url: https://www.ncbi.nlm.nih.gov/pubmed/28531163/ doi: 10.3390/molecules22050857 id: cord-329396-cl28bjnd author: Carrico, Adam W. title: Double Jeopardy: Methamphetamine Use and HIV as Risk Factors for COVID-19 date: 2020-04-07 words: 2317.0 sentences: 109.0 pages: flesch: 40.0 cache: ./cache/cord-329396-cl28bjnd.txt txt: ./txt/cord-329396-cl28bjnd.txt summary: In our prior bio-behavioral research conducted with MSM with treated HIV infection who use meth, those who provided a urine sample that was reactive for stimulants (i.e., meth or cocaine) displayed differential expression of genes and 2-directional perturbation of pathways relevant to systemic immune activation and inflammation [25] . The clinical relevance of these findings is supported by the fact that markers of systemic immune activation and inflammation are implicated in multiple, chronic medical conditions such as cardiovascular disease in people living with HIV, which have been identified as key risk factors for COVID-19 progression [28, 29] . Smoking is a prevalent mode of administration for meth and crack-cocaine that could enhance local immune dysregulation in the lungs and modify the expression of ACE-2 receptors to increase vulnerability to SARS-CoV-2 infection and COVID-19 progression. Further clinical research is needed to characterize the psychiatric consequences of the COVID-19 pandemic and test novel mHealth approaches to improve adherence to social distancing guidelines in MSM who use meth and other stimulants. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32266501/ doi: 10.1007/s10461-020-02854-w id: cord-272925-xag1yaie author: Carter, Gemma C. title: HIV entry in macrophages is dependent on intact lipid rafts date: 2009-03-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Macrophages are an important natural target cell for HIV-1, but previous studies of virus entry into these cells are limited, and the involvement of membrane cholesterol and lipid rafts is unknown. Cholesterol disruption of macrophage membranes using four pharmacological agents acting by different mechanisms: methyl-β cyclodextrin, nystatin, filipin complex and Lovastatin, all significantly inhibited productive HIV entry and reverse transcription. The inhibitory effects of these drugs resulted in decreased virus release from infected cells, and could be substantially reversed by the addition of water-soluble cholesterol. The virus bound equally to cholesterol-disrupted cells even though HIV receptor expression levels were significantly reduced. Macrophage CD4 and CCR5 were found to partition with the detergent-resistant membranes with a typical raft-associating protein flotillin-1. HIV particles were observed co-localising with a marker of lipid rafts (CTB-FITC) early post infection. These data suggest that macrophage membrane cholesterol is essential for HIV entry, and implicate lipid raft involvement. url: https://www.sciencedirect.com/science/article/pii/S0042682208008556 doi: 10.1016/j.virol.2008.12.031 id: cord-309489-ubf55eux author: Carvalho, John J. title: OUR COMMON ENEMY: COMBATTING THE WORLD''S DEADLIEST VIRUSES TO ENSURE EQUITY HEALTH CARE IN DEVELOPING NATIONS date: 2009-02-19 words: 5291.0 sentences: 231.0 pages: flesch: 44.0 cache: ./cache/cord-309489-ubf55eux.txt txt: ./txt/cord-309489-ubf55eux.txt summary: Of the emerging viruses, five have particular importance for what scientists and world leaders can learn concerning their impact on geopolitical stability, human rights, and equity health care for the underprivileged in both developed and developing nations. For example, in Latin America, population growth and uncontrolled migration from the countryside to the cities have resulted in poor housing conditions, inappropriate disposal of waste, and lack of adequate food, clean water and health care-all of which are concurrent with an increase in infected mosquitoes carrying different versions of dengue virus (Torres and Castro 2007) . Continuing with these themes, it is clear that the geographical expansion of three viruses (HIV, dengue, and rotavirus), the increase in frequency of the infectious diseases they cause, and the relationship between these viruses and geopolitical stability, human rights, and equity health care for developing nations are problems of great concern promoted not only by biological and technological factors but also by social, religious, and cultural ones. abstract: In a previous issue of Zygon (Carvalho 2007), I explored the role of scientists—especially those engaging the science‐religion dialogue—within the arena of global equity health, world poverty, and human rights. I contended that experimental biologists, who might have reduced agency because of their professional workload or lack of individual resources, can still unite into collective forces with other scientists as well as human rights organizations, medical doctors, and political and civic leaders to foster progressive change in our world. In this article, I present some recent findings from research on three emerging viruses—HIV, dengue, and rotavirus—to explore the factors that lead to the geographical expansion of these viruses and the increase in frequency of the infectious diseases they cause. I show how these viruses are generating problems for geopolitical stability, human rights, and equity health care for developing nations that are already experiencing a growing poverty crisis. I suggest some avenues of future research for the scientific community for the movement toward resolution of these problems and indicate where the science‐religion field can be of additional aid. url: https://www.ncbi.nlm.nih.gov/pubmed/32336872/ doi: 10.1111/j.1467-9744.2009.00985.x id: cord-340703-vtuy806l author: Cascio, Antonio title: Low bone mineral density in HIV-positive young Italians and migrants date: 2020-09-03 words: 4488.0 sentences: 230.0 pages: flesch: 55.0 cache: ./cache/cord-340703-vtuy806l.txt txt: ./txt/cord-340703-vtuy806l.txt summary: We aimed to evaluate the bone mineral density (BMD) in naïve antiretroviral (ARV) treated HIV positive patients comparing native Italian group (ItG) to a Migrants group (MiG) upon arrival in Italy. Lumbar site low BMD is an initial condition of bone loss in HIV young patients, especially in female migrants. Our study aims to emphasize the burden of bone health in naïve ARV HIV positive patients and compare the bone density of the native Italian population group (ItG) with that of HIV Migrants (MiG) upon arrival in Italy. Finally, in Table 3 , we report the logistic regression analysis between Low BMD variable (dichotomous) and the independent variables: Gender (dichotomous), BMI (continuous), Hydroxy-Vitamin D (continuous), CD4 (continuous), and Previous Fractures (dichotomous) for the total sample, ItG, and MiG. Our previous reports [13, 14] on the prevalence of Low-BMD in HIV mono-infected patients who underwent ARV therapy showed higher percentage rates of osteopenia (44.9%) and osteoporosis (20.9%) than an agerelated healthy Italian population (18%) [16] . abstract: BACKGROUND: Human immunodeficiency virus (HIV) infected individuals may have osteoporosis. We aimed to evaluate the bone mineral density (BMD) in naïve antiretroviral (ARV) treated HIV positive patients comparing native Italian group (ItG) to a Migrants group (MiG) upon arrival in Italy. METHODS: We conducted a cross-sectional study on 83 HIV patients less than 50 years old. We used the dual-energy X-ray absorptiometry (DXA) within six months from the HIV diagnosis. Participants were categorized as having low BMD if the femoral neck or total lumbar spine Z-score was– 2 or less. RESULTS: MiG showed low BMD more often than ItG (37.5% vs.13.6%), especially for the female gender (16.7% vs. 0.0%). A low CD4 rate (<200 cells/μl) was most often detected in MiG than ItG. In particular, we found most often male Italians with abnormal CD4 than male migrants (67.8% vs. 33.3%) and vice versa for females (30.5% vs. 66.7%). We found an abnormal bone mineral density at the lumbar site. Low BMD at the lumbar site was more frequently observed in female migrants than female Italians. Both male and female migrants had a Z-score value significantly lower than male and female Italians, respectively. By logistic regression low vitamin-D level was positively correlated to low BMD in ItG only. All data were verified and validated using a triple code identifier. CONCLUSIONS: Both DXA and vitamin-D evaluation should be offered after the diagnosis of HIV infection. Lumbar site low BMD is an initial condition of bone loss in HIV young patients, especially in female migrants. Vitamin D levels and supplementation may be considered after HIV diagnosis independently of age to improve bone health. HIGHLIGHTS: This study evaluates the frequency of bone mineral density in HIV positive patients naive to antiretroviral therapy. It compares the density of the native Italian population with that of HIV Migrants upon arrival in Italy. The results show that HIV positive migrants, even if younger than 50 years of age, are at risk for osteoporosis, especially if they are female. url: https://doi.org/10.1371/journal.pone.0237984 doi: 10.1371/journal.pone.0237984 id: cord-015958-68dmza13 author: Ceccherini-Nelli, Luca title: Globalizzazione in medicina: l’emergenza HIV date: 2007 words: 5163.0 sentences: 529.0 pages: flesch: 59.0 cache: ./cache/cord-015958-68dmza13.txt txt: ./txt/cord-015958-68dmza13.txt summary: L''ottimismo generato dalle migliori condizioni di vita (cibo e acqua più sani, migliori sistemi di raccolta rifiuti e di discarica, nuove conoscenze nella biologia e nella medicina capaci di consentire lo sviluppo e l''uso diffuso di vaccini, la produzione di antinfettivi e di antiparassitari più sicuri ed efficaci) che avevano portato nel mondo occidentale all''allungamento dell''aspettativa di vita da una media di 46,5 anni nel 1950 a 65 anni nel 2002 (51 anni per i redditi bassi, 78 per gli alti), negli anni Ottanta si era già esaurito per l''emergenza di agenti infettivi "nuovi" (non riconosciuti prima) e per la riemergenza di altri già noti, a causa sia di fattori determinati dall''agente infettante stesso, quali l''acquisizione della capacità di salto di specie o la formazione di varianti farmacoresistenti, che di fattori determinati dall''ospite, quali: 1) manovre invasive iatrogene responsabili di infezioni ospedaliere; 2) cambiamenti climatici capaci di favorire il diffondersi di parassiti vettori di infezione e alterazioni degli ecosistemi (con prevalenza incontrollata di predatori o di prede); 3) esplosione demografica con ripercussioni importanti sulle tecnologie industriali di produzione alimentare, sullo sviluppo economico-urbanistico tumultuoso, sulle migrazioni di rifugiati; 4) promiscuità sessuale e turismo sessuale; 5) tossicodipendenza, e infine 6) spostamenti delle persone e delle merci che sono sempre stati fonte di diffusione degli agenti infettivi, ma che avevano raggiunto livelli di quantità e frequenza impensabili precedentemente [1] (vedi anche i Capitoli pubblicati altrove in questo volume). abstract: L’ottimismo generato dalle migliori condizioni di vita (cibo e acqua più sani, migliori sistemi di raccolta rifiuti e di discarica, nuove conoscenze nella biologia e nella medicina capaci di consentire lo sviluppo e l’uso diffuso di vaccini, la produzione di antinfettivi e di antiparassitari più sicuri ed efficaci) che avevano portato nel mondo occidentale all’allungamento dell’aspettativa di vita da una media di 46,5 anni nel 1950 a 65 anni nel 2002 (51 anni per i redditi bassi, 78 per gli alti), negli anni Ottanta si era già esaurito per l’emergenza di agenti infettivi “nuovi” (non riconosciuti prima) e per la riemergenza di altri già noti, a causa sia di fattori determinati dall’agente infettante stesso, quali l’acquisizione della capacità di salto di specie o la formazione di varianti farmacoresistenti, che di fattori determinati dall’ospite, quali: 1) manovre invasive iatrogene responsabili di infezioni ospedaliere; 2) cambiamenti climatici capaci di favorire il diffondersi di parassiti vettori di infezione e alterazioni degli ecosistemi (con prevalenza incontrollata di predatori o di prede); 3) esplosione demografica con ripercussioni importanti sulle tecnologie industriali di produzione alimentare, sullo sviluppo economico-urbanistico tumultuoso, sulle migrazioni di rifugiati; 4) promiscuità sessuale e turismo sessuale; 5) tossicodipendenza, e infine 6) spostamenti delle persone e delle merci che sono sempre stati fonte di diffusione degli agenti infettivi, ma che avevano raggiunto livelli di quantità e frequenza impensabili precedentemente [1] (vedi anche i Capitoli pubblicati altrove in questo volume). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120090/ doi: 10.1007/978-88-470-0609-6_8 id: cord-265600-lnik974k author: Celerino da Silva, Ronaldo title: Role of DC-SIGN and L-SIGN receptors in HIV-1 vertical transmission date: 2011-01-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The innate immune system acts in the first line of host defense against pathogens. One of the mechanisms used involves the early recognition and uptake of microbes by host professional phagocytes, through pattern recognition receptors (PRRs). These PRRs bind to conserved microbial ligands expressed by pathogens and initiate both innate and adaptative immune responses. Some PRRs located on the surface of dendritic cells (DCs) and other cells seem to play an important role in human immunodeficiency virus type 1 (HIV-1) transmission. Dendritic cell–specific intercellular adhesion molecule–3 grabbing non-integrin, CD209 (DC-SIGN) and its homolog, DC-SIGN-related (DC-SIGNR or L-SIGN) receptors are PPRs able to bind the HIV-1 gp120 envelope protein and, because alterations in their expression patterns also occur, they might play a role in both horizontal and vertical transmission as well as in disseminating the virus within the host. This review aims to explore the involvement of the DC-SIGN and L-SIGN receptors in HIV-1 transmission from mother to child. url: https://www.ncbi.nlm.nih.gov/pubmed/21277928/ doi: 10.1016/j.humimm.2011.01.012 id: cord-027678-k64whepc author: Chan, Kai Man title: Pneumonia date: 2020-06-22 words: 6626.0 sentences: 414.0 pages: flesch: 40.0 cache: ./cache/cord-027678-k64whepc.txt txt: ./txt/cord-027678-k64whepc.txt summary: The differential diagnosis and the likely causative organisms can be narrowed by using epidemiological clues, the most important of which are whether the pneumonia is community-acquired or healthcare-associated and whether the patient is immunocompromised. An acute infection of the pulmonary parenchyma that is associated with at least some symptoms of acute infection, accompanied by an acute infiltrate on a chest radiograph (CXR), or auscultatory findings consistent with pneumonia (e.g. altered breath sounds, localised crackles) in a patient not hospitalised or residing in a long-term care facility for ≥14 days prior to the onset of symptoms. Diagnosis may be difficult: the clinical features of pneumonia are non-specific and many non-infectious conditions (e.g. atelectasis, pulmonary embolus, aspiration, heart Table 36 .2 Procedure for obtaining microbiological samples using bronchoscopy and protected specimen brushing and/or bronchoalveolar lavage 35, 49 Infection control abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7310946/ doi: 10.1016/b978-0-7020-4762-6.00036-9 id: cord-316904-g7dli0a8 author: Chang, Hernan R. title: Role of cytokines in AIDS wasting date: 1998-12-31 words: 8300.0 sentences: 433.0 pages: flesch: 40.0 cache: ./cache/cord-316904-g7dli0a8.txt txt: ./txt/cord-316904-g7dli0a8.txt summary: Indeed, although wasting is not universally observed in AIDS patients, the wasting syndrome in a human immunodeficiency virus (HIV)-seropositive individual is generally utilized to establish the diagnosis of AIDS 1 and is defined by a decrease in body mass greater than 10% in the absence of concomitant opportunistic infections, malignancies, and other identifiable causes of weight loss. 33 It is against this background presentation of the interacting factors contributing to malnutrition and functional impairment in HIVinfected patients-namely anorexia, malabsorption, hypermetabolism, lethargy, and impaired fat and protein metabolism-that the role of cytokines in the AIDS wasting syndrome is discussed in the following sections. In addition to their pleiotropic actions on many body systems, they could potentially contribute to the wasting and cachexia of AIDS by their ability to induce anorexia, alter energy expenditure, increase muscle proteolysis and net protein breakdown, and initiate various abnormalities of lipid metabolism. abstract: Abstract There is now a large literature implicating cytokines in the development of wasting and cachexia commonly observed in a variety of pathophysiologic conditions. In the acquired immunodeficiency syndrome (AIDS), cytokines elicited by primary and secondary infections seem to exert subtle and sustained effects on behavioral, hormonal, and metabolic axes, and their combined effects on appetite and metabolism have been postulated to drive wasting. However, correlations of increased blood levels of a particular cytokine with wasting in AIDS have not been consistent observations, perhaps because cytokines act principally as paracrine and autocrine hormones, as well as indirectly by activating other systems. A better understanding of the mechanisms underlying the catabolic effects of cytokines is clearly needed if more efficacious strategies are to be developed for the prevention and treatment of wasting in AIDS. In this review we first examine the interacting factors contributing to the AIDS wasting syndrome. We then analyze the complex and overlapping role of cytokines in the pathophysiology of this condition, and put forward a number of hypotheses to explain some of the most important features of this syndrome. url: https://www.sciencedirect.com/science/article/pii/S0899900798001087 doi: 10.1016/s0899-9007(98)00108-7 id: cord-274663-zyzgk2z3 author: Chang, Stewart T. title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line date: 2011-09-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4(+) T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. url: https://www.ncbi.nlm.nih.gov/pubmed/21933919/ doi: 10.1128/mbio.00134-11 id: cord-010689-d2qn1doq author: Chehardoli, Gholamabbas title: Synthetic strategies, SAR studies, and computer modeling of indole 2 and 3-carboxamides as the strong enzyme inhibitors: a review date: 2020-05-12 words: 6179.0 sentences: 348.0 pages: flesch: 42.0 cache: ./cache/cord-010689-d2qn1doq.txt txt: ./txt/cord-010689-d2qn1doq.txt summary: In this review, synthetic strategies of indole 2 and 3-carboxamide derivatives, the type, and mode of interaction of these derivatives against HLGP, HIV-1, renin enzyme, and structure–activity studies of these compounds were investigated. Based on our experiences on synthesis of various heterocycle compounds, such as: quinoxalines [15] , epoxides [16] , urazoles [17, 18] , pyrazolone [19] , benzoxazine [20] and especially the synthesis of 3H-indoles [21] , in this paper, we wish to present a comprehensive review about the synthesis, structure-activity relationship studies and computer modeling of indole 2 and 3-carboxamides as potent inhibitors of various enzymes. According to the results of docking calculations, the presences of indole ring and carboxamide moiety have a decisive role in the inhibitory activity of these compounds. According to the research conducted up to 2008, the presence of carboxamide moiety in the indole derivatives is essential for their inhibitory activity against HLGP. abstract: ABSTRACT: Indole derivatives have been the focus of many researchers in the study of pharmaceutical compounds for many years. Researchers have investigated the effect of carboxamide moiety at positions 2 and 3, giving unique inhibitory properties to these compounds. The presence of carboxamide moiety in indole derivatives causes hydrogen bonds with a variety of enzymes and proteins, which in many cases, inhibits their activity. In this review, synthetic strategies of indole 2 and 3-carboxamide derivatives, the type, and mode of interaction of these derivatives against HLGP, HIV-1, renin enzyme, and structure–activity studies of these compounds were investigated. It is hoped that indole scaffolds will be tested in the future for maximum activity in pharmacological compounds. GRAPHIC ABSTRACT: [Image: see text] url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214098/ doi: 10.1007/s11030-020-10061-x id: cord-326558-6tss9ydx author: Chen, Jiao title: A binning tool to reconstruct viral haplotypes from assembled contigs date: 2019-11-04 words: 6709.0 sentences: 429.0 pages: flesch: 54.0 cache: ./cache/cord-326558-6tss9ydx.txt txt: ./txt/cord-326558-6tss9ydx.txt summary: CONCLUSIONS: In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. These methods usually estimate the bin number by aligning metagenomic data to a pre-established marker gene database, and then assign assembled contigs to different bins using sequence composition information and read coverage levels. We evaluate the haplotype number estimation and clustering performance of VirBin on both simulated and mock HIV quasispecies sequencing data. It uses bowtie2 to map reads to a set of universal genes and infers the within-species strains abundances by Fig. 3 The recall and precision of contig binning results by MaxBin. X-axis represents each haplotype, in decreasing order of relative abundance. Although abundance-based clustering has been used for contig binning from multiple samples [15, 19] , existing tools are not designed Fig. 7 The pipeline of VirBin to tackle key challenges of distinguishing contigs of different haplotypes. abstract: BACKGROUND: Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed. RESULTS: We developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction. CONCLUSIONS: In this work, we presented VirBin, a new contig binning tool for distinguishing contigs from different viral haplotypes with high sequence similarity. It competes favorably with other tools on viral contig binning. The source codes are available at: https://github.com/chjiao/VirBin. url: https://www.ncbi.nlm.nih.gov/pubmed/31684876/ doi: 10.1186/s12859-019-3138-1 id: cord-255683-2eq24jth author: Chen, Weizao title: Cross-Reactive Human IgM-Derived Monoclonal Antibodies that Bind to HIV-1 Envelope Glycoproteins date: 2010-02-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Elicitation of antibodies with potent and broad neutralizing activity against HIV by immunization remains a challenge. Several monoclonal antibodies (mAbs) isolated from humans with HIV-1 infection exhibit such activity but vaccine immunogens based on structures containing their epitopes have not been successful for their elicitation. All known broadly neutralizing mAbs (bnmAbs) are immunoglobulin (Ig) Gs (IgGs) and highly somatically hypermutated which could impede their elicitation. Ig Ms (IgMs) are on average significantly less divergent from germline antibodies and are relevant for the development of vaccine immunogens but are underexplored compared to IgGs. Here we describe the identification and characterization of several human IgM-derived mAbs against HIV-1 which were selected from a large phage-displayed naive human antibody library constructed from blood, lymph nodes and spleens of 59 healthy donors. These antibodies bound with high affinity to recombinant envelope glycoproteins (gp140s, Envs) of HIV-1 isolates from different clades. They enhanced or did not neutralize infection by some of the HIV-1 primary isolates using CCR5 as a coreceptor but neutralized all CXCR4 isolates tested although weakly. One of these antibodies with relatively low degree of somatic hypermutation was more extensively characterized. It bound to a highly conserved region partially overlapping with the coreceptor binding site and close to but not overlapping with the CD4 binding site. These results suggest the existence of conserved structures that could direct the immune response to non-neutralizing or even enhancing antibodies which may represent a strategy used by the virus to escape neutralizing immune responses. Further studies will show whether such a strategy plays a role in HIV infection of humans, how important that role could be, and what the mechanisms of infection enhancement are. The newly identified mAbs could be used as reagents to further characterize conserved non-neutralizing, weakly neutralizing or enhancing epitopes and modify or remove them from candidate vaccine immunogens. url: https://www.ncbi.nlm.nih.gov/pubmed/21755021/ doi: 10.3390/v2020547 id: cord-255697-trig04hd author: Cheng, Vincent Chi-Chung title: Viral Infections, an Overview with a Focus on Prevention of Transmission date: 2016-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses are obligatory intracellular pathogens with a simple structure consisting of assembled proteins enclosing the nucleic acid genome with or without a lipid envelope. Despite increasing availability of rapid nucleic acid amplification assays for laboratory diagnosis, effective antivirals, and safe vaccines, the control of most viral infections depends on time-honored surveillance and infection control measures. Moreover most viruses can be readily destroyed by common disinfectants. This article is focused on the epidemiology, diagnosis, and control of common and emerging viral diseases. url: https://www.sciencedirect.com/science/article/pii/B9780128036785005142 doi: 10.1016/b978-0-12-803678-5.00514-2 id: cord-321773-5fw9abzl author: Cheng, Wenyu title: DDX5 RNA Helicases: Emerging Roles in Viral Infection date: 2018-04-09 words: 6739.0 sentences: 370.0 pages: flesch: 48.0 cache: ./cache/cord-321773-5fw9abzl.txt txt: ./txt/cord-321773-5fw9abzl.txt summary: Given the crucial roles of DDX5 in RNA biology, several RNA viruses were found to interact with the protein to promote viral replication (Table 1) , including severe acute respiratory syndrome (SARS) coronavirus (CoV) [16] , human immunodeficiency virus 1 (HIV-1) [17] , hepatitis C virus (HCV) [18] , Japanese encephalitis virus (JEV) [19] , porcine reproductive and respiratory syndrome virus (PRRSV) [20] , and influenza virus [21] . There are several studies that focus on specific inhibitors or drugs of the host DEAD-box helicase to inhibit virus replication or treat cancers [65] [66] [67] , but it remains to be determined whether small molecular inhibitors of the interaction between DDX5 and Rev can be found. The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3 UTR The DEAD-box RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro abstract: Asp-Glu-Ala-Asp (DEAD)-box polypeptide 5 (DDX5), also called p68, is a prototypical member of the large ATP-dependent RNA helicases family and is known to participate in all aspects of RNA metabolism ranging from transcription to translation, RNA decay, and miRNA processing. The roles of DDX5 in cell cycle regulation, tumorigenesis, apoptosis, cancer development, adipogenesis, Wnt-β-catenin signaling, and viral infection have been established. Several RNA viruses have been reported to hijack DDX5 to facilitate various steps of their replication cycles. Furthermore, DDX5 can be bounded by the viral proteins of some viruses with unknown functions. Interestingly, an antiviral function of DDX5 has been reported during hepatitis B virus and myxoma virus infection. Thus, the precise roles of this apparently multifaceted protein remain largely obscure. Here, we provide a rapid and critical overview of the structure and functions of DDX5 with a particular emphasis on its role during virus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/29642538/ doi: 10.3390/ijms19041122 id: cord-327135-4c2flue4 author: Chinnaswamy, S title: Gene–disease association with human IFNL locus polymorphisms extends beyond hepatitis C virus infections date: 2016-06-09 words: 9813.0 sentences: 499.0 pages: flesch: 48.0 cache: ./cache/cord-327135-4c2flue4.txt txt: ./txt/cord-327135-4c2flue4.txt summary: Interferon (IFN) lambda (IFN-λ or type III IFN) gene polymorphisms were discovered in the year 2009 to have a strong association with spontaneous and treatment-induced clearance of hepatitis C virus (HCV) infection in human hosts. Three independent groups conducted genome-wide association studies (GWASs) involving treatment response to chronic hepatitis C virus (HCV) infections, in three different geographical regions of the world, and reported that single-nucleotide polymorphisms (SNPs) in the IFNL locus (Figure 1 ), had strong association with treatment-induced HCV clearance irrespective of ethnicity and geographical location of the hosts. 49 In stark contrast, a dominant model of inheritance (of the non-beneficial IFNL SNP minor allele) has consistently given the best explanation on the observed phenotypes in association studies with both spontaneous clearance and IFN-based treatment response in chronic HCV infections. abstract: Interferon (IFN) lambda (IFN-λ or type III IFN) gene polymorphisms were discovered in the year 2009 to have a strong association with spontaneous and treatment-induced clearance of hepatitis C virus (HCV) infection in human hosts. This landmark discovery also brought renewed interest in type III IFN biology. After more than half a decade since this discovery, we now have reports that show that genetic association of IFNL gene polymorphisms in humans is not limited only to HCV infections but extends beyond, to include varied diseases such as non-alcoholic fatty liver disease, allergy and several other viral diseases including that caused by the human immunodeficiency virus. Notably, all these conditions have strong involvement of host innate immune responses. After the discovery of a deletion polymorphism that leads to the expression of a functional IFN-λ4 as the prime ‘functional’ variant, the relevance of other polymorphisms regulating the expression of IFN-λ3 is in doubt. Herein, I seek to critically address these issues and review the current literature to provide a framework to help further understanding of IFN-λ biology. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/gene.2016.24) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/gene.2016.24 doi: 10.1038/gene.2016.24 id: cord-027242-7qq82j2f author: Chrissafidou, Angeliki title: Infektionen, Impfungen, Reisemedizin date: 2008-12-11 words: 6531.0 sentences: 1335.0 pages: flesch: 55.0 cache: ./cache/cord-027242-7qq82j2f.txt txt: ./txt/cord-027242-7qq82j2f.txt summary: 9 HIV und AIDS 543 9.9.1 Epidemiologie und Ü bertragungswege 543 9.9.2 Labordiagnostik 546 9.9.3 Stadieneinteilung und Verlauf 548 9.9.4 Diagnostik bei HIV-Positiven 548 9.9.5 Hä ufige Krankheitsbilder bei AIDS 554 9.9.6 Therapie 560 9.9.7 Medikamente bei HIV-Patienten 564 9.9.8 Vorgehen bei Kontakt mit HIVkontaminiertem Material und Postexpositionsprophylaxe (PEP) 567 9.10 Reisemedizin 567 9.10.1 Allgemeine Empfehlungen zur Reisefä higkeit 572 9.10.2 Empfehlungen fü r Schwangere 573 9.10.3 Empfehlungen fü r ä ltere Menschen 574 9.10.4 Empfehlungen fü r Kinder und Sä uglinge 575 9.10.5 Empfehlungen fü r chronisch Kranke 577 9.10.6 Reisevorbereitungen/Prophylaxen 580 9.10.7 Reiseimpfungen und Chemoprophylaxe 587 9.10.8 Gesundheitsrisiken auf Reisen 596 9.10.9 Screening nach Reiseende 597 9.11 Infektionsschutzgesetz 9.1 Die Immunisierung durch Impfungen ist eine der wichtigsten und wirksamsten Maßnahmen zum Schutz vor Infektionskrankheiten. Aktive Immunisierung: Der Organismus wird mit Antigenen von Krankheitserregern konfrontiert und muss selbst eine Immunität ausbilden. Totimpfstoffe: Abgetö tete Krankheitserreger oder aufbereitete Antigene; keine Impfinfektion mö glich, deshalb auch bei Pat. mit Immundefekten applizierbar. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7303566/ doi: 10.1016/b978-343722442-3.50016-6 id: cord-254098-4imkkptg author: Chutiwitoonchai, Nopporn title: Characteristics of IFITM, the newly identified IFN-inducible anti-HIV-1 family proteins date: 2013-01-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: IFN-inducible IFITM proteins (IFITM1, 2, and 3) inhibit the replication of various viruses including HIV-1 through poorly understood mechanisms. Here, we further analyzed characteristics of these newly identified HIV-1 restriction factors. Firstly, in contrast to other anti-HIV-1 proteins, such as tetherin and APOBEC3G, IFITMs were resistant to a down-regulation of surface expression or degradation by HIV-1 proteins. Secondly, the enforced expression of IFITMs reduced the production of HIV-1 viruses from cells transfected with proviral plasmids containing whole viral sequences. Although their inhibitory activities were modest when compared to that of tetherin, IFITMs, but not tetherin, directly reduced the expression of HIV-1 proteins including Gag, Vif and Nef. Of importance, however, IFITMs had no inhibitory effect when these viral proteins were expressed by codon-optimized cDNAs that bypassed the viral-specific expression machinery. Indeed, our results supported the idea that IFITMs interfere with viral protein expression mediated by double-stranded viral RNAs, such as RRE and TAR. Finally, the S-palmitoylation of IFITMs, which is crucial for their anti-influenza virus activity, was not required for their anti-HIV-1 activity, indicating that IFITMs restrict these viruses at different steps. These characteristics lead to a better understanding of the mechanism by which IFITMs restrict HIV-1 and other viruses. url: https://www.sciencedirect.com/science/article/pii/S1286457913000191 doi: 10.1016/j.micinf.2012.12.003 id: cord-317277-rr9zue4l author: Cifuentes-Munoz, Nicolas title: Viral cell-to-cell spread: Conventional and non-conventional ways date: 2020-09-29 words: 13085.0 sentences: 638.0 pages: flesch: 45.0 cache: ./cache/cord-317277-rr9zue4l.txt txt: ./txt/cord-317277-rr9zue4l.txt summary: Cell-free viral particles can be released into the extracellular space through different mechanisms, such as: (a) cell lysis induced by viral proteins, as is the case for many non-enveloped viruses such as reoviruses, rotaviruses, adenoviruses and picornaviruses (Giorda and Hebert, 2013; Hu et al., 2012; Nieva et al., 2012) ; (b) by budding directly from the plasma membrane, where virions acquire their envelope, as is the case of human immunodeficiency virus (HIV-1), influenza, paramyxoviruses, and pneumoviruses (Lorizate and Krausslich, 2011; Votteler and Sundquist, 2013; Weissenhorn et al., 2013) ; (c) by exocytosis of intracellularly assembled viral particles, as is the case for bunyaviruses, flaviviruses and coronaviruses (Cifuentes-Munoz et al., 2014; Lorizate and Krausslich, 2011) . An interesting observation made for alphaviruses is that the filopodia-like extensions are not able to transfer cytosolic or plasma membrane components, suggesting they are not openended connections like TNTs. Instead, viral particles are hypothesized to bud into a protected space at the filopodial tip and then rapidly enter the target cell, preventing access of neutralizing antibodies. abstract: A critical step in the life cycle of a virus is spread to a new target cell, which generally involves the release of new viral particles from the infected cell which can then initiate infection in the next target cell. While cell-free viral particles released into the extracellular environment are necessary for long distance spread, there are disadvantages to this mechanism. These include the presence of immune system components, the low success rate of infection by single particles, and the relative fragility of viral particles in the environment. Several mechanisms of direct cell-to-cell spread have been reported for animal viruses which would avoid the issues associated with cell-free particles. A number of viruses can utilize several different mechanisms of direct cell-to-cell spread, but our understanding of the differential usage by these pathogens is modest. Although the mechanisms of cell-to-cell spread differ among viruses, there is a common exploitation of key pathways and components of the cellular cytoskeleton. Remarkably, some of the viral mechanisms of cell-to-cell spread are surprisingly similar to those used by bacteria. Here we summarize the current knowledge of the conventional and non-conventional mechanisms of viral spread, the common methods used to detect viral spread, and the impact that these mechanisms can have on viral pathogenesis. url: https://www.sciencedirect.com/science/article/pii/S0065352720300427 doi: 10.1016/bs.aivir.2020.09.002 id: cord-048467-1dus0u4m author: Civaner, Murat title: Can "presumed consent" justify the duty to treat infectious diseases? An analysis date: 2008-03-06 words: 7746.0 sentences: 303.0 pages: flesch: 51.0 cache: ./cache/cord-048467-1dus0u4m.txt txt: ./txt/cord-048467-1dus0u4m.txt summary: The purpose of this study was to investigate the opinions and beliefs held by both physicians and dentists regarding the occupational risks of infectious diseases, and to analyze the argument that the notion of "presumed consent" on the part of professionals may be grounds for supporting the duty to treat. CONCLUSION: If we use the presumed consent argument to establish the duty of the HCW to provide care, we are confronted with problems ranging over the difficulty of choosing a profession autonomously, the constant level of uncertainty present in the medical profession, the near-impossibility of being able to evaluate retrospectively whether every individual was informed, and the seemingly inescapable problem that this practice would legitimize, and perhaps even foster, discrimination against patients with certain diseases. In order to carry out this analysis, the opinions and beliefs of physicians and dentists regarding the occupational risks of infectious diseases were investigated; and, by extension, the argument that the notion of "presumed consent" may be grounds for supporting the HCWs'' duty to treat was also analyzed. abstract: BACKGROUND: AIDS, SARS, and the recent epidemics of the avian-flu have all served to remind us the debate over the limits of the moral duty to care. It is important to first consider the question of whether or not the "duty to treat" might be subject to contextual constraints. The purpose of this study was to investigate the opinions and beliefs held by both physicians and dentists regarding the occupational risks of infectious diseases, and to analyze the argument that the notion of "presumed consent" on the part of professionals may be grounds for supporting the duty to treat. METHODS: For this cross-sectional survey, the study population was selected from among physicians and dentists in Ankara. All of the 373 participants were given a self-administered questionnaire. RESULTS: In total, 79.6% of the participants said that they either had some degree of knowledge about the risks when they chose their profession or that they learned of the risks later during their education and training. Of the participants, 5.2% said that they would not have chosen this profession if they had been informed of the risks. It was found that 57% of the participants believed that there is a standard level of risk, and 52% of the participants stated that certain diseases would exceed the level of acceptable risk unless specific protective measures were implemented. CONCLUSION: If we use the presumed consent argument to establish the duty of the HCW to provide care, we are confronted with problems ranging over the difficulty of choosing a profession autonomously, the constant level of uncertainty present in the medical profession, the near-impossibility of being able to evaluate retrospectively whether every individual was informed, and the seemingly inescapable problem that this practice would legitimize, and perhaps even foster, discrimination against patients with certain diseases. Our findings suggest that another problem can be added to the list: one-fifth of the participants in this study either lacked adequate knowledge of the occupational risks when they chose the medical profession or were not sufficiently informed of these risks during their faculty education and training. Furthermore, in terms of the moral duty to provide care, it seems that most HCWs are more concerned about the availability of protective measures than about whether they had been informed of a particular risk beforehand. For all these reasons, the presumed consent argument is not persuasive enough, and cannot be used to justify the duty to provide care. It is therefore more useful to emphasize justifications other than presumed consent when defining the duty of HCWs to provide care, such as the social contract between society and the medical profession and the fact that HCWs have a greater ability to provide medical aid. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2311313/ doi: 10.1186/1471-2334-8-29 id: cord-337720-kmwft059 author: Closson, Kalysha title: When Home is Not a Safe Place: Impacts of Social Distancing Directives on Women Living with HIV date: 2020-06-02 words: 1741.0 sentences: 84.0 pages: flesch: 48.0 cache: ./cache/cord-337720-kmwft059.txt txt: ./txt/cord-337720-kmwft059.txt summary: As HIV care, research participation, and workplace settings are being transitioned to virtual and telephone-based methods, women living with HIV experiencing violence are less able to connect to critical social and protective networks [18] . As such, necessary social distancing measures have the potential to impact the rates and consequences of IPV, increasing social isolation and mental health concerns, which taken together can hinder women living with HIV''s access to, and use of, HIV treatment and violence support, further than they already experience [9, 17] . As social distancing measures limit access to supports, such as family, friends, and health care provides, that help women living with HIV cope with experiences of violence and histories of trauma, research is needed to understand the unique ways in which women living with HIV have developed resilience and coping strategies during COVID-19 restrictions and how these can be best supported. abstract: nan url: https://doi.org/10.1007/s10461-020-02941-y doi: 10.1007/s10461-020-02941-y id: cord-303189-ktl4jw8v author: Coccia, Eliana M. title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 words: 15202.0 sentences: 738.0 pages: flesch: 40.0 cache: ./cache/cord-303189-ktl4jw8v.txt txt: ./txt/cord-303189-ktl4jw8v.txt summary: Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. In these cells, the HCV-induced miR-21 has been recently reported to be involved in evasion of IFN-I production and stimulation of HCV replication, upon suppression of MyD88 and IRAK1 expression, that is required for the TLR7-mediated sensing of the virus [100] . Amongst RNA viruses that, as HCV, can establish a persistent infection, HIV-1, a lentivirus from the Retroviridae family, represents a paradigm for its ability to prevent or circumvent the innate immune response mediated by IFN-I. Overall, viruses as HCV and HIV-1 have evolved nifty strategies to dampen the host innate response in cells where a productive infection may take place, while they induce infection-independent mechanisms in non-permissive cells to facilitate the viral life cycle and promote a chronic inflammation. abstract: Abstract Type I interferon (IFN) comprises a class of cytokines first discovered more than 50 years ago and initially characterized for their ability to interfere with viral replication and restrict locally viral propagation. As such, their induction downstream of germ-line encoded pattern recognition receptors (PRRs) upon recognition of pathogen-associated molecular patterns (PAMPs) is a hallmark of the host antiviral response. The acknowledgment that several PAMPs, not just of viral origin, may induce IFN, pinpoints at these molecules as a first line of host defense against a number of invading pathogens. Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. On the other hand an inverse interference to escape the IFN system is largely exploited by pathogens through a number of tactics and tricks aimed at evading, inhibiting or manipulating the IFN pathway, that result in progression of infection or establishment of chronic disease. In this review we discuss the interplay between the IFN system and some selected clinically important and challenging viruses and bacteria, highlighting the wide array of pathogen-triggered molecular mechanisms involved in evasion strategies. url: https://doi.org/10.1016/j.smim.2015.03.005 doi: 10.1016/j.smim.2015.03.005 id: cord-326642-kc85pev4 author: Cohen, Adam L. title: Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 date: 2015-09-19 words: 4060.0 sentences: 176.0 pages: flesch: 48.0 cache: ./cache/cord-326642-kc85pev4.txt txt: ./txt/cord-326642-kc85pev4.txt summary: title: Parainfluenza Virus Infection Among Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Children and Adults Hospitalized for Severe Acute Respiratory Illness in South Africa, 2009–2014 After adjusting for age, HIV serostatus, and respiratory viral coinfection, the attributable fraction for PIV was 65.6% (95% CI [confidence interval], 47.1–77.7); PIV contributed to SARI among HIV-infected and -uninfected children <5 years of age and among individuals infected with PIV types 1 and 3. Parainfluenza virus causes substantial severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV. In this study, we aimed to describe the epidemiological and clinical characteristics of HIV-infected and -uninfected children and adults hospitalized with PIV-associated pneumonia in South Africa. Parainfluenza virus is associated with a significant amount of severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV. abstract: Background. Parainfluenza virus (PIV) is a common cause of acute respiratory tract infections, but little is known about PIV infection in children and adults in Africa, especially in settings where human immunodeficiency virus (HIV) prevalence is high. Methods. We conducted active, prospective sentinel surveillance for children and adults hospitalized with severe acute respiratory illness (SARI) from 2009 to 2014 in South Africa. We enrolled controls (outpatients without febrile or respiratory illness) to calculate the attributable fraction for PIV infection. Respiratory specimens were tested by multiplex real-time reverse-transcription polymerase chain reaction assay for parainfluenza types 1, 2, and 3. Results. Of 18 282 SARI cases enrolled, 1188 (6.5%) tested positive for any PIV type: 230 (19.4%) were type 1; 168 (14.1%) were type 2; 762 (64.1%) were type 3; and 28 (2.4%) had coinfection with 2 PIV types. After adjusting for age, HIV serostatus, and respiratory viral coinfection, the attributable fraction for PIV was 65.6% (95% CI [confidence interval], 47.1–77.7); PIV contributed to SARI among HIV-infected and -uninfected children <5 years of age and among individuals infected with PIV types 1 and 3. The observed overall incidence of PIV-associated SARI was 38 (95% CI, 36–39) cases per 100 000 population and was highest in children <1 year of age (925 [95% CI, 864–989] cases per 100 000 population). Compared with persons without HIV, persons with HIV had an increased relative risk of PIV hospitalization (9.4; 95% CI, 8.5–10.3). Conclusions. Parainfluenza virus causes substantial severe respiratory disease in South Africa among children <5 years of age, especially those that are infected with HIV. url: https://www.ncbi.nlm.nih.gov/pubmed/26566534/ doi: 10.1093/ofid/ofv139 id: cord-004501-guiy89x8 author: Cojocaru, Florina-Daniela title: Nanomaterials Designed for Antiviral Drug Delivery Transport across Biological Barriers date: 2020-02-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral infections are a major global health problem, representing a significant cause of mortality with an unfavorable continuously amplified socio-economic impact. The increased drug resistance and constant viral replication have been the trigger for important studies regarding the use of nanotechnology in antiviral therapies. Nanomaterials offer unique physico-chemical properties that have linked benefits for drug delivery as ideal tools for viral treatment. Currently, different types of nanomaterials namely nanoparticles, liposomes, nanospheres, nanogels, nanosuspensions and nanoemulsions were studied either in vitro or in vivo for drug delivery of antiviral agents with prospects to be translated in clinical practice. This review highlights the drug delivery nanosystems incorporating the major antiviral classes and their transport across specific barriers at cellular and intracellular level. Important reflections on nanomedicines currently approved or undergoing investigations for the treatment of viral infections are also discussed. Finally, the authors present an overview on the requirements for the design of antiviral nanotherapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076512/ doi: 10.3390/pharmaceutics12020171 id: cord-270868-4s3q2i6v author: Collins, Lauren F. title: Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia date: 2020-10-01 words: 2170.0 sentences: 119.0 pages: flesch: 48.0 cache: ./cache/cord-270868-4s3q2i6v.txt txt: ./txt/cord-270868-4s3q2i6v.txt summary: title: Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia BACKGROUND: There are limited data describing the presenting characteristics and outcomes among US persons with HIV (PWH) requiring hospitalization for coronavirus disease 2019 (COVID-19). CONCLUSION: The multisite series in the Southern United States provides characteristics and early outcomes of hospitalized PWH with COVID-19. To understand how COVID-19 may affect persons with HIV (PWH) in the Southern United States, a prematurely aging population with a high comorbidity burden [3, 4] , we analyzed cases among hospitalized PWH in Atlanta, Georgia. The prevalence and burden of non-AIDS comorbidities among women living with or at-risk for HIV infection in the United States Presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with COVID-19 in the New York City area Characteristics and clinical outcomes of adult patients hospitalized with COVID-19 -Georgia abstract: BACKGROUND: There are limited data describing the presenting characteristics and outcomes among US persons with HIV (PWH) requiring hospitalization for coronavirus disease 2019 (COVID-19). METHODS: We performed a case series of all PWH sequentially admitted with COVID-19 from 8 March 2020 to 23 April 2020 at three hospitals in Atlanta, Georgia. Sociodemographic, clinical and HIV-associated characteristics were collected. RESULTS: Of 530 confirmed COVID-19 cases hospitalized during this period, 20 occurred among PWH (3.8%). The median age was 57 (Q1–Q3, 48–62) years, 65% were men, and 85% were non-Hispanic Black. Presenting median symptom duration was 5 (Q1–Q3, 3–7) days; cough (90%), fever (65%), malaise (60%) and dyspnea (60%) were most common. On admission, 40% of patients required oxygenation support and 65% had an abnormal chest radiograph. Median length of hospitalization was 5 (Q1–Q3, 4–12) days, 30% required intensive care, 15% required intubation, and 15% died. Median CD4(+) cell count prior to admission was 425 (Q1–Q3, 262–815) cells/μl and 90% of patients had HIV-1 RNA less than 200 copies/ml. Half of the patients had at least five comorbidities; hypertension (70%), dyslipidemia (60%) and diabetes (45%) were most prevalent. All three patients who died had CD4(+) cell count more than 200, HIV suppression and each had a total of five comorbidities. CONCLUSION: The multisite series in the Southern United States provides characteristics and early outcomes of hospitalized PWH with COVID-19. Nearly all patients had controlled HIV and a high comorbidity burden. Additional study of COVID-19 among PWH is needed to determine the role of age, comorbidities and HIV control in mediating COVID-19 presentation and its sequelae. url: https://doi.org/10.1097/qad.0000000000002632 doi: 10.1097/qad.0000000000002632 id: cord-006716-n371b91w author: Cone, A. M. title: Flumazenil reverses diazepam-induced neonatal apnoea and hypotonia date: 1993 words: 1621.0 sentences: 90.0 pages: flesch: 59.0 cache: ./cache/cord-006716-n371b91w.txt txt: ./txt/cord-006716-n371b91w.txt summary: These strategies are required in some European countries where the large proportion of intravenous drug user (IVDU) women of child-bearing age leads to increasing numbers of perinatally infected children [2] . These mechanisms have been already identified [1] and, as in others'' data [1] , a prior unharmed experience seems to be a factor influencing reproductive decision; (2) HIV-1 testing in pregnancy is mostly useful for sexually infected women often unconscious of their condition. Sir: We describe a case in which flumazenil, a specific benzodiazepine antagonist, reversed diazepam-induced neonatal apnoea and hypotonia. Diazepam levels were not measured, but in view of the prolonged half-life of this drug, it was likely that the infant would remain susceptible to its effects after cessation of the flumazenil infusion. Complement activation and the prognostic value of C3 a in patients at risk of the adult respiratory distress syndrome abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102282/ doi: 10.1007/bf01955914 id: cord-347356-uc9dqhyq author: Cooper, TJ title: Coronavirus disease 2019 (COVID‐19) outcomes in HIV/AIDS patients: a systematic review date: 2020-07-15 words: 3949.0 sentences: 228.0 pages: flesch: 54.0 cache: ./cache/cord-347356-uc9dqhyq.txt txt: ./txt/cord-347356-uc9dqhyq.txt summary: OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The aim of this systematic review was to identify studies that discuss PLHIV who have been infected with SARS-CoV-2 and that report whether coinfection results in a greater risk of adverse outcomes and, furthermore, whether controlled HIV infection vs. A comprehensive literature search was carried out in Global Health, SCOPUS, Medline and EMBASE to identify articles that discussed HIV-positive patients and the clinical implications of HIV infection in COVID-19 in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines [13] . [21] , also highlighted a case study of a HIV patient with SARS-CoV2 co-infection, diagnosis of viral pneumonia was made on clinical examination and chest CT findings. abstract: OBJECTIVES: The aim of the study was to systematically review current studies reporting on clinical outcomes in people living with HIV (PLHIV) infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). METHODS: We conducted a systematic review using the Preferred Reporting Items for Systematic Reviews and Meta‐analysis (PRISMA) guidelines. A comprehensive literature search was conducted in Global Health, SCOPUS, Medline and EMBASE using pertinent key words and Medical Subject Headings (MeSH) terms relating to coronavirus disease 2019 (COVID‐19) and HIV. A narrative synthesis was undertaken. Articles are summarized in relevant sections. RESULTS: Two hundred and eighty‐five articles were identified after duplicates had been removed. After screening, eight studies were analysed, totalling 70 HIV‐infected patients (57 without AIDS and 13 with AIDS). Three themes were identified: (1) controlled HIV infection does not appear to result in poorer COVID‐19 outcomes, (2) more data are needed to determine COVID‐19 outcomes in patients with AIDS and (3) HIV‐infected patients presenting with COVID‐19 symptoms should be investigated for superinfections. CONCLUSIONS: Our findings suggest that PLHIV with well‐controlled disease are not at risk of poorer COVID‐19 disease outcomes than the general population. It is not clear whether those with poorly controlled HIV disease and AIDS have poorer outcomes. Superimposed bacterial pneumonia may be a risk factor for more severe COVID‐19 but further research is urgently needed to elucidate whether PLHIV are more at risk than the general population. url: https://doi.org/10.1111/hiv.12911 doi: 10.1111/hiv.12911 id: cord-000158-d08buwtu author: Corti, Davide title: Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals date: 2010-01-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The isolation of human monoclonal antibodies (mAbs) that neutralize a broad spectrum of primary HIV-1 isolates and the characterization of the human neutralizing antibody B cell response to HIV-1 infection are important goals that are central to the design of an effective antibody-based vaccine. METHODS AND FINDINGS: We immortalized IgG(+) memory B cells from individuals infected with diverse clades of HIV-1 and selected on the basis of plasma neutralization profiles that were cross-clade and relatively potent. Culture supernatants were screened using various recombinant forms of the envelope glycoproteins (Env) in multiple parallel assays. We isolated 58 mAbs that were mapped to different Env surfaces, most of which showed neutralizing activity. One mAb in particular (HJ16) specific for a novel epitope proximal to the CD4 binding site on gp120 selectively neutralized a multi-clade panel of Tier-2 HIV-1 pseudoviruses, and demonstrated reactivity that was comparable in breadth, but distinct in neutralization specificity, to that of the other CD4 binding site-specific neutralizing mAb b12. A second mAb (HGN194) bound a conserved epitope in the V3 crown and neutralized all Tier-1 and a proportion of Tier-2 pseudoviruses tested, irrespective of clade. A third mAb (HK20) with broad neutralizing activity, particularly as a Fab fragment, recognized a highly conserved epitope in the HR-1 region of gp41, but showed striking assay-dependent selectivity in its activity. CONCLUSIONS: This study reveals that by using appropriate screening methods, a large proportion of memory B cells can be isolated that produce mAbs with HIV-1 neutralizing activity. Three of these mAbs show unusual breadth of neutralization and therefore add to the current panel of HIV-1 neutralizing antibodies with potential for passive protection and template-based vaccine design. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808385/ doi: 10.1371/journal.pone.0008805 id: cord-316273-vo6j8zb0 author: Cosset, François-Loic title: Cell Entry of Enveloped Viruses date: 2011-02-08 words: 23421.0 sentences: 1013.0 pages: flesch: 40.0 cache: ./cache/cord-316273-vo6j8zb0.txt txt: ./txt/cord-316273-vo6j8zb0.txt summary: On the one hand, they acquired a domain to bind to a specific cellular protein, named "receptor." On the other hand, they developed in a different manner, according to the genus of the virus, a function of fusion that allows the destabilization of the membrane and the opening of a pore through which the genetic material will enter the cell. Thus, we need to distinguish cell surface molecules such as heparan sulfate proteoglycans, DC-SIGN, or integrins that can enhance infections by concentrating retroviruses onto cells (Bounou et al., 2002; Geijtenbeek et al., 2000; Jinno-Oue et al., 2001; Mondor et al., 1998; Pohlmann et al., 2001; Saphire et al., 2001) from authentic receptors that induce conformational changes in EnvGP that are a prerequisite for fusion of the viral and cellular membranes. abstract: Enveloped viruses penetrate their cell targets following the merging of their membrane with that of the cell. This fusion process is catalyzed by one or several viral glycoproteins incorporated on the membrane of the virus. These envelope glycoproteins (EnvGP) evolved in order to combine two features. First, they acquired a domain to bind to a specific cellular protein, named “receptor.” Second, they developed, with the help of cellular proteins, a function of finely controlled fusion to optimize the replication and preserve the integrity of the cell, specific to the genus of the virus. Following the activation of the EnvGP either by binding to their receptors and/or sometimes the acid pH of the endosomes, many changes of conformation permit ultimately the action of a specific hydrophobic domain, the fusion peptide, which destabilizes the cell membrane and leads to the opening of the lipidic membrane. The comprehension of these mechanisms is essential to develop medicines of the therapeutic class of entry inhibitor like enfuvirtide (Fuzeon) against human immunodeficiency virus (HIV). In this chapter, we will summarize the different envelope glycoprotein structures that viruses develop to achieve membrane fusion and the entry of the virus. We will describe the different entry pathways and cellular proteins that viruses have subverted to allow infection of the cell and the receptors that are used. Finally, we will illustrate more precisely the recent discoveries that have been made within the field of the entry process, with a focus on the use of pseudoparticles. These pseudoparticles are suitable for high-throughput screenings that help in the development of natural or artificial inhibitors as new therapeutics of the class of entry inhibitors. url: https://doi.org/10.1016/b978-0-12-380860-8.00004-5 doi: 10.1016/b978-0-12-380860-8.00004-5 id: cord-025172-qg3jxgch author: Covarrubias, Jose title: Trauma patients with human immunodeficiency virus (HIV): a propensity matched analysis date: 2020-05-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Given the growing number of people worldwide living with huma immunodeficiency virus (HIV), a larger subset of these patients are now susceptible to sustaining a traumatic injury. However, the impact of HIV on outcomes in trauma with modern antiretroviral treatment remains unclear. We hypothesized mortality and rates of infectious and inflammatory complications would be higher in HIV positive (HIV+) trauma patients. METHODS: The Trauma Quality Improvement Program was queried to identify trauma patients ≥ 18 years of age with HIV. Due to the imbalance between HIV+ and HIV negative (HIV−) trauma patients, a 1:2 propensity-matched model was utilized. Matched variables included age, injury severity score, mechanism of injury, systolic blood pressure, pulse rate, Glasgow Coma Scale score, and patient comorbidities. RESULTS: 84 HIV+ patients were matched to 168 HIV− patients. Compared to HIV− patients, HIV+ patients had no significant differences in mortality rate (9.5% vs. 4.8%, p = 0.144) or infectious complications, including pneumonia (6.0% vs. 4.2%, p = 0.530), urinary tract infection (1.2% vs. 1.2%, p = 1.000), or severe sepsis (1.2% vs. 0.0%, p = 0.156). However, higher rates of acute respiratory distress syndrome (ARDS) (9.5% vs. 0.6%, p < 0.001) and acute kidney injury (AKI) (4.8% vs. 0.0%, p = 0.004) were observed. CONCLUSION: HIV+ trauma patients are not at higher risk of mortality or infectious complications, likely due to the advent and prevalence of combination antiretroviral therapy. However, HIV positivity appears to increase the risk of AKI and ARDS in trauma patients. Further research is needed to confirm this finding to elucidate the etiology underlying this association. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246034/ doi: 10.1007/s00068-020-01402-4 id: cord-262232-7ecg1iha author: Crakes, Katti R title: Efficacy of silk fibroin biomaterial vehicle for in vivo mucosal delivery of Griffithsin and protection against HIV and SHIV infection ex vivo date: 2020-10-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: The majority of new HIV infections occur through mucosal transmission. The availability of readily applicable and accessible platforms for anti‐retroviral (ARV) delivery is critical for the prevention of HIV acquisition through sexual transmission in both women and men. There is a compelling need for developing new topical delivery systems that have advantages over the pills, gels and rings, which currently fail to guarantee protection against mucosal viral transmission in vulnerable populations due to lack of user compliance. The silk fibroin (SF) platform offers another option that may be better suited to individual circumstances and preferences to increase efficacy through user compliance. The objective of this study was to test safety and efficacy of SF for anti‐HIV drug delivery to mucosal sites and for viral prevention. METHODS: We formulated a potent HIV inhibitor Griffithsin (Grft) in a mucoadhesive silk fibroin (SF) drug delivery platform and tested the application in a non‐human primate model in vivo and a pre‐clinical human cervical and colorectal tissue explant model. Both vaginal and rectal compartments were assessed in rhesus macaques (Mucaca mulatta) that received SF (n = 4), no SF (n = 7) and SF‐Grft (n = 11). In this study, we evaluated the composition of local microbiota, inflammatory cytokine production, histopathological changes in the vaginal and rectal compartments and mucosal protection after ex vivo SHIV challenge. RESULTS: Effective Grft release and retention in mucosal tissues from the SF‐Grft platform resulted in protection against HIV in human cervical and colorectal tissue as well as against SHIV challenge in both rhesus macaque vaginal and rectal tissues. Mucoadhesion of SF‐Grft inserts did not cause any inflammatory responses or changes in local microbiota. CONCLUSIONS: We demonstrated that in vivo delivery of SF‐Grft in rhesus macaques fully protects against SHIV challenge ex vivo after two hours of application and is safe to use in both the vaginal and rectal compartments. Our study provides support for the development of silk fibroin as a highly promising, user‐friendly HIV prevention modality to address the global disparity in HIV infection. url: https://doi.org/10.1002/jia2.25628 doi: 10.1002/jia2.25628 id: cord-021326-yx0eb885 author: Croser, David title: Infection control since HIV date: 2020-04-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149282/ doi: 10.1038/s41404-020-0359-y id: cord-252433-0e9lonq4 author: Cullen, Bryan R. title: Viral RNAs: Lessons from the Enemy date: 2009-02-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses are adept at evolving or co-opting genomic elements that allow them to maximize their replication potential in the infected host. This evolutionary plasticity makes viruses an invaluable system to identify new mechanisms used not only by viruses but also by vertebrate cells to modulate gene expression. Here, I discuss the identification and characterization of viral mRNA structures and noncoding RNAs that have led to important insights into the molecular mechanisms of eukaryotic cells. url: https://doi.org/10.1016/j.cell.2009.01.048 doi: 10.1016/j.cell.2009.01.048 id: cord-007188-tcq8lnwg author: Cunningham, Anthony L. title: Gastrointestinal Viral Infections in Homosexual Men Who were Symptomatic and Seropositive for Human Immunodeficiency Virus date: 1988-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Gastrointestinal viruses, predominantly rotaviruses and adenoviruses, were detected by enzyme-linked immunosorbent assay, electron microscopy, or cell culture in >50% of two groups of homosexual men with symptomatic human immunodeficiency virus (HIV) infection, who did (54%) or did not (50%) have diarrhea. Lower detection rates were observed in HIV-seronegative (15%) and asymptomatic HIV-seropositive (16%) men. In the patients with diarrhea, 95% of the isolates of virus were found in the most immuno suppressed patients, those patients with AIDS-related complex or opportunistic infections associated with AIDS. High excretion rates of these viruses are probably associated with both anal-oral transmission and immunosuppression. These viruses apparently cause acute episodes or relapses of diarrhea in some patients but may be co-pathogens or noncontributory to chronic diarrhea in others. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109796/ doi: 10.1093/infdis/158.2.386 id: cord-279849-zzkliu76 author: DaPalma, T. title: A systematic approach to virus–virus interactions date: 2010-01-20 words: 8230.0 sentences: 366.0 pages: flesch: 36.0 cache: ./cache/cord-279849-zzkliu76.txt txt: ./txt/cord-279849-zzkliu76.txt summary: Therefore, in this review we identify known and potential types of virus-virus interactions (VVIs) and organize them into three categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) a subset of indirect interactions called immunological interactions, unique to organisms equipped with an adaptive immune system. One of the first helper-dependent viruses described was bacteriophage P4, a bacteria-infecting virus that is able to replicate its own genome, but requires the presence of a coinfecting bacteriophage, such as P2, to provide capsid components and cell lysis (Shore et al., 1978; Six and Klug, 1973) . While direct binding and activation of viral transactivating proteins to heterologous viral promoters has been documented, more common are reports of viral infections inducing increased expression or activation of cellular transcription factors, which then act on promoters of coinfecting viruses. Human cytomegalovirus TRS1 and IRS1 gene products block the double-stranded-RNA-activated host protein shutoff response induced by herpes simplex virus type 1 infection abstract: A virus–virus interaction is a measurable difference in the course of infection of one virus as a result of a concurrent or prior infection by a different species or strain of virus. Many such interactions have been discovered by chance, yet they have rarely been studied systematically. Increasing evidence suggests that virus–virus interactions are common and may be critical to understanding viral pathogenesis in natural hosts. In this review we propose a system for classifying virus–virus interactions by organizing them into three main categories: (1) direct interactions of viral genes or gene products, (2) indirect interactions that result from alterations in the host environment, and (3) immunological interactions. We have so far identified 15 subtypes of interaction and assigned each to one of these categories. It is anticipated that this framework will provide for a more systematic approach to investigating virus–virus interactions, both at the cellular and organismal levels. url: https://doi.org/10.1016/j.virusres.2010.01.002 doi: 10.1016/j.virusres.2010.01.002 id: cord-292546-un0blb3w author: Dandachi, Dima title: Characteristics, Comorbidities, and Outcomes in a Multicenter Registry of Patients with HIV and Coronavirus Disease-19 date: 2020-09-09 words: 3438.0 sentences: 274.0 pages: flesch: 57.0 cache: ./cache/cord-292546-un0blb3w.txt txt: ./txt/cord-292546-un0blb3w.txt summary: BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. [12] [13] [14] [15] Some of these studies reported that PWH with COVID-19 had similar clinical characteristics and comparable risk of severe disease to the general population. Study variables included patient demographics, HIV-associated variables, underlying medical problems, COVID-19 clinical presentation as reported by patients, laboratory values, treatment, and clinical outcomes. In a multivariable analysis, older age, lower CD4 count, chronic lung disease, hypertension, and high comorbidity burden were significantly associated with severe outcomes (Table 4) . As reported in multiple other studies in people without HIV, we found that age, chronic lung disease, and comorbidity burden were associated with increased rates of severe outcomes. In addition, among HIV-specific factors, we found that a lower CD4 count (< 200 cells/mm3) was associated with poor outcomes, including higher hospitalization rates, lower ICU-free survival, and overall survival. abstract: BACKGROUND: People with HIV (PWH) may have numerous risk factors for acquiring Coronavirus disease-19 (COVID-19) and developing severe outcomes, but current data are conflicting. METHODS: Healthcare providers enrolled consecutively by non-random sampling PWH with lab-confirmed COVID-19, diagnosed at their facilities between April 1st and July 1st, 2020. De-identified data were entered into an electronic Research Electronic Data Capture (REDCap). The primary endpoint was severe outcome, defined as a composite endpoint of intensive care unit (ICU) admission, mechanical ventilation, or death. The secondary outcome was the need for hospitalization. RESULTS: 286 patients were included; the mean age was 51.4 years (SD, 14.4), 25.9% were female, and 75.4% were African-American or Hispanic. Most patients (94.3%) were on antiretroviral therapy (ART), 88.7% had HIV virologic suppression, and 80.8% had comorbidities. Within 30 days of positive SARS-CoV-2 testing, 164 (57.3%) patients were hospitalized, and 47 (16.5%) required ICU admission. Mortality rates were 9.4% (27/286) overall, 16.5% (27/164) among those hospitalized, and 51.5% (24/47) among those admitted to an ICU. The primary composite endpoint occurred in 17.5% (50/286) of all patients and 30.5% (50/164) of hospitalized patients. Older age, chronic lung disease, and hypertension were associated with severe outcomes. A lower CD4 count (<200 cells/mm³) was associated with the primary and secondary endpoints. There was no association between the antiretroviral regimen or lack of viral suppression and predefined outcomes. CONCLUSION: Severe clinical outcomes occurred commonly in PWH and COVID-19. The risk for poor outcomes was higher in those with comorbidities and lower CD4 cell counts, despite HIV viral suppression. url: https://doi.org/10.1093/cid/ciaa1339 doi: 10.1093/cid/ciaa1339 id: cord-017629-fuv157f1 author: De Groot, Anne S. title: Epitope-Based Immunome-Derived Vaccines: A Strategy for Improved Design and Safety date: 2008-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vaccine science has extended beyond genomics to proteomics and has come to also encompass ‘immunomics,’ the study of the universe of pathogen-derived or neoplasm-derived peptides that interface with B and T cells of the host immune system. It has been theorized that effective vaccines can be developed using the minimum essential subset of T cell and B cell epitopes that comprise the ‘immunome.’ Researchers are therefore using bioinformatics sequence analysis tools, epitope-mapping tools, microarrays, and high-throughput immunology assays to discover the minimal essential components of the immunome. When these minimal components, or epitopes, are packaged with adjuvants in an appropriate delivery vehicle, the complete package comprises an epitope-based immunome-derived vaccine. Such vaccines may have a significant advantage over conventional vaccines, as the careful selection of the components may diminish undesired side effects such as have been observed with whole pathogen and protein subunit vaccines. This chapter will review the pre-clinical and anticipated clinical development of computer-driven vaccine design and the validation of epitope-based immunome-derived vaccines in animal models; it will also include an overview of heterologous immunity and other emerging issues that will need to be addressed by vaccines of all types in the future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122239/ doi: 10.1007/978-0-387-79208-8_3 id: cord-026112-58sa5z03 author: Dehghani-Dehej, Farzaneh title: Prevalence of HCV and/or HBV coinfection in Iranian HIV-infected patients date: 2020-04-24 words: 4005.0 sentences: 198.0 pages: flesch: 47.0 cache: ./cache/cord-026112-58sa5z03.txt txt: ./txt/cord-026112-58sa5z03.txt summary: This study aimed to investigate molecular epidemiology of HBV and HCV coinfection in Iranian HIV-infected individuals. Materials & methods: In this cross-sectional study, serological markers of HBV and HCV infection (hepatitis B surface antigen [HBsAg], hepatitis B e-antigen [HBeAg], hepatitis B e-antibody [HBeAb] and hepatitis B core antibody [HBcAb]) and anti-HCV antibodies [anti-HCV Abs] were tested in 198 Iranian HIV-infected patients. HIV/HBV-coinfected people have a higher rate of progression to liver fibrosis, cirrhosis, HCC, less clearance of HBsAg and occult HBV infections (OBI) are more frequent in these patients [13] . The aim for this study is to investigate the prevalence of HCV and/or HBV coinfection in Iranian HIV-infected individuals. According to a previous study, prevalence of cirrhosis in HIV/HBV/HCV triple-infected patients was higher than HIV/HBV-or HIV/HCV-coinfected individuals [57] . abstract: Aim: HIV-infected patients risk coinfection with HBV and HCV. This study aimed to investigate molecular epidemiology of HBV and HCV coinfection in Iranian HIV-infected individuals. Materials & methods: In this cross-sectional study, serological markers of HBV and HCV infection (hepatitis B surface antigen [HBsAg], hepatitis B e-antigen [HBeAg], hepatitis B e-antibody [HBeAb] and hepatitis B core antibody [HBcAb]) and anti-HCV antibodies [anti-HCV Abs] were tested in 198 Iranian HIV-infected patients. From plasma, HBV viral load was determined using COBAS TaqMan 48, and HCV-RNA was detected by reverse transcriptase-nested PCR. Results: 85 out of 198 (42.9%) patients were anti-HCV Ab positive and 42/198 (21.2%) had detectable HCV-RNA. Eight (4.0%) had traceable HBV-DNA. All these patients were infected by HBV genotype D. 55 (27.8%) were HBcAb positive. Nine (4.4%) were HBsAg and anti-HCV Ab positive. Conclusion: None were HIV-RNA/HCV-RNA/HBV-DNA positive, 21.2% were HIV-RNA/HCV-RNA positive and 4.0% were HIV-RNA/HBV-DNA positive. Therefore, studies on diagnosing these infections in HIV-infected individuals may be valuable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273902/ doi: 10.2217/fvl-2019-0066 id: cord-339879-92esdjy9 author: Delhalle, Sylvie title: Phages and HIV-1: From Display to Interplay date: 2012-04-13 words: 21838.0 sentences: 978.0 pages: flesch: 44.0 cache: ./cache/cord-339879-92esdjy9.txt txt: ./txt/cord-339879-92esdjy9.txt summary: The BNtAb IgG1 b12 was the first neutralizing MAb selected from a phage-displayed Fab (antibody fragment composed of one constant and one variable domain of the heavy (CH1 and VH) and the light (CL and VL) chains linked together) library derived from an HIV-1-infected donor (See section 3.1.1.1.1.) [41] . At the end of the second round, selected phages displaying longer inserts of 40 to 50 AA corresponding to the N-and C-terminal regions of Gag were identified, revealing the presence of two distinct antigenic regions in Gag. This study demonstrated that gene-fragment phage display could be used to identify epitopes targeted by polyclonal Abs. Although they occur at a very low frequency in humans, antibodies targeting host proteins involved in HIV-1 infection have been reported in immunized animals. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries abstract: The complex hide-and-seek game between HIV-1 and the host immune system has impaired the development of an efficient vaccine. In addition, the high variability of the virus impedes the long-term control of viral replication by small antiviral drugs. For more than 20 years, phage display technology has been intensively used in the field of HIV-1 to explore the epitope landscape recognized by monoclonal and polyclonal HIV-1-specific antibodies, thereby providing precious data about immunodominant and neutralizing epitopes. In parallel, biopanning experiments with various combinatorial or antibody fragment libraries were conducted on viral targets as well as host receptors to identify HIV-1 inhibitors. Besides these applications, phage display technology has been applied to characterize the enzymatic specificity of the HIV-1 protease. Phage particles also represent valuable alternative carriers displaying various HIV-1 antigens to the immune system and eliciting antiviral responses. This review presents and summarizes the different studies conducted with regard to the nature of phage libraries, target display mode and biopanning procedures. url: https://www.ncbi.nlm.nih.gov/pubmed/22606007/ doi: 10.3390/ijms13044727 id: cord-322915-zrjx31ev author: Demain, Arnold L title: Microbial drug discovery: 80 years of progress date: 2009-01-09 words: 11246.0 sentences: 688.0 pages: flesch: 40.0 cache: ./cache/cord-322915-zrjx31ev.txt txt: ./txt/cord-322915-zrjx31ev.txt summary: Evidence of the importance of natural products in the discovery of leads for the development of drugs for the treatment of human diseases is provided by the fact that close to half of the best selling pharmaceuticals in 1991 were either natural products or their derivatives. In addition to the antibiotic-resistance problem, new families of anti-infective compounds are needed to enter the marketplace at regular intervals to tackle the new diseases caused by evolving pathogens. 28 Among the novel class of antimicrobial agents used in treating resistance to Gram-positive infections, we can also mention the cyclic lipopeptide antibiotic daptomycin produced by Streptomyces roseosporus. 44 Other applications include antitumor drugs, enzyme inhibitors, gastrointestinal motor stimulator agents, hypocholesterolemic drugs, ruminant growth stimulants, insecticides, herbicides, coccidiostats, antiparasitics vs coccidia, helminths and other pharmacological activities. Considering that animal health research and the development of new anti-infective product discovery have decreased, the discovery of new antibiotics has decreased over the past 15 years, with few new drug approvals. abstract: Microbes have made a phenomenal contribution to the health and well-being of people throughout the world. In addition to producing many primary metabolites, such as amino acids, vitamins and nucleotides, they are capable of making secondary metabolites, which constitute half of the pharmaceuticals on the market today and provide agriculture with many essential products. This review centers on these beneficial secondary metabolites, the discovery of which goes back 80 years to the time when penicillin was discovered by Alexander Fleming. url: https://doi.org/10.1038/ja.2008.16 doi: 10.1038/ja.2008.16 id: cord-315687-stgj6olw author: Demma, LJ title: Evolution of the uniquely adaptable lentiviral envelope in a natural reservoir host date: 2006-03-20 words: 6439.0 sentences: 322.0 pages: flesch: 46.0 cache: ./cache/cord-315687-stgj6olw.txt txt: ./txt/cord-315687-stgj6olw.txt summary: To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time. Although phylogenetic analyses of SIV sequences reveal considerable viral genetic diversity between different infected individuals [19] , the magnitude of intra-animal viral diversity, the substrate for selection in cross-species transmission events, has not been studied. The pre-existence of viral env variants in naturally infected SMs that are capable of replicating to high levels in a new host species pointed to the importance of SIVsm diversity in the reservoir host in enabling cross-species transmission. Here we describe extraordinarily high intra-host SIVsm env V1V2 diversity in naturally infected SMs, maintained by its high replication rate and positive selection most likely mediated by antibody responses. The similar levels of viral variation may also indicate that selective forces acting on env V1V2 are comparable in both SIVsm-infected natural mangabey reservoir hosts and in HIV-infected humans. abstract: BACKGROUND: The ability of emerging pathogens to infect new species is likely related to the diversity of pathogen variants present in existing reservoirs and their degree of genomic plasticity, which determines their ability to adapt to new environments. Certain simian immunodeficiency viruses (SIVcpz, SIVsm) have demonstrated tremendous success in infecting new species, including humans, resulting in the HIV-1 and HIV-2 epidemics. Although SIV diversification has been studied on a population level, the essential substrates for cross-species transmission, namely SIV sequence diversity and the types and extent of viral diversification present in individual reservoir animals have not been elucidated. To characterize this intra-host SIV diversity, we performed sequence analyses of clonal viral envelope (env) V1V2 and gag p27 variants present in individual SIVsm-infected sooty mangabeys over time. RESULTS: SIVsm demonstrated extensive intra-animal V1V2 length variation and amino acid diversity (le38%), and continual variation in V1V2 N-linked glycosylation consensus sequence frequency and location. Positive selection was the predominant evolutionary force. Temporal sequence shifts suggested continual selection, likely due to evolving antibody responses. In contrast, gag p27 was predominantly under purifying selection. SIVsm V1V2 sequence diversification is at least as great as that in HIV-1 infected humans, indicating that extensive viral diversification in and of itself does not inevitably lead to AIDS. CONCLUSION: Positive diversifying selection in this natural reservoir host is the engine that has driven the evolution of the uniquely adaptable SIV/HIV envelope protein. These studies emphasize the importance of retroviral diversification within individual host reservoir animals as a critical substrate in facilitating cross-species transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/16549011/ doi: 10.1186/1742-4690-3-19 id: cord-004600-5lhnzzvg author: Dennin, Reinhard H. title: HIV-Infektion – Grenzen der Präventionskonzepte: Überlegungen zur Verantwortung der Betroffenen, der Politik und der Gesellschaft* date: 2007-03-26 words: 2694.0 sentences: 329.0 pages: flesch: 50.0 cache: ./cache/cord-004600-5lhnzzvg.txt txt: ./txt/cord-004600-5lhnzzvg.txt summary: Die HIV-Epidemie ist bestimmt durch ein komplexes Zusammenwirken von personengebundener Transmission, über eine Dekade langer, klinisch asymptomatischer Zeit bis zur Manifestation der Krankheit, bei permanenter Infektiosität. Die individuelle intime Sphäre des Sexualverhaltens ist durch unsere gesellschaftliche Verhaltensnormen geschützt; somit kann die HIV-Infektion als personengebundene Transmission nicht wie andere Infektionen, die den community acquired infections zugerechnet werden, z. Angewandt auf die Präventionskonzepte gegen die Ausbreitung von HIV war damit ein Vertrauens-und Erwartungsvorschuss für bereits von der HIV-Infektion betroffene wie noch HIV-naive Mitmenschen verbunden, sich den an die kognitive Ebene richtenden rationalen Präventionsbotschaften entsprechend zu verhalten, d. Die Argumente von Vertretern der wesentlich auf Konzepten der NPH basierenden HIV-Präventionskampagnen, diese hätten wesentlich zu den "geringen" Zuwachsraten an HIV-Infizierten in Deutschland und -wegen der europäischen Abstimmung -auch in Europa beigetragen, sind nach der derzeitigen Datenlage weder zu widerlegen noch zu belegen, da ein anderes Modell der Prävention nicht eingeführt wurde. abstract: Despite the introduction of campaigns to prevent the continued spread of HIV/AIDS in Germany, the number of annual firsttime HIV-diagnoses is continuing steadily. The concepts behind the current campaigns are largely based on models of New Public Health, of which social learning strategies are an essential element. The established personal and individual rights should be unimpeachable but the right not to know the status of HIV infection should be questioned for those people who spread their HIV infection intentionally and wilfully. Confronted with more than 10,000 people in Germany unconscious of their HIV infection, easy access to HIV testing and access of opportune therapy should be offered with the goal of reducing the number of new infections. Expanded strategies on the responsibility to one’s personal health and that of the partner, understandable and adapted to special groups of the society, should be established and maintained at a high level of awareness. All measures must be performed voluntarily. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080062/ doi: 10.1007/s00103-007-0212-z id: cord-281367-qm5a5c4b author: Des Jarlais, Don C title: Patterns of HIV prevalence among injecting drug users in the cross-border area of Lang Son Province, Vietnam, and Ning Ming County, Guangxi Province, China date: 2005-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: To assess patterns of injecting drug use and HIV prevalence among injecting drug users (IDUs) in an international border area along a major heroin trans-shipment route. METHODS: Cross-sectional surveys of IDUs in 5 sites in Lang Son Province, Vietnam (n = 348) and 3 sites in Ning Ming County, Guangxi Province, China (n = 308). Respondents were recruited through peer referral ("snowball") methods in both countries, and also from officially recorded lists of IDUs in Vietnam. A risk behavior questionnaire was administered and HIV counseling and testing conducted. RESULTS: Participants in both countries were largely male, in their 20s, and unmarried. A majority of subjects in both countries were members of ethnic minority groups. There were strong geographic gradients for length of drug injecting and for HIV seroprevalence. Both mean years injecting and HIV seroprevalence declined from the Vietnamese site farthest from the border to the Chinese site farthest from the border. 10.6% of participants in China and 24.5% of participants in Vietnam reported crossing the international border in the 6 months prior to interview. Crossing the border by IDUs was associated with (1) distance from the border, (2) being a member of an ethnic minority group, and (3) being HIV seropositive among Chinese participants. CONCLUSION: Reducing the international spread of HIV among IDUs will require programs at the global, regional, national, and "local cross border" levels. At the local cross border level, the programs should be coordinated on both sides of the border and on a sufficient scale that IDUs will be able to readily obtain clean injection equipment on the other side of the border as well as in their country of residence. url: https://www.ncbi.nlm.nih.gov/pubmed/16120225/ doi: 10.1186/1471-2458-5-89 id: cord-004827-bnf3mvaf author: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087184/ doi: 10.1007/s00705-004-0466-9 id: cord-331289-02411gfv author: Di Minno, Giovanni title: Current concepts in the prevention of pathogen transmission via blood/plasma-derived products for bleeding disorders() date: 2015-07-20 words: 8171.0 sentences: 395.0 pages: flesch: 43.0 cache: ./cache/cord-331289-02411gfv.txt txt: ./txt/cord-331289-02411gfv.txt summary: In general, clinicians assess the level of risk associated with the use of blood/ plasma-derived products by evaluating factors such as patient characteristics (e.g. age, immune status, geographical location, lifestyle) and the nature of the pathogen (e.g. physical characteristics, level of virulence, chronicity of infection, prevalence). Current donor selection and screening practices have improved our ability to detect or reduce the presence of pathogens in blood/plasma-derived products; for example, the residual risk of transfusion-transmitted infection (TTI) with HIV/HBV/HCV has fallen to near or less than 1 per million transfused units [14, 15] . Since TTV is often detected in healthy individuals and is not associated with any particular disease, routine screening for this virus is not considered to be necessary; even a test with excellent sensitivity/specificity would not contribute to increase the level of safety of blood/plasma-derived products with regard to TTV. abstract: The pathogen safety of blood/plasma-derived products has historically been a subject of significant concern to the medical community. Measures such as donor selection and blood screening have contributed to increase the safety of these products, but pathogen transmission does still occur. Reasons for this include lack of sensitivity/specificity of current screening methods, lack of reliable screening tests for some pathogens (e.g. prions) and the fact that many potentially harmful infectious agents are not routinely screened for. Methods for the purification/inactivation of blood/plasma-derived products have been developed in order to further reduce the residual risk, but low concentrations of pathogens do not necessarily imply a low level of risk for the patient and so the overall challenge of minimising risk remains. This review aims to discuss the variable level of pathogenic risk and describes the current screening methods used to prevent/detect the presence of pathogens in blood/plasma-derived products. url: https://www.sciencedirect.com/science/article/pii/S0268960X15000594 doi: 10.1016/j.blre.2015.07.004 id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 words: 9235.0 sentences: 480.0 pages: flesch: 45.0 cache: ./cache/cord-312332-rwmuucsp.txt txt: ./txt/cord-312332-rwmuucsp.txt summary: title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the ''knowns'' and ''unknowns'' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . abstract: RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the ‘knowns’ and ‘unknowns’ regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32921578/ doi: 10.1016/j.semcdb.2020.08.002 id: cord-324690-82qsirnk author: Dieffenbach, Carl W title: The search for an HIV vaccine, the journey continues date: 2020-05-16 words: 1469.0 sentences: 73.0 pages: flesch: 51.0 cache: ./cache/cord-324690-82qsirnk.txt txt: ./txt/cord-324690-82qsirnk.txt summary: Over the past decade, three different vaccine approaches have been implemented, possible correlates of protection identified, and two have moved through clinical evaluation to advanced clinical trials. Analysis of the correlates of protection seen in the non-human primate studies point to qualitatively different responses than those observed in RV144, and the trials are evaluating in silico designed immunogens to present the most globally conserved HIV sequences to trigger quantitatively superior CD8 + T cell responses [8, 9] . The Antibody Mediated Protection (AMP) trials are currently evaluating VRC01, the CD4 binding site targeted bNAb, to determine the ability of this single antibody to prevent HIV infection in women in Southern Africa and MSM and transgender persons in the Americas [13] . The authors thank the trial participants, community members, activists and researchers who have so willingly participated in the challenging work of HIV vaccine discovery and development. abstract: nan url: https://doi.org/10.1002/jia2.25506 doi: 10.1002/jia2.25506 id: cord-270726-w59fu9c9 author: Dikman, Andrew E. title: Human Immunodeficiency Virus-Associated Diarrhea: Still an Issue in the Era of Antiretroviral Therapy date: 2015-03-14 words: 5191.0 sentences: 279.0 pages: flesch: 43.0 cache: ./cache/cord-270726-w59fu9c9.txt txt: ./txt/cord-270726-w59fu9c9.txt summary: The etiology of noninfectious diarrhea in patients with HIV is multifactorial and includes ART-associated diarrhea and gastrointestinal damage related to HIV infection (i.e., HIV enteropathy). A basic algorithm for the diagnosis of diarrhea in patients with HIV includes physical examination, a review of medical history, assessment of HIV viral load and CD4+ T cell count, stool microbiologic assessment, and endoscopic evaluation, if needed. In addition, these agents can be associated with treatment-limiting adverse events (AEs), such as drug–drug interactions with ART regimens, abuse liability, and additional gastrointestinal AEs. Currently, crofelemer, an antisecretory agent, is the only therapy approved in the USA for the symptomatic relief of noninfectious diarrhea in patients with HIV on ART. While infection has historically been the major cause of diarrhea in patients with HIV, with the widespread use of ART therapy, noninfectious diarrhea has become a burden in this population. abstract: Over half of patients with human immunodeficiency virus (HIV) experience diarrhea that contributes negatively to quality of life and adherence to antiretroviral therapy (ART). Opportunistic infectious agents that cause diarrhea in patients with HIV span the array of protozoa, fungi, viruses, and bacteria. With global use of ART, the incidence of diarrhea because of opportunistic infections has decreased; however, the incidence of noninfectious diarrhea has increased. The etiology of noninfectious diarrhea in patients with HIV is multifactorial and includes ART-associated diarrhea and gastrointestinal damage related to HIV infection (i.e., HIV enteropathy). A basic algorithm for the diagnosis of diarrhea in patients with HIV includes physical examination, a review of medical history, assessment of HIV viral load and CD4+ T cell count, stool microbiologic assessment, and endoscopic evaluation, if needed. For patients with negative diagnostic results, the diagnosis of noninfectious diarrhea may be considered. Pharmacologic options for the treatment of noninfectious diarrhea are primarily supportive; however, the use of many unapproved agents is based on unstudied and anecdotal information. In addition, these agents can be associated with treatment-limiting adverse events (AEs), such as drug–drug interactions with ART regimens, abuse liability, and additional gastrointestinal AEs. Currently, crofelemer, an antisecretory agent, is the only therapy approved in the USA for the symptomatic relief of noninfectious diarrhea in patients with HIV on ART. url: https://doi.org/10.1007/s10620-015-3615-y doi: 10.1007/s10620-015-3615-y id: cord-017070-05vlz5dn author: Dimitrov, Dimiter S. title: Human Monoclonal Antibodies Against HIV and Emerging Viruses date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121542/ doi: 10.1007/978-1-59745-569-5_34 id: cord-022128-r8el8nqm author: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Genetic variation is a necessity of all biological systems. Viruses use all known mechanisms of variation; mutation, several forms of recombination, and segment reassortment in the case of viruses with a segmented genome. These processes are intimately connected with the replicative machineries of viruses, as well as with fundamental physical-chemical properties of nucleotides when acting as template or substrate residues. Recombination has been viewed as a means to rescue viable genomes from unfit parents or to produce large modifications for the exploration of phenotypic novelty. All types of genetic variation can act conjointly as blind processes to provide the raw materials for adaptation to the changing environments in which viruses must replicate. A distinction is made between mechanistically unavoidable and evolutionarily relevant mutation and recombination. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153327/ doi: 10.1016/b978-0-12-816331-3.00002-7 id: cord-298033-kzdp9edn author: Domingo, Esteban title: Quasispecies dynamics in disease prevention and control date: 2019-11-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Medical interventions to prevent and treat viral disease constitute evolutionary forces that may modify the genetic composition of viral populations that replicate in an infected host and influence the genomic composition of those viruses that are transmitted and progress at the epidemiological level. Given the adaptive potential of viruses in general and the RNA viruses in particular, the selection of viral mutants that display some degree of resistance to inhibitors or vaccines is a tangible challenge. Mutant selection may jeopardize control of the viral disease. Strategies intended to minimize vaccination and treatment failures are proposed and justified based on fundamental features of viral dynamics explained in the preceding chapters. The recommended use of complex, multiepitopic vaccines, and combination therapies as early as possible after initiation of infection falls under the general concept that complexity cannot be combated with simplicity. It also follows that sociopolitical action to interrupt virus replication and spread as soon as possible is as important as scientifically sound treatment designs to control viral disease on a global scale. url: https://www.sciencedirect.com/science/article/pii/B9780128163313000088 doi: 10.1016/b978-0-12-816331-3.00008-8 id: cord-306111-wn1gxhk9 author: Dommett, R. M. title: Mannose‐binding lectin in innate immunity: past, present and future date: 2006-09-01 words: 9061.0 sentences: 436.0 pages: flesch: 43.0 cache: ./cache/cord-306111-wn1gxhk9.txt txt: ./txt/cord-306111-wn1gxhk9.txt summary: Third MBL mutation in codon 52 (variant D) described (52) 1995 Polymorphisms found in promoter region of MBL gene (55) 1997 Second MASP found to activate complement (20) MBL mutations are an important risk factor for infections in children (132) 1998 Reconstitution of opsonizing activity by infusion of purified MBL into MBL-deficient humans (112) 1999 Truncated form of MASP-2 -MAp19 (21) 2000 Complement-activating complex of ficolins and MASP (133) MBL shown to bind to clinically relevant organisms (15) Structural aspects of MBL abstract: The human collectin, mannose‐binding lectin (MBL), is an important protein of the humoral innate immune system. With multiple carbohydrate‐recognition domains, it is able to bind to sugar groups displayed on the surfaces of a wide range of microorganisms and thereby provide first‐line defence. Importantly, it also activates the complement system through a distinctive third pathway, independent of both antibody and the C1 complex. Three single point mutations in exon 1 of the expressed human MBL‐2 gene appear to impair the generation of functional oligomers. Such deficiencies of functional protein are common in certain populations, e.g. in sub‐Saharan Africa, but virtually absent in others, e.g. indigenous Australians. MBL disease association studies have been a fruitful area of research and implicate a role for MBL in infective, inflammatory and autoimmune disease processes. Overall, there appears to be a genetic balance in which individuals generally benefit from high levels of the protein. However, in certain situations, reduced levels of circulating MBL may be beneficial to the host and this may explain the persistence of the deleterious gene polymorphisms in many population groups. url: https://www.ncbi.nlm.nih.gov/pubmed/16948640/ doi: 10.1111/j.1399-0039.2006.00649.x id: cord-309900-4nln90jn author: Doornekamp, Laura title: Experience with a Multinational, Secondary School Education Module with a Focus on Prevention of Virus Infections date: 2017-07-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Worldwide, virus infections are responsible for many diseases in terms of morbidity and mortality. Vaccinations and therapies are only available for relatively few virus infections and not always where they are needed. However, knowledge of transmission routes can prevent virus infection. In the context of this study, we measured the effects of a secondary school education module, named Viruskenner, on knowledge, attitude, and risk behavior as these relate to virus infections. A nonrandomized intervention study was conducted between April and August 2015 to assess the effect of this 2-month education module on knowledge, attitude, and behavior of 684 secondary school students in the Netherlands, Suriname, and Indonesia. For the Netherlands, a control group of a further 184 students was added. Factor analysis was performed on questions pertaining to attitude and behavior. Comparative analyses between pre- and posttest per country were done using multiple linear regression, independent sample T-tests, and one-way analysis of variance. These showed a significant increase in knowledge about virus infections and the prevention of infectious diseases among the Dutch and Surinamese groups, whereas a trend of increased knowledge was evident among the Indonesian participants. The Dutch control group showed an overall decrease in knowledge. Regression analyses showed that there was a significant interaction effect between participation and time on knowledge, attitude, and awareness and behavior and risk infection. Attitudes improved significantly in the intervention group. Pearson correlation coefficients between knowledge, attitude, and behavior were found to be positive. url: https://www.ncbi.nlm.nih.gov/pubmed/28719318/ doi: 10.4269/ajtmh.16-0661 id: cord-018545-fk17n2bx author: Dorofaeff, Tavey title: Infections in the PICU date: 2012 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123446/ doi: 10.1007/978-3-642-02202-9_268 id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses are the smallest known microbes, yet they cause the most significant losses in human health. Most of the time, the best-known cure for viruses is the innate immunological defense system of the host; otherwise, the initial prevention of viral infection is the only alternative. Therefore, diagnosis is the primary strategy toward the overarching goal of virus control and elimination. The introduction of a new class of nanoscale materials with multiple unique properties and functions has sparked a series of breakthrough applications. Gold nanoparticles (AuNPs) are widely reported to guide an impressive resurgence in biomedical and diagnostic applications. Here, we review the applications of AuNPs in virus testing and detection. The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. We pay particular attention to highlighting the functional role and activity of each core Au nanostructure and the resultant detection improvements in terms of sensitivity, detection range, and time. In addition, we provide a general summary of the contributions of AuNPs to the mainstream methods of virus detection, technical measures, and recommendations required in guidance toward commercial in-field applications. url: https://doi.org/10.7150/thno.23856 doi: 10.7150/thno.23856 id: cord-011903-zqt6vu6d author: Duby, Zoe title: “As a Young Pregnant Girl… The Challenges You Face”: Exploring the Intersection Between Mental Health and Sexual and Reproductive Health Amongst Adolescent Girls and Young Women in South Africa date: 2020-07-18 words: 7227.0 sentences: 295.0 pages: flesch: 47.0 cache: ./cache/cord-011903-zqt6vu6d.txt txt: ./txt/cord-011903-zqt6vu6d.txt summary: Poor mental health, including depressive disorders and stress, contributes significantly to the burden of disease in South Africa, and other parts of sub-Saharan Africa, and is also associated with negative sexual and reproductive health (SRH) outcomes for women, such as ''unintended'' or early pregnancy, and increased risk behaviours for HIV [1] [2] [3] . In the accounts of AGYW, poor mental health, including depression and suicidal risk were linked to sexual/ romantic relationship challenges, early pregnancy and child-bearing, parenting responsibilities, experiences of violence/abuse, HIV status, and lack of emotional support. Building on previous research that has found associations between depressive symptoms and psychological distress related to pregnancy, combined with a lack of social support amongst South African women [16] , our findings provide rich descriptive data on the lived reality of the interconnected psychosocial risks including stress, emotional isolation, feelings of depression and suicidal ideation, with ''unintended'' pregnancy and HIV that AGYW in South Africa face, from their own perspectives. abstract: In South Africa, adolescent girls and young women (AGYW) are at risk of poor mental health, HIV infection and early pregnancy. Poor mental health in AGYW is associated with increased sexual risk behaviours, and impeded HIV testing and care. Using in-depth interviews and focus group discussions, we explored subjective experiences of mental health and sexual and reproductive health (SRH) amongst 237 AGYW aged 15–24 years in five South African districts. Respondents shared narratives of stress, emotional isolation, feelings of depression, and suicidal ideation, interconnected with HIV, pregnancy and violence in relationships. Findings show that AGYW in South Africa face a range of mental health stressors and lack sufficient support, which intersect with SRH challenges to heighten their vulnerability. Framed within the syndemic theory, our findings suggest that South African AGYW’s vulnerability towards early pregnancy, HIV infection and poor mental health are bidirectional and interconnected. Considering the overlaps and interactions between mental health and SRH amongst AGYW, it is critical that mental health components are integrated into SRH interventions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368608/ doi: 10.1007/s10461-020-02974-3 id: cord-278156-zd039ohv author: Dumas, Fabrice title: Membrane organization of virus and target cell plays a role in HIV entry date: 2014-09-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The initial steps of the Human Immunodeficiency Virus (HIV) replication cycle play a crucial role that arbitrates viral tropism and infection efficiency. Before the release of its genome into the host cell cytoplasm, viruses operate a complex sequence of events that take place at the plasma membrane of the target cell. The first step is the binding of the HIV protein envelope (Env) to the cellular receptor CD4. This triggers conformational changes of the gp120 viral protein that allow its interaction with a co-receptor that can be either CCR5 or CXCR4, defining the tropism of the virus entering the cell. This sequential interaction finally drives the fusion of the viral and host cell membrane or to the endocytosis of the viruses. Here, we discuss how the membrane composition and organization of both the virus and the target cell can affect these steps and thus influence the capability of the viruses to infect cells. url: https://doi.org/10.1016/j.biochi.2014.08.015 doi: 10.1016/j.biochi.2014.08.015 id: cord-333622-0ddutmdd author: Dyer, Wayne B title: Mechanisms of HIV non-progression; robust and sustained CD4+ T-cell proliferative responses to p24 antigen correlate with control of viraemia and lack of disease progression after long-term transfusion-acquired HIV-1 infection date: 2008-12-11 words: 5615.0 sentences: 243.0 pages: flesch: 44.0 cache: ./cache/cord-333622-0ddutmdd.txt txt: ./txt/cord-333622-0ddutmdd.txt summary: title: Mechanisms of HIV non-progression; robust and sustained CD4+ T-cell proliferative responses to p24 antigen correlate with control of viraemia and lack of disease progression after long-term transfusion-acquired HIV-1 infection Early studies on this cohort of TAHIV patients led to the identification of the Sydney Blood Bank Cohort (SBBC) of long-term survivors [8] , and that an attenuated nef-deleted strain of HIV-1, transmitted from a single donor resulted in slow to non-progression in these individuals [9] . In addition to the well described host genetic factors which may prolong non-progression [7] , recent studies have suggested an influence from innate immune mechanisms, including polymorphisms that decrease TLR function thereby reducing immune activation upon exposure to infections diseases [18] , or the FcγRIIA polymorphism (R/R) which is strongly associated with progressive HIV disease as a result of impaired elimination of HIV immune complexes [19] . abstract: BACKGROUND: Elite non-progressors (plasma viral load <50 copies/ml while antiretroviral naive) constitute a tiny fraction of HIV-infected individuals. After 12 years follow-up of a cohort of 13 long-term non-progressors (LTNP) identified from 135 individuals with transfusion-acquired HIV infection, 5 remained LTNP after 23 to 26 years infection, but only 3 retained elite LTNP status. We examined the mechanisms that differentiated delayed progressors from LTNP in this cohort. RESULTS: A survival advantage was conferred on 12 of 13 subjects, who had at least one host genetic factor (HLA, chemokine receptor or TLR polymorphisms) or viral attenuating factor (defective nef) associated with slow progression. However, antiviral immune responses differentiated the course of disease into and beyond the second decade of infection. A stable p24-specific proliferative response was associated with control of viraemia and retention of non-progressor status, but this p24 response was absent or declined in viraemic subjects. Strong Gag-dominant cytotoxic T lymphocyte (CTL) responses were identified in most LTNP, or Pol dominant-CTL in those with nef-defective HIV infection. CTL were associated with control of viraemia when combined with p24 proliferative responses. However, CTL did not prevent late disease progression. Individuals with sustained viral suppression had CTL recognising numerous Gag epitopes, while strong but restricted responses to one or two immunodominant epitopes was effective for some time, but failed to contain viraemia over the course of this study. Viral escape mutants at a HLA B27-restricted Gag-p24 epitope were detected in only 1 of 3 individuals, whereas declining or negative p24 proliferative responses occurred in all 3 concurrent with an increase in viraemia. CONCLUSION: Detectable viraemia at study entry was predictive of loss of LTNP status and/or disease progression in 6 of 8, and differentiated slow progressors from elite LTNP who retained potent virological control. Sustained immunological suppression of viraemia was independently associated with preserved p24 proliferative responses, regardless of the strength and breadth of the CTL response. A decline in this protective p24 response preceded or correlated with loss of non-progressor status and/or signs of disease progression. url: https://doi.org/10.1186/1742-4690-5-112 doi: 10.1186/1742-4690-5-112 id: cord-332588-k4tghibp author: D’Alessandro, Sarah title: The Use of Antimalarial Drugs against Viral Infection date: 2020-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In recent decades, drugs used to treat malaria infection have been shown to be beneficial for many other diseases, including viral infections. In particular, they have received special attention due to the lack of effective antiviral drugs against new emerging viruses (i.e., HIV, dengue virus, chikungunya virus, Ebola virus, etc.) or against classic infections due to drug-resistant viral strains (i.e., human cytomegalovirus). Here, we reviewed the in vitro/in vivo and clinical studies conducted to evaluate the antiviral activities of four classes of antimalarial drugs: Artemisinin derivatives, aryl-aminoalcohols, aminoquinolines, and antimicrobial drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/31936284/ doi: 10.3390/microorganisms8010085 id: cord-301704-mb2oylqb author: Eapen, Paul title: In Preparation for Outdoor Pharming: Griffithsin Can Be Expressed in Nicotiana excelsiana and Retains Activity After Storage as Silage date: 2020-03-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Griffithsin is an algae-derived lectin with strong anti-viral activity against HIV and a positive safety profile. Multiple clinical studies are investigating griffithsin's utility as topical HIV microbicide. HIV microbicides are an extremely cost-sensitive market and plant-based griffithsin protein expression has the potential to meet those demands. The griffithsin product used in the clinic has been expressed and purified in N. benthamiana, using a TMV-based viral vector system, Geneware®. Outdoor pharming of biopharmaceuticals would further alleviate startup costs for biotechnology firms and may allow broader product accessibility. Therefore, this study assessed expression in a hybrid tobacco line, N. excelsiana, that is susceptible to TMV-based viral vectors and can be grown outdoors. In addition to using this hybrid line we expand on methods for in planta storage of griffithsin in leafy plants by ensiling kilogram quantities of griffithsin. The ensiling process allows year-round biomanufacturing, minimal environmental-controlled storage, and reduces the industry need for multiple growth areas to maintain multi-product manufacturing of plant-based pharmaceuticals. This study shows that griffithsin can be expressed in N. excelsiana and is stable, recoverable, and active from ensiled tissue. These studies can pave the way for future plant-based pharmaceuticals to be expressed and stored in this manner. url: https://doi.org/10.3389/fbioe.2020.00199 doi: 10.3389/fbioe.2020.00199 id: cord-354029-mp5r82g4 author: Earp, L. J. title: The Many Mechanisms of Viral Membrane Fusion Proteins date: 2005 words: 12130.0 sentences: 702.0 pages: flesch: 50.0 cache: ./cache/cord-354029-mp5r82g4.txt txt: ./txt/cord-354029-mp5r82g4.txt summary: Despite their differences, common principles for how fusion proteins function are emerging: In response to an activating trigger, the metastable fusion protein converts to an extended, in some cases rodlike structure, which inserts into the target membrane via its fusion peptide. Although several viral fusion proteins, such as influenza hemagglutinin (HA) and the human immunodeficiency virus (HIV) envelope glycoprotein (Env), have emerged as paradigms, it is important to realize that there are many distinguishing features among viral fusion proteins (Table 1 ). We now review a lipid rearrangement model and focus on the roles of different regions of viral fusion proteins in choreographing the structural changes that the membranes undergo throughout the fusion cascade (Fig. 3) . Cellular membrane-binding ability of the C-terminal cytoplasmic domain of human immunodeficiency virus type 1 envelope transmembrane protein gp41 Role of the N-terminal peptides of viral envelope proteins in membrane fusion abstract: Every enveloped virus fuses its membrane with a host cell membrane, thereby releasing its genome into the cytoplasm and initiating the viral replication cycle. In each case, one or a small set of viral surface transmembrane glycoproteins mediates fusion. Viral fusion proteins vary in their mode of activation and in structural class. These features combine to yield many different fusion mechanisms. Despite their differences, common principles for how fusion proteins function are emerging: In response to an activating trigger, the metastable fusion protein converts to an extended, in some cases rodlike structure, which inserts into the target membrane via its fusion peptide. A subsequent conformational change causes the fusion protein to fold back upon itself, thereby bringing its fusion peptide and its transmembrane domain—and their attached target and viral membranes—into intimate contact. Fusion ensues as the initial lipid stalk progresses through local hemifusion, and then opening and enlargement of a fusion pore. Here we review recent advances in our understanding of how fusion proteins are activated, how fusion proteins change conformation during fusion, and what is happening to the lipids during fusion. We also briefly discuss the therapeutic potential of fusion inhibitors in treating viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/15609500/ doi: 10.1007/3-540-26764-6_2 id: cord-338654-ma9ayu80 author: Eaton, Lisa A. title: Social and behavioral health responses to COVID-19: lessons learned from four decades of an HIV pandemic date: 2020-04-25 words: 3425.0 sentences: 160.0 pages: flesch: 39.0 cache: ./cache/cord-338654-ma9ayu80.txt txt: ./txt/cord-338654-ma9ayu80.txt summary: The current state of COVID-19 disease transmission has left our public health approaches to be heavily dependent on social and behavioral change strategies to halt transmissions. We focus on multiple levels of intervention including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. We focus on multiple levels of intervention including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. The model has multiple foci, including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. Interventions to address stigma have been developed that target individuals, health care workers, communities, and social figures, which will likely find new purpose in COVID-19 (Andersson et al., 2020; Rao et al., 2019; Stangl et al., 2013) . abstract: Our public health approaches to addressing COVID-19 are heavily dependent on social and behavioral change strategies to halt transmissions. To date, biomedical forms of curative and preventative treatments for COVID-19 are at best limited. Four decades into the HIV epidemic we have learned a considerable amount of information regarding social and behavioral approaches to addressing disease transmission. Here we outline broad, scoping lessons learned from the HIV literature tailored to the nature of what we currently know about COVID-19. We focus on multiple levels of intervention including intrapersonal, interpersonal, community, and social factors, each of which provide a reference point for understanding and elaborating on social/behavioral lessons learned from HIV prevention and treatment research. The investments in HIV prevention and treatment research far outweigh any infectious disease in the history of public health, that is, until now with the emergence of COVID-19. url: https://doi.org/10.1007/s10865-020-00157-y doi: 10.1007/s10865-020-00157-y id: cord-004198-h8ch3x14 author: Ebuy, Hiluf title: HIV testing, test results and factors influencing among infants born to HIV positive mothers in public hospitals of Mekelle City, North Ethiopia: a cross-sectional study date: 2020-01-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Timely infant testing for HIV is critical to ensure optimal treatment outcomes among exposed infants. While world health organization recommends HIV exposed infants to be tested between 4 to 6 weeks of age, in developing countries like Ethiopia, access to timely infant testing is still very limited. The study is intended to assess timely infant testing, testing for HIV at the 18th month, test results and factors influencing HIV positivity among infants born to HIV positive mothers in public hospitals of Mekelle, Ethiopia. METHODS: A cross-sectional study design was employed on 558 HIV exposed infants, using consecutive sampling technique. A checklist was used to extract 4 years (January 2014–December 2017) secondary data, collected from January–April 2018. Data were analyzed using SPSS version 20, and binary logistic regression model was used to examine the association of independent variables with the outcome variables. RESULTS: Timely infant testing for HIV accounted for 346(62.0%). Mothers who attended antenatal care (AOR: 2.77; 95% CI: 1.17, 6.55) and who were counselled on feeding options (AOR: 2.01; 95% CI: 1.11, 3.65) were strongly associated with timely infant testing. Poor maternal adherence status was associated with infants’ HIV positivity at the 18th month of antibody test (AOR: 15.93; 95% CI: 2.21, 94.66). Being rural resident (AOR: 4.0; 95% CI: 1.23, 13.04), being low birth weight (AOR: 5.64; 95% CI: 2.00, 16.71) and not receiving ARV prophylaxis (AOR: 4.70; 95% CI: 1.15, 19.11) were positively associated with the overall HIV positivity. CONCLUSIONS: A considerable proportion of exposed infants did not undergo timely testing for HIV. Antenatal care follow-up and counselling on feeding options were associated with timely infant testing. Mother’s poor adherence status was associated with infant’s HIV positivity at the 18th month of antibody testing. Being rural resident, being low birth weight, and not receiving ARV prophylaxis were the factors that enhance the overall HIV positivity. Timely infant testing, counselling on feeding options and adherence should be intensified, and prevention of mother-to-child transmission program in rural settings need to be strengthened. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6975065/ doi: 10.1186/s12879-020-4790-9 id: cord-322256-mv9ll0h4 author: Edelman, E. Jennifer title: Confronting Another Pandemic: Lessons from HIV can Inform Our COVID-19 Response date: 2020-05-12 words: 1747.0 sentences: 73.0 pages: flesch: 40.0 cache: ./cache/cord-322256-mv9ll0h4.txt txt: ./txt/cord-322256-mv9ll0h4.txt summary: We reflect on how this relates to (1) testing, including contact tracing; (2) health system redesign; (3) telehealth; (4) health disparities; (5) political denial, with inadequate and uncoordinated governmental response; (6) occupational exposure; and (7) complex reactions among healthcare providers. Experiences with HIV and partner services has taught us the critical role of public health collaboration to promote contact tracing to ensure that individuals who have been exposed to an infectious disease receive appropriate counseling, testing, and treatment [2] . The differences in routes of transmission render COVID-19 many fold more dangerous than HIV in the health care setting and mandates the need for ensuring adequate PPE for healthcare workers and others providing care for individuals exposed by aerosols and contact with patients with COVID-19 and cannot be overstated. abstract: The novel coronavirus 2019 illness (COVID-19) has completely transformed and uprooted lives across the globe. While different diseases, there are critical observations and lessons to be learned from the ongoing HIV epidemic to inform our response to COVID-19. We reflect on how this relates to (1) testing, including contact tracing; (2) health system redesign; (3) telehealth; (4) health disparities; (5) political denial, with inadequate and uncoordinated governmental response; (6) occupational exposure; and (7) complex reactions among healthcare providers. Decades of experiences with HIV provide an important framework for moving forward as we combat COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32399798/ doi: 10.1007/s10461-020-02908-z id: cord-285151-zynor0b2 author: Eisenhut, Michael title: Neopterin in Diagnosis and Monitoring of Infectious Diseases date: 2013-12-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Neopterin is produced by activated monocytes, macrophages, and dendritic cells upon stimulation by interferon gamma produced by T-lymphocytes. Quantification of neopterin in body fluids has been achieved by standard high-performance liquid chromatography, radioimmunoassays, and enzyme-linked immunosorbent assays. Neopterin levels predict HIV-related mortality more efficiently than clinical manifestations. Successful highly active antiretroviral therapy is associated with a decrease in neopterin levels. Elevated neopterin levels were associated with hepatitis by hepatitis A, B, and C viruses. Serum neopterin levels were found to be a predictor of response to treatment of chronic HCV infection with pegylated interferon combined with ribavirin. Neopterin levels of patients with pulmonary tuberculosis were found to be higher in patients with more extensive radiological changes. Elimination of blood donors with elevated neopterin levels to reduce risk of transmission of infections with known and unknown viral pathogens has been undertaken. Neopterin measurement is hereby more cost effective but less sensitive than screening using polymerase chain reaction based assays. In conclusion neopterin is a nonspecific marker of activated T-helper cell 1 dominated immune response. It may be a useful marker for monitoring of infectious disease activity during treatment and for more accurate estimation of extent of disease and prognosis. url: https://doi.org/10.1155/2013/196432 doi: 10.1155/2013/196432 id: cord-000868-vnwpzsu8 author: Eissmann, Kristin title: HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop date: 2013-01-22 words: 9072.0 sentences: 425.0 pages: flesch: 51.0 cache: ./cache/cord-000868-vnwpzsu8.txt txt: ./txt/cord-000868-vnwpzsu8.txt summary: Performing a virus-cell fusion assay and temperature-arrested HIV-infection kinetics, we provide evidence that the HIV-inhibitory E2 peptides interfere with late HIV-1 entry steps after the engagement of gp120 with CD4 receptor and coreceptor. Using synthetic peptides presenting different regions of E2, we recently demonstrated that this interference with HIV-1 entry can be ascribed to the N-terminal part of the GBV-C E2 protein ranging from residue 29 to 72 (according to GenBank accession no. The Effect of GBV-C E2 Peptides Arises After gp120/CD4 and gp120/coreceptor engagement To find out whether early or late steps of HIV-1 entry are affected by the E2 peptides, the E2 peptide activity was determined before and after gp120/CD4 engagement using the Vpr-b-lactamase (Vpr-BlaM) enzyme-based virus-cell fusion assay under standard (pre-CD4 binding) and temperature-arrested state (TAS; post-CD4 binding) conditions, respectively. abstract: A strategy for antiviral drug discovery is the elucidation and imitation of viral interference mechanisms. HIV-1 patients benefit from a coinfection with GB Virus C (GBV-C), since HIV-positive individuals with long-term GBV-C viraemia show better survival rates than HIV-1 patients without persisting GBV-C. A direct influence of GBV-C on HIV-1 replication has been shown in coinfection experiments. GBV-C is a human non-pathogenic member of the flaviviridae family that can replicate in T and B cells. Therefore, GBV-C shares partly the same ecological niche with HIV-1. In earlier work we have demonstrated that recombinant glycoprotein E2 of GBV-C and peptides derived from the E2 N-terminus interfere with HIV entry. In this study we investigated the underlying mechanism. Performing a virus-cell fusion assay and temperature-arrested HIV-infection kinetics, we provide evidence that the HIV-inhibitory E2 peptides interfere with late HIV-1 entry steps after the engagement of gp120 with CD4 receptor and coreceptor. Binding and competition experiments revealed that the N-terminal E2 peptides bind to the disulfide loop region of HIV-1 transmembrane protein gp41. In conjunction with computational analyses, we identified sequence similarities between the N-termini of GBV-C E2 and the HIV-1 glycoprotein gp120. This similarity appears to enable the GBV-C E2 N-terminus to interact with the HIV-1 gp41 disulfide loop, a crucial domain involved in the gp120-gp41 interface. Furthermore, the results of the present study provide initial proof of concept that peptides targeted to the gp41 disulfide loop are able to inhibit HIV fusion and should inspire the development of this new class of HIV-1 entry inhibitors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551756/ doi: 10.1371/journal.pone.0054452 id: cord-332396-nattdect author: Ejima, K. title: HIV testing by public health centers and municipalities, and new HIV cases during the COVID-19 pandemic in Japan date: 2020-10-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background: During the COVID-19 outbreak, medical resources were primarily allocated to COVID-19, which might have reduced facility capacity for HIV testing. Further, people may have opted against HIV testing during this period to avoid COVID-19 exposure. We investigate the influence of the COVID-19 pandemic on HIV testing and its consequences in Japan. Methods: We analysed quarterly HIV/AIDS-related data from 2015 to the second quarter of 2020 using an anomaly detection approach. The data included the number of consultations that public health centers received, the number of HIV tests performed by public health centers or municipalities, and the number of newly reported HIV cases with and without AIDS diagnosis. As sensitivity analyses, we performed the same analysis for two subgroups: men who have sex with men (MSM) and non-Japanese. Findings: The number of HIV tests (9,584 vs. 35,908 in the year-before period) and consultations (11,689 vs. 32,565) performed by public health centers significantly declined in the second quarter of 2020, while the proportion of HIV cases with AIDS diagnosis among all HIV cases (36.2% vs. 26.4%) significantly increased after removing the trend and seasonality effects. The number of HIV cases without AIDS diagnosis numerically decreased (166 vs. 217), although the reduction was not significant. We confirmed similar trend for the MSM and non-Japanese groups. Interpretation: The current HIV testing system including public health centers misses more HIV cases at the early phase of the infection during the pandemic. Given that the clear epidemiological picture of HIV incidence during the pandemic is still uncertain, continuously monitoring the situation as well as securing sufficient test resources using self-test is essential. url: http://medrxiv.org/cgi/content/short/2020.10.16.20213959v1?rss=1 doi: 10.1101/2020.10.16.20213959 id: cord-020778-4jslid14 author: El Sayed, Khalid A. title: Natural Products as Antiviral Agents date: 2007-09-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since the ancient times, natural products have served as a major source of drugs. About fifty percent of today's pharmaceutical drugs are derived from natural origin. Interest in natural products as a source of new drugs is growing due to many factors that will be discussed in this article. Viruses have been resistant to therapy or prophylaxis longer than any other form of life. Currently, there are only few drugs available for the cure of viral diseases including acyclovir which is modeled on a natural product parent. In order to combat viruses which have devastating effects on humans, animals, insects, crop plants, fungi and bacteria, many research efforts have been devoted for the discovery of new antiviral natural products. Recent analysis of the number and sources of antiviral agents reported mainly in the annual reports of medicinal chemistry from 1984 to 1995 indicated that seven out of ten synthetic agents approved by FDA between 1983-1994, are modeled on a natural product parent. It has been estimated that only 5-15% of the approximately 250,000 species of higher plants have been systematically investigated for the presence of bioactive compounds while the potential of the marine environment has barely been tapped. The aim of this review is to provide an overview on the central role of natural products in the discovery and development of new antiviral drugs by displaying 340 structures of plant, marine and microbial origin that show promising in vitro antiviral activity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147881/ doi: 10.1016/s1572-5995(00)80051-4 id: cord-306315-vt2e0crh author: Elabbadi, Alexandre title: Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study) date: 2020-09-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: Acute respiratory failure is the main reason for admission to the intensive care unit (ICU) in HIV-infected adults. There is little data about the epidemiology of respiratory viruses in this population. METHODS: HIV-infected adults admitted to two intensive care units over a 6-year period for an acute respiratory failure and explored for respiratory viruses with multiplex polymerase chain reaction (mPCR) were retrospectively selected. Objectives were to describe the prevalence of respiratory viruses, coinfections with non-viral pathogens, and hospital outcome. RESULTS: A total of 123 episodes were included. An HIV infection was newly diagnosed in 9% of cases and 72% of the population were on antiretroviral therapy. Real-time mPCR tests identified at least one respiratory virus in the respiratory tract of 33 (27%) patients, but with a non-viral copathogen in two-thirds of cases. Rhinovirus was predominant, documented in 15 patients, followed by Influenza and Respiratory Syncytial Viruses (both n = 6). The prevalence of respiratory virus-associated infection did not vary along with the level of the CD4 T-cell deficiency, except for Rhinovirus which was more prevalent in patients with a CD4 lymphocyte count below 200 cells/µL (n = 13 (20%) vs. n = 2 (4%), p < 0.01). In multivariate analysis, respiratory virus-associated infection was not associated with a worse prognosis. CONCLUSIONS: Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Rhinovirus is the predominant viral specie; its prevalence is highest in patients with a CD4 lymphocyte count below 200 cells/µL. url: https://doi.org/10.1186/s13613-020-00738-9 doi: 10.1186/s13613-020-00738-9 id: cord-344084-z4t2wkgk author: Ellwanger, Joel Henrique title: Beyond HIV infection: neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases date: 2020-05-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The interactions between chemokine receptors and their ligands may affect susceptibility to infectious diseases as well as their clinical manifestations. These interactions mediate both the traffic of inflammatory cells and virus-associated immune responses. In the context of viral infections, the human C-C chemokine receptor type 5 (CCR5) receives great attention from the scientific community due to its role as an HIV-1 co-receptor. The genetic variant CCR5Δ32 (32 base-pair deletion in CCR5 gene) impairs CCR5 expression on the cell surface and is associated with protection against HIV infection in homozygous individuals. Also, the genetic variant CCR5Δ32 modifies the CCR5-mediated inflammatory responses in various conditions, such as inflammatory and infectious diseases. CCR5 antagonists mimic, at least in part, the natural effects of the CCR5Δ32 in humans, which explains the growing interest in the potential benefits of using CCR5 modulators for the treatment of different diseases. Nevertheless, beyond HIV infection, understanding the effects of the CCR5Δ32 variant in multiple viral infections is essential to shed light on the potential effects of the CCR5 modulators from a broader perspective. In this context, this review discusses the involvement of CCR5 and the effects of the CCR5Δ32 in human infections caused by the following pathogens: West Nile virus, Influenza virus, Human papillomavirus, Hepatitis B virus, Hepatitis C virus, Poliovirus, Dengue virus, Human cytomegalovirus, Crimean-Congo hemorrhagic fever virus, Enterovirus, Japanese encephalitis virus, and Hantavirus. Subsequently, this review addresses the impacts of CCR5 gene editing and CCR5 modulation on health and viral diseases. Also, this article connects recent findings regarding extracellular vesicles (e.g., exosomes), viruses, and CCR5. Neglected and emerging topics in “CCR5 research” are briefly described, with focus on Rocio virus, Zika virus, Epstein-Barr virus, and Rhinovirus. Finally, the potential influence of CCR5 on the immune responses to coronaviruses is discussed. url: https://api.elsevier.com/content/article/pii/S0168170220302938 doi: 10.1016/j.virusres.2020.198040 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. url: https://api.elsevier.com/content/article/pii/S0580951715000069 doi: 10.1016/bs.mim.2015.04.005 id: cord-325936-rwxg187r author: Eyal, Nir title: AIDS Activism and Coronavirus Vaccine Challenge Trials date: 2020-06-26 words: 2220.0 sentences: 115.0 pages: flesch: 51.0 cache: ./cache/cord-325936-rwxg187r.txt txt: ./txt/cord-325936-rwxg187r.txt summary: To minimize risk to participants, live SARS-CoV-2 vaccine challenge trials would need to recruit participants who, in the-likely-event of infection, would remain at relatively low fatality risk. Shortly after HIV sterilizing cure trials transplanted allogenic stem cell in participants, with well over a thousand times the fatal risk of SARS-Cov-2 infection in healthy young participants [17, 18] , AIDS activist David Evans interviewed the participants of these risky trials and concluded, "We should recognize their great capacity to understand the risks they may confront as research participants and, after a careful ethical and scientific review, respect the motivations of those who decide that the benefits of knowing that their contributions may help others outweighs the risks" [19] . That is not the case for COVID-19, which means that adequately communicating about and assessing potential risks and benefits of participating in a challenge study and ensuring appropriate informed consent may be impossible. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32591984/ doi: 10.1007/s10461-020-02953-8 id: cord-340389-0fybiybv author: Fahrioglu, Umut title: CCR5-Δ32 gene variant frequency in the Turkish Cypriot population date: 2020-07-31 words: 3532.0 sentences: 202.0 pages: flesch: 57.0 cache: ./cache/cord-340389-0fybiybv.txt txt: ./txt/cord-340389-0fybiybv.txt summary: In the current study, we aimed to determine the CCR5-Δ32 allele frequency in the Turkish Cypriot population with 326 subjects, 141 men (43.1%) and 185 (56.9%) women. In the current study, we aimed to determine the CCR5-Δ32 allele frequency in the Turkish Cypriot population. As the results of our study suggest, most of the Turkish Cypriot population is at greater risk of HIV infection and faster disease progression due to a very low frequency of the Δ32 allele. By keeping the greater risk in mind and using studies like ours, a dialog with health authorities must begin in order to develop a more structured and up-to-date strategy for testing and preventing HIV with the hopes of eliminating HIV/AIDS from the Turkish Cypriot population. Frequencies of 32 base pair deletion of the (Delta 32) allele of the CCR5 HIV-1 co-receptor gene in Caucasians: a comparative analysis abstract: Recent UNAIDS reports (December 2019) indicate that 37.9 million people have been affected by HIV infection around the globe in 2018, of which 1.7 million are cited as new infections. Human immunodeficiency virus-1 (HIV-1) requires both the CD4 receptor, as the primary receptor, and a chemokine co-receptor to gain entry into the cell. In addition to the WT allele for C–C motif chemokine receptor 5 (CCR5-wt), there is another allele with a 32 bp deletion in the protein coding region (CCR5-Δ32). Individuals who are homozygous for the mutant allele are resistant towards M-tropic HIV infections. In the current study, we aimed to determine the CCR5-Δ32 allele frequency in the Turkish Cypriot population with 326 subjects, 141 men (43.1%) and 185 (56.9%) women. The region of the CCR5 gene containing the Δ32 deletion was amplified using flanking primers. The CCR5 gene Δ32 allele frequency was calculated at 3% and only observed in heterozygous individuals. We hope that our current publication could be a point of dialog between the physicians, the government officials and the public set up a more modern and well-structured HIV screening program in an effort to control and hopefully eliminate HIV from the Turkish Cypriot population. url: https://www.ncbi.nlm.nih.gov/pubmed/32734471/ doi: 10.1007/s42770-020-00352-8 id: cord-253182-s60vzf3q author: Fang, Evandro F. title: A research agenda for ageing in China in the 21st century (2nd edition): Focusing on basic and translational research, long-term care, policy and social networks date: 2020-09-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: One of the key issues facing public healthcare is the global trend of an increasingly ageing society which continues to present policy makers and caregivers with formidable healthcare and socio-economic challenges. Ageing is the primary contributor to a broad spectrum of chronic disorders all associated with a lower quality of life in the elderly. In 2019, the Chinese population constituted 18 % of the world population, with 164.5 million Chinese citizens aged 65 and above (65+), and 26 million aged 80 or above (80+). China has become an ageing society, and as it continues to age it will continue to exacerbate the burden borne by current family and public healthcare systems. Major healthcare challenges involved with caring for the elderly in China include the management of chronic non-communicable diseases (CNCDs), physical frailty, neurodegenerative diseases, cardiovascular diseases, with emerging challenges such as providing sufficient dental care, combating the rising prevalence of sexually transmitted diseases among nursing home communities, providing support for increased incidences of immune diseases, and the growing necessity to provide palliative care for the elderly. At the governmental level, it is necessary to make long-term strategic plans to respond to the pressures of an ageing society, especially to establish a nationwide, affordable, annual health check system to facilitate early diagnosis and provide access to affordable treatments. China has begun work on several activities to address these issues including the recent completion of the of the Ten-year Health-Care Reform project, the implementation of the Healthy China 2030 Action Plan, and the opening of the National Clinical Research Center for Geriatric Disorders. There are also societal challenges, namely the shift from an extended family system in which the younger provide home care for their elderly family members, to the current trend in which young people are increasingly migrating towards major cities for work, increasing reliance on nursing homes to compensate, especially following the outcomes of the ‘one child policy’ and the ‘empty-nest elderly’ phenomenon. At the individual level, it is important to provide avenues for people to seek and improve their own knowledge of health and disease, to encourage them to seek medical check-ups to prevent/manage illness, and to find ways to promote modifiable health-related behaviors (social activity, exercise, healthy diets, reasonable diet supplements) to enable healthier, happier, longer, and more productive lives in the elderly. Finally, at the technological or treatment level, there is a focus on modern technologies to counteract the negative effects of ageing. Researchers are striving to produce drugs that can mimic the effects of ‘exercising more, eating less’, while other anti-ageing molecules from molecular gerontologists could help to improve ‘healthspan’ in the elderly. Machine learning, ‘Big Data’, and other novel technologies can also be used to monitor disease patterns at the population level and may be used to inform policy design in the future. Collectively, synergies across disciplines on policies, geriatric care, drug development, personal awareness, the use of big data, machine learning and personalized medicine will transform China into a country that enables the most for its elderly, maximizing and celebrating their longevity in the coming decades. This is the 2nd edition of the review paper (Fang EF et al., Ageing Re. Rev. 2015). url: https://www.ncbi.nlm.nih.gov/pubmed/32971255/ doi: 10.1016/j.arr.2020.101174 id: cord-272051-arz8r204 author: Federico, Maurizio title: HIV-protease inhibitors block the replication of both vesicular stomatitis and influenza viruses at an early post-entry replication step date: 2011-08-15 words: 6772.0 sentences: 320.0 pages: flesch: 49.0 cache: ./cache/cord-272051-arz8r204.txt txt: ./txt/cord-272051-arz8r204.txt summary: Since the replication of many virus species requires the activity of host cell proteases, investigating the effects of PIs on the life cycle of viruses other than HIV would be of interest. Considering that PIs are well tolerated drugs in vivo, and that many relevant human pathogens belong to the family of RNA viruses infecting cells through an endocytic pathway, this finding would open the way towards a broader therapeutic use of PIs. HIV virions emerging from cells treated with PIs remain immature viral particles as a consequence of the block of Gag polyprotein cleavage. Cells were treated overnight with the PI doses most effective against VSV and/or influenza virus replication, then labeled with LysoSensor Green DND-189 for 30 min in the presence of PIs, and finally analyzed by FACS. abstract: The inhibitors of HIV-1 protease (PIs) have been designed to block the activity of the viral aspartyl-protease. However, it is now accepted that this family of inhibitors can also affect the activity of cell proteases. Since the replication of many virus species requires the activity of host cell proteases, investigating the effects of PIs on the life cycle of viruses other than HIV would be of interest. Here, the potent inhibition induced by saquinavir and nelfinavir on the replication of both vesicular stomatitis and influenza viruses is described. These are unrelated enveloped RNA viruses infecting target cells upon endocytosis and intracellular fusion. The PI-induced inhibition was apparently a consequence of a block at the level of the fusion between viral envelope and endosomal membranes. These findings would open the way towards the therapeutic use of PIs against enveloped RNA viruses other than HIV. url: https://www.sciencedirect.com/science/article/pii/S0042682211002157 doi: 10.1016/j.virol.2011.05.002 id: cord-268977-hcg2rrhl author: Feikin, Daniel R. title: Etiology and Incidence of Viral and Bacterial Acute Respiratory Illness among Older Children and Adults in Rural Western Kenya, 2007–2010 date: 2012-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Few comprehensive data exist on disease incidence for specific etiologies of acute respiratory illness (ARI) in older children and adults in Africa. METHODOLOGY/PRINCIPAL FINDINGS: From March 1, 2007, to February 28, 2010, among a surveillance population of 21,420 persons >5 years old in rural western Kenya, we collected blood for culture and malaria smears, nasopharyngeal and oropharyngeal swabs for quantitative real-time PCR for ten viruses and three atypical bacteria, and urine for pneumococcal antigen testing on outpatients and inpatients meeting a ARI case definition (cough or difficulty breathing or chest pain and temperature >38.0°C or oxygen saturation <90% or hospitalization). We also collected swabs from asymptomatic controls, from which we calculated pathogen-attributable fractions, adjusting for age, season, and HIV-status, in logistic regression. We calculated incidence by pathogen, adjusting for health-seeking for ARI and pathogen-attributable fractions. Among 3,406 ARI patients >5 years old (adjusted annual incidence 12.0 per 100 person-years), influenza A virus was the most common virus (22% overall; 11% inpatients, 27% outpatients) and Streptococcus pneumoniae was the most common bacteria (16% overall; 23% inpatients, 14% outpatients), yielding annual incidences of 2.6 and 1.7 episodes per 100 person-years, respectively. Influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human metapneumovirus were more prevalent in swabs among cases (22%, 6%, 8% and 5%, respectively) than controls. Adenovirus, parainfluenza viruses, rhinovirus/enterovirus, parechovirus, and Mycoplasma pneumoniae were not more prevalent among cases than controls. Pneumococcus and non-typhi Salmonella were more prevalent among HIV-infected adults, but prevalence of viruses was similar among HIV-infected and HIV-negative individuals. ARI incidence was highest during peak malaria season. CONCLUSIONS/SIGNFICANCE: Vaccination against influenza and pneumococcus (by potential herd immunity from childhood vaccination or of HIV-infected adults) might prevent much of the substantial ARI incidence among persons >5 years old in similar rural African settings. url: https://www.ncbi.nlm.nih.gov/pubmed/22937071/ doi: 10.1371/journal.pone.0043656 id: cord-256477-dftt5m6i author: Feller, John M. title: Potential Ebola prophylaxis date: 2015-07-01 words: 604.0 sentences: 43.0 pages: flesch: 53.0 cache: ./cache/cord-256477-dftt5m6i.txt txt: ./txt/cord-256477-dftt5m6i.txt summary: The hypothesis that CQ might afford Ebola prophylaxis comes from our own work showing hydroxychloroquine (HCQ) induces apoptosis (programmed cell death) in peripheral blood mononuclear cells. 4, 5 A randomised controlled trial (RCT) in 13 ART-naïve patients found CQ was associated with decreased memory CD8 T-cell activation, CD4 and CD8 T-cell proliferation and lipopolysaccharide levels compared with baseline, but there were no changes in plasma HIV RNA. 6 However, another RCT of HCQ in ART-naïve patients demonstrated no change in T-cell activation and proliferation, an increase in HIV RNA and a decrease in CD4 T-cell counts. Ebola infects dendritic cells, which display signals of infection on their surfaces to activate T lymphocytes that destroy other infected cells before the virus replicates further. Reduction of immune activation with chloroquine therapy during chronic HIV infection Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial abstract: nan url: https://doi.org/10.1111/jpc.12955 doi: 10.1111/jpc.12955 id: cord-031722-n5ja5oqw author: Fields, Errol L. title: Mind the Gap: HIV Prevention Among Young Black Men Who Have Sex with Men date: 2020-09-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PURPOSE OF REVIEW: Young Black men who have sex with men (YBMSM) suffer profound health inequities in new HIV diagnoses and clinical outcomes. While the evolution of HIV prevention options has become increasingly biomedical, inequities in access and uptake of these modalities persist. RECENT FINDINGS: Studies suggest that while YBMSM display interest and acceptability of varied HIV prevention options, uptake lags due to the lingering effects of intersectional oppression from racism and sexual prejudice, HIV stigma, institutional and provider bias, and unresolved health policy barriers. Promising avenues to address these barriers have yet to be fully explored. SUMMARY: We have the tools to effectively prevent HIV transmission and acquisition among YBMSM, but we have not yet effectively implemented these tools for this priority population. To end the epidemic, we must tailor and adapt HIV prevention strategies to meet the unique intersecting needs, identities, and social contexts of YBMSM. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7483045/ doi: 10.1007/s11904-020-00532-z id: cord-330852-n7j0c4ne author: Fischer, Wolfgang B. title: Mechanism of Function of Viral Channel Proteins and Implications for Drug Development date: 2012-02-23 words: 23680.0 sentences: 1178.0 pages: flesch: 53.0 cache: ./cache/cord-330852-n7j0c4ne.txt txt: ./txt/cord-330852-n7j0c4ne.txt summary: By adding data from functional studies like Cys scanning and electrophysiological measurements as mentioned as well as computational modeling data (Sansom and Kerr, 1993; Sansom et al., 1997; Zhong et al., 1998) , an approximate structural model of the tetrameric assembly of the TMDs of M2 with the histidines and tryptophans as important pore lining residues has been generated. Amiloride derivatives block ion channel activity and enhancement of virus-like particle budding caused by HIV-1 protein Vpu Backbone structure of the amantadine-blocked trans-membrane domain M2 protein channel from influenza A virus Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the Human Immunodeficiency Virus HIV-1 Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1 abstract: Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo. url: https://doi.org/10.1016/b978-0-12-394305-7.00006-9 doi: 10.1016/b978-0-12-394305-7.00006-9 id: cord-264994-j8iawzp8 author: Fitzpatrick, Meagan C. title: Modelling microbial infection to address global health challenges date: 2019-09-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The continued growth of the world’s population and increased interconnectivity heighten the risk that infectious diseases pose for human health worldwide. Epidemiological modelling is a tool that can be used to mitigate this risk by predicting disease spread or quantifying the impact of different intervention strategies on disease transmission dynamics. We illustrate how four decades of methodological advances and improved data quality have facilitated the contribution of modelling to address global health challenges, exemplified by models for the HIV crisis, emerging pathogens and pandemic preparedness. Throughout, we discuss the importance of designing a model that is appropriate to the research question and the available data. We highlight pitfalls that can arise in model development, validation and interpretation. Close collaboration between empiricists and modellers continues to improve the accuracy of predictions and the optimization of models for public health decision-making. url: https://doi.org/10.1038/s41564-019-0565-8 doi: 10.1038/s41564-019-0565-8 id: cord-305039-grsv06j7 author: Flego, Michela title: Clinical development of monoclonal antibody-based drugs in HIV and HCV diseases date: 2013-01-04 words: 10985.0 sentences: 476.0 pages: flesch: 37.0 cache: ./cache/cord-305039-grsv06j7.txt txt: ./txt/cord-305039-grsv06j7.txt summary: As for HIV, mAbs directed against spike viral proteins, as well as against host receptors, may act at an early stage of infection by preventing the binding of the virus on the cell surface. In some chronic viral infections, virus-specific immune cells may persist in a ''non-functional'' state, because of an imbalance of immunoregulatory signals involving multiple inhibitory and activating receptors, triggered by soluble factors and/or cell surface ligands. Therapeutic approaches using specific mAbs to block host immunosuppressive molecules (antagonism) or to trigger activating receptors (agonism) may be a valid strategy to restore immune cell function and treat various chronic viral infections. In a proof-of-concept passive immunization trial with humans, it has been demonstrated that a cocktail of the three broadly neutralizing mAbs -2G12, 4E10 and 2F5was able to delay viral rebound in patients whose infections were fully suppressed by antiretroviral treatment before administration of the antibodies [76] . abstract: Today there are many licensed antiviral drugs, but the emergence of drug resistant strains sometimes invalidates the effects of the current therapies used in the treatment of infectious diseases. Compared to conventional antiviral drugs, monoclonal antibodies (mAbs) used as pharmacological molecules have particular physical characteristics and modes of action, and, therefore, they should be considered as a distinct therapeutic class. Despite being historically validated, antibodies may represent a novel tool for combatting infectious diseases. The current high cost of mAbs' production, storage and administration (by injection only) and the consequent obstacles to development are outweighed by mAbs' clinical advantages. These are related to a low toxicity combined with high specificity and versatility, which allows a specific antibody to mediate various biological effects, ranging from the virus neutralization mechanisms to the modulation of immune responses. This review briefly summarizes the recent technological advances in the field of immunoglobulin research, and the current status of mAb-based drugs in clinical trials for HIV and HCV diseases. For each clinical trial the available data are reported and the emerging conceptual problems of the employed mAbs are highlighted. This overview helps to give a clear picture of the efficacy and challenges of the mAbs in the field of these two infectious diseases which have such a global impact. url: https://www.ncbi.nlm.nih.gov/pubmed/23289632/ doi: 10.1186/1741-7015-11-4 id: cord-299762-qr6kbwuo author: Fok, Jelle Anthony title: Genetic code expansion strategies for vaccine development date: 2020-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: By providing long‐term protection against infectious diseases vaccinations have significantly reduced death and morbidity world‐wide. In the 21 st century, (bio)technological advances have paved the way for developing prophylactic vaccines that are safer and more effective as well as enabled the use of vaccines as therapeutics to treat human diseases. Here, we provide a focused review on the utility of genetic code expansion as an emerging tool for the development of vaccines. Specifically, we discuss how the incorporation of immunogenic non‐canonical amino acids can aid in eliciting immune responses against adverse self‐proteins and highlight the potential of an expanded genetic code for the construction of replication‐incompetent viruses. We close the review by discussing future prospects and remaining challenges for the application of these approaches in the development of both prophylactic and therapeutic vaccines in the near future. url: https://doi.org/10.1002/cbic.202000343 doi: 10.1002/cbic.202000343 id: cord-017782-dtveihrj author: Fong, I. W. title: Litigations for HIV Related Complications date: 2010-11-30 words: 6292.0 sentences: 332.0 pages: flesch: 54.0 cache: ./cache/cord-017782-dtveihrj.txt txt: ./txt/cord-017782-dtveihrj.txt summary: Specific charges were: (1) the GP should have repeated the HIV serology to confirm that the plaintiff was HIV infected, (2) the defendant was negligent in starting treatment for HIV infection without proof of disease, (3) the physician lacked knowledge of HIV infection and should have referred the patient to a specialist or HIV clinic, (4) treatment of toxic medications were given for several years without any clear indication, and (5) the GP did not adequately inform the patient on the pros and cons of therapy, nor explain the potential toxicities and side-effects. Although the CD4 + T lymphocyte quantitative count is a very useful and standard test to monitor patients for progression of HIV disease or response to therapy, it can be low in many conditions. Long-term non-progression or elite controllers represent <5% of HIV-infected subjects who maintain relatively normal CD4 + cell count and very low or immeasurable viral load for 8 years to decades without therapy. abstract: In 1992, a 27-year-old male with same sex exposure requested human immuno-deficiency virus (HIV) testing anonymously at a walk-in clinic. He was advised that the test (HIV serology) was positive and he requested a repeat test (anonymously) 1 month later, which was also reported as being positive. About 2 years later, he was assessed by a general practitioner for symptoms of depression and continued medical care. At that time, investigations revealed a CD4 T-cell count of about 700 cells/uL. Sometime in 1996 a repeat blood test revealed a CD4 cell count just <500 cells/uL. No consultation to an infectious diseases specialist or HIV clinic was made. The GP(general practitioner) then initiated a regimen consisting of didanosine, lamivudine, and saquinavir for HIV infection. At that time, testing for HIV viral load was not generally available to the medical community, but became procurable in 1997. Initially, the patient tolerated the regimen well and over the next 3 years his CD4 cell count was maintained above 600–700 cells/uL and the HIV viral load remained undetectable (<50 copies). However, the patient started to show morphologic changes of moderate facial and peripheral lipoatrophy, developed mild sensory peripheral neuropathy, and increased liver enzymes attributable to fatty liver, and elevations of the fasting serum glucose. In the summer of 2000, although the CD4 cell count remained stable, the HIV viral load was reported as being over 7,000 copies/uL. At this time, the patient was referred to a university hospital HIV clinic. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122441/ doi: 10.1007/978-1-4419-8053-3_13 id: cord-270399-yfko8mpc author: Foster, Allison title: It’s complicated: A case report on a COVID-19-positive HIV patient presenting with rhabdomyolysis and acute kidney injury date: 2020-10-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The SARS-Cov-2/COVID-19 pandemic in early 2020 has had a devastating impact on health systems around the world. While viral pneumonia remains the most common complication, reports are surfacing of cases with neurological, cardiac, and renal involvement. Even less is known about the implications in special high-risk populations. In this report, we discuss a unique case of an HIV-positive patient in New York City who presented with a 2-week history of worsening fatigue, cough, dyspnea, and myalgias and was found to have COVID-19 pneumonia and acute kidney injury. He was managed for severe uremic metabolic acidosis and electrolyte abnormalities with emergent hemodialysis and supportive therapy with subsequent improvement. Direct involvement of SARS-CoV-2 and pneumonia-induced rhabdomyolysis were identified as the precipitating factors of his acute kidney injury. The pathophysiologic mechanisms of acute kidney injury, SARS-CoV-2 renal tropism, and the impact of highly active antiretroviral therapy on COVID-19 pneumonia are discussed. We highlight the importance of clinician awareness of this potentially fatal complication of COVID-19 pneumonia, particularly in the HIV-positive population as early recognition and management can have favorable outcomes. url: https://doi.org/10.1177/2050313x20965423 doi: 10.1177/2050313x20965423 id: cord-259237-aty0vrat author: Frabutt, Dylan A. title: Arms Race between Enveloped Viruses and the Host ERAD Machinery date: 2016-09-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Enveloped viruses represent a significant category of pathogens that cause serious diseases in animals. These viruses express envelope glycoproteins that are singularly important during the infection of host cells by mediating fusion between the viral envelope and host cell membranes. Despite low homology at protein levels, three classes of viral fusion proteins have, as of yet, been identified based on structural similarities. Their incorporation into viral particles is dependent upon their proper sub-cellular localization after being expressed and folded properly in the endoplasmic reticulum (ER). However, viral protein expression can cause stress in the ER, and host cells respond to alleviate the ER stress in the form of the unfolded protein response (UPR); the effects of which have been observed to potentiate or inhibit viral infection. One important arm of UPR is to elevate the capacity of the ER-associated protein degradation (ERAD) pathway, which is comprised of host quality control machinery that ensures proper protein folding. In this review, we provide relevant details regarding viral envelope glycoproteins, UPR, ERAD, and their interactions in host cells. url: https://www.ncbi.nlm.nih.gov/pubmed/27657106/ doi: 10.3390/v8090255 id: cord-009096-3c5t70an author: Frankish, Helen title: New WHO chief promises greater commitment to HIV/AIDS date: 2003-07-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135582/ doi: 10.1016/s0140-6736(03)14007-x id: cord-016472-jj7fqcen author: Freudenberg, Nicholas title: Health Research Behind Bars: A Brief Guide to Research in Jails and Prisons date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: While most people make staying out of jail and prison a priority, a growing number of researchers are eager to get into correctional facilities in order to study the criminal justice system, the causes and consequences of incarceration, and the role of corrections in our society. For health researchers and their collaborators, the audience for this chapter, correctional facilities offer several unique advantages: a population at high risk of many health problems including infectious and chronic diseases, substance abuse, and mental health problems; social and physical environments that can enhance or impede well-being; a setting that is a focal point for the class, racial/ethnic, and gender differences that divide the United States; a site where health and mental health services and prevention programs are offered and can be evaluated; a controlled environment for administration of treatments such as directly observed therapy for tuberculosis; and a stopping point in the cycle of incarceration and reentry that so profoundly affects community well-being. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120758/ doi: 10.1007/978-0-387-71695-4_24 id: cord-332569-af8oq2d6 author: Friedman, Henry title: The Critical Role of Nonhuman Primates in Medical Research date: 2017-08-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The sponsors of this report endorse carefully regulated research with nonhuman primates. This research is essential to learning about the biology, treatment and prevention of diseases and conditions that cause human suffering. url: https://www.ncbi.nlm.nih.gov/pubmed/29034361/ doi: 10.20411/pai.v2i3.186 id: cord-346424-gfccstoz author: Friedrich, Brian M title: A Functional Role for ADAM10 in Human Immunodeficiency Virus Type-1 Replication date: 2011-05-11 words: 6319.0 sentences: 330.0 pages: flesch: 46.0 cache: ./cache/cord-346424-gfccstoz.txt txt: ./txt/cord-346424-gfccstoz.txt summary: RESULTS: Silencing ADAM10 expression with small interfering RNA (siRNA) 48 hours before infection significantly inhibited HIV-1 replication in primary human monocyte-derived macrophages and in CD4(+ )cell lines. In studies reported herein, it was found that transfecting cells with ADAM10 small interfering RNA (siRNA) dramatically inhibited replication of X4 and R5 HIV-1 strains, both in primary human monocyte-derived macrophages and in CD4 + cell lines. Figure 1A shows that ADAM10 silencing effectively inhibited R5-tropic HIV-1 replication when human monocyte-derived macrophages were transfected with siRNAs 48 h prior to infection. To determine whether ADAM10 is required for entry or HIV-1 reverse transcription, small non-genomic DNA was isolated from control-and ADAM10 siRNA-transfected macrophages at 48 h post-infection for quantification by real-time PCR. To determine the effect of silencing cellular genes on HIV-1 replication, TZM-bl cells or primary human macrophages were transfected with siRNA SMARTpools for 48 h prior to infection. abstract: BACKGROUND: Gene trap insertional mutagenesis was used as a high-throughput approach to discover cellular genes participating in viral infection by screening libraries of cells selected for survival from lytic infection with a variety of viruses. Cells harboring a disrupted ADAM10 (A Disintegrin and Metalloprotease 10) allele survived reovirus infection, and subsequently ADAM10 was shown by RNA interference to be important for replication of HIV-1. RESULTS: Silencing ADAM10 expression with small interfering RNA (siRNA) 48 hours before infection significantly inhibited HIV-1 replication in primary human monocyte-derived macrophages and in CD4(+ )cell lines. In agreement, ADAM10 over-expression significantly increased HIV-1 replication. ADAM10 down-regulation did not inhibit viral reverse transcription, indicating that viral entry and uncoating are also independent of ADAM10 expression. Integration of HIV-1 cDNA was reduced in ADAM10 down-regulated cells; however, concomitant 2-LTR circle formation was not detected, suggesting that HIV-1 does not enter the nucleus. Further, ADAM10 silencing inhibited downstream reporter gene expression and viral protein translation. Interestingly, we found that while the metalloprotease domain of ADAM10 is not required for HIV-1 replication, ADAM15 and γ-secretase (which proteolytically release the extracellular and intracellular domains of ADAM10 from the plasma membrane, respectively) do support productive infection. CONCLUSIONS: We propose that ADAM10 facilitates replication at the level of nuclear trafficking. Collectively, our data support a model whereby ADAM10 is cleaved by ADAM15 and γ-secretase and that the ADAM10 intracellular domain directly facilitates HIV-1 nuclear trafficking. Thus, ADAM10 represents a novel cellular target class for development of antiretroviral drugs. url: https://doi.org/10.1186/1742-4690-8-32 doi: 10.1186/1742-4690-8-32 id: cord-104490-t42eccng author: Frimpong, Shadrack title: A Case for Girl-child Education to Prevent and Curb the Impact of Emerging Infectious Diseases Epidemics date: 2020-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Not only do epidemics such as HIV/AIDS, Ebola Virus Disease (EVD), and the current Coronavirus Disease (COVID-19) cause the loss of millions of lives, but they also cost the global economy billions of dollars. Consequently, there is an urgent need to formulate interventions that will help control their spread and impact when they emerge. The education of young girls and women is one such historical approach. They are usually the vulnerable targets of disease outbreaks – they are most likely to be vehicles for the spread of epidemics due to their assigned traditional roles in resource-limited countries. Based on our work and the work of others on educational interventions, we propose six critical components of a cost-effective and sustainable response to promote girl-child education in resource-limited settings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7513442/ doi: nan id: cord-004002-b35wm2db author: Gaborit, Benjamin Jean title: Outcome and prognostic factors of Pneumocystis jirovecii pneumonia in immunocompromised adults: a prospective observational study date: 2019-11-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) remains a severe disease associated with high rates of invasive mechanical ventilation (MV) and mortality. The objectives of this study were to assess early risk factors for severe PJP and 90-day mortality, including the broncho-alveolar lavage fluid cytology profiles at diagnosis. METHODS: We prospectively enrolled all patients meeting pre-defined diagnostic criteria for PJP admitted at Nantes university hospital, France, from January 2012 to January 2017. Diagnostic criteria for PJP were typical clinical features with microbiological confirmation of P. jirovecii cysts by direct examination or a positive specific quantitative real-time polymerase chain reaction (PCR) assay. Severe PJP was defined as hypoxemic acute respiratory failure requiring high-flow nasal oxygen with at least 50% FiO(2), non-invasive ventilation, or MV. RESULTS: Of 2446 respiratory samples investigated during the study period, 514 from 430 patients were positive for P. jirovecii. Of these 430 patients, 107 met criteria for PJP and were included in the study, 53 (49.5%) patients had severe PJP, including 30 who required MV. All patients were immunocompromised with haematological malignancy ranking first (n = 37, 35%), followed by solid organ transplantation (n = 27, 25%), HIV-infection (n = 21, 20%), systemic diseases (n = 13, 12%), solid tumors (n = 12, 11%) and primary immunodeficiency (n = 6, 8%). By multivariate analysis, factors independently associated with severity were older age (OR, 3.36; 95% CI 1.4–8.5; p < 0.05), a P. jirovecii microscopy-positive result from bronchoalveolar lavage (BAL) (OR, 1.3; 95% CI 1.54–9.3; p < 0.05); and absence of a BAL fluid alveolitis profile (OR, 3.2; 95% CI 1.27–8.8; p < 0.04). The 90-day mortality rate was 27%, increasing to 50% in the severe PJP group. Factors independently associated with 90-day mortality were worse SOFA score on day 1 (OR, 1.05; 95% CI 1.02–1.09; p < 0.001) whereas alveolitis at BAL was protective (OR, 0.79; 95% CI 0.65–0.96; p < 0.05). In the subgroup of HIV-negative patients, similar findings were obtained, then viral co-infection were independently associated with higher 90-day mortality (OR, 1.25; 95% CI 1.02–1.55; p < 0.05). CONCLUSIONS: Older age and P. jirovecii oocysts at microscopic examination of BAL were independently associated with severe PJP. Both initial PJP severity as evaluated by the SOFA score and viral co-infection predicted 90-day mortality. Alveolitis at BAL examination was associated with less severe PJP. The pathophysiological mechanism underlying this observation deserves further investigation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6881486/ doi: 10.1186/s13613-019-0604-x id: cord-260444-ooi5x9p3 author: Gadelha Farias, Luís Arthur Brasil title: Case Report: Coronavirus Disease and Pulmonary Tuberculosis in Patients with Human Immunodeficiency Virus: Report of Two Cases date: 2020-08-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Coinfection of SARS-CoV-2/Mycobacterium tuberculosis (MTB) in patients with HIV/AIDS has not been previously reported. Here, we present two cases of coinfection of SARS-CoV-2 and MTB in patients with HIV. The first case is a 39-year-old patient who was admitted with a 7-day history of fever, myalgia, headache, and cough. The second patient is a 43-year-old man who had a 1-month history of cough with hemoptoic sputum, evolving to mild respiratory distress in the last 7 days. Both patients already had pulmonary tuberculosis and subsequently developed SARS-CoV-2 infection during the 2020 pandemic. Nonadherence to antiretroviral treatment may have been a factor in the clinical worsening of the patients. url: https://doi.org/10.4269/ajtmh.20-0737 doi: 10.4269/ajtmh.20-0737 id: cord-254194-962vynwk author: Galdiero, Stefania title: Silver Nanoparticles as Potential Antiviral Agents date: 2011-10-24 words: 10034.0 sentences: 447.0 pages: flesch: 38.0 cache: ./cache/cord-254194-962vynwk.txt txt: ./txt/cord-254194-962vynwk.txt summary: Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. Theoretically, any metal could be analysed for antiviral activity, however, little effort has been done to determine the interactions of metal nanoparticles with viruses, and only recently some studies have emerged showing that metal nanoparticles can be effective antiviral agents against HIV-1 [37] [38] [39] [40] , hepatitis B virus [41] , respiratory syncytial virus [42] , herpes simplex virus type 1 [43, 44] , monkeypox virus [45] , influenza virus [46] and Tacaribe virus [47] . abstract: Virus infections pose significant global health challenges, especially in view of the fact that the emergence of resistant viral strains and the adverse side effects associated with prolonged use continue to slow down the application of effective antiviral therapies. This makes imperative the need for the development of safe and potent alternatives to conventional antiviral drugs. In the present scenario, nanoscale materials have emerged as novel antiviral agents for the possibilities offered by their unique chemical and physical properties. Silver nanoparticles have mainly been studied for their antimicrobial potential against bacteria, but have also proven to be active against several types of viruses including human imunodeficiency virus, hepatitis B virus, herpes simplex virus, respiratory syncytial virus, and monkey pox virus. The use of metal nanoparticles provides an interesting opportunity for novel antiviral therapies. Since metals may attack a broad range of targets in the virus there is a lower possibility to develop resistance as compared to conventional antivirals. The present review focuses on the development of methods for the production of silver nanoparticles and on their use as antiviral therapeutics against pathogenic viruses. url: https://doi.org/10.3390/molecules16108894 doi: 10.3390/molecules16108894 id: cord-302530-pp6bl941 author: Gale, Paul title: How virus size and attachment parameters affect the temperature sensitivity of virus binding to host cells: Predictions of a thermodynamic model for arboviruses and HIV date: 2020-03-12 words: 14797.0 sentences: 905.0 pages: flesch: 66.0 cache: ./cache/cord-302530-pp6bl941.txt txt: ./txt/cord-302530-pp6bl941.txt summary: These are:-1 The predicted effect of the magnitude of ΔC p on the temperature dependence of Dengue virus (DENV) transmission by Aedes albopictus; 2 The predicted effect of the magnitude of ΔC p on the temperature peak observed for the specific binding of Western equine encephalitis virus (WEEV) to susceptible Culex tarsalis brush border fragments (BBFs); 3 A large negative ΔC p for a protein:protein GP/Cr system as represented by HIV gp120:CD4 diminishes host cell binding at human body temperature; 4 A large virus diameter as for the HIV virion diminishes host cell binding at the higher temperature of the human body through the large negative ΔS a_immob ; 5 Non-specific attachment factors may partially overcome the unfavourable ΔS a_immob and hence enhance specific HIV binding through Env:CD4 interactions at human body temperature; and 6 Increasing the number, n, of GP/Cr contacts with temperature to reproduce the data of Frey et al. abstract: Virus binding to host cells involves specific interactions between viral (glyco)proteins (GP) and host cell surface receptors (Cr) (protein or sialic acid (SA)). The magnitude of the enthalpy of association changes with temperature according to the change in heat capacity (ΔC(p)) on GP/Cr binding, being little affected for avian influenza virus (AIV) haemagglutinin (HA) binding to SA (ΔC(p) = 0 kJ/mol/K) but greatly affected for HIV gp120 binding to CD4 receptor (ΔC(p) = −5.0 kJ/mol/K). A thermodynamic model developed here predicts that values of ΔC(p) from 0 to ~−2.0 kJ/mol/K have relatively little impact on the temperature sensitivity of the number of mosquito midgut cells with bound arbovirus, while intermediate values of ΔC(p) of ~−3.0 kJ/mol/K give a peak binding at a temperature of ~20 °C as observed experimentally for Western equine encephalitis virus. More negative values of ΔC(p) greatly decrease arbovirus binding at temperatures below ~20 °C. Thus to promote transmission at low temperatures, arboviruses may benefit from ΔC(p) ~ 0 kJ/mol/K as for HA/SA and it is interesting that bluetongue virus binds to SA in midge midguts. Large negative values of ΔC(p) as for HIV gp120:CD4 diminish binding at 37 °C. Of greater importance, however, is the decrease in entropy of the whole virus (ΔS(a_immob)) on its immobilisation on the host cell surface. ΔS(a_immob) presents a repulsive force which the enthalpy-driven GP/Cr interactions weakened at higher temperatures struggle to overcome. ΔS(a_immob) is more negative (less favourable) for larger diameter viruses which therefore show diminished binding at higher temperatures than smaller viruses. It is proposed that small size phenotype through a less negative ΔS(a_immob) is selected for viruses infecting warmer hosts thus explaining the observation that virion volume decreases with increasing host temperature from 0 °C to 40 °C in the case of dsDNA viruses. Compared to arboviruses which also infect warm-blooded vertebrates, HIV is large at 134 nm diameter and thus would have a large negative ΔS(a_immob) which would diminish its binding at human body temperature. It is proposed that prior non-specific binding of HIV through attachment factors takes much of the entropy loss for ΔS(a_immob) so enhancing subsequent specific gp120:CD4 binding at 37 °C. This is consistent with the observation that HIV attachment factors are not essential but augment infection. Antiviral therapies should focus on increasing virion size, for example through binding of zinc oxide nanoparticles to herpes simplex virus, hence making ΔS(a_immob) more negative, and thus reducing binding affinity at 37 °C. url: https://www.ncbi.nlm.nih.gov/pubmed/32292808/ doi: 10.1016/j.mran.2020.100104 id: cord-284385-ster02o9 author: Gambichler, Thilo title: On the use of immune checkpoint inhibitors in patients with viral infections including COVID-19 date: 2020-07-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The present review summarizes up-to-date evidence addressing the frequently discussed clinical controversies regarding the use of immune checkpoint inhibitors (ICIs) in cancer patients with viral infections, including AIDS, hepatitis B and C, progressive multifocal leukoencephalopathy, influenza, and COVID-19. In detail, we provide available information on (1) safety regarding the risk of new infections, (2) effects on the outcome of pre-existing infections, (3) whether immunosuppressive drugs used to treat ICI-related adverse events affect the risk of infection or virulence of pre-existing infections, (4) whether the use of vaccines in ICI-treated patients is considered safe, and (5) whether there are beneficial effects of ICIs that even qualify them as a therapeutic approach for these viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32611687/ doi: 10.1136/jitc-2020-001145 id: cord-316534-ep7ezoko author: Gamble, Lena J title: Current progress in the development of a prophylactic vaccine for HIV-1 date: 2010-12-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since its discovery and characterization in the early 1980s as a virus that attacks the immune system, there has been some success for the treatment of human immunodeficiency virus-1 (HIV-1) infection. However, due to the overwhelming public health impact of this virus, a vaccine is needed urgently. Despite the tireless efforts of scientist and clinicians, there is still no safe and effective vaccine that provides sterilizing immunity. A vaccine that provides sterilizing immunity against HIV infection remains elusive in part due to the following reasons: 1) degree of diversity of the virus, 2) ability of the virus to evade the hosts’ immunity, and 3) lack of appropriate animal models in which to test vaccine candidates. There have been several attempts to stimulate the immune system to provide protection against HIV-infection. Here, we will discuss attempts that have been made to induce sterilizing immunity, including traditional vaccination attempts, induction of broadly neutralizing antibody production, DNA vaccines, and use of viral vectors. Some of these attempts show promise pending continued research efforts. url: https://www.ncbi.nlm.nih.gov/pubmed/21267356/ doi: 10.2147/dddt.s6959 id: cord-001532-kz3b01wq author: Gantt, Soren title: Nelfinavir Impairs Glycosylation of Herpes Simplex Virus 1 Envelope Proteins and Blocks Virus Maturation date: 2015-01-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Nelfinavir (NFV) is an HIV-1 aspartyl protease inhibitor that has numerous effects on human cells, which impart attractive antitumor properties. NFV has also been shown to have in vitro inhibitory activity against human herpesviruses (HHVs). Given the apparent absence of an aspartyl protease encoded by HHVs, we investigated the mechanism of action of NFV herpes simplex virus type 1 (HSV-1) in cultured cells. Selection of HSV-1 resistance to NFV was not achieved despite multiple passages under drug pressure. NFV did not significantly affect the level of expression of late HSV-1 gene products. Normal numbers of viral particles appeared to be produced in NFV-treated cells by electron microscopy but remain within the cytoplasm more often than controls. NFV did not inhibit the activity of the HSV-1 serine protease nor could its antiviral activity be attributed to inhibition of Akt phosphorylation. NFV was found to decrease glycosylation of viral glycoproteins B and C and resulted in aberrant subcellular localization, consistent with induction of endoplasmic reticulum stress and the unfolded protein response by NFV. These results demonstrate that NFV causes alterations in HSV-1 glycoprotein maturation and egress and likely acts on one or more host cell functions that are important for HHV replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325974/ doi: 10.1155/2015/687162 id: cord-306050-y8i8759c author: García, Juan Ignacio title: Accuracy of the tuberculosis point-of-care Alere determine lipoarabinomannan antigen diagnostic test using α-mannosidase treated and untreated urine in a cohort of people living with HIV in Guatemala date: 2020-10-19 words: 5288.0 sentences: 263.0 pages: flesch: 48.0 cache: ./cache/cord-306050-y8i8759c.txt txt: ./txt/cord-306050-y8i8759c.txt summary: title: Accuracy of the tuberculosis point-of-care Alere determine lipoarabinomannan antigen diagnostic test using α-mannosidase treated and untreated urine in a cohort of people living with HIV in Guatemala The aim of the study is to evaluate the performance of the lipoarabinomannan antigen test (LAM-test) with and without α-mannosidase pre-treated urine in a cohort of PLWH in primary care clinics in Guatemala. A composite reference standard of either a positive Mycobacterium tuberculosis complex culture and/or GeneXpert(®) MTB/RIF (Xpert, Cepheid, Sunnyvale, CA, USA) results was used in the LAM-test diagnostic accuracy studies. We also determined if a 30 min α-mannosidase pre-treatment of urine using an enzyme that removes the mannose caps of LAM could improve the sensitivity of the LAM-test as we have shown in the laboratory settings [14] , and further correlated LAM-test results with TB incidence, mortality rates, and risk factors in our cohort of PLWH. abstract: BACKGROUND: Improved point-of-care diagnostic tests for tuberculosis (TB) in severe immune suppressed people living with HIV (PLWH) are needed to decrease morbidity and mortality outcomes. The aim of the study is to evaluate the performance of the lipoarabinomannan antigen test (LAM-test) with and without α-mannosidase pre-treated urine in a cohort of PLWH in primary care clinics in Guatemala. We further determined TB incidence, and mortality rates and its risk factors in PLWH with TB symptoms. METHODS: Prospective longitudinal study of PLWH with TB symptoms. Urine samples were collected at 2 HIV sites to test the sensitivity of the LAM-test in urine with and without α-mannosidase pre-treatment. A composite reference standard of either a positive Mycobacterium tuberculosis complex culture and/or GeneXpert(®) MTB/RIF (Xpert, Cepheid, Sunnyvale, CA, USA) results was used in the LAM-test diagnostic accuracy studies. Cox proportional hazards regression was used to study mortality predictors. RESULTS: The overall sensitivity of the LAM-test was of 56.1% with 95% CI of (43.3–68.3). There were no differences in the LAM-test sensitivity neither by hospital nor by CD4 T cell values. LAM-test sensitivity in PLWH with < 200 CD4 T cells/µl was of 62.2% (95% CI 46.5–76.2). There were no significant differences in sensitivity when comparing LAM-test results obtained from untreated vs. α-mannosidase treated urine [55.2% (95% CI 42.6–67.4) vs. 56.9% (95% CI 44–69.2), respectively]. TB incidence in our cohort was of 21.4/100 person years (PYs) (95% CI 16.6–27.6), and mortality rate was of 11.1/100 PYs (95% CI 8.2–15.0). Importantly, PLWH with a positive LAM-test result had an adjusted hazard ratio (aHR) of death of 1.98 (1.0–3.8) with a significant p value of 0.044 when compared to PLWH with a negative LAM-test result. CONCLUSIONS: In this study, α-mannosidase treatment of urine did not significantly increase the LAM-test performance, however; this needs to be further evaluated in a large-scale study due to our study limitations. Importantly, high rates of TB incidence and mortality were found, and a positive LAM-test result predicted mortality in PLWH with TB clinical symptoms. url: https://www.ncbi.nlm.nih.gov/pubmed/33076996/ doi: 10.1186/s12981-020-00318-8 id: cord-277417-f71jwdzj author: Geoghegan, Jemma L. title: The phylogenomics of evolving virus virulence date: 2018-10-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study. url: https://doi.org/10.1038/s41576-018-0055-5 doi: 10.1038/s41576-018-0055-5 id: cord-341838-lkz8ro90 author: Gervasoni, Cristina title: Clinical features and outcomes of HIV patients with coronavirus disease 2019 date: 2020-05-14 words: 1794.0 sentences: 117.0 pages: flesch: 59.0 cache: ./cache/cord-341838-lkz8ro90.txt txt: ./txt/cord-341838-lkz8ro90.txt summary: The aim of this retrospective study was to describe the clinical characteristics and outcomes of HIVinfected patients with a probable/proven diagnosis of SARS-CoV-2 infection who have been regularly followed up by our hospital. As in the general population, the large majority of our patients were males, but their mean age was nearly 10 years lower than that observed in HIV-negative COVID-19 patients. 16 Furthermore, the findings of this study document favourable outcomes in HIV patients treated mainly with integrase inhibitors (11% protease inhibitors), which apparently indicates that antiretroviral therapy does not play a key role, A c c e p t e d M a n u s c r i p t 8 although a potentially protective effect of tenofovir cannot be ruled out given its recently reported effect against SARS-CoV-2 RNA-dependent RNA polymerase. In conclusion, our findings suggest that HIV-positive patients with SARS-CoV-2 infection are not at greater risk of severe disease or death than HIV-negative patients. abstract: Little is known about the clinical outcomes of HIV patients infected with SARS-CoV-2. We describe 47 patients referred to our hospital between 21 February and 16 April 2020 with proven/probable COVID-19, 45 (96%) of whom fully recovered and two died. url: https://doi.org/10.1093/cid/ciaa579 doi: 10.1093/cid/ciaa579 id: cord-293857-o8rlqsq5 author: Ghosh, Arun K. title: Organic Carbamates in Drug Design and Medicinal Chemistry date: 2015-01-07 words: 18165.0 sentences: 1121.0 pages: flesch: 41.0 cache: ./cache/cord-293857-o8rlqsq5.txt txt: ./txt/cord-293857-o8rlqsq5.txt summary: Also, we will outline successful designs of organic carbamates, including a variety of cyclic ether-derived carbamates, as suitable amide bond surrogates leading to a wide range of novel organic carbamates as potent HIV-1 protease, βsecretase, serine protease, and cysteine protease inhibitors. 172−174 A number of FDA-approved HIV protease inhibitor drugs contain an important carbamate functionality. 179, 230 Further development of carbamate-derived novel HIV-1 protease inhibitors is shown in Figure 12 . This backbone binding strategy to combat drug resistance led to the development of a series of very potent carbamate-derived protease inhibitors. Carbamate derivative 281 (Figure 24 ), a diphenyl phosphonate ester containing a Cbz group and bearing a single amino acid side chain, showed very good inhibitory activity against human plasma kallikrein, useful for the treatment of hereditary angioedema. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation abstract: [Image: see text] The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug–target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry. url: https://doi.org/10.1021/jm501371s doi: 10.1021/jm501371s id: cord-260422-z22t57ju author: Godet, Julien title: Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1 date: 2012-06-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: RNA chaperones are proteins able to rearrange nucleic acid structures towards their most stable conformations. In retroviruses, the reverse transcription of the viral RNA requires multiple and complex nucleic acid rearrangements that need to be chaperoned. HIV-1 has evolved different viral-encoded proteins with chaperone activity, notably Tat and the well described nucleocapsid protein NCp7. We propose here an overview of the recent reports that examine and compare the nucleic acid chaperone properties of Tat and NCp7 during reverse transcription to illustrate the variety of mechanisms of action of the nucleic acid chaperone proteins. url: https://www.sciencedirect.com/science/article/pii/S0168170212002183 doi: 10.1016/j.virusres.2012.06.021 id: cord-261382-cyty5noi author: Goffinet, Christine title: Cellular Antiviral Factors that Target Particle Infectivity of HIV-1 date: 2016-05-17 words: 4084.0 sentences: 177.0 pages: flesch: 35.0 cache: ./cache/cord-261382-cyty5noi.txt txt: ./txt/cord-261382-cyty5noi.txt summary: Whereas well-established restriction factors interfere with early post-entry steps and release of HIV-1, recent research has revealed a diverse set of proteins that reduce the infectious quality of released particles using individual, to date poorly understood modes of action. Alternatively, alteration of the virus membrane fluidity, restriction of the accessibility of the HIV-1 Env glycoprotein to the HIV-1 receptor/coreceptor complex by steric hindrance through an incorporated protein or inhibition of the maturation-induced clustering of HIV-1 Env trimers could represent mechanisms of cellular defense that target particle infectivity. Since it shares mRNA upregulation in CD4+ T-cells of HIV-1 infected individuals [11] and type I IFN-induced expression [10, 12, 13] with established restriction factors of HIV-1, it was included in a functional screen of candidate ISGs for antiviral activity (Goffinet, unpublished data). Additional family members, including IFITM5, whose expression is restricted to osteoblasts [22] , and 10 additional, recently discovered human ifitm genes [21] probably do not contribute to inhibition of HIV-1 infection or haven''t yet been tested for antiviral activity, respectively. abstract: Background: In the past decade, the identification and characterization of antiviral genes with the ability to interfere with virus replication has established cell-intrinsic innate immunity as a third line of antiviral defense in addition to adaptive and classical innate immunity. Understanding how cellular factors have evolved to inhibit HIV-1 reveals particularly vulnerable points of the viral replication cycle. Many, but not all, antiviral proteins share type I interferon-upregulated expression and sensitivity to viral counteraction or evasion measures. Whereas well-established restriction factors interfere with early post-entry steps and release of HIV-1, recent research has revealed a diverse set of proteins that reduce the infectious quality of released particles using individual, to date poorly understood modes of action. These include induction of paucity of mature glycoproteins in nascent virions or self-incorporation into the virus particle, resulting in poor infectiousness of the virion and impaired spread of the infection. Conclusion: A better understanding of these newly discovered antiviral factors may open new avenues towards the design of drugs that repress the spread of viruses whose genomes have already integrated. url: https://www.ncbi.nlm.nih.gov/pubmed/26674651/ doi: 10.2174/1570162x14666151216145521 id: cord-306701-hs9cfdsu author: Gona, Philimon N. title: Burden and changes in HIV/AIDS morbidity and mortality in Southern Africa Development Community Countries, 1990–2017 date: 2020-06-05 words: 6030.0 sentences: 278.0 pages: flesch: 50.0 cache: ./cache/cord-306701-hs9cfdsu.txt txt: ./txt/cord-306701-hs9cfdsu.txt summary: We conducted a descriptive epidemiological analysis of HIV/AIDS burden for the 16 SADC countries using secondary data from the Global Burden of Diseases, Injuries and Risk Factor (GBD) Study. We assessed morbidity and mortality in the 16 SADC countries using a descriptive epidemiological analysis of HIV/AIDS burden based on secondary data from GBD study in 1990, 2005, 2010 , and 2017. The GBD study estimates country-specific incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to diseases such as HIV/AIDS. To facilitate comparison of HIV/AIDS outcomes of morbidity and mortality across countries, time, age-groups, and sex, the Institute for Health Metrics and Evaluation (IHME) improved previously established metrics like prevalence and incidence. The five leading countries with the proportion deaths attributable to HIV/AIDS in 2017 were Botswana, South Africa, Lesotho, eSwatini, and Mozambique, also had the highest age-standardized mortality, YLL, YLD rates. abstract: BACKGROUND: The 16 Southern Africa Development Community (SADC) countries remain the epicentre of the HIV/AIDS epidemic with the largest number of people living with HIV/AIDS. Anti-retroviral treatment (ART) has improved survival and prevention of mother-to-child transmission (PMTCT) of HIV, but the disease remains a serious cause of mortality. We conducted a descriptive epidemiological analysis of HIV/AIDS burden for the 16 SADC countries using secondary data from the Global Burden of Diseases, Injuries and Risk Factor (GBD) Study. METHODS: The GBD study is a systematic, scientific effort by the Institute for Health Metrics and Evaluation (IHME) to quantify the comparative magnitude of health loss due to diseases, injuries, and risk factors by age, sex, and geographies for specific points in time. We analyzed the following outcomes: mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to HIV/AIDS for SADC. Input data for GBD was extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service utilisation, disease notifications, and other sources. Country- and cause-specific HIV/AIDS-related death rates were calculated using the Cause of Death Ensemble model (CODEm) and spatiotemporal Gaussian process regression (ST-GPR). Deaths were multiplied by standard life expectancy at each age-group to calculate YLLs. Cause-specific mortality was estimated using a Bayesian meta-regression modelling tool, DisMod-MR. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases to calculate YLDs. Crude and age-adjusted rates per 100,000 population and changes between 1990 and 2017 were determined for each country. RESULTS: In 2017, HIV/AIDS caused 336,175 deaths overall in SADC countries, and more than 20 million DALYs. This corresponds to a 3-fold increase from 113,631 deaths (6,915,170 DALYs) in 1990. The five leading countries with the proportion of deaths attributable to HIV/AIDS in 2017 were Botswana at the top with 28.7% (95% UI; 23.7–35.2), followed by South Africa 28.5% (25.8–31.6), Lesotho, 25.1% (21.2–30.4), eSwatini 24.8% (21.3–28.6), and Mozambique 24.2% (20.6–29.3). The five countries had relative attributable deaths that were at least 14 times greater than the global burden of 1.7% (1.6–1.8). Similar patterns were observed with YLDs, YLLs, and DALYs. Comoros, Seychelles and Mauritius were on the lower end, with attributable proportions less than 1%, below the global proportion. CONCLUSIONS: Great progress in reducing HIV/AIDS burden has been achieved since the peak but more needs to be done. The post-2005 decline is attributed to PMTCT of HIV, resources provided through the US President’s Emergency Plan For AIDS Relief (PEPFAR), and behavioural change. The five countries with the highest burden of HIV/AIDS as measured by proportion of death attributed to HIV/AIDS and age-standardized mortaility rate were Botswana, South Africa, Lesotho, eSwatini, and Mozambique. SADC countries should cooperate, work with donors, and embrace the UN Fast-Track approach, which calls for frontloading investment from domestic or other sources to prevent and treat HIV/AIDS. Robust tracking, testing, and early treatment are required, as well as refinement of individual treatment strategies for transient individuals in the region. url: https://doi.org/10.1186/s12889-020-08988-9 doi: 10.1186/s12889-020-08988-9 id: cord-319354-jbain7n6 author: Gondim, Ana C. S. title: Potent antiviral activity of carbohydrate-specific algal and leguminous lectins from the Brazilian biodiversity date: 2019-01-14 words: 4052.0 sentences: 201.0 pages: flesch: 52.0 cache: ./cache/cord-319354-jbain7n6.txt txt: ./txt/cord-319354-jbain7n6.txt summary: For example, lectins from Bryothamnion triquetrum (BTL) and Bryothamnion seaforthii (BSL) have been used to differentiate human colon carcinoma cell variants, 10 while the algal (cyanobacterial) lectin cyanovirin-N (CV-N) shows not only potent antiviral activity against HIV-1 and HIV-2, but also against influenza virus and Ebola virus. Given the potent anti-HIV activity of several lectins, and their pronounced effect on syncytium formation in SupT1-HUT-78/HIV-1 co-cultures, the binding of the lectins to the HIV-1 envelope glycoproteins gp120 and gp41 and the cellular CD4 receptor was investigated by surface plasmon resonance (SPR) technology. The leguminous lectins (DLasiL, DSclerL, ConBr, ConM) appeared to show higher binding to the three glycoproteins than the algal (SfL, HML) lectins (Table S1 †) . Thus, these and other lectins might act as antiviral compounds efficiently preventing viral entry into the host cells, which generally occurs through specific interactions of the lectins with glycans exposed on the gp120 (and gp41) glycoproteins (in the case of HIV) of the virus surface. abstract: Brazil has one of the largest biodiversities in the world. The search for new natural products extracted from the Brazilian flora may lead to the discovery of novel drugs with potential to treat infectious and other diseases. Here, we have investigated 9 lectins extracted and purified from the Northeastern Brazilian flora, from both leguminous species: Canavalia brasiliensis (ConBr), C. maritima (ConM), Dioclea lasiocarpa (DLasiL) and D. sclerocarpa (DSclerL), and algae Amansia multifida (AML), Bryothamniom seaforthii (BSL), Hypnea musciformis (HML), Meristiella echinocarpa (MEL) and Solieria filiformis (SfL). They were exposed to a panel of 18 different viruses, including HIV and influenza viruses. Several lectins showed highly potent antiviral activity, often within the low nanomolar range. DSclerL and DLasiL exhibited EC(50) values (effective concentration of lectin required to inhibit virus-induced cytopathicity by 50%) of 9 nM to 46 nM for HIV-1 and respiratory syncytial virus (RSV), respectively, DLasiL also inhibited feline corona virus at an EC(50) of 5 nM, and DSclerL, ConBr and ConM showed remarkably low EC(50) values ranging from 0.4 to 6 nM against influenza A virus strain H3N2 and influenza B virus. For HIV, evidence pointed to the blockage of entry of the virus into its target cells as the underlying mechanism of antiviral action of these lectins. Overall, the most promising lectins based on their EC(50) values were DLasiL, DSclerL, ConBr, ConM, SfL and HML. These novel findings indicate that lectins from the Brazilian flora may provide novel antiviral compounds with therapeutic potential. url: https://www.ncbi.nlm.nih.gov/pubmed/30996857/ doi: 10.1039/c8md00508g id: cord-287286-4l963z2q author: Green, Victoria A. title: Molecular mechanisms of viral infection and propagation: An overview of the second Advanced Summer School in Africa date: 2010-07-28 words: 7368.0 sentences: 363.0 pages: flesch: 43.0 cache: ./cache/cord-287286-4l963z2q.txt txt: ./txt/cord-287286-4l963z2q.txt summary: The main themes of discussion at the summer school were: 1) why viral infection can lead to cancer; 2) how a greater understanding of the mechanisms underpinning human immunodeficiency virus (HIV) propagation can inform new antiviral strategies; 3) the abilities of viruses to evade the immune system and the obstacles to the development of effective vaccines; and, 4) the potential afforded by viruses as research tools. The import of the host, including an ability to regulate viral gene expression in different tissues and to mount an effective immune response, is becoming increasingly apparent in determining the molecular basis of HPV-associated tumor progression. Advantages CoVs possess over other viruses as expression vectors include: 1) the possibility of spike protein manipulation, to engineer virus tropism (88, 89) ; 2) the replication of the RNA genome in the cytoplasm, side-stepping potential problems associated with integration (90); 3) the existence of nonpathogenic strains that infect a wide range of species of health and economic importance; 4) the ability to carry large genomes (27-30 kb) , which could favor the introduction of extensive foreign genes (91); and 5) the availability of cDNA clones derived from infectious strains (92, 93) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/20681023/ doi: 10.1002/iub.364 id: cord-285430-o086q2qa author: Gribble, Karleen title: Mistakes from the HIV pandemic should inform the COVID-19 response for maternal and newborn care date: 2020-07-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: In an effort to prevent infants being infected with SARS-CoV-2, some governments, professional organisations, and health facilities are instituting policies that isolate newborns from their mothers and otherwise prevent or impede breastfeeding. WEIGHING OF RISKS IS NECESSARY IN POLICY DEVELOPMENT: Such policies are risky as was shown in the early response to the HIV pandemic where efforts to prevent mother to child transmission by replacing breastfeeding with infant formula feeding ultimately resulted in more infant deaths. In the COVID-19 pandemic, the risk of maternal SARS-CoV-2 transmission needs to be weighed against the protection skin-to-skin contact, maternal proximity, and breastfeeding affords infants. CONCLUSION: Policy makers and practitioners need to learn from the mistakes of the HIV pandemic and not undermine breastfeeding in the COVID-19 pandemic. It is clear that in order to maximise infant health and wellbeing, COVID-19 policies should support skin-to-skin contact, maternal proximity, and breastfeeding. url: https://doi.org/10.1186/s13006-020-00306-8 doi: 10.1186/s13006-020-00306-8 id: cord-340763-cxnu9g8y author: Grimm, Sebastian K. title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies date: 2015-02-17 words: 7822.0 sentences: 341.0 pages: flesch: 45.0 cache: ./cache/cord-340763-cxnu9g8y.txt txt: ./txt/cord-340763-cxnu9g8y.txt summary: title: Directed Evolution of a Yeast-Displayed HIV-1 SOSIP gp140 Spike Protein toward Improved Expression and Affinity for Conformational Antibodies Because the intrinsic instability and complexity of this trimeric glycoprotein has greatly impeded the development of immunogens that properly represent the structure of native envelope, this platform addresses an essential need for methodologies with the capacity to rapidly engineer HIV spike proteins towards improved homogeneity, stability, and presentation of neutralizing epitopes. The rationally designed d-SOSIP variant and a mutant with disrupted CD4 binding site (CD4bs)-specific Ab binding (d-SOSIP D368R) were displayed as Aga2 fusion proteins on yeast ( Fig. 2A ), and compared for display level and binding to a panel of HIV bnAbs together with the well-characterized and folded YU2 gp120 core [47] and an unrelated viral envelope protein (E2) derived from Hepatitis C virus (HCV E2) as positive and negative controls Fig. 2) . abstract: Design of an envelope-based immunogen capable of inducing a broadly neutralizing antibody response is thought to be key to the development of a protective HIV-1 vaccine. However, the broad diversity of viral variants and a limited ability to produce native envelope have hampered such design efforts. Here we describe adaptation of the yeast display system and use of a combinatorial protein engineering approach to permit directed evolution of HIV envelope variants. Because the intrinsic instability and complexity of this trimeric glycoprotein has greatly impeded the development of immunogens that properly represent the structure of native envelope, this platform addresses an essential need for methodologies with the capacity to rapidly engineer HIV spike proteins towards improved homogeneity, stability, and presentation of neutralizing epitopes. We report for the first time the display of a designed SOSIP gp140 on yeast, and the in vitro evolution of derivatives with greatly improved expression and binding to conformation-dependent antibodies. These efforts represent an initial and critical step toward the ability to rapidly engineer HIV-1 envelope immunogens via directed evolution. url: https://doi.org/10.1371/journal.pone.0117227 doi: 10.1371/journal.pone.0117227 id: cord-351004-h6fde7vm author: Gudipati, Smitha title: Descriptive Analysis of Patients Living With HIV Affected by COVID-19 date: 2020-07-13 words: 2472.0 sentences: 151.0 pages: flesch: 54.0 cache: ./cache/cord-351004-h6fde7vm.txt txt: ./txt/cord-351004-h6fde7vm.txt summary: METHODS: This is a case series that included 14 PLWH with laboratory-confirmed COVID-19 infection who were evaluated at Henry Ford Hospital in Detroit, Michigan, between March 20, 2020, and April 30, 2020. CONCLUSION: Although the clinical spectrum of COVID-19 among PLWH cannot be fully ascertained by this report, it adds to the data that suggest that HIV-positive patients with SARS-CoV-2 infection are not at a greater risk of severe disease or death as compared to HIV-negative patients. This is a case series that included 14 PLWH who were evaluated in the Henry Ford Hospital (HFH) emergency department for laboratory-confirmed COVID-19 infection, between March 20, 2020, and April 30, 2020. Our case series, the current published literature on HIV and SARS-CoV-2, and the published data from HFH on COVID-19 patients without known HIV supports the theory that there is not an excess morbidity and mortality among PLWH affected by COVID-19 compared with the general public. abstract: COVID-19 disease has spread globally and was declared a pandemic on March 11, 2020, by the World Health Organization. On March 10, the State of Michigan confirmed its first 2 cases of COVID-19, and the number of confirmed cases has reached 47,182 as of May 11, 2020, with 4555 deaths. SETTING: Currently, little is known if patients living with HIV (PLWH) are at a higher risk of severe COVID-19 or if their antiretrovirals are protective. This study presents epidemiologic and clinical features of COVID-19 infected PLWH in Detroit, Michigan. METHODS: This is a case series that included 14 PLWH with laboratory-confirmed COVID-19 infection who were evaluated at Henry Ford Hospital in Detroit, Michigan, between March 20, 2020, and April 30, 2020. RESULTS: Fourteen PLWH were diagnosed with COVID-19. Twelve patients were men and 2 were women; 13 patients were virally suppressed. Eight patients were hospitalized, and 6 patients were told to self-quarantine at home after their diagnoses. Three patients who were admitted expired during their hospital stay. No patient required bilevel positive airway pressure or nebulizer use in the emergency department, and none developed acute respiratory distress syndrome, pulmonary embolism, deep venous thrombosis, or a cytokine storm while on therapy for COVID-19. CONCLUSION: Although the clinical spectrum of COVID-19 among PLWH cannot be fully ascertained by this report, it adds to the data that suggest that HIV-positive patients with SARS-CoV-2 infection are not at a greater risk of severe disease or death as compared to HIV-negative patients. url: https://doi.org/10.1097/qai.0000000000002450 doi: 10.1097/qai.0000000000002450 id: cord-013481-3zwq67do author: Guo, Kejun title: Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis date: 2020-10-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The Type I Interferons (IFN-Is) are innate antiviral cytokines that include 12 different IFNα subtypes and IFNβ that signal through the IFN-I receptor (IFNAR), inducing hundreds of IFN-stimulated genes (ISGs) that comprise the ‘interferome’. Quantitative differences in IFNAR binding correlate with antiviral activity, but whether IFN-Is exhibit qualitative differences remains controversial. Moreover, the IFN-I response is protective during acute HIV-1 infection, but likely pathogenic during the chronic stages. To gain a deeper understanding of the IFN-I response, we compared the interferomes of IFNα subtypes dominantly-expressed in HIV-1-exposed plasmacytoid dendritic cells (1, 2, 5, 8 and 14) and IFNβ in the earliest cellular targets of HIV-1 infection. Primary gut CD4 T cells from 3 donors were treated for 18 hours ex vivo with individual IFN-Is normalized for IFNAR signaling strength. Of 1,969 IFN-regulated genes, 246 ‘core ISGs’ were induced by all IFN-Is tested. However, many IFN-regulated genes were not shared between the IFNα subtypes despite similar induction of canonical antiviral ISGs such as ISG15, RSAD2 and MX1, formally demonstrating qualitative differences between the IFNα subtypes. Notably, IFNβ induced a broader interferome than the individual IFNα subtypes. Since IFNβ, and not IFNα, is upregulated during chronic HIV-1 infection in the gut, we compared core ISGs and IFNβ-specific ISGs from colon pinch biopsies of HIV-1-uninfected (n = 13) versus age- and gender-matched, antiretroviral-therapy naïve persons with HIV-1 (PWH; n = 19). Core ISGs linked to inflammation, T cell activation and immune exhaustion were elevated in PWH, positively correlated with plasma lipopolysaccharide (LPS) levels and gut IFNβ levels, and negatively correlated with gut CD4 T cell frequencies. In sharp contrast, IFNβ-specific ISGs linked to protein translation and anti-inflammatory responses were significantly downregulated in PWH, negatively correlated with gut IFNβ and LPS, and positively correlated with plasma IL6 and gut CD4 T cell frequencies. Our findings reveal qualitative differences in interferome induction by diverse IFN-Is and suggest potential mechanisms for how IFNβ may drive HIV-1 pathogenesis in the gut. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7592919/ doi: 10.1371/journal.ppat.1008986 id: cord-291534-c6cjxq07 author: Gwyer Findlay, Emily title: Cationic Host Defence Peptides: Potential as Antiviral Therapeutics date: 2013-05-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: There is a pressing need to develop new antiviral treatments; of the 60 drugs currently available, half are aimed at HIV-1 and the remainder target only a further six viruses. This demand has led to the emergence of possible peptide therapies, with 15 currently in clinical trials. Advancements in understanding the antiviral potential of naturally occurring host defence peptides highlights the potential of a whole new class of molecules to be considered as antiviral therapeutics. Cationic host defence peptides, such as defensins and cathelicidins, are important components of innate immunity with antimicrobial and immunomodulatory capabilities. In recent years they have also been shown to be natural, broad-spectrum antivirals against both enveloped and non-enveloped viruses, including HIV-1, influenza virus, respiratory syncytial virus and herpes simplex virus. Here we review the antiviral properties of several families of these host peptides and their potential to inform the design of novel therapeutics. url: https://doi.org/10.1007/s40259-013-0039-0 doi: 10.1007/s40259-013-0039-0 id: cord-260191-0u0pu0br author: Haas, W. title: „Emerging Infectious Diseases“: Dengue-Fieber, West-Nil-Fieber, SARS, Vogelgrippe, HIV date: 2004-05-29 words: 2431.0 sentences: 335.0 pages: flesch: 51.0 cache: ./cache/cord-260191-0u0pu0br.txt txt: ./txt/cord-260191-0u0pu0br.txt summary: Abstract Some emerging infectious diseases have recently become endemic in Germany.Others remain confined to specific regions in the world.Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms.Several of these emerging infections will be explained.HIV is an example for an imported pathogen which has become endemic in Germany.SARS and avian influenza are zoonoses with the potential to spread from person to person.Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain.Outbreaks of dengue fever in endemic areas are reflected in increased infec-gehäuften Erkrankungen bei Rückkehrern wieder.West-Nil-Virus-Erkrankungen kommen derzeit nur als importierte Erkrankungen in Deutschland vor.Wichtig ist,diese Erkrankungen frühzeitig in die differenzialdiagnostischen Überlegungen des Klinikers einzubeziehen,um die erforderlichen Maßnahmen zur Diagnostik,Therapie und zum Infektionsschutz rechtzeitig einleiten zu können.Dies erfordert ein gutes Zusammenspiel mit dem Labor und dem öffentlichen Gesundheitsdienst. abstract: Some emerging infectious diseases have recently become endemic in Germany. Others remain confined to specific regions in the world. Physicians notice them only when travelers after infection in endemic areas present themselves with symptoms. Several of these emerging infections will be explained. HIV is an example for an imported pathogen which has become endemic in Germany. SARS and avian influenza are zoonoses with the potential to spread from person to person. Avian influenza in humans provides a possibility for the reassortment of a potential new pandemic strain. Outbreaks of dengue fever in endemic areas are reflected in increased infections in travelers returning from these areas. Currently, West-Nile-virus infections are only imported into Germany. The timely implementation of diagnostic, therapeutic and infection control measures requires physicians to include these diseases in their differential diagnosis. To achieve this goal, good cooperation between physicians, laboratories and the public health service is essential. url: https://www.ncbi.nlm.nih.gov/pubmed/15107983/ doi: 10.1007/s00108-004-1199-2 id: cord-256324-w3bejmy5 author: Hamada, Yoshio title: New directions for protease inhibitors directed drug discovery date: 2016-07-22 words: 5066.0 sentences: 292.0 pages: flesch: 55.0 cache: ./cache/cord-256324-w3bejmy5.txt txt: ./txt/cord-256324-w3bejmy5.txt summary: 23 Most b-secretase inhibitors possess a transition state analogue at the P 1 position and are designed based on the amino acid sequence of Swedish mutant APP, which has a double mutation around the b-site (at the K670N and M671L residues). Many inhibitors with an aromatic ring at the P 1 position were subsequently reported; for example, a research group at Merck Sharp and Dohme (MSD) reported the potent inhibitors 50 63, 64 Although 18 was designed based on peptidomimetic inhibitors by using the SBDD approach, it is notable because it forms a unique cyclic structure at the P 1 position where the hydroxyl and amino groups on the cyclic sulfone ring of 18 appear to interact with two Asp residues at the active site of b-secretase as well as acting as a transition state analogue. abstract: Proteases play crucial roles in various biological processes, and their activities are essential for all living organisms—from viruses to humans. Since their functions are closely associated with many pathogenic mechanisms, their inhibitors or activators are important molecular targets for developing treatments for various diseases. Here, we describe drugs/drug candidates that target proteases, such as malarial plasmepsins, β‐secretase, virus proteases, and dipeptidyl peptidase‐4. Previously, we reported inhibitors of aspartic proteases, such as renin, human immunodeficiency virus type 1 protease, human T‐lymphotropic virus type I protease, plasmepsins, and β‐secretase, as drug candidates for hypertension, adult T‐cell leukaemia, human T‐lymphotropic virus type I‐associated myelopathy, malaria, and Alzheimer's disease. Our inhibitors are also described in this review article as examples of drugs that target proteases. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 563–579, 2016. url: https://doi.org/10.1002/bip.22780 doi: 10.1002/bip.22780 id: cord-320832-q1oojklw author: Hanum, Nadia title: Use of HIV pre-exposure prophylaxis among men who have sex with men in England: data from the AURAH2 prospective study date: 2020-09-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Since October, 2017 (and until October, 2020), pre-exposure prophylaxis (PrEP) has only been available in England, UK, through the PrEP Impact Trial, by purchasing it from some genitourinary medicine clinics, or via online sources. Here we report changes from 2013 to 2018 in PrEP and postexposure prophylaxis (PEP) awareness and use among HIV-negative gay, bisexual, and other men who have sex with men (MSM) and assess predictors of PrEP initiation. METHODS: In the prospective cohort study Attitudes to, and Understanding of Risk of Acquisition of HIV 2 (AURAH2), MSM were recruited from three sexual health clinics in England: two in London and one in Brighton, UK. Men were eligible if they were aged 18 years or older and HIV-negative or of unknown HIV status. Participants self-completed a baseline paper questionnaire at one of the three clinics between July 30, 2013, and April 30, 2016, and were subsequently able to complete 4-monthly and annual online questionnaires, which were available between March 1, 2015, and March 31, 2018, and collected information on sociodemographics, health and wellbeing, HIV status, and sexual behaviours. PrEP and PEP use in the previous 12 months was obtained at baseline and in annual questionnaires. We assessed trends over calendar time in 3-month periods from first enrolment to the end of the study period (July–December, 2013, was counted as one period) in use of PrEP and PEP using generalised estimating equation logistic models. We used age-adjusted Poisson models to assess factors associated with PrEP initiation among participants who reported never having used PrEP at baseline. FINDINGS: 1162 men completed a baseline questionnaire, among whom the mean age was 34 years (SD 10·4), and of those with available data, 942 (82%) of 1150 were white, 1076 (94%) of 1150 were gay, and 857 (74%) of 1159 were university educated. 622 (54%) of 1162 men completed at least one follow-up online questionnaire, of whom 483 (78%) completed at least one annual questionnaire. Overall, PrEP use in the past year increased from 0% (none of 28 respondents) in July to December, 2013, to 43% (23 of 53) in January to March, 2018. The corresponding increase in PrEP use among men who reported condomless sex with two or more partners was from 0% (none of 13 respondents) to 78% (21 of 27). PEP use peaked in April to June, 2016, at 28% (41 of 147 respondents), but decreased thereafter to 8% (four of 53) in January to March, 2018. Among 460 men who had never used PrEP at baseline, predictors of initiating PrEP included age 40–44 years (incidence rate ratio [IRR] 4·25, 95% CI 1·14–15·79) and 45 years and older (3·59, 1·08–11·97) versus younger than 25 years; and after adjustment for age, recent HIV test (5·17, 1·89–14·08), condomless sex (5·01, 2·16–11·63), condomless sex with two or more partners (5·43, 2·99–9·86), group sex (1·69, 1·01–2·84), and non-injection chemsex-related drugs use (2·86, 1·67–4·91) in the past 3 months, PEP use (4·69, 2·83–7·79) in the past 12 months, and calendar year (Jan 1, 2017, to March 31, 2018 vs July 30, 2013, to Dec 31, 2015: 21·19, 9·48–47·35). Non-employment (0·35, 0·14–0·91) and unstable or no housing (vs homeowner 0·13, 0·02–0·95) were associated with reduced rates of PrEP initiation after adjustment for age. About half of PrEP was obtained via the internet, even after the PrEP Impact trial had started (11 [48%] of 23 respondents in January to March, 2018). INTERPRETATION: PrEP awareness and use increased substantially from 2013 to 2018 among a cohort of MSM in England. Improving access to PrEP by routine commissioning by National Health Service England could increase PrEP use among all eligible MSM, but should include public health strategies to target socioeconomic and demographic disparities in knowledge and use of PrEP. FUNDING: National Institute for Health Research. url: https://doi.org/10.1016/s2468-2667(20)30186-9 doi: 10.1016/s2468-2667(20)30186-9 id: cord-273777-qb0vp9gr author: Happel, Anna-Ursula title: The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? date: 2020-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Besides bacteria, fungi, protists and archaea, the vaginal ecosystem also contains a range of prokaryote- and eukaryote-infecting viruses, which are collectively referred to as the “virome”. Despite its well-described role in the gut and other environmental niches, the vaginal virome remains understudied. With a focus on sexual and reproductive health, we summarize the currently known components of the vaginal virome, its relationship with other constituents of the vaginal microbiota and its association with adverse health outcomes. While a range of eukaryote-infecting viruses has been described to be present in the female genital tract (FGT), few prokaryote-infecting viruses have been described. Literature suggests that various vaginal viruses interact with vaginal bacterial microbiota and host immunity and that any imbalance thereof may contribute to the risk of adverse reproductive health outcomes, including infertility and adverse birth outcomes. Current limitations of vaginal virome research include experimental and analytical constraints. Considering the vaginal virome may represent the missing link in our understanding of the relationship between FGT bacteria, mucosal immunity, and adverse sexual and reproductive health outcomes, future studies evaluating the vaginal microbiome and its population dynamics holistically will be important for understanding the role of the vaginal virome in balancing health and disease. url: https://doi.org/10.3390/v12080832 doi: 10.3390/v12080832 id: cord-076081-ue9azoyf author: Hardon, Anita title: Alternative medicines for AIDS in resource-poor settings: Insights from exploratory anthropological studies in Asia and Africa date: 2008-07-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The emergence of alternative medicines for AIDS in Asia and Africa was discussed at a satellite symposium and the parallel session on alternative and traditional treatments of the AIDSImpact meeting, held in Marseille, in July 2007. These medicines are heterogeneous, both in their presentation and in their geographic and cultural origin. The sessions focused on the role of these medications in selected resource poor settings in Africa and Asia now that access to anti-retroviral therapy is increasing. The aims of the sessions were to (1) identify the actors involved in the diffusion of these alternative medicines for HIV/AIDS, (2) explore uses and forms, and the way these medicines are given legitimacy, (3) reflect on underlying processes of globalisation and cultural differentiation, and (4) define priority questions for future research in this area. This article presents the insights generated at the meeting, illustrated with some findings from the case studies (Uganda, Senegal, Benin, Burkina Faso, China and Indonesia) that were presented. These case studies reveal the wide range of actors who are involved in the marketing and supply of alternative medicines. Regulatory mechanisms are weak. The efficacy claims of alternative medicines often reinforce a biomedical paradigm for HIV/AIDS, and fit with a healthy living ideology promoted by AIDS care programs and support groups. The AIDSImpact session concluded that more interdisciplinary research is needed on the experience of people living with HIV/AIDS with these alternative medicines, and on the ways in which these products interact (or not) with anti-retroviral therapy at pharmacological as well as psychosocial levels. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2503967/ doi: 10.1186/1746-4269-4-16 id: cord-016283-b6yywn9f author: Hasan, Ashfaq title: Clinical Aspects and Principles of Management of Tuberculosis date: 2019-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Tuberculosis over the ages, has killed more people than any other infection has. Notwithstanding the advances in modern science, clinical diagnosis sometimes remains elusive, owing principally to the frequent paucibacillary occurrence of the disease and the slow doubling time of the organism; empiric treatment is often fraught with risks in the era of increasing drug resistance. This chapter attempts to provide an overview of the disease, beginning with the pathogenesis and its protean clinical presentations. It also discusses the recent evolution of molecular methods that have lately provided an impetus to early diagnosis with a clear opportunity to unmask drug resistance before initiating “blind”, potentially ineffective, and sometimes harmful treatment with standard therapy. The chapter also provides insight into tuberculosis in special situations, and discusses briefly the treatments in uncomplicated cases as well as in special situations, and in instances of drug resistance. Preventive methods including current and upcoming vaccines are mentioned. Finally, a short discussion of the sequelae of tuberculosis—which have the potential to be confused with active disease—is presented. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120521/ doi: 10.1007/978-981-32-9413-4_20 id: cord-018070-js9vvsud author: Hayes, Anna Marie title: Human Insecurity in the People’s Republic of China: The Vulnerability of Chinese Women to HIV/AIDS date: 2011-10-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: HIV/AIDS has become one of the world’s leading causes of human insecurity for both men and women. In addition to physiological factors, women’s vulnerability to HIV transmission is primarily fuelled by gender inequality and gender-based discrimination and violence. Therefore, women’s vulnerability to HIV transmission is closely linked to issues of empowerment and gender-based power relations. Even with this realization however, women are still sometimes overlooked in many HIV/AIDS prevention and treatment campaigns, such as those in the People’s Republic of China (PRC), and responses to HIV/AIDS do not always actively seek to empower women. Therefore, a deficiency in women’s human security increases their HIV/AIDS vulnerability. This chapter examines the intersection of gender inequality and HIV vulnerability as it applies to women in the PRC. The unequal status of many women in China, and the privileged position accorded to Chinese men, strongly indicates that Chinese women face a heightened vulnerability to HIV transmission. While many of these vulnerabilities are similar to women elsewhere in the world and certainly are not unique to China, by overlooking the many social, cultural, economic and political factors that contribute to HIV/AIDS vulnerability and transmission of the virus, particularly those faced by women, China has a long way to go before Chinese women are protected from HIV transmission. Given that HIV/AIDS heightens human insecurity, the stage is set for Chinese women (and men) to face an insecure future if the Chinese government does not fully implement international best practice, meaning a gendered response, into its overall HIV/AIDS response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122858/ doi: 10.1007/978-94-007-1799-2_2 id: cord-314098-1i6c0l3e author: Hayward, Joshua A title: Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity date: 2018-03-29 words: 6805.0 sentences: 379.0 pages: flesch: 50.0 cache: ./cache/cord-314098-1i6c0l3e.txt txt: ./txt/cord-314098-1i6c0l3e.txt summary: Several bat APOBEC3 proteins are antiviral as demonstrated by restriction of retroviral infectivity using HIV-1 as a model, and recombinant A3Z1 subtypes possess strong DNA deaminase activity. In this study, pteropid A3 loci were generated through the step-wise extension of cDNA-mapped gene scaffolds followed by remapping of sequence read archives, supported experimentally by an A3 expression analysis of bat spleen tissue. The antiviral activity of bat A3 proteins was determined by assessing the capacity of representatives of each bat A3 subtype to restrict HIV-1 infectivity in target cells. doi:10.1093/molbev/msy048 MBE Ancient Bat Retroviruses Were Hypermutated by APOBEC3 A3 activity results in C to U lesions in the negative (cDNA) strand, which lead to positive (genomic) strand G to A mutations in endogenous retroviruses (ERVs) within host genomes (Perez-Caballero et al. abstract: Bats have attracted attention in recent years as important reservoirs of viruses deadly to humans and other mammals. These infections are typically nonpathogenic in bats raising questions about innate immune differences that might exist between bats and other mammals. The APOBEC3 gene family encodes antiviral DNA cytosine deaminases with important roles in the suppression of diverse viruses and genomic parasites. Here, we characterize pteropid APOBEC3 genes and show that species within the genus Pteropus possess the largest and most diverse array of APOBEC3 genes identified in any mammal reported to date. Several bat APOBEC3 proteins are antiviral as demonstrated by restriction of retroviral infectivity using HIV-1 as a model, and recombinant A3Z1 subtypes possess strong DNA deaminase activity. These genes represent the first group of antiviral restriction factors identified in bats with extensive diversification relative to homologues in other mammals. url: https://www.ncbi.nlm.nih.gov/pubmed/29617834/ doi: 10.1093/molbev/msy048 id: cord-262143-s01jrtbb author: Head, Michael G title: The allocation of US$105 billion in global funding from G20 countries for infectious disease research between 2000 and 2017: a content analysis of investments date: 2020-09-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Each year, billions of US$ are spent globally on infectious disease research and development. However, there is little systematic tracking of global research and development. We present research on investments into infectious diseases research from funders in the G20 countries across an 18-year time period spanning 2000–17, comparing amounts invested for different conditions and considering the global burden of disease to identify potential areas of relative underfunding. METHODS: The study examined research awards made between 2000 and 2017 for infectious disease research from G20-based public and philanthropic funders. We searched research databases using a range of keywords, and open access data were extracted from funder websites. Awards were categorised by type of science, specialty, and disease or pathogen. Data collected included study title, abstract, award amount, funder, and year. We used descriptive statistics and Spearman's correlation coefficient to investigate the association between research investment and disease burden, using Global Burden of Disease 2017 study data. FINDINGS: The final 2000–17 dataset included 94 074 awards for infectious disease research, with a sum investment of $104·9 billion (annual range 4·1 billion to 8·4 billion) and a median award size of $257 176 (IQR 62 562–770 661). Pre-clinical research received $61·1 billion (58·2%) across 70 337 (74·8%) awards and public health research received $29·5 billion (28·1%) from 19 197 (20·4%) awards. HIV/AIDS received $42·1 billion (40·1%), tuberculosis received $7·0 billion (6·7%), malaria received $5·6 billion (5·3%), and pneumonia received $3·5 billion (3·3%). Funding for Ebola virus ($1·2 billion), Zika virus ($0·3 billion), influenza ($4·4 billion), and coronavirus ($0·5 billion) was typically highest soon after a high-profile outbreak. There was a general increase in year-on-year investment in infectious disease research between 2000 and 2006, with a decline between 2007 and 2017. Funders based in the USA provided $81·6 billion (77·8%). Based on funding per 2017 disability-adjusted life years (DALYs), HIV/AIDS received the greatest relative investment ($772 per DALY), compared with tuberculosis ($156 per DALY), malaria ($125 per DALY), and pneumonia ($33 per DALY). Syphilis and scabies received the least relative investment (both $9 per DALY). We observed weak positive correlation (r=0·30) between investment and 2017 disease burden. INTERPRETATION: HIV research received the highest amount of investment relative to DALY burden. Scabies and syphilis received the lowest relative funding. Investments for high-threat pathogens (eg, Ebola virus and coronavirus) were often reactive and followed outbreaks. We found little evidence that funding is proactively guided by global burden or pandemic risk. Our findings show how research investments are allocated and how this relates to disease burden and diseases with pandemic potential. FUNDING: Bill & Melinda Gates Foundation. url: https://api.elsevier.com/content/article/pii/S2214109X20303570 doi: 10.1016/s2214-109x(20)30357-0 id: cord-338804-nreqluol author: Heise, M.T. title: Viral Pathogenesis date: 2014-11-28 words: 6413.0 sentences: 232.0 pages: flesch: 35.0 cache: ./cache/cord-338804-nreqluol.txt txt: ./txt/cord-338804-nreqluol.txt summary: Viral interactions with these receptors can have a significant impact upon several aspects of viral pathogenesis, including determining the cell or tissue tropism of a virus or even whether a virus can efficiently infect and cause disease in a specific host species. Therefore, viruses that are defective in their ability to antagonize the host type I interferon system are often unable to replicate and spread efficiently within the host, illustrating the importance of viral immune evasion strategies in determining whether a virus will be pathogenic ( Figure 2) . (b) If the virus effectively interferes with the type I interferon response, interferon will be prevented from inducing a robust antiviral state within the host, and the virus is able to replicate to higher levels, will spread more efficiently, and may cause more severe disease. Therefore, like other aspects of viral pathogenesis, a complex series of virus-host interactions determines whether infection with cancer associated viruses ultimately results in disease development. abstract: Viral pathogenesis describes the processes by which viral infections cause diseases and involves virus–host interactions at the cellular and systemic level that determine whether a virus will cause a disease, what form that disease takes, and how severe the disease will be. Though the pathogenesis of each virus is unique, there are several common points in the virus life cycle that are shared between all pathogenic viruses, and by considering these common aspects of the virus-induced disease process, we can explore some general concepts in viral pathogenesis while illustrating some of the virus specific processes that shape disease outcomes. url: https://www.sciencedirect.com/science/article/pii/B9780128012383000799 doi: 10.1016/b978-0-12-801238-3.00079-9 id: cord-010203-dt9m596i author: Hellen, Christopher U.T. title: Viral proteases as targets for chemotherapeutic intervention date: 2004-08-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Many viruses encode proteinases that are essential for infectivity, and are consequently attractive chemotherapeutic targets. The biochemistry and structure of the human immunodeficiency virus proteinase have been characterized extensively, and potent peptide-mimetic inhibitors have been developed. Techniques and strategies used to improve the efficiency of these compounds are likely to be applicable to other viral proteinases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172713/ doi: 10.1016/0958-1669(92)90010-g id: cord-016041-427mbaqc author: Hengge, Ulrich R. title: Gentherapie date: 2008 words: 7287.0 sentences: 824.0 pages: flesch: 46.0 cache: ./cache/cord-016041-427mbaqc.txt txt: ./txt/cord-016041-427mbaqc.txt summary: Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (>Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (>Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. Neue Verfahren des Vektor-Targetings sowie interessante Techniken wie Elektroporation und hydrodynamische Injektion konnten die Transgenexpression in vivo verbessern, indem eine verbesserte Verteilung der Plasmid-DNA im Zielorgan erreicht wurde (Wolff u. Bei einer weiteren Zytokin-Gentherapie wurde Melanompatienten intratumoral ein Canarypox-Virus-Vektor injiziert, der das IL-12-Gen exprimierte, und zur T-Zell-Akkumulation in injizierten Melanomen führte (Triozzi et al. Es ist jedoch schwierig, einen Zusammenhang zwischen Tumorregression und der Existenz einer durch die Vakzinierung induzierten zytotoxischen T-Zell-Antwort unzweifelhaft festzustellen, da nicht alle Patienten mit zellulären Immunantworten auf den Tumor eine Regression desselben zeigen. Ein Paradebeispiel hierfür ist das p53-Protein, das erst nach einem aufgetretenen DNA-Schaden den Zellzyklus blockiert und die Zellen der Apoptose unterwirft (Roth 2006) . abstract: Die Gentherapie ist eine junge Wissenschaft, die Nukleinsäuren zur Therapie einsetzt (Hengge u. Bardenheuer 2004). Die somatische Gentherapie befasst sich mit der Behandlung von somatischen (Körper-)Zellen (⧁ Tab. 4.1.1), wobei das therapeutische Gen ein im Organismus benötigtes Protein kodiert. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120194/ doi: 10.1007/978-3-540-69414-4_16 id: cord-017012-yl0vanuh author: Herberg, Jethro title: Infectious Diseases and the Kidney date: 2009 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The kidney is involved in a wide range of bacterial, viral, fungal, and parasitic diseases. In most systemic infections, renal involvement is a minor component of the illness, but in some, renal failure may be the presenting feature and the major problem in management. Although individual infectious processes may have a predilection to involve the renal vasculature, glomeruli, interstitium, or collecting systems, a purely anatomic approach to the classification of infectious diseases affecting the kidney is rarely helpful because most infections may involve several different aspects of renal function. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121468/ doi: 10.1007/978-3-540-76341-3_52 id: cord-314528-5yq95giq author: Hirayama, Makoto title: High-Mannose Specific Lectin and Its Recombinants from a Carrageenophyta Kappaphycus alvarezii Represent a Potent Anti-HIV Activity Through High-Affinity Binding to the Viral Envelope Glycoprotein gp120 date: 2015-12-12 words: 8228.0 sentences: 437.0 pages: flesch: 56.0 cache: ./cache/cord-314528-5yq95giq.txt txt: ./txt/cord-314528-5yq95giq.txt summary: title: High-Mannose Specific Lectin and Its Recombinants from a Carrageenophyta Kappaphycus alvarezii Represent a Potent Anti-HIV Activity Through High-Affinity Binding to the Viral Envelope Glycoprotein gp120 We previously reported that a high-mannose binding lectin KAA-2 from the red alga Kappaphycus alvarezii, which is an economically important species and widely cultivated as a source of carrageenans, had a potent anti-influenza virus activity. They consisted of four internal tandem-repeated domains, which are conserved in high-mannose specific lectins from lower organisms, including a cyanobacterium Oscillatoria agardhii and a red alga Eucheuma serra. alvarezii preferentially recognized high-mannose-type oligosaccharides bearing an exposed α1-3 Man at the nonreducing end in D2 arm and inhibited infection of various influenza virus strains with EC 50 s of low nanomolar levels through direct binding to the viral envelope hemagglutinin protein, which has several high-mannose N-glycans (Sato et al. abstract: We previously reported that a high-mannose binding lectin KAA-2 from the red alga Kappaphycus alvarezii, which is an economically important species and widely cultivated as a source of carrageenans, had a potent anti-influenza virus activity. In this study, the full-length sequences of two KAA isoforms, KAA-1 and KAA-2, were elucidated by a combination of peptide mapping and cDNA cloning. They consisted of four internal tandem-repeated domains, which are conserved in high-mannose specific lectins from lower organisms, including a cyanobacterium Oscillatoria agardhii and a red alga Eucheuma serra. Using an Escherichia coli expression system, an active recombinant form of KAA-1 (His-tagged rKAA-1) was successfully generated in the yield of 115 mg per a litter of culture. In a detailed oligosaccharide binding analysis by a centrifugal ultrafiltration-HPLC method with 27 pyridylaminated oligosaccharides, His-tagged rKAA-1 and rKAA-1 specifically bound to high-mannose N-glycans with an exposed α1-3 mannose in the D2 arm as the native lectin did. Predicted from oligosaccharide-binding specificity, a surface plasmon resonance analysis revealed that the recombinants exhibit strong interaction with gp120, a heavily glycosylated envelope glycoprotein of HIV with high association constants (1.48–1.61 × 10(9) M(−1)). Native KAAs and the recombinants inhibited the HIV-1 entry at IC(50)s of low nanomolar levels (7.3–12.9 nM). Thus, the recombinant proteins would be useful as antiviral reagents targeting the viral surface glycoproteins with high-mannose N-glycans, and the cultivated alga K. alvarezii could also be a good source of not only carrageenans but also this functional lectin(s). url: https://www.ncbi.nlm.nih.gov/pubmed/26661793/ doi: 10.1007/s10126-015-9684-2 id: cord-334133-61om170g author: Hollier, Mark J. title: The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function date: 2005-07-05 words: 8424.0 sentences: 437.0 pages: flesch: 57.0 cache: ./cache/cord-334133-61om170g.txt txt: ./txt/cord-334133-61om170g.txt summary: For example, the GL envelope protein of equine arteritis virus is proposed to have 1 or 3 MSDs (Snijder and Meulenberg, 1998) , the M protein of transmissible gastroenteritis coronavirus and equine arteritis virus, and the S antigen of hepatitis B virus are proposed to have three or four MSDs (Prange and Streeck, 1995; Risco et al., 1995; Snijder and Meulenberg, 1998) , and the herpes simplex virus glycoprotein B (Pellett et al., 1985) , and the Epstein -Barr virus 58 kDa latent protein Hennessy et al., 1984) both have multiple MSDs. Based on an analysis of their sequence and structure, we propose that the gp41 transmembrane region and C-terminal tail of all HIV-1 clades A to D can exist in two conformations, with either 1 MSD (the conventional structure) or with 3 MSDs. We suggest that these are, respectively, the majority and minority forms of intracellular Env. In the 3-MSD form, MSD 1 and MSD 2 are separated by a highly conserved beta turn, while the MSD 2 and MSD 3 support an unstructured hydrophilic loop/minor ectodomain of 41 residues that in clade B strains is highly antibody-reactive and involved in fusion. abstract: In addition to the major ectodomain, the gp41 transmembrane glycoprotein of HIV-1 is now known to have a minor ectodomain that is part of the long C-terminal tail. Both ectodomains are highly antigenic, carry neutralizing and non-neutralizing epitopes, and are involved in virus-mediated fusion activity. However, data have so far been biologically based, and derived solely from T cell line-adapted (TCLA), B clade viruses. Here we have carried out sequence and theoretically based structural analyses of 357 gp41 C-terminal sequences of mainly primary isolates of HIV-1 clades A, B, C, and D. Data show that all these viruses have the potential to form a tail loop structure (the minor ectodomain) supported by three, β-sheet, membrane-spanning domains (MSDs). This means that the first (N-terminal) tyrosine-based sorting signal of the gp41 tail is situated outside the cell membrane and is non-functional, and that gp41 that reaches the cell surface may be recycled back into the cytoplasm through the activity of the second tyrosine-sorting signal. However, we suggest that only a minority of cell-associated gp41 molecules – those destined for incorporation into virions – has 3 MSDs and the minor ectodomain. Most intracellular gp41 has the conventional single MSD, no minor ectodomain, a functional first tyrosine-based sorting signal, and in line with current thinking is degraded intracellularly. The gp41 structural diversity suggested here can be viewed as an evolutionary strategy to minimize HIV-1 envelope glycoprotein expression on the cell surface, and hence possible cytotoxicity and immune attack on the infected cell. url: https://www.ncbi.nlm.nih.gov/pubmed/15913700/ doi: 10.1016/j.virol.2005.04.015 id: cord-004247-lagv3tp7 author: Hooft van Huijsduijnen, Rob title: Reassessing therapeutic antibodies for neglected and tropical diseases date: 2020-01-30 words: 6756.0 sentences: 314.0 pages: flesch: 42.0 cache: ./cache/cord-004247-lagv3tp7.txt txt: ./txt/cord-004247-lagv3tp7.txt summary: This mAb was protective in an in vitro, antigen-dependent, cellular cytotoxicity assay with rat macrophages or eosinophils and also in vivo during the early phase of infection Second, beyond the cell-surface proteins, schistosomes also express a large number of glycans as part of their glycoprotein and glycolipid repertoire, and an antibody response against those glycans is mounted by the infected host [80] . In addition to antibodies that directly target and inhibit the fungal pathogen, mAbs can be directed to checkpoints that control the host immune response. In addition to highlighting the potential of mAbs as therapeutics, these studies have demonstrated the diversity of inhibitory actions that mAbs can perform on cryptococcal cells, which can include opsonization and increased phagocytosis, inhibition of fungal growth, capsular polysaccharide release and biofilm formation, antibody-mediated target cleavage, and augmentation of the host response [104] [105] [106] [107] . abstract: In the past two decades there has been a significant expansion in the number of new therapeutic monoclonal antibodies (mAbs) that are approved by regulators. The discovery of these new medicines has been driven primarily by new approaches in inflammatory diseases and oncology, especially in immuno-oncology. Other recent successes have included new antibodies for use in viral diseases, including HIV. The perception of very high costs associated with mAbs has led to the assumption that they play no role in prophylaxis for diseases of poverty. However, improvements in antibody-expression yields and manufacturing processes indicate this is a cost-effective option for providing protection from many types of infection that should be revisited. Recent technology developments also indicate that several months of protection could be achieved with a single dose. Moreover, new methods in B cell sorting now enable the systematic identification of high-quality antibodies from humanized mice, or patients. This Review discusses the potential for passive immunization against schistosomiasis, fungal infections, dengue, and other neglected diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991954/ doi: 10.1371/journal.pntd.0007860 id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro.2016.182) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro.2016.182 doi: 10.1038/nrmicro.2016.182 id: cord-292521-tpb12dkq author: Howard, John title: Widely Disseminated Cryptococcosis Manifesting in a Previously Undiagnosed Human Immunodeficiency Virus (HIV)-Positive 18-Year-Old date: 2020-10-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Patient: Male, 18-year-old Final Diagnosis: Disseminated cryptococcosis in previously undiagnosed HIV Symptoms: Diarhea • lymphadenopathy Medication: — Clinical Procedure: — Specialty: General and Internal Medicine • Pathology OBJECTIVE: Unusual clinical course BACKGROUND: After initial infection with HIV, loss of CD4+ T cells progresses along a predictable timeline. The clinical latency stage lasts an average of 10 years, until the CD4+ T cell count falls below 200 cells/uL or the patient develops an AIDS-defining opportunistic infection/cancer. This report describes an unusual opportunistic infection in a young patient with no prior clinical evidence of HIV infection. CASE REPORT: An 18-year-old man presented with fever, abdominal pain, and dyspnea for the previous 2 weeks and was symptomatically treated for gastroenteritis. He presented 2 weeks later with extreme fatigue, and a CT scan revealed diffuse lymphadenopathy. He was transferred to a regional hospital, but upon arrival and prior to detailed investigative work-up, he developed cardiac arrest. Despite maximal resuscitative efforts, he died approximately 8 h after admission. At autopsy, diffuse lymphadenopathy, splenomegaly, and pulmonary congestion were noted. Disseminated cryptococcal infection involving almost every organ system was identified at autopsy. A postmortem HIV-1 antibody test was positive. The cause of death was severe immunodeficiency as a result of advanced HIV infection resulting in disseminated cryptococcal infection, with cerebral edema, herniation, and respiratory failure. CONCLUSIONS: This patient’s non-specific symptoms in conjunction with his rapid decline made arriving at a correct diagnosis challenging. Only during autopsy was the disseminated fungal infection discovered, leading to suspicion of HIV infection. HIV autopsies are not uncommon, but the clinical history is usually known beforehand. This case report highlights the importance of considering HIV-related conditions in patients presenting with this array of symptoms, as well as to alert healthcare providers and staff to the need for increased biosafety precautions. url: https://doi.org/10.12659/ajcr.924410 doi: 10.12659/ajcr.924410 id: cord-006381-fsg9x8n7 author: Howard, O. M. Zack title: Chemokines as Molecular Targets for Therapeutic Intervention date: 1999 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite the youth of the chemokine field, many antagonists of chemokine function have already been identified and tested at the preclinical level. These include neutralizing antibodies, peptidyl and non-peptidyl antagonists and non-specific immunosuppressive agents. These early studies suggest that chemokine agonists have the potential to regulate many diseases, ranging from HIV-1 infection and tumor growth to acute and chronic inflammation. Clinical application will depend on pharmaceutical development. Great strides have been made in defining structural domains of the chemokines involved in receptor binding and activation. The identification of receptors is rapidly progressing, but with 50 potential ligands and 15 characterized receptors, it is obvious that additional molecular studies are needed. The intriguing observation that several pathogens either use chemokine receptors as entry portals or produce chemokine decoys to subvert the immune system suggests that there is much to be learned about the immune system from studies of “virokines.” Future studies should lead to the discovery and design of more effective inhibitors and antagonists with therapeutic benefit. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101721/ doi: 10.1023/a:1020587407535 id: cord-265146-j0n3a4m6 author: Hsieh, Ying-Hen title: Ascertaining the 2004–2006 HIV type 1 CRF07_BC outbreak among injecting drug users in Taiwan date: 2013-02-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To ascertain the explosive 2004–2006 outbreak of HIV-1 CRF07_BC among intravenous drug users (IDU) in Taiwan, which more than doubled the total number of reported HIV cases in less than 3 years, resulting in a 45-fold increase in cumulative IDU/HIV cases and a 40-fold increase in previously seldom-reported female IDU/HIV cases. METHODS: A mathematical model was utilized to fit the monthly case data, in order to estimate the turning points (peak incidence) and the reproduction number R of the outbreak. Furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female IDUs. RESULTS: Model fit revealed a two-wave epidemic during April 2004–March 2007. The larger second wave started shortly after May 2005 and peaked in October 2005 before gradually subsiding. R was estimated to be 3.15 (3.14–3.16) and 27.21 (26.73–28.05) for the two respective waves. The time series of monthly differences in male and female case data were found to be most significantly correlated at lag 0 (i.e., r > 0.7) with r = 0.906 and 0.804, respectively in each direction. The Granger causality test indicated that the male time series caused the corresponding female time series with a lag of 2 months or less. CONCLUSIONS: The modeling results revealed the presence of a small first wave in 2004, before an explosion of cases after May 2005. Furthermore, a harm reduction program implemented in August 2005 contributed to the downturn in the epidemic after October. Correlation results also suggest that the upsurge in male HIV cases led to the subsequent drastic surge in female cases. url: https://doi.org/10.1016/j.ijid.2013.01.002 doi: 10.1016/j.ijid.2013.01.002 id: cord-030427-fn9pfqts author: Huang, Feifei title: Acculturation, HIV-Related Stigma, Stress, and Patient-Healthcare Provider Relationships Among HIV-Infected Asian Americans: A Path Analysis date: 2020-08-13 words: 3439.0 sentences: 162.0 pages: flesch: 42.0 cache: ./cache/cord-030427-fn9pfqts.txt txt: ./txt/cord-030427-fn9pfqts.txt summary: title: Acculturation, HIV-Related Stigma, Stress, and Patient-Healthcare Provider Relationships Among HIV-Infected Asian Americans: A Path Analysis A bias-corrected factor score path analysis was performed to examine the proposed model of relations among acculturation, stigma, stress, and patient-HCP relationships. A convenience sample of 69 HIV-positive Asian Americans in San Francisco, Los Angeles, and New York City were recruited and collect data were collected on demographics, HIV-related stigma, stress, and patient-HCP relationships. Similar to other people living with HIV/AIDS (PLWHA), HIV-infected Asian Americans may also suffer from HIV-related stigma and stress, which in turn influences their patient-healthcare provider (HCP) relationships [4, 5] . The present study showed that acculturation is beneficial for patient-HCP relationships to the extent that it decreases perceived stigma and stress in Asian American PLWHA. In this paper, we examined the associations among acculturation, HIV-related stigma, stress, and patient-HCP relationships among Asian American PLWHA. abstract: Acculturation may limit HIV-positive Asian Americans’ active interactions with patient-healthcare providers (HCP) and utilization of HIV healthcare services; however, the specific mediation effect of acculturation still unknown. A bias-corrected factor score path analysis was performed to examine the proposed model of relations among acculturation, stigma, stress, and patient-HCP relationships. A convenience sample of 69 HIV-positive Asian Americans in San Francisco, Los Angeles, and New York City were recruited and collect data were collected on demographics, HIV-related stigma, stress, and patient-HCP relationships. HIV stigma and stress had a direct, negative effect on patient-HCP relationships. Acculturation had a positive total effect on patient-HCP relationships, and was mediated by HIV stigma and stress. A acculturation also had a direct impact on stigma and stress. Acculturation, HIV-related stigma, and stress are key elements to achieving good patient-HCP relationships, and provide insights on the design of culturally sensitive interventions to improve patient-HCP relationships. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424136/ doi: 10.1007/s10903-020-01068-5 id: cord-017439-0c6ohmmg author: Hughes-Oliver, Jacqueline M. title: Pooling Experiments for Blood Screening and Drug Discovery date: 2006 words: 7874.0 sentences: 461.0 pages: flesch: 51.0 cache: ./cache/cord-017439-0c6ohmmg.txt txt: ./txt/cord-017439-0c6ohmmg.txt summary: Today, pooling experiments are driven by the potential cost savings and precision gains that can result, and they are making a substantial impact on blood screening and drug discovery. A general review of pooling experiments is given here, with additional details and discussion of issues and methods for two important application areas, namely, blood testing and drug discovery. Recognizing that developing countries can ill-afford the cost of 100% one-at-a-time screening, WHO issued recommendations for testing for HIV antibody on serum pools (WHO, 1991) in areas where seroprevalence is less than 2%. Since the late 1980s, statistical contributions to pooling for blood testing have focused on the following aspects: assessing changes in sensitivity and specificity due to pooling, designing pooling strategies to accommodate both cheap initial screens and gold-standard confirmatory screens, and estimation of covariate-dependent prevalences. On the information and accuracy of pooled testing in estimating prevalence of a rare disease: Application to HIV screening abstract: Pooling experiments date as far back as 1915 and were initially used in dilution studies for estimating the density of organisms in some medium. These early uses of pooling were necessitated by scientific and technical limitations. Today, pooling experiments are driven by the potential cost savings and precision gains that can result, and they are making a substantial impact on blood screening and drug discovery. A general review of pooling experiments is given here, with additional details and discussion of issues and methods for two important application areas, namely, blood testing and drug discovery. The blood testing application is very old, from 1943, yet is still used today, especially for HIV antibody screening. In contrast, the drug discovery application is relatively new, with early uses occurring in the period from the late 1980s to early 1990s. Statistical methods for this latter application are still actively being investigated and developed through both the pharmaceutical industries and academic research. The ability of pooling to investigate synergism offers exciting prospects for the discovery of combination therapies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122002/ doi: 10.1007/0-387-28014-6_3 id: cord-017227-66dx2dkv author: Humphreys, Hilary title: Immunocompromised Patients date: 2012-08-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The ominous prognosis of cancer patients with or without neutropenia in need of critical care has led to reservations with regard to admission of cancer patients to the ICU. However, significant improvements in ICU and in-hospital survival of cancer patients in ICU have been demonstrated in studies in recent years [1–4]. Risk factors for mortality have shifted from those related to the underlying condition to those related to the severity of acute illness similar to other critically-ill patients. Neutropenia per se and the underlying malignancy (solid and hematological) do not have an impact on the outcome of patients in ICU. Recent chemotherapy is associated rather with improved survival [3, 5–7], while organ dysfunction, severity of disease scores, need for vasopressor treatment, need for mechanical ventilation immediately or after noninvasive ventilation, no definite diagnosis and a non-infectious diagnosis are associated with mortality [1–3, 8]. Invasive aspergillosis is also associated with very high mortality rates in ICU (see below). In several studies, admission to ICU in the early stages of sepsis or other acute event was associated with better survival than admission later, after development of organ dysfunction. Performance status is perhaps the most important and only variable relating to the underlying condition that is correlated with ICU death. The prognosis remains guarded for certain cancer patients, including patients after allogeneic hematopoietic stem cell transplantation (HSCT) with active uncontrolled graft versus host disease, those with relapse of the primary disease after allogeneic HSCT and special cases of solid cancer including pulmonary carcinomatous lymphangitis and carcinomatous meningitis with coma [9]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121735/ doi: 10.1007/978-1-4471-4318-5_10 id: cord-259131-36udb7uc author: Hunegnaw, Ruth title: Alveolar Macrophage Dysfunction and Increased PD-1 Expression During Chronic SIV Infection of Rhesus Macaques date: 2019-07-03 words: 7426.0 sentences: 376.0 pages: flesch: 46.0 cache: ./cache/cord-259131-36udb7uc.txt txt: ./txt/cord-259131-36udb7uc.txt summary: AM expression of proinflammatory cytokines TNF-α, IL-6, IL-1β, and chemokine RANTES drastically increased 2-wpi compared to AMs of naïve macaques (p < 0.0001 for all), but dropped significantly with progression to chronic infection. AM expression of proinflammatory cytokines TNF-α, IL-6, IL-1β, and chemokine RANTES drastically increased 2-wpi compared to AMs of naïve macaques (p < 0.0001 for all), but dropped significantly with progression to chronic infection. In addition, the low proinflammatory cytokine response in chronic infection was not associated with an increase in IL-10-expressing AMs. To investigate AM activation, BAL cells obtained from naïve and acute and chronically infected macaques at weeks 2, 4, 8, 12, and 20 wpi, were incubated with native gp120 from R5 tropic SIV or LPS for 6 h, and intracellular expression of MIP-1β and IL-6 was assessed (Figures 3A,B) . Decreased Fc receptor expression on innate immune cells is associated with impaired antibody-mediated cellular phagocytic activity in chronically HIV-1 infected individuals abstract: HIV infected individuals have been shown to be pre-disposed to pulmonary infections even while receiving anti-retroviral therapy. Alveolar macrophages (AMs) play a critical role in lung innate immunity, but contradictory results have been reported regarding their functionality following HIV infection. Here, using the SIV rhesus macaque model, we document the effect of SIV infection on the phenotypic and functional properties of AMs. Following infection with SIV(mac251), AMs in bronchoalveolar lavage (BAL) sampled over 2- to 20-weeks post-infection (wpi) were compared to those in BAL samples from naïve macaques. AM expression of proinflammatory cytokines TNF-α, IL-6, IL-1β, and chemokine RANTES drastically increased 2-wpi compared to AMs of naïve macaques (p < 0.0001 for all), but dropped significantly with progression to chronic infection. Phagocytic activity of AMs 2-and 4-wpi was elevated compared to AMs of naive animals (p = 0.0005, p = 0.0004, respectively) but significantly decreased by 12-wpi (p = 0.0022, p = 0.0019, respectively). By 20-wpi the ability of AMs from chronically infected animals to perform SIV-specific antibody-dependent phagocytosis (ADP) was also diminished (p = 0.028). Acute SIV infection was associated with increased FcγRIII expression which subsequently declined with disease progression. Frequency of FcγRIII(+) AMs showed a strong trend toward correlation with SIV-specific ADP, and at 2-wpi FcγRIII expression negatively correlated with viral load (r = −0.6819; p = 0.0013), suggesting a contribution to viremia control. Importantly, PD-1 was found to be expressed on AMs and showed a strong trend toward correlation with plasma viral load (r = 0.8266; p = 0.058), indicating that similar to over-expression on T-cells, PD-1 expression on AMs may also be associated with disease progression. Further, AMs predominantly expressed PD-L2, which remained consistent over the course of infection. PD-1 blockade enhanced SIV-specific ADP by AMs from chronic infection indicating that the PD-1/PD-L2 pathway may modulate functional activity of AMs at that stage. These findings provide new insight into the dynamics of SIV infection leading to AM dysfunction and alteration of pulmonary innate immunity. Our results suggest new pathways to exploit in developing therapies targeting pulmonary disease susceptibility in HIV-infected individuals. url: https://doi.org/10.3389/fimmu.2019.01537 doi: 10.3389/fimmu.2019.01537 id: cord-018646-fqy82sm6 author: Huremović, Damir title: Brief History of Pandemics (Pandemics Throughout History) date: 2019-05-16 words: 6864.0 sentences: 333.0 pages: flesch: 56.0 cache: ./cache/cord-018646-fqy82sm6.txt txt: ./txt/cord-018646-fqy82sm6.txt summary: Starting with religious texts, which heavily reference plagues, this chapter establishes the fundamentals for our understanding of the scope, social, medical, and psychological impact that some pandemics effected on civilization, including the Black Death (a plague outbreak from the fourteenth century), the Spanish Flu of 1918, and the more recent outbreaks in the twenty-first century, including SARS, Ebola, and Zika. This includes the unexamined ways pandemic outbreaks might have shaped the specialty of psychiatry; psychoanalysis was gaining recognition as an established treatment within medical community at the time the last great pandemic was making global rounds a century ago. Stemming from Doric Greek word plaga (strike, blow), the word plague is a polyseme, used interchangeably to describe a particular, virulent contagious febrile disease caused by Yersinia pestis, as a general term for any epidemic disease causing a high rate of mortality, or more widely, as a metaphor for any sudden outbreak of a disastrous evil or affliction [4] . abstract: Intermittent outbreaks of infectious diseases have had profound and lasting effects on societies throughout history. Those events have powerfully shaped the economic, political, and social aspects of human civilization, with their effects often lasting for centuries. Epidemic outbreaks have defined some of the basic tenets of modern medicine, pushing the scientific community to develop principles of epidemiology, prevention, immunization, and antimicrobial treatments. This chapter outlines some of the most notable outbreaks that took place in human history and are relevant for a better understanding of the rest of the material. Starting with religious texts, which heavily reference plagues, this chapter establishes the fundamentals for our understanding of the scope, social, medical, and psychological impact that some pandemics effected on civilization, including the Black Death (a plague outbreak from the fourteenth century), the Spanish Flu of 1918, and the more recent outbreaks in the twenty-first century, including SARS, Ebola, and Zika. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123574/ doi: 10.1007/978-3-030-15346-5_2 id: cord-016075-ind62t53 author: Hwang, Stephen W. title: Homeless People date: 2005 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120238/ doi: 10.1007/0-387-25822-1_2 id: cord-292830-gcfx1095 author: Ianevski, Aleksandr title: Novel activities of safe-in-human broad-spectrum antiviral agents date: 2018-04-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: According to the WHO, there is an urgent need for better control of viral diseases. Re-positioning existing safe-in-human antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. We tested 55 of these compounds against eight different RNA and DNA viruses. We found novel activities for dalbavancin against echovirus 1, ezetimibe against human immunodeficiency virus 1 and Zika virus, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against Rift valley fever virus. Thus, the spectrum of antiviral activities of existing antiviral agents could be expanded towards other viral diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/29698664/ doi: 10.1016/j.antiviral.2018.04.016 id: cord-018040-k0h5ejjt author: Ilyinskii, P. title: Aspects of Microparticle Utilization for Potentiation of Novel Vaccines: Promises and Risks date: 2009 words: 6930.0 sentences: 309.0 pages: flesch: 41.0 cache: ./cache/cord-018040-k0h5ejjt.txt txt: ./txt/cord-018040-k0h5ejjt.txt summary: Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. The size of these vectors is generally within 10-1000 nm and it is a specific mechanism by which our immune system recognizes such particles that underlies their adjuvant potencies (in addition, many carriers protect proteins/NA from rapid degradation in vivo and release them into the organism during prolonged periods of time, which also results in higher immunogenicity). Several VLPbased vaccines have been licensed for general use, many of them against HBV, which are composed of HBV surface antigen (HBsAg), which is a main component of currently used protein-based, alum adjuvant-potentiated vaccine. abstract: Many recombinant vaccines against novel (HIV, HCV) or ever-changing (influenza) infectious agents require the presence of adjuvants/delivery vehicles to induce strong immune responses. The necessity of their improvement led to the major effort towards development of vaccine delivery systems that are generally particulate (e.g., nano- and microparticles) and have comparable dimensions to the pathogens (viruses or bacteria). The mode of action of these adjuvants is not fully understood but implies the stimulation of the innate or antigen-specific immune responses, and/or the increase of antigen uptake or processing by antigen-presenting cells (APC). Moreover, enhancement of adjuvant activity through the use of micro- and nanoparticulate delivery systems often resulted from the synergistic effects producing immune responses stronger than those elicited by the adjuvant or delivery system alone. Among particulate adjuvants, biodegradable micro- and nanoparticles of poly(D,L-lactide-co-glycoside) (PLGA) or poly(D,L-lactide) (PLA) have been reported to enhance both humoral and cellular immune responses against an encapsulated protein antigen. Cationic and anionic polylactide co-glycolide (PLG) microparticles have been successfully used to adsorb a variety of agents, which include plasmid DNA, recombinant proteins and adjuvant active oligonucleotides and are also currently tested in several vaccine applications. Another approach envisions specific targeting of APC, especially peripheral DC and exploitation of particulate systems that are small enough for lymphatic uptake (polystyrene nanobeads). Micro- and nanoparticles offer the possibility of enhancement of their uptake by appropriate cells through manipulation of their surface properties. Still, questions regarding toxicity and molecular interaction between micro- and nano-particles and immune cells, tissues and whole organisms remain to be addressed. These risks and other possible side effects should be assessed in detail especially if mass-production and massive administration of such preparations is to be considered. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122810/ doi: 10.1007/978-90-481-2523-4_26 id: cord-312513-mad9xkz8 author: Iordanou, Stelios title: Severe SARS‐CoV‐2 pneumonia in a 58‐year‐old patient with HIV: a clinical case report from the Republic of Cyprus date: 2020-05-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: HIV and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) co‐infection is a major challenge for the clinicians as it urged the importance of developing an optimal pharmaceutical scheme and patient's management. The reports that have been recently published regarding the course of SARS‐CoV‐2 in patients with HIV are sparse. In this brief report we describe, our first single‐centre experience from a 58‐year‐old Caucasian male patient with HIV who developed a severe SARS‐CoV‐2 infection, including clinical characteristics, treatment, and outcomes. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26053 doi: 10.1002/jmv.26053 id: cord-010845-pakh49dy author: Isiguzo, Godsent title: Diagnosis and Management of Tuberculous Pericarditis: What Is New? date: 2020-01-15 words: 4108.0 sentences: 176.0 pages: flesch: 37.0 cache: ./cache/cord-010845-pakh49dy.txt txt: ./txt/cord-010845-pakh49dy.txt summary: The statement is particularly true for tuberculous pericarditis (TBP), where lack of understanding of this severe form of extra-pulmonary tuberculosis (EPTB) has hampered discovery and translation of cost-effective, rapid diagnostic tests and host-directed therapies able to prevent its debilitating complications and associated mortality. Finally, recent reports suggest that among both HIV-infected and HIVuninfected patients with culture-positive pericardial fluid, Mtb bacillary loads are as high as 3.91 log 10 CFU/mL (range 0.5-8.96), with bacillary loads over 5.53 log 10 CFU/mL being significantly associated with mortality [18] . Diagnostic accuracy of quantitative PCR (Xpert MTB/RIF) for tuberculous pericarditis compared to adenosine deaminase and unstimulated interferon-γ in a high burden setting: a prospective study Diagnostic accuracy of quantitative PCR (Xpert MTB/RIF) for tuberculous pericarditis compared to adenosine deaminase and unstimulated interferon-gamma in a high burden setting: a prospective study abstract: PURPOSE OF REVIEW: This review provides an update on the immunopathogenesis of tuberculous pericarditis (TBP), investigations to confirm tuberculous etiology, the limitations of anti-tuberculous therapy (ATT), and recent efficacy trials. RECENT FINDINGS: A profibrotic immune response characterizes TBP, with low levels of AcSDKP, high levels of γ-interferon and IL-10 in the pericardium, and high levels of TGF-β and IL-10 in the blood. These findings may have implications for future therapeutic targets. Despite advances in nucleic acid amplification approaches, these tests remain disappointing for TBP. Trials of corticosteroids and colchicine have had mixed results, with no impact on mortality, evidence of a reduction in rates of constrictive pericarditis and potential harm in those with advanced HIV. Small studies suggest that ATT penetrates the pericardium poorly. Given that there is a close association between high bacillary burden and mortality, a rethink about the optimal drug doses and duration may be required. SUMMARY: The high mortality and morbidity from TBP despite use of anti-tuberculous drugs call for researches targeting host-directed immunological determinants of treatment outcome. There is also a need for the identification of steps in clinical management where interventions are needed to improve outcomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11886-020-1254-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222865/ doi: 10.1007/s11886-020-1254-1 id: cord-331879-w7008uyy author: Iversen, Jenny title: COVID‐19, HIV and key populations: cross‐cutting issues and the need for population‐specific responses date: 2020-10-01 words: 3688.0 sentences: 143.0 pages: flesch: 36.0 cache: ./cache/cord-331879-w7008uyy.txt txt: ./txt/cord-331879-w7008uyy.txt summary: However, the conditions faced by specific populations vary according to social, structural and environmental factors, including stigma and discrimination, criminalization, social and economic safety nets and the local epidemiology of HIV and COVID‐19, which determine risk of exposure and vulnerability to adverse health outcomes, as well as the ability to comply with measures such as physical distancing. Significant heterogeneity in the COVID‐19 pandemic, the underlying HIV epidemic and the ability of key populations to protect themselves means that people who inject drugs and sex workers face particular challenges, including indirect impacts as a result of police targeting, loss of income and sometimes both. Global networks, including the International Network of People who use Drugs (INPUD), the Global Network of Sex Work Projects (NSWP), the Global Network of People Living with HIV (GNP+) and MPact Global Action for Gay Men''s Health and Rights have issued statements calling for urgent action to protect their communities and to address population-specific needs for prevention, care and treatment [9,18-20]. abstract: INTRODUCTION: Key populations at elevated risk to contract or transmit HIV may also be at higher risk of COVID‐19 complications and adverse outcomes associated with public health prevention measures. However, the conditions faced by specific populations vary according to social, structural and environmental factors, including stigma and discrimination, criminalization, social and economic safety nets and the local epidemiology of HIV and COVID‐19, which determine risk of exposure and vulnerability to adverse health outcomes, as well as the ability to comply with measures such as physical distancing. This commentary identifies common vulnerabilities and cross‐cutting themes in terms of the impacts of COVID‐19 on key populations before addressing issues and concerns specific to particular populations. DISCUSSION: Cross‐cutting themes include direct impacts such as disrupted access to essential medicines, commodities and services such as anti‐retroviral treatment, HIV pre‐exposure prophylaxis, opioid agonist treatment, viral load monitoring, HIV and sexually transmitted infections testing, condoms and syringes. Indirect impacts include significant collateral damage arising from prevention measures which restrict human rights, increase or impose criminal penalties, and expand police powers to target vulnerable and criminalized populations. Significant heterogeneity in the COVID‐19 pandemic, the underlying HIV epidemic and the ability of key populations to protect themselves means that people who inject drugs and sex workers face particular challenges, including indirect impacts as a result of police targeting, loss of income and sometimes both. Geographical variations mean that transgender people and men who have sex with men in regions like Africa and the middle east remain criminalized, as well as stigmatized and discriminated against, increasing their vulnerability to adverse outcomes in relation to COVID‐19. CONCLUSIONS: Disruptions to both licit and illicit supply chains, loss of income and livelihoods and changes in behaviour as a result of lockdowns and physical distancing have the potential to exacerbate the impacts of the COVID‐19 pandemic on key populations. While these impacts will vary significantly, human‐rights approaches to COVID‐19 emergency laws and public health prevention measures that are population‐specific and sensitive, will be key to reducing adverse health outcomes and ensuring that no one is left behind. url: https://doi.org/10.1002/jia2.25632 doi: 10.1002/jia2.25632 id: cord-018017-c8myq6bi author: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious disease represent the most significant threat to human health. Significant geologic cataclysmic events have caused the extinction of countless species, but these “Wrath of God” events predate the emergence of Homo sapiens. Pandemic infections have accompanied the rise of human civilization frequently re-occurring leaving a lasting imprint on human history punctuated by profound loss of life. Emerging infections become endemic and are here to stay marking their presence with an annual death toll. Each decade brings a new onslaught of emerging infectious agents. We are surprised again and again but are never prepared. The long-term consequences often remain unrecognized and are always inconvenient including cancer, cardiovascular disease and immune associated diseases that threaten our health. Reliance on clusters of clinical symptoms in the face of diverse and non-descriptive viral infection symptoms is a foolhardy form of crisis management. Viral success is based on rapid replication resulting in large numbers. Single-stranded RNA viruses with their high replication error rate represent a paradigm for resilience. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122756/ doi: 10.1007/978-3-319-98164-2_3 id: cord-029423-o24dthlk author: Iwuji, Collins C. title: A phase IV randomised, open-label pilot study to evaluate switching from protease-inhibitor based regimen to Bictegravir/Emtricitabine/Tenofovir Alafenamide single tablet regimen in Integrase inhibitor-naïve, virologically suppressed HIV-1 infected adults harbouring drug resistance mutations (PIBIK study): study protocol for a randomised trial date: 2020-07-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Currently recommended boosted protease-inhibitor (bPI) regimens may be associated with increased risk of cardiovascular or chronic kidney diseases; in addition, boosted regimens are particularly associated with drug-drug interactions. Since both cardiovascular and renal disease, and polypharmacy, are common in ageing people with HIV, there is a need for alternative efficacious regimens. bPI-based regimens are often the treatment of choice for individuals with pre-treatment or treatment-acquired resistance but it is plausible that carefully selected HIV-positive individuals with drug resistance, who are virologically suppressed on their current bPI regimen, could maintain virological efficacy when switched to bictegravir, emtricitabine and tenofovir alafenamide (B/F/TAF) fixed dose combination (FDC). METHODS/DESIGN: A phase IV, investigator-initiated, multicentre, open label pilot, randomised two-arm study to assess the safety and efficacy of switching from bPI regimen to B/F/TAF single tablet regimen in integrase inhibitor-naïve, virologically suppressed adults with HIV-1 infection harbouring drug resistance mutations. Eligible individuals will either continue on their bPI regimen or switch to B/F/TAF FDC. After 24 weeks, all participants in the bPI arm will be switched to B/F/TAF and followed for a further 24 weeks and all participants will be followed for 48 weeks. The primary efficacy endpoint is the proportion of participants with HIV-1 RNA < 50 copies/mL at week 24 using pure virologic response whilst the secondary efficacy endpoint is the proportion of participants with HIV-1 RNA < 50 copies/mL at Week 48. Other secondary outcome measures include between arm comparisons of drug resistance at virological failure, safety and tolerability and patient-reported outcome measures. DISCUSSION: We aim to provide preliminary evidence of the efficacy of switching to B/F/TAF in patients with virological suppression on a bPI-based regimen who harbour select drug resistance mutations. TRIAL REGISTRATION: ISRCTN 44453201, registered 19 June 2019 and EudraCT 2018–004732-30. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370264/ doi: 10.1186/s12879-020-05240-y id: cord-277818-8w15dz20 author: Jaichenco, Andre L. title: Infectious Disease Considerations for the Operating Room date: 2018-02-09 words: 9728.0 sentences: 528.0 pages: flesch: 39.0 cache: ./cache/cord-277818-8w15dz20.txt txt: ./txt/cord-277818-8w15dz20.txt summary: Hand hygiene is a well-known and effective solution to the problem of bacterial transmission within and across patients and is considered the most important and cost-effective individual intervention in the prevention of health care–associated infections in children and health care providers Compliance with the current "5 moments" World Health Organization guidelines could make a major inroad into reducing provider hand and workspace contamination. These findings have clinical implications for the risk of colonization and subsequent HCIs-for example, SSIs. This calls attention to the need to develop and enforce strict hand hygiene guidelines for personnel who are providing anesthesia care, but more importantly the need to increase compliance with environmental disinfection of the OR (between cases and terminal cleaning), and to study further the directions of the spread of pathogens in the OR and anesthesia work areas. abstract: The risk of infection transmission by anesthesia providers in their work area environment is reviewed. The dynamics of transmission and the strategies for preventing infection transmission in health care institutions are discussed. Anesthesiologists have long been patient safety advocates and have taken on increasing responsibility for preventing health care–associated infections. Anesthesia providers practice in a nonsterile environment within the operating room and have an impact on bacterial transmission and infection rates. Understanding the characteristics of transmission elements provides the practicing anesthesiologist with methods to protect susceptible patients and themselves to avoid spreading infection. It is vital to have in place proper systems to remove contaminated air to minimize the risk of airborne pathogens being transmitted by children. Preoperative patient skin and other bacterial reservoir decontamination and hand hygiene by anesthesia providers reduces contamination of the work area and IV access ports. Hand hygiene is a well-known and effective solution to the problem of bacterial transmission within and across patients and is considered the most important and cost-effective individual intervention in the prevention of health care–associated infections in children and health care providers Compliance with the current “5 moments” World Health Organization guidelines could make a major inroad into reducing provider hand and workspace contamination. Surgical antimicrobial prophylaxis is an essential tool to reduce the risk of postoperative infections, and the anesthesia team plays a central role in ensuring the proper timing of drug administration. Protocols, although effective, require continuous feedback and revision. url: https://api.elsevier.com/content/article/pii/B9780323429740000501 doi: 10.1016/b978-0-323-42974-0.00050-1 id: cord-341503-3cvtoc2j author: Jaiswal, J. title: Disinformation, Misinformation and Inequality-Driven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism date: 2020-05-21 words: 2551.0 sentences: 146.0 pages: flesch: 39.0 cache: ./cache/cord-341503-3cvtoc2j.txt txt: ./txt/cord-341503-3cvtoc2j.txt summary: Much of the evidence needed to fully inform clinical and public health responses is not yet available, making COVID-19 uniquely vulnerable to a proliferation of disinformation, misinformation, and medical mistrust, including what are often called "conspiracy beliefs" [6, 7] . The purpose of this commentary is to suggest that understanding the etiologies of disinformation, misinformation, and medical mistrust must be an important component of the public health response to COVID-19. It is vital to consider how people, as individuals and as members of groups, experience and interpret social and economic inequality, and how those experiences affect their trust in or mistrust of evidence-based public health messaging, as well as their readiness to accept any promulgated misinformation or disinformation [64] . Public health and medical professionals have a responsibility to communicate science in an effective, accurate and accessible manner, without bias-and with the understanding that structural racism and other forms of oppression are root causes of inequality-driven mistrust. abstract: nan url: https://doi.org/10.1007/s10461-020-02925-y doi: 10.1007/s10461-020-02925-y id: cord-306972-alyyju5x author: James, Peter Bai title: An assessment of Ebola-related stigma and its association with informal healthcare utilisation among Ebola survivors in Sierra Leone: a cross-sectional study date: 2020-02-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: We examined the magnitude and correlates of Ebola virus disease (EVD)-related stigma among EVD survivors in Sierra Leone since their return to their communities. In addition, we determined whether EVD-related stigma is a predictor of informal health care use among EVD survivors. METHODS: We conducted a cross-sectional study among 358 EVD survivors in five districts across all four geographic regions (Western Area, Northern Province, Eastern Province and Southern Province) of Sierra Leone. Ebola-related stigma was measured by adapting the validated HIV related stigma for people living with HIV/AIDS instrument. We also measured traditional and complementary medicine (T&CM) use (as a measure of informal healthcare use). Data were analysed using descriptive statistics and regression analysis. RESULTS: EVD survivors report higher levels of internalised stigma (0.92 ± 0.77) compared to total enacted stigma (0.71 ± 0.61). Social isolation (0.96 ± 0.88) was the highest reported enacted stigma subscale. Ebola survivors who identified as Christians [AOR = 2.51, 95%CI: 1.15–5.49, p = 0.021], who perceived their health to be fair/poor [AOR = 2.58, 95%CI: 1.39–4.77. p = 0.003] and who reside in the northern region of Sierra Leone [AOR = 2.80, 95%CI: 1.29–6.07, p = 0.009] were more likely to experience internalised stigma. Verbal abuse [AOR = 1.95, 95%CI: 1.09–3.49, p = 0.025] and healthcare neglect [AOR = 2.35, 95%CI: 1.37–4.02, p = 0.002] were independent predictors of T&CM use among EVD survivors. CONCLUSION: Our findings suggest EVD-related stigma (internalised and enacted) is prevalent among EVD survivors since their return to their communities. Religiosity, perceived health status and region were identified as independent predictors of internalised stigma. Verbal abuse and healthcare neglect predict informal healthcare use. EVD survivor-centred and community-driven anti-stigma programs are needed to promote EVD survivors’ recovery and community re-integration. url: https://www.ncbi.nlm.nih.gov/pubmed/32020858/ doi: 10.1186/s12889-020-8279-7 id: cord-276006-mjjnkqv6 author: Jarach, Natanel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Antiviral polymers are part of a major campaign led by the scientific community in recent years. Facing this most demanding of campaigns, two main approaches have been undertaken by scientists. First, the classic approach involves the development of relatively small molecules having antiviral properties to serve as drugs. The other approach involves searching for polymers with antiviral properties to be used as prescription medications or viral spread prevention measures. This second approach took two distinct directions. The first, using polymers as antiviral drug-delivery systems, taking advantage of their biodegradable properties. The second, using polymers with antiviral properties for on-contact virus elimination, which will be the focus of this review. Anti-viral polymers are obtained by either the addition of small antiviral molecules (such as metal ions) to obtain ion-containing polymers with antiviral properties or the use of polymers composed of an organic backbone and electrically charged moieties like polyanions, such as carboxylate containing polymers, or polycations such as quaternary ammonium containing polymers. Other approaches include moieties hybridized by sulphates, carboxylic acids, or amines and/or combining repeating units with a similar chemical structure to common antiviral drugs. Furthermore, elevated temperatures appear to increase the anti-viral effect of ions and other functional moieties. url: https://doi.org/10.3390/polym12081727 doi: 10.3390/polym12081727 id: cord-346314-o9fjpqaj author: Jarboui, Mohamed Ali title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 words: 10004.0 sentences: 521.0 pages: flesch: 36.0 cache: ./cache/cord-346314-o9fjpqaj.txt txt: ./txt/cord-346314-o9fjpqaj.txt summary: Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. Following the detailed annotation of the quantitative abundance changes in the nucleolar protein composition upon Tat expression, we focussed on the Tat-affected cellular complexes and signalling pathways associated with ribosome biogenesis, spliceosome, molecular chaperones, DNA replication and repair and metabolism and discuss their potential involvement in HIV-1 pathogenesis. In this study, we investigated the quantitative changes in the nucleolar proteome of Jurkat T cells constitutively expressing HIV-1 Tat (86aa) versus their Tat-negative counterpart, using stable isotope labelling with amino acids in cell culture (SILAC) technology, followed by ESI tandem mass spectrometry and implemented the experimental approach described in Figure 1A . abstract: The trans-activator Tat protein is a viral regulatory protein essential for HIV-1 replication. Tat trafficks to the nucleoplasm and the nucleolus. The nucleolus, a highly dynamic and structured membrane-less sub-nuclear compartment, is the site of rRNA and ribosome biogenesis and is involved in numerous cellular functions including transcriptional regulation, cell cycle control and viral infection. Importantly, transient nucleolar trafficking of both Tat and HIV-1 viral transcripts are critical in HIV-1 replication, however, the role(s) of the nucleolus in HIV-1 replication remains unclear. To better understand how the interaction of Tat with the nucleolar machinery contributes to HIV-1 pathogenesis, we investigated the quantitative changes in the composition of the nucleolar proteome of Jurkat T-cells stably expressing HIV-1 Tat fused to a TAP tag. Using an organellar proteomic approach based on mass spectrometry, coupled with Stable Isotope Labelling in Cell culture (SILAC), we quantified 520 proteins, including 49 proteins showing significant changes in abundance in Jurkat T-cell nucleolus upon Tat expression. Numerous proteins exhibiting a fold change were well characterised Tat interactors and/or known to be critical for HIV-1 replication. This suggests that the spatial control and subcellular compartimentaliation of these cellular cofactors by Tat provide an additional layer of control for regulating cellular machinery involved in HIV-1 pathogenesis. Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. We present here the first differential profiling of the nucleolar proteome of T-cells expressing HIV-1 Tat. We discuss how these proteins collectively participate in interconnected networks converging to adapt the nucleolus dynamic activities, which favor host biosynthetic activities and may contribute to create a cellular environment supporting robust HIV-1 production. url: https://www.ncbi.nlm.nih.gov/pubmed/23166591/ doi: 10.1371/journal.pone.0048702 id: cord-303208-4bui0ioe author: Jarlais, Don C Des title: Increasing HIV prevention and care for injecting drug users date: 2010-02-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1016/s0140-6736(10)60314-5 doi: 10.1016/s0140-6736(10)60314-5 id: cord-274688-cr1rvy8u author: Jewell, Britta L title: Potential effects of disruption to HIV programmes in sub-Saharan Africa caused by COVID-19: results from multiple mathematical models date: 2020-08-06 words: 1865.0 sentences: 90.0 pages: flesch: 48.0 cache: ./cache/cord-274688-cr1rvy8u.txt txt: ./txt/cord-274688-cr1rvy8u.txt summary: METHODS: In this modelling study, we used five well described models of HIV epidemics (Goals, Optima HIV, HIV Synthesis, an Imperial College London model, and Epidemiological MODeling software [EMOD]) to estimate the effect of various potential disruptions to HIV prevention, testing, and treatment services on HIV-related deaths and new infections in sub-Saharan Africa lasting 6 months over 1 year from April 1, 2020. FINDINGS: A 6-month interruption of supply of antiretroviral therapy (ART) drugs across 50% of the population of people living with HIV who are on treatment would be expected to lead to a 1·63 times (median across models; range 1·39–1·87) increase in HIV-related deaths over a 1-year period compared with no disruption. The HIV-related death rate for people living with HIV who were on ART, but who stopped treatment due to potential disruption on the antiretroviral (ARV) drug supply as a result of the COVID-19 pandemic was modeled to represent findings from the SMART Study (1). abstract: BACKGROUND: The COVID-19 pandemic could lead to disruptions to provision of HIV services for people living with HIV and those at risk of acquiring HIV in sub-Saharan Africa, where UNAIDS estimated that more than two-thirds of the approximately 38 million people living with HIV resided in 2018. We aimed to predict the potential effects of such disruptions on HIV-related deaths and new infections in sub-Saharan Africa. METHODS: In this modelling study, we used five well described models of HIV epidemics (Goals, Optima HIV, HIV Synthesis, an Imperial College London model, and Epidemiological MODeling software [EMOD]) to estimate the effect of various potential disruptions to HIV prevention, testing, and treatment services on HIV-related deaths and new infections in sub-Saharan Africa lasting 6 months over 1 year from April 1, 2020. We considered scenarios in which disruptions affected 20%, 50%, and 100% of the population. FINDINGS: A 6-month interruption of supply of antiretroviral therapy (ART) drugs across 50% of the population of people living with HIV who are on treatment would be expected to lead to a 1·63 times (median across models; range 1·39–1·87) increase in HIV-related deaths over a 1-year period compared with no disruption. In sub-Saharan Africa, this increase amounts to a median excess of HIV deaths, across all model estimates, of 296 000 (range 229 023–420 000) if such a high level of disruption occurred. Interruption of ART would increase mother-to-child transmission of HIV by approximately 1·6 times. Although an interruption in the supply of ART drugs would have the largest impact of any potential disruptions, effects of poorer clinical care due to overstretched health facilities, interruptions of supply of other drugs such as co-trimoxazole, and suspension of HIV testing would all have a substantial effect on population-level mortality (up to a 1·06 times increase in HIV-related deaths over a 1-year period due to disruptions affecting 50% of the population compared with no disruption). Interruption to condom supplies and peer education would make populations more susceptible to increases in HIV incidence, although physical distancing measures could lead to reductions in risky sexual behaviour (up to 1·19 times increase in new HIV infections over a 1-year period if 50% of people are affected). INTERPRETATION: During the COVID-19 pandemic, the primary priority for governments, donors, suppliers, and communities should focus on maintaining uninterrupted supply of ART drugs for people with HIV to avoid additional HIV-related deaths. The provision of other HIV prevention measures is also important to prevent any increase in HIV incidence. FUNDING: Bill & Melinda Gates Foundation. url: https://www.ncbi.nlm.nih.gov/pubmed/32771089/ doi: 10.1016/s2352-3018(20)30211-3 id: cord-324984-ojrpsdt9 author: Ji, Xingyue title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Direct‐acting antiviral agents (DAAs) represent a class of drugs targeting viral proteins and have been demonstrated to be very successful in combating viral infections in clinic. However, DAAs suffer from several inherent limitations, including narrow‐spectrum antiviral profiles and liability to drug resistance, and hence there are still unmet needs in the treatment of viral infections. In comparison, host targeting antivirals (HTAs) target host factors for antiviral treatment. Since host proteins are probably broadly required for various viral infections, HTAs are not only perceived, but also demonstrated to exhibit broad‐spectrum antiviral activities. In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. In this review, we summarize various host proteins as antiviral targets from a medicinal chemistry prospective. Challenges and issues associated with HTAs are also discussed. url: https://doi.org/10.1002/med.21664 doi: 10.1002/med.21664 id: cord-288440-w7g2agaf author: Jia, Rui title: The C-Terminal Sequence of IFITM1 Regulates Its Anti-HIV-1 Activity date: 2015-03-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The interferon-inducible transmembrane (IFITM) proteins inhibit a wide range of viruses. We previously reported the inhibition of human immunodeficiency virus type 1 (HIV-1) strain BH10 by human IFITM1, 2 and 3. It is unknown whether other HIV-1 strains are similarly inhibited by IFITMs and whether there exists viral countermeasure to overcome IFITM inhibition. We report here that the HIV-1 NL4-3 strain (HIV-1(NL4-3)) is not restricted by IFITM1 and its viral envelope glycoprotein is partly responsible for this insensitivity. However, HIV-1(NL4-3) is profoundly inhibited by an IFITM1 mutant, known as Δ(117–125), which is deleted of 9 amino acids at the C-terminus. In contrast to the wild type IFITM1, which does not affect HIV-1 entry, the Δ(117–125) mutant diminishes HIV-1(NL4-3) entry by 3-fold. This inhibition correlates with the predominant localization of Δ(117–125) to the plasma membrane where HIV-1 entry occurs. In spite of strong conservation of IFITM1 among most species, mouse IFITM1 is 19 amino acids shorter at its C-terminus as compared to human IFITM1 and, like the human IFITM1 mutant Δ(117–125), mouse IFITM1 also inhibits HIV-1 entry. This is the first report illustrating the role of viral envelope protein in overcoming IFITM1 restriction. The results also demonstrate the importance of the C-terminal region of IFITM1 in modulating the antiviral function through controlling protein subcellular localization. url: https://www.ncbi.nlm.nih.gov/pubmed/25738301/ doi: 10.1371/journal.pone.0118794 id: cord-349790-dezauioa author: Johnson, Stephanie title: Ethical challenges in pathogen sequencing: a systematic scoping review date: 2020-06-03 words: 6222.0 sentences: 273.0 pages: flesch: 41.0 cache: ./cache/cord-349790-dezauioa.txt txt: ./txt/cord-349790-dezauioa.txt summary: Methods: We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. Implementation science research may also inform best practices for discussing the meaning and limitations of sequence data and cluster membership with community members and help to identify acceptable and evidence-based approaches that impose the least risk to persons within specific contexts. Many noted that there are important reasons to ensure that the public and individuals understand the uses of data collected as part of a sequencing studies, and the potential risks. abstract: Background: Going forward, the routine implementation of genomic surveillance activities and outbreak investigation is to be expected. We sought to systematically identify the emerging ethical challenges; and to systematically assess the gaps in ethical frameworks or thinking and identify where further work is needed to solve practical challenges. Methods: We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation. Results: 28 articles were identified; nine United States, five United Kingdom, five The Netherlands, three Canada, two Switzerland, one Australia, two South Africa, and one Italy. Eight articles were specifically about the use of sequencing in HIV. Eleven were not specific to a particular disease. Results were organized into four themes: tensions between public and private interests; difficulties with translation from research to clinical and public health practice; the importance of community trust and support; equity and global partnerships; and the importance of context. Conclusion: While pathogen sequencing has the potential to be transformative for public health, there are a number of key ethical issues that must be addressed, particularly around the conditions of use for pathogen sequence data. Ethical standards should be informed by public values, and further empirical work investigating stakeholders’ views are required. Development in the field should also be under-pinned by a strong commitment to values of justice, in particular global health equity. url: https://www.ncbi.nlm.nih.gov/pubmed/32864469/ doi: 10.12688/wellcomeopenres.15806.1 id: cord-010001-u0d5jkp1 author: KOTWAL, GIRISH J. title: Anti‐HIV, Anti‐Poxvirus, and Anti‐SARS Activity of a Nontoxic, Acidic Plant Extract from the Trifollium Species Secomet‐V/anti‐Vac Suggests That It Contains a Novel Broad‐Spectrum Antiviral date: 2006-01-22 words: 2608.0 sentences: 123.0 pages: flesch: 51.0 cache: ./cache/cord-010001-u0d5jkp1.txt txt: ./txt/cord-010001-u0d5jkp1.txt summary: With a well-established infrastructure and the methodology to cultivate and to titer viruses accurately 6 to evaluate antiviral effects, it was possible to show that indeed a small volume of the plant extract termed Secomet-V was able to inactivate approximately 1 million virus particles of the attenuated recombinant vaccinia virus vGK5 7 in 1 minute consistently and reproducibly. Secomet-V, an extract of an African plant also found elsewhere in Asia, has been found to have potent antiviral activity against a poxvirus (vaccinia virus), rendering about 1 million particles noninfectious in 1 min with a 50th of a milliliter in in vitro assays (FIG. HIV-infected cells treated with plant extract showed no significant effect on the viral levels (TABLE 1) . There was no difference in the effectiveness of the plant extract in rendering vaccinia virus noninfectious whether it was autoclaved or not, suggesting that the bioactive agent is most likely but not necessarily a heat-stable compound and not a small peptide. abstract: Enveloped animal viruses such as human immunodeficiency virus (HIV), hepatitis B virus, hepatitis C virus, human papillomavirus, Marburg, and influenza are major public health concerns around the world. The prohibitive cost of antiretroviral (ARV) drugs for most HIV‐infected patients in sub‐Saharan Africa and the serious side effects in those who have access to ARV drugs make a compelling case for the study of complementary and alternative therapies. Such therapies should have scientifically proved antiviral activity and minimal toxic effects. A plant extract, Secomet‐V, with an anecdotal indication in humans for promise as an anti‐HIV treatment, was investigated. Using a previously described attenuated vaccinia virus vGK5, we established the antiviral activity of Secomet‐V. Chemical analysis showed that it has an acidic pH, nontoxic traces of iron (<10 ppm), and almost undetectable levels of arsenic (<1.0 ppm). The color varies from colorless to pale yellow to dark brown. The active agent is heat stable at least up to sterilizing temperature of 121°C. The crude plant extract is a mixture of several small molecules separable by high‐pressure liquid chromatography. The HIV viral loads were significantly reduced over several months in a few patients monitored after treatment with Secomet‐V. Secomet‐V was also found to have antiviral activity against the SARS virus but not against the West Nile virus. Secomet‐V, therefore, is a broad‐spectrum antiviral, which possibly works by neutralizing viral infectivity, resulting in the prevention of viral attachment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167892/ doi: 10.1196/annals.1352.014 id: cord-317988-1buh1wm0 author: Kalichman, Seth C. title: Intersecting Pandemics: Impact of SARS-CoV-2 (COVID-19) Protective Behaviors on People Living With HIV, Atlanta, Georgia date: 2020-06-05 words: 4040.0 sentences: 216.0 pages: flesch: 47.0 cache: ./cache/cord-317988-1buh1wm0.txt txt: ./txt/cord-317988-1buh1wm0.txt summary: At follow-up, in the first month of responding to COVID-19, engaging in more social distancing behaviors was related to difficulty accessing food and medications and increased cancelation of health care appointments, both by self and providers. These results suggest social responses to COVID-19 adversely impacted the health care of people living with HIV, supporting continued monitoring to determine the long-term effects of co-occurring HIV and COVID-19 pandemics. 15 High prevalence of substance use and co-occurring underlying health conditions have the potential to amplify the severity of COVID-19 in people living with HIV. 43 Although people with HIV will recognize their increased risks due to an immune suppressive condition, the added burden of smoking and other substance use, as well as underlying conditions common to HIV infection, have not been included in Centers for Disease Control and Prevention reports of severe case outcomes and have not been included in public health messaging. abstract: COVID-19 and its social responses threaten the health of people living with HIV. We conducted a rapid-response interview to assess COVID-19 protective behaviors of people living with HIV and the impact of their responses on HIV-related health care. METHOD: Men and women living with HIV (N = 162) aged 20–37 years participating in a longitudinal study of HIV treatment and care completed routine study measures and an assessment of COVID-19–related experiences. RESULTS: At baseline, most participants demonstrated HIV viremia, markers indicative of renal disorders, and biologically confirmed substance use. At follow-up, in the first month of responding to COVID-19, engaging in more social distancing behaviors was related to difficulty accessing food and medications and increased cancelation of health care appointments, both by self and providers. We observed antiretroviral therapy adherence had improved during the initial month of COVID-19 response. CONCLUSIONS: Factors that may pose added risk for COVID-19 severity were prevalent among people living with HIV, and those with greater risk factors did not practice more COVID-19 protective behaviors. Social distancing and other practices intended to mitigate the spread of COVID-19 interfered with HIV care, and impeded access to food and medications, although an immediate adverse impact on medication adherence was not evident. These results suggest social responses to COVID-19 adversely impacted the health care of people living with HIV, supporting continued monitoring to determine the long-term effects of co-occurring HIV and COVID-19 pandemics. url: https://www.ncbi.nlm.nih.gov/pubmed/32530862/ doi: 10.1097/qai.0000000000002414 id: cord-304873-ppb9k3zu author: Kang, Hunseung title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 date: 1998-04-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Programmed ribosomal frameshifting in viral messenger RNA occurs in response to neighboring sequence elements consisting of: a frameshift site, a spacer, and a downstream enhancer sequence. In human immunodeficiency virus type 1 (HIV-1) mRNA, this sequence element has a potential to form either a stem-loop or a pseudoknot structure. Based on many mutational studies, the stem-loop structure has been proposed for the downstream enhancer region of the HIV-1 mRNA. This stimulatory stem-loop structure is separated from the shift site by a spacer of seven nucleotides. In contrast, a recent report has proposed an alternative model in which the bases in the spacer sequence form a pseudoknot structure as the downstream enhancer sequence [Du et al., Biochemistry 35 (1996) 4187–4198.]. Using UV melting and enzymatic mapping analyses, we have investigated the conformation of the sequence region involved in ribosomal frameshifting in HIV-1. Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. This finding further supports the stem-loop structure proposed by many mutational studies for the downstream enhancer sequence of the HIV-1 mRNA. url: https://www.sciencedirect.com/science/article/pii/S0167478198000049 doi: 10.1016/s0167-4781(98)00004-9 id: cord-311559-vkb7a4cm author: Kanwugu, Osman N. title: HIV/SARS‐CoV‐2 coinfection: A global perspective date: 2020-07-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since its first appearance in Wuhan, China, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has rapidly spread throughout the world and has become a global pandemic. Several medical comorbidities have been identified as risk factors for coronavirus disease 2019 (COVID‐19). However, it remains unclear whether people living with human immunodefeciency virus (PLWH) are at an increased risk of COVID‐19 and severe disease manifestation, with controversial suggestion that HIV‐infected individuals could be protected from severe COVID‐19 by means of antiretroviral therapy or HIV‐related immunosuppression. Several cases of coinfection with HIV and SARS‐CoV‐2 have been reported from different parts of the globe. This review seeks to provide a holistic overview of SARS‐CoV‐2 infection in PLWH. url: https://www.ncbi.nlm.nih.gov/pubmed/32692406/ doi: 10.1002/jmv.26321 id: cord-350569-dtxtjtfo author: Kasoka, Kasoka title: Autonomy in HIV testing: a call for a rethink of personal autonomy in the HIV response in sub-Saharan Africa date: 2020-06-13 words: 13925.0 sentences: 639.0 pages: flesch: 51.0 cache: ./cache/cord-350569-dtxtjtfo.txt txt: ./txt/cord-350569-dtxtjtfo.txt summary: In most SSA countries the ethic or value of personal autonomy or self-determination is promoted as primary in HIV testing decision-making. Without rethinking the value of autonomy in HIV testing decision-making, the article cautions that attainment of the Sustainable Development Goal (SDG) 3 and the UNAIDS fast-track strategy that explicitly call to end the epidemic by 2030 will not be feasible for SSA. 9 My article interrogates the personal autonomy arguments and reaches a conclusion that the philosophy surrounding the value is problematic, as well as, it is silent on the ethics of the actual implications of an autonomous decision in HIV testing (Selemogo 2010) . HIV testing ethics, in particular informed consent requirements that are now premised on personal autonomy, should reflect a human being who is unique and yet a creature of the inescapable inculcating environment that makes her the ''I That Is We''. abstract: The author reviews various conceptions of autonomy to show that humans are actually not autonomous, strictly speaking. He argues for a need to rethink the personal autonomy approaches to HIV testing in sub-Saharan Africa (SSA) countries. HIV/AIDS has remained a leading cause of disease burden in SSA. It is important to bring this disease burden under control, especially given the availability of current effective antiretroviral regimens in low- and middle-income countries. In most SSA countries the ethic or value of personal autonomy or self-determination is promoted as primary in HIV testing decision-making. SSA policymakers have an ontological and moral duty to adopt HIV testing policies that reflect human and medical realities, relationships, local contexts, and respect human rights for both individuals and others who are affected by HIV in society. Without rethinking the value of autonomy in HIV testing decision-making, the article cautions that attainment of the Sustainable Development Goal (SDG) 3 and the UNAIDS fast-track strategy that explicitly call to end the epidemic by 2030 will not be feasible for SSA. url: https://doi.org/10.1007/s11019-020-09959-y doi: 10.1007/s11019-020-09959-y id: cord-015831-s78omm53 author: Kaufman, Joan title: Civil Society Involvement in National HIV/AIDS Programs date: 2019-05-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Globally, the AIDS response relies on active participation of nongovernmental organizations (NGOs) and civil society. In China, the government is the main provider of health and social services, and the role of NGOs is more limited than in other countries. Despite this, China has opened the door for NGO participation in its AIDS response, initially because of donor pressure but increasingly due to official acknowledgment of the important role these groups play in controlling the epidemic. Since the first AIDS NGOs were established in China in the 1990s, Chinese AIDS NGOs have made unique contributions to China’s AIDS response in critical areas like access to drugs, support for treatment compliance, outreach to marginalized at-risk groups, and efforts to reduce stigma among marginalized populations. However, there has been a substantial drop-off in donor funding in recent years, and although the Chinese government has filled the funding gap, demonstrating its commitment to the sector, recent policy moves toward greater control over the work and funding of NGOs threatens their survival. Thus far, China’s AIDS response has been noteworthy, but these new NGO funding and regulatory developments pose significant challenges to the next phase of outreach, prevention, treatment, and care. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119907/ doi: 10.1007/978-981-13-8518-6_22 id: cord-005882-iodfgzjf author: Kaufmann, Stefan H E title: Annulling a dangerous liaison: vaccination strategies against AIDS and tuberculosis date: 2005-04-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human immunodeficiency virus (HIV) and Mycobacterium tuberculosis annually cause 3 million and 2 million deaths, respectively. Last year, 600,000 individuals, doubly infected with HIV and M. tuberculosis, died. Since World War I, approximately 150 million people have succumbed to these two infections—more total deaths than in all wars in the last 2,000 years. Although the perceived threats of new infections such as SARS, new variant Creutzfeldt-Jakob disease and anthrax are real, these outbreaks have caused less than 1,000 deaths globally, a death toll AIDS and tuberculosis exact every 2 h. In 2003, 40 million people were infected with HIV, 2 billion with M. tuberculosis, and 15 million with both. Last year, 5 million and 50 million were newly infected with HIV or M. tuberculosis, respectively, with 2 million new double infections. Better control measures are urgently needed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095892/ doi: 10.1038/nm1221 id: cord-353895-tgn1kk07 author: Kavanagh, Matthew M title: Reckoning with mortality: global health, HIV, and the politics of data date: 2020-07-03 words: 1848.0 sentences: 94.0 pages: flesch: 46.0 cache: ./cache/cord-353895-tgn1kk07.txt txt: ./txt/cord-353895-tgn1kk07.txt summary: Studies in South Africa, Kenya, Zambia, and the Democratic Republic of the Congo have shown that most patients with HIV admitted to hospital have already been on antiretroviral therapy (often for years) but they either stop treatment or are on a treatment regimen that is not effectively suppressing the virus. In South Africa, in particular, tracking the mortality of young people using systems at the local level helped monitor the effectiveness of HIV programmes. 20 Hopefully, this step will improve patient outcomes by incentivising effective interventions for advanced HIV disease and support for people who have stopped treatment to re-enter care. 17 Third, we can move towards a variety of outcomeoriented global health programmes beyond HIV, for which measures of success move from the number of patients receiving services to explicit reductions in mortality rates. abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0140673620310461 doi: 10.1016/s0140-6736(20)31046-1 id: cord-324056-cvvyf3cb author: Kelley, Patrick W. title: Global Health: Governance and Policy Development date: 2011-06-30 words: 5948.0 sentences: 334.0 pages: flesch: 48.0 cache: ./cache/cord-324056-cvvyf3cb.txt txt: ./txt/cord-324056-cvvyf3cb.txt summary: Owing to the increasing recognition that health is fundamental to the broader UN goals of fostering the international rule of law, global security, economic development, social progress, human rights, and world peace, health issues have now taken a more prominent place than they had in the United Nation''s first 50 years. GAVI also supports innovative financing Box 3 The goals and targets of the US government global health initiative HIV/AIDS: The US President''s Emergency Plan for AIDS Relief will: (1) support the prevention of more than 12 million new HIV infections; (2) provide direct support for more than 4 million people on treatment; and (3) support care for more than 12 million people, including 5 million orphans and vulnerable children. Reflecting the emergence of the new era in global health governance, in 1998 the Rockefeller Foundation established an initiative to create innovative new public-private partnerships, including the Medicines for Malaria Venture, the Global Alliance for TB Drug Development, and the International Partnership on Microbicides. abstract: Global health policy is now being influenced by an ever-increasing number of nonstate and non-intergovernmental actors to include influential foundations, multinational corporations, multi-sectoral partnerships, and civil society organizations. This article reviews how globalization is a key driver for the ongoing evolution of global health governance. It describes the massive increases in bilateral and multilateral investments in global health and it highlights the current global and US architecture for performing global health programs. The article closes describing some of the challenges and prospects that characterize global health governance today. url: https://doi.org/10.1016/j.idc.2011.02.014 doi: 10.1016/j.idc.2011.02.014 id: cord-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 words: 12734.0 sentences: 684.0 pages: flesch: 44.0 cache: ./cache/cord-349358-leicos9j.txt txt: ./txt/cord-349358-leicos9j.txt summary: During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. abstract: Silencing gene expression through a process known as RNA interference (RNAi) has been known in the plant world for many years. In recent years, knowledge of the prevalence of RNAi and the mechanism of gene silencing through RNAi has started to unfold. It is now believed that RNAi serves in part as an innate response against invading viral pathogens and, indeed, counter silencing mechanisms aimed at neutralizing RNAi have been found in various viral pathogens. During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Furthermore, it is now apparent that in in vitro and in some in vivo models, the prospects for this technology in developing therapeutic applications are robust. However, many key questions and obstacles in the translation of RNAi into a potential therapeutic platform still remain, including the specificity and longevity of the silencing effect, and, most importantly, the delivery of the dsRNA that induces the system. It is expected that for the specific examples in which the delivery issue could be circumvented or resolved, RNAi may hold promise for the development of gene‐specific therapeutics. Copyright © 2006 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16779870/ doi: 10.1002/jgm.929 id: cord-351740-779g8tr1 author: Khaba, Moshawa Calvin title: COVID-19 in an HIV-infected patient. Lessons learned from an autopsy case date: 2020-09-25 words: 1830.0 sentences: 126.0 pages: flesch: 55.0 cache: ./cache/cord-351740-779g8tr1.txt txt: ./txt/cord-351740-779g8tr1.txt summary: We report the first autopsy case of HIV-infected individual with COVID-19 as the cause of death. The first confirmed case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was reported in China in December 2019. To the best of our knowledge, this manuscript represents the first published report of an autopsy performed on an HIV infected patient with cause of death attributed to COVID-19. The final cause of death was SARS-CoV-2 (COVID-19) infection in HIV infected patient. In accord to what is already published, the lung findings on the index patient showed early phase of diffuse alveolar damage with associated microthrombi which is seen in COVID-19. Whilst HIV infected people on treatment with normal CD4 count and low viral load may not be at a high risk of serious illness, the presence of other chronic conditions may increase their overall risk (7) The fact that SARS-CoV-2 can cause transient immune deficiency, it denotes that HIV and COVID-19 interaction may have adverse immunological and clinical outcomes. abstract: Despite measures put in places to curb the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across South Africa, there has been a rapid spread which caused extensive morbidity and mortality. Whilst there is currently increased COVID-19 associated death, autopsies on COVID positive individuals are not routinely performed. An autopsy was performed on a 19 years old African patient who was recently diagnosed with human immunodeficiency virus (HIV). He presented with clinical features of SARS-CoV-2 which subsequently tested positive for. Important histopathological findings included diffuse alveolar damage and fibrin thrombi. No superimposed infections were noted. The cause of death was attributed to COVID-19. We report the first autopsy case of HIV-infected individual with COVID-19 as the cause of death. url: https://doi.org/10.1016/j.ijid.2020.09.1435 doi: 10.1016/j.ijid.2020.09.1435 id: cord-254187-dcdc6sqi author: Kimball, AM title: “What, me worry?” Businesses and AIDS at Davos date: 2005-04-05 words: 1836.0 sentences: 103.0 pages: flesch: 57.0 cache: ./cache/cord-254187-dcdc6sqi.txt txt: ./txt/cord-254187-dcdc6sqi.txt summary: At the Davos Summit in February, 2005, the World Economic Forum released its current survey on businesses and HIV/AIDS. In Asia, the prospective new epicentre of the epidemic, the efforts of the Thailand Business Coalition on AIDS and the Tata Group in India highlight roles business can play: prevention and education for workers; workplace programmes to prevent discrimination; and public-private collaboration and funding for effective programmes. 5 The most recent survey of the World Economic Forum''s Global Health Initiative 6 shows that awareness by business that AIDS will affect operations and profits reflects the level of efforts to combat the disease. 6 The Global Health Initiative worked with several South African firms to organise case studies, which vividly illustrate the imperatives and benefits for companies offering antiretrovirals to their employees. A role for business in HIV/AIDS in Asia abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0140673605747929 doi: 10.1016/s0140-6736(05)74792-9 id: cord-264699-l8db5gll author: Kino, Tomoshige title: Virus-mediated modulation of the host endocrine signaling systems: clinical implications date: 2007-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses, which are among the simplest infective pathogens, can produce characteristic endocrine manifestations in infected patients. In addition to the classic modification of the host endocrine system by either direct or indirect destruction of the endocrine organs and/or effects exerted by systemic production of inflammatory and/or stress mediators, recent progress in molecular virology and endocrinology has revealed that virus-encoded molecules might alter the host endocrine-signaling systems by affecting extracellular and/or intracellular signal transduction and hormone sensitivity of host target tissues. Here, we provide a brief overview of such viral-mediated modulation of host endocrine signaling systems. We propose that virus-encoded molecules and the signaling systems they influence are potential therapeutic targets for the treatment of disorders that are associated with some viral infections. url: https://api.elsevier.com/content/article/pii/S104327600700046X doi: 10.1016/j.tem.2007.03.003 id: cord-011457-hqxybv1k author: Kirui, James title: Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release date: 2020-05-19 words: 5612.0 sentences: 249.0 pages: flesch: 46.0 cache: ./cache/cord-011457-hqxybv1k.txt txt: ./txt/cord-011457-hqxybv1k.txt summary: To enable simple and highly sensitive measurement of virus release from transfected cells, we generated HIV-1 reporter viruses in which Nanoluciferase (NanoLuc) was inserted between the MA and CA domains of Gag (Gag-iNanoLuc). We generated viruses using the pNL4-3 Gag-iNanoLuc vector complemented with different ratios of the WT HIV-1 molecular clone pNL4-3 and tested their infectivity by measuring the HIV-1 Tat-driven firefly luciferase activity in TZM-bl cells. These results demonstrate that the Gag-iNanoLuc vector provides a highly sensitive and quantitative tool for measuring the effects of Gag mutations, host cell restriction factors, and small-molecule inhibitors on HIV-1 particle assembly and release. The Gag-NanoLuc fusion protein is expressed in the cell and released at similar levels to WT Gag, thereby enabling simple yet highly sensitive quantification of viral gene expression and virus particle production by measurement of the NanoLuc reporter protein bioluminescent activity in the cell lysates and supernatants. abstract: BACKGROUND: The continued persistence of HIV-1 as a public health concern due to the lack of a cure calls for the development of new tools for studying replication of the virus. Here, we used NanoLuc, a small and extremely bright luciferase protein, to develop an HIV-1 bioluminescent reporter virus that simplifies functional measurement of virus particle production. RESULTS: The reporter virus encodes a Gag protein containing NanoLuc inserted between the matrix (MA) and capsid (CA) domains of Gag, thereby generating virus particles that package high levels of the NanoLuc reporter. We observe that inserting the NanoLuc protein within HIV-1 Gag has minimal impact on Gag expression and virus particle release. We show that the reporter virus recapitulates inhibition of HIV-1 particle release by Gag mutations, the restriction factor tetherin, and the small-molecule inhibitor amphotericin-B methyl ester. CONCLUSION: These results demonstrate that this vector will provide a simple and rapid tool for functional studies of virus particle assembly and release and high-throughput screening for cellular factors and small molecules that promote or inhibit HIV-1 particle production. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235552/ doi: 10.1186/s12977-020-00521-5 id: cord-326725-0jgw083h author: Klamroth, Robert title: Pathogen inactivation and removal methods for plasma‐derived clotting factor concentrates date: 2013-09-30 words: 5972.0 sentences: 303.0 pages: flesch: 41.0 cache: ./cache/cord-326725-0jgw083h.txt txt: ./txt/cord-326725-0jgw083h.txt summary: These measures include selection of donors, screening of donations and plasma pools for markers of infection with known viruses, and a manufacturing process with a high capacity to inactivate and/or remove viruses by selected steps validated for their virus reduction capacity. [7] [8] [9] Although screening for viral markers by serology and virus nucleic acid by nucleic acid testing (NAT) ensures that nearly all plasma units entering production are free of HBV, HCV, and HIV, inactivation and removal steps are necessary to reduce any viruses that may enter the plasma pool during a "window period" before markers can be detected. 46 Although B19V was reduced by dry heat in validation studies, the reduction factor may not be sufficient for complete inactivation of the virus load in the final product; asymptomatic B19V infection was detected in a patient who received FVIII concentrate treated at 80°C for 72 hours. abstract: Pathogen safety is crucial for plasma‐derived clotting factor concentrates used in the treatment of bleeding disorders. Plasma, the starting material for these products, is collected by plasmapheresis (source plasma) or derived from whole blood donations (recovered plasma). The primary measures regarding pathogen safety are selection of healthy donors donating in centers with appropriate epidemiologic data for the main blood‐transmissible viruses, screening donations for the absence of relevant infectious blood‐borne viruses, and release of plasma pools for further processing only if they are nonreactive for serologic markers and nucleic acids for these viruses. Despite this testing, pathogen inactivation and/or removal during the manufacturing process of plasma‐derived clotting factor concentrates is required to ensure prevention of transmission of infectious agents. Historically, hepatitis viruses and human immunodeficiency virus have posed the greatest threat to patients receiving plasma‐derived therapy for treatment of hemophilia or von Willebrand disease. Over the past 30 years, dedicated virus inactivation and removal steps have been integrated into factor concentrate production processes, essentially eliminating transmission of these viruses. Manufacturing steps used in the purification of factor concentrates have also proved to be successful in reducing potential prion infectivity. In this review, current techniques for inactivation and removal of pathogens from factor concentrates are discussed. Ideally, production processes should involve a combination of complementary steps for pathogen inactivation and/or removal to ensure product safety. Finally, potential batch‐to‐batch contamination is avoided by stringent cleaning and sanitization methods as part of the manufacturing process. url: https://doi.org/10.1111/trf.12423 doi: 10.1111/trf.12423 id: cord-300968-dtaasxk1 author: Kliger, Yossef title: From genome to antivirals: SARS as a test tube date: 2005-03-01 words: 5104.0 sentences: 272.0 pages: flesch: 46.0 cache: ./cache/cord-300968-dtaasxk1.txt txt: ./txt/cord-300968-dtaasxk1.txt summary: Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. This strategy seems promising in developing anti-viral therapeutic peptides to other viruses that possess type 1 viral fusion proteins [e.g. measles virus and respiratory syncytial virus (RSV)], which share some structural motifs with HIV. Similar to HIV, binding of the viral spike glycoprotein to some receptor(s) on host cells is the first step in SARS-CoV infection. HIV entry involves the binding of the viral envelope glycoproteins (comprising gp120 and gp41, which are the homologous of SARS-CoV S1 and S2, respectively) to CD4 on the host cell plasma membrane. Following the rule: formation of the 6-helix bundle of the fusion core from severe acute respiratory syndrome coronavirus spike protein and identification of potent peptide inhibitors Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoproteinmediated viral entry Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeatderived peptides abstract: Abstract The severe acute respiratory syndrome (SARS) epidemic brought into the spotlight the need for rapid development of effective anti-viral drugs against newly emerging viruses. Researchers have leveraged the 20-year battle against AIDS into a variety of possible treatments for SARS. Most prominently, based solely on viral genome information, silencers of viral genes, viral-enzyme blockers and viral-entry inhibitors were suggested as potential therapeutic agents for SARS. In particular, inhibitors of viral entry, comprising therapeutic peptides, were based on the recently launched anti-HIV drug enfuvirtide. This could represent one of the most direct routes from genome sequencing to the discovery of antiviral drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/15749283/ doi: 10.1016/s1359-6446(04)03320-3 id: cord-017506-t86v3zw3 author: Knox, Tamsin A. title: Alcohol, HIV/AIDS, and Liver Disease date: 2012-04-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Globally, there are over 33 million persons living with HIV/AIDS resulting in 1.8 million deaths annually. While the rate of HIV transmission is slowing, it is estimated that 2.6 million new infections occur yearly [1]. In the United States, there are approximately 1.2 million living with HIV/AIDS, with 50,000 new HIV infections and 17,000 deaths from the disease annually [2]. For those who can obtain effective antiretroviral therapy (ART), HIV/AIDS has become a chronic disease with life expectancies over 30 years [3]. Research in the last 10 years has revealed the importance of alcohol in the HIV/AIDS epidemic. Alcohol use, in moderate or hazardous amounts, has been associated with increased acquisition of HIV infection, progression of HIV infection, deleterious effects on HIV treatment, and acceleration in the comorbidities of HIV infection [4–9]. Yet alcohol remains the “forgotten drug” of the HIV/AIDS epidemic [10]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122083/ doi: 10.1007/978-1-62703-047-2_23 id: cord-266294-ua22udlc author: Koch, Oliver title: 29 Antiviral drugs date: 2010-12-31 words: 10777.0 sentences: 526.0 pages: flesch: 47.0 cache: ./cache/cord-266294-ua22udlc.txt txt: ./txt/cord-266294-ua22udlc.txt summary: Metabolism The hemochromatosis gene polymorphism HFE 187C> G and possibly mitochondrial haplogroup J gave relative protection against lipoatrophy during antiretroviral drug therapy in a trial in which 96 patients were randomized to didanosine þ stavudine or zidovudine þ lamivudine, combined with efavirenz and/ or nelfinavir in AIDS Clinical Trials Group (ACTG) 384 sub-study A5005s (20 C ). Gastrointestinal In a retrospective obser vational study of highly active antiretroviral therapy (HAART), 27 of 50 patients who took indinavir in combination with zidovudine and lamivudine developed nausea and were significantly more likely to stop taking the treatment than those who were taking zidovudine þ lamivudine þ tenofovir (24 c ). abstract: Publisher Summary This chapter discusses the adverse effects of antiviral drugs used against cytomegalovirus, herpesviruses, hepatitis viruses, against HIV, and against influenza viruses. The cidofovir, drug active against cytomegalovirus, has been associated with bronchiolitis obliterans. Aciclovir and valaciclovir has been reported with renal insufficiency. Adefovir , a drug active against hepatitis viruses, is associated with the fall in creatinine clearance in patients with lamivudine-resistant HBe antigen (HBeAg)negative disease. Drugs active against HIV are comprehensively reviewed as in combination, nucleoside analogue reverse transcriptase inhibitors, nucleoside analogue reverse transcriptase inhibitors, and protease inhibitors. In a randomized controlled trial of indinavir, saquinavir and lopinavir in combination with low-dose ritonavir in 656 patients, median total cholesterol increased by 0.5 mmol/l in the patients with the highest minimum drug plasma concentrations. In patients with AIDS-associated AIDS dementia complex taking optimal stable background antiretroviral therapy including either abacavir or placebo, there was significantly more nausea in those who took abacavir. url: https://www.sciencedirect.com/science/article/pii/S0378608010320290 doi: 10.1016/s0378-6080(10)32029-0 id: cord-287018-g4y5kjju author: Konstantinova, P title: Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA date: 2006-05-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Inhibition of virus replication by means of RNA interference has been reported for several important human pathogens, including human immunodeficiency virus type 1 (HIV-1). RNA interference against these pathogens has been accomplished by introduction of virus-specific synthetic small interfering RNAs (siRNAs) or DNA constructs encoding short-hairpin RNAs (shRNAs). Their use as therapeutic antiviral against HIV-1 is limited, because of the emergence of viral escape mutants. In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. Expression of lhRNAs in mammalian cells may result in the synthesis of many siRNAs targeting different viral sequences, thus providing more potent inhibition and reducing the chance of viral escape. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. Our results show that DNA constructs encoding virus-specific lhRNAs are capable of inhibiting HIV-1 production in a sequence-specific manner, without inducing the class I interferon genes. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/sj.gt.3302786) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/16708080/ doi: 10.1038/sj.gt.3302786 id: cord-303408-coesfldm author: Konstantinova, Pavlina title: Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome date: 2007-03-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) can be inhibited by means of RNA silencing or interference (RNAi) using synthetic short interfering RNAs (siRNAs) or gene constructs encoding short hairpin RNAs (shRNAs) or long hairpin RNAs (lhRNAs). The use of siRNA and shRNA as antiviral therapeutic is limited because of the emergence of viral escape mutants. This problem is theoretically prevented by intracellular expression of lhRNAs generating multiple siRNAs that target the virus simultaneously, thus reducing the chance of viral escape. However, gene constructs encoding lhRNA molecules face problems with delivery to the right cells in an infected individual. In order to solve this problem, we constructed an HIV-1 variant with a 300 bp long hairpin structure in the 3' part of the genome corresponding to the Nef gene (HIV-lhNef). RESULTS: Intriguingly, HIV-lhNef potently inhibited wild-type HIV-1 production in trans. However, HIV-lhNef demonstrated a severe production and replication defect, which we were able to solve by selecting spontaneous virus variants with truncated hairpin structures. Although these escape variants lost the ability to trans-inhibit HIV-1, they effectively outgrew the wild-type virus in competition experiments in SupT1 cells. CONCLUSION: Expression of the lhNef hairpin within the HIV-1 genome results in potent trans-inhibition of wild-type HIV-1. Although the mechanism of trans-inhibition is currently unknown, it remains of interest to study the molecular details because the observed effect is extremely potent. This may have implications for the development of virus strains to be used as live-attenuated virus vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/17331227/ doi: 10.1186/1742-4690-4-15 id: cord-257553-479x7av6 author: Kortepeter, Mark G. title: Health Care Workers and Researchers Traveling to Developing-World Clinical Settings: Disease Transmission Risk and Mitigation date: 2010-12-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: With the recent emphasis on funding and training opportunities for global health and humanitarian aid and the increased interest in the field, many health care workers and medical researchers are traveling from resource-replete to resource-limited settings. This type of travel brings unique disease risks not routinely considered for the business or vacationing traveler. This review provides practical advice for this special population of travelers, targeted to specific health care-related risks (needlestick, hemorrhagic fever viruses, severe viral respiratory disease, and tuberculosis), with suggestions for risk mitigation. url: https://doi.org/10.1086/657115 doi: 10.1086/657115 id: cord-329223-f84gjxm1 author: Kouokam, Joseph Calvin title: Investigation of Griffithsin''s Interactions with Human Cells Confirms Its Outstanding Safety and Efficacy Profile as a Microbicide Candidate date: 2011-08-02 words: 8837.0 sentences: 382.0 pages: flesch: 47.0 cache: ./cache/cord-329223-f84gjxm1.txt txt: ./txt/cord-329223-f84gjxm1.txt summary: In contrast to several other antiviral lectins however, GRFT treatment induces only minimal changes in secretion of inflammatory cytokines and chemokines by epithelial cells or human PBMC, has no measureable effect on cell viability and does not significantly upregulate markers of T-cell activation. When freshly-isolated PBMC were pre-incubated for 24 hrs with GRFT at various concentrations, washed and then infected with HIV-1 R5 strain BaL (without adding new compound), GRFT inhibited viral replication for 9 days of cell culture (Fig. 2) . In addition, the numbers of CD4 2 /CD25 + cells were elevated when PBMC were cultured in presence of PHA or ConA compared to their PBS and GRFT counterpart (Fig. 6 , left panel and data not shown). The heat map shown in Fig. 9A indicates that cells exposed for 24 hours to GRFT Lec-(1 and 8 mM), and low concentrations of GRFT (0.1 mM ) and CV-N (0.05 mM) showed comparable gene expression profiles to those that were incubated in presence of PBS alone. abstract: Many natural product-derived lectins such as the red algal lectin griffithsin (GRFT) have potent in vitro activity against viruses that display dense clusters of oligomannose N-linked glycans (NLG) on their surface envelope glycoproteins. However, since oligomannose NLG are also found on some host proteins it is possible that treatment with antiviral lectins may trigger undesirable side effects. For other antiviral lectins such as concanavalin A, banana lectin and cyanovirin-N (CV-N), interactions between the lectin and as yet undescribed cellular moieties have been reported to induce undesirable side effects including secretion of inflammatory cytokines and activation of host T-cells. We show that GRFT, unlike CV-N, binds the surface of human epithelial and peripheral blood mononuclear cells (PBMC) through an exclusively oligosaccharide-dependent interaction. In contrast to several other antiviral lectins however, GRFT treatment induces only minimal changes in secretion of inflammatory cytokines and chemokines by epithelial cells or human PBMC, has no measureable effect on cell viability and does not significantly upregulate markers of T-cell activation. In addition, GRFT appears to retain antiviral activity once bound to the surface of PBMC. Finally, RNA microarray studies show that, while CV-N and ConA regulate expression of a multitude of cellular genes, GRFT treatment effects only minimal alterations in the gene expression profile of a human ectocervical cell line. These studies indicate that GRFT has an outstanding safety profile with little evidence of induced toxicity, T-cell activation or deleterious immunological consequence, unique attributes for a natural product-derived lectin. url: https://doi.org/10.1371/journal.pone.0022635 doi: 10.1371/journal.pone.0022635 id: cord-009446-8keu2uay author: Kreer, Christoph title: Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies date: 2020-01-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7157687/ doi: 10.3390/vaccines8010013 id: cord-268901-7cm6m1ol author: Ku, Therese title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 date: 2019-07-01 words: 7766.0 sentences: 507.0 pages: flesch: 67.0 cache: ./cache/cord-268901-7cm6m1ol.txt txt: ./txt/cord-268901-7cm6m1ol.txt summary: title: Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. The organozinc was added dropwise to a mixture of 15 (451 mg, 1.0 mmol), Pd (PPh 3 ) 4 (115 mg, 0.1 mmol) and CuI (10 mg, 0.05 mmol) in 40 mL of anhydrous THF and allowed to stir at room temperature for 24 h. abstract: Abstract Anti-HIV-1 drug design has been notably challenging due to the virus’ ability to mutate and develop immunity against commercially available drugs. The aims of this project were to develop a series of fleximer base analogues that not only possess inherent flexibility that can remain active when faced with binding site mutations, but also target a non-canonical, highly conserved target: the nucleocapsid protein of HIV (NC). The compounds were predicted by computational studies not to function via zinc ejection, which would endow them with significant advantages over non-specific and thus toxic zinc-ejectors. The target fleximer bases were synthesized using palladium-catalyzed cross-coupling techniques and subsequently tested against NC and HIV-1. The results of those studies are described herein. url: https://www.ncbi.nlm.nih.gov/pubmed/31126822/ doi: 10.1016/j.bmc.2019.05.019 id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 words: 9406.0 sentences: 511.0 pages: flesch: 37.0 cache: ./cache/cord-317037-1qydcc5e.txt txt: ./txt/cord-317037-1qydcc5e.txt summary: Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. abstract: Extracellular vesicles (EVs) have shown their potential as a carrier of molecular information, and they have been involved in physiological functions and diseases caused by viral infections. Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. They are released via a direct outward budding and fission of plasma membrane blebs into the extracellular space to either facilitate virus propagation or regulate the immune responses. Moreover, EVs generated by virus-infected cells can incorporate virulence factors including viral protein and viral genetic material, and thus can resemble noninfectious viruses. Interactions of EVs with recipient cells have been shown to activate signaling pathways that may contribute to a sustained cellular response towards viral infections. EVs, by utilizing a complex set of cargos, can play a regulatory role in viral infection, both by facilitating and suppressing the infection. EV-based antiviral and antiretroviral drug delivery approaches provide an opportunity for targeted drug delivery. In this review, we summarize the literature on EVs, their associated involvement in transmission in viral infections, and potential therapeutic implications. url: https://doi.org/10.3390/v12080887 doi: 10.3390/v12080887 id: cord-000849-rrezynbs author: Kumar, Rajesh title: A novel strategy for efficient production of anti-V3 human scFvs against HIV-1 clade C date: 2012-11-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Production of human monoclonal antibodies that exhibit broadly neutralizing activity is needed for preventing HIV-1 infection, however only a few such antibodies have been generated till date. Isolation of antibodies by the hybridoma technology is a cumbersome process with fewer yields. Further, the loss of unstable or slowly growing clones which may have unique binding specificities often occurs during cloning and propagation and the strongly positive clones are often lost. This has been avoided by the process described in this paper, wherein, by combining the strategy of EBV transformation and recombinant DNA technology, we constructed human single chain variable fragments (scFvs) against the third variable region (V3) of the clade C HIV-1 envelope. RESULTS: An antigen specific phage library of 7000 clones was constructed from the enriched V3- positive antibody secreting EBV transformed cells. By ligation of the digested scFv DNA into phagemid vector and bio panning against the HIV-1 consensus C and B V3 peptides followed by random selection of 40 clones, we identified 15 clones that showed V3 reactivity in phage ELISA. DNA fingerprinting analysis and sequencing showed that 13 out of the 15 clones were distinct. Expression of the positive clones was tested by SDS-PAGE and Western blot. All the 13 anti-V3 scFvs showed cross-reactivity against both the clade C and B V3 peptides and did not show any reactivity against other unrelated peptides in ELISA. Preliminary neutralization assays indicated varying degrees of neutralization of clade C and B viruses. EBV transformation, followed by antigen selection of lines to identify specific binders, enabled the selection of phage from un-cloned lines for scFv generation, thus avoiding the problems of hybridoma technology. Moreover, as the clones were pretested for antigen binding, a comparatively small library sufficed for the selection of a considerable number of unique antigen binding phage. After selection, the phage clones were propagated in a clonal manner. CONCLUSIONS: This strategy can be efficiently used and is cost effective for the generation of diverse recombinant antibodies. This is the first study to generate anti-V3 scFvs against HIV-1 Clade C. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536577/ doi: 10.1186/1472-6750-12-87 id: cord-345342-04tvuj9f author: Kumar, Rebecca N. title: COVID‐19 in an HIV‐positive Kidney Transplant Recipient date: 2020-05-26 words: 1451.0 sentences: 93.0 pages: flesch: 50.0 cache: ./cache/cord-345342-04tvuj9f.txt txt: ./txt/cord-345342-04tvuj9f.txt summary: This case describes the clinical course of a symptomatic kidney transplant recipient with HIV who tested positive for SARS-CoV-2. A 50-year-old HIV+ (CD4 395 cells/µL, CD4% 28%, HIV RNA < 20 copies/mL) African-American male with deceased donor kidney transplantation 14 months earlier for end-stage renal disease secondary to HIV-associated nephropathy (HIVAN)/focal segmental glomerulosclerosis (FSGS) presented to the Emergency Department (ED) complaining of fevers for two days, with temperatures to 101°F, chills, nasal congestion, and mild cough. All rights reserved There have been reported cases of COVID-19 in HIV-infected patients and cases of COVID-19 in transplant recipients [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] . However, this case is the first detailed report of an HIVpositive kidney transplant recipient who developed and recovered from COVID-19. Case Report: A Kidney Transplant Patient with Mild COVID-19 Case report of COVID-19 in a kidney transplant recipient: Does immunosuppression alter the clinical presentation? abstract: We report a case of a 50‐year‐old male with a history of HIV and kidney transplant who presented with SARS‐CoV‐2. We also present a review of COVID‐19 cases in kidney transplant recipients. url: https://www.ncbi.nlm.nih.gov/pubmed/32453483/ doi: 10.1111/tid.13338 id: cord-297530-7zbvgvk8 author: Kühnert, Denise title: Phylogenetic and epidemic modeling of rapidly evolving infectious diseases date: 2011-08-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Epidemic modeling of infectious diseases has a long history in both theoretical and empirical research. However the recent explosion of genetic data has revealed the rapid rate of evolution that many populations of infectious agents undergo and has underscored the need to consider both evolutionary and ecological processes on the same time scale. Mathematical epidemiology has applied dynamical models to study infectious epidemics, but these models have tended not to exploit – or take into account – evolutionary changes and their effect on the ecological processes and population dynamics of the infectious agent. On the other hand, statistical phylogenetics has increasingly been applied to the study of infectious agents. This approach is based on phylogenetics, molecular clocks, genealogy-based population genetics and phylogeography. Bayesian Markov chain Monte Carlo and related computational tools have been the primary source of advances in these statistical phylogenetic approaches. Recently the first tentative steps have been taken to reconcile these two theoretical approaches. We survey the Bayesian phylogenetic approach to epidemic modeling of infection diseases and describe the contrasts it provides to mathematical epidemiology as well as emphasize the significance of the future unification of these two fields. url: https://api.elsevier.com/content/article/pii/S156713481100284X doi: 10.1016/j.meegid.2011.08.005 id: cord-300642-c7adeis1 author: Lai, Andrew SH title: Viral nephropathy date: 2006 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral infections can cause many glomerular diseases. The diagnostic criteria for virus-related nephropathy include detailed clinical and laboratory data, and tissue molecular analysis. Several mechanisms are involved in the pathogenesis of virus-related nephropathy, including tropism of the virus in the kidney, induction of abnormal immune complexes, direct cytopathogenic effects, and multiorgan failure. Hepatitis B virus is associated with membranous nephropathy and mesangiocapillary glomerulonephritis in endemic areas. Hepatitis C virus causes various forms of glomerulonephritis, including cryoglobulinemia-mediated glomerulonephritis. Infection with HIV is associated with a collapsing focal segmental glomerulosclerosis, a distinctive disease that affects mainly Africans and African Americans. In the course of HIV infection, other types of immune complex glomerulonephritis can occur, most frequently in whites. Recent reports indicate a role for parvovirus B19 in 'idiopathic' collapsing focal segmental glomerulosclerosis. Both hantaviruses, and coronaviruses associated with severe acute respiratory syndrome, can lead to acute renal failure. Renal biopsy followed by appropriate serological and molecular testing is essential for defining virus-related glomerular lesions and guiding prognostic and therapeutic evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/16932438/ doi: 10.1038/ncpneph0166 id: cord-017831-anadq4j9 author: Lai, Yi-Horng title: Network Analysis of Comorbidities: Case Study of HIV/AIDS in Taiwan date: 2015-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Comorbidities are the presence of one or more additional disorders or diseases co-occurring with a primary disease or disorder. The purpose of this study is to identify diseases that co-occur with HIV/AIDS and analyze the gender differences. Data was collected from 536 HIV/AIDS admission medical records out of 1,377,469 admission medical records from 1997 to 2010 in Taiwan. In this study, the comorbidity relationships are presented in the phenotypic disease network (PDN), and φ-correlation is used to measure the distance between two diseases on the network. The results show that there is a high correlation in the following pairs/triad of diseases: human immunodeficiency virus infection with specified conditions (042) and pneumocystosis pneumonia (1363), human immunodeficiency virus infection with specified malignant neoplasms (0422) and kaposi’s sarcoma of other specified sites (1768), human immunodeficiency virus acquired immunodeficiency syndrome, and unspecified (0429) and progressive multifocal leukoencephalopathy (0463), and lastly, human immunodeficiency virus infection with specified infections (0420), meningoencephalitis due to toxoplasmosis (1300), and human immunodeficiency virus infection specified infections causing other specified infections (0421). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122503/ doi: 10.1007/978-3-662-48319-0_14 id: cord-354790-xx6imhzb author: Lambour, Jennifer title: Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play date: 2016-08-17 words: 6499.0 sentences: 324.0 pages: flesch: 33.0 cache: ./cache/cord-354790-xx6imhzb.txt txt: ./txt/cord-354790-xx6imhzb.txt summary: 31 In addition to controlling the viral propagation by these mechanisms, the opsonization of viral particles and/or infected cells by therapeutic antiviral mAbs of the IgG type leads to the formation of immune complexes (ICs) recognizable by the FcγRs expressed on antigen-presenting cells (APCs) such as DCs. This can potentially affect the endogenous antiviral adaptive immune response of passive immunotherapy-treated individuals. Moreover, as the in vivo activity of anti-HIV-1 bNAbs, including viral load control, was recently shown to crucially depend on Fc effector functions, 53,54 an important issue is identifying that Fc-FcγRs interactions are involved in the induction of vaccinelike effects by antiviral mAbs. To understand the mechanisms underlying the enhancement of antiviral responses by ICs, several in vitro studies have addressed whether antibody-mediated viral uptake by DCs could lead to stronger activation of these cells and the development of stronger virus-specific CD4 + and CD8 + T-cell responses in an Fc-dependent manner. abstract: Monoclonal antibodies (mAbs), which currently constitute the main class of biotherapeutics, are now recognized as major medical tools that are increasingly being considered to fight severe viral infections. Indeed, the number of antiviral mAbs developed in recent years has grown exponentially. Although their direct effects on viral blunting have been studied in detail, their potential immunomodulatory actions have been overlooked until recently. The ability of antiviral mAbs to modulate antiviral immune responses in infected organisms has recently been revealed. More specifically, upon recognition of their cognate antigens, mAbs form immune complexes (ICs) that can be recognized by the Fc receptors expressed on different immune cells of infected individuals. This binding may be followed by the modulation of the host immune responses. Harnessing this immunomodulatory property may facilitate improvements in the therapeutic potential of antiviral mAbs. This review focuses on the role of ICs formed with different viral determinants and mAbs in the induction of antiviral immune responses in the context of both passive immunotherapies and vaccination strategies. Potential deleterious effects of ICs on the host immune response are also discussed. url: https://doi.org/10.1038/emi.2016.97 doi: 10.1038/emi.2016.97 id: cord-273324-xhpv783y author: Land, Kevin J. title: REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: 2018-12-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Lack of access to quality diagnostics remains a major contributor to health burden in resource-limited settings. It has been more than 10 years since ASSURED (affordable, sensitive, specific, user-friendly, rapid, equipment-free, delivered) was coined to describe the ideal test to meet the needs of the developing world. Since its initial publication, technological innovations have led to the development of diagnostics that address the ASSURED criteria, but challenges remain. From this perspective, we assess factors contributing to the success and failure of ASSURED diagnostics, lessons learnt in the implementation of ASSURED tests over the past decade, and highlight additional conditions that should be considered in addressing point-of-care needs. With rapid advances in digital technology and mobile health (m-health), future diagnostics should incorporate these elements to give us REASSURED diagnostic systems that can inform disease control strategies in real-time, strengthen the efficiency of health care systems and improve patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/30546093/ doi: 10.1038/s41564-018-0295-3 id: cord-305085-bv7udg9k author: Lawrence, Robert M. title: Chapter 13 Transmission of Infectious Diseases Through Breast Milk and Breastfeeding date: 2011-12-31 words: 45849.0 sentences: 2358.0 pages: flesch: 45.0 cache: ./cache/cord-305085-bv7udg9k.txt txt: ./txt/cord-305085-bv7udg9k.txt summary: Postnatal exposure of susceptible infants to CMV, including premature infants without passively acquired maternal antibodies against CMV, infants born to CMV-seronegative mothers, and immunodeficient infants, can cause significant clinical illness (pneumonitis, hepatitis, thrombocytopenia).* In one study of premature infants followed up to 12 months, Vochem et al 430 found CMV transmission in 17 of 29 infants (59%) exposed to CMV virolactia and breastfed compared with no infants infected of 27 exposed to breast milk without CMV. 38, 104, 121 Laboratory reports demonstrate the presence of cell-free virus and cell-associated virus in breast milk as well as various immunologic factors that could block or limit infection.* A dose-response relationship has been observed, correlating the HIV viral load in human milk as well as a mother'' s plasma viral load with an increased transmission risk for the breastfed infant. 76 No case of transmission of yellow fever virus from an infected mother to her infant via breastfeeding or breast milk has been reported. abstract: nan url: https://api.elsevier.com/content/article/pii/B9781437707885100136 doi: 10.1016/b978-1-4377-0788-5.10013-6 id: cord-312167-d16ylykc author: Lazzarin, Serena Marita title: Successful treatment of HIV-associated tumefactive demyelinating lesions with corticosteroids and cyclophosphamide: a case report date: 2020-11-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33141250/ doi: 10.1007/s00415-020-10296-6 id: cord-334454-cqaado3u author: Leal, Rodolfo Oliveira title: The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives date: 2016-10-27 words: 4320.0 sentences: 201.0 pages: flesch: 41.0 cache: ./cache/cord-334454-cqaado3u.txt txt: ./txt/cord-334454-cqaado3u.txt summary: title: The Use of Recombinant Feline Interferon Omega Therapy as an Immune-Modulator in Cats Naturally Infected with Feline Immunodeficiency Virus: New Perspectives More than summarizing the main conclusions about rFeIFN-ω in cats, this review emphasizes the immune-modulation properties of IFN therapy, opening new perspectives for its use in retroviral infections. Firstly, the effect of rFeIFN-ω licensed protocol in cats living in an animal shelter was evaluated, assessing clinical improvement and monitoring concurrent viral excretion (namely herpesvirus, calicivirus, and coronavirus) [26] . Following the same methodology of previous studies, the clinical improvement, concurrent viral excretion, APP profiles, and different hematology and biochemistry parameters in FIV-infected cats treated with the oral protocol were assessed. Only one study had previously reported that the licensed protocol does not change viremia or proviral load in treated FIV-infected cats, suggesting that this compound may not act on acquired immunity [17] . abstract: Type I interferons (IFNs) are well-known cytokines that, among their main functions, are key components of the host immune response against viral infections. Due to its immune modulation properties, they are commonly used in the therapeutic approach of various retroviral infections, namely human immunodeficiency virus (HIV) and feline immunodeficiency virus (FIV). In HIV infection, it has been shown that IFN therapy limits early viral replication, particularly useful on post-exposure prophylaxis. In veterinary medicine, recombinant feline interferon omega (rFeIFN-ω) was the first interferon licensed for use in cats. Several studies have recently shown that this compound seems to stimulate the innate immunity, decreasing clinical signs and co-infections in naturally FIV-infected cats. More than summarizing the main conclusions about rFeIFN-ω in cats, this review emphasizes the immune-modulation properties of IFN therapy, opening new perspectives for its use in retroviral infections. Either in FIV-infected cats or in HIV individuals, type I IFNs seem to induce an innate immune-modulation and should not be overlooked as a therapeutic option in retroviral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/29056740/ doi: 10.3390/vetsci3040032 id: cord-266226-gxbrgy6g author: Lee, Choongho title: Griffithsin, a Highly Potent Broad-Spectrum Antiviral Lectin from Red Algae: From Discovery to Clinical Application date: 2019-10-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Virus entry into a susceptible host cell is the first step in the formation of all viral diseases. Controlling viral infections by disrupting viral entry is advantageous for antibody-mediated neutralization by the host’s immune system and as a preventive and therapeutic antiviral strategy. Recently, several plant-derived carbohydrate-binding proteins (lectins) have emerged as a new class of antiviral biologics by taking advantage of a unique glycosylation pattern only found on the surface of viruses. In particular, a red algae-derived griffithsin (GRFT) protein has demonstrated superior in vitro and in vivo antiviral activity with minimum host toxicity against a variety of clinically relevant, enveloped viruses. This review examines the structural characteristics of GRFT, focusing on its carbohydrate-binding capability. Its in vitro antiviral profiles against human immunodeficiency virus (HIV) are also discussed followed by a description of the results from a combination study using anti-HIV drugs. The results of several studies regarding its novel antiviral mechanism of action are provided in conjunction with an explanation of viral resistance profiles to GRFT. In addition, its in vitro and in vivo host toxicity profiles are summarized with its pharmacokinetic behavior using in vivo efficacy study results. Also, a large-scale production and formulation strategy, as well as a drug delivery strategy, for GRFT as a new class of broad-spectrum microbicides is discussed. Finally, results from two ongoing clinical studies examining GRFT’s effects on viruses are presented. url: https://doi.org/10.3390/md17100567 doi: 10.3390/md17100567 id: cord-102905-rlee32x7 author: Leis, Jonathan title: Ilaprazole and other novel prazole-based compounds that bind Tsg101 inhibit viral budding of HSV-1/2 and HIV from cells date: 2020-05-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In many enveloped virus families, including HIV and HSV, a crucial, yet unexploited, step in the viral life cycle is releasing particles from the infected cell membranes. This release process is mediated by host ESCRT complex proteins, which is recruited by viral structural proteins and provides the mechanical means for membrane scission and subsequent viral budding. The prazole drug, tenatoprazole, was previously shown to bind to ESCRT complex member Tsg101 and quantitatively block the release of infectious HIV-1 from cells in culture. In this report we show that tenatoprazole and a related prazole drug, ilaprazole, effectively block infectious Herpes Simplex Virus (HSV)-1/2 release from Vero cells in culture. By electron microscopy, we found that both prazole drugs block the release of HSV particles from the cell nuclear membrane resulting in their accumulation in the nucleus. Ilaprazole also quantitatively blocks the release of HIV-1 from 293T cells with an EC50 of 0.8 μM, which is more potent than tenatoprazole. Finally, we synthesized and tested multiple novel prazole-based analogs that demonstrate both binding to Tsg101 and inhibition of viral egress in the nanomolar range of HIV-1 from 293T cells. Our results indicate that prazole-based compounds may represent a class of drugs with potential to be broad-spectrum antiviral agents against multiple enveloped viruses, by interrupting cellular Tsg101 interaction with maturing virus, thus blocking the budding process that releases particles from the cell. Importance These results provide the basis for the development of drugs that target enveloped virus budding that can be used ultimately to control multiple virus infections in humans. url: https://doi.org/10.1101/2020.05.04.075036 doi: 10.1101/2020.05.04.075036 id: cord-355439-eqtk51q3 author: Lesko, Catherine R title: HIV and SARS-CoV-2: Intersecting Epidemics with Many Unknowns date: 2020-07-22 words: 3288.0 sentences: 154.0 pages: flesch: 46.0 cache: ./cache/cord-355439-eqtk51q3.txt txt: ./txt/cord-355439-eqtk51q3.txt summary: Surveillance data, such as those available from South Africa or Wuhan, will provide the most complete picture of COVID-19 risk among PLWH (e.g., by not restricting to PLWH who are in care and who are more likely to have wellcontrolled HIV disease); however clinical data, such as those from Madrid, may provide the most depth (e.g., by allowing examination of the role of comorbidities, medications, and COVID-19 treatments) as long as potential selection bias is considered. Despite some good telehealth outcomes for some PLWH, telehealth has the potential to exacerbate disparities in care for people with lower socio-economic status: lack of necessary technology and services, technology literacy, and safe, confidential surroundings to participate fully in telehealth may be barriers to engagement in care (32 distancing restrictions if they need to go outside their homes to access alcohol or other drugs, or critically, medication assisted treatments (such as methadone or buprenorphine). abstract: As of July 2020, approximately 6 months into the pandemic of novel coronavirus disease 2019 (COVID-19), whether people living with HIV (PLWH) are disproportionately affected remains an unanswered question. Thus far, risk of COVID-19 in people with and without HIV appears similar but data are sometimes contradictory. Some uncertainty is due to the recency of the emergence of COVID-19 and sparsity of data; some is due to imprecision about what it means for HIV to be a “risk factor” for COVID-19. Forthcoming studies on the risk of COVID-19 to PLWH should differentiate between 1) the unadjusted, excess burden of disease among PLWH to inform surveillance efforts; and 2) any excess risk of COVID-19 among PLWH due to biological effects of HIV, independent of comorbidities that confound rather than mediate this effect. PLWH bear a disproportionate burden of alcohol, other drug use, mental health disorders, and other structural vulnerabilities, which may increase their risk of COVID-19. In addition to any direct effects of COVID-19 on the health of PLWH, we need to understand how physical distancing restrictions impact secondary health outcomes, and the need for, accessibility of, and impact of alternative modalities of providing ongoing medical, mental health, and substance use treatment that comply with physical distancing restrictions (e.g., telemedicine). url: https://www.ncbi.nlm.nih.gov/pubmed/32696057/ doi: 10.1093/aje/kwaa158 id: cord-332093-iluqwwxs author: Lessler, Justin title: Mechanistic Models of Infectious Disease and Their Impact on Public Health date: 2016-02-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: From the 1930s through the 1940s, Lowell Reed and Wade Hampton Frost used mathematical models and mechanical epidemic simulators as research tools and to teach epidemic theory to students at the Johns Hopkins Bloomberg School of Public Health (then the School of Hygiene and Public Health). Since that time, modeling has become an integral part of epidemiology and public health. Models have been used for explanatory and inferential purposes, as well as in planning and implementing public health responses. In this article, we review a selection of developments in the history of modeling of infectious disease dynamics over the past 100 years. We also identify trends in model development and use and speculate as to the future use of models in infectious disease dynamics. url: https://doi.org/10.1093/aje/kww021 doi: 10.1093/aje/kww021 id: cord-012503-8rv2xof7 author: Levintow, Sara N. title: Estimating the Effect of Depression on HIV Transmission Risk Behaviors Among People Who Inject Drugs in Vietnam: A Causal Approach date: 2020-08-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The burden of depression and HIV is high among people who inject drugs (PWID), yet the effect of depression on transmission risk behaviors is not well understood in this population. Using causal inference methods, we analyzed data from 455 PWID living with HIV in Vietnam 2009–2013. Study visits every 6 months over 2 years measured depressive symptoms in the past week and injecting and sexual behaviors in the prior 3 months. Severe depressive symptoms (vs. mild/no symptoms) increased injection equipment sharing (risk difference [RD] = 3.9 percentage points, 95% CI −1.7, 9.6) but not condomless sex (RD = −1.8, 95% CI −6.4, 2.8) as reported 6 months later. The cross-sectional association with injection equipment sharing at the same visit (RD = 6.2, 95% CI 1.4, 11.0) was stronger than the longitudinal effect. Interventions on depression among PWID may decrease sharing of injection equipment and the corresponding risk of HIV transmission. Clinical trial registration ClinicalTrials.gov NCT01689545. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10461-020-03007-9) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7444452/ doi: 10.1007/s10461-020-03007-9 id: cord-016690-3gsq724l author: Li, Hongjun title: HIV/AIDS Related Respiratory Diseases date: 2013-09-30 words: 26772.0 sentences: 1583.0 pages: flesch: 46.0 cache: ./cache/cord-016690-3gsq724l.txt txt: ./txt/cord-016690-3gsq724l.txt summary: Its difference from the clinical manifestations of non-HIV infected patients is as the following: (1) More common pulmonary infi ltration with multiple involvements and rare cavities; (2) Higher incidence of dissemination (87-96 %) commonly along with blood fl ow and higher incidence of extrapulmonary tuberculosis (60-70 %); (3) More common lymph node tuberculosis, such as hilar, mediastinal and extrapleural lymphadenectasis; (4) Lower positive rate of tuberculin test (PPD); (5) More patients with no expectoration, with sputum smear for acid-fast bacilli staining is negative; (6) Higher incidence of resistant strains, high recurrence rate, and higher mortality (Table 17 .1 ). Based on the course of the disease, the diagnostic imaging demonstrations of Rhodococcus equi pulmonary infection can be divided into early stage, showing round liked fl aky blurry shadows surrounding unilateral hilum that has blurry boundary; middle stage (parenchymal change), showing central sphere liked high density shadow surrounding unilateral hilum, in parenchymal changes and with clear boundary; advanced stage (necrosis) showing secondary cavity of the pulmonary mass, possibly with hydropneumothorax and pleurisy. abstract: Lungs are the most commonly involved organ by HIV/AIDS related diseases, and pulmonary infections are the main reasons for the increasing death rate from AIDS. Pathogens of HIV related pulmonary infections include parasites, fungi, mycobacteria, viruses, bacteria and toxoplasma gondii. According to international reports, pathogens have different geographical distribution, which is also closely related to the socioeconomic status of the region to produce varied AIDS related diseases spectra. For instance, in the United States, pneumocystis carnii pneumonia (PCP), tuberculosis and recurrent bacterial pneumonia (at least twice within 1 year) occur frequently in HIV infected patients. An international report published 10 years ago indicated that PCP is the most common and serious pulmonary opportunistic infections in HIV infected patients. Now its incidence has dropped with the application of antiretroviral treatment and preventive measures. PCP will continue to occur initially in patients who are aware of their HIV infection. In addition, HIV related viral and parasitic infections have been reported both domestically and internationally. In this section, the clinical manifestations and imaging findings of HIV related pulmonary infections are analyzed and discussed, which provide effective diagnosis basis, so as to reduce the incidence of HIV-related pulmonary infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121050/ doi: 10.1007/978-94-007-7823-8_17 id: cord-340879-gu91cact author: Li, Miao title: Isolation and Characterization of a Phaseolus vulgaris Trypsin Inhibitor with Antiproliferative Activity on Leukemia and Lymphoma Cells date: 2017-01-23 words: 4150.0 sentences: 228.0 pages: flesch: 48.0 cache: ./cache/cord-340879-gu91cact.txt txt: ./txt/cord-340879-gu91cact.txt summary: title: Isolation and Characterization of a Phaseolus vulgaris Trypsin Inhibitor with Antiproliferative Activity on Leukemia and Lymphoma Cells The intent of the present study was to isolate a trypsin inhibitor from the gold bean and to test it for inhibitory action on tumor cells, viral enzymes, and fungal growth. Gold bean trypsin inhibitor is also devoid of any inhibitory effect on HIV-1 integrase and SARS coronavirus proteinase. Gold bean trypsin inhibitor is also devoid of any inhibitory effect on HIV-1 integrase and SARS coronavirus proteinase. A lectin, an antifungal protein and a trypsin inhibitor can be isolated from the gold bean [24, 25] . A homodimeric sporamin-type trypsin inhibitor with antiproliferative, hiv reverse transcriptase-inhibitory and antifungal activities from wampee (clausena lansium) seeds The isolation of two proteins, glycoprotein i and a trypsin inhibitor, from the seeds of kidney bean (Phaseolus vulgaris) abstract: A 17.5-kDa trypsin inhibitor was purified from Phaseolus vulgaris cv. “gold bean” with an isolation protocol including ion exchange chromatography on DEAE-cellulose (Diethylaminoethyl-cellulose), affinity chromatography on Affi-gel blue gel, ion exchange chromatography on SP-sepharose (Sulfopropyl-sepharose), and gel filtration by FPLC (Fast protein liquid chromatography) on Superdex 75. It dose-dependently inhibited trypsin with an IC(50) value of 0.4 μM, and this activity was reduced in the presence of dithiothreitol in a dose- and time-dependent manner, signifying the importance of the disulfide linkage to the activity. It inhibited [methyl-(3)H] thymidine incorporation by leukemia L1210 cells and lymphoma MBL2 cells with an IC(50) value of 2.3 μM and 2.5 μM, respectively. The inhibitor had no effect on fungal growth and the activities of various viral enzymes when tested up to 100 μM. url: https://www.ncbi.nlm.nih.gov/pubmed/28125005/ doi: 10.3390/molecules22010187 id: cord-262752-bwofzbwa author: Li, Qianqian title: Current status on the development of pseudoviruses for enveloped viruses date: 2017-12-07 words: 3268.0 sentences: 179.0 pages: flesch: 37.0 cache: ./cache/cord-262752-bwofzbwa.txt txt: ./txt/cord-262752-bwofzbwa.txt summary: Early work by Witte and colleagues showed that when they used VSV to infect the cells in which MLV is packaged, they were able to harvest pseudovirus for use in neutralization antibody assays. Development of in vitro and in vivo rabies virus neutralization assays based on a high-titer pseudovirus system Development of a pseudotyped-lentiviral-vector-based neutralization assay for chikungunya virus infection Second generation of pseudotype-based serum neutralization assay for Nipah virus antibodies: sensitive and high-throughput analysis utilizing secreted alkaline phosphatase Use of vesicular stomatitis virus pseudotypes bearing Hantaan or Seoul virus envelope proteins in a rapid and safe neutralization test A neutralization test for specific detection of Nipah virus antibodies using pseudotyped vesicular stomatitis virus expressing green fluorescent protein Truncation of the human immunodeficiency virus-type-2 envelope glycoprotein allows efficient pseudotyping of murine leukemia virus retroviral vector particles Cholesterol supplementation during production increases the infectivity of retroviral and Lentiviral vectors pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G) abstract: Emerging and reemerging infectious diseases have a strong negative impact on public health. However, because many of these pathogens must be handled in biosafety level, 3 or 4 containment laboratories, research and development of antivirals or vaccines against these diseases are often impeded. Alternative approaches to address this issue have been vigorously pursued, particularly the use of pseudoviruses in place of wild‐type viruses. As pseudoviruses have been deprived of certain gene sequences of the virulent virus, they can be handled in biosafety level 2 laboratories. Importantly, the envelopes of these viral particles may have similar conformational structures to those of the wild‐type viruses, making it feasible to conduct mechanistic investigation on viral entry and to evaluate potential neutralizing antibodies. However, a variety of challenging issues remain, including the production of a sufficient pseudovirus yield and the inability to produce an appropriate pseudotype of certain viruses. This review discusses current progress in the development of pseudoviruses and dissects the factors that contribute to low viral yields. url: https://doi.org/10.1002/rmv.1963 doi: 10.1002/rmv.1963 id: cord-304816-7gg6pxnt author: Li, Wei title: Letter to the Editor: The characteristics of two patients co‐infected with SARS‐CoV‐2 and HIV in Wuhan, China date: 2020-06-10 words: 1000.0 sentences: 69.0 pages: flesch: 57.0 cache: ./cache/cord-304816-7gg6pxnt.txt txt: ./txt/cord-304816-7gg6pxnt.txt summary: In the present study, we reported two young male COVID-19 patients co-infected with HIV and analyzed the clinical and laboratory features of them. It will provide clues for the diagnosis and treatment of COVID-19 patients co-infected with HIV. The laboratory test results showed that the protein synthesis by hepatocytes like TP or ALB were decreased and the hepatocellular enzymes ALT or AST were significantly increased, the absolute count of lymphocytes was lower than the normal reference value. We reported two cases of COVID-19 patients co-infected with HIV. Although there is a lack of epidemiological investigation on whether HIV patients are susceptible to COVID-19, the above cases presented the following distinctive clinical course and manifestations. Co-infection of SARS-CoV-2 and HIV in a patient in Wuhan city COVID-19 in a patient with HIV infection Clinical features and outcome of HIV/SARS-CoV-2 co-infected patients in the Bronx abstract: We reported two cases of COVID‐19 patients co‐infected with HIV. The SARS‐CoV‐2 nucleic acid test of patients turned negative while the clinical symptoms persisted, and interstitial pneumonia gradually deteriorated. The cases provided evidences to clinicians for the diagnosis and treatment of COVID‐19 patients co‐infected with HIV. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26155 doi: 10.1002/jmv.26155 id: cord-295494-wal0gtrs author: Limeres Posse, Jacobo title: Infection Transmission by Saliva and the Paradoxical Protective Role of Saliva date: 2017-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Saliva is produced by both major (parotid and submandibular and sublingual) and minor (located in the mouth) glands, with different constituents and properties between the two groups. In the mouth saliva is a colorless, odorless, tasteless, watery liquid containing 99% water and 1% organic and inorganic substances and dissolved gases, mainly oxygen and carbon dioxide. Salivary constituents can be grouped into proteins (e.g., amylase and lysozyme), organic molecules (e.g., urea, lipids, and glucose mainly), and electrolytes (e.g., sodium, calcium, chlorine, and phosphates). Cellular elements such as epithelial cells, leukocytes and various hormones, and vitamins have also been detected. The composition of saliva is modified, depending on factors such as secreted amount, circadian rhythm, duration and nature of stimuli, diet, and medication intake, among others. url: https://api.elsevier.com/content/article/pii/B9780128136812000019 doi: 10.1016/b978-0-12-813681-2.00001-9 id: cord-264159-e9071tyv author: Lin, Weikang Nicholas title: The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date: 2020-06-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host–pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development. url: https://www.ncbi.nlm.nih.gov/pubmed/32531928/ doi: 10.3390/cells9061440 id: cord-022168-qautse9a author: Liu, Li title: Clinical Use of DNA Vaccines date: 2017-07-25 words: 7120.0 sentences: 321.0 pages: flesch: 38.0 cache: ./cache/cord-022168-qautse9a.txt txt: ./txt/cord-022168-qautse9a.txt summary: Specifically, the strategies that allow DNA vaccines to overcome antigenic diversity for viral infection and break immune tolerance for cancer therapy are explored. To overcome these obstacles, several approaches focusing on augmenting DNA uptake, maximizing protein expression, and enhancing antigen immunogenicity have been developed and tested in clinical trials. Therefore, one key element to improve DNA vaccine efficacy is to formulate a vaccine with an immunogenic cancer antigen so that it can prime T cells for immune responses. To date, the most successful and encouraging outcomes of using DNA vaccine in the clinical setting were obtained from treatment of malignant diseases where the etiological agent is of foreign viral origin, such as the human papillomavirus (HPV), as these viral agents can readily induce a strong immune response against cancerous cells harboring viral antigens. abstract: Owing to their unique advantages in simplicity, safety, scalability, and possibility of repeated administrations, DNA vaccines represent an appealing and competitive immunization approach for a wide array of conditions, including but not limited to infectious diseases and cancer immunotherapy. Despite the exciting efficacy observed in preclinical studies, DNA vaccines have faced challenges in inducing strong immune responses in humans. This unexpected poor immunogenicity has severely hampered the translation of DNA vaccines from investigational medications to licensed products. To overcome this obstacle, tremendous efforts have been made to improve antigen expression and enhance immunogenicity. Among these endeavors, in vivo DNA electroporation (EP) has proved to be a breakthrough technology capable of mediating efficient DNA uptake and resulting in enhanced antigen expression and vaccine immunogenicity. EP-mediated DNA delivery has become one of the major platforms used in clinical trials to evaluate DNA vaccines in humans. In this chapter, in addition to EP delivery, other progress made in DNA vaccine development including plasmid optimization, antigen design, and immunologic adjuvants is also reviewed. Finally, the use of DNA vaccines in the context of clinical trials for infectious diseases and cancer immunotherapy is summarized. Specifically, the strategies that allow DNA vaccines to overcome antigenic diversity for viral infection and break immune tolerance for cancer therapy are explored. Based on the advantages of DNA vaccines and the immense progress, led by the electroporation-mediated vaccine delivery, DNA vaccines appear to have the potential to fundamentally transform the vaccine field, providing important benefits for preventing and curing diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153459/ doi: 10.1007/978-3-319-32886-7_106 id: cord-271188-ewlxy5po author: Liu, Wei title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 words: 4237.0 sentences: 245.0 pages: flesch: 42.0 cache: ./cache/cord-271188-ewlxy5po.txt txt: ./txt/cord-271188-ewlxy5po.txt summary: Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 abstract: PURPOSE OF THE REVIEW: The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) in China is lifting widespread concerns. Thus, therapeutic options are urgently needed, and will be discussed in this review. RECENT FINDINGS: Iron-containing enzymes are required for viruses most likely including coronaviruses (CoVs) to complete their replication process. Moreover, poor prognosis occurred in the conditions of iron overload for patients upon infections of viruses. Thus, limiting iron represents a promising adjuvant strategy in treating viral infection through oral uptake or venous injection of iron chelators, or through the manipulation of the key iron regulators. For example, treatment with iron chelator deferiprone has been shown to prolong the survival of acquired immunodeficiency syndrome (AIDS) patients. Increasing intracellular iron efflux via increasing iron exporter ferroportin expression also exhibits antiviral effect on human immunodeficiency virus (HIV). The implications of other metals besides iron are also briefly discussed. SUMMARY: For even though we know little about iron regulation in COVID-19 patients thus far, it could be deduced from other viral infections that iron chelation might be an alternative beneficial adjuvant in treating COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32318324/ doi: 10.1007/s40588-020-00140-w id: cord-262076-b5u5hp2r author: Liu, Ying Poi title: Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron date: 2008-03-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: RNA interference (RNAi) is a powerful approach to inhibit human immunodeficiency virus type 1 (HIV-1) replication. However, HIV-1 can escape from RNAi-mediated antiviral therapy by selection of mutations in the targeted sequence. To prevent viral escape, multiple small interfering RNAs (siRNAs) against conserved viral sequences should be combined. Ideally, these RNA inhibitors should be expressed simultaneously from a single transgene transcript. In this study, we tested a multiplex microRNA (miRNA) expression strategy by inserting multiple effective anti-HIV siRNA sequences in the miRNA polycistron mir-17-92. Individual anti-HIV miRNAs that resemble the natural miRNA structures were optimized by varying the siRNA position in the hairpin stem to obtain maximal effectiveness against luciferase reporters and HIV-1. We show that an antiviral miRNA construct can have a greater intrinsic inhibitory activity than a conventional short hairpin (shRNA) construct. When combined in a polycistron setting, the silencing activity of an individual miRNA is strongly boosted. We demonstrate that HIV-1 replication can be efficiently inhibited by simultaneous expression of four antiviral siRNAs from the polycistronic miRNA transcript. These combined results indicate that a multiplex miRNA strategy may be a promising therapeutic approach to attack escape-prone viral pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/18346971/ doi: 10.1093/nar/gkn109 id: cord-305602-yzc4bosn author: Llano, Manuel title: Chapter Seven Defining Pharmacological Targets by Analysis of Virus–Host Protein Interactions date: 2018-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Viruses are obligate parasites that depend on cellular factors for replication. Pharmacological inhibition of essential viral proteins, mostly enzymes, is an effective therapeutic alternative in the absence of effective vaccines. However, this strategy commonly encounters drug resistance mechanisms that allow these pathogens to evade control. Due to the dependency on host factors for viral replication, pharmacological disruption of the host-pathogen protein–protein interactions (PPIs) is an important therapeutic alternative to block viral replication. In this review we discuss salient aspects of PPIs implicated in viral replication and advances in the development of small molecules that inhibit viral replication through antagonism of these interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/29459033/ doi: 10.1016/bs.apcsb.2017.11.001 id: cord-323261-1of5ertf author: Lo, Catherine Yuk-ping title: Securitizing HIV/AIDS: a game changer in state-societal relations in China? date: 2018-05-16 words: 9433.0 sentences: 400.0 pages: flesch: 46.0 cache: ./cache/cord-323261-1of5ertf.txt txt: ./txt/cord-323261-1of5ertf.txt summary: Considering the low priority of health policies since the economic reform, the limitation of the "third sector" activity permitted in authoritarian China, together with the political sensitivity of the HIV/AIDS problem in the country, this article aims to explain the proliferation of HIV/AIDS-focused NGOs in China with the usage of the securitization framework in the field of international relations (IR). Based on the discourse analysis of the official documents and newspaper articles, it is argued that Chinese national leaders followed suit the international move (i.e. UNSC Resolution 1308) to securitize HIV/AIDS in the country, framing HIV/ AIDS as a threat with social, political, economic, and security implications. Along with the weakening of international securitization efforts and the rise of Chinese government''s involvement in managing NGOs in the post-Global Fund era, the continuous proliferation of NGOs is further complicated by the fragmented nature of HIV/AIDS-focused civil society groups in China. abstract: BACKGROUND: China has experienced unprecedented economic growth since the 1980s. Despite this impressive economic development, this growth exists side by side with the human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) and severe acute respiratory syndrome (SARS) crises and the persisting deficiencies in public health provision in China. Acknowledging the prevailing health problems, the Chinese government has encouraged the development of health non-governmental organizations (NGOs) to respond to the health challenges and address the gaps in public health provision of the government. HIV/AIDS-focused NGOs have been perceived as the most outstanding civil society group developed in China. Considering the low priority of health policies since the economic reform, the limitation of the “third sector” activity permitted in authoritarian China, together with the political sensitivity of the HIV/AIDS problem in the country, this article aims to explain the proliferation of HIV/AIDS-focused NGOs in China with the usage of the securitization framework in the field of international relations (IR). METHODS: The research that underpins this article is based on a desk-based literature review as well as in-depth field interviews with individuals working in HIV/AIDS-focused NGOs in China. Face-to-face interviews for this research were conducted between January and May in 2011, and between December 2016 and January 2017, in China. Discourse analysis was in particular employed in the study of the security-threat framing process (securitization) of HIV/AIDS in China. RESULTS: This article argues that the proliferation of HIV/AIDS-related NGOs in China is largely attributed to the normative and technical effects of HIV/AIDS securitization ushered in by the United Nations Security Council (UNSC) and supported by the Global Fund to Fight AIDS, Tuberculosis, and Malaria (hereinafter Global Fund) observed in China. Despite depicting a positive scenario, the development of HIV/AIDS-focused NGOs in China generated by the international securitization efforts is largely limited. An internal and external factor was identified to verify the argument, namely (1) the reduction of international financial commitments, as well as (2) the fragmentation of HIV/AIDS-focused NGO community in China. CONCLUSIONS: This article shows that international securitization weakened with the rise of Chinese commitment on HIV/AIDS interventions. In other words, HIV/AIDS-related responses delivered by the national government are no longer checked by the global mechanism of HIV/AIDS; thus it is unclear whether these NGOs would remain of interest as partners for the government. The fragmentation of the HIV/AIDS community would further hinder the development, preventing from NGOs with the same interest forming alliances to call for changes in current political environment. Such restriction on the concerted efforts of HIV/AIDS-related NGOs in China would make achievement of the Sustainable Development Goals (SDGs) to foster stronger partnerships between the government and civil society difficult, which in turn hindering the realization of ending HIV/AIDS in the world by 2030. url: https://www.ncbi.nlm.nih.gov/pubmed/29769102/ doi: 10.1186/s12992-018-0364-7 id: cord-341323-mw352rr1 author: Logie, Carmen H title: Lessons learned from HIV can inform our approach to COVID‐19 stigma date: 2020-05-04 words: 1560.0 sentences: 100.0 pages: flesch: 50.0 cache: ./cache/cord-341323-mw352rr1.txt txt: ./txt/cord-341323-mw352rr1.txt summary: We are moving away from siloed stigma research on individual health conditions (e.g. HIV, mental health), social identities (e.g. race, sexual orientation) and practices (e.g., sex work, drug use) [15] . Intersecting stigmasuch as racism and povertyinteract with HIV-related stigma to harm health engagement and outcomes [16, 17] and may present analogous barriers to COVID-19 testing and treatment [14] . There are complex associations between HIV-related stigma and age, whereby older persons living with HIV may experience reduced health effects of stigma [21, 22] . The contact approach involves people who have experienced the stigma being targeted (e.g. persons living with HIV, persons experiencing COVID-19 stigma) delivering the intervention to provide a face to the pandemic that in turn can foster empathy and reduce othering [26, 27] . Creating space for stories of COVID-19 that reveal stigma and solidarity, of front-line healthcare workers'' experiences, and of people living in quarantine, can reduce fear and spark empathy by helping us to see ourselves and our communities reflected in the pandemic [28] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32365283/ doi: 10.1002/jia2.25504 id: cord-017412-1avevzya author: Losada, Liliana title: The Human Lung Microbiome date: 2010-10-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The human lower respiratory tract is considered sterile in normal healthy individuals (Flanagan et al., 2007; Speert, 2006) despite the fact that every day we breathe in multiple microorganisms present in the air and aspirate thousands of organisms from the mouth and nasopharynx. This apparent sterility is maintained by numerous interrelated components of the lung physical structures such as the mucociliary elevator and components of the innate and adaptive immune systems (discussed below) (reviewed in (Diamond et al., 2000; Gerritsen, 2000)). However, it is possible that the observed sterility might be a result of the laboratory practices applied to study the flora of the lungs. Historically, researchers faced with a set of diseases characterized by a changing and largely cryptic lung microbiome have lacked tools to study lung ecology as a whole and have concentrated on familiar, cultivatable candidate pathogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121966/ doi: 10.1007/978-1-4419-7089-3_7 id: cord-253997-imwjoecx author: Lotter-Stark, Hester C.T. title: Plant made anti-HIV microbicides—A field of opportunity date: 2012-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract HIV remains a significant global burden and without an effective vaccine, it is crucial to develop microbicides to halt the initial transmission of the virus. Several microbicides have been researched with various levels of success. Amongst these, the broadly neutralising antibodies and peptide lectins are promising in that they can immediately act on the virus and have proven efficacious in in vitro and in vivo protection studies. For the purpose of development and access by the relevant population groups, it is crucial that these microbicides be produced at low cost. For the promising protein and peptide candidate molecules, it appears that current production systems are overburdened and expensive to establish and maintain. With recent developments in vector systems for protein expression coupled with downstream protein purification technologies, plants are rapidly gaining credibility as alternative production systems. Here we evaluate the advances made in host and vector system development for plant expression as well as the progress made in expressing HIV neutralising antibodies and peptide lectins using plant-based platforms. url: https://api.elsevier.com/content/article/pii/S0734975012001073 doi: 10.1016/j.biotechadv.2012.06.002 id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 words: 7555.0 sentences: 343.0 pages: flesch: 36.0 cache: ./cache/cord-307817-2vy28i4m.txt txt: ./txt/cord-307817-2vy28i4m.txt summary: The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. abstract: The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. Virus-targeting antivirals can function directly or indirectly to inhibit the biological functions of viral proteins, mostly enzymatic activities, or to block viral replication machinery. Host-targeting antivirals target the host proteins that are involved in the viral life cycle, regulating the function of the immune system or other cellular processes in host cells. Here we review key targets and considerations for the development of both antiviral strategies. url: https://www.sciencedirect.com/science/article/pii/S0165614713002265 doi: 10.1016/j.tips.2013.11.006 id: cord-327461-ohgkgvry author: Lu, Ying title: Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial date: 2020-06-12 words: 4420.0 sentences: 221.0 pages: flesch: 47.0 cache: ./cache/cord-327461-ohgkgvry.txt txt: ./txt/cord-327461-ohgkgvry.txt summary: title: Monetary incentives and peer referral in promoting digital network-based secondary distribution of HIV self-testing among men who have sex with men in China: study protocol for a three-arm randomized controlled trial Digital network-based secondary distribution is considered as an effective model to enhance HIV self-testing (HIVST) among key populations. We describe a three-arm randomized controlled trial to examine the effect of monetary incentives and peer referral in promoting digital network-based secondary distribution of HIVST among MSM in China. Our trial aims to enable more Chinese MSM to receive HIV self-testing, reach more first-time HIV testing alters, and identify more people with an HIV-positive (reactive) result by implementing the photo-verified HIV self-testing method under different scenarios, i.e., standard secondary distribution, secondary distribution with monetary incentives and secondary distribution with monetary incentives plus peer-referral links. Hypothesis 2: Compared with standard secondary distribution, secondary distribution with monetary incentives plus peer referral will promote index MSM to distribute more HIVST kits to people within their social network. abstract: BACKGROUND: Human immunodeficiency virus (HIV) testing is a crucial strategy for HIV prevention. HIV testing rates remain low among men who have sex with men (MSM) in China. Digital network-based secondary distribution is considered as an effective model to enhance HIV self-testing (HIVST) among key populations. Digital platforms provide opportunities for testers to apply for HIVST kits by themselves, and secondary distribution allows them to apply for multiple kits to deliver to their sexual partners or members within their social network. We describe a three-arm randomized controlled trial to examine the effect of monetary incentives and peer referral in promoting digital network-based secondary distribution of HIVST among MSM in China. METHODS: Three hundred MSM in China will be enrolled through a digital platform for data collection. The eligibility criteria include being biological male, 18 years of age or over, ever having had sex with another man, being able to apply for kits via the online platform, and being willing to provide personal telephone number for follow-up. Eligible participants will be randomly allocated into one of the three arms: standard secondary distribution arm, secondary distribution with monetary incentives arm, and secondary distribution with monetary incentives plus peer referral arm. Participants (defined as “index”) will distribute actual HIV self-test kits to members within their social network (defined as “alter”) or share referral links to encourage alters to apply HIV self-test kits by themselves. All index participants will be requested to complete a baseline survey and a 3-month follow-up survey. Both indexes and alters will complete a survey upon returning the results by taking a photo of the used kits with the unique identification number. DISCUSSION: HIV testing rates remain suboptimal among MSM in China. Innovative interventions are needed to further expand the uptake of HIV testing among key populations. The findings of the trial can provide scientific evidence and experience on promoting secondary distribution of HIVST to reach key populations who have not yet been covered by existing testing services. TRIAL REGISTRATION: The study was registered in the Chinese Clinical Trial Registry (ChiCTR1900025433) on 26, August 2019, http://www.chictr.org.cn/showproj.aspx?proj=42001. Prospectively registered. url: https://doi.org/10.1186/s12889-020-09048-y doi: 10.1186/s12889-020-09048-y id: cord-287337-2ljbsia2 author: Ludwig, Christine title: Virus-like particles—universal molecular toolboxes date: 2008-01-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Virus-like particles (VLPs) are highly organised spheres that self-assemble from virus-derived structural antigens. These stable and versatile subviral particles possess excellent adjuvant properties capable of inducing innate and cognate immune responses. Commercialised VLP-based vaccines have been successful in protecting humans from hepatitis B virus (HBV) and human papillomavirus (HPV) infection and are currently explored for their potential to combat other infectious diseases and cancer. Much insight into VLP-mediated immune stimulation and optimised VLP design has been gained from human immunodeficiency virus (HIV)-derived VLPs presenting promising components of current AIDS vaccine approaches. Owing to their unique features, VLPs and virosomes, the in vitro-reconstituted VLP counterparts, have recently gained ground in the field of nanobiotechnology as organic templates for the development of new biomaterials. url: https://api.elsevier.com/content/article/pii/S0958166907001462 doi: 10.1016/j.copbio.2007.10.013 id: cord-029416-738t6rk1 author: Mandal, Sandip title: The potential impact of preventive therapy against tuberculosis in the WHO South-East Asian Region: a modelling approach date: 2020-07-20 words: 5177.0 sentences: 255.0 pages: flesch: 43.0 cache: ./cache/cord-029416-738t6rk1.txt txt: ./txt/cord-029416-738t6rk1.txt summary: The 2018 World Health Organization (WHO) guidelines on eligibility for preventive therapy to treat latent TB infection (LTBI) include people living with human immunodeficiency virus (PLHIV), household contacts of TB patients including children, and those with clinical conditions including silicosis, dialysis, transplantation, etc. Relative to both scenarios, for each country in the region, we projected TB cases and deaths averted between 2020 and 2030, by full uptake of preventive therapy, defined as comprehensive coverage amongst eligible populations as per WHO guidelines, and assuming outcomes consistent with clinical trials. In the absence of a widely deployable test to identify who would benefit most from preventive therapy, World Health Organization (WHO) guidelines identify high-risk groups for eligibility: for example, those with human immunodeficiency virus (HIV) coinfection [10] and, in the most recently updated guidelines, all household contacts of diagnosed TB cases and those with clinical conditions including silicosis, those on anti-TNF treatment, and other country-specific groups [11] . abstract: BACKGROUND: The prevention of tuberculosis (TB) is key for accelerating current, slow declines in TB burden. The 2018 World Health Organization (WHO) guidelines on eligibility for preventive therapy to treat latent TB infection (LTBI) include people living with human immunodeficiency virus (PLHIV), household contacts of TB patients including children, and those with clinical conditions including silicosis, dialysis, transplantation, etc. and other country-specific groups. We aimed to estimate the potential impact of full implementation of these guidelines in the WHO South-East Asian (SEA) Region, which bears the largest burden of TB and LTBI amongst the WHO regions. METHODS: We developed mathematical models of TB transmission dynamics, calibrated individually to each of the 11 countries in the region. We modelled preventive therapy in the absence of other TB interventions. As an alternative comparator, reflecting ongoing developments in TB control in the region, we also simulated improvements in the treatment cascade for active TB, including private sector engagement and intensified case-finding. Relative to both scenarios, for each country in the region, we projected TB cases and deaths averted between 2020 and 2030, by full uptake of preventive therapy, defined as comprehensive coverage amongst eligible populations as per WHO guidelines, and assuming outcomes consistent with clinical trials. We also performed sensitivity analysis to illustrate impact under less-than-optimal conditions. RESULTS: At the regional level, full uptake of preventive therapy amongst identified risk groups would reduce annual incidence rates in 2030 by 8.30% (95% CrI 6.48–10.83) relative to 2015, in the absence of any additional interventions. If implemented against a backdrop of improved TB treatment cascades, preventive therapy would achieve an incremental 6.93 percentage points (95% CrI 5.81–8.51) of reduction in annual incidence rates, compared to 2015. At the regional level, the numbers of individuals with latent TB infection that need to be treated to avert 1 TB case is 64 (95% CrI 55–74). Sensitivity analysis illustrates that results for impact are roughly proportional to ‘effective coverage’ (the product of actual coverage and effectiveness of the regimen). CONCLUSIONS: Full implementation of WHO guidelines is important for ending TB in the SEA Region. Although future strategies will need to be expanded to the population level, to achieve large declines in TB incidence, the uptake of current tools can offer a valuable step in this direction. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7369473/ doi: 10.1186/s12916-020-01651-5 id: cord-314560-rswa5zdn author: Manjunath, N. title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 words: 5875.0 sentences: 352.0 pages: flesch: 48.0 cache: ./cache/cord-314560-rswa5zdn.txt txt: ./txt/cord-314560-rswa5zdn.txt summary: RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. However, in recent years, a new type of genomic immunity mediated by RNA interference (RNAi) has emerged and has sparked intense interest as a potential treatment strategy for a variety of diseases, including viral infections, cancer and degenerative diseases [1] [2] [3] [4] . In RNAi, long double-stranded (ds) RNA generated during viral infection is cleaved by an enzyme termed Dicer into short, 21-23 nucleotide (nt) dsRNA molecules termed small interfering (si)RNAs that mediate sequence-specific gene silencing [5, 6] . A landmark development in the field occurred with the discovery that the introduction of 21-nt-long synthetic RNA resembling the Dicer-processed siRNA into mammalian cells induces sequence-specific gene silencing without evoking the interferon response [10] . abstract: RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. Its potential to inhibit the replication of a variety of viruses has been demonstrated in vitro and in vivo in mouse and monkey models. These results have generated profound interest in the use of this technology as a potential treatment strategy for viral infections for which vaccines and drugs are unavailable or inadequate. In this review, we discuss the progress made within the past 2–3 years towards harnessing the potential of RNAi for clinical application in viral infections and the hurdles that have yet to be overcome. url: https://www.ncbi.nlm.nih.gov/pubmed/16753342/ doi: 10.1016/j.it.2006.05.006 id: cord-007237-8y7218oj author: Manning, Ashleigh title: Comparison of Tissue Distribution, Persistence, and Molecular Epidemiology of Parvovirus B19 and Novel Human Parvoviruses PARV4 and Human Bocavirus date: 2007-05-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background. PARV4 and human bocavirus (HBoV) are newly discovered human parvoviruses with poorly understood epidemiologies and disease associations. We investigated the frequencies of persistence, tissue distribution, and influence of immunosuppression on replication of these viruses. Methods. At autopsy, bone marrow, lymphoid tissue, and brain tissue from human immunodeficiency virus (HIV)—infected individuals with acquired immunodeficiency syndrome (AIDS) and those without AIDS and from HIV-uninfected individuals were screened for parvovirus B19, PARV4, and HBoV DNA by means of quantitative polymerase chain reaction analyses. Results. B19 DNA was detected both in HIV-infected study subjects (13 of 24) and in HIV-uninfected study subjects (8 of 8), whereas PARV4 DNA was detected only in HIV-infected study subjects (17 of 24). HBoV DNA was not detected in any study subjects. The degree of immunosuppression with HIV infection did not influence B19 or PARV4 viral loads. B19 or PARV4 plasma viremia was not detected in any study subjects (n = 76; viral load <25 DNA copies/mL). A significantly older age distribution was found for study subjects infected with B19 genotype 2, compared with those infected with B19 genotype 1. Two genotypes of PARV4 were detected; study subjects carrying prototype PARV4 (genotype 1) were younger (all born after 1958) than those infected with genotype 2 (PARV5; study subjects born between 1949 and 1956). Conclusions. Tight immune control of replication of B19 and PARV4 was retained despite profound immunosuppression. Recent genotype replacement of PARV4, combined with absent sequence diversity among genotype 1 sequences, suggests a recent, epidemic spread in the United Kingdom, potentially through transmission routes shared by HIV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109978/ doi: 10.1086/513280 id: cord-314753-xflhxb13 author: Manso, Carmen F. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 words: 6333.0 sentences: 296.0 pages: flesch: 48.0 cache: ./cache/cord-314753-xflhxb13.txt txt: ./txt/cord-314753-xflhxb13.txt summary: The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration. abstract: RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 10(4) and 10(3) IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/28646219/ doi: 10.1038/s41598-017-02239-5 id: cord-330465-16j5vm7h author: Marciniec, Krzysztof title: Phosphate Derivatives of 3-Carboxyacylbetulin: SynThesis, In Vitro Anti-HIV and Molecular Docking Study date: 2020-08-05 words: 6908.0 sentences: 396.0 pages: flesch: 48.0 cache: ./cache/cord-330465-16j5vm7h.txt txt: ./txt/cord-330465-16j5vm7h.txt summary: The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. In order to check the potential toxic properties of the compounds 3-5, docking study of phosphate betulin derivatives to cellular proteins was carried out. According to the results of docking (Table S1 ) obtained from AutoDock Vina, four potential SARS-CoV-2 inhibitors (BVM, betulinic acid, and compounds 4 and 6) were selected based on a lower negative dock energy value. abstract: Lupane-type pentacyclic triterpenes such as betulin and betulinic acid play an important role in the search for new therapies that would be effective in controlling viral infections. The aim of this study was the synthesis and evaluation of in vitro anti-HIV-1 activity for phosphate derivatives of 3-carboxyacylbetulin 3–5 as well as an in silico study of new compounds as potential ligands of the C-terminal domain of the HIV-1 capsid–spacer peptide 1 (CA-CTD-SP1) as a molecular target of HIV-1 maturation inhibitors. In vitro studies showed that 28-diethoxyphosphoryl-3-O-(3′,3′-dimethylsuccinyl)betulin (compound 3), the phosphate analog of bevirimat (betulinic acid derivative, HIV-1 maturation inhibitor), has IC(50) (half maximal inhibitory concentration) equal to 0.02 μM. Compound 3 inhibits viral replication at a level comparable to bevirimat and is also more selective (selectivity indices = 1250 and 967, respectively). Molecular docking was used to examine the probable interaction between the phosphate derivatives of 3-carboxyacylbetulin and C-terminal domain (CTD) of the HIV-1 capsid (CA)–spacer peptide 1 (SP1) fragment of Gag protein, designated as CTD-SP1. Compared with interactions between bevirimat (BVM) and the protein, an increased number of strong interactions between ligand 3 and the protein, generated by the phosphate group, were observed. These compounds might have the potential to also inhibit SARS-CoV2 proteins, in as far as the intrinsically imprecise docking scores suggest. url: https://www.ncbi.nlm.nih.gov/pubmed/32764519/ doi: 10.3390/biom10081148 id: cord-354972-nc496v6s author: Margolin, Emmanuel title: Prospects for SARS-CoV-2 diagnostics, therapeutics and vaccines in Africa date: 2020-09-10 words: 10919.0 sentences: 464.0 pages: flesch: 37.0 cache: ./cache/cord-354972-nc496v6s.txt txt: ./txt/cord-354972-nc496v6s.txt summary: As of 8 August 2020, there have been over 1.2 million confirmed cases of COVID-19 in Africa, with 29,833 deaths reported (Africa CDC) There is concern that the pandemic may pose an even greater risk to countries in Africa owing to their weak health-care infrastructure, large burden of co-infections, including HIV-1 and tuberculosis, and ongoing outbreaks of emerging and re-emerging infections such as Ebola virus (Democratic Republic of Congo) and Lassa haemorrhagic fever (Nigeria) that will divert much-needed resources away from the fight against COVID-19 (ref. Given the optimistic development timeline of 12-18 months before any vaccines could be available for widespread use, it is clear that these efforts will not Box 1 | Potential impact of climate on SArS-coV-2 dissemination the comparatively low incidence of coronavirus disease-2019 (COviD19) in africa has raised the possibility that climate could influence the spread of severe acute respiratory syndrome coronavirus 2 (sars-Cov-2). abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a global pandemic, prompting unprecedented efforts to contain the virus. Many developed countries have implemented widespread testing and have rapidly mobilized research programmes to develop vaccines and therapeutics. However, these approaches may be impractical in Africa, where the infrastructure for testing is poorly developed and owing to the limited manufacturing capacity to produce pharmaceuticals. Furthermore, a large burden of HIV-1 and tuberculosis in Africa could exacerbate the severity of infection and may affect vaccine immunogenicity. This Review discusses global efforts to develop diagnostics, therapeutics and vaccines, with these considerations in mind. We also highlight vaccine and diagnostic production platforms that are being developed in Africa and that could be translated into clinical development through appropriate partnerships for manufacture. url: https://www.ncbi.nlm.nih.gov/pubmed/32913297/ doi: 10.1038/s41579-020-00441-3 id: cord-326833-boxgt4kb author: Marimuthu, Janakiram title: HIV and SARS CoV‐2 co‐infection: A retrospective, record based, case series from South India date: 2020-07-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: HIV prevalence in India is about 0.22%, with the total number of people living with HIV/AIDS (PLHA) is estimated at 21.40 lakhs, constituting third largest epidemic in world. However, no study on HIV‐COVID‐19 co‐infection has been reported from India. We conducted a retrospective, record based case series including three males, 2 females and 1 transgender PLHA co‐infected with SARS CoV‐2 in the Indian state of Tamil Nadu. Fever (5), followed by cough (2) and sore throat (1), were the presenting symptoms. Latest Median CD4 count among our patients was 535 cells/ mm3. One of the patients was not under clinical HIV control, with an opportunistic infection Two among our patients were having hypertension. The mainstay of treatment given for the patients consisted of multi‐vitamins in addition to the ARV drugs, anti‐pyretics and anti‐tussives. One of the patient was on low dose Ritonavir boosted HAART regimen. All patients had stable vitals at room conditions, did not have any complications during their entire stay in health care facility for COVID‐19, treated and discharged. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32633846/ doi: 10.1002/jmv.26271 id: cord-330581-g5r2b043 author: Marini, Elena title: HIV‐1 matrix protein p17 binds to monocytes and selectively stimulates MCP‐1 secretion: role of transcriptional factor AP‐1 date: 2007-10-26 words: 8241.0 sentences: 419.0 pages: flesch: 52.0 cache: ./cache/cord-330581-g5r2b043.txt txt: ./txt/cord-330581-g5r2b043.txt summary: C. AP-1 protein family profiling for DNA-binding activity of an ELISA-based transcription factor assay kit using nuclear extracts (4 mg per sample) from human monocytes cultured for 1 h in the presence or absence of p17-and AP-1-specific oligonucleotides immobilized to a 96-well plate. Due to the large number of primary monocytes required for the analysis of transcription factor DNA-binding activity in protein nuclear extracts, we further investigated the involvement of AP-1 transcription factor in p17-induced MCP-1 transcriptional events using the monocytic cell line THP-1, which constitutively expresses p17Rs on its surface (data not shown). Among these, the HIV-1 matrix protein p17 has been recently identified as a critical determinant in AIDS pathogenesis as it binds to a cellular receptor expressed on immune cells and enhances viral replication and infectivity (De Francesco et al., 1998) , through a combination of different effector functions (De Francesco et al., 2002; Vitale et al., 2003) . abstract: HIV‐1 matrix protein p17 activates a variety of cell responses which play a critical role in viral replication and infection. Its activity depends on the expression of p17 receptors (p17R) on the surface of target cells. Whether p17 also plays a role in stimulating human monocytes, a major HIV‐1 reservoir, is not known. Here we show that human monocytes constitutively express p17Rs and that p17 selectively triggers these cells to produce MCP‐1. The effect of p17 on MCP‐1 expression was observed at the transcriptional level and was primarily dependent on the activation of the transcription factor AP‐1. p17 increased the binding activity of AP‐1 complexes in a time‐ and dose‐dependent manner. Deletion of the AP‐1 binding sites in the MCP‐1 promoter resulted in the lack of p17‐induced MCP‐1 transcription. In particular, the P3 binding site located between −69 and −63 position seems to be essential to MCP‐1 mRNA induction in p17‐treated monocytes. An ever increasing amount of evidences shows a tight link between biologically dysregulated monocytes, AP‐1 activation, MCP‐1 release and HIV‐1 pathogenesis. Overall our results suggest that p17 may play a critical role in the monocyte‐mediated inflammatory processes, which are suspected to be major precipitating events in AIDS‐defining diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/18042260/ doi: 10.1111/j.1462-5822.2007.01073.x id: cord-337458-dc90ecfe author: Markwalter, Christine F. title: Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date: 2018-12-04 words: 40568.0 sentences: 2391.0 pages: flesch: 40.0 cache: ./cache/cord-337458-dc90ecfe.txt txt: ./txt/cord-337458-dc90ecfe.txt summary: In this review, we define the components of a diagnostic to include: (1) the target biomarker, an endogenous indicator of a disease state, which is most often a pathogen or host protein, carbohydrate, or nucleic acid sequence, (2) sample preparation, which allows for biomarker isolation, purification, and/or concentration from complex biological matrices, (3) molecular recognition elements, which specifically capture and detect the target biomarker, (4) signal generation and amplification, and (5) instrumentation for signal read-out. 113, 114 In subsequent studies, the group developed and optimized a hand-held, easy-to-use device 85, 115 (Figure 8A ) in which HRP2-bound, IMAC-functionalized magnetic beads were directly transferred to the sample pad of commercial malaria lateral flow assays. If combined with one of the sample preparation strategies discussed previously (section 3) or integrated with paper or another field-ready substrate, this Ir(III)-based detection strategy could produce a robust and sensitive assay that is applicable in low-resource diagnostic settings. abstract: [Image: see text] Infectious diseases claim millions of lives each year. Robust and accurate diagnostics are essential tools for identifying those who are at risk and in need of treatment in low-resource settings. Inorganic complexes and metal-based nanomaterials continue to drive the development of diagnostic platforms and strategies that enable infectious disease detection in low-resource settings. In this review, we highlight works from the past 20 years in which inorganic chemistry and nanotechnology were implemented in each of the core components that make up a diagnostic test. First, we present how inorganic biomarkers and their properties are leveraged for infectious disease detection. In the following section, we detail metal-based technologies that have been employed for sample preparation and biomarker isolation from sample matrices. We then describe how inorganic- and nanomaterial-based probes have been utilized in point-of-care diagnostics for signal generation. The following section discusses instrumentation for signal readout in resource-limited settings. Next, we highlight the detection of nucleic acids at the point of care as an emerging application of inorganic chemistry. Lastly, we consider the challenges that remain for translation of the aforementioned diagnostic platforms to low-resource settings. url: https://doi.org/10.1021/acs.chemrev.8b00136 doi: 10.1021/acs.chemrev.8b00136 id: cord-257272-4q52p1pd author: Marsh, Mark title: Roles for endocytosis in lentiviral replication date: 1997-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Endocytosis is essential for the entry of many viruses into cells. The primate lentiviruses [human immunodeficiency virus (HIV) 1 and 2, and the simian immunodeficiency viruses (SIVs)], however, use endocytosis in other aspects of their life cycles. Here, the authors describe the ways in which the endocytic pathway is used by HIV and SIV and discuss the mechanisms through which endocytosis may contribute to the pathogenic properties of these viruses. url: https://www.sciencedirect.com/science/article/pii/S0962892497200383 doi: 10.1016/s0962-8924(97)20038-3 id: cord-295062-8rl4kswe author: Marsh, Mark title: Virus Entry: Open Sesame date: 2006-02-24 words: 8504.0 sentences: 401.0 pages: flesch: 42.0 cache: ./cache/cord-295062-8rl4kswe.txt txt: ./txt/cord-295062-8rl4kswe.txt summary: Virus Particles as Devices for Targeted Gene Transfer A viral particle is composed of nucleic acids (RNA or DNA), protein, and, in the case of enveloped viruses, membrane lipids. Viruses use signaling activities to induce changes in the cell that promote viral entry and early cytoplasmic events, as well as to optimize later processes in the replication cycle. Like cholera toxin, these viruses bind to the sugar moiety of gangliosides and enter cells via caveolar/raft pathways that are dependent on cholesterol ( Figures 2D and 2E ) and the activation of tyrosine-kinase signaling cascades (Anderson et al., 1996; Pelkmans et al., 2001; Smith et al., 2003a; Stang et al., 1997; Tsai et al., 2003) . Nevertheless, in the majority of cases, the transfer of viral genomes from cell to cell appears to occur through the formation of virus particles that are released from infected cells and use the mechanisms described above to enter new uninfected hosts. abstract: Detailed information about the replication cycle of viruses and their interactions with host organisms is required to develop strategies to stop them. Cell biology studies, live-cell imaging, and systems biology have started to illuminate the multiple and subtly different pathways that animal viruses use to enter host cells. These insights are revolutionizing our understanding of endocytosis and the movement of vesicles within cells. In addition, such insights reveal new targets for attacking viruses before they can usurp the host-cell machinery for replication. url: https://www.sciencedirect.com/science/article/pii/S0092867406001826 doi: 10.1016/j.cell.2006.02.007 id: cord-287348-00yaxpkp author: Martinez, Maria Jose Abad title: Antiviral Activities of Polysaccharides from Natural Sources date: 2005-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The ever increasing resistance of human pathogens to current anti-infective agents is a serious medical problem, leading to the need to develop novel antibiotic prototype molecules. In the case of viruses, the search for antiviral agents involves additional difficulties, particularly due to the nature of the infectious viral agents. Thus, many compounds that may cause the death of viruses are also very likely to injure the host cell that harbours them. Natural products are increasingly appreciated as leads for drug discovery and development. Screening studies have been carried out in order to find antiviral agents from natural sources, and the occurrence of antiviral activity in extracts of plants, marine organisms and fungi is frequent. The evidence indicates that there may be numerous potentially useful antiviral phytochemicals in nature, waiting to be evaluated and exploited. In addition, other plants, not previously utilized medicinally, may also reveal antivirals. Among natural antiviral agents, recent investigations have reconsidered the interest of phyto-polysaccharides, which act as potent inhibitors of different viruses. This chapter will illustrate a variety of antiviral polysaccharides from natural sources since 1990, with the aim of making this matter more accessible to drug development url: https://www.sciencedirect.com/science/article/pii/S1572599505800389 doi: 10.1016/s1572-5995(05)80038-9 id: cord-347992-coby2m6e author: Marton, Soledad title: In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules date: 2010-06-28 words: 10035.0 sentences: 535.0 pages: flesch: 45.0 cache: ./cache/cord-347992-coby2m6e.txt txt: ./txt/cord-347992-coby2m6e.txt summary: Although ribozymes and DNAzymes have been extensively assayed as potential therapeutic agents, and different clinical trials have already tested their efficiency against various diseases [49] [50] [51] [52] , very few reports have described the direct application of in vitro selection strategies in the development of potentially therapeutic catalytic nucleic acids. Molecular studies have shown that this aptamer binds to the cell surface protein nucleolin and inhibits the activity of NF-KB, a ubiquitous transcription factor, through intracellular complex formation [108] . In a different approach, SELEX has been performed with the E2F1 protein to find in vitro selected RNA aptamers that bind to and inhibit E2F activity. Astier-Gi''s group described the characterization of two DNA aptamers (27v and 127v) that specifically bind to hepatitis C virus (HCV) RNA polymerase (NS5B), inhibiting its activity in vitro [146] . In vitro selection procedures for identifying DNA and RNA aptamers targeted to nucleic acids and proteins abstract: It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids. url: https://www.ncbi.nlm.nih.gov/pubmed/20657381/ doi: 10.3390/molecules15074610 id: cord-263157-8jin6oru author: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Therapeutic options against the human immunodeficiency virus type 1 (HIV-1) continue to expand with the development of new drugs and new therapeutic strategies. Nevertheless, management of HIV-1 infected individuals has become increasingly complex. The emergence of drug-resistant variants, the growing recognition of the long-term toxicity of antiretroviral therapies and the persistence of viral reservoirs justify the continued efforts to develop new anti-HIV-1 strategies. Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Here, the recent advances in siRNA-based therapies are reviewed. url: https://www.ncbi.nlm.nih.gov/pubmed/19301656/ doi: 10.1007/978-1-60327-547-7_17 id: cord-319263-g49jma8n author: Marziali, Megan E. title: Physical Distancing in COVID-19 May Exacerbate Experiences of Social Isolation among People Living with HIV date: 2020-04-23 words: 1289.0 sentences: 75.0 pages: flesch: 48.0 cache: ./cache/cord-319263-g49jma8n.txt txt: ./txt/cord-319263-g49jma8n.txt summary: title: Physical Distancing in COVID-19 May Exacerbate Experiences of Social Isolation among People Living with HIV We have discussed that people living with HIV (PLHIV) are at greater risk of experiencing social isolation [13] . Therefore, due to the various shelter-in-place and physical distancing measures, it is likely that this disease is resulting in more social isolation, and in greater severity, than previously experienced among PLHIV. Among participants with poor self-rated physical health, of whom 42% are living with HIV, 87% experienced loneliness. This study provides further support for the notion that social isolation and loneliness can have a tangible impact on the health of an individual. Therefore, it is necessary to also focus on evaluating mental health of PLHIV, during and after the COVID-19 control measures, to better understand and address loneliness in this population. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32328849/ doi: 10.1007/s10461-020-02872-8 id: cord-023669-3ataw6gy author: Masur, Henry title: Critically Ill Immunosuppressed Host date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173421/ doi: 10.1016/b978-032304841-5.50056-x id: cord-339341-c2o42b5j author: Matibag, Gino C. title: Advocacy, promotion and e-learning: Supercourse for zoonosis date: 2005-09-01 words: 5855.0 sentences: 317.0 pages: flesch: 44.0 cache: ./cache/cord-339341-c2o42b5j.txt txt: ./txt/cord-339341-c2o42b5j.txt summary: This paper discusses the history of emerging infectious diseases, risk communication and perception, and the Supercourse lectures as means to strengthen the concepts and definition of risk management and global governance of zoonosis. The overall goal of the "Supercourse for Zoonosis" is to show the most recent development in the knowledge of SARS and other zoonotic diseases such as avian influenza and bovine spongiform encephalopathy (BSE), inter alia, which have significant global impact not only on health but also on the economy. The specific objectives of "Supercourse for Zoonosis" are to develop a set of educational materials for the control of zoonotic diseases, to disseminate them effectively via the Internet, to facilitate their use in the prevention and control of the diseases, and to promote human health while minimizing their economic impact. abstract: This paper discusses the history of emerging infectious diseases, risk communication and perception, and the Supercourse lectures as means to strengthen the concepts and definition of risk management and global governance of zoonosis. The paper begins by outlining some of the key themes and issues in infectious diseases, highlighting the way which historical analysis challenges ideas of the ‘newness’ of some of these developments. It then discusses the role of risk communication to public accountability. The bulk of the paper presents an overview of developments of the Internet-based learning system through the Supercourse lectures that may prove to be a strong arm for the promotion of the latest medical information particularly to developing countries. url: https://doi.org/10.1007/bf02897702 doi: 10.1007/bf02897702 id: cord-268776-yfq9oky5 author: Mattson, Mark P. title: Infectious agents and age-related neurodegenerative disorders date: 2003-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: As with other organ systems, the vulnerability of the nervous system to infectious agents increases with aging. Several different infectious agents can cause neurodegenerative conditions, with prominent examples being human immunodeficiency virus (HIV-1) dementia and prion disorders. Such infections of the central nervous system (CNS) typically have a relatively long incubation period and a chronic progressive course, and are therefore increasing in frequency as more people live longer. Infectious agents may enter the central nervous system in infected migratory macrophages, by transcytosis across blood–brain barrier cells or by intraneuronal transfer from peripheral nerves. Synapses and lipid rafts are important sites at which infectious agents may enter neurons and/or exert their cytotoxic effects. Recent findings suggest the possibility that infectious agents may increase the risk of common age-related neurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS) and stroke. While scenarios can be envisioned whereby viruses such as Chlamydia pneumoniae, herpes simplex and influenza promote damage to neurons during aging, there is no conclusive evidence for a major role of these pathogens in neurodegenerative disorders. In the case of stroke, blood vessels may be adversely affected by bacteria or viruses resulting in atherosclerosis. url: https://www.sciencedirect.com/science/article/pii/S1568163703000394 doi: 10.1016/j.arr.2003.08.005 id: cord-341097-c96hm610 author: Mayer, Craig S. title: Analysis of data dictionary formats of HIV clinical trials date: 2020-10-05 words: 6899.0 sentences: 366.0 pages: flesch: 57.0 cache: ./cache/cord-341097-c96hm610.txt txt: ./txt/cord-341097-c96hm610.txt summary: To facilitate aggregation across studies, we defined three types of data dictionary (data element, forms, and permissible values) and created a simple information model for each type. The presented study is limited to data dictionary analysis, although the motivation is to later analyze a large body of past HIV data elements to inform data-driven consensus on CDEs. This study is part of a larger research project titled ''Identification of Research Common Data Elements in HIV/AIDS using data science methods'' [12] . We use the term Forms Data Dictionary (or forms dictionary in shorter form) to refer to a data dictionary that provides a full list of titles and descriptions of all Case Report Forms (CRFs) used in the study (or other relevant metadata for data element grouping). Use of categorical data elements in research is extremely common and, as stated earlier, most studies would be expected to provide a permissible value dictionary. abstract: BACKGROUND: Efforts to define research Common Data Elements try to harmonize data collection across clinical studies. OBJECTIVE: Our goal was to analyze the quality and usability of data dictionaries of HIV studies. METHODS: For the clinical domain of HIV, we searched data sharing platforms and acquired a set of 18 HIV related studies from which we analyzed 26 328 data elements. We identified existing standards for creating a data dictionary and reviewed their use. To facilitate aggregation across studies, we defined three types of data dictionary (data element, forms, and permissible values) and created a simple information model for each type. RESULTS: An average study had 427 data elements (ranging from 46 elements to 9 945 elements). In terms of data type, 48.6% of data elements were string, 47.8% were numeric, 3.0% were date and 0.6% were date-time. No study in our sample explicitly declared a data element as a categorical variable and rather considered them either strings or numeric. Only for 61% of studies were we able to obtain permissible values. The majority of studies used CSV files to share a data dictionary while 22% of the studies used a non-computable, PDF format. All studies grouped their data elements. The average number of groups or forms per study was 24 (ranging between 2 and 124 groups/forms). An accurate and well formatted data dictionary facilitates error-free secondary analysis and can help with data de-identification. CONCLUSION: We saw features of data dictionaries that made them difficult to use and understand. This included multiple data dictionary files or non-machine-readable documents, data elements included in data but not in the dictionary or missing data types or descriptions. Building on experience with aggregating data elements across a large set of studies, we created a set of recommendations (called CONSIDER statement) that can guide optimal data sharing of future studies. url: https://doi.org/10.1371/journal.pone.0240047 doi: 10.1371/journal.pone.0240047 id: cord-332610-t99l3zii author: Mayer, J.D. title: Emerging Diseases: Overview date: 2008-08-26 words: 9596.0 sentences: 469.0 pages: flesch: 52.0 cache: ./cache/cord-332610-t99l3zii.txt txt: ./txt/cord-332610-t99l3zii.txt summary: The potential for new diseases to emerge in the United States was there, and it took just a few years until this happened, catching the medical and public health communities by surprise. The issue at the time was whether legionnaires disease and toxic shock syndrome were anomalies, whether the assumption of the conquest of infectious diseases had clearly been erroneous, or whether these two outbreaks were harbingers of a new stage in ''epidemiologic history''a historical period during which emerging infections would become common and would catch the attention of the public, the public health community, the medical community, and government agencies. Severe acute respiratory syndrome (SARS) proved to be of great import in both the public awareness of emerging infectious diseases and in the testing and real-time construction of both domestic and international systems of public health surveillance and response. abstract: Emerging infectious diseases are diseases that are either new, are newly recognized, or are increasing in prevalence in new areas. Resurgent diseases are also usually grouped in this category, as is antimicrobial resistance. These diseases have been given formal recognition in the past two decades, although a historical outlook demonstrates that the phenomenon has probably been persistent, although largely undetected, through recorded history. Emergence has accelerated recently, driven by factors such as demographic change, land use change, increased rapidity and frequency of intercontinental transportation, and other mostly social trends. Continued infectious disease emergence poses, and will continue to pose, significant challenges for public health and for basic science. url: https://api.elsevier.com/content/article/pii/B9780123739605004536 doi: 10.1016/b978-012373960-5.00453-6 id: cord-017885-cz19y60u author: Maziarz, Eileen K. title: Cryptococcosis date: 2014-11-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Cryptococcosis is an infectious disease caused by the encapsulated fungi Cryptococcus neoformans and Cryptococcus gattii. Once a relatively uncommon cause of human disease, cryptococcal infection can develop in apparently immunocompetent hosts and has emerged as an important opportunistic infection in humans over the past several decades as immunocompromised populations expand in the setting of HIV/AIDS, organ transplantation, malignancies, and treatment for other conditions. Clinical manifestations are myriad but pulmonary and central nervous system (CNS) infections are the most common. Improvements in diagnostic testing and standardized approaches to antifungal therapy, when available, have made considerable impact in the management of this infection. While the widespread use of highly active antiretroviral therapy (HAART) has improved the outcome of cryptococcosis in many HIV-infected patients, cryptococcosis remains an entity of considerable morbidity and mortality in many parts of the world, and restoration of host immunity can present management challenges that require individualized management. As immunocompromised populations continue to expand, it is likely that cryptococcosis will remain an important opportunistic fungal infection of humans requiring ongoing investigation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122569/ doi: 10.1007/978-3-319-13090-3_15 id: cord-267182-ctvnmjsl author: Mboowa, Gerald title: Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies date: 2018-03-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers. url: https://www.ncbi.nlm.nih.gov/pubmed/29755620/ doi: 10.1155/2018/1875217 id: cord-313729-mydyc68y author: McDiarmid, Melissa A. title: Hazards of the Health Care Sector: Looking Beyond Infectious Disease date: 2014-11-25 words: 2949.0 sentences: 156.0 pages: flesch: 47.0 cache: ./cache/cord-313729-mydyc68y.txt txt: ./txt/cord-313729-mydyc68y.txt summary: BACKGROUND: Possessing every hazard class, the health care sector poses significant health threats to its workforce in both high-resource settings and lowand middle-income countries (LMICs). 5 Although preventing exposure to infectious agents and musculoskeletal injuries resulting from patient lifting have been the primary focus of employee safety programs, the chemical hazards in health care have been more slowly recognized. 10 Bloodborne pathogens, which include viruses capable of causing hepatitis or HIV infections continue to threaten health workers in both high-resource areas and in LMICs. 17 In developing countries, 40% to 65% of hepatitis B (HBV) and C virus (HCV) infections in health care workers were attributed to percutaneous occupational exposure. 29 The basic occupational health approach to minimizing exposure to any workplace hazard uses a combination of protective industrial hygiene control methods that are applied in a specified order or hierarchy. abstract: BACKGROUND: Possessing every hazard class, the health care sector poses significant health threats to its workforce in both high-resource settings and low- and middle-income countries (LMICs). OBJECTIVES: The aim of this paper was to examine the applicability of the classical hierarchy of hazard control technologies in resource-constrained health care settings. METHODS: Using a biologic and chemical hazard example, the hazard control hierarchy was applied for risk mitigation. FINDINGS: Even when resource constraints force a reordered selection of hazard control elements, risk reduction can be achieved across a variety of hazard classes. CONCLUSION: For LMICs with limited resources, the hazard control hierarchy can be effectively employed, although the selection of methods may be reordered, to achieve significant hazard control. Such prevention strategies can thereby strengthen and sustain a critical pillar of the health system, its workforce. url: https://doi.org/10.1016/j.aogh.2014.08.001 doi: 10.1016/j.aogh.2014.08.001 id: cord-304748-ddwawfv2 author: Mendelsohn, Andrea S. title: COVID-19 and Antiretroviral Therapies: South Africa’s Charge Towards 90–90–90 in the Midst of a Second Pandemic date: 2020-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32356032/ doi: 10.1007/s10461-020-02898-y id: cord-340619-3tjquzx8 author: Menghua, Wu title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count date: 2020-07-23 words: 1601.0 sentences: 119.0 pages: flesch: 63.0 cache: ./cache/cord-340619-3tjquzx8.txt txt: ./txt/cord-340619-3tjquzx8.txt summary: title: Case report: one case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a normal CD4(+) T cell count Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. Here we reported a case of HIV and SARS-CoV-2 coinfection who had a prolonged viral shedding duration about 28 days. [11] reported a patient with kidney transplantation who had a prolonged viral shedding duration for 63 days. This is the first report of a patient co-infected with HIV and SARS-CoV-2 who showed a prolonged viral shedding duration. The lymphocyte count of our case was also less than 2.0 × 10 9 /L, which might be a co-factor for the prolonged viral shedding duration. Viral shedding prolongation in a kidney transplant patient with COVID-19 pneumonia abstract: BACKGROUND: The COVID-19 has been a severe pandemic all around the world. Nowadays the patient with co-infection of HIV and SARS-CoV-2 was rarely reported. Here we reported a special case with HIV and SARS-CoV-2 co-infection, which showed a prolonged viral shedding duration. CASE PRESENTATION: The patient was infected with HIV 8 years ago through sexual transmission and had the normal CD4(+)T cell count. She was found SARS-CoV-2 positive using real-time Polymerase Chain Reaction (RT-PCR) during the epidemic. Most importantly, the patient had a prolonged viral shedding duration of SARS-CoV-2 about 28 days. CONCLUSION: The viral shedding duration may be prolonged in people living with HIV. The 14 days isolation strategy might not be long enough for them. The isolation or discharge of these patients needs further confirmation for preventing epidemics. url: https://doi.org/10.1186/s12981-020-00301-3 doi: 10.1186/s12981-020-00301-3 id: cord-314331-7k0oym5i author: Menza, Timothy W. title: Rapid Uptake of Home-Based HIV Self-testing During Social Distancing for SARS-CoV2 Infection in Oregon date: 2020-06-27 words: 2378.0 sentences: 112.0 pages: flesch: 57.0 cache: ./cache/cord-314331-7k0oym5i.txt txt: ./txt/cord-314331-7k0oym5i.txt summary: We implemented a pilot home HIV self-testing program one week after a stay-home order for SARS-CoV2 was enacted in Oregon. In addition, 77% of MSM who use apps wanted social or sexual networking apps to add a feature that would allow them to order an HIV home test from the app. We implemented a pilot home-based HIV testing program to increase access to HIV testing separate from the SARS-CoV2 pandemic; however, its launch coincided with rising SARS-CoV2 cases and the stay-home order in Oregon. One-third of program participants had never tested before, a proportion greater than that found in a prior survey of MSM who use apps and in a trial of home HIV self-testing [9, 10] . Based on the feedback provided by participants, home self-testing appears to ameliorate several barriers to accessing an HIV test. Finally, home HIV testing allowed participants to test without risking exposure to SARS-CoV2 infection in a healthcare setting. abstract: We implemented a pilot home HIV self-testing program one week after a stay-home order for SARS-CoV2 was enacted in Oregon. We advertised the program on a geospatial networking app and community partner websites targeting men who have sex with men; nine percent of web visits resulted in an order. Over 70% of the kits initially allotted to the program were ordered in the first 24 h of launch. One-third of participants had never tested for HIV. We found enthusiasm for discreet, free, home-based testing and uncovered an unmet need for HIV testing as clinical and outreach programs shuttered in Oregon. url: https://www.ncbi.nlm.nih.gov/pubmed/32594272/ doi: 10.1007/s10461-020-02959-2 id: cord-023884-etkhrgxp author: Meremikwu, Martin title: Malaria in Women and Children date: 2009-05-18 words: 8513.0 sentences: 412.0 pages: flesch: 46.0 cache: ./cache/cord-023884-etkhrgxp.txt txt: ./txt/cord-023884-etkhrgxp.txt summary: falciparum infections (often in persons who have no immunity to malaria or whose immunity has decreased) are complicated by serious organ failures or abnormalities in the patient''s blood or metabolism, resulting in cerebral malaria, with abnormal behavior, impairment of consciousness, seizures, coma, or other neurologic abnormalities, severe anemia due to hemolysis (destruction of the red blood cells), hemoglobinuria (hemoglobin in the urine) due to hemolysis, pulmonary edema (fluid buildup in the lungs) or acute respiratory distress syndrome (ARDS), which may occur even after the parasite counts have decreased in response to treatment, abnormalities in blood coagulation and thrombocytopenia (decrease in blood platelets), cardiovascular collapse, shock, acute kidney failure, hyperparasitemia, where more than 5% of the red blood cells are infected by malaria parasites, metabolic acidosis (excessive acidity in the blood and tissue fluids), often in association with hypoglycemia (low blood glucose). A review of studies in areas of sub-Saharan Africa with high and stable malaria transmission shows that HIV-1 infection and clinically diagnosed AIDS increased the incidence of malaria 1.2-fold and 2fold, respectively (Korenromp et al. Achieving high coverage of insecticide-treated bed nets (ITNs) use and prompt access to treatment with artemisininbased combination treatments (ACTs) would contribute to the reduction in the morbidity and Source: WHO-AFRO (2004) mortality attributable to HIV co-infection with malaria in high transmission areas. abstract: After reading this chapter and answering the discussion questions that follow, you should be able to: Explain the global burden of malaria, discuss its clinical manifestations, and appraise its health impact on women and children. Analyze the mechanisms and consequences of malaria and HIV co-infection and discuss current treatment, control and prevention strategies. Describe the challenges posed by vector resistance to insecticides, parasite resistance to antimalarials, climate change, wars/conflicts, and HIV/AIDS to malaria control and prevention efforts. Evaluate social, cultural, and economic limitations of community-based programs for malaria control and prevention. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176232/ doi: 10.1007/b106524_12 id: cord-337315-qv8ycdhe author: Miller, Maureen title: Integrated biological–behavioural surveillance in pandemic-threat warning systems date: 2017-01-01 words: 4629.0 sentences: 267.0 pages: flesch: 40.0 cache: ./cache/cord-337315-qv8ycdhe.txt txt: ./txt/cord-337315-qv8ycdhe.txt summary: 13 Similar surveillance could help identify behavioural risk factors and high-risk subgroups for zoonotic infections such as Ebola -potentially before diseases of pandemic potential are identified in clinical settings or major outbreaks occur in communities. When designed according to Strengthening the Reporting of Observational Studies in Epidemiology criteria, integrated surveillance requires that both behavioural risk factors -i.e. exposure variables -and disease-indicator outcome variables be measured in behavioural surveys. 22 In the development of pandemic-threat warning systems, integrated biological-behavioural surveillance can be tightly focused on specific viral families in the high-risk population subgroups that live in identified hotspots and are environmentally or occupationally exposed to animals. The remainder of this article presents an overview of issues relevant to the design of rigorous behavioural surveys to assess the spillover of emerging zoonotic disease and the associated transmission risk factors, which is the first step in designing effective integrated surveillance. abstract: Economically and politically disruptive disease outbreaks are a hallmark of the 21st century. Although pandemics are driven by human behaviours, current surveillance systems for identifying pandemic threats are largely reliant on the monitoring of disease outcomes in clinical settings. Standardized integrated biological–behavioural surveillance could, and should, be used in community settings to complement such clinical monitoring. The usefulness of such an approach has already been demonstrated in studies on human immunodeficiency virus, where integrated surveillance contributed to a biologically based and quantifiable understanding of the behavioural risk factors associated with the transmission dynamics of the virus. When designed according to Strengthening the Reporting of Observational Studies in Epidemiology criteria, integrated surveillance requires that both behavioural risk factors – i.e. exposure variables – and disease-indicator outcome variables be measured in behavioural surveys. In the field of pandemic threats, biological outcome data could address the weaknesses of self-reported data collected in behavioural surveys. Data from serosurveys of viruses with pandemic potential, collected under non-outbreak conditions, indicate that serosurveillance could be used to predict future outbreaks. When conducted together, behavioural surveys and serosurveys could warn of future pandemics, potentially before the disease appears in clinical settings. Traditional disease-outcome surveillance must be frequent and ongoing to remain useful but behavioural surveillance remains informative even if conducted much less often, since behaviour change occurs slowly over time. Only through knowledge of specific behavioural risk factors can interventions and policies that can prevent the next pandemic be developed. url: https://doi.org/10.2471/blt.16.175984 doi: 10.2471/blt.16.175984 id: cord-302403-kahi8cbc author: Miller, Robert F. title: Pulmonary Infections date: 2009-05-15 words: 18163.0 sentences: 918.0 pages: flesch: 43.0 cache: ./cache/cord-302403-kahi8cbc.txt txt: ./txt/cord-302403-kahi8cbc.txt summary: Before HAART, defined as a combination of medications that usually includes at least three potent anti-HIV agents, treatment largely consisted of specific opportunistic infection management and less effective antiretroviral therapy. In many parts of the world, the main causes of death in patients with HIV infection include bacterial pneumonia, tuberculosis, and PCP. Recent work has shown chronic obstructive pulmonary disease (COPD) and lung cancer occur more frequently among HIV-infected individuals compared with the general population. In addition to pulmonary tuberculosis, extrapulmonary disease occurs in a high proportion of HIV-infected individuals with low CD4 lymphocyte counts (<150 cells/mL). Hence, some centers advocate use of empirical therapy for HIV-infected patients who are seen with symptoms and chest radiographic and blood gas abnormalities typical of mild PCP, without the need for bronchoscopy. On the basis of current evidence, patients with CD4 counts >200 cells/mL have a low risk of HIV disease progression or death during 6 months of treatment for tuberculosis. abstract: nan url: https://api.elsevier.com/content/article/pii/B9780323048255100340 doi: 10.1016/b978-032304825-5.10034-0 id: cord-022521-r72jtoso author: Miller, Tracie L. title: Gastrointestinal Complications of Secondary Immunodeficiency Syndromes date: 2010-12-27 words: 13694.0 sentences: 812.0 pages: flesch: 36.0 cache: ./cache/cord-022521-r72jtoso.txt txt: ./txt/cord-022521-r72jtoso.txt summary: However, in the United States and other developed countries, severe malnutrition and new cases of perinatal HIV-1 disease are rare because of relatively high standards of living and effective highly active antiretroviral therapies (HAART) given to pregnant HIV-infected women that prevent transmission of HIV to the infants. Examination of both acute simian immunodeficiency virus (SIV) and HIV infection have documented reduced CD4 cell levels in GALT prior to a detectable reduction in T cells of the peripheral blood, highlighting the gastrointestinal tract''s role and susceptibility. Previous studies have shown that activated mucosal T cells play a role in the pathogenesis of enteropathy in the human small intestine 37 and can affect the morphology of the villi and crypts in a manner similar to that seen in patients with HIV-1 infection. Immune restoration disease after the treatment of immunodeficient HIV-infected patients with highly active antiretroviral therapy abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158192/ doi: 10.1016/b978-1-4377-0774-8.10042-9 id: cord-326744-eled2tgo author: Millett, Gregorio A. title: White Counties Stand Apart: The Primacy of Residential Segregation in COVID-19 and HIV Diagnoses date: 2020-10-01 words: 3228.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-326744-eled2tgo.txt txt: ./txt/cord-326744-eled2tgo.txt summary: 28 Attributing racial disparities to underlying conditions implicitly blames communities of color for COVID-19 disparities due to poor health decisions; but there is ample literature showing how social determinants contribute to worse health outcomes in communities of color, 29 including well-cited HIV research studies of youth, gay men, and PWID, which show that HIV disparities persist in black communities despite similar or fewer behavioral risks than whites. A CDC demonstration project that scaled up HIV testing efforts in black and Latino communities in the District of Columbia dramatically reduced the proportion of concurrent AIDS diagnoses at first positive test; 46 and encouraging data from a recent study 35 show shifts in COVID-19 testing from wealthier and white neighborhoods to poorer and more diverse neighborhoods in cities initially hit by the COVID-19 pandemic. abstract: Emerging epidemiological data suggest that white Americans have a lower risk of acquiring COVID-19. Although many studies have pointed to the role of systemic racism in COVID-19 racial/ethnic disparities, few studies have examined the contribution of racial segregation. Residential segregation is associated with differing health outcomes by race/ethnicity for various diseases, including HIV. This commentary documents differing HIV and COVID-19 outcomes and service delivery by race/ethnicity and the crucial role of racial segregation. Using publicly available Census data, we divide US counties into quintiles by percentage of non-Hispanic white residents and examine HIV diagnoses and COVID-19 per 100,000 population. HIV diagnoses decrease as the proportion of white residents increase across US counties. COVID-19 diagnoses follow a similar pattern: Counties with the highest proportion of white residents have the fewest cases of COVID-19 irrespective of geographic region or state political party inclination (i.e., red or blue states). Moreover, comparatively fewer COVID-19 diagnoses have occurred in primarily white counties throughout the duration of the US COVID-19 pandemic. Systemic drivers place racial minorities at greater risk for COVID-19 and HIV. Individual-level characteristics (e.g., underlying health conditions for COVID-19 or risk behavior for HIV) do not fully explain excess disease burden in racial minority communities. Corresponding interventions must use structural- and policy-level solutions to address racial and ethnic health disparities. url: https://www.ncbi.nlm.nih.gov/pubmed/32833494/ doi: 10.1089/apc.2020.0155 id: cord-301349-m4nr3pqx author: Mirza, Muhammad Usman title: Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore‐based virtual screening approach date: 2020-09-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca(2+) mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC(50) values ranging from 10.64 to 64.56 μM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies. url: https://www.sciencedirect.com/science/article/pii/S0928098720303250?v=s5 doi: 10.1016/j.ejps.2020.105537 id: cord-286194-2emwfx89 author: Mirzaei, Hossein title: COVID-19 Among People Living with HIV: A Systematic Review date: 2020-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This systematic review summarizes the evidence on the earliest patients with COVID-19-HIV co-infection. We searched PubMed, Scopus, Web of Science, Embase, preprint databases, and Google Scholar from December 01, 2019, to June 1, 2020. From an initial 547 publications and 75 reports, 25 studies provided specific information on COVID-19 patients living with HIV. Studies described 252 patients, 80.9% were male, the mean age was 52.7 years, and 98% were on antiretroviral treatment (ART). Co-morbidities in addition to HIV and COVID-19 (multimorbidity) included hypertension (39.3%), obesity or hyperlipidemia (19.3%), chronic obstructive pulmonary disease (18.0%), and diabetes (17.2%). Two-thirds (66.5%) had mild to moderate symptoms, the most common being fever (74.0%) and cough (58.3%). Among patients who died, the majority (90.5%) were over 50 years old, male (85.7%), and had multimorbidity (64.3%). Our findings highlight the importance of identifying co-infections, addressing co-morbidities, and ensuring a secure supply of ART for PLHIV during the COVID-19 pandemic. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10461-020-02983-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s10461-020-02983-2 doi: 10.1007/s10461-020-02983-2 id: cord-310867-78cx3o29 author: Mo, Phoenix K. H. title: Stigmatization among people living with HIV in Hong Kong: A qualitative study date: 2017-02-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: HIV/AIDS is one of the most stigmatized medical conditions across the world. Self‐stigma is prevalent among people living with HIV (PLHIV) and a major obstacle to HIV prevention and care. OBJECTIVE: This study aimed to describe the experiences of stigmatization and explore the possible factors that might be associated with stigmatization among PLHIV in Hong Kong. DESIGN: Qualitative in‐depth interviews were conducted. SETTING AND PARTICIPANTS: 15 PLHIV were recruited from two local non‐governmental organizations on HIV prevention. MAIN VARIABLES STUDIED: Participants were interviewed about their views and feelings towards oneself as a PLHIV and contributing factors, experiences of discriminations, stigmatizing behaviours, issues about disclosure, social relationships and potential impact of HIV. RESULTS AND CONCLUSIONS: Thematic analyses revealed three levels of factors which might be associated with stigmatization: (i) intrapersonal level (misconceptions about HIV, attribution of self‐responsibility, severe state of illness, side‐effects of medication), (ii) interpersonal level (discrimination, social rejection) and (iii) social level (mass media, public stereotypes). Findings provide important insights into which interventions to reduce stigmatization of PLHIV could be designed. url: https://www.ncbi.nlm.nih.gov/pubmed/28195685/ doi: 10.1111/hex.12535 id: cord-322581-v96k4yxg author: Mockiene, Vida title: Nurses'' willingness to take care of people living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) — does a teaching intervention make a difference? date: 2011-08-31 words: 4347.0 sentences: 219.0 pages: flesch: 56.0 cache: ./cache/cord-322581-v96k4yxg.txt txt: ./txt/cord-322581-v96k4yxg.txt summary: Summary The aim of this study is to describe the impact of an education intervention programme on nurses'' willingness to care for HIV-positive people in Lithuania. The MEDLINE, Cochrane Library, ERIC databases, and Lithuanian AIDS Centre were searched for relevant English-language citations between 2000 and 2010 using the following search terms: education intervention, HIV, Lithuania, nurse, and willingness to take care. The aim of the study is to explore the impact of an intervention programme on nurses'' willingness to take care of HIV-positive people in Lithuania. The aim of this study was to ascertain what kind of impact the intervention has on nurses'' willingness to take care of HIV-positive people or those with AIDS in Lithuania. abstract: Summary The aim of this study is to describe the impact of an education intervention programme on nurses' willingness to care for HIV-positive people in Lithuania. Methods The study utilizes a randomized controlled trial design (RCT). The total sample comprises 185 nurses working in medical, surgical and gynaecological units, and primary health care centres from the same hospital areas in three Lithuanian hospitals. The data were analyzed using SPSS 12.0 and descriptive statistics. Findings Our educational intervention did not have an impact on the nurses' willingness to take care of people living with HIV (PLHIV), as their level of willingness was high already before the education intervention. Conclusions Further research on this issue is needed to try to understand the forces acting on our nursing staff in order to ensure appropriate care for PLHIV. url: https://www.sciencedirect.com/science/article/pii/S0260691710002066 doi: 10.1016/j.nedt.2010.10.021 id: cord-349104-p0egfpx9 author: Modi, Anita R. title: Coronavirus disease 2019 in an orthotopic liver transplant recipient living with human immunodeficiency virus date: 2020-06-17 words: 1207.0 sentences: 76.0 pages: flesch: 38.0 cache: ./cache/cord-349104-p0egfpx9.txt txt: ./txt/cord-349104-p0egfpx9.txt summary: Yet immunocompromised status alone, in the absence of other comorbidities, may not necessarily predict severe illness presentations and poorer clinical outcomes as indicated by recent reports of COVID‐19‐infected solid organ transplant recipients and people living with human immunodeficiency virus (HIV). Yet immunocompromised status alone, in the absence of other comorbidities, may not necessarily predict severe illness presentations and poorer clinical outcomes as indicated by recent reports of COVID-19-infected solid organ transplant recipients and people living with human immunodeficiency virus (HIV). COVID-19, HIV, hydroxychloroquine, immunocompromised, orthotopic liver transplantation Solid organ transplant recipients living with HIV uniquely demonstrate features of both immune suppression and immune activation, as evidenced by the increased rates of allograft rejection in such patients. We hope to contribute to the literature of COVID-19 in immunocompromised patients by describing an orthotopic liver transplant (OLT) recipient with well-controlled HIV who experienced a mild flu-like illness attributed to SARS-CoV-2. abstract: Coronavirus disease 2019 (COVID‐19), mediated by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), can manifest with flu‐like illness and severe pneumonia with acute respiratory distress syndrome (ARDS). Immunocompromised patients merit particular attention as altered host immunity may influence both disease severity and duration of viral shedding as is described with several other ribonucleic acid respiratory viruses. Yet immunocompromised status alone, in the absence of other comorbidities, may not necessarily predict severe illness presentations and poorer clinical outcomes as indicated by recent reports of COVID‐19‐infected solid organ transplant recipients and people living with human immunodeficiency virus (HIV). Such patients may even be spared the robust inflammatory response that precipitates ARDS associated with COVID‐19, complicating the management of iatrogenic immunosuppression in this setting. We present a case of an orthotopic liver transplant recipient with well‐controlled HIV who successfully recovered from a mild, flu‐like illness attributed to SARS‐CoV‐2. url: https://www.ncbi.nlm.nih.gov/pubmed/32500666/ doi: 10.1111/tid.13351 id: cord-291063-de7v4e5s author: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases. url: https://doi.org/10.1155/2009/419539 doi: 10.1155/2009/419539 id: cord-260496-s2ba7uy3 author: Moncany, Maurice L.J. title: Identification of conserved lentiviral sequences as landmarks of genomic flexibility date: 2006-08-08 words: 5991.0 sentences: 296.0 pages: flesch: 51.0 cache: ./cache/cord-260496-s2ba7uy3.txt txt: ./txt/cord-260496-s2ba7uy3.txt summary: Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). Immunodeficiency lentiviral genomes correspond to 171 human viruses (155 HIV-1s and 16 HIV-2s), 33 simian viruses (3 CPZ, 9 AGM, 8 Macaque, 2 Mandrill, 10 Sooty Mangabey, 1 Sykes'' monkey viruses) and 33 non-primate mammal viruses (2 bovine, 2 caprine, 11 equine, 9 feline, 3 ovine and 6 ovine/caprine viruses). From the particular organization of the HIV-1 and HIV-2 ( Fig. 1) , AGM and macaque (Fig. 2) , CPZ, feline, equine and D-particle-forming viruses (Fig. 3) and that of sooty mangabey, mandrill and other non-primate lentiviruses (supplementary data), it appears that a given CLS occupied on the viral genome a specific position that was roughly conserved in the different viral families. abstract: Considering that recombinations produce quasispecies in lentivirus spreading, we identified and localized highly conserved sequences that may play an important role in viral ontology. Comparison of entire genomes, including 237 human, simian and non-primate mammal lentiviruses and 103 negative control viruses, led to identify 28 Conserved Lentiviral Sequences (CLSs). They were located mainly in the structural genes forming hot spots particularly in the gag and pol genes and to a lesser extent in LTRs and regulatory genes. The CLS pattern was the same throughout the different HIV-1 subtypes, except for some HIV-1-O strains. Only CLS 3 and 4 were detected in both negative control HTLV-1 oncornaviruses and D-particle-forming simian viruses, which are not immunodeficiency inducers and display a genetic stability. CLSs divided the virus genomes into domains allowing us to distinguish sequence families leading to the notion of ‘species self’ besides that of ‘lentiviral self’. Most of acutely localized CLSs in HIV-1s (82%) corresponded to wide recombination segments being currently reported. To cite this article: M.L.J. Moncany et al., C. R. Biologies 329 (2006). url: https://www.sciencedirect.com/science/article/pii/S1631069106001661 doi: 10.1016/j.crvi.2006.07.001 id: cord-328287-3qgzulgj author: Moni, Mohammad Ali title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies date: 2014-10-24 words: 10643.0 sentences: 547.0 pages: flesch: 43.0 cache: ./cache/cord-328287-3qgzulgj.txt txt: ./txt/cord-328287-3qgzulgj.txt summary: Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). To observe the association of SARS and HIV infections with other 7 important diseases (chronic heart failure, kidney disorders, breast cancer, parkinson, osteoporosis, type 1 and type 2 diabetes), we have collected mRNA microarray raw data associated with each disease from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) accession numbers are GSE9006, GSE9128, GSE15072, GSE7158, GSE8977 and GSE7621 [59] . abstract: BACKGROUND: Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I’d rather have HIV than diabetes" as life expectancy among diabetes patients is lower than that of HIV. However, HIV has a comorbidity impact on the diabetes. RESULTS: We present a quantitative framework to compare and explore comorbidity between diseases. By using neighbourhood based benchmark and topological methods, we have built comorbidity relationships network based on the OMIM and our identified significant genes. Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). Phenotypic association is measured by calculating both the Relative Risk as the quantified measures of comorbidity tendency of two disease pairs and the ϕ-correlation to measure the robustness of the comorbidity associations. The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). HIV-1 induces comorbidities relationship with many other diseases, particularly strong correlation with the neurological, cancer, metabolic and immunological diseases. Similar comorbidities risk is observed from the clinical information. Moreover, SARS and HIV infections dysregulate 4 genes (ANXA3, GNS, HIST1H1C, RASA3) and 3 genes (HBA1, TFRC, GHITM) respectively that affect the ageing process. It is notable that HIV and SARS similarly dysregulated 11 genes and 3 pathways. Only 4 significantly dysregulated genes are common between SARS-CoV and MERS-CoV, including NFKBIA that is a key regulator of immune responsiveness implicated in susceptibility to infectious and inflammatory diseases. CONCLUSIONS: Our method presents a ripe opportunity to use data-driven approaches for advancing our current knowledge on disease mechanism and predicting disease comorbidities in a quantitative way. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2105-15-333) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/1471-2105-15-333 doi: 10.1186/1471-2105-15-333 id: cord-304188-1nm1tbig author: Moody, M. Anthony title: Modulation of HIV-1 immunity by adjuvants date: 2014-04-10 words: 5154.0 sentences: 249.0 pages: flesch: 43.0 cache: ./cache/cord-304188-1nm1tbig.txt txt: ./txt/cord-304188-1nm1tbig.txt summary: Although no vaccine formulation has yet succeeded in eliciting broad neutralizing antibodies against HIV-1, the ability of adjuvants to direct the immune response to immunogens suggests they will be critically important in any successful HIV-1 vaccine. This is accomplished in one of two ways -through the incorporation of active compounds in a vaccine formulation (e.g., formulating a protein immunogen in a liposome containing a TLR4 agonist) or by incorporating elements in the vaccine that result in the production of immune stimulants (e.g., addition of plasmids expressing cytokines in a DNA vaccine regimen). [12] reported in 1993 on another group of chimpanzees immunized with formaldehyde-inactivated HIV-1 adjuvanted with alum, Freund''s incomplete adjuvant (an oil-in-water emulsion), or with a zinc hydroxide/lecithin-based adjuvant; in this study, antibody titers were best with the lecithin-based adjuvant, although proliferation and antibodydependent cell-mediated cytotoxicity (ADCC) responses were similar between lecithin and alum arms. abstract: PURPOSE OF REVIEW: To summarize the role of adjuvants in eliciting desirable antibody responses against HIV-1 with particular emphasis on both historical context and recent developments. RECENT FINDINGS: Increased understanding of the role of pattern recognition receptors such as Toll-like receptors in recruiting and directing the immune system has increased the variety of adjuvant formulations being tested in animal models and humans. Across all vaccine platforms, adjuvant formulations have been shown to enhance desirable immune responses such as higher antibody titers and increased functional activity. Although no vaccine formulation has yet succeeded in eliciting broad neutralizing antibodies against HIV-1, the ability of adjuvants to direct the immune response to immunogens suggests they will be critically important in any successful HIV-1 vaccine. SUMMARY: The parallel development of adjuvants along with better HIV-1 immunogens will be needed for a successful AIDS vaccine. Additional comparative testing will be required to determine the optimal adjuvant and immunogen regimen that can elicit antibody responses capable of blocking HIV-1 transmission. url: https://doi.org/10.1097/coh.0000000000000052 doi: 10.1097/coh.0000000000000052 id: cord-333405-ji58jbct author: Morens, David M. title: The challenge of emerging and re-emerging infectious diseases date: 2004-07-08 words: 6421.0 sentences: 315.0 pages: flesch: 41.0 cache: ./cache/cord-333405-ji58jbct.txt txt: ./txt/cord-333405-ji58jbct.txt summary: Of the ''newly emerging'' and ''re-emerging/resurging'' diseases that have followed the appearance of AIDS (Fig. 1) , some have been minor curiosities, such as the 2003 cases of monkeypox imported into the United States 4 , whereas others, such as severe acute respiratory syndrome (SARS), which emerged in the same year 5 , have had a worldwide impact. The impact of both new and re-emerging infectious diseases on human populations is affected by the rate and degree to which they spread across geographical areas, depending on the movement of human hosts or of the vectors or reservoirs of infections. Immune deficiency associated with AIDS, and with chemotherapy for cancer, immune-mediated diseases and transplantation, has contributed to an enormous global increase in the numbers of immunosuppressed people over the past few decades (probably more than 1% of the world''s population), setting the stage for the re-emergence of many opportunistic infections. abstract: Infectious diseases have for centuries ranked with wars and famine as major challenges to human progress and survival. They remain among the leading causes of death and disability worldwide. Against a constant background of established infections, epidemics of new and old infectious diseases periodically emerge, greatly magnifying the global burden of infections. Studies of these emerging infections reveal the evolutionary properties of pathogenic microorganisms and the dynamic relationships between microorganisms, their hosts and the environment. url: https://www.ncbi.nlm.nih.gov/pubmed/15241422/ doi: 10.1038/nature02759 id: cord-263645-wupre5uj author: Morgan, Brittany S title: Insights into the development of chemical probes for RNA date: 2018-09-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Over the past decade, the RNA revolution has revealed thousands of non-coding RNAs that are essential for cellular regulation and are misregulated in disease. While the development of methods and tools to study these RNAs has been challenging, the power and promise of small molecule chemical probes is increasingly recognized. To harness existing knowledge, we compiled a list of 116 ligands with reported activity against RNA targets in biological systems (R-BIND). In this survey, we examine the RNA targets, design and discovery strategies, and chemical probe characterization techniques of these ligands. We discuss the applicability of current tools to identify and evaluate RNA-targeted chemical probes, suggest criteria to assess the quality of RNA chemical probes and targets, and propose areas where new tools are particularly needed. We anticipate that this knowledge will expedite the discovery of RNA-targeted ligands and the next phase of the RNA revolution. url: https://doi.org/10.1093/nar/gky718 doi: 10.1093/nar/gky718 id: cord-341298-mqpovrms author: Morse, S.A. title: Viruses and Bioterrorism date: 2016-10-31 words: 4787.0 sentences: 224.0 pages: flesch: 44.0 cache: ./cache/cord-341298-mqpovrms.txt txt: ./txt/cord-341298-mqpovrms.txt summary: Requirements for an ideal biological warfare agent may include: availability; ease of production; stability after production; a susceptible population (human or animal); absence of specific treatment; ability to incapacitate or kill the host; appropriate particle size in aerosols so that the virus can be carried long distances by prevailing winds and inhaled deeply into the lungs of unsuspecting victims; ability to be disseminated via food or water; and, the availability of a vaccine to protect certain groups. Classification of viral agents that are considered to be of concern for bioterrorism and biowarfare and those that have been weaponized or studied for offensive or defensive purposes as part of former or current national biological weapons programs incapacitating (eg, VEE) or lethal infections (EEE case fatality rates range from 50 to 75%) (Sidwell and Smee, 2003) . An Australian research group (Jackson et al., 2001) was investigating virally vectored immunocontraceptive vaccines based on ectromelia virus, the causative agent of the disease termed mousepox. abstract: The target for a terrorist attack with a viral agent can range from humans to animals and plants. However, the use of a viral agent may pose a challenge due to problems associated with acquisition, cultivation, and dissemination. Agricultural targets are of concern as they would require relatively little specialized expertise and technology and can have large economic consequences. Viral agents are prone to genetic variation and mutation, and can be manipulated or created in the laboratory. Unlike bacterial diseases, many of which are treatable with antimicrobials, there are fewer medical countermeasures to employ when dealing with viral infections. url: https://www.sciencedirect.com/science/article/pii/B9780128096338110076 doi: 10.1016/b978-0-12-809633-8.11007-6 id: cord-275859-ix8du1er author: Mouzakis, Kathryn D. title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date: 2012-12-15 words: 6721.0 sentences: 322.0 pages: flesch: 50.0 cache: ./cache/cord-275859-ix8du1er.txt txt: ./txt/cord-275859-ix8du1er.txt summary: In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Here, we investigate the role of the HIV-1 RNA structure in frameshifting, focusing on elucidating the relationships between frameshift efficiency and (i) the downstream RNA stem-loop thermodynamic stability, (ii) spacer length and (iii) surrounding genomic secondary structure. Our data further indicate that the base pairs important for frameshifting are located at a distance of 8 nt from the slippery site, which corresponds to the length of the spacer and is consistent with a structural model of the ribosome paused at the frameshift site. Instead, we observe a strong correlation (R 2 = 0.88) between frameshift efficiency and local stability of the first 3 bp at the base of the stem-loop using a one-phase exponential decay function ( Figure 3C and Supplementary Table S3 ). abstract: The human immunodeficiency virus (HIV) requires a programmed −1 ribosomal frameshift for Pol gene expression. The HIV frameshift site consists of a heptanucleotide slippery sequence (UUUUUUA) followed by a spacer region and a downstream RNA stem–loop structure. Here we investigate the role of the RNA structure in promoting the −1 frameshift. The stem–loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. No correlation between overall stability and frameshift efficiency is observed. In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Insertion or deletions in the spacer region appear to correspondingly change the identity of the base pairs encountered 8 nt downstream of the slippery site. Finally, the role of the surrounding genomic secondary structure was investigated and found to have a modest impact on frameshift efficiency, consistent with the hypothesis that the genomic secondary structure attenuates frameshifting by affecting the overall rate of translation. url: https://www.ncbi.nlm.nih.gov/pubmed/23248007/ doi: 10.1093/nar/gks1254 id: cord-315918-12rbbe8c author: Mukherjee, Pulok K. title: Antiviral Evaluation of Herbal Drugs date: 2019-06-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The viral infection and resistance to the existing antiviral drugs are alarming, which is a serious public health concern. Medicinal plants are valuable resources for treatment of viral infections and can be used for the management of infections like herpes simplex virus (HSV), human immunodeficiency virus (HIV), influenza, etc. The antiviral screening of plant extracts should be highly selective, specific, and sensitive for bioactivity guided isolation of the active compounds from the plant extracts. The antiviral screening system should be validated for accuracy, reproducibility, simplicity, and cost effectiveness. This chapter highlights on various aspects for screening and evaluation of antiviral natural components including factors affecting antiviral in vivo studies, host cells, organisms, and culture media followed by different virus-specific assays for antiviral screening of natural products. url: https://api.elsevier.com/content/article/pii/B9780128133743000168 doi: 10.1016/b978-0-12-813374-3.00016-8 id: cord-048351-4y8ghcpq author: Murdoch, David M title: Immune reconstitution inflammatory syndrome (IRIS): review of common infectious manifestations and treatment options date: 2007-05-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The immune reconstitution inflammatory syndrome (IRIS) in HIV-infected patients initiating antiretroviral therapy (ART) results from restored immunity to specific infectious or non-infectious antigens. A paradoxical clinical worsening of a known condition or the appearance of a new condition after initiating therapy characterizes the syndrome. Potential mechanisms for the syndrome include a partial recovery of the immune system or exuberant host immunological responses to antigenic stimuli. The overall incidence of IRIS is unknown, but is dependent on the population studied and its underlying opportunistic infectious burden. The infectious pathogens most frequently implicated in the syndrome are mycobacteria, varicella zoster, herpesviruses, and cytomegalovirus (CMV). No single treatment option exists and depends on the underlying infectious agent and its clinical presentation. Prospective cohort studies addressing the optimal screening and treatment of opportunistic infections in patients eligible for ART are currently being conducted. These studies will provide evidence for the development of treatment guidelines in order to reduce the burden of IRIS. We review the available literature on the pathogenesis and epidemiology of IRIS, and present treatment options for the more common infectious manifestations of this diverse syndrome and for manifestations associated with a high morbidity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1871602/ doi: 10.1186/1742-6405-4-9 id: cord-001707-piyo00yg author: Murray, Jillian title: Determining the Provincial and National Burden of Influenza-Associated Severe Acute Respiratory Illness in South Africa Using a Rapid Assessment Methodology date: 2015-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Local disease burden data are necessary to set national influenza vaccination policy. In 2010 the population of South Africa was 50 million and the HIV prevalence was 11%. We used a previously developed methodology to determine severe influenza burden in South Africa. Hospitalized severe acute respiratory illness (SARI) incidence was calculated, stratified by HIV status, for four age groups using data from population-based surveillance in one site situated in Gauteng Province for 2009–2011. These rates were adjusted for each of the remaining 8 provinces based on their prevalence of risk factors for pneumonia and healthcare-seeking behavior. We estimated non-hospitalized influenza-associated SARI from healthcare utilization surveys at two sites and used the percent of SARI cases positive for influenza from sentinel surveillance to derive the influenza-associated SARI rate. We applied rates of hospitalized and non-hospitalized influenza-associated SARI to census data to calculate the national number of cases. The percent of SARI cases that tested positive for influenza ranged from 7–17% depending on age group, year, province and HIV status. In 2010, there were an estimated 21,555 total severe influenza cases in HIV-uninfected individuals and 13,876 in HIV-infected individuals. In 2011, there were an estimated 29,892 total severe influenza cases in HIV-uninfected individuals and 17,289 in HIV-infected individuals. The incidence of influenza-associated SARI was highest in children <5 years and was higher in HIV-infected than HIV-uninfected persons in all age groups. Influenza virus was associated with a substantial amount of severe disease, especially in young children and HIV-infected populations in South Africa. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4496064/ doi: 10.1371/journal.pone.0132078 id: cord-013442-kjfk7hq6 author: Muñoz-Laboy, Miguel title: “En la Lucha”: Strategies to Improve HIV Care for Puerto Ricans with Opioids Use Disorders date: 2020-10-30 words: 7646.0 sentences: 386.0 pages: flesch: 52.0 cache: ./cache/cord-013442-kjfk7hq6.txt txt: ./txt/cord-013442-kjfk7hq6.txt summary: Based on more than two decades of organizational experiences since the onset of the HIV epidemic in Philadelphia, and the review of the scientific literature in HIV care continuum outcomes, the leadership of both organizations and the intervention designers decided to establish Clínica Bienestar as guided by three principles: (1) Colocation of services for transnational groups to increase utilization of HIV services by minimizing unnecessary navigation through complex health care systems (primary care services, HIV services, substance use disorder treatment) while decreasing duplicative costs to achieve similar health outcomes [27] . (2) HIV diagnosis and trajectory to engagement in care at Clínica Bienestar Philadelphia; (3) Substance use trajectory into current treatment and recovery; (4) Mapping of kinship and community support systems; (5) Services received for the past 24 months at Clínica Bienestar. abstract: BACKGROUND: Clínica Bienestar is a comprehensive HIV primary care clinic for Spanish-speaking Latinx with opioids use disorders (OUD). This article describes the barriers and trajectories to HIV viral suppression for Puerto Ricans with a transnational profile and dual diagnoses (HIV and OUD), and the strategies applied to increase retention in care. METHODS: Case study methodology was used to select two patient life histories that illustrate the most common pathways to success in reducing HIV viral load to undetectable and achieving OUD long-term recovery. RESULTS AND DISCUSSION: Patients’ major challenges included: (1) Persistent migrating while seeking substance use treatment services with limited or no support from their sending and hosting communities; (2) Intersectional stigmas; (3) Untreated trauma; (4) Language and cultural barriers. Clínica Bienestar’s service model included ten strategies to retain patients in care (e.g., Case management to identify cases with high social isolation), six emerged as central to addressing transnational challenges. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7596834/ doi: 10.1007/s10903-020-01091-6 id: cord-008672-luoxomif author: Mwachari, C. title: Chronic diarrhoea among HIV-infected adult patients in Nairobi, Kenya date: 2004-10-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVES: Chronic diarrhoea and wasting are well recognized features of AIDS in Africa. However, because of resource constraints few ocmprehensive aetiological studies have conducted in sub-Saharan Africa which have included a broad range of microbiological investigations. We undertook a prospective cross-sectional study of adult patients admitted to a government hospital in Nairobi, Kenya, to determine possible bacterial, mycobacterial, parasitic and viral causes of diarrhoca; to consider which may be treatable; and to relate microbiological findings to clinical outcome. METHODS: Stool specimens from 75 consecutive HIV-seropositive patients with chronic diarrhoca admitted to a Nairobi hospital were subjected to microbiological investigation and results were compared with clinical findings and outcome. Stool samples were cultured for bacteria and mycobacteria and underwent light and electron microscopy; lawns of Escherichica coli were probed for pathogenic types and aliquots were tested for the presence of Clostridium difficile cytotoxin. Blood cultures for mycobacteria and other bacterial pathogens were performed as clinically indicated. RESULTS: Thirty-nine (52%) patients yielded putative pathogens, the most common being Cryptosporidium sp. (17%), Salmonella typhimurium (13%), and Mycobacterium tuberculosis (13%). Of 41 patients investigated for pathogenic Escherichia coli, enteroaggregative E. coli and diffusely adherent E. coli were each found in four patients. Thirty-one (41%) patients died. Detection of cryptosporidium cysts was the single most significant predictor of death (X(2) = 5.2, P<0.05). Many patients did not improve (21; 285) or self-discharged whilst still sick (5; 7%) but five (7%) were diagnosed ante mortem with tuberculosis and treated and a further 13 (17%) showed improvement by time of discharge. CONCLUSIONS: HIV-infected patients with chronic diarrhoea in Nairobi have a poor outcome overall, and even with extensive investigation a putative pathogen was identified in only just over half the patients. The most important step is to exclude tuberculosis: and the most useful investigation appears to be Ziehl-Neelsen staining. Other potentially treatable Gram-negative bacterial pathogens, S. typhimurium, Shigella sp. and adherent E. coli were, however, common but require culture facilities which are not widely accessible for definitive identification. Further studies focussing on simple ways to identify sub-groups of patients with treatable infections are warranted. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133614/ doi: 10.1016/s0163-4453(98)90561-8 id: cord-304794-z2kx314h author: Métifiot, Mathieu title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 words: 9102.0 sentences: 490.0 pages: flesch: 47.0 cache: ./cache/cord-304794-z2kx314h.txt txt: ./txt/cord-304794-z2kx314h.txt summary: Conversely, a G-quadruplex or G4 is formed by nucleic acid sequences (DNA or RNA) containing G-tracts or Gblocks (adjacent runs of guanines) and composed of various numbers of guanines. Short RNA templates from the central region of the HIV-1 genome contain G-rich sequences near the central polypurine tract (cPPT) at the 3 end of the pol gene (IN coding sequence); this is a region where one of the two primers used for synthesizing the (−) strand DNA is produced during reverse transcription. In addition, one could imagine alternative therapeutic strategies focused on targeting RNA structures within viral ORFs to interfere with the virus cycle as well as to promote antigen presentation and to stimulate the host immune response. Topology of a DNA G-quadruplex structure formed in the HIV-1 promoter: a potential target for anti-HIV drug development U3 Region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence abstract: G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300 000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein–Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools. url: https://doi.org/10.1093/nar/gku999 doi: 10.1093/nar/gku999 id: cord-032438-cpoalxyd author: Nachega, Jean B title: The where, when, and how of community-based versus clinic-based ART delivery in South Africa and Uganda date: 2020-09-21 words: 1286.0 sentences: 59.0 pages: flesch: 40.0 cache: ./cache/cord-032438-cpoalxyd.txt txt: ./txt/cord-032438-cpoalxyd.txt summary: In this issue of The Lancet Global Health, Ruanne Barnabas and colleagues report results of the Delivery Optimization of Antiretroviral Therapy (DO-ART) study, a multicentre, randomised trial comparing community-based ART initiation, monitoring, and resupply with use of a hybrid approach (ART initiation at the clinic with community monitoring and resupply), and with standard clinicbased ART delivery among individuals from South Africa and Uganda with detectable HIV viral load. 7 However, most communitybased differentiated service delivery models for ART delivery have been developed for patients who are already stable on ART, and the most important contribution of the study by Barnabas and colleagues is that community-based, same-day ART initiation in individuals with elevated viral load was safe and resulted in improved viral suppression after 12 months, particularly among men. Community-based antiretroviral therapy versus standard clinic-based services for HIV in South Africa and Uganda (DO ART): a randomised trial abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505575/ doi: 10.1016/s2214-109x(20)30385-5 id: cord-338572-5ifc2lx6 author: Nagarakanti, Sandhya R. title: Clinical outcomes of patients with COVID‐19 and HIV coinfection date: 2020-09-19 words: 1598.0 sentences: 103.0 pages: flesch: 55.0 cache: ./cache/cord-338572-5ifc2lx6.txt txt: ./txt/cord-338572-5ifc2lx6.txt summary: We present the clinical outcomes of HIV patients hospitalized for COVID‐19 in a matched comparison with historical controls. Data on baseline clinical characteristics and hospital course was documented and compared with that of a matched control group of COVID‐19 patients who had no history of HIV. CONCLUSIONS: In our cohort of HIV infected patients hospitalized for COVID‐19, there was no difference in mortality, ICU admission and the need for mechanical ventilation when compared to a matched control of COVID ‐19 patients with HIV. We evaluated their clinical outcomes and compared them to that of a well-matched control group of patients with no HIV. These data points included HIV-associated characteristics such as most recent CD4+ T cells, CD4/CD8 ratio, ( obtained by flow cytometry Clinical outcomes of hospitalized patients were compared to that of a propensity matched cohort of COVID-19 patients who had no history of HIV infection. abstract: BACKGROUND: Patients with Human Immune Deficiency Virus (HIV) infection may be at an increased risk for morbidity and mortality from the Coronavirus disease‐2019 (COVID‐19). We present the clinical outcomes of HIV patients hospitalized for COVID‐19 in a matched comparison with historical controls. METHODS: We conducted retrospective cohort study of HIV patients who were admitted for COVID‐19 between March 2020 and April 2020 to Newark Beth Israel Medical Center. Data on baseline clinical characteristics and hospital course was documented and compared with that of a matched control group of COVID‐19 patients who had no history of HIV. Kaplan Meier Survival curves and the log‐rank tests were used to estimate and compare in‐hospital survival between both unmatched and matched groups. RESULTS: Twenty‐three patients with HIV were hospitalized with COVID‐19. Median age was 59 years. The rates of in‐hospital death, the need for mechanical ventilation and intensive care unit admission were 13% (n=3), 9% (n=2) and 9% (n=2) respectively. The HIV infection was well controlled in all patients except for 3 patients who had presented with acquired immune deficiency syndrome (AIDS). All AIDS patients were discharged home uneventfully. A one‐to‐one propensity matching identified 23 COVID‐19 patients who served as a control group. In both pre‐ and post‐match cohorts, survival between HIV and control groups were comparable. CONCLUSIONS: In our cohort of HIV infected patients hospitalized for COVID‐19, there was no difference in mortality, ICU admission and the need for mechanical ventilation when compared to a matched control of COVID ‐19 patients with HIV. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.26533 doi: 10.1002/jmv.26533 id: cord-004986-en7taikk author: Nagy, Nathalie title: Infections gastro-intestinales chez le patient immunocompromis date: 2002 words: 6147.0 sentences: 672.0 pages: flesch: 58.0 cache: ./cache/cord-004986-en7taikk.txt txt: ./txt/cord-004986-en7taikk.txt summary: Dans 44 h 68 % des patients sida prEsentant une entEropathie due ~un ou plusieurs agents pathogEnes concomitant, des symptEmes gastro-intestinaux sont retrouvEs. Le diagnostic d''infections opportunistes est en gEnEral base sur une combinaison de culture de selles, examen direct des selles ~ la recherche d''ceufs ou de larves, et d''une biopsie endoscopique. L''infection herpEtique semble 6tre plus frEquente chez le patient HIV que chez les autres patients immunodEprimEs. Dans une importante Etude prospective r6alisEe sur 100 patients HIV pr6sentant une cesophagite her-pEtique, le virus HSV n''a 6tE identifi6 que darts 5 % des cas alors que la prevalence du virus CMV atteignait 50 % [4] . Les infections ~ Campylobacter ont 6t6 identifi6es dans approximativement 11% des coprocultures des patients sida, qu''ils souffrent ou non de diarrh6es ; ces patients, pr6sentant une incidence d''infection, sont 39 fois plus importants que dans la population g6n6rale. Cependant une colonisation m6me par des agents non pathog6nes peut 8tre responsable d''affections s6vhres chez les patients immunocompromis [6] . abstract: The gastrointestinal tract is frequently involved in immunocompromised hosts. The most common digestive manifestations are dysphagia, odynophagia and diarrhea. These diseases are more frequent in patients with acquired immunodeficiency virus (AIDS). These GI diseases are of several categories: HIV related inflammatory conditions (HIV related enteropathy, idiopathic esophageal ulceration), infections due to germs also commonly present in immunocompetent patients (Salmonellosis, shigellosis,…), opportunistic infections (CMV, Mucormycosis,Cryptosporidium, Mycobacterium, Isospora belli,…). The prevalence, pathogenesis, clinical manifestation, gross pathological findings and microscopic features are discussed for each entity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087899/ doi: 10.1007/bf03016656 id: cord-259846-oxbmtend author: Naik, Parvaiz Ahmad title: Global dynamics of a fractional order model for the transmission of HIV epidemic with optimal control date: 2020-06-18 words: 8469.0 sentences: 533.0 pages: flesch: 53.0 cache: ./cache/cord-259846-oxbmtend.txt txt: ./txt/cord-259846-oxbmtend.txt summary: Furthermore, for the fractional optimal control problem associated with the control strategies such as condom use for exposed class, treatment for aware infectives, awareness about disease among unaware infectives and behavioral change for susceptibles, we formulated a fractional optimality condition for the proposed model. We incorporate into the model time dependent controls such as condom use for exposed individuals, treatment for infected female sex workers, awareness about the disease among unaware infectives and behavioral change for susceptibles in order to reduce the risk of the spread of HIV/AIDS disease. In order to justify our theoretical findings, we introduced in this section some numerical experiments obtained for different instances of fractional power κ for the HIV epidemic model without control (9) and with control (24) along with adjoint variable systems and the control strategies. We present the numerical results for the model (9) when all control measures are absent and also to examine the role of fractional order κ on the HIV disease spread. abstract: In this paper, a nonlinear fractional order epidemic model for HIV transmission is proposed and analyzed by including extra compartment namely exposed class to the basic SIR epidemic model. Also, the infected class of female sex workers is divided into unaware infectives and the aware infectives. The focus is on the spread of HIV by female sex workers through prostitution, because in the present world sexual transmission is the major cause of the HIV transmission. The exposed class contains those susceptible males in the population who have sexual contact with the female sex workers and are exposed to the infection directly or indirectly. The Caputo type fractional derivative is involved and generalized Adams-Bashforth-Moulton method is employed to numerically solve the proposed model. Model equilibria are determined and their stability analysis is considered by using fractional Routh-Hurwitz stability criterion and fractional La-Salle invariant principle. Analysis of the model demonstrates that the population is free from the disease if [Formula: see text] and disease spreads in the population if [Formula: see text]. Meanwhile, by using Lyapunov functional approach, the global dynamics of the endemic equilibrium point is discussed. Furthermore, for the fractional optimal control problem associated with the control strategies such as condom use for exposed class, treatment for aware infectives, awareness about disease among unaware infectives and behavioral change for susceptibles, we formulated a fractional optimality condition for the proposed model. The existence of fractional optimal control is analyzed and the Euler-Lagrange necessary conditions for the optimality of fractional optimal control are obtained. The effectiveness of control strategies is shown through numerical simulations and it can be seen through simulation, that the control measures effectively increase the quality of life and age limit of the HIV patients. It significantly reduces the number of HIV/AIDS patients during the whole epidemic. url: https://api.elsevier.com/content/article/pii/S0960077920302265 doi: 10.1016/j.chaos.2020.109826 id: cord-018785-tcr5xlf8 author: Nambiar, Puja title: Infection in Kidney Transplantation date: 2018-06-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infection is an important cause of morbidity and mortality after kidney transplantation. It has been estimated that 70% of kidney transplant recipients will experience an infection episode within the first 3 years after transplantation (Dharnidharka et al. 2007). After cardiovascular disease, infection is the second leading cause of death in recipients with allograft function (Snyder et al. 2009). The immunosuppressive therapy required to prevent organ rejection places the kidney transplant recipient at increased risk for donor-derived, nosocomial, and community-acquired infections as well as reactivation of latent pathogens. Pretransplant screening, immunizations, and optimal antibacterial and antiviral prophylaxis can help to reduce the impact of infection. Awareness of the approach to infection in the transplant recipient including diagnostic and management strategies is essential to optimizing outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123753/ doi: 10.1007/978-3-319-19617-6_22 id: cord-251939-dvbua4pf author: Nepal, Binod title: AIDS denial in Asia: Dimensions and roots date: 2007-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract AIDS denial has long been viewed as the obstacle to forging effective response in many Asian countries. This article examines the dimensions and roots of this phenomenon. It identifies seven types of views, attitudes, or tendencies that can be described as denial, dissent, disagreements, or doubts. Three major factors underlying the AIDS denial are discussed. These are (1) historical impressions that STDs are Western diseases, (2) desire of some Asian leaders to forge Eastern points of view, and (3) long-held negative image towards the peoples or groups who happened to be at the front-line of the population groups exposed to the epidemic. The third factor is the most important source of denial. AIDS denial is not a new and isolated phenomenon but the one shaped by the global and historical institutions. Asian AIDS denial reflects the authoritarian and moralist grievances arising from the perceived deterioration of traditional moral order. url: https://api.elsevier.com/content/article/pii/S0168851007001157 doi: 10.1016/j.healthpol.2007.04.011 id: cord-297303-cpajrgba author: Nguyen, Annie L. title: Leaning on Community-Based Participatory Research to Respond During COVID-19 date: 2020-05-14 words: 1175.0 sentences: 54.0 pages: flesch: 53.0 cache: ./cache/cord-297303-cpajrgba.txt txt: ./txt/cord-297303-cpajrgba.txt summary: Located in Palm Springs, California (a popular retirement community in the Coachella Valley with the highest proportion of people aging with HIV in the United States), we have been working over the past five years to prepare stakeholders to conduct innovative and local research. Since the committee is responsive to current needs, they shifted their efforts to COVID-19 with the idea to conduct a needs and post-traumatic stress disorder (PTSD) assessment survey of older adults living with HIV in the Coachella Valley. In the implementation phase of the study, we reached out to local service-based groups in the Coachella Valley known to assist older adults living with HIV and distributed recruitment emails to their members through their mailing lists. Our next step is to provide data in real-time to local service based groups in the Coachella Valley, so organizations can respond to the emergent needs of older adults living with HIV. abstract: nan url: https://doi.org/10.1007/s10461-020-02922-1 doi: 10.1007/s10461-020-02922-1 id: cord-000065-6c3zb3g4 author: Nguyen, Thu Anh title: Health workers' views on quality of prevention of mother-to-child transmission and postnatal care for HIV-infected women and their children date: 2009-05-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Prevention of mother-to-child transmission has been considered as not a simple intervention but a comprehensive set of interventions requiring capable health workers. Viet Nam's extensive health care system reaches the village level, but still HIV-infected mothers and children have received inadequate health care services for prevention of mother-to-child transmission. We report here the health workers' perceptions on factors that lead to their failure to give good quality prevention of mother-to-child transmission services. METHODS: Semistructured interviews with 53 health workers and unstructured observations in nine health facilities in Hanoi were conducted. Selection of respondents was based on their function, position and experience in the development or implementation of prevention of mother-to-child transmission policies/programmes. RESULTS: Factors that lead to health workers' failure to give good quality services for prevention of mother-to-child transmission include their own fear of HIV infection; lack of knowledge on HIV and counselling skills; or high workloads and lack of staff; unavailability of HIV testing at commune level; shortage of antiretroviral drugs; and lack of operational guidelines. A negative attitude during counselling and provision of care, treating in a separate area and avoidance of providing service at all were seen by health workers as the result of fear of being infected, as well as distrust towards almost all HIV-infected patients because of the prevailing association with antisocial behaviours. Additionally, the fragmentation of the health care system into specialized vertical pillars, including a vertical programme for HIV/AIDS, is a major obstacle to providing a continuum of care. CONCLUSION: Many hospital staff were not being able to provide good care or were even unwilling to provide appropriate care for HIV-positive pregnant women The study suggests that the quality of prevention of mother-to-child transmission service could be enhanced by improving communication and other skills of health workers, providing them with greater support and enhancing their motivation. Reduction of workload would also be important. Development of a practical strategy is needed to strengthen and adapt the referral system to meet the needs of patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684067/ doi: 10.1186/1478-4491-7-39 id: cord-016704-99v4brjf author: Nicholson, Felicity title: Infectious Diseases: The Role of the Forensic Physician date: 2005 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infections have plagued doctors for centuries, in both the diagnosis of the specific diseases and the identification and subsequent management of the causative agents. There is a constant need for information as new organisms emerge, existing ones develop resistance to current drugs or vaccines, and changes in epidemiology and prevalence occur. In the 21st century, obtaining this information has never been more important. Population migration and the relatively low cost of flying means that unfamiliar infectious diseases may be brought into industrialized countries. An example of this was an outbreak of severe acute respiratory syndrome (SARS), which was first recognized in 2003. Despite modern technology and a huge input of money, it took months for the agent to be identified, a diagnostic test to be produced, and a strategy for disease reporting and isolation to be established. There is no doubt that other new and fascinating diseases will continue to emerge. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121068/ doi: 10.1385/1-59259-913-3:235 id: cord-301449-5okb7wf2 author: Nixon, Douglas F. title: Comments on “coinfection of SARS‐CoV‐2 and HIV in a patient in Wuhan city, China” date: 2020-04-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Zhu et al. report in their letter, Co-infection of SARS-CoV-2 and HIV in a patient in Wuhan city, China, a case of COVID19 in an HIV infected patient1 . However, from the details given in the report, there are doubts that this patient is living with HIV, and additional information would be needed to confirm it. In addition, the antiretroviral drug treatment mentioned is not within the standard guidelines for someone infected with HIV. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25821 doi: 10.1002/jmv.25821 id: cord-297612-swc2pitd author: Nosyk, Bohdan title: Contact tracing for COVID-19: An opportunity to reduce health disparities and End the HIV/AIDS Epidemic in the US date: 2020-04-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: SARS-CoV2 testing and contact tracing have been proposed as critical components of a safe and effective COVID-19 public health strategy. We argue that COVID-19 contact tracing may provide a unique opportunity to also conduct widespread HIV testing, among other health promotion activities. url: https://www.ncbi.nlm.nih.gov/pubmed/32339245/ doi: 10.1093/cid/ciaa501 id: cord-257217-f9sdt7ax author: Nunes, Marta C. title: Clinical Epidemiology of Bocavirus, Rhinovirus, Two Polyomaviruses and Four Coronaviruses in HIV-Infected and HIV-Uninfected South African Children date: 2014-02-03 words: 4629.0 sentences: 215.0 pages: flesch: 43.0 cache: ./cache/cord-257217-f9sdt7ax.txt txt: ./txt/cord-257217-f9sdt7ax.txt summary: We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and –KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI). METHODS: Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and –uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and influenza A/B. The aim of this study was to identify the prevalence of hBoV, hRV, WUPyV, KIPyV, CoV-OC43, CoV-NL63, CoV-HKU1 and CoV-229E among HIV-infected and -uninfected children who were hospitalized for LRTI using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Very few viral aetiology studies have been conducted in Africa: in a Mozambican study of virus-associated acute respiratory infections (ARI) in infants with an estimated 3-5% HIV prevalence, the most frequently detected viruses were hRV (26%), influenza (15%) and adenovirus (14%) [27] . abstract: BACKGROUND: Advances in molecular diagnostics have implicated newly-discovered respiratory viruses in the pathogenesis of pneumonia. We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and –KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI). METHODS: Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and –uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I–III, adenovirus and influenza A/B. RESULTS: At least one of these viruses were identified in 274 (53.0%) of 517 and in 509 (54.0%) of 943 LRTI-episodes in HIV-infected and -uninfected children, respectively. Human rhinovirus was the most prevalent in HIV-infected (31.7%) and –uninfected children (32.0%), followed by CoV-OC43 (12.2%) and hBoV (9.5%) in HIV-infected; and by hBoV (13.3%) and WUPyV (11.9%) in HIV-uninfected children. Polyomavirus-KI (8.9% vs. 4.8%; p = 0.002) and CoV-OC43 (12.2% vs. 3.6%; p<0.001) were more prevalent in HIV-infected than –uninfected children. Combined with previously-tested viruses, respiratory viruses were identified in 60.9% of HIV-infected and 78.3% of HIV-uninfected children. The newly tested viruses were detected at high frequency in association with other respiratory viruses, including previously-investigated viruses (22.8% in HIV-infected and 28.5% in HIV–uninfected children). CONCLUSIONS: We established that combined with previously-investigated viruses, at least one respiratory virus was identified in the majority of HIV-infected and HIV-uninfected children hospitalized for LRTI. The high frequency of viral co-infections illustrates the complexities in attributing causality to specific viruses in the aetiology of LRTI and may indicate a synergetic role of viral co-infections in the pathogenesis of childhood LRTI. url: https://doi.org/10.1371/journal.pone.0086448 doi: 10.1371/journal.pone.0086448 id: cord-320156-xs936r6u author: Nunes, Marta C. title: Polyomaviruses-associated respiratory infections in HIV-infected and HIV-uninfected children date: 2014-10-28 words: 3682.0 sentences: 186.0 pages: flesch: 44.0 cache: ./cache/cord-320156-xs936r6u.txt txt: ./txt/cord-320156-xs936r6u.txt summary: OBJECTIVES: To determine the prevalence and clinical manifestations of WUPyV and KIPyV-associated lower respiratory tract infections (LRTIs) hospitalization in HIV-infected and -uninfected children; and probe the role of pneumococcal co-infection. Co-infections with other respiratory-viruses were detected in 65.5% of WUPyV-positive LRTIs and in 75.0% of KIPyV-positive LRTIs. Among HIV-uninfected children, there was a lower incidence of hospitalization for clinical pneumonia episodes in which KIPyV (80%; 95% CI: 41, 93) and WUPyV (49%; 95% CI: 9, 71) were identified among PCV9-recipients compared to placebo-recipients. The aim of this study was to determine the burden and clinical features of WUPyV and KIPyV infections in HIV-infected and HIV-uninfected children hospitalized for LRTIs. Furthermore, as an exploratory analysis we used the design of a RCT of a 9-valent PCV (PCV9) to probe whether pneumococcal co-infection may contribute to hospitalization for PyV-associated pneumonia. abstract: BACKGROUND: Two recently discovered polyomaviruses (PyV), WU and KI, have been identified in respiratory-tract specimens from children with acute respiratory infections, although there are limited data in HIV-infected children. OBJECTIVES: To determine the prevalence and clinical manifestations of WUPyV and KIPyV-associated lower respiratory tract infections (LRTIs) hospitalization in HIV-infected and -uninfected children; and probe the role of pneumococcal co-infection. STUDY DESIGN: Nasopharyngeal aspirates were collected from a cohort of 39,836 children randomized to receive 9-valent pneumococcal conjugate vaccine (PCV9) or placebo when hospitalized for LRTIs, and were screened by PCR for WUPyV, KIPyV and other respiratory viruses. RESULTS: In placebo-recipients the prevalence of WUPyV was 6.3% (18/285) in HIV-infected and 13.9% (66/476) in HIV-uninfected children (p = 0.002). In WUPyV-positive LRTIs HIV-infected children had lower oxygen saturation at admission and a higher case fatality rate (11.1% vs. 0%; p = 0.04). KIPyV was identified in 10.2% (29/285) of HIV-infected and in 7.4% (35/476) of HIV-uninfected placebo-recipients with LRTIs (p = 0.13). HIV-infected compared to HIV-uninfected children with KIPyV-positive LRTIs had lower oxygen saturation, higher respiratory rate and longer duration of hospitalization. Co-infections with other respiratory-viruses were detected in 65.5% of WUPyV-positive LRTIs and in 75.0% of KIPyV-positive LRTIs. Among HIV-uninfected children, there was a lower incidence of hospitalization for clinical pneumonia episodes in which KIPyV (80%; 95% CI: 41, 93) and WUPyV (49%; 95% CI: 9, 71) were identified among PCV9-recipients compared to placebo-recipients. CONCLUSIONS: Polyomaviruses were commonly identified in HIV-infected and -uninfected children hospitalized for LRTIs, frequently in association with other viruses and may contribute to the pathogenesis of pneumococcal pneumonia. url: https://api.elsevier.com/content/article/pii/S1386653214004004 doi: 10.1016/j.jcv.2014.10.013 id: cord-304157-u0mlee6u author: Nyasulu, Juliet title: The effects of coronavirus disease 2019 pandemic on the South African health system: A call to maintain essential health services date: 2020-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: South Africa had its first coronavirus disease 2019 (COVID-19) case on 06 March 2020 in an individual who travelled overseas. Since then, cases have constantly increased and the pandemic has taken a toll on the health system. This requires extra mobilisation of resources to curb the disease and overcome financial loses whilst providing social protection to the poor. Assessing the effects of COVID-19 on South African health system is critical to identify challenges and act timely to strike a balance between managing the emergency and maintaining essential health services. We applied the World Health Organization (WHO) health systems framework to assess the effects of COVID-19 on South African health system, and proposed solutions to address the gaps, with a focus on human immunodeficiency virus (HIV) and expanded programme on immunisation (EPI) programmes. The emergence of COVID-19 pandemic has direct impact on the health system, negatively affecting its functionality, as depletion of resources to curb the emergency is eminent. Diversion of health workforce, suspension of services, reduced health-seeking behaviour, unavailability of supplies, deterioration in data monitoring and funding crunches are some of the noted challenges. In such emergencies, the ability to deliver essential services is dependent on baseline capacity of health system. Our approach advocates for close collaboration between essential services and COVID-19 teams to identify priorities, restructure essential services to accommodate physical distancing, promote task shifting at primary level, optimise the use of mobile/web-based technologies for service delivery/training/monitoring and involve private sector and non-health departments to increase management capacity. Strategic responses thus planned can assist in mitigating the adverse effects of the pandemic whilst preventing morbidity and mortality from preventable diseases in the population. url: https://www.ncbi.nlm.nih.gov/pubmed/32787396/ doi: 10.4102/phcfm.v12i1.2480 id: cord-271948-iq29xqrn author: Obeng, Billal Musah title: Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana date: 2020-07-24 words: 3572.0 sentences: 203.0 pages: flesch: 56.0 cache: ./cache/cord-271948-iq29xqrn.txt txt: ./txt/cord-271948-iq29xqrn.txt summary: title: Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana BACKGROUND: Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana. This study found major drug resistance mutations, E138A and K65R that respectively confer high level resistance to NNRTIs and NRTIs. Although, CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. The data obtained is useful for the selection of drugs for ART initiation to maximize therapeutic outcomes in drug-naïve HIV-1 patients in Ghana. abstract: BACKGROUND: Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. Globally, limited data exist on TDR and SD among blood donors. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. METHODS: Purposive sampling method was used to collect 81 HIV sero-positive blood samples from the Southern Area Blood Center and confirmed by INNO-LIA as HIV-1 and/or HIV-2. Viral RNA was only extracted from plasma samples confirmed as HIV-1 positive. Complementary DNA (cDNA) was synthesized using the RNA as a template and subsequently amplified by nested PCR with specific primers. The expected products were verified, purified and sequenced. Neighbour-joining tree with the Kimura’s 2-parameter distances was generated with the RT sequences using Molecular Evolutionary Genetic Analysis version 6.0 (MEGA 6.0). RESULTS: Out of the 81 plasma samples, 60 (74%) were confirmed as HIV-1 sero-positive by INNO-LIA HIVI/II Score kit with no HIV-2 and dual HIV-1/2 infections. The remaining samples, 21 (26%) were confirmed as HIV sero-negative. Of the 60 confirmed positive samples, (32) 53% and (28) 47% were successfully amplified in the RT and PR genes respectively. Nucleotide sequencing of amplified samples revealed the presence of major drug resistance mutations in two (2) samples; E138A in one sample and another with K65R. HIV-1 Subtypes including subtypes A, B, CRF02_AG and CRF09_cpx were found. CONCLUSION: This study found major drug resistance mutations, E138A and K65R in the RT gene that confer high level resistance to most NNRTIs and NRTI respectively. CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. However, a more prospective and detailed analysis is needed to establish this phenomenon. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana. url: https://www.ncbi.nlm.nih.gov/pubmed/32709248/ doi: 10.1186/s12985-020-01386-y id: cord-001228-4eh22ek7 author: Ofori, Leslie O. title: High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity date: 2014-01-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: [Image: see text] The life cycle of the human immunodeficiency virus type 1 (HIV-1) has an absolute requirement for ribosomal frameshifting during protein translation in order to produce the polyprotein precursor of the viral enzymes. While an RNA stem-loop structure (the “HIV-1 Frameshift Stimulating Signal”, or HIV-1 FSS) controls the frameshift efficiency and has been hypothesized as an attractive therapeutic target, developing compounds that selectively bind this RNA and interfere with HIV-1 replication has proven challenging. Building on our prior discovery of a “hit” molecule able to bind this stem-loop, we now report the development of compounds displaying high affinity for the HIV-1 FSS. These compounds are able to enhance frameshifting more than 50% in a dual-luciferase assay in human embryonic kidney cells, and they strongly inhibit the infectivity of pseudotyped HIV-1 virions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954503/ doi: 10.1021/jm401438g id: cord-316789-nb4437qs author: Omel’yanchuk, L. V. title: Drosophila melanogaster as a model for studying the function of animal viral proteins date: 2011-07-16 words: 3481.0 sentences: 174.0 pages: flesch: 52.0 cache: ./cache/cord-316789-nb4437qs.txt txt: ./txt/cord-316789-nb4437qs.txt summary: Studies in which Drosophila melanogaster individuals carrying transgenes of animal viruses were used to analyze the action of animal viral proteins on the cell are reviewed. At the same time, it is commonly known that in addition to these proteins serving the structural function viral genomes contain genes responsible for finer aspects of interaction with host cells: cell proliferation (in fact, isolation of oncogenes was made on the basis of this property) and cell apoptosis. Drosophila was successfully used to study viral genes and proteins inhibiting programmed death (apoptosis) of host cells. The authors of the work [19] cloned the HIV tat gene in the pCasPeR vector containing the hs promoter capable of heat shock activation of transgene expression in all tissues. abstract: Studies in which Drosophila melanogaster individuals carrying transgenes of animal viruses were used to analyze the action of animal viral proteins on the cell are reviewed. The data presented suggest that host specificity of viruses is determined by their proteins responsible for the penetration of the virus into the cell, while viral proteins responsible for interactions with the host cell are much less host-specific. Due to this, the model of Drosophila with its developed system of searching for genetic interactions can be used to find intracellular targets for the action of viral proteins of the second group. url: https://doi.org/10.1134/s1022795411040090 doi: 10.1134/s1022795411040090 id: cord-287949-243xlmep author: Onovo, A. A. title: Using Supervised Machine Learning and Empirical Bayesian Kriging to reveal Correlates and Patterns of COVID-19 Disease outbreak in sub-Saharan Africa: Exploratory Data Analysis date: 2020-05-02 words: 4908.0 sentences: 233.0 pages: flesch: 51.0 cache: ./cache/cord-287949-243xlmep.txt txt: ./txt/cord-287949-243xlmep.txt summary: Explanatory or independent variables in the model included total population, GDP per capita, percentage of population with access to electricity, percentage of population with access to basic drinking water, incidence of malaria (per 1,000 population at risk), percentage of men and women aged 15 and over who currently smoke any tobacco product, Diarrhea treatment (percent of children under 5 receiving oral rehydration and continued feeding), percentage of infants who received third-dose of pneumococcal conjugate-based vaccine (PCV), incidence of tuberculosis (per 100,000 people), percent out-of-pocket expenditure, life expectancy at birth, Health Systems Performance Index, estimated incidence rate (new HIV infection per 1,000 uninfected population, children aged 0-14 years), estimated incidence rate (new HIV infection per 1,000 uninfected population, adolescents aged 10-19 years), HIV prevalence among people aged 15-49 years, transmission classification of COVID-19 disease (1=imported, 2=local transmission), income group (1=High Income, 2=Low income, 3=Lower middle income, 4=Upper middle income), Geocoordinates of SSA countries (latitude and longitude), and Time (days) between the first and last reported coronavirus cases. abstract: Introduction: Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan, China, and has subsequently spread worldwide. Knowledge of coronavirus-related risk factors can help countries build more systematic and successful responses to COVID-19 disease outbreak. Here we used Supervised Machine Learning and Empirical Bayesian Kriging (EBK) techniques to reveal correlates and patterns of COVID-19 Disease outbreak in sub-Saharan Africa (SSA). Methods: We analyzed time series aggregate data compiled by Johns Hopkins University on the outbreak of COVID-19 disease across SSA. COVID-19 data was merged with additional data on socio-demographic and health indicator survey data for 39 of SSA 48 countries that reported confirmed cases and deaths from coronavirus between February 28, 2020 through March 26, 2020. We used supervised machine learning algorithm, Lasso for variable selection and statistical inference. EBK was used to also create a raster estimating the spatial distribution of COVID-19 disease outbreak. Results: The lasso Cross-fit partialing out predictive model ascertained seven variables significantly associated with the risk of coronavirus infection (i.e. new HIV infections among pediatric, adolescent, and middle-aged adult PLHIV, time (days), pneumococcal conjugate-based vaccine, incidence of malaria and diarrhea treatment). Our study indicates, the doubling time in new coronavirus cases was 3 days. The steady three-day decrease in coronavirus outbreak rate of change (ROC) from 37% on March 23, 2020 to 23% on March 26, 2020 indicates the positive impact of countries' steps to stymie the outbreak. The interpolated maps show that coronavirus is rising every day and appears to be severely confined in South Africa. In the West African region (i.e. Burkina Faso, Ghana, Senegal, CotedIviore, Cameroon, and Nigeria), we predict that new cases and deaths from the virus are most likely to increase. Interpretation: Integrated and efficiently delivered interventions to reduce HIV, pneumonia, malaria and diarrhea, are essential to accelerating global health efforts. Scaling up screening and increasing COVID-19 testing capacity across SSA countries can help provide better understanding on how the pandemic is progressing and possibly ensure a sustained decline in the ROC of coronavirus outbreak. Funding: Authors were wholly responsible for the costs of data collation and analysis. url: https://doi.org/10.1101/2020.04.27.20082057 doi: 10.1101/2020.04.27.20082057 id: cord-346153-9162w7il author: Openshaw, P J title: Crossing barriers: infections of the lung and the gut date: 2008-12-24 words: 1716.0 sentences: 90.0 pages: flesch: 43.0 cache: ./cache/cord-346153-9162w7il.txt txt: ./txt/cord-346153-9162w7il.txt summary: Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. However, the coronavirus copy number in some studies showed an increase between day 5 and day 10, so that maximal infectivity followed the fever, 7 leading perhaps to a false sense of security amongst those caring for SARS patients. e reason for these interactions are incompletely understood, but intriguing recent study show that in uenza and respiratory syndrome virus are both capable of causing a persistent inhibition of the innate response to bacterial superinfection, and therefore to increased bacterial replication and disease. Highly pathogenic strains of in uenza also cause intense systemic symptoms, sometimes associated with gastrointestinal disease. Microbial translocation is a cause of systemic immune activation in chronic HIV infection abstract: Although known as respiratory pathogens, severe acute respiratory syndrome (SARS) and its sister coronaviruses frequently cause enteric symptoms. In addition, other classically non-enteric viruses (such as HIV and influenza) may also have enteric effects that are crucial in their pathogeneses. These effects can be due to direct infection of the gut mucosa, but can also be because of decreased antibacterial defenses, increased mucosal permeability, bacterial translocation, and systemic leak of endotoxin. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/mi.2008.79) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/19129753/ doi: 10.1038/mi.2008.79 id: cord-310931-5165078t author: Oppong, Joseph R. title: Globalization of Communicable Diseases date: 2019-12-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Fueled by globalization and human behavior, communicable diseases pose a serious threat to humankind despite unparalleled technological advances. New viruses and devastating communicable diseases such as Ebola and Zika are emerging; diseases previously considered eradicated such as measles are reemerging, while antibiotic resistance is increasing to dangerously high levels worldwide. Increased human population and accelerated global travel make local outbreaks instant global threats. Researchers are concerned that an avian influenza outbreak could kill many more people when it emerges because of the absence of immunity and human travel interaction patterns. Yet the threat of communicable disease varies by geographic location—where you live matters. This entry examines the spatial patterns of familiar communicable diseases, including the syndemic of human immunodeficiency virus (HIV) and tuberculosis, as well as new diseases such as Ebola, Zika, and dengue. It highlights the huge potential of mapping communicable disease genotypes while raising the alarm on the urgent need for effective global disease surveillance systems and new tools for fighting communicable diseases. Because communicable diseases do not respect political boundaries, global cooperation is vital to prevent this threat to humankind. url: https://api.elsevier.com/content/article/pii/B978008102295510438X doi: 10.1016/b978-0-08-102295-5.10438-x id: cord-285603-f4572w5m author: Ortega, Joseph T. title: Class A G Protein-Coupled Receptor Antagonist Famotidine as a Therapeutic Alternative against SARS-CoV2: An In Silico Analysis date: 2020-06-24 words: 5994.0 sentences: 348.0 pages: flesch: 47.0 cache: ./cache/cord-285603-f4572w5m.txt txt: ./txt/cord-285603-f4572w5m.txt summary: In order to gain a deeper understanding if the pharmacokinetic parameters of the SARS-CoV2 protease inhibitors could be related to positive outcomes in the therapy, we analyzed the ADME parameters of famotidine and compared with several known antiviral drugs such as ribavirin, lopinavir, and nafamostat, which were evaluated against SARS-CoV2. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Chemical structures and administration, distribution, metabolism, and elimination (ADME) parameters for famotidine, ribavirin, lopinavir, and nafamostat, drugs that were evaluated as SARS-CoV2 inhibitors, are shown. Altogether, in this study, we showed that famotidine could be used as an antiviral agent against SARS-CoV2, targeting proteases involved in the virus replication, mostly the main protease, as well as the viral PLpro and human host Tmprss2. abstract: The pandemic associated with Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV2) and its disease named COVID-19 challenged the scientific community to discover effective therapeutic solutions in a short period. Repurposing existing drugs is one viable approach that emphasizes speed during these urgent times. Famotidine, a class A G protein-coupled receptor antagonist used for the treatment of gastroesophageal reflux was recently identified in an in silico screening. Additionally, a recent retrospective clinical report showed that the treatment with famotidine provided a good outcome in patients infected with SARS-CoV2. A clinical trial testing effectiveness of famotidine in combination with hydroxychloroquine is currently ongoing in the United States (US). In the 1990s, famotidine was described as an antiviral agent against human immunodeficiency virus (HIV). Interestingly, some HIV protease inhibitors are presently being used against SARS-CoV2. However, it is not clear if famotidine could be effective against SARS-CoV2. Thus, by using a computational analysis, we aimed to examine if the antiviral effect of famotidine could be related to the inhibition of proteases involved in the virus replication. Our results showed that famotidine could interact within the catalytic site of the three proteases associated with SARS-CoV2 replication. However, weak binding affinity of famotidine to these proteases suggests that a successful famotidine therapy could likely be achieved only in combination with other antiviral drugs. Finally, analysis of famotidine’s pharmacokinetic parameters indicated that its effect against SARS-CoV2 infection could be reached only upon intravenous administration. This work will contribute to the pharmacological knowledge of famotidine as an antiviral agent against SARS-CoV2. url: https://www.ncbi.nlm.nih.gov/pubmed/32599963/ doi: 10.3390/biom10060954 id: cord-265699-0socw0hp author: Ortega, Miguel Ángel title: Dendrimers and Dendritic Materials: From Laboratory to Medical Practice in Infectious Diseases date: 2020-09-14 words: 11148.0 sentences: 591.0 pages: flesch: 41.0 cache: ./cache/cord-265699-0socw0hp.txt txt: ./txt/cord-265699-0socw0hp.txt summary: This review provides the reader a general overview about the uses of dendrimers and dendritic materials in the treatment, prevention, and diagnosis of highly prevalent infectious diseases, and their advantages compared to traditional approaches. Key commercial successes include the Stratus CS Acute Care Diagnostic System (Siemens Healthcare GmbH, Erlangen, Germany), for emergency diagnosis of cardiovascular infarctions; VivaGel ® products (Starpharma, Melbourne, Australia), for the prevention and treatment of sexually transmitted infections (STIs); Targeted DEP ® and Priostar ® (Starpharma), for the delivery of anticancer drugs and agrochemical products, respectively; or SpheriCal (Polymer Factory, Stockholm, Sweden), as mass spectrometry standards [59] . Key commercial successes include the Stratus CS Acute Care Diagnostic System (Siemens Healthcare GmbH, Erlangen, Germany), for emergency diagnosis of cardiovascular infarctions; VivaGel ® products (Starpharma, Melbourne, Australia), for the prevention and treatment of sexually transmitted infections (STIs); Targeted DEP ® and Priostar ® (Starpharma), for the delivery of anticancer drugs and agrochemical products, respectively; or SpheriCal (Polymer Factory, Stockholm, Sweden), as mass spectrometry standards [59] . abstract: Infectious diseases are one of the main global public health risks, predominantly caused by viruses, bacteria, fungi, and parasites. The control of infections is founded on three main pillars: prevention, treatment, and diagnosis. However, the appearance of microbial resistance has challenged traditional strategies and demands new approaches. Dendrimers are a type of polymeric nanoparticles whose nanometric size, multivalency, biocompatibility, and structural perfection offer boundless possibilities in multiple biomedical applications. This review provides the reader a general overview about the uses of dendrimers and dendritic materials in the treatment, prevention, and diagnosis of highly prevalent infectious diseases, and their advantages compared to traditional approaches. Examples of dendrimers as antimicrobial agents per se, as nanocarriers of antimicrobial drugs, as well as their uses in gene transfection, in vaccines or as contrast agents in imaging assays are presented. Despite the need to address some challenges in order to be used in the clinic, dendritic materials appear as an innovative tool with a brilliant future ahead in the clinical management of infectious diseases and many other health issues. url: https://doi.org/10.3390/pharmaceutics12090874 doi: 10.3390/pharmaceutics12090874 id: cord-017887-pj6pal35 author: OuYang, Bo title: Structural and Functional Properties of Viral Membrane Proteins date: 2018-06-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses have developed a large variety of transmembrane proteins to carry out their infectious cycles. Some of these proteins are simply anchored to membrane via transmembrane helices. Others, however, adopt more interesting structures to perform tasks such as mediating membrane fusion and forming ion-permeating channels. Due to the dynamic or plastic nature shown by many of the viral membrane proteins, structural and mechanistic understanding of these proteins has lagged behind their counterparts in prokaryotes and eukaryotes. This chapter provides an overview of the use of NMR spectroscopy to unveil the transmembrane and membrane-proximal regions of viral membrane proteins, as well as their interactions with potential therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122571/ doi: 10.1007/978-981-13-0532-0_6 id: cord-340777-d1vwjqk6 author: O’Byrne, Patrick title: Immediate PrEP after PEP: Results from an Observational Nurse-Led PEP2PrEP Study date: 2020-08-28 words: 4855.0 sentences: 229.0 pages: flesch: 55.0 cache: ./cache/cord-340777-d1vwjqk6.txt txt: ./txt/cord-340777-d1vwjqk6.txt summary: 3 This last point has led some guidelines to suggest that PEP use more than once warrants preexposure prophylaxis (PrEP), which is the use antiretroviral medications before a potential HIV exposure to prevent seroconversion. 4, 5 To inform this decision and address high seroconversion rates among PEP patients, we began offering PEP2PrEP to patients who (1) initiated PEP at our sexually transmitted infection (STI) testing clinic, (2) reported good adherence to the PEP, and (3) had no serologic or physical evidence of HIV infection. Extracted data focused on demographics (age, gender, income), sexual and drug use practices (sex practices, gender of partners, substance use), mental health (depression, anxiety, using the patient health questionnaire 9 [PHQ9], and generalized anxiety 7 scale [GAD7], respectively), reason for PEP use and follow-up details (practices that warranted PEP, symptoms, test results), and information on PrEP visits (attendance, symptoms, results). abstract: Patients who use post-exposure prophylaxis (PEP) are at ongoing risk for HIV acquisition after completing PEP. While the Centers for Disease Control and Prevention recommends pre-exposure prophylaxis (PrEP) use immediately after PEP, some practitioners are hesitant to offer PEP-to-PrEP (PEP2PrEP). We began offering PEP2PrEP in the sexually transmitted infection clinic in Ottawa, Canada on August 5, 2018. During the first 16 months of PEP2PrEP, 61 patients requested PEP and 46 were initiated; 30 of these patients agreed to PEP2PrEP and 26 followed through. None of our PEP patients had confirmed HIV exposures; all fulfilled the initiation criterion of condomless anal sex with a male partner of unknown HIV-status. During the study, the number of PEP requests and initiations was statistical unchanged, yet the seroconversion rate among patients who used PEP decreased from 1.7% pre-PEP2PrEP to 0% post-PEP2PrEP. Regarding follow-up, most discontinuations occurred between the PrEP intake and 1-month follow-up visit. url: https://doi.org/10.1177/2325958220939763 doi: 10.1177/2325958220939763 id: cord-027859-citynr6c author: P. Shetty, Nandini title: Epidemiology of Disease in the Tropics date: 2020-06-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315327/ doi: 10.1016/b978-1-4160-4470-3.50007-0 id: cord-285898-rtqkvf63 author: Padberg, Stephanie title: Anti-infective Agents date: 2014-09-29 words: 23992.0 sentences: 1446.0 pages: flesch: 42.0 cache: ./cache/cord-285898-rtqkvf63.txt txt: ./txt/cord-285898-rtqkvf63.txt summary: In the case of clarithromycin, there was some 2.6 Anti-infective Agents 2 Pregnancy initial concern as animal experiments demonstrated teratogenic effects, and for instance, in some studies cardiovascular defects were induced in rats. In a prospective cohort study with 949 women who were exposed to a fluorquinolone during the first trimester, neither the rate of major birth defects, nor the risk of spontaneous abortion were increased compared to a control group (Padberg 2014) . Danish cohort studies based on a prescription register also could not find an increased risk of birth defects after first trimester exposure in several thousand pregnant women (Nørgaard 2008 , Sørensen 1999 ). Data from the Antiretroviral Pregnancy Registry (2013) with 27 birth defects in 905 cases, indicate a malformation rate of 3.0% after exposure during the first trimester, similarly as seen in the general population of the USA. Three birth defects were observed among 141 pregnant women with first trimester exposures reported to the Antiretroviral Pregnancy Registry (2013). abstract: Infections may be hazardous to the health of the mother, the course of pregnancy, and the unborn child. They can lead to premature labor or premature rupture of membranes and thereby increase the risk for spontaneous abortion and prematurity. Furthermore, certain germs can pass to the unborn child and harm it directly. Therefore, an anti-infective treatment which should be both effective and safe for the mother and the unborn child is often required. The use of penicillines and older cephalosporines is well documented and considered to be safe. Consequently, they are the drug of choice during pregnancy. In selected cases of bacterial resistance or intolerance to first-line antibiotics, other anti-infective agents might be recommended. Especially for life-threatening infections, a therapy with not so well-tried agents might be needed. The potential benefit of treatment in such cases most often outbalances the potential risk for the unborn child. url: https://www.sciencedirect.com/science/article/pii/B978012408078200007X doi: 10.1016/b978-0-12-408078-2.00007-x id: cord-022380-49oti4zg author: Panlilio, Adelisa L title: Occupational Infectious Diseases date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155632/ doi: 10.1016/b978-0-7216-8974-6.50026-9 id: cord-003895-m1y76ee5 author: Parcesepe, Angela M. title: Gender, HIV-Related Stigma, and Health-Related Quality of Life Among Adults Enrolling in HIV Care in Tanzania date: 2019-03-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: HIV-related stigma has been associated with worse health-related quality of life (HRQoL) among people living with HIV (PLWH). Little is known about how different types of HIV-related stigma (i.e., anticipatory, internalized, or enacted HIV-related stigma) influence HRQoL and whether these relationships differ by gender. The sample included 912 PLWH aged 18 years or older enrolling in HIV care at four health facilities in Tanzania. HRQoL was assessed with the life satisfaction and overall function subscales of the HIV/AIDS-Targeted Quality of Life (HAT-QoL) instrument. Sex-stratified multivariable logistic regression modeled the association of anticipatory, internalized, and enacted HIV-related stigma on poor HRQoL. Across all participants, the mean life satisfaction score was 63.4 (IQR: 43.8, 81.3) and the mean overall function score was 72.0 (IQR: 58.3, 91.7). Mean HRQoL scores were significantly higher for women compared to men for overall function (5.1 points higher) and life satisfaction (4.3 points higher). Fourteen percent of respondents reported recent enacted HIV-related stigma and 13% reported recent medium or high levels of internalized stigma. In multivariable models, high internalized and high anticipatory stigma were significantly associated with higher odds of poor life satisfaction and poor overall function in both men and women. Psychosocial interventions to prevent or reduce the impact of internalized and anticipatory stigma may improve HRQoL among persons in HIV care. Future research should longitudinally examine mechanisms between HIV-related stigma, poor HRQoL, and HIV care outcomes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768763/ doi: 10.1007/s10461-019-02480-1 id: cord-304427-r7jt95ko author: Pasquato, A. title: Heparin enhances the furin cleavage of HIV-1 gp160 peptides date: 2007-12-22 words: 3356.0 sentences: 176.0 pages: flesch: 54.0 cache: ./cache/cord-304427-r7jt95ko.txt txt: ./txt/cord-304427-r7jt95ko.txt summary: The 18mer, 41mer, and 51mer were synthesized on a semi-automatic synthesizer (Applied Biosystems, Mod. 431A) using a Rink amide MBHA resin Abbreviations: HIV-1, human immunodeficiency virus type 1; GAGs, glycosaminoglycans; CD, circular dichroism; AIDS, acquired immunodeficiency syndrome; RP-HPLC, reverse phase high performance liquid chromatography; PC, proprotein convertase; BTMD, before trans membrane domain; MS, mass spectrometry; AMC, 7-amino-4methyl-coumarin; MCA, 7-amido-4-methylcoumarin; TFE, trifluoroethanol; SDS, sodium dodecyl sulfate; Tris-HCl, Tris-(hydroxymethyl) aminomethane-HCl; DMSO, dimethyl sulfoxide; HF, hydrofluoric acid; cmk, chloromethylketone; PBS, phosphate buffer saline (NovaBiochem, La Jolla, 0.48 mmol/g, 0.25 mmol), Boc chemistry and HBTU/HOBt activation. Similarly, peptides derived from the cleavage site of the human respiratory syncytial virus (RSV) fusion glycoprotein bind heparin and cellular GAGs [26] . Heparin was shown to strongly interact with the 41mer and 51mer peptides, inducing conformational changes, thereby exposing site1 for cleavage. abstract: Infectious HIV-1 requires gp160 cleavage by furin at the REKR(511)↓ motif (site1) into the gp120/gp41 complex, whereas the KAKR(503) (site2) sequence remains uncleaved. We synthesized 41mer and 51mer peptides, comprising site1 and site2, to study their conformation and in vitro furin processing. We found that, while the previously reported 19mer and 13mer analogues represent excellent in vitro furin substrates, the present extended sequences require heparin for optimal processing. Our data support the hypothesis of a direct binding of heparin with site1 and site2, allowing selective exposure/accessibility of the REKR sequence, which is only then optimally cleaved by furin. url: https://api.elsevier.com/content/article/pii/S0014579307011945 doi: 10.1016/j.febslet.2007.11.050 id: cord-341304-jdvzpvdx author: Pata, Rama Kanth title: Human Immunodeficiency Virus: A Dark Cloud With Silver Lining During the COVID-19 Pandemic date: 2020-07-20 words: 1871.0 sentences: 105.0 pages: flesch: 53.0 cache: ./cache/cord-341304-jdvzpvdx.txt txt: ./txt/cord-341304-jdvzpvdx.txt summary: In December 2019, China reported a cluster of pneumonia patients infected by a new virus from the coronavirus family called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus quickly spread around the world and infected millions of people, and the World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020. On March 22, 2020, a 67-year-old female with a past medical history of asthma, coronary artery disease (status post-coronary artery bypass graft two years ago), hypertension, hyperlipidemia, and HIV on antiretroviral medications [bictegrav/emtricit/tenofov ala (Biktarvy® 50-200-25 mg tablet, Gilead Sciences, Foster City, CA) and darunavir/cobicistat (Prezcobix® 800 mg-150 mg tablet, Janssen Pharmaceutica, Beerse, Belgium)] was brought in by emergency medical services (EMS) for progressively worsening shortening of breath associated with weakness and two episodes of watery non-bloody diarrhea for one day. showed clinical improvement in the first case of COVID-19 in the United States after the use of remdesivir [8] . abstract: In December 2019, China reported a cluster of pneumonia patients infected by a new virus from the coronavirus family called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus quickly spread around the world and infected millions of people, and the World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a pandemic on March 11, 2020. Although some patients show only mild or even asymptomatic response to this infection, severe disease with rapid progression to acute respiratory distress and multiorgan failure is also commonly seen. In this report, we discuss three cases of HIV patients who survived COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32832299/ doi: 10.7759/cureus.9302 id: cord-355475-kdubhh73 author: Patton, Lauren L. title: Viral Pandemics and Oral Health: Lessons Learned From HIV to SARS-CoV-2 date: 2020-11-05 words: 2161.0 sentences: 104.0 pages: flesch: 45.0 cache: ./cache/cord-355475-kdubhh73.txt txt: ./txt/cord-355475-kdubhh73.txt summary: An early survey in May and June 2020 of practicing dentists in private practice and public health settings in the United States (U.S.), a short 2 months after the first COVID-19 wave and national shortages of personal protective equipment caused offices to move to emergency only dental care, showed that 99.7% of offices had implemented enhanced infection control procedures. While hope for a COVID-19 vaccine to quell transmission is widespread, we must not lose sight of the fact that diverse vaccine development technologies and novel drug discovery efforts made today will benefit our response to the next pandemic. 14 When the diversity of oral mucosal and salivary gland disorders were observed in HIV/AIDS patients, international collaborative groups such as the European Community We learned from HIV disease management that the antiretroviral drugs can have acute and long-term toxicities including ulcers, xerostomia/parotid lipomatosis, taste disturbances, perioral paresthesia, erythema multiforme and facial fat wasting. abstract: nan url: https://api.elsevier.com/content/article/pii/S2212440320313146 doi: 10.1016/j.oooo.2020.10.022 id: cord-318591-ssnlfjap author: Pecego, AC title: Etiology, clinical, and epidemiological characteristics of severe respiratory infection in people living with HIV date: 2020-01-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: People living with HIV (PLWH) are more prone to severe respiratory infections. We used the severe acute respiratory infection (SARI) definition to describe the etiology, clinical, and epidemiological characteristics in this population. This was a prospective observational study including PLWH hospitalized with fever and cough. Those with symptom onset up to 10 days were classified as severe acute respiratory infection and 11–30 days as non-severe acute respiratory infection. Blood, urine samples and nasopharyngeal swabs were collected. Data were extracted from patient charts during their hospital stay. Forty-nine patients were included, median CD4 cell count: 80 cells/mm(3), median time since HIV diagnosis and hospital admission: 84 months and 80% were antiretroviral therapy exposed. Twenty-seven patients were classified as SARI. Etiology was identified in 69%, 47% were polymicrobial. Respiratory virus (9 SARI vs. 13 non-SARI), bacteria (5 SARI vs. 4 non-SARI), Mycobacterium tuberculosis (6 SARI group vs. 7 non-SARI group), Pneumocystis jirovecii (4 SARI vs. 1 non-SARI), Cryptococcus neoformans (1 SARI vs. 3 non-SARI), and influenza A (1 SARI vs. 2 non-SARI). Dyspnea was statistically more prevalent in SARI (78% vs. 36%, p = 0.011) but the risk of death was higher in the non-SARI (4% vs. 36%, p = 0.0067). In the severely immunocompromised PLWH, severe acute respiratory infection can be caused by multiple pathogens and codetection is a common feature. url: https://www.ncbi.nlm.nih.gov/pubmed/31969059/ doi: 10.1177/0956462419882587 id: cord-288982-63ddlh20 author: Peeling, Rosanna W. title: Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date: 2015-11-09 words: 4391.0 sentences: 216.0 pages: flesch: 44.0 cache: ./cache/cord-288982-63ddlh20.txt txt: ./txt/cord-288982-63ddlh20.txt summary: Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. In the last decade, rapid point-of-care (POC) diagnostic tests fulfilling the ASSURED criteria (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable) have become commercially available and are widely used for infectious diseases such as malaria, HIV and syphilis. abstract: Diagnostics play a critical role in clinical decision making, and in disease control and prevention. Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. A new generation of POC molecular tests that are highly sensitive and specific, robust and easy to use are now available for deployment in low resource settings. Decentralisation of testing outside of the laboratory can put tremendous stress on the healthcare system and presents challenges for training and quality assurance. A feature of many of these POC molecular devices is that they are equipped with data transmission capacities. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. Data connectivity also allows control programmes to monitor the quality of tests and testing, and optimise supply chain management; thus, increasing the efficiency of healthcare systems and improving patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/26553825/ doi: 10.1093/inthealth/ihv062 id: cord-004335-bw3tziup author: Perez-Zsolt, Daniel title: When Dendritic Cells Go Viral: The Role of Siglec-1 in Host Defense and Dissemination of Enveloped Viruses date: 2019-12-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Dendritic cells (DCs) are among the first cells that recognize incoming viruses at the mucosal portals of entry. Initial interaction between DCs and viruses facilitates cell activation and migration to secondary lymphoid tissues, where these antigen presenting cells (APCs) prime specific adaptive immune responses. Some viruses, however, have evolved strategies to subvert the migratory capacity of DCs as a way to disseminate infection systemically. Here we focus on the role of Siglec-1, a sialic acid-binding type I lectin receptor potently upregulated by type I interferons on DCs, that acts as a double edge sword, containing viral replication through the induction of antiviral immunity, but also favoring viral spread within tissues. Such is the case for distant enveloped viruses like human immunodeficiency virus (HIV)-1 or Ebola virus (EBOV), which incorporate sialic acid-containing gangliosides on their viral membrane and are effectively recognized by Siglec-1. Here we review how Siglec-1 is highly induced on the surface of human DCs upon viral infection, the way this impacts different antigen presentation pathways, and how enveloped viruses have evolved to exploit these APC functions as a potent dissemination strategy in different anatomical compartments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7019426/ doi: 10.3390/v12010008 id: cord-285443-9y2kkmby author: Pessi, Antonello title: Cholesterol‐conjugated peptide antivirals: a path to a rapid response to emerging viral diseases date: 2014-10-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: While it is now possible to identify and genetically fingerprint the causative agents of emerging viral diseases, often with extraordinary speed, suitable therapies cannot be developed with equivalent speed, because drug discovery requires information that goes beyond knowledge of the viral genome. Peptides, however, may represent a special opportunity. For all enveloped viruses, fusion between the viral and the target cell membrane is an obligatory step of the life cycle. Class I fusion proteins harbor regions with a repeating pattern of amino acids, the heptad repeats (HRs), that play a key role in fusion, and HR‐derived peptides such as enfuvirtide, in clinical use for HIV, can block the process. Because of their characteristic sequence pattern, HRs are easily identified in the genome by means of computer programs, providing the sequence of candidate peptide inhibitors directly from genomic information. Moreover, a simple chemical modification, the attachment of a cholesterol group, can dramatically increase the antiviral potency of HR‐derived inhibitors and simultaneously improve their pharmacokinetics. Further enhancement can be provided by dimerization of the cholesterol‐conjugated peptide. The examples reported so far include inhibitors of retroviruses, paramyxoviruses, orthomyxoviruses, henipaviruses, coronaviruses, and filoviruses. For some of these viruses, in vivo efficacy has been demonstrated in suitable animal models. The combination of bioinformatic lead identification and potency/pharmacokinetics improvement provided by cholesterol conjugation may form the basis for a rapid response strategy, where development of an emergency cholesterol‐conjugated therapeutic would immediately follow the availability of the genetic information of a new enveloped virus. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/25331523/ doi: 10.1002/psc.2706 id: cord-354974-bh2expef author: Peterson, Ingrid title: Respiratory Virus–Associated Severe Acute Respiratory Illness and Viral Clustering in Malawian Children in a Setting With a High Prevalence of HIV Infection, Malaria, and Malnutrition date: 2016-09-13 words: 3863.0 sentences: 192.0 pages: flesch: 45.0 cache: ./cache/cord-354974-bh2expef.txt txt: ./txt/cord-354974-bh2expef.txt summary: BACKGROUND: We used data from 4 years of pediatric severe acute respiratory illness (SARI) sentinel surveillance in Blantyre, Malawi, to identify factors associated with clinical severity and coviral clustering. A total of 605 SARI cases (26.8%) had warning signs, which were positively associated with HIV infection (adjusted risk ratio [aRR], 2.4; 95% confidence interval [CI], 1.4–3.9), respiratory syncytial virus infection (aRR, 1.9; 95% CI, 1.3–3.0) and rainy season (aRR, 2.4; 95% CI, 1.6–3.8). In the context of a low-income population with multiple drivers of immune compromise (eg, human immunodeficiency virus [HIV] infection, malnutrition, and malaria) [11] , we conducted active surveillance at a large urban teaching hospital in Malawi to estimate the incidence of childhood SARI and explore the association of SARI clinical severity with HIV infection and clustering of respiratory viral coinfection. After adjustment for age, sex, and HIV status, rainy season recruitment was significantly associated with SARI with warning signs in influenza virus-positive patients with SARI (aRR, 3.42; 95% CI, 1.37-8.53; analysis not shown). abstract: BACKGROUND: We used data from 4 years of pediatric severe acute respiratory illness (SARI) sentinel surveillance in Blantyre, Malawi, to identify factors associated with clinical severity and coviral clustering. METHODS: From January 2011 to December 2014, 2363 children aged 3 months to 14 years presenting to the hospital with SARI were enrolled. Nasopharyngeal aspirates were tested for influenza virus and other respiratory viruses. We assessed risk factors for clinical severity and conducted clustering analysis to identify viral clusters in children with viral codetection. RESULTS: Hospital-attended influenza virus–positive SARI incidence was 2.0 cases per 10 000 children annually; it was highest among children aged <1 year (6.3 cases per 10 000), and human immunodeficiency virus (HIV)–infected children aged 5–9 years (6.0 cases per 10 000). A total of 605 SARI cases (26.8%) had warning signs, which were positively associated with HIV infection (adjusted risk ratio [aRR], 2.4; 95% confidence interval [CI], 1.4–3.9), respiratory syncytial virus infection (aRR, 1.9; 95% CI, 1.3–3.0) and rainy season (aRR, 2.4; 95% CI, 1.6–3.8). We identified 6 coviral clusters; 1 cluster was associated with SARI with warning signs. CONCLUSIONS: Influenza vaccination may benefit young children and HIV-infected children in this setting. Viral clustering may be associated with SARI severity; its assessment should be included in routine SARI surveillance. url: https://academic.oup.com/jid/article-pdf/214/11/1700/18070040/jiw426.pdf doi: 10.1093/infdis/jiw426 id: cord-017600-4e7mw041 author: Pfister, H. -W. title: Infektionen date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Trotz Weiterentwicklung moderner Antibiotika in den letzten Jahren sind die Letalitätszahlen der bakteriellen (eitrigen) Meningitis weiterhin hoch; Überlebende haben häufig neurologische Residuen. Die ungünstigen klinischen Verläufe der bakteriellen Meningitis sind meist Folge intrakranieller Komplikationen, wie z. B. eines generalisierten Hirnödems, einer zerebrovaskulären arteriellen oder venösen Beteiligung oder eines Hydrozephalus. Als Folge dieser Komplikationen kommt es häufig zu einem Anstieg des intrakraniellen Drucks. Bei schweren, komplizierten klinischen Verläufen der bakteriellen Meningitis kommen oft adjuvante Therapiemaßnahmen (z. B. intravenöse Gabe von hyperosmolaren Substanzen, externe Ventrikeldrainage) zum Einsatz. Bei Nachweis einer meningitisassoziierten septischen Sinus-/Venenthrombose erfolgt die dosisadaptierte intravenöse Heparintherapie. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122197/ doi: 10.1007/978-3-540-68317-9_35 id: cord-254951-anfkuigj author: Pierre, Gashema title: Attendance to HIV Antiretroviral Collection Clinic Appointments During COVID-19 Lockdown. A Single Center Study in Kigali, Rwanda date: 2020-06-25 words: 1213.0 sentences: 66.0 pages: flesch: 57.0 cache: ./cache/cord-254951-anfkuigj.txt txt: ./txt/cord-254951-anfkuigj.txt summary: According to The Joint United Nations Programme on HIV and AIDS (UNAIDS) and the World Health Organization (WHO), a 6-month disruption of antiretroviral therapy (ART) during the COVID-19 pandemic in sub-Saharan Africa will increase HIV-related death rate by more than half a million [8] . Given the recent total lockdown in Rwanda, this note presents findings from a study aimed to assess attendance to ART collection clinic appointments in the period 21 March to 30 April 2020 in Kigali, Rwanda. Less than half (48%) had attended scheduled ART collection clinic appointments during the lockdown period of 21 March to 30 April 2020. There was an association between place of residence and attendance status (p = 0.040), 50% staying within Kigali attended scheduled ART collection clinic appointments during the lockdown period compared to 35% among those living outside Kigali. abstract: nan url: https://doi.org/10.1007/s10461-020-02956-5 doi: 10.1007/s10461-020-02956-5 id: cord-350540-s6is9ndm author: Pinto, Rogério M. title: COVID-19 Pandemic Disrupts HIV Continuum of Care and Prevention: Implications for Research and Practice Concerning Community-Based Organizations and Frontline Providers date: 2020-04-28 words: 2028.0 sentences: 100.0 pages: flesch: 49.0 cache: ./cache/cord-350540-s6is9ndm.txt txt: ./txt/cord-350540-s6is9ndm.txt summary: title: COVID-19 Pandemic Disrupts HIV Continuum of Care and Prevention: Implications for Research and Practice Concerning Community-Based Organizations and Frontline Providers Community-based organizations (CBOs) employ frontline service providers-social workers, health educators, navigators-to help (1) individuals of unknown HIV status access testing; (2) those at high-risk for HIV but who test negative to access physicians who can prescribe PrEP; Nonetheless, community-engaged research suggests that, prior to the COVID-19 pandemic, these frontline providers had not been consistent in how often or in how they linked clients to care continuum services. Providers having day-to-day interactions with clients in primary care, outpatient, and prevention settings are poised to help PLWH and vulnerable individuals overcome HIV-related stigma, PrEP stigma, inadequate health insurance, and can help improve HIV testing rates [20] [21] [22] [23] [24] [25] . abstract: nan url: https://doi.org/10.1007/s10461-020-02893-3 doi: 10.1007/s10461-020-02893-3 id: cord-264050-6zpw6itb author: Pirofski, Liise-anne title: Immune-Mediated Damage Completes the Parabola: Cryptococcus neoformans Pathogenesis Can Reflect the Outcome of a Weak or Strong Immune Response date: 2017-12-12 words: 2752.0 sentences: 121.0 pages: flesch: 36.0 cache: ./cache/cord-264050-6zpw6itb.txt txt: ./txt/cord-264050-6zpw6itb.txt summary: The demonstration that host-mediated damage can drive cryptococcal disease provides proof of concept that the parabola put forth in the damage-response framework has the flexibility to depict complex and changing outcomes of host-microbe interaction. However, the emergence of Cryptococcus gattii in apparently healthy persons in the Pacific Northwest (7) and the unexpected appearance of immune reconstitution inflammatory syndrome (IRIS)-associated cryptococcosis in patients with HIV/AIDS after initiation of antiretroviral therapy (ART) (8, 9) revealed that the host immune response itself can contribute to the pathogenesis of cryptococcosis. The emergence of IRIS-associated cryptococcosis in the setting of ART initiation provided clear evidence that host damage in patients with cryptococcal disease may be driven by inflammation (12) . Chemokine levels and chemokine receptor expression in the blood and the cerebrospinal fluid of HIV-infected patients with cryptococcal meningitis and cryptococcosis-associated immune reconstitution inflammatory syndrome abstract: Cryptococcosis occurs most frequently in immunocompromised individuals. This has led to the prevailing view that this disease is the result of weak immune responses that cannot control the fungus. However, increasingly, clinical and experimental studies have revealed that the host immune response can contribute to cryptococcal pathogenesis, including the recent study of L. M. Neal et al. (mBio 8:e01415-17, 2017, https://doi.org/10.1128/mBio.01415-17) that reports that CD4(+) T cells mediate tissue damage in experimental murine cryptococcosis. This finding has fundamental implications for our understanding of the pathogenesis of cryptococcal disease; it helps explain why immunotherapy has been largely unsuccessful in treatment and provides insight into the paradoxical observation that HIV-associated cryptococcosis may have a better prognosis than cryptococcosis in those with no known immune impairment. The demonstration that host-mediated damage can drive cryptococcal disease provides proof of concept that the parabola put forth in the damage-response framework has the flexibility to depict complex and changing outcomes of host-microbe interaction. url: https://www.ncbi.nlm.nih.gov/pubmed/29233901/ doi: 10.1128/mbio.02063-17 id: cord-005335-u04cxiej author: Podder, C. N. title: Mathematical Analysis of a Model for Assessing the Impact of Antiretroviral Therapy, Voluntary Testing and Condom Use in Curtailing the Spread of HIV date: 2011-05-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This paper presents a deterministic model for evaluating the impact of anti-retroviral drugs (ARVs), voluntary testing (using standard antibody-based and a DNA-based testing methods) and condom use on the transmission dynamics of HIV in a community. Rigorous qualitative analysis of the model show that it has a globally-stable disease-free equilibrium whenever a certain epidemiological threshold, known as the effective reproduction number [Formula: see text], is less than unity. The model has an endemic equilibrium whenever [Formula: see text]. The endemic equilibrium is shown to be locally-asymptotically stable for a special case. Numerical simulations of the model show that the use of the combined testing and treatment strategy is more effective than the use of the standard ELISA testing method with ARV treatment, even for the use of condoms as a singular strategy. Furthermore, the universal strategy (which involves the use of condoms, the two testing methods and ARV treatment) is always more effective than the combined use of the standard ELISA testing method and ARVs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090688/ doi: 10.1007/s12591-011-0090-6 id: cord-260695-qwepi0we author: Postler, Thomas S. title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Long non-coding RNAs (lncRNAs) are rapidly emerging as important regulators of a diverse array of cellular functions. Here, we describe a meta-analysis of two independent RNA-seq studies to identify lncRNAs that are differentially expressed upon HIV-1 infection. Only three lncRNA genes exhibited altered expression of ≥2-fold in HIV-1-infected cells. Of these, the uncharacterized lncRNA LINC00173 was chosen for further study. Both transcript variants of LINC00173 (lnc173 TSV1 and 2) could be detected by qPCR, localized predominantly to the nucleus and were reproducibly up-regulated during infection. Knock-out of the LINC00173 locus did not have detectable effects on HIV-1 replication. Interestingly, however, stimulation of Jurkat T cells with PMA/ionomycin resulted in a decrease of lnc173 expression, and Jurkat cells deficient for lnc173 on average expressed higher levels of specific cytokines than control cells. These data suggest that lnc173 may have a role in the regulation of cytokines in T cells. url: https://doi.org/10.1016/j.virol.2017.08.006 doi: 10.1016/j.virol.2017.08.006 id: cord-252167-2zxw3sh8 author: Poteat, Tonia C title: Celebrating the struggle against homophobia, transphobia and biphobia as central to ending HIV transmission by 2030 date: 2020-05-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32407566/ doi: 10.1002/jia2.25532 id: cord-284409-xiyeceib author: Prabakaran, Ponraj title: The Antibody Germline/Maturation Hypothesis, Elicitation of Broadly Neutralizing Antibodies Against HIV-1 and Cord Blood IgM Repertoires date: 2014-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We have previously observed that all known potent broadly neutralizing antibodies (bnAbs) against HIV-1 are highly divergent from their putative germline predecessors in contrast to bnAbs against viruses causing acute infections such as henipaviruses and SARS CoV, which are much less divergent from their germline counterparts. Consequently, we have hypothesized that germline antibodies may not bind to the HIV-1 envelope glycoprotein (Env) because they are so different compared to the highly somatically mutated HIV-1-specific bnAbs. We have further hypothesized that the immunogenicity of highly conserved epitopes on the HIV-1 envelope glycoproteins (Envs) may be reduced or eliminated by their very weak or absent interactions with germline antibodies and immune responses leading to the elicitation of bnAbs may not be initiated and/or sustained. Even if such responses are initiated, the maturation pathways are so extraordinarily complex that prolonged periods of time may be required for elicitation of bnAbs with defined unique sequences. We provided the initial evidence supporting this antibody germline/maturation hypothesis, which prompted a number of studies to design vaccine immunogens that could bind putative germline predecessors of known bnAbs and to explore complex B cell lineages. However, guiding the immune system through the exceptionally complex antibody maturation pathways to elicit known bnAbs remains a major challenge. Here, we discuss studies exploring the antibody germline/maturation hypothesis as related to elicitation of bnAbs against HIV-1 and present our recent data demonstrating the existence of germline-like precursors of VRC01 antibodies in a human cord blood IgM library. url: https://doi.org/10.3389/fimmu.2014.00398 doi: 10.3389/fimmu.2014.00398 id: cord-302854-buzyani0 author: Prabakaran, Ponraj title: Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing date: 2012-08-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Our understanding of how antibodies are generated and function could help develop effective vaccines and antibody-based therapeutics against viruses such as HIV-1, SARS coronavirus (SARS CoV), and Hendra and Nipah viruses (henipaviruses). Although broadly neutralizing antibodies (bnAbs) against the HIV-1 were observed in patients, elicitation of such bnAbs remains a major challenge when compared to other viral targets. We previously hypothesized that HIV-1 could have evolved a strategy to evade the immune system due to absent or very weak binding of germline antibodies to the conserved epitopes that may not be sufficient to initiate and/or maintain an effective immune response. To further explore our hypothesis, we used the 454 sequence analysis of a large naïve library of human IgM antibodies which had been used for selecting antibodies against SARS CoV receptor-binding domain (RBD), and soluble G proteins (sG) of henipaviruses. We found that the human IgM repertoires from the 454 sequencing have diverse germline usages, recombination patterns, junction diversity, and a lower extent of somatic mutation. In this study, we identified antibody maturation intermediates that are related to bnAbs against the HIV-1 and other viruses as observed in normal individuals, and compared their genetic diversity and somatic mutation level along with available structural and functional data. Further computational analysis will provide framework for understanding the underlying genetic and molecular determinants related to maturation pathways of antiviral bnAbs that could be useful for applying novel approaches to the design of effective vaccine immunogens and antibody-based therapeutics. url: https://doi.org/10.3389/fmicb.2012.00277 doi: 10.3389/fmicb.2012.00277 id: cord-029450-4rnrq78l author: Prattichizzo, Francesco title: Response to: Letter to the Editor on “Bonafè M, Prattichizzo F, Giuliani A, Storci G, Sabbatinelli J, Olivieri F. Inflamm-aging: Why older men are the most susceptible to SARS-CoV-2 complicated outcomes. Cytokine Growth Factor Rev” by Eugenia Quiros-Roldan, Giorgio Biasiotto and Isabella Zanella date: 2020-07-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368416/ doi: 10.1016/j.cytogfr.2020.07.013 id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Real-time PCR array for rapid detection of multiple viral pathogens should be highly useful in cases where the sample volume and the time of testing are limited, i.e. in the eligibility testing of tissue and organ donors. FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). One hundred twenty (120) primers were designed using a combination of bioinformatics approaches, and, after experimental testing, 24 primer sets targeting eight viral pathogens were selected to set up the array with SYBR Green chemistry. The specificity and sensitivity of the virus-specific primer sets selected for the array were evaluated using analytical panels with known amounts of viruses spiked into human plasma. The array detected: 10 genome equivalents (geq)/ml of HIV-2 and HCV, 50 geq of HIV-1 (subtype B), HBV (genotype A) and WNV. It detected 100–1,000 geq/ml of plasma of HIV-1 subtypes (A – G), group N and CRF (AE and AG) isolates. Further evaluation with a panel consisting of 28 HIV-1 and HIV-2 clinical isolates revealed no cross-reactivity of HIV-1 or HIV-2 specific primers with another type of HIV. All 28 viral isolates were identified with specific primer sets targeting the most conserved genome areas. The PCR array correctly identified viral infections in a panel of 17 previously quantified clinical plasma samples positive for HIV-1, HCV or HBV at as low as several geq per PCR reaction. CONCLUSIONS: The viral array described here demonstrated adequate performance in the testing of donors’ clinical samples. Further improvement in its sensitivity for the broad spectrum of HIV-1 subtypes is under development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422334/ doi: 10.1371/journal.pone.0043246 id: cord-261287-l4649du3 author: Puoti, Massimo title: A randomized, controlled trial of triple antiviral therapy as initial treatment of chronic hepatitis C in HIV-infected patients() date: 2004-05-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND/AIMS: Interferon and ribavirin combination therapy for chronic hepatitis C induces a low response rate in human immunodeficiency virus (HIV) infected patients. To assess the impact of intensification of interferon administration and of the addition of amantadine on the efficacy and safety of standard anti-hepatitis C virus (HCV) treatment in HIV-infected patients. METHODS: Multicentre, prospective, open-label, randomized, phase III clinical trial. Eighty co-infected patients were randomized to receive ribavirin 800–1000 mg/day in combination with, group A: interferon alpha2a 3 MIU thrice weekly; group B: IFNα2a 3 MIU daily, plus amantadine 200 mg/day; treatment duration was 24–48 weeks according to HCV genotype. RESULTS: Forty-one patients were randomized in group A and 39 in group B. Intention-to-treat analysis showed a sustained virological response, defined as HCV-RNA negativization, 6 months after stopping treatment in 22% of patients from group A and 13% from group B (P>0.05). The lack of a 2-log drop in HCV-RNA levels after 12 weeks of treatment showed a 100% predictive value of lack of sustained response. CONCLUSIONS: Amantadine addition and interferon intensification do not improve the low efficacy of combination of interferon alfa plus ribavirin in HIV/HCV co-infected patients. Patients with no early virologic response did not have any probability of sustained response. url: https://www.ncbi.nlm.nih.gov/pubmed/15288482/ doi: 10.1016/j.jhep.2004.04.016 id: cord-018864-c1r2n17o author: Pöhlmann, Stefan title: Attachment of human immunodeficiency virus to cells and its inhibition date: 2007 words: 5827.0 sentences: 238.0 pages: flesch: 38.0 cache: ./cache/cord-018864-c1r2n17o.txt txt: ./txt/cord-018864-c1r2n17o.txt summary: In fact, the determinant role played by dendritic cells (DCs) in HIV-1 transmission might rely on specific interactions between gp120 and C-type lectins, of which the DC-specific intercellular adhesion molecule-3 (ICAM-3) grabbing nonintegrin (DC-SIGN) and DC-SIGNR (for DC-SIGN-related) are the best studied [10, 11]. In addition to its own virus-encoded envelope glycoproteins, the virus incorporates many different cellular proteins normally found on the cell surface (reviewed in [12] [13] [14] [15] The process of incorporation of host cell membrane proteins was found to be conserved among all tested HIV-1 subtypes and strains that were expanded in natural cellular reservoirs, such as mitogen-activated peripheral blood lymphocytes and human lymphoid tissue cultured ex vivo [27] [28] [29] [30] [31] [32] . Statin compounds reduce human immunodeficiency virus type 1 replication by preventing the interaction between virion-associated host intercellular adhesion molecule 1 and its natural cell surface ligand LFA-1 A dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN)-related protein is highly expressed on human liver sinusoidal endothelial cells and promotes HIV-1 infection abstract: The entry of enveloped viruses involves virus adsorption followed by close apposition of the viral and plasma membranes. This multistep process is initiated by specific binding interactions between glycoproteins in the viral envelope and appropriate receptors on the cell surface. In the case of HIV-1, attachment of virions to the cell surface is attributed to a high affinity interaction between envelope spike glycoproteins (Env, composed of the surface protein gp120 and the transmembrane protein gp41) and a complex made of the primary CD4 receptor and a seven-transmembrane co-receptor (e.g., CXCR4 or CCR5) (reviewed in [1]). Then a chain of dynamic events take place that enable the viral nucleocapsid to penetrate within the target cell following the destabilization of membrane microenvironment and the formation of a fusion pore. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123856/ doi: 10.1007/978-3-7643-7783-0_3 id: cord-302321-6x7hyald author: Qiao, Shan title: Disparity in HIV Service Interruption in the Outbreak of COVID-19 in South Carolina date: 2020-08-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: To examine HIV service interruptions during the COIVD-19 outbreak in South Carolina (SC) and identify geospatial and socioeconomic correlates of such interruptions, we collected qualitative, geospatial, and quantitative data from 27 Ryan White HIV clinics in SC in March, 2020. HIV service interruptions were categorized (none, minimal, partial, and complete interruption) and analyzed for geospatial heterogeneity. Nearly 56% of the HIV clinics were partially interrupted and 26% were completely closed. Geospatial heterogeneity of service interruption existed but did not exactly overlap with the geospatial pattern of COVID-19 outbreak. The percentage of uninsured in the service catchment areas was significantly correlated with HIV service interruption (F = 3.987, P = .02). This mixed-method study demonstrated the disparity of HIV service interruptions in the COVID-19 in SC and suggested a contribution of existing socioeconomic gaps to this disparity. These findings may inform the resources allocation and future strategies to respond to public health emergencies. url: https://www.ncbi.nlm.nih.gov/pubmed/32856176/ doi: 10.1007/s10461-020-03013-x id: cord-329890-wg23sa1u author: Quah, Stella R. title: Public image and governance of epidemics: Comparing HIV/AIDS and SARS date: 2007-02-28 words: 9734.0 sentences: 423.0 pages: flesch: 49.0 cache: ./cache/cord-329890-wg23sa1u.txt txt: ./txt/cord-329890-wg23sa1u.txt summary: Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people''s lifestyles and approaches to the control and prevention of epidemics. The second assumption is that in contrast to SARS, the overall negative public ''image'' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people''s perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. The second assumption to be explored here is that in contrast to SARS, the overall negative social ''image'' of HIV/AIDS as a disease associated with particular types of individuals tends to weaken people''s perception of susceptibility and, correspondingly, tends to discourage public support for robust preventive efforts at the community level. abstract: Abstract A comparative analysis of the 2002–2003 infectious disease outbreak, severe acute respiratory syndrome (SARS), and the HIV/AIDS epidemic that has affected the world over the past two decades reveals the significant role of socio-cultural beliefs and attitudes in the shaping of people's lifestyles and approaches to the control and prevention of epidemics. The main research question is: what can we learn from the SARS experience about effective prevention of HIV/AIDS? The sources of data include population figures on the development of these epidemics and findings from two sociological studies of representative samples of Singapore's multi-ethnic population. The comparative study illustrates the impact of cultural beliefs and attitudes in shaping the public image of these two different infectious diseases; the relevance of public image of the disease for effective prevention and control of epidemics. url: https://www.ncbi.nlm.nih.gov/pubmed/16632071/ doi: 10.1016/j.healthpol.2006.03.002 id: cord-317990-61is0hgm author: Quinn, Katherine G. title: Applying the Popular Opinion Leader Intervention for HIV to COVID-19 date: 2020-06-25 words: 2198.0 sentences: 104.0 pages: flesch: 41.0 cache: ./cache/cord-317990-61is0hgm.txt txt: ./txt/cord-317990-61is0hgm.txt summary: have recently noted, the spread of medical mistrust and public health misinformation evident in the current COVID-19 pandemic mirrors long-standing challenges in the HIV epidemic [1] . Accordingly, we can take lessons learned from the HIV epidemic about the spread of public health information and its effects on behavior change apply them to the current pandemic. This Note focuses on social networks and the popular opinion leader model, which may be key in disseminating trusted information about COVID-19 in a rapidly changing public health landscape. Yet, engaging trusted community leaders and social influencers to disseminate accurate public health information may help overcome these challenges to address inequities reduce COVID-19 stigma, and strengthen norms that contribute to sustained behavior change (e.g. social distancing, mask wearing, hand washing). Aligned with social distancing guidelines for COVID-19 prevention, we are using online social networks as an efficient and effective way to disseminate accurate information and influence community norms and behaviors [36] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32588259/ doi: 10.1007/s10461-020-02954-7 id: cord-278456-gsv6dh36 author: Qureshi, Abid title: AVCpred: an integrated web server for prediction and design of antiviral compounds date: 2016-09-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral infections constantly jeopardize the global public health due to lack of effective antiviral therapeutics. Therefore, there is an imperative need to speed up the drug discovery process to identify novel and efficient drug candidates. In this study, we have developed quantitative structure–activity relationship (QSAR)‐based models for predicting antiviral compounds (AVCs) against deadly viruses like human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human herpesvirus (HHV) and 26 others using publicly available experimental data from the ChEMBL bioactivity database. Support vector machine (SVM) models achieved a maximum Pearson correlation coefficient of 0.72, 0.74, 0.66, 0.68, and 0.71 in regression mode and a maximum Matthew's correlation coefficient 0.91, 0.93, 0.70, 0.89, and 0.71, respectively, in classification mode during 10‐fold cross‐validation. Furthermore, similar performance was observed on the independent validation sets. We have integrated these models in the AVCpred web server, freely available at http://crdd.osdd.net/servers/avcpred. In addition, the datasets are provided in a searchable format. We hope this web server will assist researchers in the identification of potential antiviral agents. It would also save time and cost by prioritizing new drugs against viruses before their synthesis and experimental testing. url: https://doi.org/10.1111/cbdd.12834 doi: 10.1111/cbdd.12834 id: cord-305195-e41yfo89 author: Rainwater-Lovett, Kaitlin title: Viral Epidemiology: Tracking Viruses with Smartphones and Social Media date: 2016-02-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The science of epidemiology has been developed over the last 200 years, using traditional methods to describe the distribution of diseases by person, place, and time. However, in the last several decades, a new set of technologies has become available, based on the methods of computer sciences, systems biology, and the extraordinary powers of the Internet. Technological and analytical advances can enhance traditional epidemiological methods to study the emergence, epidemiology, and transmission dynamics of viruses and associated diseases. Social media are increasingly used to detect the emergence and geographic spread of viral disease outbreaks. Large-scale population movement can be estimated using satellite imagery and mobile phone use, and fine-scale population movement can be tracked using global positioning system loggers, allowing estimation of transmission pathways and contact patterns at different spatial scales. Advances in genomic sequencing and bioinformatics permit more accurate determination of viral evolution and the construction of transmission networks, also at different spatial and temporal scales. Phylodynamics links evolutionary and epidemiological processes to better understand viral transmission patterns. More complex and realistic mathematical models of virus transmission within human and animal populations, including detailed agent-based models, are increasingly used to predict transmission patterns and the impact of control interventions such as vaccination and quarantine. In this chapter, we will briefly review traditional epidemiological methods and then describe the new technologies with some examples of their application. url: https://api.elsevier.com/content/article/pii/B9780128009642000185 doi: 10.1016/b978-0-12-800964-2.00018-5 id: cord-275677-hbv49e01 author: Ramana, Lakshmi Narashimhan title: Targeting strategies for delivery of anti-HIV drugs date: 2014-10-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human Immunodeficiency Virus (HIV) infection remains a significant cause of mortality globally. Though antiretroviral therapy has significantly reduced AIDS-related morbidity and mortality, there are several drawbacks in the current therapy, including toxicity, drug–drug interactions, development of drug resistance, necessity for long-term drug therapy, poor bio-availability and lack of access to tissues and reservoirs. To circumvent these problems, recent anti-HIV therapeutic research has focused on improving drug delivery systems through drug delivery targeted specifically to host cells infected with HIV or could potentially get infected with HIV. In this regard, several surface molecules of both viral and host cell origin have been described in recent years, that would enable targeted drug delivery in HIV infection. In the present review, we provide a comprehensive overview of the need for novel drug delivery systems, and the successes and challenges in the identification of novel viral and host-cell molecules for the targeted drug delivery of anti-HIV drugs. Such targeted anti-retroviral drug delivery approaches could pave the way for effective treatment and eradication of HIV from the body. url: https://api.elsevier.com/content/article/pii/S0168365914005835 doi: 10.1016/j.jconrel.2014.08.003 id: cord-278174-znc99yos author: Ramsey, Glenn title: Managing recalls and withdrawals of blood components date: 2004-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Donor centers are issuing a growing number of recalls and market withdrawals to hospital transfusion services about blood components. More than 1 in 2,000 units were recalled in the late 1990s in the United States. The most common reason for these notices from donor centers is postdonation donor information. Most of these units had been transfused, and many present a “risk of a risk” (ie, a problem might have been present that might have affected the recipient). A few regulations and standards address recalls in general terms, but transfusion services generally have wide discretion in the management of specific common recall problems. The Food and Drug Administration (FDA) is now including posttransfusion evaluations in its guidelines for emerging infectious threats to the blood supply. We suggest that hospital transfusion services should have standard operating procedures for managing recalls and that the hospital transfusion committee and the quality management program should provide local input or oversight. Using the FDA’s categories of donor center biological product deviations, we provide recommendations to consider for when to notify the recipient’s physician, after postdonation information is received about a previously transfused blood component. More study of this important everyday issue in transfusion medicine is highly desirable. url: https://www.ncbi.nlm.nih.gov/pubmed/14689376/ doi: 10.1016/j.tmrv.2003.10.005 id: cord-009891-gqrhbhbn author: Rassool, G. Hussein title: Current issues and forthcoming events date: 2003-09-03 words: 3466.0 sentences: 168.0 pages: flesch: 49.0 cache: ./cache/cord-009891-gqrhbhbn.txt txt: ./txt/cord-009891-gqrhbhbn.txt summary: The Centers for Disease Control and Prevention (CDC), USA, reports that ''transmission to health care workers appears to have occurred after close contact with symptomatic individuals (e.g. persons with fever or respiratory symptoms) before recommended infection control precautions for SARS were implemented (i.e. unprotected exposures).'' There is also a possibility that the causative agent can remain viable for extended periods of time after drying on environmental surfaces. Preliminary results of a large-scale trial of a candidate AIDS vaccine announced by the US-based biotechnology company VaxGen suggest that it is possible to protect some individuals from HIV infection. The result is that poor diagnosis of pain in cancer patients remains a significant problem, with many physicians finding it difficult to differentiate between the various pain types; and, many underestimating its severity. Poor diagnosis, poor assessment, the choice of less appropriate treatments, plus patients and physicians fears about controlled drugs such as morphine all contribute to under treatment of cancer pain. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166755/ doi: 10.1046/j.1365-2648.2003.02701.x-i2 id: cord-011155-zraqyx78 author: Reif, Lindsey K. title: Interventions to Improve Antiretroviral Therapy Adherence Among Adolescents and Youth in Low- and Middle-Income Countries: A Systematic Review 2015–2019 date: 2020-03-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Adolescents and youth living with HIV have poorer antiretroviral treatment (ART) adherence and viral suppression outcomes than all other age groups. Effective interventions promoting adherence are urgently needed. We reviewed and synthesized recent literature on interventions to improve ART adherence among this vulnerable population. We focus on studies conducted in low- and middle-income countries (LMIC) where the adolescent and youth HIV burden is greatest. Articles published between September 2015 and January 2019 were identified through PubMed. Inclusion criteria were: [1] included participants ages 10–24 years; [2] assessed the efficacy of an intervention to improve ART adherence; [3] reported an ART adherence measurement or viral load; [4] conducted in a LMIC. Articles were reviewed for study population characteristics, intervention type, study design, outcomes measured, and intervention effect. Strength of each study’s evidence was evaluated according to an adapted World Health Organization GRADE system. Articles meeting all inclusion criteria except being conducted in an LMIC were reviewed for results and potential transportability to a LMIC setting. Of 108 articles identified, 7 met criteria for inclusion. Three evaluated patient-level interventions and four evaluated health services interventions. Of the patient-level interventions, two were experimental designs and one was a retrospective cohort study. None of these interventions improved ART adherence or viral suppression. Of the four health services interventions, two targeted stable patients and reduced the amount of time spent in the clinic or grouped patients together for bi-monthly meetings, and two targeted patients newly diagnosed with HIV or not yet deemed clinically stable and augmented clinical care with home-based case-management. The two studies targeting stable patients used retrospective cohort designs and found that adolescents and youth were less likely to maintain viral suppression than children or adults. The two studies targeting patients not yet deemed clinically stable included one experimental and one retrospective cohort design and showed improved ART adherence and viral suppression outcomes. ART adherence and viral suppression outcomes remain a major challenge among adolescents and youth. Intensive home-based case management models of care hold promise for improving outcomes in this population and warrant further research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223708/ doi: 10.1007/s10461-020-02822-4 id: cord-331673-xv1tcugl author: Reina, Giacomo title: Hard Nanomaterials in Time of Viral Pandemics date: 2020-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: [Image: see text] The SARS-Cov-2 pandemic has spread worldwide during 2020, setting up an uncertain start of this decade. The measures to contain infection taken by many governments have been extremely severe by imposing home lockdown and industrial production shutdown, making this the biggest crisis since the second world war. Additionally, the continuous colonization of wild natural lands may touch unknown virus reservoirs, causing the spread of epidemics. Apart from SARS-Cov-2, the recent history has seen the spread of several viral pandemics such as H2N2 and H3N3 flu, HIV, and SARS, while MERS and Ebola viruses are considered still in a prepandemic phase. Hard nanomaterials (HNMs) have been recently used as antimicrobial agents, potentially being next-generation drugs to fight viral infections. HNMs can block infection at early (disinfection, entrance inhibition) and middle (inside the host cells) stages and are also able to mitigate the immune response. This review is focused on the application of HNMs as antiviral agents. In particular, mechanisms of actions, biological outputs, and limitations for each HNM will be systematically presented and analyzed from a material chemistry point-of-view. The antiviral activity will be discussed in the context of the different pandemic viruses. We acknowledge that HNM antiviral research is still at its early stage, however, we believe that this field will rapidly blossom in the next period. url: https://doi.org/10.1021/acsnano.0c04117 doi: 10.1021/acsnano.0c04117 id: cord-263965-i8yutik6 author: Relf, Michael V. title: What's Old is New! Similarities Between SARS-CoV-2 and HIV date: 2020-04-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32282428/ doi: 10.1097/jnc.0000000000000174 id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 words: 10548.0 sentences: 574.0 pages: flesch: 43.0 cache: ./cache/cord-330800-s91zfzfi.txt txt: ./txt/cord-330800-s91zfzfi.txt summary: e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. abstract: Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32908530/ doi: 10.1155/2020/8832728 id: cord-001385-rb5vwolt author: Reuven, Eliran Moshe title: The HIV-1 Envelope Transmembrane Domain Binds TLR2 through a Distinct Dimerization Motif and Inhibits TLR2-Mediated Responses date: 2014-08-14 words: 6147.0 sentences: 318.0 pages: flesch: 51.0 cache: ./cache/cord-001385-rb5vwolt.txt txt: ./txt/cord-001385-rb5vwolt.txt summary: Figure 1A and B show that 20 minutes after addition of LTA to RAW cells that were pre-incubated with the gp41 TMD peptide, there was a significant decrease in ERK1,2 phosphorylation compared to nontreated cells, indicating less receptor activation. We next measured the expression levels of NFkB downstream genes; Tumor Necrosis Factor a (TNFa), a hallmark cytokine of TLR activation, and Monocyte Chemotactic Protein 1 (MCP-1), a major chemokine mainly secreted by macrophages [22] , in order to ensure that the inhibitive effect on ERK1,2 phosphorylation is a result of inhibition of TLR2 signaling. IL-6 is an additional target gene of TLR2 but it is transcribed via a different transcription factor complex than TNFa. Cells were pre-incubated with ENV TMD peptides for two hours prior to LTA activation. In order to confirm this hypothesis we utilized the ectopic expression of HIV-1 ENV-YFP chimeric protein in RAW 264.7 cells, which mimics the HIV-1 infection of macrophages, and tested their responsiveness to LTA by measuring TNFa secretion. abstract: HIV-1 uses a number of means to manipulate the immune system, to avoid recognition and to highjack signaling pathways. HIV-1 infected cells show limited Toll-Like Receptor (TLR) responsiveness via as yet unknown mechanisms. Using biochemical and biophysical approaches, we demonstrate that the trans-membrane domain (TMD) of the HIV-1 envelope (ENV) directly interacts with TLR2 TMD within the membrane milieu. This interaction attenuates TNFα, IL-6 and MCP-1 secretion in macrophages, induced by natural ligands of TLR2 both in in vitro and in vivo models. This was associated with decreased levels of ERK phosphorylation. Furthermore, mutagenesis demonstrated the importance of a conserved GxxxG motif in driving this interaction within the membrane milieu. The administration of the ENV TMD in vivo to lipotechoic acid (LTA)/Galactosamine-mediated septic mice resulted in a significant decrease in mortality and in tissue damage, due to the weakening of systemic macrophage activation. Our findings suggest that the TMD of ENV is involved in modulation of the innate immune response during HIV infection. Furthermore, due to the high functional homology of viral ENV proteins this function may be a general character of viral-induced immune modulation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133399/ doi: 10.1371/journal.ppat.1004248 id: cord-261830-5o5epn6v author: Rheinemann, Lara title: Virus Budding date: 2020-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Enveloped viruses exit producer cells and acquire their external lipid envelopes by budding through limiting cellular membranes. Most viruses encode multifunctional structural proteins that coordinate the processes of virion assembly, membrane envelopment, budding, and maturation. In many cases, the cellular ESCRT pathway is recruited to facilitate the membrane fission step of budding, but alternative strategies are also employed. Recently, many viruses previously considered to be non-enveloped have been shown to exit cells non-lytically within vesicles, adding further complexity to the intricacies of virus budding and egress. url: https://www.sciencedirect.com/science/article/pii/B9780128145159000230 doi: 10.1016/b978-0-12-814515-9.00023-0 id: cord-253556-p1y0zeo1 author: Rhodes, Scott D. title: A rapid qualitative assessment of the impact of the COVID-19 pandemic on a racially/ethnically diverse sample of gay, bisexual, and other men who have sex with men living with HIV in the US South date: 2020-08-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Persons living with HIV (PLWH) may be at increased risk for severe COVID-19-related illness. Our community-based participatory research partnership collected and analyzed semi-structured interview data to understand the early impact of the COVID-19 pandemic on a sample of racially/ethnically diverse gay, bisexual, and other men who have sex with men living with HIV. Fifteen cisgender men participated; their mean age was 28. Six participants were Black/African American, five were Spanish-speaking Latinx, and four were White. Seventeen themes emerged that were categorized into six domains: knowledge and perceptions of COVID-19; COVID-19 information sources and perceptions of trustworthiness; impact of COVID-19 on behaviors, health, and social determinants of health; and general COVID-19-related concerns. Interventions are needed to ensure that PLWH have updated information and adhere to medication regimens, and to reduce the impact of COVID-19 on social isolation, economic stability, healthcare access, and other social determinants of health within this vulnerable population. url: https://www.ncbi.nlm.nih.gov/pubmed/32818212/ doi: 10.21203/rs.3.rs-57507/v1 id: cord-274019-dao10kx9 author: Rife, Brittany D title: Phylodynamic applications in 21(st) century global infectious disease research date: 2017-05-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21(st) century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics. RESULTS: The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus. CONCLUSIONS: Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s41256-017-0034-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s41256-017-0034-y doi: 10.1186/s41256-017-0034-y id: cord-255690-xc4bxin4 author: Rolain, Jean-Marc title: Recycling of chloroquine and its hydroxyl analogue to face bacterial, fungal and viral infections in the 21st century date: 2007-07-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Chloroquine (CQ) and its hydroxyl analogue hydroxychloroquine (HCQ) are weak bases with a half-century long use as antimalarial agents. Apart from this antimalarial activity, CQ and HCQ have gained interest in the field of other infectious diseases. One of the most interesting mechanisms of action is that CQ leads to alkalinisation of acid vesicles that inhibit the growth of several intracellular bacteria and fungi. The proof of concept of this effect was first used to restore intracellular pH allowing antibiotic efficacy for Coxiella burnetii, the agent of Q fever, and doxycycline plus HCQ is now the reference treatment for chronic Q fever. There is also strong evidence of a similar effect in vitro against Tropheryma whipplei, the agent of Whipple's disease, and a clinical trial is in progress. Other bacteria and fungi multiply in an acidic environment and encouraging in vitro data suggest that this concept may be generalised for all intracellular organisms that multiply in an acidic environment. For viruses, CQ led to inhibition of uncoating and/or alteration of post-translational modifications of newly synthesised proteins, especially inhibition of glycosylation. These effects have been well described in vitro for many viruses, with human immunodeficiency virus (HIV) being the most studied. Preliminary in vivo clinical trials suggest that CQ alone or in combination with antiretroviral drugs might represent an interesting way to treat HIV infection. In conclusion, our review re-emphasises the paradigm that activities mediated by lysosomotropic agents may offer an interesting weapon to face present and future infectious diseases worldwide. url: https://api.elsevier.com/content/article/pii/S0924857907002580 doi: 10.1016/j.ijantimicag.2007.05.015 id: cord-011064-1d3v87km author: Roskin, Krishna M. title: Aberrant B cell repertoire selection associated with HIV neutralizing antibody breadth date: 2020-01-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A goal of HIV vaccine development is to elicit antibodies with neutralizing breadth. Broadly neutralizing antibodies (bNAbs) to HIV often have unusual sequences with long heavy-chain complementarity-determining region loops, high somatic mutation rates and polyreactivity. A subset of HIV-infected individuals develops such antibodies, but it is unclear whether this reflects systematic differences in their antibody repertoires or is a consequence of rare stochastic events involving individual clones. We sequenced antibody heavy-chain repertoires in a large cohort of HIV-infected individuals with bNAb responses or no neutralization breadth and uninfected controls, identifying consistent features of bNAb repertoires, encompassing thousands of B cell clones per individual, with correlated T cell phenotypes. These repertoire features were not observed during chronic cytomegalovirus infection in an independent cohort. Our data indicate that the development of numerous B cell lineages with antibody features associated with autoreactivity may be a key aspect in the development of HIV neutralizing antibody breadth. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223457/ doi: 10.1038/s41590-019-0581-0 id: cord-271241-w1q46y63 author: Ruggiero, Emanuela title: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date: 2020-05-18 words: 8912.0 sentences: 495.0 pages: flesch: 45.0 cache: ./cache/cord-271241-w1q46y63.txt txt: ./txt/cord-271241-w1q46y63.txt summary: Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. 1 In the past few decades, pharmaceutical and biotechnological advance has succeeded in developing new therapeutics for the management of different viral diseases: for example, anti-retroviral therapy against the human immunodeficiency virus (HIV), or the pan-genotypic direct-acting antiviral drugs used for hepatitis C (HCV) management. In addition, such PQSs are highly conserved, despite the high recombination rates that characterize viruses, suggesting a crucial role for G4s in viral evolution and replication, and corroborating their targeting as a valid pharmacological approach for antiviral therapy. abstract: Viruses are the most abundant organisms on our planet, affecting all living beings: some of them are responsible for massive epidemics that concern health, national economies and the overall welfare of societies. Although advances in antiviral research have led to successful therapies against several human viruses, still some of them cannot be eradicated from the host and most of them do not have any treatment available. Consequently, innovative antiviral therapies are urgently needed. In the past few years, research on G-quadruplexes (G4s) in viruses has boomed, providing powerful evidence for the regulatory role of G4s in key viral steps. Comprehensive bioinformatics analyses have traced putative G4-forming sequences in the genome of almost all human viruses, showing that their distribution is statistically significant and their presence highly conserved. Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. Recent studies have demonstrated the formation and function of G4s in pathogens responsible for serious diseases, such as HIV-1, Hepatitis B and C, Ebola viruses, to cite a few. In this chapter, we present the state of the art on the structural and functional characterization of viral G4s in RNA viruses, DNA viruses and retroviruses. We also present the G4 ligands that provide further details on the viral G4 role and which, showing promising antiviral activity, which could be exploited for the development of innovative antiviral agents. url: https://api.elsevier.com/content/article/pii/S0065774320300142 doi: 10.1016/bs.armc.2020.04.001 id: cord-319116-2ts6zpdb author: Ruggiero, Emanuela title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date: 2018-04-20 words: 9124.0 sentences: 410.0 pages: flesch: 42.0 cache: ./cache/cord-319116-2ts6zpdb.txt txt: ./txt/cord-319116-2ts6zpdb.txt summary: Since the number of reports describing the presence of G4s in virus genomes has boomed in the past 2 years and treatment with several G4 ligands has shown potentially interesting therapeutic activity, we here aim at presenting, organizing and discussing an up-to-date close-up of the literature on G4s in viruses and the classes of molecules that have shown antiviral activity by viral G4 targeting. The research of G4s in the HIV-1 genome has been quite productive, concerning not only the two RNA viral genome copies, but also the integrated proviral genome, specifically For each virus the following information is shown: virion structure and dimension, genome size and organization; schematic representation of the G4 (red dots) location in the viral genomes or in the mRNA and G4 binding proteins; number of G4s assessed through bioinformatics analysis, according to the corresponding references; G4 ligands reported to date to display antiviral effect and corresponding references. abstract: G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing interest. Indeed, G4s have been reported in several viruses, including those involved in recent epidemics, such as the Zika and Ebola viruses. Viral G4s are usually located in regulatory regions of the genome and implicated in the control of key viral processes; in some cases, they have been involved also in viral latency. In this context, G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle, and as therapeutic agents. In general, G4 ligands showed promising antiviral activity, with G4-mediated mechanisms of action both at the genome and transcript level. This review aims to provide an updated close-up of the literature on G4s in viruses. The current state of the art of G4 ligands in antiviral research is also reported, with particular focus on the structural and physicochemical requirements for optimal biological activity. The achievements and the to-dos in the field are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/29554280/ doi: 10.1093/nar/gky187 id: cord-264408-vk4lt83x author: Ruiz, Sara I. title: Animal Models of Human Viral Diseases date: 2017-06-23 words: 34464.0 sentences: 1865.0 pages: flesch: 47.0 cache: ./cache/cord-264408-vk4lt83x.txt txt: ./txt/cord-264408-vk4lt83x.txt summary: Well-developed animal models are necessary to understand disease progression, pathogenesis, and immunologic responses to viral infections in humans. NHPs including marmosets, cotton-top tamarins, and rhesus macaques infected with Norwalk virus are monitored for the extent of viral shedding; however, no clinical disease is observed in these models. Intracerebral and IN routes of infection resulted in a fatal disease that was highly dependent on dose while intradermal (ID) and subQ inoculations caused only 50% fatality in mice regardless of the amount of virus (liu et al., 1970) . Ferrets infected with Hendra or Nipah virus display the same clinical disease as seen in the hamster model and human cases (Bossart et al., 2009; Pallister et al., 2011) . Characterization studies with IFNAr −/− mice challenged with different routes (IP, IN, IM, and subQ) showed that CCHFV causes acute disease with high viral loads, pathology in liver and lymphoid tissues, increased proinflammatory response, severe thrombocytopenia, coagulopathy, and death, all of which are characteristics of human disease . abstract: As the threat of exposure to emerging and reemerging viruses within a naïve population increases, it is vital that the basic mechanisms of pathogenesis and immune response be thoroughly investigated. Recent outbreaks of Middle East respiratory syndrome corona virus, Ebola virus, Chikungunya virus, and Zika virus illustrate the emerging threats that are encountered. By utilizing animal models in this endeavor, the host response to viruses can be studied in a more complex and integrated context to identify novel drug targets, and assess the efficacy and safety of new products rapidly. This is especially true in the advent and implementation of the FDA animal rule. Although no one animal model is able to recapitulate all aspects of human disease, understanding the current limitations allows for a more targeted experimental design. Important facets to consider prior to an animal study are route of viral exposure, species of animal, biomarkers of disease, and a humane endpoint. This chapter covers the current animal models for medically important human viruses, and demonstrates where the gaps in knowledge exist. url: https://www.sciencedirect.com/science/article/pii/B9780128094686000334 doi: 10.1016/b978-0-12-809468-6.00033-4 id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29292156/ doi: 10.1016/j.biotechadv.2017.12.016 id: cord-018137-rmtyrbg0 author: Saad, Farouk Tijjani title: Global Stability Analysis of HIV+ Model date: 2018-12-29 words: 2932.0 sentences: 168.0 pages: flesch: 57.0 cache: ./cache/cord-018137-rmtyrbg0.txt txt: ./txt/cord-018137-rmtyrbg0.txt summary: Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio [Formula: see text] was also calculated by the use of next generation matrix. Efforts to improve the use of antiretroviral treatment in some part of the world were still not enough to reduce a significant number of deaths, the HIV/AIDS epidemic claimed 3.1 million lives in 2005, of which about 570000 were children (UNAIDS/WHO [8] ). We shall study the global stabilities of both disease free and endemic equilibria by the use of Lyapunov function. Here we use the real data obtained from MOH, in which there were a total of 13646 HIV-1 positive reported cases in the year 2016, in the year 2016 to study and predict the dynamics of HIV in Turkey using our model. Stability analysis of an HIV/Aids epidemic model with treatment Stability analysis of an HIV/AIDS epidemic model with screening Global analysis of an HIV/AIDS epidemic model abstract: We developed and studied a mathematical model of HIV+. Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio [Formula: see text] was also calculated by the use of next generation matrix. Global stability analysis of the equilibria was carried out by the use of Lyapunov function, and it was shown that the stability of the equilibria depends on the magnitude of the basic reproduction ratio. When [Formula: see text] , the disease free equilibrium is globally asymptotically stable, and disease dies out. On the other hand if [Formula: see text] , the endemic equilibrium is globally asymptotically stable and epidemics occurs. Reported cases of 13646 HIV-1 positive were obtained in the year 2016 from Ministry of Health, Turkey (MOH). This data is used to present the numerical simulations, which supports the analytic result. [Formula: see text] was found to be 1.98998, which is bigger than 1, this shows the threat posed by HIV in Turkey. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122938/ doi: 10.1007/978-3-030-04164-9_109 id: cord-282063-tkp1tifx author: Saberi, Parya title: Research in the Time of Coronavirus: Continuing Ongoing Studies in the Midst of the COVID-19 Pandemic date: 2020-04-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32303924/ doi: 10.1007/s10461-020-02868-4 id: cord-282675-s4zmffj3 author: Sagaon-Teyssier, Luis title: Assessment of mental health outcomes and associated factors among workers in community-based HIV care centers in the early stage of the COVID-19 outbreak in Mali date: 2020-10-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: • Malian healthcare workers presented mental disorders in the early stage of COVID-19. • Nurses were at lower risk of mental health disorders than other worker categories. • Women were at greater risk of mental health disorders than men. • A lack of protection equipment and nurses was associated with mental disorders. url: https://www.sciencedirect.com/science/article/pii/S2590229620300150?v=s5 doi: 10.1016/j.hpopen.2020.100017 id: cord-259925-g28sx9qu author: Saleemi, Mansab Ali title: Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date: 2020-10-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The emergence of a new coronavirus, in around late December 2019 which had first been reported in Wuhan, China has now developed into a massive threat to global public health. The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. The person-to-person transmission of this virus is ongoing despite drastic public health mitigation measures such as social distancing and movement restrictions implemented in most countries. Understanding the source of such an infectious pathogen is crucial to develop a means of avoiding transmission and further to develop therapeutic drugs and vaccines. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. In this context, this review is devoted to understanding the taxonomic characteristics of SARS-CoV-2 and HIV. Herein, we discuss the emergence and molecular mechanisms of both viral infections. Nevertheless, no vaccine or therapeutic drug is yet to be approved for the treatment of SARS-CoV-2, although it is highly likely that new effective medications that target the virus specifically will take years to establish. Therefore, this review reflects the latest repurpose of existing antiviral therapeutic drug choices available to combat SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S1567134820304147?v=s5 doi: 10.1016/j.meegid.2020.104583 id: cord-304214-66nxk4e8 author: Sanders, John W. title: Vectored immunoprophylaxis: an emerging adjunct to traditional vaccination date: 2017-02-10 words: 3742.0 sentences: 173.0 pages: flesch: 36.0 cache: ./cache/cord-304214-66nxk4e8.txt txt: ./txt/cord-304214-66nxk4e8.txt summary: Rather than passively transfering pre-formed antibodies, VIP is a process in which genes encoding previously characterized neutralizing antibodies are vectored into non-hematopoietic cells which then secrete the monoclonal antibodes encoded by those genes [1] (See Fig. 1 .) This vectored delivery and production of specified antibodies allows for protection without generating a standard immune response and results in endogenous antibody production that has the potential to be sustained [9] . Saunders, et al., used an rAAV serotype 8 vector to produce a full length IgG of a simianized form of the broadly neutralizing antibody VRC07 in macaques which was protective against simian-human immunodeficiency virus (SHIV) infection 5.5 weeks after treatment [24] . Using HIV-1-infected humanized mice, Horwitz, et al., demonstrated that following initial treatment with anti-retroviral therapy (ART), a single injection of adeno-associated virus directing expression of broadly neutralizing antibody 10-1074, produced durable viremic control after the ART was stopped [26] . abstract: The successful development of effective vaccines has been elusive for many of the world’s most important infectious diseases. Additionally, much of the population, such as the aged or immunocompromised, are unable to mount an effective immunologic response for existing vaccines. Vectored Immunoprophylaxis (VIP) is a novel approach designed to address these challenges. Rather than utilizing an antigen to trigger a response from the host’s immune system as is normally done with traditional vaccines, VIP genetically engineers the production of tailored antibodies from non-hematopoietic cells, bypassing the humoral immune system. Direct administration of genes encoding for neutralizing antibodies has proven to be effective in both preventing and treating several infectious diseases in animal models. While, a significant amount of work has focused on HIV, including an ongoing clinical trial, the approach has also been shown to be effective for malaria, dengue, hepatitis C, influenza, and more. In addition to presenting itself as a potentially efficient approach to solving long-standing vaccine challenges, the approach may be the best, if not only, method to vaccinate immunocompromised individuals. Many issues still need to be addressed, including which tissue(s) makes the most suitable platform, which vector(s) are most efficient at transducing the platform tissue used to secrete the antibodies, and what are the long-term effects of such a treatment. Here we provide a brief overview of this approach, and its potential application in treating some of the world’s most intractable infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/28883973/ doi: 10.1186/s40794-017-0046-0 id: cord-300522-okbupw61 author: Sansone, Clementina title: Marine Algal Antioxidants as Potential Vectors for Controlling Viral Diseases date: 2020-05-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: As the COVID-19 epidemic expands in the world, and with the previous SARS epidemic, avian flu, Ebola and AIDS serving as a warning, biomedical and biotechnological research has the task to find solutions to counteract viral entry and pathogenesis. A novel approach can come from marine chemodiversity, recognized as a relevant source for developing a future natural “antiviral pharmacy”. Activities of antioxidants against viruses can be exploited to cope with human viral infection, from single individual infections to protection of populations. There is a potentially rich and fruitful reservoir of such compounds thanks to the plethora of bioactive molecules and families present in marine microorganisms. The aim of this communication is to present the state-of-play of what is known on the antiviral activities recognized in (micro)algae, highlighting the different molecules from various algae and their mechanisms of actions, when known. Given the ability of various algal molecules—mainly sulfated polysaccharides—to inhibit viral infection at Stage I (adsorption and invasion of cells), we envisage a need to further investigate the antiviral ability of algae, and their mechanisms of action. Given the advantages of microalgal production compared to other organisms, the opportunity might become reality in a short period of time. url: https://doi.org/10.3390/antiox9050392 doi: 10.3390/antiox9050392 id: cord-311679-m6poosn3 author: Santos, Glenn-Milo title: Economic, Mental Health, HIV Prevention and HIV Treatment Impacts of COVID-19 and the COVID-19 Response on a Global Sample of Cisgender Gay Men and Other Men Who Have Sex with Men date: 2020-07-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: There is an urgent need to measure the impacts of COVID-19 among gay men and other men who have sex with men (MSM). We conducted a cross-sectional survey with a global sample of gay men and other MSM (n = 2732) from April 16, 2020 to May 4, 2020, through a social networking app. We characterized the economic, mental health, HIV prevention and HIV treatment impacts of COVID-19 and the COVID-19 response, and examined whether sub-groups of our study population are disproportionately impacted by COVID-19. Many gay men and other MSM not only reported economic and mental health consequences, but also interruptions to HIV prevention and testing, and HIV care and treatment services. These consequences were significantly greater among people living with HIV, racial/ethnic minorities, immigrants, sex workers, and socio-economically disadvantaged groups. These findings highlight the urgent need to mitigate the negative impacts of COVID-19 among gay men and other MSM. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10461-020-02969-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32654021/ doi: 10.1007/s10461-020-02969-0 id: cord-311366-uodq4foi author: Sanyal, Anwesha title: Neisseria gonorrhoeae uses cellular proteins CXCL10 and IL8 to enhance HIV‐1 transmission across cervical mucosa date: 2019-04-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: PROBLEM: Neisseria gonorrhoeae (NG) infection has been shown to increase sexual transmission of HIV‐1. However, the mechanism of NG‐induced enhanced HIV‐1 transmission is unknown. METHODS: (a) The cervical tissues were exposed to NG, and cytokine induction was monitored by measuring cytokine proteins in culture supernatants and cytokine mRNAs in tissues. (b) Transcription and replication of HIV‐1 in TZM‐bl, U1, and ACH2 cells were measured by Beta‐Gal activity and p24 proteins in the supernatant, respectively. (c) HIV‐1 transmission was assayed in an organ culture system by measuring transmitted HIV‐1 in supernatant and HIV‐1 gag mRNA in the tissues. (d) Transcriptome analysis was done using second generation sequencing. RESULTS: (a) NG induced membrane ruffling of epithelial layer, caused migration of CD3+ cells to the intraepithelial region, and induced high levels of inflammatory cytokines IL‐1β and TNF‐α. (b) NG‐induced supernatants (NGIS) increased HIV‐1 transcription, induced HIV‐1 from latently infected cells, and increased transmission of HIV‐1 across cervical mucosa. (c) Transcriptome analysis of the epithelial layer of the tissues exposed to NG, and HIV‐1 showed significant upregulation of CXCL10 and IL8. IL‐1β increased the induction of CXCL10 and IL‐8 expression in cervical mucosa with a concomitant increase in HIV‐1 transmission. CONCLUSION: We present a model in which IL‐1β produced from cervical epithelium during NG exposure increases CXCL10 and IL8 in epithelia. This in turn causes upon HIV‐1 infection, the migration of HIV‐1 target cells toward the subepithelium, resulting in increased HIV‐1 transcription in the sub‐mucosa and subsequent enhancement of transmission across cervical mucosa. url: https://www.ncbi.nlm.nih.gov/pubmed/30903720/ doi: 10.1111/aji.13111 id: cord-324137-nau83mjv author: Saranathan, Nandhini title: G-Quadruplexes: More Than Just a Kink in Microbial Genomes date: 2018-09-14 words: 6722.0 sentences: 379.0 pages: flesch: 42.0 cache: ./cache/cord-324137-nau83mjv.txt txt: ./txt/cord-324137-nau83mjv.txt summary: Several reports convincingly demonstrate antimicrobial activity of quadruplex-binding ligands against clinically challenging pathogens, including HIV-1, HCV, Ebola virus, Plasmodium falciparum, and Mycobacterium tuberculosis. An earlier study reports that, following concatemeric replication of HHV-1, the cleavage of unit length genomes and their encapsidation is achieved by the binding of virus proteins to a DNA secondary structure formed by a DNA packaging sequence (pac-1) [50] . G4s have been shown to inhibit the transcription or translation of structural and nonstructural proteins in viruses, deleteriously affecting the virus loads and their pathogenicity; the stabilization of these quadruplexes with ligands has been investigated as a potential mechanism for targeting viruses. Negative regulation of virus transcription, translation or replication by quadruplex motifs in virus genomes forms the basis of using G4-binding ligands as antiviral agents. G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions abstract: G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein–Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy. url: https://api.elsevier.com/content/article/pii/S0966842X18301951 doi: 10.1016/j.tim.2018.08.011 id: cord-006260-ux32zanj author: Sarkar, Paul title: Antimicrobial Agents are Societal Drugs: How Should This Influence Prescribing? date: 2012-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This paper is concerned with how those who prescribe antimicrobials should consider the wider repercussions of their actions. It is accepted that in an ecological system, pressure will cause evolution; this is also the case with antimicrobials, the result being the development of resistance and the therapeutic failure of drugs. To an extent, this can be ameliorated through advances by the pharmaceutical industry, but that should not stop us from critically appraising our use and modifying our behavior to slow this process down. Up to 50% of prescribing in human medicine and 80% in veterinary medicine and farming has been considered questionable. The Alliance for the Prudent Use of Antimicrobials (APUA) was approached by the WHO to review the situation. Their recommendations include decreasing the prescribing of antibacterials for nonbacterial infections. In the UK, there has been an initiative called ‘the path of least resistance’. This encourages general practitioners to avoid prescribing or reduce the duration of prescriptions for conditions such as upper respiratory tract infections and uncomplicated urinary tract infections; this approach has been successful. Another recommendation is to reduce the prescribing of broad-spectrum antibacterials. In UK hospitals, the problems identified with the inappropriate use of antibacterials are insufficient training in infectious disease, difficulty in selecting empirical antibacterial therapy, poor use of available microbiological information, the fear of litigation and the fact that the majority of antibacterials are prescribed by the least experienced doctors. With close liaison between the laboratories and clinicians, and the development of local protocols, this can be addressed. Another recommendation is to tighten the use of antibacterial prophylaxis and to improve patient compliance. Through a combination of improved education for doctors and patients, and improved communication skills, these problems can be addressed. A further recommendation is to encourage teaching methods that modify prescribing habits. It has been shown that workshops have led to a significant reduction in the prescribing of broad-spectrum antibacterials in the community. Auditing the prescribing of antibacterials has also been recommended. Surveillance systems around the world monitor trends in resistance: the European Antimicrobial Resistance Surveillance Progamme (EARSS) monitors antibacterial resistance; the WHO and the International Union Against Tuberculosis and Lung Disease collaborate to monitor tuberculosis; the WHO and the International AIDS Society monitor HIV. In the third world, a bigger problem than resistance is whether drugs are even effective, as they are often spoiled by climactic conditions, and poor quality generics and counterfeit drugs are common. Also, patients may not be able to complete a course for financial reasons. Facts about Antimicrobial resistance in Animals (and agriculture) and Impact on Resistance (FAAIR) was commissioned by APUA. They conclude that the nonhuman use of antibacterials can lead to the development of antibacterial resistance in human pathogens. The European commission banned the use of antibacterials as growth promoters in 1999. In the Western world, we should improve our diagnosis of sepsis, access local guidelines and consider withholding treatment pending investigations, decide if treatment can be stopped earlier and treat the patient not the result. Many developing countries need improved access to more antimicrobials, preferably in the controlled environment of appropriate medical advice. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100809/ doi: 10.2165/00003495-200666070-00001 id: cord-015376-z739ifu5 author: Savarino, Andrea title: Potential therapies for coronaviruses date: 2006-08-31 words: 6361.0 sentences: 313.0 pages: flesch: 48.0 cache: ./cache/cord-015376-z739ifu5.txt txt: ./txt/cord-015376-z739ifu5.txt summary: These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. abstract: Coronavirus replication offers several attractive targets for chemotherapy. These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. Lessons should be learnt from AIDS research for choosing the best strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103690/ doi: 10.1517/13543776.16.9.1269 id: cord-297257-lzybfwc2 author: Savarino, Andrea title: Chloroquine and beyond: exploring anti-rheumatic drugs to reduce immune hyperactivation in HIV/AIDS date: 2015-06-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The restoration of the immune system prompted by antiretroviral therapy (ART) has allowed drastically reducing the mortality and morbidity of HIV infection. However, one main source of clinical concern is the persistence of immune hyperactivation in individuals under ART. Chronically enhanced levels of T-cell activation are associated with several deleterious effects which lead to faster disease progression and slower CD4(+) T-cell recovery during ART. In this article, we discuss the rationale, and review the results, of the use of antimalarial quinolines, such as chloroquine and its derivative hydroxychloroquine, to counteract immune activation in HIV infection. Despite the promising results of several pilot trials, the most recent clinical data indicate that antimalarial quinolines are unlikely to exert a marked beneficial effect on immune activation. Alternative approaches will likely be required to reproducibly decrease immune activation in the setting of HIV infection. If the quinoline-based strategies should nevertheless be pursued in future studies, particular care must be devoted to the dosage selection, in order to maximize the chances to obtain effective in vivo drug concentrations. url: https://doi.org/10.1186/s12977-015-0178-0 doi: 10.1186/s12977-015-0178-0 id: cord-268712-rxdw553c author: Sawyer, Alexandra title: Posttraumatic growth and adjustment among individuals with cancer or HIV/AIDS: A meta-analysis date: 2010-03-02 words: 8820.0 sentences: 475.0 pages: flesch: 46.0 cache: ./cache/cord-268712-rxdw553c.txt txt: ./txt/cord-268712-rxdw553c.txt summary: Consequently, this meta-analysis explored the relationship between posttraumatic growth and psychological and physical wellbeing in adults diagnosed with cancer or HIV/AIDS and examined potential moderators of these relationships. As such the aim of the current paper is to present a meta-analysis of the existing literature that will aim to objectively summarize PTG and its relation to adjustment in individuals living with a life threatening illness (cancer or HIV/ AIDS) and to examine potential moderators of this relationship. Primarily it is concerned with estimating the overall effect size of the relationship between PTG following a life threatening illness (cancer or HIV/AIDS) and various indicators of adjustment. This meta-analytic review summarized the findings from 38 studies examining the association between PTG following cancer or HIV/AIDS and positive psychological adjustment, negative psychological adjustment, and subjective physical health. abstract: There is increasing research on posttraumatic growth after life-threatening illnesses such as cancer and HIV/AIDS, although it is unclear whether growth confers any psychological or physical benefits in such samples. Consequently, this meta-analysis explored the relationship between posttraumatic growth and psychological and physical wellbeing in adults diagnosed with cancer or HIV/AIDS and examined potential moderators of these relationships. Analysis of 38 studies (N = 7927) of posttraumatic growth after cancer or HIV/AIDS revealed that growth was related to increased positive mental health, reduced negative mental health and better subjective physical health. Moderators of these relationships included time since the event, age, ethnicity, and type of negative mental health outcome. It is hoped that this synthesis will encourage further examination of the potentially complex relationship between posttraumatic growth and adjustment in individuals living with life-threatening medical conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/20350775/ doi: 10.1016/j.cpr.2010.02.004 id: cord-023841-amfb4jft author: Scherr, Johannes title: Bewegung und Erkrankungen des Immunsystems date: 2017 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Die Effektivität von körperlicher Aktivität in der Primär- als auch Sekundär- und Tertiärprävention ist hinlänglich bekannt. Das Immunsystem spielt eine entscheidende Rolle bei einer Vielzahl von Erkrankungen, da es durch seine Botenfunktion (z. B. durch Zytokine) in einer Vielzahl der Regulationsprozesse mit involviert ist. So kommt es durch moderat-intensive körperliche Aktivität zu einer Stärkung des Immunsystems mit konsekutiv verminderter Infektanfälligkeit sowie eher anti-inflammatorischen Effekten, wohingegen langandauernde und höher intensive Belastungen zu einer Schwächung der Abwehrfunktion sowie einem pro-inflammatorischen Effekt führen. Somit stellt eine adäquat dosierte körperliche Aktivität eine erfolgversprechende Therapieoption bei Erkrankungen des infektiologischen Formenkreises sowie des Immunsystems dar. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176187/ doi: 10.1007/978-3-662-50335-5_17 id: cord-003307-snruk3j2 author: Schmidt, Julius J. title: Clinical course, treatment and outcome of Pneumocystis pneumonia in immunocompromised adults: a retrospective analysis over 17 years date: 2018-11-19 words: 4068.0 sentences: 239.0 pages: flesch: 51.0 cache: ./cache/cord-003307-snruk3j2.txt txt: ./txt/cord-003307-snruk3j2.txt summary: BACKGROUND: Despite modern intensive care with standardized strategies against acute respiratory distress syndrome (ARDS), Pneumocystis pneumonia (PcP) remains a life-threatening disease with a high mortality rate. Based on the high burden of PcP and the likelihood of unfavorable outcome particularly in non-HIV-positive patients, chemoprophylaxis with trimethoprim-sulfame thoxazole (TMP-SMX) is recommended in high-risk populations [13] . We here report comprehensive epidemiological, clinical, laboratory, therapeutic and outcome data on 240 cases of PcP, including a high percentage of non-HIV-positive patients, in a tertiary care center over the last 17 years. For every patient, clinical data on demographic characteristics, underlying disease, status of immune competence, treatment regimens of immunosuppression, PcP therapy regimen and mortality, were gathered in the study database. Outcomes and prognostic factors of non-HIV patients with pneumocystis jirovecii pneumonia and pulmonary CMV co-infection: a retrospective cohort study abstract: BACKGROUND: Despite modern intensive care with standardized strategies against acute respiratory distress syndrome (ARDS), Pneumocystis pneumonia (PcP) remains a life-threatening disease with a high mortality rate. Here, we analyzed a large mixed cohort of immunocompromised patients with PcP, with regard to clinical course and treatment, and aimed at identifying predictors of outcome. METHODS: This was a single-center retrospective analysis in a tertiary care institution across 17 years. Diagnosis of PcP required typical clinical features and microbiological confirmation of Pneumocystis jirovecii. Epidemiological, clinical, laboratory and outcome data were collected from patient records. RESULTS: A total of 52,364 specimens from 7504 patients were sent for microbiological assessment (3653 with clinical suspicion of Pneumocystis pneumonia). PcP was confirmed in 240 patients, about half of them HIV positive (52%). The remaining subjects were either solid organ transplant recipients (16.3%) or suffered from malignancy (15.8%) or autoimmune diseases (11.7%). Of note, 95% of patients with PcP were not receiving chemoprophylaxis. Overall in-hospital mortality was 25.4%, increasing to 58% if ICU admission was required. Multivariable regression identified lactate dehydrogenase (LDH) as predictor of in-hospital mortality (adjusted OR 1.17 (95% CI 1.09–1.27), p < 0.0001). Mortality in LDH quartiles increased from 8% to 49%, and a cutoff value of 495 U/L predicted mortality with sensitivity and specificity of 70%. With regard to treatment, 40% of patients received trimethoprim-sulfamethoxazole at doses that were lower than recommended, and these patients had a higher mortality risk (HR 1.80 (95% CI 1.10–3.44), p = 0.02). CONCLUSIONS: PcP remains a life-threatening disease among immunocompromised patients. About half of patients with PcP do not have HIV infection. Initial LDH values might serve as a stratifying tool to identify those patients at high risk of death among patients with HIV and without HIV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13054-018-2221-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245758/ doi: 10.1186/s13054-018-2221-8 id: cord-022535-08hqmwlg author: Schmiedel, Stefan title: Infektionen, Impfungen, Reisemedizin date: 2013-06-26 words: 6075.0 sentences: 1245.0 pages: flesch: 50.0 cache: ./cache/cord-022535-08hqmwlg.txt txt: ./txt/cord-022535-08hqmwlg.txt summary: • Kinder > 1 J.: Zuwarten bei Fieber bis 3 d, so weit kein klarer Lokalbefund vorliegt und der AZ es erlaubt, rein symptomatische Ther. Facharztüberweisung oder Klinikeinweisung bei reduziertem AZ, bei hohem Fieber und Vorliegen eines Immundefekts (HIV-Inf., immunsuppressive Ther., Z.n. Splenektomie), sowie bei Fortbestehen des Fiebers über 1 Wo. hinaus. Die Immunisierung durch Impfungen ist eine der wichtigsten und wirksamsten Maßnahmen zum Schutz vor Infektionskrankheiten. • Nach Auftreten von KO bei einer Impfung besteht bis zur Klärung der Ursachen eine KI für denselben Impfstoff. • Bei 2 Tetanus-Impfungen in der Vorgeschichte und wenn die Verletzung nicht länger als 24 h zurückliegt, nur Impfung und kein Tetanus-Immunglobulin. Durch Impfung bleiben später der Stress und die Kosten des Varizellen-Immunglobulins bei Varizellen-Exposition von seroneg. Impfbefreiungszeugnis Falls obligatorische Impfungen bei Reisenden kontraindiziert sind, muss ein Impfbefreiungszeugnis mit Unterschrift des Arztes und einem Beglaubigungsstempel mitgeführt werden; je nach Reiseland in englischer oder französischer Sprache und evtl abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158279/ doi: 10.1016/b978-3-437-22443-0.10009-2 id: cord-033558-lcgo1tiy author: Schmiedel, Stefan title: Infektionen, Impfungen, Reisemedizin date: 2020-10-09 words: 5008.0 sentences: 1080.0 pages: flesch: 52.0 cache: ./cache/cord-033558-lcgo1tiy.txt txt: ./txt/cord-033558-lcgo1tiy.txt summary: 9 HIV und AIDS 524 9.9.1 Epidemiologie und Übertragungswege 524 9.9.2 Labordiagnostik 524 9.9.3 Stadieneinteilung und Verlauf 527 9.9.4 Diagnostik bei HIV-Positiven 529 9.9.5 Häufige Krankheitsbilder bei AIDS 529 9.9.6 Therapie 534 9.9.7 Medikamente bei HIV-Patienten 539 9.9.8 Vorgehen bei Kontakt mit HIVkontaminiertem Material und Postexpositionsprophylaxe (PEP) 542 9.9.9 Präexpositionsprophylaxe (PREP) 543 9.10 Reisemedizin 544 9.10.1 Allgemeines 544 9.10.2 Allgemeine Empfehlungen zur Reisefähigkeit 544 9.10.3 Empfehlungen für Schwangere 549 9.10.4 Empfehlungen für ältere Menschen 550 9.10.5 Empfehlungen für Kinder und Säuglinge 551 9.10.6 Empfehlungen für chronisch Kranke 553 9.10.7 Reisevorbereitungen/ Prophylaxen 555 9.10.8 Reiseimpfungen u. Die Immunisierung durch Impfungen ist eine der wichtigsten u. B. Hühnereiweiß, ▶ 9.2.4) • Nach Auftreten von KO bei einer Impfung besteht bis zur Klärung der Ursachen eine KI für denselben Impfstoff • Es gibt keine unzulässig großen Abstände zwischen Impfungen. Bei Impfungen, die nur bis zu einem bestimmten Alter empfohlen werden, sollen keine weiteren Dosen verabreicht werden, wenn Pat. dieses Alter überschritten hat. Impfung gegen Influenza in der Klinik • Grad 3: Pat. mit Sofortreaktion nach Verzehr von Hühnereiweiß mit Urtikaria, Laryngo-/Bronchospasmus, RR-Abfall. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545216/ doi: 10.1016/b978-3-437-22449-2.00009-5 id: cord-020494-d5sreohg author: Schmutzhard, E. title: Entzündliche Erkrankungen date: 2006 words: 9279.0 sentences: 1352.0 pages: flesch: 45.0 cache: ./cache/cord-020494-d5sreohg.txt txt: ./txt/cord-020494-d5sreohg.txt summary: Die antibiotische Therapie der bakteriellen Meningitis wird von den epidemiologischen Gegebenheiten, insbesondere dem Alter des Patienten, der regionalen Resistenzsituation der jeweiligen Erreger und von evtl. ⊡ Tabelle 32.4 zeigt die wahrscheinlichsten Erreger in den entsprechenden Altersgruppen und gibt das antibiotische Regime, das sofort nach der Diagnose einer eitrigen Meningitis verabreicht werden soll, an. Die klinische Symptomatik und der klinisch-neurologische Verlauf bei einem Patienten mit einem/mehreren Hirnabszessen kann von mild über protrahiert bis zu fulminant sein. Bei begründetem Verdacht auf einen Hirnabszess ist eine Lumbalpunktion kontraindiziert, da der diagnostische Wert der Liquoruntersuchung nur sehr gering ist und die LP die Gefahr einer Einklemmung mit sich bringt. Ein Subduralempyem sollte bei jedem Patienten mit Meningismus und fokalem neurologischem Defizit vermutet werden, insbesondere, wenn sich die Klinik sehr rasch verschlechtert und auf eine Hirnhemi sphäre beschränkt ist. Diese anamnestischen Angaben sind aber keine obligatorische Voraussetzung für die Diagnose einer Neuroborreliose, da das Frühstadium klinisch stumm verlaufen kann und der Zeckenstich vom Patienten nicht immer bemerkt wird. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136898/ doi: 10.1007/3-540-31176-9_32 id: cord-309242-ilsupfl8 author: Schuchat, Anne title: Global health and the US Centers for Disease Control and Prevention date: 2014-07-02 words: 2886.0 sentences: 161.0 pages: flesch: 50.0 cache: ./cache/cord-309242-ilsupfl8.txt txt: ./txt/cord-309242-ilsupfl8.txt summary: CDC staff work with peers in Ministries of Health and other host country entities to implement eff ective national programmes in HIV care and treatment, tuberculosis-HIV integration, maternal and child health, HIV prevention, and HIV counselling and testing. President Obama announced in December, 2011, ambitious new targets for priority evidence-based interventions that were to be realised in just 2 years'' time: PEPFAR, in 2013, was committed to directly support 6 million patients receiving treatment, an increase of 50% over the previous target; provision of therapy to 1·5 million pregnant women to prevent vertical infection of HIV; and to cumulatively reach 4·7 million men with voluntary medical male circumcisions. 5 CDC implemented an innovative approach to prevent mother-to-child transmission of HIV in Malawi by working with the Ministry of Health and local partners. abstract: nan url: https://api.elsevier.com/content/article/pii/S0140673614605705 doi: 10.1016/s0140-6736(14)60570-5 id: cord-023854-w8kx5n8k author: Schuster, V. title: Virusinfektionen date: 2019 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Dieses Kapitel behandelt Klinik, Komplikationen, Diagnostik, Prophylaxe und Therapie der wesentlichen Virusinfektionen im Kindes- und Jugendlichenalter, u. a. Virusinfektionen der Herpes-Gruppe (HSV1 und 2 [u. a. schwere neonatale Infektionen, Herpesenzephalitis]), VZV [u. a. neonatale VZV-Infektionen, Herpes-Zoster], EBV, CMV, HHV6–7 [Dreitagefieber], HHV8 [Kaposi-Sarkom]. Unter den Virushepatititiden spielen bei Kindern die Hepatitis A, B (chronische Hepatitis B) sowie C (chronische Hepatitis B) die größte Rolle. Weitere bedeutsame Viren sind Parvovirus-B19 (Ursache der Ringelröteln, einer aplastischen Krise oder eines Hydrops fetalis), humane Papillomaviren (bedeutsam v. a. Genitalwarzen, Larynxpapillome und Karzinome), Rotaviren (bedeutsame Gastroenteritiserreger), FSME, HIV sowie die „typischen Kinderkrankheiten“ Masern, Mumps und Röteln. Häufige Erreger des oberen und unteren Respirationstrakts sind Rhinoviren, das RS-Virus, das humane Metapneumovirus (hMPV), das humane Bocavirus (hBoV), das humane Coronavirus (HCoV) sowie Influenza- und Parainfluenzaviren. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176200/ doi: 10.1007/978-3-662-57295-5_14 id: cord-018721-othar2uv author: Schwab, Stefan title: Infektionen date: 2012-03-17 words: 13415.0 sentences: 1662.0 pages: flesch: 40.0 cache: ./cache/cord-018721-othar2uv.txt txt: ./txt/cord-018721-othar2uv.txt summary: Zusammenfassend kann aufgrund der zur Verfügung stehenden Daten die Gabe von Dexamethason bei erwachsenen Patienten mit Verdacht auf eine bakterielle Meningitis (d. Für Entwicklungsländer mit eingeschränkter medizinischer Versorgung und einem hohen Anteil HIV-positiver Patienten konnte keine Wirksamkeit für Dexamethason bei der bakteriellen Meningitis nachgewiesen werden [32] , [33] , [34] . HIV-positive Patienten mit intrakraniellen Tuberkulomen können im Rahmen des "immune reconstitution syndrome" (IRIS) eine durchaus dramatische klinisch neurologische Verschlechterung erfahren, mit Zunahme der neurologi-z Diagnostik Die Untersuchung des Liquor cerebrospinalis ist für die Diagnose einer chronischen Meningitis unverzichtbar, der Liquor ist typischerweise klar, bei deutlich erhöhtem Eiweiß auch xanthochrom wirkend. Da bei der Pathogenese dieser Enzephalitis auch Autoimmunmechanismen eine wichtige Rolle spielen, scheint unter einer kombinierten Th erapie mit Aciclovir und Dexamethason die Rate von Patienten mit schlechtem Outcome geringer zu sein als unter alleiniger Th erapie mit Aciclovir [158] . abstract: Trotz Weiterentwicklung moderner Antibiotika in den letzten Jahren sind die Letalitätszahlen der bakteriellen (eitrigen) Meningitis weiterhin hoch; Überlebende haben häufig neurologische Residuen. Die ungünstigen klinischen Verläufe der bakteriellen Meningitis sind meist Folge intrakranieller Komplikationen, wie z. B. eines generalisierten Hirnödems, einer zerebrovaskulären arteriellen oder venösen Beteiligung oder eines Hydrozephalus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123678/ doi: 10.1007/978-3-642-16911-3_32 id: cord-030368-6z99rm0a author: Schwegler, Ute title: Infektionskrankheiten date: 2012 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Virale Infektionen zählen immer noch weltweit, besonders in den Entwicklungsländern, zu den häufigsten Todesursachen. Durch internationale systematische Impfkampagnen der WHO ist die Welt Pocken-frei geworden. Die Inzidenz der Infektionen, die durch eine Immunprophylaxe verhindert werden können, wurde drastisch gesenkt (Poliomyelitis, Tollwut). In den 1980er Jahren trat eine neue Tierseuche beim Rind auf, die bovine spongyforme Enzephalopathie (BSE), die mit der neuen Variante der Creutzfeldt-Jakob-Krankheit (vCJK) in Zusammenhang steht (Nahrungskette). Im selben Zeitraum begann die explosionsartige weltweite Verbreitung eines neuen Retrovirus, des HIV. Trotz intensiver Aufklärungskampagnen und neuen therapeutischen Möglichkeiten (HAART, hoch aktive antiretrovirale Therapie) ist es bis zur Jahrtausendwende nicht gelungen, die weitere Ausbreitung der HIV-Infektion zu verhindern. Seit 2007 ist eine allmähliche Eindämmung der Infektion zu erkennen, die Neuinfektionen sind weltweit rückläufig. Durch den breiteren Einsatz der HAART sind Lebensqualität und Lebenserwartung enorm gestiegen, die Sterberate der AIDS-Infizierten ist seit 2005 um mehr als 50 % zurückgegangen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418528/ doi: 10.1007/978-3-642-21081-5_27 id: cord-304251-dohglrm1 author: Scully, C title: Emerging and changing viral diseases in the new millennium date: 2015-08-06 words: 6254.0 sentences: 322.0 pages: flesch: 47.0 cache: ./cache/cord-304251-dohglrm1.txt txt: ./txt/cord-304251-dohglrm1.txt summary: Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. Gradually, however, the unexpected consequences of some oral viral infections have emerged and been recognised, not without some surprise (Scully, 1983) especially the oncogenicity of some herpesviruses (Eglin et al, 1983) and human papillomaviruses (HPVs) which we (Eglin et al, 1983; Maitland et al, 1987; Cox et al, 1993 ) and many others (e.g. Lind et al, 1986) have explored, culminating in the appreciation of unanticipated transmission routes for some cancers, such as sexual (Scully, 2002) . The recent several decades have also seen a most dramatic change with the emergence globally of new viral infectionsnotably human immunodeficiency viruses (HIV)and the appearance also in resource-rich countries, of some other dangerous and sometimes lethal infections hitherto latent, unrecognised or unappreciated in resource-poor areas. abstract: Most viral infections encountered in resource‐rich countries are relatively trivial and transient with perhaps fever, malaise, myalgia, rash (exanthema) and sometimes mucosal manifestations (enanthema), including oral in some. However, the apparent benignity may be illusory as some viral infections have unexpected consequences – such as the oncogenicity of some herpesviruses and human papillomaviruses. Infections are transmitted from various human or animal vectors, especially by close proximity, and the increasing movements of peoples across the globe, mean that infections hitherto confined largely to the tropics now appear worldwide. Global warming also increases the range of movement of vectors such as mosquitoes. Thus recent decades have seen a most dramatic change with the emergence globally also of new viral infections – notably human immunodeficiency viruses (HIV) – and the appearance of some other dangerous and sometimes lethal infections formerly seen mainly in, and reported from, resource‐poor areas especially in parts of Asia, Latin America and Africa. This study offers a brief update of the most salient new aspects of the important viral infections, especially those with known orofacial manifestations or other implications for oral health care. url: https://doi.org/10.1111/odi.12356 doi: 10.1111/odi.12356 id: cord-306266-8qdrshz3 author: Scully, Crispian title: Respiratory medicine date: 2014-06-25 words: 13246.0 sentences: 698.0 pages: flesch: 42.0 cache: ./cache/cord-306266-8qdrshz3.txt txt: ./txt/cord-306266-8qdrshz3.txt summary: Other factors that have been studied include: ■ air pollution -There is an association between air pollution and aggravation of existing asthma ■ allergen avoidance -There is no consistent evidence of benefit ■ breast-feeding -There is evidence of a protective effect in relation to early asthma ■ electrolytes -There is no consistent evidence of benefit ■ fish oils and fatty acid -There is no consistent evidence of benefit ■ house dust mites -Measures to reduce the numbers of house dust mites do not affect asthma severity ■ immunotherapy -Allergenspecific immunotherapy is beneficial in allergic asthma ■ microbial exposure -There is insufficient evidence to indicate that the use of probiotics in pregnancy reduces the incidence of childhood asthma ■ modified milk formulae -There is no consistent evidence of benefit pets -There are no controlled trials on the benefits of removing pets from the home ■ tobacco -Exposure to cigarette smoke adversely affects quality of life, lung function, need for rescue medications and longterm control with inhaled steroids. abstract: ●. Upper respiratory infections are commonplace, especially in young people, and are often contagious; ●. Lower respiratory infections are often contagious and some are potentially fatal; ●. Asthma is common and may be life-threatening; ●. Chronic obstructive pulmonary disease is common and disabling; ●. Tuberculosis worldwide is an important infection, affecting people with HIV/AIDS or malnutrition particularly; ●. Lung cancer is common and usually has a poor prognosis. url: https://api.elsevier.com/content/article/pii/B9780702054013000151 doi: 10.1016/b978-0-7020-5401-3.00015-1 id: cord-260476-whfyczcj author: Seissler, Tanja title: Hijacking of the Ubiquitin/Proteasome Pathway by the HIV Auxiliary Proteins date: 2017-10-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The ubiquitin-proteasome system (UPS) ensures regulation of the protein pool in the cell by ubiquitination of proteins followed by their degradation by the proteasome. It plays a central role in the cell under normal physiological conditions as well as during viral infections. On the one hand, the UPS can be used by the cell to degrade viral proteins, thereby restricting the viral infection. On the other hand, it can also be subverted by the virus to its own advantage, notably to induce degradation of cellular restriction factors. This makes the UPS a central player in viral restriction and counter-restriction. In this respect, the human immunodeficiency viruses (HIV-1 and 2) represent excellent examples. Indeed, many steps of the HIV life cycle are restricted by cellular proteins, some of which are themselves components of the UPS. However, HIV itself hijacks the UPS to mediate defense against several cellular restriction factors. For example, the HIV auxiliary proteins Vif, Vpx and Vpu counteract specific restriction factors by the recruitment of cellular UPS components. In this review, we describe the interplay between HIV and the UPS to illustrate its role in the restriction of viral infections and its hijacking by viral proteins for counter-restriction. url: https://www.ncbi.nlm.nih.gov/pubmed/29088112/ doi: 10.3390/v9110322 id: cord-023729-dipjubn7 author: Serlin, Michael H. title: Gastrointestinal Disorders in HIV date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173545/ doi: 10.1016/b978-1-4160-2882-6.50027-7 id: cord-287853-cob7ur35 author: Sharma, Vaneet Kumar title: The expanding role of mass spectrometry in the field of vaccine development date: 2018-05-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Biological mass spectrometry has evolved as a core analytical technology in the last decade mainly because of its unparalleled ability to perform qualitative as well as quantitative profiling of enormously complex biological samples with high mass accuracy, sensitivity, selectivity and specificity. Mass spectrometry‐based techniques are also routinely used to assess glycosylation and other post‐translational modifications, disulfide bond linkage, and scrambling as well as for the detection of host cell protein contaminants in the field of biopharmaceuticals. The role of mass spectrometry in vaccine development has been very limited but is now expanding as the landscape of global vaccine development is shifting towards the development of recombinant vaccines. In this review, the role of mass spectrometry in vaccine development is presented, some of the ongoing efforts to develop vaccines for diseases with global unmet medical need are discussed and the regulatory challenges of implementing mass spectrometry techniques in a quality control laboratory setting are highlighted. url: https://doi.org/10.1002/mas.21571 doi: 10.1002/mas.21571 id: cord-256459-6h358si5 author: Sharpstone, D title: Gastrointestinal manifestations of HIV infection date: 1996-08-10 words: 3644.0 sentences: 201.0 pages: flesch: 36.0 cache: ./cache/cord-256459-6h358si5.txt txt: ./txt/cord-256459-6h358si5.txt summary: Mucosal biopsy: Although diagnosis by stool analysis alone has been suggested by Johanson and Sonnenberg, 32 this study may have overestimated the value of symptomatic treatment and ignored the possibility that cytomegalovirus infection sometimes responds to therapy. Analysis of six stool samples and histological examination of small and large bowel biopsy speicmens detect more than 90% of infectious causes of diarrhoea in HIV-seropositive individuals. Since diagnosis of cytomegalovirus enteritis is improving, patients with milder symptoms are being detected and the quality of life with treatment-anti-CMV agents have to be given intravenously and have considerable toxicitymay not be enhanced compared with no therapy. The other origin of abdominal pain unique to HIV-seropositive patients is an AIDS-related sclerosing cholangitis caused by various opportunists including Microsporidia, CMV, and Cryptosporidia. Effects of zidovudine treatment on the small intestinal mucosa in patients infected with the human immunodeficiency virus Atrovaquone is effective treatment for the symptoms of gastrointestinal microsporidiosis in HIV-1 infected patients abstract: The harrowing picture of emaciated terminally ill AIDS patients is a reminder of our lack of understanding of immunological mechanisms that normally control opportunistic infections. Many gastrointestinal pathogens in patients with AIDS are resistant to treatment and lead inexorably to weight loss and death. Although knowledge of the pathogenesis and clinical significance of weight loss has improved considerably, this has not yet led to a sustained effort to improve nutritional status during early stages of disease. url: https://www.sciencedirect.com/science/article/pii/S0140673696010343 doi: 10.1016/s0140-6736(96)01034-3 id: cord-021966-5m21bsrw author: Shaw, Alan R. title: Vaccines date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152278/ doi: 10.1016/b978-0-323-04404-2.10092-2 id: cord-011855-0vetk6jd author: Shayo, Elizabeth title: Ethical issues in intervention studies on the prevention and management of diabetes and hypertension in sub-Saharan Africa date: 2020-07-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7342469/ doi: 10.1136/bmjgh-2019-002193 id: cord-262892-n38r8n70 author: Sheikh, Jamila title: Nutritional Care of the Child with Human Immunodeficiency Virus Infection in the United States: A Historical and Contemporary Perspective date: 2015-05-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In well-resourced settings, early infant diagnosis and administration of life-saving antiretrovirals (ARVs) have significantly improved clinical outcomes in pediatric human immunodeficiency virus (HIV) infection. The dramatic increase in survival rates is associated with enhancements in overall quality of life, which reflect a multidisciplinary, holistic approach to care. Current optimism starkly contrasts with the outlook and prognosis two decades ago, when failure to thrive and wasting syndrome from uncontrolled pediatric HIV infection resulted from poor oral intake, malabsorption, chronic diarrhea, and a persistently catabolic state. The tenets of care developed from that era still hold true in that all infants, children, and adolescents with HIV require comprehensive nutritional services in addition to effective combination antiretroviral therapy (cART). This chapter will review the principles of nutrition in the pre- and post-cART eras and discuss the etiologic factors associated with malnutrition, with an emphasis on interventions that have favorably impacted the growth and body composition of infants, children and adolescents with HIV. url: https://www.sciencedirect.com/science/article/pii/B9780128007693000093 doi: 10.1016/b978-0-12-800769-3.00009-3 id: cord-354050-kcn67stj author: Shi, Guoli title: More than meets the I: the diverse antiviral and cellular functions of interferon-induced transmembrane proteins date: 2017-11-21 words: 6846.0 sentences: 313.0 pages: flesch: 36.0 cache: ./cache/cord-354050-kcn67stj.txt txt: ./txt/cord-354050-kcn67stj.txt summary: Most of what we know about the antiviral activities of IFITM proteins results from work using IAV and vesicular stomatitis virus (VSV), which perform pH-dependent fusion reactions in endosomes to gain access to the cell interior [22] . As the primary determinant for virus-cell attachment and the subsequent fusion reaction, the viral envelope glycoprotein (Env) was suspected to play an important role in whether or not HIV-1 and related lentiviruses are subject to inhibition by IFITM proteins. In addition to restricting virus entry, recent findings indicate that IFITM proteins perform antiviral functions impacting late stages of the HIV-1 life cycle. This antiviral activity is enhanced upon expression of an IFITM3 mutant that is defective for endocytosis, indicating that restriction of HIV-1 virion infectivity is performed at the plasma membrane [5] . Nonetheless, the recent identification of Env variants that are resistant to the IFITM3-mediated restriction of virion infectivity confirms this viral protein as an important determinant. abstract: The first responders of human antiviral immunity are components of the intrinsic immune response that reside within each and every one of our cells. This cell-autonomous arsenal consists of nucleic acid sensors and antiviral effectors strategically placed by evolution to detect and restrict invading viruses. While some factors are present at baseline to allow for constant surveillance of the cell interior, others are upregulated by cytokines (such as interferons) that signal a viral infection underway in neighboring cells. In this review, we highlight the multiple roles played by the interferon-induced transmembrane (IFITM) proteins during viral infection, with focuses on IFITM3 and HIV-1. Moreover, we discuss the cellular pathways in which IFITM proteins are intertwined and the various functions they have been ascribed outside the context of infection. While appreciated as broadly-acting, potent restriction factors that prevent virus infection and pathogenesis in cell culture and in vivo, questions remain regarding their precise mode of action and importance in certain viral contexts. Continued efforts to study IFITM protein function will further cement their status as critical host determinants of virus susceptibility and prioritize them in the development of new antiviral therapies. url: https://doi.org/10.1186/s12977-017-0377-y doi: 10.1186/s12977-017-0377-y id: cord-003764-141u6ax7 author: Shrestha, Ashish C. title: Cytolytic Perforin as an Adjuvant to Enhance the Immunogenicity of DNA Vaccines date: 2019-04-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: DNA vaccines present one of the most cost-effective platforms to develop global vaccines, which have been tested for nearly three decades in preclinical and clinical settings with some success in the clinic. However, one of the major challenges for the development of DNA vaccines is their poor immunogenicity in humans, which has led to refinements in DNA delivery, dosage in prime/boost regimens and the inclusion of adjuvants to enhance their immunogenicity. In this review, we focus on adjuvants that can enhance the immunogenicity of DNA encoded antigens and highlight the development of a novel cytolytic DNA platform encoding a truncated mouse perforin. The application of this innovative DNA technology has considerable potential in the development of effective vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630607/ doi: 10.3390/vaccines7020038 id: cord-284608-ba7wq52t author: Sias, Catia title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples date: 2019-03-04 words: 5645.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-284608-ba7wq52t.txt txt: ./txt/cord-284608-ba7wq52t.txt summary: title: Alpha, Beta, gamma human PapillomaViruses (HPV) detection with a different sets of primers in oropharyngeal swabs, anal and cervical samples BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. In this study, we analyzed the presence of HPV DNA in oral, anal, and cervical specimens collected from HIV positive and HIV negative individuals, living in the same geographic area (regione Lazio) by using MY09/11 [20, 21] FAP59/64 primers [22] . abstract: BACKGROUND: Recent studies have shown a 13-fold increase of oropharyngeal cancer in the presence of HPV, while α-HPV detection seems to be rare in oral cavity in comparison to anal or cervical district, many novel β and γ types have been isolated in this anatomical site suggesting a wide tropism range. Currently, there are no guidelines recommending HPV oral cavity screening as a mandatory test, and it remains unknown which HPV types should be included in HPV screening programs. Our goal was to assess HPV prevalence in oropharyngeal, anal, and cervical swabs using different sets of primers,which are able to amplify α, β, γ HPV types. METHODS: We analysed the presence of HPV DNA in oropharyngeal (n = 124), anal (n = 186), cervical specimens (n = 43) from HIV positive and negative patients using FAP59/64 and MY09/11 primers. All untyped strains were genetically characterized through PCR amplification and direct sequencing of partial L1 region, and the resulting sequences were classified through phylogenetic analysis. RESULTS: HPV prevalence was 20.9% in 124 oropharyngeal swab samples, including infections with multiple HPV types (5.6%). HPV prevalence in this anatomical site was significantly associated with serostatus: 63.3%in HIV positive and 36.3% in HIV negative patients (p < 0.05). Unclassified types were detected in 6 specimens. In our analysis, we did not observe any difference in HPV (α, β, γ) prevalence between men and women. Overall, β species were the most frequently detected 69.7%. When using anal swabs, for HIV positive patients, β genus prevalence was 1% and γ genus was 3.7% including 6 unclassified types. In cervical samples from 43 HIV positive women (18 HPV negative and 25 positive by MY09/11 PCR), only one sample was positivite for β(1) species (2.4%) using FAP primers. Six of the untyped strains clustered with sequences from species 7, 9, 10, 8,12 of γ genus. Four sequences remained unclassified. Finally, β and γ HPV prevalence was significantly lower than their respective HPV prevalence as identified by the Luminex system in all anatomical sites that were analyzed in previous studies. CONCLUSION: This study provides new information about viral isolates present in oropharyngeal site and it will contribute to improve the monitoring of HPV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1132-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30832688/ doi: 10.1186/s12985-019-1132-x id: cord-022141-yxttl3gh author: Siegel, Frederic R. title: Progressive Adaptation: The Key to Sustaining a Growing Global Population date: 2014-08-23 words: 11114.0 sentences: 489.0 pages: flesch: 52.0 cache: ./cache/cord-022141-yxttl3gh.txt txt: ./txt/cord-022141-yxttl3gh.txt summary: Adaptation by the global community as a unit is vital to cope with the effects of increasing populations, global warming/climate change, the chemical, biological, and physical impacts on life-sustaining ecosystems, and competition for life sustaining and economically important natural resources. The chronic malnutrition that about 1 billion people suffered from in 2013 is likely to grow in number in some regions due to global warming/climate change because humans cannot adapt to less food if they are already at subsistence rations. As the global population increases and more people in developing and less developed nations have more disposable income, there will be a growing draw on natural resources other than water and food to service their industrial, agricultural, and manufacturing needs and wants. The effects of higher temperatures from global warming and climate change included what has been discussed in previous chapters of this book: heat, drought, sea level rise, coastal zones, typhoons, flooding, river runoff, water availability, ecosystem shifts, crop yields, fishing, aquaculture, livestock, health and poverty, and tourism. abstract: Adaptation is an evolving long-term process during which a population of life forms adjusts to changes in its habitat and surrounding environments. Adaptation by the global community as a unit is vital to cope with the effects of increasing populations, global warming/climate change, the chemical, biological, and physical impacts on life-sustaining ecosystems, and competition for life sustaining and economically important natural resources. The latter include water, food, energy, metal ores, industrial minerals, and wood. Within this framework, it is necessary to adapt as well to changes in local and regional physical conditions brought on by natural and anthropogenic hazards, by health threats of epidemic or pandemic reach, by social conditions such as conflicts driven by religious and ethnic fanaticism, and by tribalism and clan ties. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153416/ doi: 10.1007/978-3-319-09686-5_9 id: cord-313617-hh7lccet author: Sigel, Keith title: Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City date: 2020-06-28 words: 2565.0 sentences: 190.0 pages: flesch: 56.0 cache: ./cache/cord-313617-hh7lccet.txt txt: ./txt/cord-313617-hh7lccet.txt summary: We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. We then compared differences in time to death to assess disease trajectory for hospitalized patients by HIV status by fitting unadjusted cumulative incidence function curves with hospital discharge as a competing risk. [7] To compare cumulative incidence of death by HIV status accounting for potential confounding factors we then fit a multivariable survival model using Fine-Grey competing risk methods, including demographics, COVID-19 severity, comorbid conditions and laboratory values that differed by HIV status. abstract: BACKGROUND: There have been limited data regarding the clinical impact of COVID-19 disease on people with HIV (PWH). In this study we compared outcomes for PWH with COVID-19 disease to a matched comparison group. DESIGN: We identified 88 PWH hospitalized with laboratory confirmed COVID-19 in our hospital system in New York between March 12 and April 23, 2020. We collected data on baseline clinical characteristics, laboratory values, HIV infection status, COVID-19 treatment, and outcomes from this group and matched comparators (one PWH to up to five patients by age, sex, race/ethnicity and calendar week of infection). We compared baseline clinical characteristics and outcomes (death, mechanical ventilation, hospital discharge) for these two groups, as well as cumulative incidence of death by HIV status. RESULTS: Patients did not differ significantly by HIV status by age, sex or race/ethnicity due to the matching algorithm. PWH hospitalized with COVID-19 had high proportions of HIV virologic control on antiretroviral therapy. PWH had greater proportions of smoking (p<0.001) and comorbid illness than demographically similar uninfected comparators. There was no difference in COVID-19 severity on admission by HIV status (p=0.15). Poor outcomes for hospitalized PWH were frequent but similar to proportions in comparators; 18% required mechanical ventilation and ultimately 21% died during follow-up (compared with 23% and 20% respectively). There was similar cumulative incidence of death over time by HIV status (p=0.94). INTERPRETATION: We found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared to a demographically similar patient group. url: https://doi.org/10.1093/cid/ciaa880 doi: 10.1093/cid/ciaa880 id: cord-021481-tvs1pnib author: Singh, Gatikrushna title: Cellular RNA Helicases Support Early and Late Events in Retroviral Replication date: 2018-08-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Retroviruses commandeer cell RNA helicases (RHs). Cell RHs are necessary for early and late events in retrovirus replication. The provirus is adopted by the cell-endogenous nuclear and cytoplasmic gene expression types of machinery. Whereas retroviruses engender the supportive activity of cell RHs, other RNA viruses provoke theantiviral role of this superfamily of conserved proteins. In this chapter, we contrast retrovirus reliance on host RNA helicases to support their replication cycle, with the virus-encoded helicaseactivity utilized by RNA viruses in cytoplasmic factories. Ironically, RHs are agonists to retroviruses and antagonists to other RNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149973/ doi: 10.1016/b978-0-12-811185-7.00007-8 id: cord-310430-7eww1oet author: Singh, Ram Sarup title: Algal lectins as promising biomolecules for biomedical research date: 2013-07-16 words: 6079.0 sentences: 347.0 pages: flesch: 45.0 cache: ./cache/cord-310430-7eww1oet.txt txt: ./txt/cord-310430-7eww1oet.txt summary: In general, marine algal lectins are monomeric, low molecular weight proteins, exhibiting high content of acidic amino acids, with isoelectric point (pI) in the range of 4-6, do not require metal ions for their biological activities and most of them show specificity for glycoproteins than monosaccharides Rogers & Hori, 1993; Shiomi et al., 1981) . They concluded that marine algal agglutinins are most sensitive to protease treated sheep erythrocytes followed by native rabbit and sheep erythrocytes, but not to human and chicken red blood cells. Lectins from cyanobacteria and other marine macro-algae are specific for high-mannose which makes them promising candidates for the prevention of transmission of various enveloped viruses such as human immunodeficiency virus (HIV), influenza virus, hepatitis C virus (HCV), Ebola virus and severe acute respiratory syndrome coronavirus (SARS-CoV) (Ziolkowska & Wlodawer, 2006) . Antinociceptive and anti-inflammatory effects of a mucin-binding agglutinin isolated from the red marine alga Hypnea cervicornis abstract: Lectins are natural bioactive ubiquitous proteins or glycoproteins of non-immune response that bind reversibly to glycans of glycoproteins, glycolipids and polysaccharides possessing at least one non-catalytic domain causing agglutination. Some of them consist of several carbohydrate-binding domains which endow them with the properties of cell agglutination or precipitation of glycoconjugates. Lectins are rampant in nature from plants, animals and microorganisms. Among microorganisms, algae are the potent source of lectins with unique properties specifically from red algae. The demand of peculiar and neoteric biologically active substances has intensified the developments on isolation and biomedical applications of new algal lectins. Comprehensively, algal lectins are used in biomedical research for antiviral, antinociceptive, anti-inflammatory, anti-tumor activities, etc. and in pharmaceutics for the fabrication of cost-effective protein expression systems and nutraceutics. In this review, an attempt has been made to collate the information on various biomedical applications of algal lectins. url: https://doi.org/10.3109/1040841x.2013.798780 doi: 10.3109/1040841x.2013.798780 id: cord-260604-lz1qd69t author: Singh, Ramendra K. title: Synthesis, structure–activity relationship and antiviral activity of 3′-N,N-dimethylamino-2′,3′-dideoxythymidine and its prodrugs date: 2010-09-30 words: 3096.0 sentences: 170.0 pages: flesch: 58.0 cache: ./cache/cord-260604-lz1qd69t.txt txt: ./txt/cord-260604-lz1qd69t.txt summary: Molecular docking studies with HIV-1 RT using DS 2.5 and pymol softwares have shown marked differences in the interaction patterns between the lead compound 4 and AZT. The lead molecule, DMAT, was designed keeping AZT, an approved NRTI drug against HIV/AIDS, in mind, where azido group has been replaced by dimethylamino function, Fig. 1 . Compounds 4 and 5 have showed similar values of CC 50 and EC 50 against all viruses studied and thus no activity was observed, while 5 0 -L-phenylalanyl derivative 6, having free amino function was potentially active at an EC 50 of 0.03 mM against VSV in HeLa and HEL cell cultures. The fact that the lead molecule DMAT (and its prodrugs) being a dideoxynucleoside and having structural features similar to AZT, did not show any activity against HIV and rather proved toxic, prompted us to study its interaction with HIV-1 RT. abstract: Abstract A probable NRTI molecule, viz. 3′-N,N-dimethylamino-2′,3′-dideoxythymidine (4) and its 5′-O-carboxyl ester prodrugs – 5′-(N-α-BOC-l-phenylalanyl)-3′-N,N-dimethylamino-2′,3′-dideoxythymidine (5), 5′-l-phenylalanyl-3′-N,N-dimethylamino-2′,3′-dideoxythymidine (6) and 5′-decanoyl-3′-N,N-dimethylamino-2′,3′-dideoxythymidine (7) have been synthesized and screened against HIV, HSV-1 and 2, parainfluenza-3, vesicular stomatitis and several other viruses. The compound 6 showed good antiviral activity with EC50 value 0.03μM (SI=8) against VSV in Hela and HEL cell lines. However, the lead compound 4 and its derivatives 5, 6 and 7 showed no remarkable activity against HIV-1 and other viruses. Molecular docking studies with HIV-1 RT using DS 2.5 and pymol softwares have shown marked differences in the interaction patterns between the lead compound 4 and AZT. url: https://www.sciencedirect.com/science/article/pii/S0223523410003685 doi: 10.1016/j.ejmech.2010.05.028 id: cord-289443-46w52de3 author: Sironi, Manuela title: Evolutionary insights into host–pathogen interactions from mammalian sequence data date: 2015-03-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infections are one of the major selective pressures acting on humans, and host-pathogen interactions contribute to shaping the genetic diversity of both organisms. Evolutionary genomic studies take advantage of experiments that natural selection has been performing over millennia. In particular, inter-species comparative genomic analyses can highlight the genetic determinants of infection susceptibility or severity. Recent examples show how evolution-guided approaches can provide new insights into host–pathogen interactions, ultimately clarifying the basis of host range and explaining the emergence of different diseases. We describe the latest developments in comparative immunology and evolutionary genetics, showing their relevance for understanding the molecular determinants of infection susceptibility in mammals. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrg3905) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrg3905 doi: 10.1038/nrg3905 id: cord-341155-3d64mso0 author: Slots, Jørgen title: Bacterial and viral pathogens in saliva: disease relationship and infectious risk date: 2010-12-07 words: 9332.0 sentences: 447.0 pages: flesch: 36.0 cache: ./cache/cord-341155-3d64mso0.txt txt: ./txt/cord-341155-3d64mso0.txt summary: Human viruses are also frequent inhabitants of the human mouth, and their presence in saliva may be caused by the direct transfer of saliva from infected individuals, a bloodborne infection of the salivary glands, infection of the oral mucosa, or serumal exudates from diseased periodontal sites. Caries risk is assessed by the levels of mutans streptococci and lactobacilli in stimulated saliva (94, 96) , and salivary transmission of cariogenic bacteria frequently occurs from the mother to her child (92, 100) . As high quantities of salivary Epstein-Barr virus DNA can be recovered from fully edentulous patients (155) , the occurrence of the virus in saliva may not be a reliable indicator of its subgingival level or of the periodontitis disease status. Taken together, the saliva of HIV-infected persons is a risk factor for the transmission of several virulent herpesvirus species, and patients receiving HAART cannot be assumed to be less infectious for herpesviruses than individuals not receiving HAART. abstract: nan url: https://doi.org/10.1111/j.1600-0757.2010.00361.x doi: 10.1111/j.1600-0757.2010.00361.x id: cord-329482-haenltxn author: Small, Eusebius title: Covid-19 and Gender in LMICs: Potential Lessons from HIV Pandemic date: 2020-05-25 words: 1581.0 sentences: 96.0 pages: flesch: 53.0 cache: ./cache/cord-329482-haenltxn.txt txt: ./txt/cord-329482-haenltxn.txt summary: According to the World Bank, almost 24 million fewer people will escape poverty in East Asia and the Pacific because of the financial impact of COVID-19 in 2020 [9] . Among the LMICs in sub-Saharan Africa, COVID-19 could push these countries farther into a spiral of poverty, ravaging their already tenuous health systems [2, 5] . During the HIV outbreak, a significant limited reproductive health care and family planning services were available to women. According to the United Nations, an unrelated crisis impacting women worldwide are the spikes in domestic violence due to COVID-19 lockdowns [7] . Additionally, women who are transgender and are living with HIV are disproportionately impacted by intimate partner violence [24] , stay at home COVID-19 orders could exacerbate their wellbeing. A pandemic of the poor: social disadvantage and the U.S. HIV epidemic Gender-Based Violence Increases Risk of HIV/AIDS for Women in Sub-Saharan Africa -Population Reference Bureau abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32451937/ doi: 10.1007/s10461-020-02932-z id: cord-355318-qm79gz8w author: Smit, Albertus J. title: Winter Is Coming: A Southern Hemisphere Perspective of the Environmental Drivers of SARS-CoV-2 and the Potential Seasonality of COVID-19 date: 2020-08-05 words: 15419.0 sentences: 706.0 pages: flesch: 41.0 cache: ./cache/cord-355318-qm79gz8w.txt txt: ./txt/cord-355318-qm79gz8w.txt summary: Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Thus, if climate factors do play a role in COVID-19 infection rates, the concurrence of transition of southern hemisphere countries to their winter season with the mid-stages of the disease transmission trajectory is of concern, especially with respect to containment policy and health system resource allocation. Environmental variables considered in preprint and peer-reviewed publications as modulators of SARS-CoV-2 transmission rates include mean, minimum and/or maximum daily temperature, and diurnal temperature range; an undefined ''humidity'' variable, relative humidity, specific humidity and absolute humidity; dew point temperature; rainfall; wind speed or wind power; air pressure; some metric of solar or UV radiation; and ''air quality'' (Supplementary Tables S1 and S2 ). The general prevalence of climatologically-coupled seasonal signals and environmental variable modulation seen in the majority of other viral respiratory diseases creates the expectation for a similar effect on SARS-CoV-2 and in COVID-19 epidemiology. abstract: SARS-CoV-2 virus infections in humans were first reported in December 2019, the boreal winter. The resulting COVID-19 pandemic was declared by the WHO in March 2020. By July 2020, COVID-19 was present in 213 countries and territories, with over 12 million confirmed cases and over half a million attributed deaths. Knowledge of other viral respiratory diseases suggests that the transmission of SARS-CoV-2 could be modulated by seasonally varying environmental factors such as temperature and humidity. Many studies on the environmental sensitivity of COVID-19 are appearing online, and some have been published in peer-reviewed journals. Initially, these studies raised the hypothesis that climatic conditions would subdue the viral transmission rate in places entering the boreal summer, and that southern hemisphere countries would experience enhanced disease spread. For the latter, the COVID-19 peak would coincide with the peak of the influenza season, increasing misdiagnosis and placing an additional burden on health systems. In this review, we assess the evidence that environmental drivers are a significant factor in the trajectory of the COVID-19 pandemic, globally and regionally. We critically assessed 42 peer-reviewed and 80 preprint publications that met qualifying criteria. Since the disease has been prevalent for only half a year in the northern, and one-quarter of a year in the southern hemisphere, datasets capturing a full seasonal cycle in one locality are not yet available. Analyses based on space-for-time substitutions, i.e., using data from climatically distinct locations as a surrogate for seasonal progression, have been inconclusive. The reported studies present a strong northern bias. Socio-economic conditions peculiar to the ‘Global South’ have been omitted as confounding variables, thereby weakening evidence of environmental signals. We explore why research to date has failed to show convincing evidence for environmental modulation of COVID-19, and discuss directions for future research. We conclude that the evidence thus far suggests a weak modulation effect, currently overwhelmed by the scale and rate of the spread of COVID-19. Seasonally modulated transmission, if it exists, will be more evident in 2021 and subsequent years. url: https://doi.org/10.3390/ijerph17165634 doi: 10.3390/ijerph17165634 id: cord-297135-mg2qs3b6 author: Smith, Kumi title: A harm reduction paradox: Comparing China''s policies on needle and syringe exchange and methadone maintenance date: 2012-07-31 words: 5305.0 sentences: 207.0 pages: flesch: 42.0 cache: ./cache/cord-297135-mg2qs3b6.txt txt: ./txt/cord-297135-mg2qs3b6.txt summary: Abstract Background China has launched methadone maintenance treatment (MMT) and needle and syringe exchange programmes (NSEP) as part of the country''s HIV prevention strategy amongst injection drug users. The State Council AIDS Working Committee, an interagency committee formed to streamline the government''s AIDS policy, created an opportunity for a rare partnership between the Ministries of Health and Public Security and this resulted in experimentation with progressive strategies including needle and syringe exchange programmes (NSEP) and methadone maintenance treatment (MMT) (State Council, People''s Republic of China, 2001 China, , 2006a . A key distinction is the international attention garnered by MMT in the form of publications, recognition from international drug policy groups-Director Zunyou Wu of the Chinese National Centre for AIDS/STD Control & Prevention (NCAIDS) was awarded the International Harm Reduction Association''s Rolleston Award for significant contributions to the field (IHRD, 2008)-and study tours by health experts from Russia, Vietnam, and Malaysia (Malinowska-Sempruch & Bartlett, 2006) . abstract: Abstract Background China has launched methadone maintenance treatment (MMT) and needle and syringe exchange programmes (NSEP) as part of the country's HIV prevention strategy amongst injection drug users. MMT is expanding, with backing from multiple government ministries, however, NSEP have received less political support and funding. Methods Semi-structured, serial interviews were conducted with key informants, knowledgeable about China's harm reduction policies. Concurrent content analysis allowed for revision of the interview guide throughout the data collection process. This was combined with a systematic analysis of official government policy documents on NSEP and MMT, including white papers, legal documents, and policy statements. Findings Early consensus between public security and public health sectors regarding methadone's dual use in HIV prevention as well as method of drug control created broad institutional support for MMT programmes amongst policy makers. In contrast, NSEP were seen as satisfying only the HIV prevention goals of the public health sector, and were perceived as condoning illicit drug use. Furthermore, NSEP's roots in China, as an experimental collaboration with international groups, created suspicion regarding its role in China's drug control policy. NSEP and MMT's distinct paths to policy development are reflected in the complex and occasionally contradictory nature of China's harm reduction strategy. Conclusions These discrepancies highlight the need for a more politically sustainable and comprehensive integration of harm reduction projects. Recommendations include improved evaluation methods for NESP, NSEP-MMT cross-referral system, and stronger NSEP advocacy within the non-profit and public health sectors. url: https://api.elsevier.com/content/article/pii/S0955395911001770 doi: 10.1016/j.drugpo.2011.09.010 id: cord-259503-dkfrk71a author: Smith, Sarah E. title: Sherlock Genomes — viral investigator date: 2013-02-15 words: 806.0 sentences: 54.0 pages: flesch: 56.0 cache: ./cache/cord-259503-dkfrk71a.txt txt: ./txt/cord-259503-dkfrk71a.txt summary: Deep sequencing technologies and stateof-the-art bioinformatics techniques have revolutionized the way that RNA viruses, a notoriously variable group of pathogens, can be identified and characterized. By using de novo assembly of short reads, the authors showed that this method could generate full genomes for viruses within all four major HIV-1 genetic groups. Even when almost nothing is known about the agent of a viral infection, deep sequencing technologies can identify a pathogen and produce the full genome, fast. When SARS-CoV began infecting people in 2002, it took a large team to generate a full genome by capillary sequencing. 2 used random priming to amplify viral RNA isolated from the Saudi Arabian patient, and then deep-sequenced the genome. Knowing the sequence of the whole genome enabled the authors to further characterize this new virus, named human CoV (HCoV)-EMC2012. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes abstract: This month's Genome Watch highlights how deep sequencing technologies have vastly reduced the time and prior knowledge needed to generate viral genomes. url: https://www.ncbi.nlm.nih.gov/pubmed/23411861/ doi: 10.1038/nrmicro2979 id: cord-000130-dqqcajjd author: Smith?, Robert J title: The OptAIDS project: towards global halting of HIV/AIDS date: 2009-11-18 words: 2383.0 sentences: 146.0 pages: flesch: 54.0 cache: ./cache/cord-000130-dqqcajjd.txt txt: ./txt/cord-000130-dqqcajjd.txt summary: The OptAIDS workshop was the first of its kind: a scientific meeting held simultaneously in both a real world location and also Second Life ® http://secondlife.com, a virtual landscape that allows real-time communication. Spending our way out of the epidemic Theme 1 comprises an introduction and overview of mathematical modeling [22] , as well as a history of AIDS in Africa and its effects on human development [23] . Theme 4 examines in-host modeling -a crucial element in tackling the disease, often overlooked by epidemiologists -by proposing new methods for evaluating the efficacy of antiretroviral treatment [31] and examining antioxidant supplementation as HIV therapy, with a focus on injecting drug users [32] . Finally, Theme 6 examines the question at the core of the OptAIDS project: spending our way out of the AIDS epidemic [6] . Predicting and preventing measles epidemics in New Zealand: application of a mathematical model Halting HIV/AIDS with avatars and havatars: a virtual world approach to modelling epidemics abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779497/ doi: 10.1186/1471-2458-9-s1-s1 id: cord-317533-xpfqdeqv author: Smuts, Heidi title: Human coronavirus NL63 infections in infants hospitalised with acute respiratory tract infections in South Africa date: 2008-07-24 words: 2374.0 sentences: 137.0 pages: flesch: 52.0 cache: ./cache/cord-317533-xpfqdeqv.txt txt: ./txt/cord-317533-xpfqdeqv.txt summary: Objective To determine the role of HCoV‐NL63 in infants and young children hospitalised with acute respiratory tract infections (ARI) in Cape Town, South Africa. A number of respiratory viruses including influenza viruses, respiratory syncytial virus (RSV), parainfluenza viruses, adenovirus and the recently described human metapneumovirus (hMPV) play an important role in acute respiratory tract infections (ARI) in children. In the South African setting, where the prevalence of HIV is high, all infant respiratory samples are routinely screened for CMV as in our setting this virus is a major cause of pneumonia in HIV-infected children. In conclusion these findings suggest that although HCoV-NL63 is circulating in the community it plays a minor role in severe respiratory tract infections in young children who require hospitalisation. A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalised with respiratory tract infections in Belgium Evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children abstract: Background Human coronavirus NL63 (HCoV‐NL63) is a novel respiratory virus which is associated with respiratory tract infections in children. Objective To determine the role of HCoV‐NL63 in infants and young children hospitalised with acute respiratory tract infections (ARI) in Cape Town, South Africa. Methods Respiratory specimens were collected from 1055 infants and young children hospitalised with ARI in 2003–2004. Samples were screened by RT‐PCR to detect HCoV‐NL63 and human metapneumovirus (hMPV). Standard shell vial culture and immunofluoresence was used to detect the common respiratory viruses including RSV, influenza A and B viruses, parainfluenza viruses 1, 2, 3, adenovirus and CMV. Results A respiratory virus was found in 401/1055 (38·0%) samples. HCoV‐NL63 was detected in 9/1055 (0·85%) with peak activity during autumn (67%). Most patients had a diagnosis of pneumonia or lower respiratory tract infection (6/9; 67%). Conclusions This is the first report of HCoV‐NL63 infections in hospitalised children in Africa. During the 2‐year period HCoV‐NL63 played a minor role in ARI in children. url: https://doi.org/10.1111/j.1750-2659.2008.00049.x doi: 10.1111/j.1750-2659.2008.00049.x id: cord-263438-9ra94uda author: Snowden, Frank M. title: Emerging and reemerging diseases: a historical perspective date: 2008-09-19 words: 14393.0 sentences: 608.0 pages: flesch: 47.0 cache: ./cache/cord-263438-9ra94uda.txt txt: ./txt/cord-263438-9ra94uda.txt summary: Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. In 1996, in addition, President Bill Clinton (28) issued a fact sheet entitled ''Addressing the Threat of Emerging Infectious Diseases'' in which he declared them ''one of the most significant health and security challenges facing the global community.'' There were also highly visible hearings on emerging infections in the US Congress (29) . The Rand Corporation intelligence report The Global Threat of New and Reemerging Infectious Diseases: Reconciling U.S. National Security and Public Health Policy (53) had two leading themes. abstract: Summary: Between mid‐century and 1992, there was a consensus that the battle against infectious diseases had been won, and the Surgeon General announced that it was time to close the book. Experience with human immunodeficiency virus/acquired immunodeficiency syndrome, the return of cholera to the Americas in 1991, the plague outbreak in India in 1994, and the emergence of Ebola in Zaire in 1995 created awareness of a new vulnerability to epidemics due to population growth, unplanned urbanization, antimicrobial resistance, poverty, societal change, and rapid mass movement of people. The increasing virulence of dengue fever with dengue hemorrhagic fever and dengue shock syndrome disproved the theory of the evolution toward commensalism, and the discovery of the microbial origins of peptic ulcer demonstrated the reach of infectious diseases. The Institute of Medicine coined the term ‘emerging and reemerging diseases’ to explain that the world had entered an era in which the vulnerability to epidemics in the United States and globally was greater than ever. The United States and the World Health Organization took devised rapid response systems to monitor and contain disease outbreaks and to develop new weapons against microbes. These mechanisms were tested by severe acute respiratory syndrome in 2003, and a series of practical and conceptual blind spots in preparedness were revealed. url: https://www.ncbi.nlm.nih.gov/pubmed/18837773/ doi: 10.1111/j.1600-065x.2008.00677.x id: cord-022348-w7z97wir author: Sola, Monica title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter argues that the vast majority of genetic changes or mutations fixed by RNA viruses are essentially neutral or nearly neutral in character. In molecular evolution one of the remarkable observations has been the uniformity of the molecular clock. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. These analyses indicate that viral protein diversification is essentially a smooth process, the major parameter being the nature of the protein more than the ecological niche it finds itself in. Synonymous changes are invariably more frequent than nonsynonymous changes. Positive selection exploits a small proportion of genetic variants, while functional sequence space is sufficiently dense, allowing viable solutions to be found. Although evolution has connotations of change, what has always counted is natural selection or adaptation. It is the only force for the genesis of a novel replicon. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155598/ doi: 10.1016/b978-012220360-2/50007-6 id: cord-006331-s2qf98lj author: Spiridonova, V. A. title: Molecular recognition elements: DNA/RNA-aptamers to proteins date: 2010-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The review summarizes data on DNA/RNA aptamers, a novel class of molecular recognition elements. Special attention is paid to the aptamers to proteins involved into pathogenesis of wide spread human diseases. These include aptamers to serine proteases, cytokines, influenza viral proteins, immune deficiency virus protein and nucleic acid binding proteins. High affinity and specific binding of aptamers to particular protein targets make them attractive as direct protein inhibitors. They can inhibit pathogenic proteins and data presented here demonstrate that the idea that nucleic acid aptamers can regulate (inhibit) activity of protein targets has been transformed from the stage of basic developments into the stage of realization of practical tasks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101625/ doi: 10.1134/s1990750810020046 id: cord-253768-y35m3vh1 author: Springer, Sandra A title: Federal and State Action Needed to End the Infectious Complications of Illicit Drug Use in the United States: IDSA and HIVMA’s Advocacy Agenda date: 2020-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In response to the opioid crisis, IDSA and HIVMA established a working group to drive an evidence- and human rights-based response to illicit drug use and associated infectious diseases. Infectious diseases and HIV physicians have an opportunity to intervene, addressing both conditions. IDSA and HIVMA have developed a policy agenda highlighting evidence-based practices that need further dissemination. This paper reviews (1) programs most relevant to infectious diseases in the 2018 SUPPORT Act; (2) opportunities offered by the “End the HIV Epidemic” initiative; and (3) policy changes necessary to affect the trajectory of the opioid epidemic and associated infections. Issues addressed include leveraging harm reduction tools and improving integrated prevention and treatment services for the infectious diseases and substance use disorder care continuum. By strengthening collaborations between infectious diseases and addiction specialists, including increasing training in substance use disorder treatment among infectious diseases and addiction specialists, we can decrease morbidity and mortality associated with these overlapping epidemics. url: https://doi.org/10.1093/infdis/jiz673 doi: 10.1093/infdis/jiz673 id: cord-302082-aaokc182 author: Stanberry, Lawrence R. title: Vaccines of the future date: 2011-08-31 words: 7736.0 sentences: 348.0 pages: flesch: 37.0 cache: ./cache/cord-302082-aaokc182.txt txt: ./txt/cord-302082-aaokc182.txt summary: To address these challenges researchers are exploring many avenues: novel adjuvants are being developed that enhance the immune response elicited by a vaccine while maintaining high levels of tolerability; methods of protective antigen identification are iterated with every success; vaccine storage and transport systems are improving (including optimising the cold chain and developing temperature-stable vaccines); and new and potentially more convenient methods of vaccine administration are being pursued. One approach to addressing the weak immunogenicity of the antigen has been to link it to a potent Toll-like receptor adjuvant such as flagellin, an approach developed by VaxInnate Inc. During primary infection of a single individual with HIV, mutations in surface proteins of the virus lead to selection of a ''cloud'' of antigenic variants that can evade the cell-mediated immune responses complicating the development of broadly effective vaccines. abstract: nan url: https://api.elsevier.com/content/article/pii/S2210762211000076 doi: 10.1016/j.pervac.2011.05.006 id: cord-004575-b0t6bsya author: Staub, Roger title: Haben HIV-Positive eine besondere Verantwortung?: Ein Diskussionsbeitrag date: 2007-03-27 words: 1953.0 sentences: 233.0 pages: flesch: 62.0 cache: ./cache/cord-004575-b0t6bsya.txt txt: ./txt/cord-004575-b0t6bsya.txt summary: Von HIV-infizierten Menschen sollten wir erwarten, dass sie den geliebten Partner, die geliebte Partnerin nicht gefährden bei sexuellen Begegnungen, die im Rahmen einer aktuellen oder erhofften zukünftigen Beziehung stattfinden. Auch von einer HIV-positiven Prostituierten oder von einem HIV-positiven Homosexuellen bei einem One-Night-Stand ist nicht zu erwarten, dass sie Verantwortung für den Schutz des anderen übernehmen. Lässt sich eine HIV-positive Person auf eine so geartete Beziehung ein, kann die Liebe nach dem Verlobungstest nur weiter gedeihen, wenn der HIV-positive oder ungetestete Partner von Anfang an seine Verantwortung wahrgenommen und für konsequenten Schutz gesorgt hat. Wenn wir es schaffen, auch von einer HIV-positiven Prostituierten nicht zu erwarten, dass sie auf das Angebot eines Freiers verzichten muss, der für "ohne" gar mehr bezahlen will, dann können wir auch mit Freiern deutlich kommunizieren und sie zum "immer mit" motivieren. abstract: In the 1980s, most Western countries decided to opt for a new public health approach based on learning strategies to fight HIV/AIDS. Within the new public health paradigm, every sexually active person protects him-/herself, whereas it is the infected people that bear the burden of prevention according to old public health. The paper begins with a clear statement for the new public health approach that includes self-protection and the protection of civil rights. It argues that this approach is still valid under the changing circumstances due to combination therapies and the developments related to them, such as the introduction of routine HIV screening in some countries. On this background, the paper examines from an ethical perspective to what extent people with HIV have a responsibility in HIV prevention. The paper argues that a person with HIV has a responsibility to protect his/her partner in the case of a relationship of love. On the other hand, in the case of "purely" sexual encounters, each person is responsible for his/her own security and should not rely on the other. This position also helps to clarify prevention messages. In conclusion, the paper shows how morality evolves into ethical positions and then translates into the law. It finally claims for stronger obligations for sex businesses to support HIV prevention. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079983/ doi: 10.1007/s00103-007-0190-1 id: cord-318587-ewvnkdr2 author: Steeds, Kimberley title: Pseudotyping of VSV with Ebola virus glycoprotein is superior to HIV-1 for the assessment of neutralising antibodies date: 2020-08-31 words: 4973.0 sentences: 244.0 pages: flesch: 46.0 cache: ./cache/cord-318587-ewvnkdr2.txt txt: ./txt/cord-318587-ewvnkdr2.txt summary: We evaluated the suitability of EBOV GP pseudotyped human immunodeficiency virus type 1 (HIV-1) and vesicular stomatitis virus (VSV) to measure the neutralising ability of plasma from EVD survivors, when compared to results from a live EBOV neutralisation assay. The aim of this study was to assess the suitability of EBOV GP pseudotyped HIV-1 and VSV systems to measure neutralisation by EVD survivor plasma, in comparison with results from a live EBOV neutralisation assay. To determine the optimal pseudotyped virus input to use in the HIV-and VSV-based assays, neutralisation of different amounts of the EBOV GP pseudotyped viruses by plasma from a Guinean EVD survivor donor or human anti-EBOV GP mAb KZ52 was assessed. When IC 50 values of EBOV GP pseudotyped HIV-1 neutralisation of the 30 EVD survivor and 10 negative plasma samples were compared with GMT values for the live EBOV neutralisation assay, a positive correlation (r s = 0.54) was determined using the nonparametric Spearman correlation coefficient (Fig. 5a) and this was statistically significant (p = 0.0004). abstract: Ebola virus (EBOV) is an enveloped, single-stranded RNA virus that can cause Ebola virus disease (EVD). It is thought that EVD survivors are protected against subsequent infection with EBOV and that neutralising antibodies to the viral surface glycoprotein (GP) are potential correlates of protection. Serological studies are vital to assess neutralising antibodies targeted to EBOV GP; however, handling of EBOV is limited to containment level 4 laboratories. Pseudotyped viruses can be used as alternatives to live viruses, which require high levels of bio-containment, in serological and viral entry assays. However, neutralisation capacity can differ among pseudotyped virus platforms. We evaluated the suitability of EBOV GP pseudotyped human immunodeficiency virus type 1 (HIV-1) and vesicular stomatitis virus (VSV) to measure the neutralising ability of plasma from EVD survivors, when compared to results from a live EBOV neutralisation assay. The sensitivity, specificity and correlation with live EBOV neutralisation were greater for the VSV-based pseudotyped virus system, which is particularly important when evaluating EBOV vaccine responses and immuno-therapeutics. Therefore, the EBOV GP pseudotyped VSV neutralisation assay reported here could be used to provide a better understanding of the putative correlates of protection against EBOV. url: https://www.ncbi.nlm.nih.gov/pubmed/32868837/ doi: 10.1038/s41598-020-71225-1 id: cord-348409-oxjd263z author: Stern, Zachariah title: The development of inovirus-associated vector vaccines using phage-display technologies date: 2019-09-08 words: 6043.0 sentences: 315.0 pages: flesch: 41.0 cache: ./cache/cord-348409-oxjd263z.txt txt: ./txt/cord-348409-oxjd263z.txt summary: Areas covered: The architectural traits of filamentous viruses and their derivatives, IAVs, facilitate the display of specific antigenic peptides which induce antibody production to prevent or curtail infection. The creation of Random Peptide Libraries (RPL), where random oligopeptides are fused to major capsid proteins (gp3 or gp8) and displayed on individual inovirus clones creating a random variety of IAVs which can be used for vaccine design via epitope mapping using monoclonal or polyclonal antibodies. Through this breakthrough technology which was the subject matter of the Nobel Prize in Chemistry 2018 (see ''Expert Commentary'' below), inovriuses displaying oligopeptides mimicking antigens (or specific epitopes of an antigen) can be used to vaccinate hosts thus inducing the desired antibody production. Unlike previous studies, which used a single specific peptide fused to a inovirus, four different antigenic peptides were displayed by inoviruses in a cocktail of recombinant IAVs. The induction of a cellular response completely vaccinated 1/3 of the pigs in the study and reduced the number of cysticerci in all other pigs [61] . abstract: Introduction: Inovirus-associated vectors (IAVs) are derived from bacterial filamentous viruses (phages). As vaccine carriers, they have elicited both cellular and humoral responses against a variety of pathogens causing infectious diseases and other non-infectious diseases. By displaying specific antigen epitopes or proteins on their coat proteins, IAVs have merited much study, as their unique abilities are exploited for widespread vaccine development. Areas covered: The architectural traits of filamentous viruses and their derivatives, IAVs, facilitate the display of specific antigenic peptides which induce antibody production to prevent or curtail infection. Inoviruses provide a foundation for cost-efficient large-scale specific phage display. In this paper, the development of different applications of inovirus-based phage display vaccines across a broad range of pathogens and hosts is reviewed. The references cited in this review were selected from established databases based on the authors’ knowledge of the study subject. Expert commentary: The importance of phage-display technology has been recently highlighted by the Nobel Prize in Chemistry 2018 awarded to George P. Smith and Sir Gregory P. Winter. Furthermore, the symbiotic nature of filamentous viruses infecting intestinal F(+) E. coli strains offers an attractive platform for the development of novel vaccines that stimulate mucosal immunity url: https://doi.org/10.1080/14760584.2019.1651649 doi: 10.1080/14760584.2019.1651649 id: cord-010699-mfe1oajn author: Suehiro, Tamy Taianne title: Cervical and oral human papillomavirus infection in women living with human immunodeficiency virus (HIV) and matched HIV-negative controls in Brazil date: 2020-05-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Despite the demonstrated role of human Papillomavirus (HPV) in the etiology of cervical cancer and the strong evidence suggesting the importance of HPV in the development of oropharyngeal cancer, several aspects of the interrelationship between HPV infection in both body sites remain unknown, specifically in female human immunodeficiency virus (HIV)-positive (HIV+) patients. We aimed to assess the prevalence, distribution, and concordance of cervical and oral HPV in HIV+ women and matched HIV-negative (HIV-) controls in Brazil. MATERIAL AND METHODS: Cervical and endocervical samples for cytological screening and HPV detection and oral samples were collected from 115 HIV+ women using highly active antiretroviral therapy (HAART) and 139 HIV-matched controls (HIV-) in Maringá City, Brazil. Risk factors were assessed using a standardized questionnaire, and the data regarding HIV infection were obtained from the patients’ medical records. HPV detection and typing were performed using the Kit Multiplex XGEN Multi HPV Chip HS12. RESULTS: HIV infection was well controlled in this cohort, but women who exhibited detectable HIV loads were significantly associated with HPV-positive status overall (P = 0.03) and in cervical mucosa (P = 0.01). HIV+ women had significantly more abnormal cytological findings (P = 0.04) than HIV- women. Of the 115 HIV+ women, 48.7% were positive for cervical and/or oral HPV DNA; of the 139 HIV- women, 41% were positive for cervical and/or oral HPV (P = 0.25). Both HIV+ and HIV- women had a statistically higher prevalence of cervical HPV infection than oral infection. The concurrent HPV infection in two anatomical sites was similar in HIV+ and HIV- women; however, HPV type concordance was not observed. HPV type distribution was different between the anatomical sites in both groups, and HIV+ women presented less common types, mainly in oral mucosa. CONCLUSION: Our data support the importance of testing HPV infection in HIV+ women, even when the HIV infection is well controlled. Prospective studies are required to better understand the natural history of HPV infection in both anatomical sites, specifically in HIV+ women. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216672/ doi: 10.1186/s13027-020-00301-y id: cord-002757-upwe0cpj author: Sullivan, Kathleen E. title: Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies date: 2017-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In today’s global economy and affordable vacation travel, it is increasingly important that visitors to another country and their physician be familiar with emerging infections, infections unique to a specific geographic region, and risks related to the process of travel. This is never more important than for patients with primary immunodeficiency disorders (PIDD). A recent review addressing common causes of fever in travelers provides important information for the general population Thwaites and Day (N Engl J Med 376:548-560, 2017). This review covers critical infectious and management concerns specifically related to travel for patients with PIDD. This review will discuss the context of the changing landscape of infections, highlight specific infections of concern, and profile distinct infection phenotypes in patients who are immune compromised. The organization of this review will address the environment driving emerging infections and several concerns unique to patients with PIDD. The first section addresses general considerations, the second section profiles specific infections organized according to mechanism of transmission, and the third section focuses on unique phenotypes and unique susceptibilities in patients with PIDDs. This review does not address most parasitic diseases. Reference tables provide easily accessible information on a broader range of infections than is described in the text. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5693703/ doi: 10.1007/s10875-017-0426-2 id: cord-301506-q2a5aogo author: Sun, Xinhua title: Evolution of information-driven HIV/AIDS policies in China date: 2010-12-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background As China continues to commit to universal access to HIV/AIDS prevention, treatment and care services, its HIV/AIDS policies have become increasingly information driven. We review China’s key national-level HIV/AIDS policies and discuss policy gaps and challenges ahead. Methods We conducted a desk review of key national-level policies that have had a major impact on China’s HIV/AIDS epidemic, and examined recent epidemiological data relevant to China’s HIV response. Results National-level policies that have had a major impact on China’s HIV/AIDS response include: ‘Four Frees and One Care’; 5-year action plans; and HIV/AIDS regulation. These landmark policies have facilitated massive scaling up of services over the past decade. For example, the number of drug users provided with methadone maintenance treatment significantly increased from 8116 in 2005 to 241 975 in 2009; almost a 30-fold increase. The ‘Four Frees and One Care’ policy has increased the number of people living with AIDS on anti-retroviral treatment from some 100 patients in 2003 to over 80 000 in 2009. However, stigma and discrimination remains major obstacles for people living with HIV/AIDS trying to access services. Conclusions China’s current national policies are increasingly information driven and responsive to changes in the epidemic. However, gaps remain in policy implementation, and new policies are needed to meet emerging challenges. url: https://www.ncbi.nlm.nih.gov/pubmed/21113036/ doi: 10.1093/ije/dyq217 id: cord-295099-ghc85pf5 author: Sun, Zehua title: Brief introduction of current technologies in isolation of broadly neutralizing HIV-1 antibodies date: 2018-01-02 words: 7441.0 sentences: 366.0 pages: flesch: 39.0 cache: ./cache/cord-295099-ghc85pf5.txt txt: ./txt/cord-295099-ghc85pf5.txt summary: Antibody responses to neutralize human immunodeficiency virus-1 (HIV-1) are mediated by direct binding to viral spikes, which are trimers composed of glycoproteins gp120 and gp41 (Pincus et al., 2017a; Pincus et al., 2017b; Blair et al., 2007; Morris et al., 2000; Micoli et al., 2000; Pegu et al., 2017; Haynes and Mascola, 2017; Liao et al., 2004; Brodine et al., 2003; Ward and Wilson, 2017; Debnath et al., 1994; Moore et al., 1993) . M43 and m44 are HIV-1 cross-reactive human monoclonal antibodies isolated from a recombinant phage display library by competitive antigen panning (Zhang et al., 2012; Zhang et al., 2008; Zhang et al., 2006; Zhang et al., 2004a; Zhang et al., 2004b) . HIV-1 specific antibodies isolated by display techniques are less potent than those isolated by micro neutralization or single B cell sorting and cloning. Anti-human immunodeficiency virus type 1 human monoclonal antibodies that bind discontinuous epitopes in the viral glycoproteins can identify mimotopes from recombinant phage peptide display libraries abstract: HIV/AIDS has become a worldwide pandemic. Before an effective HIV-1 vaccine eliciting broadly neutralizing monoclonal antibodies (bnmAbs) is fully developed, passive immunization for prevention and treatment of HIV-1 infection may alleviate the burden caused by the pandemic. Among HIV-1 infected individuals, about 20% of them generated cross-reactive neutralizing antibodies two to four years after infection, the details of which could provide knowledge for effective vaccine design. Recent progress in techniques for isolation of human broadly neutralizing antibodies has facilitated the study of passive immunization. The isolation and characterization of large panels of potent human broadly neutralizing antibodies has revealed new insights into the principles of antibody-mediated neutralization of HIV. In this paper, we review the current effective techniques in broadly neutralizing antibody isolation. url: https://doi.org/10.1016/j.virusres.2017.10.011 doi: 10.1016/j.virusres.2017.10.011 id: cord-264225-vzcfeh7t author: Talbert-Slagle, Kristina title: Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body date: 2014-05-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://doi.org/10.1371/journal.ppat.1004092 doi: 10.1371/journal.ppat.1004092 id: cord-264986-glm2qcuz author: Tam, Cheuk Chi title: Psychological Distress Among HIV Healthcare Providers During the COVID-19 Pandemic in China: Mediating Roles of Institutional Support and Resilience date: 2020-10-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Psychological distress among healthcare providers is concerning during COVID-19 pandemic due to extreme stress at healthcare facilities, including HIV clinics in China. The socioecological model suggests that psychological distress could be influenced by multi-level factors. However, limited COVID-19 research examined the mechanisms of psychological distress among HIV healthcare providers. This study examined organizational and intrapersonal factors contributing to psychological health during COVID-19 pandemic. Data were collected via online anonymous surveys from 1029 HIV healthcare providers in Guangxi, China during April–May 2020. Path analysis was utilized to test a mediation model among COVID-19 stressors, institutional support, resilience, and psychological distress (PHQ-4). Thirty-eight percent of the providers experienced psychological distress (PHQ-4 score > 3). Institutional support and resilience mediated the relationship between COVID-19 stressors and psychological distress. Psychological distress was common among Chinese HIV healthcare providers during COVID-19 pandemic. Psychological health intervention should attend to institutional support and resilience. url: https://doi.org/10.1007/s10461-020-03068-w doi: 10.1007/s10461-020-03068-w id: cord-103350-jj9pc4a6 author: Tang, Pingtao title: An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy date: 2020-05-08 words: 4041.0 sentences: 204.0 pages: flesch: 46.0 cache: ./cache/cord-103350-jj9pc4a6.txt txt: ./txt/cord-103350-jj9pc4a6.txt summary: rAd-Tat and LacZ control vectors (2 × 109) were expressed in the kidney of newborn wild type and HIV-transgenic (Tg26) FVB/N mice without significant proteinuria (n = 5 8 per group). Results HIV-Tat induced the expression of HIV-1 genes (env) and heparin binding growth factors in the kidney of HIV-Tg26 mice, and precipitated HIVAN in the first month of life. Summary statement We developed a new inducible mouse model system of childhood HIV-associated nephropathy, and demonstrated that HIV-Tat plays a critical role in this renal disease acting in synergy with other HIV-1 genes and heparin binding cytokines. Therefore, we carried out this study to determine whether the HIV-1 trans-activator (Tat) gene precipitates HIVAN in young mice, and define whether this approach could be used to generate an inducible mouse model system of childhood HIVAN. Our study showed that the activation and basic binding domains of Tat are sufficient to induce the renal expression of HIV-genes and precipitate HIVAN in young mice. abstract: Background Modern antiretroviral therapies (ART) have decreased the prevalence of HIV-associated nephropathy (HIVAN). Nonetheless, we continue to see children and adolescents with HIVAN all over the world. Furthermore, once HIVAN is established in children, it is difficult to revert its long-term progression, and we need better animal models of childhood HIVAN to test new treatments. Objectives To define whether the HIV-1 trans-activator (Tat) gene precipitates HIVAN in young mice, and to develop an inducible mouse model of childhood HIVAN. Design/Methods An HIV-Tat gene cloned from a child with HIVAN was used to generate recombinant adenoviral vectors (rAd-Tat). rAd-Tat and LacZ control vectors (2 × 109) were expressed in the kidney of newborn wild type and HIV-transgenic (Tg26) FVB/N mice without significant proteinuria (n = 5 - 8 per group). Mice were sacrificed 7 and 35 days later to assess their renal outcome, the expression of HIV-genes and growth factors, and markers of cell growth and differentiation by RT-qPCR, immunohistochemistry, and/or Western blots. Results HIV-Tat induced the expression of HIV-1 genes (env) and heparin binding growth factors in the kidney of HIV-Tg26 mice, and precipitated HIVAN in the first month of life. No significant renal changes were detected in wild type mice infected with rAd-Tat vectors, suggesting that HIV-Tat alone does not induce renal disease. Conclusion This new mouse model of childhood HIVAN highlights the critical role that HIV-Tat plays in the pathogenesis of HIVAN, and could be used to study the pathogenesis and treatment of HIVAN in children and adolescents. Summary statement We developed a new inducible mouse model system of childhood HIV-associated nephropathy, and demonstrated that HIV-Tat plays a critical role in this renal disease acting in synergy with other HIV-1 genes and heparin binding cytokines. url: https://doi.org/10.1101/2020.05.06.081851 doi: 10.1101/2020.05.06.081851 id: cord-278831-gwnfcfvk author: Taniwaki, Sueli Akemi title: Virus–host interaction in feline immunodeficiency virus (FIV) infection date: 2013-08-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Feline immunodeficiency virus (FIV) infection has been the focus of several studies because this virus exhibits genetic and pathogenic characteristics that are similar to those of the human immunodeficiency virus (HIV). FIV causes acquired immunodeficiency syndrome (AIDS) in cats, nevertheless, a large fraction of infected cats remain asymptomatic throughout life despite of persistent chronic infection. This slow disease progression may be due to the presence of factors that are involved in the natural resistance to infection and the immune response that is mounted by the animals, as well as due to the adaptation of the virus to the host. Therefore, the study of virus–host interaction is essential to the understanding of the different patterns of disease course and the virus persistence in the host, and to help with the development of effective vaccines and perhaps the cure of FIV and HIV infections. url: https://api.elsevier.com/content/article/pii/S0147957113000556 doi: 10.1016/j.cimid.2013.07.001 id: cord-103662-a4ok5wqc author: Tarek, M. title: Custommune: a web tool to design personalized and population-targeted vaccine epitopes date: 2020-04-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Computational prediction of immunogenic epitopes is a promising platform for therapeutic and preventive vaccine design. A potential target for this strategy is human immunodeficiency virus (HIV-1), for which, despite decades of efforts, no vaccine is available. In particular, a therapeutic vaccine devised to eliminate infected cells would represent a key component of cure strategies. HIV peptides designed based on individual viro-immunological data from people living with HIV/AIDS have recently shown able to induce post-therapy viral set point abatement. However, the reproducibility and scalability of this method is curtailed by the errors and arbitrariness associated with manual peptide design as well as by the time-consuming process. We herein introduce Custommune, a user-friendly web tool to design personalized and population-targeted vaccines. When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. Of note, Custommune predictions compared favorably with manually designed peptides administered in a recent phase II clinical trial (NCT02961829). Furthermore, we utilized Custommune to design preventive vaccines targeted for populations highly affected by COVID-19. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Overall, our data describe a new tool for rapid development of personalized or population-based immunotherapy against chronic and acute viral infections. url: http://medrxiv.org/cgi/content/short/2020.04.25.20079426v1?rss=1 doi: 10.1101/2020.04.25.20079426 id: cord-023168-cd7adns8 author: Thachil, Jecko title: Haematological Diseases in the Tropics date: 2013-10-21 words: 30224.0 sentences: 1724.0 pages: flesch: 44.0 cache: ./cache/cord-023168-cd7adns8.txt txt: ./txt/cord-023168-cd7adns8.txt summary: The most useful laboratory measure of iron status Low value is diagnostic in the presence of anaemia Very high values (>100 µg/L) usually exclude iron deficiency'' Being an acute-phase protein, it increases in inflammatory conditions, and certain malignancies, making it unreliable Also increased in tissue damage especially of the liver Levels are falsely decreased in vitamin C deficiency and hypothyroidism Erythrocyte zinc protoporphyrin An intermediate in haem biosynthesis and elevated concentrations indicate interrupted haem synthesis due to iron deficiency when zinc is incorporated in place of iron Can be measured on a drop of blood with a portable haematofluorometer Small sample size makes it very useful as a screening test in field surveys, particularly in children, and pregnant women where inflammatory states may not co-exist Red cells should be washed before measurement (serum bilirubin and fluorescent compounds like some drugs can give falsely high values) although not often done Lead poisoning can give falsely high values Rarely acute myeloid leukaemia and sideroblastic anaemia give slightly high values Useful in that it is not increased in thalassaemias WHO recommends normal level >70 µmol/mol haem Iron studies Serum iron concentration represents the iron entering and leaving the circulation. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167525/ doi: 10.1016/b978-0-7020-5101-2.00066-2 id: cord-322503-fynprt6f author: Thakur, Aarzoo title: Physiologically‐Based Pharmacokinetic Modeling to Predict the Clinical Efficacy of the Coadministration of Lopinavir and Ritonavir against SARS‐CoV‐2 date: 2020-08-07 words: 3527.0 sentences: 210.0 pages: flesch: 48.0 cache: ./cache/cord-322503-fynprt6f.txt txt: ./txt/cord-322503-fynprt6f.txt summary: Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. To address this possibility, we utilized physiologically-based pharmacokinetic (PBPK) modeling to simulate the unbound lung concentration of lopinavir achieved by 400/100 mg twice daily dose of lopinavir/ritonavir in both Caucasians and Chinese populations. 14, 15 Therefore, we derived unbound EC 50 (EC 50,unbound ) values against SARS-CoV-2 from various literature reports and compared it against the predicted C u,lung values to determine if clinically used doses of 400/100 mg twice a day would reach efficacious lung concentrations in Caucasian and Chinese populations. The impact of protein binding on PK/PD assessments were then assessed by comparing the predicted total and unbound lung concentrations of 400/100 mg twice daily lopinavir/ritonavir with EC 50 and EC 50,unbound values of lopinavir against SARS-CoV-2 respectively. abstract: Lopinavir/ritonavir, originally developed for treating the human immunodeficiency virus (HIV), is currently undergoing clinical studies for treating the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Although recent reports suggest that lopinavir exhibits in vitro efficacy against SARS‐CoV‐2, it is a highly protein bound drug and it remains unknown if it reaches adequate in vivo unbound (free) concentrations in lung tissue. We built a physiologically‐based pharmacokinetic (PBPK) model of lopinavir/ritonavir in Caucasian and Chinese populations. Our aim was to perform pharmacokinetic/pharmacodynamic correlations by comparing simulated free plasma and lung concentration values achieved using different dosing regimens of lopinavir/ritonavir with EC(50,unbound) and EC(90,unbound) values of lopinavir against SARS‐CoV‐2. The model was validated against multiple observed clinical datasets for single and repeated dosing of lopinavir/ritonavir. Predicted pharmacokinetic parameters such as the maximum plasma concentration, area under the plasma concentration‐time profile, oral clearance, half‐life and minimum plasma concentration at steady state were within two‐fold of clinical values for both populations. Using the current lopinavir/ritonavir regimen of 400/100 mg twice daily, lopinavir does not achieve sufficient free lung concentrations for efficacy against SARS‐CoV‐2. Although the Chinese population reaches greater plasma and lung concentrations as compared to Caucasians, our simulations suggest that a significant dose increase from the current clinically used dosing regimen is necessary to reach the EC(50,unbound) value for both populations. Based on safety data, higher doses would likely lead to QT prolongation and gastrointestinal disorders (nausea, vomiting and diarrhea), thus, any dose adjustment must be carefully weighed alongside these safety concerns. url: https://www.ncbi.nlm.nih.gov/pubmed/32767755/ doi: 10.1002/cpt.2014 id: cord-001079-v01vwu00 author: Thoden, J. title: Therapy and prophylaxis of opportunistic infections in HIV-infected patients: a guideline by the German and Austrian AIDS societies (DAIG/ÖAG) (AWMF 055/066) date: 2013-09-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: There was a growing need for practical guidelines for the most common OIs in Germany and Austria under consideration of the local epidemiological conditions. MATERIALS AND METHODS: The German and Austrian AIDS societies developed these guidelines between March 2010 and November 2011. A structured Medline research was performed for 12 diseases, namely Immune reconstitution inflammatory syndrome, Pneumocystis jiroveci pneumonia, cerebral toxoplasmosis, cytomegalovirus manifestations, candidiasis, herpes simplex virus infections, varizella zoster virus infections, progressive multifocal leucencephalopathy, cryptosporidiosis, cryptococcosis, nontuberculosis mycobacteria infections and tuberculosis. Due to the lack of evidence by randomized controlled trials, part of the guidelines reflects expert opinions. The German version was accepted by the German and Austrian AIDS Societies and was previously published by the Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften (AWMF; German Association of the Scientific Medical Societies). CONCLUSION: The review presented here is a translation of a short version of the German–Austrian Guidelines of opportunistic infections in HIV patients. These guidelines are well-accepted in a clinical setting in both Germany and Austria. They lead to a similar treatment of a heterogeneous group of patients in these countries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776256/ doi: 10.1007/s15010-013-0504-1 id: cord-262017-utvy0i8l author: Tobar Vega, Pool title: Talaromyces marneffei laboratory cross reactivity with Histoplasma and Blastomyces urinary antigen date: 2019-06-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Talaromyces marneffei is a fungal opportunistic infection usually seen in immunocompromised patients from eastern countries. In the US when examining HIV-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. We present the case of a 35-year-old HIV patient originally from Thailand in which urine lab results were positive for Blastomyces and Histoplasma antigen, but biopsy showed T. marneffei. Concomitantly the patient presented with hyponatremia which was deemed to be from SIADH. We present the first case of a patient with T. marneffei cross reactivity with Blastomyces, Histoplasma and SIADH due to pulmonary disease. url: https://www.ncbi.nlm.nih.gov/pubmed/31229614/ doi: 10.1016/j.ijid.2019.06.018 id: cord-289274-3g67f8sw author: Tosoni, Elena title: Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription date: 2015-10-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Folding of the LTR promoter into dynamic G-quadruplex conformations has been shown to suppress its transcriptional activity in HIV-1. Here we sought to identify the proteins that control the folding of this region of proviral genome by inducing/stabilizing G-quadruplex structures. The implementation of electrophorethic mobility shift assay and pull-down experiments coupled with mass spectrometric analysis revealed that the cellular protein nucleolin is able to specifically recognize G-quadruplex structures present in the LTR promoter. Nucleolin recognized with high affinity and specificity the majority, but not all the possible G-quadruplexes folded by this sequence. In addition, it displayed greater binding preference towards DNA than RNA G-quadruplexes, thus indicating two levels of selectivity based on the sequence and nature of the target. The interaction translated into stabilization of the LTR G-quadruplexes and increased promoter silencing activity; in contrast, disruption of nucleolin binding in cells by both siRNAs and a nucleolin binding aptamer greatly increased LTR promoter activity. These data indicate that nucleolin possesses a specific and regulated activity toward the HIV-1 LTR promoter, which is mediated by G-quadruplexes. These observations provide new essential insights into viral transcription and a possible low mutagenic target for antiretroviral therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/26354862/ doi: 10.1093/nar/gkv897 id: cord-317213-vhprfb1o author: Tram, Dai Thien Nhan title: Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases date: 2016-09-26 words: 11575.0 sentences: 794.0 pages: flesch: 48.0 cache: ./cache/cord-317213-vhprfb1o.txt txt: ./txt/cord-317213-vhprfb1o.txt summary: This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases. • no tagging is required • about two orders of magnitude more sensitive than some common colorimetric techniques • selectivity down to the level of single-base mismatch • quantitative signal intensity varied with the length of target RNA sequence (Nam et al., 2004) Analyte: nucleotide sequence indicative of anthrax lethal factor Sample size: 30 μl Assay time: 3-4 h Detection range: 500 zM-5 fM Performance: abstract: Nanotechnology has gained much attention over the last decades, as it offers unique opportunities for the advancement of the next generation of sensing tools. Point-of-care (POC) devices for the selective detection of biomolecules using engineered nanoparticles have become a main research thrust in the diagnostic field. This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/27686397/ doi: 10.1016/j.biotechadv.2016.09.003 id: cord-345771-3v2avxiv author: Traub, Ariana Moriah title: Multimonth Dispensing of Antiretroviral Therapy Protects the Most Vulnerable From 2 Pandemics at Once date: 2020-06-30 words: 703.0 sentences: 44.0 pages: flesch: 56.0 cache: ./cache/cord-345771-3v2avxiv.txt txt: ./txt/cord-345771-3v2avxiv.txt summary: We encourage governments in countries that have a high prevalence of people living with HIV to implement multimonth dispensing of antiretroviral therapy to safeguard both patients with HIV and health care workers from coronavirus disease 2019. 2,3 However, as with other infectious diseases, it is expected that PLHIV who are not virally suppressed and/or on antiretroviral therapy (ART) might be at an increased risk of COVID-19 infection, severe disease, and poor health outcomes. Thus, policy makers-including the U.S. President''s Emergency Plan for AIDS Relief-are encouraging countries to provide PLHIV with a multimonth supply of ART as a key strategy to safeguard PLHIV and health care workers involved in providing HIV services. As a key strategy to safeguard patients and health care workers providing HIV services, MMD also reduces clinic visits, improves viral suppression, encourages social distancing, and potentially saves patients from the dual threat of SARS-CoV-2 and HIV. abstract: We encourage governments in countries that have a high prevalence of people living with HIV to implement multimonth dispensing of antiretroviral therapy to safeguard both patients with HIV and health care workers from coronavirus disease 2019. url: https://www.ncbi.nlm.nih.gov/pubmed/32606089/ doi: 10.9745/ghsp-d-20-00160 id: cord-343470-w215pzdc author: Tsai, Kevin title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 words: 9761.0 sentences: 452.0 pages: flesch: 41.0 cache: ./cache/cord-343470-w215pzdc.txt txt: ./txt/cord-343470-w215pzdc.txt summary: Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. First, the viral protein VP16, which is packaged into the tegument layer of incoming virions, recruits host proteins, including host-cell factor 1 (HCF-1) and octamer-binding factor (Oct-1), in order to form a complex that recruits the histone demethylases lysine-specific demethylase 1 (LSD1) and Jumonji domain 2 (JMJD2) family members as a means to remove repressive H3K9 marks from viral immediate early promoters 42 Upon entry into the cell nucleus, the DNA of many viruses initiates the replication process adjacent to subnuclear structures called pro-myelocytic leukaemia nuclear bodies (PML-NBs). abstract: Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. However, viruses have evolved countermeasures that prevent the epigenetic silencing of their genes during lytic replication, and they can also take advantage of epigenetic silencing to establish latent infections. By contrast, the various covalent modifications added to RNAs, termed epitranscriptomic modifications, can positively regulate mRNA translation and/or stability, and both DNA and RNA viruses have evolved to utilize epitranscriptomic modifications as a means to maximize viral gene expression. As a consequence, both chromatin and RNA modifications could serve as novel targets for the development of antivirals. In this Review, we discuss how host epigenetic and epitranscriptomic processes regulate viral gene expression at the levels of chromatin and RNA function, respectively, and explore how viruses modify, avoid or utilize these processes in order to regulate viral gene expression. url: https://www.ncbi.nlm.nih.gov/pubmed/32533130/ doi: 10.1038/s41579-020-0382-3 id: cord-333730-qsx0m68e author: Tsai, Y. C. title: Oral disease-modifying antirheumatic drugs and immunosuppressants with antiviral potential, including SARS-CoV-2 infection: a review date: 2020-09-03 words: 4920.0 sentences: 297.0 pages: flesch: 35.0 cache: ./cache/cord-333730-qsx0m68e.txt txt: ./txt/cord-333730-qsx0m68e.txt summary: However, some immunosuppressants or disease-modifying antirheumatic drugs (DMARDs) show antiviral activity and may be safely used or even beneficial in patients with selected concomitant viral infections. In vitro anti-CMV properties of leflunomide were not through blocking the replication of viral DNA, so it is effective even in patients with direct antiviral drug-resistance history. The combination of MMF and highly active antiretroviral therapy improved the control of viral replication and delayed viral-load rebound in a randomized pilot study (n = 17 The effectiveness of thalidomide for KS might be related to anti-angiogenesis, and experts hypothesized the modulation of the immune system to trigger an antiviral action. Although in most instances, the antiviral activity of DMARDs is based on in vitro or small-scale controlled studies, this property would be useful in the choice of DMARDs for patients with concomitant viral infections. Effects of hydroxychloroquine on immune activation and disease progression among HIV-infected patients not receiving antiretroviral therapy: a randomized controlled trial abstract: There have been several episodes of viral infection evolving into epidemics in recent decades, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the latest example. Its high infectivity and moderate mortality have resulted in an urgent need to find an effective treatment modality. Although the category of immunosuppressive drugs usually poses a risk of infection due to interference of the immune system, some of them have been found to exert antiviral properties and are already used in daily practice. Recently, hydroxychloroquine and baricitinib have been proposed as potential drugs for SARS-CoV-2. In fact, there are other immunosuppressants known with antiviral activities, including cyclosporine A, hydroxyurea, minocycline, mycophenolic acid, mycophenolate mofetil, leflunomide, tofacitinib, and thalidomide. The inherent antiviral activity could be a treatment choice for patients with coexisting rheumatological disorders and infections. Clinical evidence, their possible mode of actions and spectrum of antiviral activities are included in this review article. LAY SUMMARY: Immunosuppressants often raise the concern of infection risks, especially for patients with underlying immune disorders. However, some disease-modifying antirheumatic drugs (DMARDs) with inherent antiviral activity would be a reasonable choice in the situation of concomitant viral infections and flare up of autoimmune diseases. This review covers DMARDs of treatment potential for SARS-CoV-2 in part I, and antiviral mechanisms plus trial evidence for viruses other than SARS-CoV-2 in part II. url: https://www.ncbi.nlm.nih.gov/pubmed/32952617/ doi: 10.1177/1759720x20947296 id: cord-009669-bcdjwpd1 author: Tsegaye, Theodros Solomon title: The multiple facets of HIV attachment to dendritic cell lectins date: 2010-09-20 words: 4852.0 sentences: 199.0 pages: flesch: 40.0 cache: ./cache/cord-009669-bcdjwpd1.txt txt: ./txt/cord-009669-bcdjwpd1.txt summary: Trans-infection was reported to depend on DC-SIGNmediated binding and cellular uptake of HIV into dendritic cells (Geijtenbeek et al., 2000; Kwon et al., 2002) , followed by intracellular transport of virions to sites of dendritic cell-T cell contact, termed infectious synapses (McDonald et al., 2003) (Fig. 1) . Finally, signalling via TLR8 and DC-SIGN was required for NFkB-dependent recruitment of the transcription factor pTEF-b to the viral promoter, and thus for the generation of full-length HIV transcripts in dendritic cells -a prerequisite for productive infection (Gringhuis et al., 2010) (Fig. 2) . Dendritic cell-mediated trans-enhancement of human immunodeficiency virus type 1 infectivity is independent of DC-SIGN The C-type lectin surface receptor DCIR acts as a new attachment factor for HIV-1 in dendritic cells and contributes to trans-and cis-infection pathways Functionally distinct transmission of human immunodeficiency virus type 1 mediated by immature and mature dendritic cells abstract: Entry of enveloped viruses into host cells depends on the interactions of viral surface proteins with cell surface receptors. Many enveloped viruses maximize the efficiency of receptor engagement by first binding to attachment‐promoting factors, which concentrate virions on target cells and thus increase the likelihood of subsequent receptor engagement. Cellular lectins can recognize glycans on viral surface proteins and mediate viral uptake into immune cells for subsequent antigen presentation. Paradoxically, many viral and non‐viral pathogens target lectins to attach to immune cells and to subvert cellular functions to promote their spread. Thus, it has been proposed that attachment of HIV to the dendritic cell lectin DC‐SIGN enables the virus to hijack cellular transport processes to ensure its transmission to adjacent T cells. However, recent studies show that the consequences of viral capture by immune cell lectins can be diverse, and can entail negative and positive regulation of viral spread. Here, we will describe key concepts proposed for the role of lectins in HIV attachment to host cells, and we will discuss recent findings in this rapidly evolving area of research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162262/ doi: 10.1111/j.1462-5822.2010.01519.x id: cord-254190-bxfne94u author: Tu, Wenwei title: Application of Humanized Mice in Immunological Research date: 2015-07-07 words: 6246.0 sentences: 254.0 pages: flesch: 34.0 cache: ./cache/cord-254190-bxfne94u.txt txt: ./txt/cord-254190-bxfne94u.txt summary: On the contrary, humanized mice established by peripheral blood cells provide a ready platform for studying the functions of mature immune cells but the length of window appropriate for research is still limited by chronic GVHD and ongoing reduced engraftment. Distinct from their T cell companion, reconstitution of functional B lymphocytes is generally poor in humanized mice and needed to improve in the future although their primary repertoire were principally unaltered by the differences between mouse and human stromal environments [ 53 ] and their ability to produce antigen-specifi c antibody was partly developed [ 54 ] . In above three studies, investigators planted solid grafts into immunodefi cient mice before reconstitution of human immune system and induced rejection by infusion of mature human cells. Humanized immune system (HIS) mice as a tool to study human NK cell development Humanized mice as a model to study human hematopoietic stem cell transplantation abstract: During the past decade, the development of humanized mouse models and their general applications in biomedical research greatly accelerated the translation of outcomes obtained from basic research into potential diagnostic and therapeutic strategies in clinic. In this chapter, we firstly present an overview on the history and current progress of diverse humanized mouse models and then focus on those equipped with reconstituted human immune system. The update advancement in the establishment of humanized immune system mice and their applications in the studies of the development of human immune system and the pathogenesis of multiple human immune-related diseases are intensively reviewed here, while the shortcoming and perspective of these potent tools are discussed as well. As a valuable bridge across the gap between bench work and clinical trial, progressive humanized mouse models will undoubtedly continue to play an indispensable role in the wide area of biomedical research. url: https://doi.org/10.1007/978-1-4939-3139-2_10 doi: 10.1007/978-1-4939-3139-2_10 id: cord-303165-ikepr2p2 author: Tulchinsky, Theodore H. title: Expanding the Concept of Public Health date: 2014-10-10 words: 33919.0 sentences: 1389.0 pages: flesch: 41.0 cache: ./cache/cord-303165-ikepr2p2.txt txt: ./txt/cord-303165-ikepr2p2.txt summary: It also demands special attention through health promotion activities of all kinds at national and local societal levels to provide access for groups with special risks and needs to medical and community health care with the currently available and newly developing knowledge and technologies. 5. Environmental, biological, occupational, social, and economic factors that endanger health and human life, addressing: (a) physical and mental illness, diseases and infirmity, trauma and injuries (b) local and global sanitation and environmental ecology (c) healthful nutrition and food security including availability, quality, safety, access, and affordability of food products (d) disasters, natural and human-made, including war, terrorism, and genocide (e) population groups at special risk and with specific health needs. It acts to improve health and social welfare, and to reduce specific determinants of diseases and risk factors that adversely affect the health, well-being, and productive capacities of an individual or society, setting targets based on the size of the problem but also the feasibility of successful intervention, in a cost-effective way. abstract: Ancient societies recognized the needs of sanitation, food safety, workers’ health, and medical care to protect against disease and to promote well-being and civic prosperity. New energies and knowledge since the eighteenth century produced landmark discoveries such as prevention of scurvy and vaccination against smallpox. The biological germ theory and competing miasma theory each proved effective in sanitation, and immunization in control of infectious diseases. Non-communicable diseases as the leading causes of mortality have responded to innovative preventive care of health risk factors, smoking, hypertension, obesity, physical inactivity, unhealthful diets, and diabetes mellitus. Health promotion proved effective to modern public health in tackling disease origins, individual behavior, and social and economic conditions. The global burden of infectious and non-communicable diseases, aging and chronic illness faces rising costs and still inadequate prevention. The evolution of concepts of public health will have to address these new challenges of population health. url: https://www.sciencedirect.com/science/article/pii/B9780124157668000021 doi: 10.1016/b978-0-12-415766-8.00002-1 id: cord-325300-wawui0fd author: Tulchinsky, Theodore H. title: 4 Communicable Diseases date: 2000-12-31 words: 31276.0 sentences: 1672.0 pages: flesch: 47.0 cache: ./cache/cord-325300-wawui0fd.txt txt: ./txt/cord-325300-wawui0fd.txt summary: No less important are organized programs to promote self protection, case finding, and effective treatment of infections to stop their spread to other susceptible persons (e.g., HIV, sexually transmitted diseases, tuberculosis, malaria). Very great progress has been made in infectious disease control by clinical, public health, and societal means since 1900 in the industrialized countries and since the 1970s in the developing world. The WHO in 1998 has declared hepatitis prevention as a major public health crisis, with an estimated 170 million persons infected worldwide (1996) , stressing that this "silent epidemic" is being neglected and that screening of blood products is vital to reduce transmission of this disease as for HIu HCV is a major cause of chronic cirrhosis and liver cancer. Varicella vaccine is now recommended for routine immunization at age 12-18 months in the United States, with catch-up for children up to age 13 years and for occupationally exposed persons in health or child care settings. abstract: Publisher Summary In a world of rapid international transport and contact between populations, systems are needed to monitor the potential explosive spread of pathogens that may be transferred from their normal habitat. The potential for the international spread of new or reinvigorated infectious diseases constitute threat to mankind akin to ecological and other man-made disasters. Public health has addressed the issues of communicable disease as one of its key issues in protecting individual and population health. Methods of intervention include classic public health through sanitation, immunization, and well beyond that into nutrition, education, case finding, and treatment, and changing human behavior. The knowledge, attitudes, beliefs, and practices of policy makers, health care providers, and parents is as important in the success of communicable disease control as are the technology available and methods of financing health systems. Together, these encompass the broad programmatic approach of the New Public Health to control of communicable diseases. url: https://api.elsevier.com/content/article/pii/B9780127033501500061 doi: 10.1016/b978-012703350-1/50006-1 id: cord-021668-33zfio0u author: Tyring, Stephen K. title: Syndromal tropical dermatology date: 2009-05-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151842/ doi: 10.1016/b978-0-443-06790-7.50005-3 id: cord-021990-a8ku5rke author: Tyring, Stephen K. title: Syndromal Tropical Dermatology date: 2016-12-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152309/ doi: 10.1016/b978-0-323-29634-2.00001-8 id: cord-252039-732z92dd author: Valdiserri, Ronald O. title: Responding to Pandemics: What We’ve Learned from HIV/AIDS date: 2020-04-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32274671/ doi: 10.1007/s10461-020-02859-5 id: cord-269222-g2ibmo75 author: Valenti, Piera title: Role of Lactobacilli and Lactoferrin in the Mucosal Cervicovaginal Defense date: 2018-03-01 words: 9642.0 sentences: 449.0 pages: flesch: 28.0 cache: ./cache/cord-269222-g2ibmo75.txt txt: ./txt/cord-269222-g2ibmo75.txt summary: Lactoferrin is strongly increased in lower genital tract mucosal fluid of women affected by Neisseria gonorrheae, Chlamydia trachomatis, and Trichomonas vaginalis infections promoting both innate and adaptive immune responses. Lactoferrin is strongly increased in lower genital tract mucosal fluid of women affected by Neisseria gonorrheae, Chlamydia trachomatis, and Trichomonas vaginalis infections promoting both innate and adaptive immune responses. Lactobacilli exert their protective effects by several mechanisms: (i) microbial competition for the nutrients and for adherence to the vaginal epithelium; (ii) reduction of the vaginal pH by the production of organic acids, especially lactic acid, through the degradation of glycogen released by vaginal cells thus exerting selective antimicrobial activity against non-resident microbiota; (iii) production of antimicrobial substances, such as bacteriocins and hydrogen peroxide (H2O2) able to suppress the growth of several microorganisms; and (iv) modulation of the local immune system (16) . abstract: The innate defense system of the female mucosal genital tract involves a close and complex interaction among the healthy vaginal microbiota, different cells, and various proteins that protect the host from pathogens. Vaginal lactobacilli and lactoferrin represent two essential actors in the vaginal environment. Lactobacilli represent the dominant bacterial species able to prevent facultative and obligate anaerobes outnumber in vaginal microbiota maintaining healthy microbial homeostasis. Several mechanisms underlie the protection exerted by lactobacilli: competition for nutrients and tissue adherence, reduction of the vaginal pH, modulation of immunity, and production of bioactive compounds. Among bioactive factors of cervicovaginal mucosa, lactoferrin, an iron-binding cationic glycoprotein, is a multifunctional glycoprotein with antibacterial, antifungal, antiviral, and antiparasitic activities, recently emerging as an important modulator of inflammation. Lactobacilli and lactoferrin are largely under the influence of female hormones and of paracrine production of various cytokines. Lactoferrin is strongly increased in lower genital tract mucosal fluid of women affected by Neisseria gonorrheae, Chlamydia trachomatis, and Trichomonas vaginalis infections promoting both innate and adaptive immune responses. In vaginal dysbiosis characterized by low amounts of vaginal lactobacilli and increased levels of endogenous anaerobic bacteria, the increase in lactoferrin could act as an immune modulator assuming the role normally played by the healthy microbiota in vaginal mucosa. Then lactoferrin and lactobacilli may be considered as biomarkers of altered microbial homeostasis at vaginal level. Considering the shortage of effective treatments to counteract recurrent and/or antibiotic-resistant bacterial infections, the intravaginal administration of lactobacilli and lactoferrin could be a novel efficient therapeutic strategy and a valuable tool to restore mucosal immune homeostasis. url: https://doi.org/10.3389/fimmu.2018.00376 doi: 10.3389/fimmu.2018.00376 id: cord-000008-3dgjv0x1 author: Vali, Bahareh title: HIV-Specific T-Cells Accumulate in the Liver in HCV/HIV Co-Infection date: 2008-10-20 words: 5253.0 sentences: 236.0 pages: flesch: 47.0 cache: ./cache/cord-000008-3dgjv0x1.txt txt: ./txt/cord-000008-3dgjv0x1.txt summary: In response to stimulation with HIV peptide pool, untreated co-infected individuals showed significantly higher frequencies of intra-hepatic CD4 + T-cells producing IFN-c, compared to HCV mono-infected [0.1660.05% vs 0.0260.01%, p,0.05], and HAART-treated co-infected individuals [0.1660.05% vs 0.0360.05%, p,0.05] (Figure 2a ). Therapy naïve co-infected subjects had greater IFN-c producing CD8 + T-cells in response to HIV peptides compared to HCV mono-infected individuals [1.3960.37% vs 0.0260.0%, p,0.05], and HAART was associated with a significant reduction in the frequencies of these cells [1.3960.37% vs 0.3060.26%, p,0.05] (figure 2b). The tetramer cytokine response pattern was shown to be different in the liver compared to blood of the same individual, with diminished intra-hepatic tetramer-specific IFN-c responses and an increase in both CD107a and TNF-a responses, with the majority of SL9 tetramer positive cells expressing these two markers. Therapy naïve co-infected individuals demonstrated a higher frequency of intra-hepatic CD8 + T-cells that produce TNF-a in response to both HCV and HIV antigen stimulation compared to HCV mono-infected individuals. abstract: BACKGROUND AND AIMS: Hepatitis C Virus (HCV)-related liver disease progresses more rapidly in individuals co-infected with Human Immunodeficiency Virus-1 (HIV), although the underlying immunologic mechanisms are unknown. We examined whether HIV-specific T-cells are identified in the liver of HCV/HIV co-infected individuals and promote liver inflammation through bystander immune responses. METHODS: Ex-vivo intra-hepatic lymphocytes from HCV mono-infected and HCV/HIV co-infected individuals were assessed for immune responses to HIV and HCV antigens by polychromatic flow cytometry. RESULTS: HCV/HIV liver biopsies had similar frequencies of lymphocytes but lower percentages of CD4(+) T-cells compared to HCV biopsies. In co-infection, intra-hepatic HIV-specific CD8(+) and CD4(+) T-cells producing IFN-γ and TNF-α were detected and were comparable in frequency to those that were HCV-specific. In co-infected individuals, viral-specific CD8(+) T-cells produced more of the fibrogenic cytokine, TNF-α. In both mono- and co-infected individuals, intra-hepatic HCV-specific T-cells were poorly functional compared to HIV-specific T-cells. In co-infection, HAART was not associated with a reconstitution of intra-hepatic CD4(+) T-cells and was associated with reduction in both HIV and HCV-specific intra-hepatic cytokine responses. CONCLUSION: The accumulation of functional HIV-specific T-cells in the liver during HCV/HIV co-infection may represent a bystander role for HIV in inducing faster progression of liver disease. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2565067/ doi: 10.1371/journal.pone.0003454 id: cord-333655-lylt7qld author: Van Breedam, Wander title: Bitter‐sweet symphony: glycan–lectin interactions in virus biology date: 2013-12-06 words: 18667.0 sentences: 875.0 pages: flesch: 42.0 cache: ./cache/cord-333655-lylt7qld.txt txt: ./txt/cord-333655-lylt7qld.txt summary: In sum, it appears that the dimeric lectin galectin-1 can enhance HIV-1 infection efficiency by cross-linking viral and host cell glycans and thereby promoting firmer adhesion of the virus to the target cell surface and facilitating virus-receptor interactions (Ouellet et al., 2005; Mercier et al., 2008; St-Pierre et al., 2011; Sato et al., 2012) . As has been shown for IAV, acquisition or deletion of glycosylation sites may affect crucial steps in the viral infection/replication process (e.g. receptor binding, fusion, release of newly formed virions) (Ohuchi et al., 1997; Wagner et al., 2000; Tsuchiya et al., 2002; Kim & Park, 2012) , alter the capacity of the virus to avoid induction of/recognition by virus-specific antibodies (glycan shielding) Wei et al., 2010; Wanzeck et al., 2011; Kim & Park, 2012; Job et al., 2013; Sun et al., 2013) , and modulate viral interaction with various immune system lectins (Reading et al., 2007; Vigerust et al., 2007; Reading et al., 2009; Tate et al., 2011a, b) . abstract: Glycans are carbohydrate modifications typically found on proteins or lipids, and can act as ligands for glycan‐binding proteins called lectins. Glycans and lectins play crucial roles in the function of cells and organs, and in the immune system of animals and humans. Viral pathogens use glycans and lectins that are encoded by their own or the host genome for their replication and spread. Recent advances in glycobiological research indicate that glycans and lectins mediate key interactions at the virus‐host interface, controlling viral spread and/or activation of the immune system. This review reflects on glycan–lectin interactions in the context of viral infection and antiviral immunity. A short introduction illustrates the nature of glycans and lectins, and conveys the basic principles of their interactions. Subsequently, examples are discussed highlighting specific glycan–lectin interactions and how they affect the progress of viral infections, either benefiting the host or the virus. Moreover, glycan and lectin variability and their potential biological consequences are discussed. Finally, the review outlines how recent advances in the glycan–lectin field might be transformed into promising new approaches to antiviral therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/24188132/ doi: 10.1111/1574-6976.12052 id: cord-319609-y0gdjn64 author: Van Duyne, Rachel title: The identification of unique serum proteins of HIV-1 latently infected long-term non-progressor patients date: 2010-07-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The search for disease biomarkers within human peripheral fluids has become a favorable approach to preventative therapeutics throughout the past few years. The comparison of normal versus disease states can identify an overexpression or a suppression of critical proteins where illness has directly altered a patient's cellular homeostasis. In particular, the analysis of HIV-1 infected serum is an attractive medium with which to identify altered protein expression due to the ease and non-invasive methods of collecting samples as well as the corresponding insight into the in vivo interaction of the virus with infected cells/tissue. The utilization of proteomic techniques to globally identify differentially expressed serum proteins in response to HIV-1 infection is a significant undertaking that is complicated due to the innate protein profile of human serum. RESULTS: Here, the depletion of 12 of the most abundant serum proteins, followed by two-dimensional gel electrophoresis coupled with identification of these proteins using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, has allowed for the identification of differentially expressed, low abundant serum proteins. We have analyzed and compared serum samples from HIV-1 infected subjects who are being treated using highly active antiretroviral therapy (HAART) to those who are latently infected but have not progressed to AIDS despite the absence of treatment, i.e. long term non-progressors (LTNPs). Here we have identified unique serum proteins that are differentially expressed in LTNP HIV-1 patients and may contribute to the ability of these patients to combat HIV-1 infection in the absence of HAART. We focused on the cdk4/6 cell cycle inhibitor p16(INK4A )and found that the treatment of HIV-1 latently infected cell lines with p16(INK4A )decreases viral production despite it not being expressed endogenously in these cells. CONCLUSIONS: Identification of these unique proteins may serve as an indication of altered viral states in response to infection as well as a natural phenotypic variability in response to HIV-1 infection in a given population. url: https://doi.org/10.1186/1742-6405-7-21 doi: 10.1186/1742-6405-7-21 id: cord-305394-wwabxlgr author: Venter, W D Francois title: COVID-19: First data from Africa date: 2020-08-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32865552/ doi: 10.1093/cid/ciaa1293 id: cord-285505-8norumv6 author: Vere Hodge, R. Anthony title: Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA date: 2014-09-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The 27th International Conference on Antiviral Research (ICAR) was held in Raleigh, North Carolina, USA from May 12 to 16, 2014. This article summarizes the principal invited lectures. John Drach (Elion Award) described the early days of antiviral drugs and their novel modes of action. Piet Herdewijn (Holý Award) used evolutionary pressure to select DNA polymerases that accept nucleoside analogs. Replacing thymine by 5-chlorouracil led to the generation of a new form of Escherichia coli. Adrian Ray (Prusoff Award) demonstrated how prodrugs can markedly improve both the efficacy and safety of potential drugs. The keynote addresses, by David Margolis and Myron Cohen, tackled two emerging areas of HIV research, to find an HIV “cure” and to prevent HIV transmission, respectively. These topics were discussed further in other presentations – a cure seems to be a distant prospect but there are exciting developments for reducing HIV transmission. TDF-containing vaginal rings and GSK-744, as a long-lasting injection, offer great hope. There were three mini-symposia. Although therapy with TDF/FTC gives excellent control of HBV replication, there are only a few patients who achieve a functional cure. Myrcludex, an entry inhibitor, is active against both HBV and HDV. The recent progress with HBV replication in cell cultures has transformed the search for new antiviral compounds. The HBV capsid protein has been recognized as key player in HBV DNA synthesis. Unexpectedly, compounds which enhance capsid formation, markedly reduce HBV DNA synthesis. The development of BCX4430, which is active against Marburg and Ebola viruses, is of great current interest. url: https://api.elsevier.com/content/article/pii/S0166354214002460 doi: 10.1016/j.antiviral.2014.08.009 id: cord-023925-qrr7jcwe author: Verhoef, Jan title: A8 Immune response in human pathology: Infections caused by bacteria, viruses, fungi, and parasites date: 2011-07-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the middle of the 19th century, it became clear that micro-organisms could cause disease. Effective treatment, however, was not possible at that time; prevention and spread of infectious diseases depended solely on proper hygienic means. At the beginning of the 20th century, passive and active vaccination procedures were developed against a number of these PATHOGENIC MICRO-ORGANISMS to prevent the diseases in question (rabies, diphtheria, tetanus, etc.). Thanks to the discovery of antimicrobial chemicals (by Paul Ehrlich) and antibiotics (by Sir Alexander Fleming), the threat of infectious diseases seemed to be minimised. Large scale vaccination programmes against childhood diseases (diphtheria, whooping cough and polio), started in the early 1950s, raised hopes of finally being able to eradicate these diseases from the planet. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178827/ doi: 10.1007/978-3-0346-0136-8_8 id: cord-264713-38dlh3wg author: Vernet, Guy title: Molecular diagnostics in virology date: 2004-08-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular biology has significantly improved diagnosis in the field of clinical virology. Virus discovery and rapid implementation of diagnostic tests for newly discovered viruses has strongly beneficiated from the development of molecular techniques. Viral load and antiviral resistance or subtyping assays are now part of the biological monitoring of patients chronically infected by human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV) and CMV. It will be important to add to this panel assays for other viruses of the herpesviridae family. Qualitative assays for the detection of blood-borne viruses have increased safety of blood donation and organ transplantation. Screening of other blood-borne viruses (parvovirus B19, HAV), multiplexing of detection and test automation to improve practicability and reduce costs will be the next steps. A major evolution in the near future will be the generalization of NAT for the diagnosis of viral etiology in patients, mostly with respiratory, CNS or gastro-intestinal diseases. Major technical improvements have been made to avoid obstacles that still limit this generalization, i.e. genetic variability of viruses, multiplex detection, contamination risk. Commercial offers already exist but menus must be extended to limit the validation and documentation work associated with home-brew assays. Real-time amplification has allowed the development of new NAT platforms but automation and integration of all steps of the reaction are still required to reduce hands-on-time, time-to-result and costs, and to increase throughput. url: https://www.sciencedirect.com/science/article/pii/S1386653204001696 doi: 10.1016/j.jcv.2004.06.003 id: cord-269759-1n1oo6wc author: Villamil-Gómez, Wilmer E. title: Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia date: 2020-02-06 words: 836.0 sentences: 55.0 pages: flesch: 50.0 cache: ./cache/cord-269759-1n1oo6wc.txt txt: ./txt/cord-269759-1n1oo6wc.txt summary: title: Fatal human coronavirus 229E (HCoV-229E) and RSV–Related pneumonia in an AIDS patient from Colombia We would like to discuss the relevance of other respiratory viruses, including other CoV different to MERS-CoV, the Severe Acute Respiratory Syndrome CoV (SARS-CoV) and the 2019 novel CoV (2019nCoV) [2] in relation to a case of coinfection between HCoV-229E, respiratory syncytial virus (RSV) and HIV we had in Colombia. There is a lack of reported cases of a human coronavirus infection in HIV infected patients from Colombia and South America, confirmed by RT-PCR. HCoV-229E causes common cold but occasionally it can be associated with more severe respiratory infections in children [3, 4] , elderly and persons with underlying illness [3, 5] , which would be the case of HIV infection, as seen in this report [4, 6] . In Colombia, the unique previous reference to coronaviruses was the identification of avian infectious bronchitis virus strains (an avian coronavirus, genus Gammacoronavirus) in Antioquia [8] , a department close to Sucre, where our patient was diagnosed. abstract: nan url: https://api.elsevier.com/content/article/pii/S1477893920300235 doi: 10.1016/j.tmaid.2020.101573 id: cord-264884-ydkigome author: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution to all life. We now know that viruses numerically dominate all habitats of life, especially the oceans. Theoretical developments in the 1970s regarding quasispecies, error rates, and error thresholds have yielded many practical insights into virus–host dynamics. The human diseases of HIV-1 and hepatitis C virus cannot be understood without this evolutionary framework. Yet recent developments with poliovirus demonstrate that viral fitness can be the result of a consortia, not one fittest type, a basic Darwinian concept in evolutionary biology. Darwinian principles do apply to viruses, such as with Fisher population genetics, but other features, such as reticulated and quasispecies-based evolution distinguish virus evolution from classical studies. The available phylogenetic tools have greatly aided our analysis of virus evolution, but these methods struggle to characterize the role of virus populations. Missing from many of these considerations has been the major role played by persisting viruses in stable virus evolution and disease emergence. In many cases, extreme stability is seen with persisting RNA viruses. Indeed, examples are known in which it is the persistently infected host that has better survival. We have also recently come to appreciate the vast diversity of phage (DNA viruses) of prokaryotes as a system that evolves by genetic exchanges across vast populations (Chapter 10). This has been proposed to be the “big bang” of biological evolution. In the large DNA viruses of aquatic microbes we see surprisingly large, complex and diverse viruses. With both prokaryotic and eukaryotic DNA viruses, recombination is the main engine of virus evolution, and virus host co-evolution is common, although not uniform. Viral emergence appears to be an unending phenomenon and we can currently witness a selective sweep by retroviruses that infect and become endogenized in koala bears. url: https://api.elsevier.com/content/article/pii/B9780123741530000217 doi: 10.1016/b978-0-12-374153-0.00021-7 id: cord-292740-b4cdj96q author: Wahid, Braira title: Immunotherapeutic strategies for sexually transmitted viral infections: HIV, HSV and HPV date: 2016-08-03 words: 10099.0 sentences: 516.0 pages: flesch: 34.0 cache: ./cache/cord-292740-b4cdj96q.txt txt: ./txt/cord-292740-b4cdj96q.txt summary: Within initial three months of infection, high concentration of antibodies is developed against different viral proteins in HIV-1 infected patients and recent studies unfolded that antibodies, CD8+ T cell activity, and CD4+ helper responses lead to control of HIV virus. Replication defective recombinant adenovirus 5 vector with HIV-1 clade B nef/gag/pol inserts was the first T-cell vaccine that underwent clinical efficacy trials and exhibited significant increase in CD8+ T cell but these CD8+ immune responses targeted the variable but not the conserved regions of virus. Immunomodulators include both immunosuppressive and immunostimulatory agents that trigger secretion of cytokines from macrophages (IL-12, IFN-12, TNF-a) leading to increased Th1 response, antibody production in response to improved antigen presentation by dendritic cells, and cell-mediated immunity which is being used clinically to cure viral infections like herpes simplex virus, human papillomavirus and cancerous lesions in immunocompromised individuals [136] . abstract: More than 1 million sexually transmitted infections (STIs) are acquired each day globally. Etiotropic drugs cannot effectively control infectious diseases therefore, there is a dire need to explore alternative strategies especially those based on the regulation of immune system. The review discusses all rational approaches to develop better understanding towards immunotherapeutic strategies based on modulation of immune system in an attempt to curb the elevating risk of infectious diseases such as HIV, HPV and HSV because of their high prevalence. Development of monoclonal antibodies, vaccines and several other immune based treatments are promising alternative strategies that are offering new opportunities to eradicate pathogens. url: https://api.elsevier.com/content/article/pii/S0008874916300648 doi: 10.1016/j.cellimm.2016.08.001 id: cord-259748-x7dq1sy4 author: Wan, Dongshan title: Research Advances in How the cGAS-STING Pathway Controls the Cellular Inflammatory Response date: 2020-04-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Double-stranded DNA (dsDNA) sensor cyclic-GMP-AMP synthase (cGAS) along with the downstream stimulator of interferon genes (STING) acting as essential immune-surveillance mediators have become hot topics of research. The intrinsic function of the cGAS-STING pathway facilitates type-I interferon (IFN) inflammatory signaling responses and other cellular processes such as autophagy, cell survival, senescence. cGAS-STING pathway interplays with other innate immune pathways, by which it participates in regulating infection, inflammatory disease, and cancer. The therapeutic approaches targeting this pathway show promise for future translation into clinical applications. Here, we present a review of the important previous works and recent advances regarding the cGAS-STING pathway, and provide a comprehensive understanding of the modulatory pattern of the cGAS-STING pathway under multifarious pathologic states. url: https://www.ncbi.nlm.nih.gov/pubmed/32411126/ doi: 10.3389/fimmu.2020.00615 id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 words: 36567.0 sentences: 2487.0 pages: flesch: 46.0 cache: ./cache/cord-347710-ff64y6ef.txt txt: ./txt/cord-347710-ff64y6ef.txt summary: hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. abstract: Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/32661235/ doi: 10.1038/s41392-020-00233-4 id: cord-013336-42thiglv author: Wang, Cheng title: Correlates of HIV self-testing among female sex workers in China: implications for expanding HIV screening date: 2020-10-22 words: 3641.0 sentences: 191.0 pages: flesch: 52.0 cache: ./cache/cord-013336-42thiglv.txt txt: ./txt/cord-013336-42thiglv.txt summary: However, there have been few studies examining HIV self-testing among female sex workers in countries outside of sub-Saharan Africa, including China [16] [17] [18] . We partnered with eight local female sex workers community-based organizations (CBO) in those eight cities with experience of conducting female sex workers outreach programs including condom promotion, sexual health education, HIV and syphilis rapid testing and counseling, and linkage to care (accompaniment to clinical services for infected individuals). Since the World Health Organization released guidelines recommending HIV self-testing among under-served and high-risk populations in 2016 [25] , many studies in the sub-Saharan Africa have shown that HIV self-testing has a good acceptability and feasibility for female sex workers [12, 14, 15, 26] . Studies have suggested that adding HIV self-testing to existing community-based testing and counseling services among female sex workers is acceptable, cost-effective and efficient to improve linkage to care [15, 26, 27] . abstract: BACKGROUND: Human immunodeficiency virus (HIV) self-testing may help improve test uptake among female sex workers. China has implemented many HIV self-testing programs among men who have sex with men, creating an opportunity for promotion among female sex workers. However, there is a limited literature on examining HIV self-testing among female sex workers. This study aimed to examine HIV self-testing experiences and its determinants among female sex workers in China. METHODS: A venue-based, cross-sectional study was conducted among Chinese female sex workers in 2019. Participants completed a survey including social-demographic characteristics, sexual behaviors, and HIV self-testing history, the distribution of which were analyzed using descriptive analysis. Multivariable logistic regression was conducted to identify associations with HIV self-testing. RESULTS: Among 1287 Chinese female sex workers, 1072 (83.3%, 95% confidence interval [CI] 81.2–85.3%) had ever tested for HIV, and 103 (8.0%, 95% CI 6.6–9.6%) had ever used HIV self-testing. More than half reported that the self-test was their first HIV test (59.2%, 61/103), around one-fifth reported HIV self-testing results influenced the price of sex (21.4%, 22/103). A minority of individuals reported ever experiencing pressure to undertake HIV self-testing (6.8%, 7/103). After adjusting for covariates, HIV self-testing was positively associated with receiving anal sex in the past month (adjusted odds ratio [aOR] = 2.2, 95% CI 1.4–3.5), using drugs before or during sex (aOR = 2.8, 95% CI 1.8–4.5), injecting drugs in the past 6 months (aOR = 2.6, 95% CI 1.2–6.0), being diagnosed with other sexually transmitted infections (aOR = 1.6, 95% CI 1.0–2.5), tested for other sexually transmitted infections in the past six months (aOR = 3.4, 95% CI 2.1–5.5), ever tested in the hospital (aOR = 3.4, 95% CI 2.0–5.6), and ever tested in the community (aOR = 1.5, 95% CI 1.2–1.9). CONCLUSIONS: Our findings suggest that HIV self-testing could expand overall HIV testing uptake, increase HIV testing frequency, reach sub-groups of high-risk female sex workers and has limited potential harms among female sex workers. HIV self-testing should be incorporated among Chinese female sex workers as a complement to facility-based HIV testing services. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583185/ doi: 10.1186/s40249-020-00765-5 id: cord-283127-jetmocvk author: Wang, Denong title: Targeting N-Glycan Cryptic Sugar Moieties for Broad-Spectrum Virus Neutralization: Progress in Identifying Conserved Molecular Targets in Viruses of Distinct Phylogenetic Origins date: 2015-03-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Identifying molecular targets for eliciting broadly virus-neutralizing antibodies is one of the key steps toward development of vaccines against emerging viral pathogens. Owing to genomic and somatic diversities among viral species, identifying protein targets for broad-spectrum virus neutralization is highly challenging even for the same virus, such as HIV-1. However, viruses rely on host glycosylation machineries to synthesize and express glycans and, thereby, may display common carbohydrate moieties. Thus, exploring glycan-binding profiles of broad-spectrum virus-neutralizing agents may provide key information to uncover the carbohydrate-based virus-neutralizing epitopes. In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA), for their viral targeting activities. Although these agents were known to be specific for oligomannosyl antigens, they differ strikingly in virus-binding activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV), and human cytomegalovirus (HCMV). In carbohydrate microarray analyses, we explored the molecular basis underlying the striking differences in the spectrum of anti-virus activities of the two probes. Unlike 2G12, which is strictly specific for the high-density Man(9)GlcNAc(2)Asn (Man9)-clusters, GNA recognizes a number of N-glycan cryptic sugar moieties. These include not only the known oligomannosyl antigens but also previously unrecognized tri-antennary or multi-valent GlcNAc-terminating N-glycan epitopes (Tri/m-Gn). These findings highlight the potential of N-glycan cryptic sugar moieties as conserved targets for broad-spectrum virus neutralization and suggest the GNA-model of glycan-binding warrants focused investigation. url: https://www.ncbi.nlm.nih.gov/pubmed/25774492/ doi: 10.3390/molecules20034610 id: cord-269862-krcu3hfa author: Wang, Shui-Mei title: APOBEC3G cytidine deaminase association with coronavirus nucleocapsid protein date: 2009-05-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We previously reported that replacing HIV-1 nucleocapsid (NC) domain with SARS-CoV nucleocapsid (N) residues 2–213, 215–421, or 234–421 results in efficient virus-like particle (VLP) production at a level comparable to that of wild-type HIV-1. In this study we demonstrate that these chimeras are capable of packaging large amounts of human APOBEC3G (hA3G), and that an HIV-1 Gag chimera containing the carboxyl-terminal half of human coronavirus 229E (HCoV-229E) N as a substitute for NC is capable of directing VLP assembly and efficiently packaging hA3G. When co-expressed with SARS-CoV N and M (membrane) proteins, hA3G was efficiently incorporated into SARS-CoV VLPs. Data from GST pull-down assays suggest that the N sequence involved in N–hA3G interactions is located between residues 86 and 302. Like HIV-1 NC, the SARS-CoV or HCoV-229E N-associated with hA3G depends on the presence of RNA, with the first linker region essential for hA3G packaging into both HIV-1 and SARS-CoV VLPs. The results raise the possibility that hA3G is capable of associating with different species of viral structural proteins through a potentially common, RNA-mediated mechanism. url: https://api.elsevier.com/content/article/pii/S0042682209001834 doi: 10.1016/j.virol.2009.03.010 id: cord-001972-1zisomq5 author: Wang, Xue title: Pandemic Influenza A (H1N1) Virus Infection Increases Apoptosis and HIV-1 Replication in HIV-1 Infected Jurkat Cells date: 2016-02-02 words: 3921.0 sentences: 197.0 pages: flesch: 46.0 cache: ./cache/cord-001972-1zisomq5.txt txt: ./txt/cord-001972-1zisomq5.txt summary: These data indicate that HIV-1 replication can be activated by pH1N1 virus in HIV-1-infected cells resulting in induction of cell death through apoptotic pathways. Cells treated with pH1N1 had higher level of NF-kB phosphorylation and increased protein expression of NFAT and AP-1 ( Figure 3B ) relative to HIV-1 infection alone, suggesting pH1N1 infection can activate host transcription factors required for HIV-1 replication in Jurkat cells. These data indicate that pandemic influenza A (H1N1) infection can increase accumulation of CD4 protein and induce T cell signaling and activate host transcription factors required for HIV-1 replication. In conclusion, our results demonstrate that pandemic influenza A (H1N1) virus infection can induce cell death through apoptotic signaling pathways and promote HIV-1 replication through the MAPK and TCR-related signaling pathways in HIV-1-infected Jurkat cells. Pandemic influenza A (H1N1) virus infection is also able to reactivate HIV-1 replication from its state of latent infection through activating apoptosis and TCR-signaling pathways. abstract: Influenza virus infection has a significant impact on public health, since it is a major cause of morbidity and mortality. It is not well-known whether influenza virus infection affects cell death and human immunodeficiency virus (HIV)-1 replication in HIV-1-infected patients. Using a lymphoma cell line, Jurkat, we examined the in vitro effects of pandemic influenza A (H1N1) virus (pH1N1) infection on cell death and HIV-1 RNA production in infected cells. We found that pH1N1 infection increased apoptotic cell death through Fas and Bax-mediated pathways in HIV-1-infected Jurkat cells. Infection with pH1N1 virus could promote HIV-1 RNA production by activating host transcription factors including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-ĸB), nuclear factor of activated T-cells (NFAT) and activator protein 1 (AP-1) through mitogen-activated protein kinases (MAPK) pathways and T-cell antigen receptor (TCR)-related pathways. The replication of HIV-1 latent infection could be reactivated by pH1N1 infection through TCR and apoptotic pathways. These data indicate that HIV-1 replication can be activated by pH1N1 virus in HIV-1-infected cells resulting in induction of cell death through apoptotic pathways. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776188/ doi: 10.3390/v8020033 id: cord-003715-deqiets2 author: Warren, Cody J. title: Selective use of primate CD4 receptors by HIV-1 date: 2019-06-10 words: 9529.0 sentences: 457.0 pages: flesch: 55.0 cache: ./cache/cord-003715-deqiets2.txt txt: ./txt/cord-003715-deqiets2.txt summary: We next tested HIV-1 pseudotyped with Envs from four macrophage-tropic viruses [31, [64] [65] [66] [67] [68] [69] [70] [71] [72] for their ability to infect cells bearing primate CD4 receptors ( Fig 3B) . (A, B) Cells stably expressing various primate CD4 receptors (x-axis), along with human CCR5, were infected with Q23ΔEnv-GFP pseudotyped with (A) early HIV-1 Envelopes (Envs) or (B) Envs from common macrophagetropic HIV-1 isolates. Collectively, these data suggest that most early HIV-1 isolates from the blood, which have lower affinity for human CD4 compared to macrophage-tropic viruses, do not bind well to chimpanzee and macaque CD4. In this study, we have shown that Envs from over 30 early and chronic HIV-1 isolates from human blood (mother-infant pairs, etc.) all demonstrate selective entry via only some primate CD4 receptors. (B) Dog thymocytes (Cf2Th cells) stably expressing human CCR5 and the indicated rhesus macaque CD4 alleles (x-axis) were infected with HIV-1 (Q23ΔEnv-GFP) bearing a subtype A (BG505) or subtype C (CAP210.2.00.E8) Envelope (Env). abstract: Individuals chronically infected with HIV-1 harbor complex viral populations within their bloodstreams. Recently, it has come to light that when these people infect others, the new infection is typically established by only one or a small number of virions from within this complex viral swarm. An important goal is to characterize the biological properties of HIV-1 virions that seed and exist early in new human infections because these are potentially the only viruses against which a prophylactic HIV-1 vaccine would need to elicit protection. This includes understanding how the Envelope (Env) protein of these virions interacts with the T-cell receptor CD4, which supports attachment and entry of HIV-1 into target cells. We examined early HIV-1 isolates for their ability to infect cells via the CD4 receptor of 15 different primate species. Primates were the original source of HIV-1 and now serve as valuable animal models for studying HIV-1. We find that most primary isolates of HIV-1 from the blood, including early isolates, are highly selective and enter cells through some primate CD4 receptor orthologs but not others. This phenotype is remarkably consistent, regardless of route of transmission, viral subtype, or time of isolation post infection. We show that the weak CD4 binding affinity of blood-derived HIV-1 isolates is what makes them sensitive to the small sequence differences in CD4 from one primate species to the next. To substantiate this, we engineered an early HIV-1 Env to have high, medium, or low binding affinity to CD4, and we show that it loses the ability to enter cells via the CD4 receptor of many primate species as the binding affinity gets weaker. Based on the phenotype of selective use of primate CD4, we find that weak CD4 binding appears to be a nearly universal property of HIV-1 circulating in the bloodstream. Therefore, weak binding to CD4 must be a selected and important property in the biology of HIV-1 in the body. We identify six primate species that encode CD4 receptors that fully support the entry of early HIV-1 isolates despite their low binding affinity for CD4. These findings will help inform long-standing efforts to model HIV-1 transmission and early disease in primates. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586362/ doi: 10.1371/journal.pbio.3000304 id: cord-263452-y2ral8nx author: Watanabe, Yasunori title: Site-specific glycan analysis of the SARS-CoV-2 spike date: 2020-05-04 words: 2073.0 sentences: 121.0 pages: flesch: 50.0 cache: ./cache/cord-263452-y2ral8nx.txt txt: ./txt/cord-263452-y2ral8nx.txt summary: To resolve the site-specific glycosylation of SARS-CoV-2 S protein and visualize the distribution of glycoforms across the protein surface, we expressed and purified three biological replicates of recombinant soluble material in an identical manner to that which was used to obtain the high-resolution cryo-electron microscopy (cryo-EM) structure, albeit without glycan processing blockade using kifunensine (4). The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, as observed on SARS-CoV-1 S (10, 13), HIV-1 Env (27) , influenza HA (28, 29) , and LASV GPC (24). For example, one of the most densely glycosylated viral spike proteins is HIV-1 Env, which exhibits ~60% oligomannose-type glycans (21, 34) . This suggests that SARS-CoV-2 S protein is less densely glycosylated and that the glycans form less of a shield compared with other viral glycoproteins including HIV-1 Env and LASV GPC, which may be beneficial for the elicitation of neutralizing antibodies. SARS-CoV-2 spike site-specific N-linked glycan analysis abstract: The emergence of the betacoronavirus, SARS-CoV-2, the causative agent of COVID-19, represents a significant threat to global human health. Vaccine development is focused on the principal target of the humoral immune response, the spike (S) glycoprotein, which mediates cell entry and membrane fusion. SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer, which likely play a role in protein folding and immune evasion. Here, using a site-specific mass spectrometric approach, we reveal the glycan structures on a recombinant SARS-CoV-2 S immunogen. This analysis enables mapping of the glycan-processing states across the trimeric viral spike. We show how SARS-CoV-2 S glycans differ from typical host glycan processing, which may have implications in viral pathobiology and vaccine design. url: https://www.ncbi.nlm.nih.gov/pubmed/32366695/ doi: 10.1126/science.abb9983 id: cord-293653-u2qrxq6t author: Watashi, Koichi title: Cyclophilin and Viruses: Cyclophilin as a Cofactor for Viral Infection and Possible Anti-Viral Target date: 2007-02-05 words: 4891.0 sentences: 304.0 pages: flesch: 46.0 cache: ./cache/cord-293653-u2qrxq6t.txt txt: ./txt/cord-293653-u2qrxq6t.txt summary: In addition to these cellular events, a number of reports demonstrated that CyP plays a critical role in the life cycle of viruses, especially human immunodeficiency virus (HIV) and hepatitis C virus (HCV). The action of PPIases leads to changes in protein conformation (Takahashi, 1999) , but the binding of CsA and FK506 to CyP and FKBP, respectively, inhibits the activity of these enzymes (Fischer et al. The CsA/CyP or FK506/FKBP complex, subsequently interacts with and inhibits calcineurin (CN), a phosphatase involved in the activation of the transcription factor NF-AT. Members of the CyP family play roles in a variety of cellular processes including the immune response, transcription, mitochondrial function, cell death, and chemotaxis, as described below. However, the best-characterized role identified for CyPA is not in normal cellular physiology, but rather as co-factor during the human immunodefi ciency virus-1 (HIV-1) viral life cycle (See below). abstract: Cyclophilin (CyP) is a peptidyl prolyl cis/trans isomerase, catalyzing the cis-trans isomerization of proline residues in proteins. CyP plays key roles in several different aspects of cellular physiology including the immune response, transcription, mitochondrial function, cell death, and chemotaxis. In addition to these cellular events, a number of reports demonstrated that CyP plays a critical role in the life cycle of viruses, especially human immunodeficiency virus (HIV) and hepatitis C virus (HCV). These two viruses are significant causes of morbidity and mortality worldwide, but current therapies are often insufficient. CyP may provide a novel therapeutic target for the management and/or cure of these diseases, in particular HCV. url: https://www.ncbi.nlm.nih.gov/pubmed/21901058/ doi: nan id: cord-293379-c4qdmkw5 author: Weiss, Robin A title: HIV and AIDS: looking ahead date: 2003 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although the future of HIV science is uncertain, we need to reappraise HIV diversity, pathogenesis and immunity. The AIDS pandemic threatens the success of existing vaccine programs and may accelerate the emergence of new infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/12835710/ doi: 10.1038/nm0703-887 id: cord-300793-tuq8z6gm author: Weiss, Robin A title: Social and environmental risk factors in the emergence of infectious diseases date: 2004 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Fifty years ago, the age-old scourge of infectious disease was receding in the developed world in response to improved public health measures, while the advent of antibiotics, better vaccines, insecticides and improved surveillance held the promise of eradicating residual problems. By the late twentieth century, however, an increase in the emergence and re-emergence of infectious diseases was evident in many parts of the world. This upturn looms as the fourth major transition in human–microbe relationships since the advent of agriculture around 10,000 years ago. About 30 new diseases have been identified, including Legionnaires' disease, human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS), hepatitis C, bovine spongiform encephalopathy (BSE)/variant Creutzfeldt-Jakob disease (vCJD), Nipah virus, several viral hemorrhagic fevers and, most recently, severe acute respiratory syndrome (SARS) and avian influenza. The emergence of these diseases, and resurgence of old ones like tuberculosis and cholera, reflects various changes in human ecology: rural-to-urban migration resulting in high-density peri-urban slums; increasing long-distance mobility and trade; the social disruption of war and conflict; changes in personal behavior; and, increasingly, human-induced global changes, including widespread forest clearance and climate change. Political ignorance, denial and obduracy (as with HIV/AIDS) further compound the risks. The use and misuse of medical technology also pose risks, such as drug-resistant microbes and contaminated equipment or biological medicines. A better understanding of the evolving social dynamics of emerging infectious diseases ought to help us to anticipate and hopefully ameliorate current and future risks. url: https://www.ncbi.nlm.nih.gov/pubmed/15577934/ doi: 10.1038/nm1150 id: cord-330970-6kkqoh7f author: Weiss, Robin A title: Apes, lice and prehistory date: 2009-02-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although most epidemic human infectious diseases are caused by recently introduced pathogens, cospeciation of parasite and host is commonplace for endemic infections. Occasional host infidelity, however, provides the endemic parasite with an opportunity to survive the potential extinction of its host. Such infidelity may account for the survival of certain types of human lice, and it is currently exemplified by viruses such as HIV. url: https://www.ncbi.nlm.nih.gov/pubmed/19232074/ doi: 10.1186/jbiol114 id: cord-021872-rhi7hi9m author: Wilkes, Rebecca P. title: Update on Antiviral Therapies date: 2015-12-04 words: 9933.0 sentences: 524.0 pages: flesch: 47.0 cache: ./cache/cord-021872-rhi7hi9m.txt txt: ./txt/cord-021872-rhi7hi9m.txt summary: Topical antiviral therapy has been mainly used for herpetic ocular disease, but studies have evaluated a systemic antiviral compound (famciclovir) for treatment of multiple clinical syndromes associated with FHV-1 infections. 7 A related drug, (R)-9-(2-phosphonylmethoxypropyl)-2,6diaminopurine (PMPDAP), has been shown previously to be a potent inhibitor of FIV replication in cell culture and has reduced the viral load in three of four cats experimentally infected with FIV when treated at 20 mg/kg SC three times per week for 6 weeks. 1 A prodrug of acyclovir, valacyclovir, was developed for increased bioavailability in humans, but use for FHV-1 treatment in experimentally infected cats induced fatal renal and hepatic necrosis and bone marrow suppression, and did not reduce viral shedding or clinical disease severity. 20 Even though this study did not mimic how cats with natural infection would be treated, results from a clinical case study suggested this drug is likely effective for treatment of clinical cases, though it was not blinded and placebo controlled. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152142/ doi: 10.1016/b978-0-323-22652-3.00007-4 id: cord-327324-4c4a4bfz author: Wilkinson, Robert J title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 date: 2020-06-13 words: 872.0 sentences: 61.0 pages: flesch: 43.0 cache: ./cache/cord-327324-4c4a4bfz.txt txt: ./txt/cord-327324-4c4a4bfz.txt summary: title: Tuberculosis and type 2 Diabetes Mellitus: an inflammatory danger signal in the time of COVID-19 Active tuberculosis has a transcriptomic signature dominated by a neutrophil-driven type 1 and 2 interferoninducible gene profile. The exaggerated inflammation that characterizes HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is triggered by Toll-like receptor and inflammasome signalling [14] . Male sex and diabetes have been identified in virtually every study as risk factors for severe COVID-19 infection, associated in the largest study to date with an adjusted hazard ratio for in-hospital death of 1.99 (male sex) and 1.50 for controlled (HbA1c < 58 mmol/mol) and 2.36 for uncontrolled DM [18] . Diabetes mellitus increases the risk of active tuberculosis: a systematic review of 13 observational studies HIV-tuberculosis-associated immune reconstitution inflammatory syndrome is characterized by Toll-like receptor and inflammasome signalling Complement pathway gene activation and rising circulating immune complexes characterize early disease in HIV-associated tuberculosis abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32533824/ doi: 10.1093/cid/ciaa747 id: cord-337659-x4oywbrj author: Wilson, Brenda A. title: Global biosecurity in a complex, dynamic world date: 2008-07-31 words: 10626.0 sentences: 469.0 pages: flesch: 45.0 cache: ./cache/cord-337659-x4oywbrj.txt txt: ./txt/cord-337659-x4oywbrj.txt summary: Although one might argue that the principal difference in the infectious disease threat today versus say 10, 25, or 50 years ago is bioterrorism, the resources spend on preparing for a bioterror attack is viewed by most scientists as grossly exorbitant [6] , particularly considering the small numbers of individuals who have been or could be affected by this type of attack and considering the relatively low medical relevance or prevalence of the diseases caused by the limited number of highpriority bioterror bioagents, the socalled ''''category A select agents.'''' And, while admittedly the preparedness and surveillance measures put in place for one has certainly helped to protect against the other (the improved global response to and curtailment of SARS coming after the anthrax bioterrorist attacks is a prime example of this), most scientists feel that the limited resources available from an already overburdened system should instead be used for studying and preparing against the looming and potentially more devastating infectious disease threats from natural or accidental exposure [7] , which could affect millions of people and animals and could have huge health and economic consequences. abstract: Biosecurity is emerging as a major global health priority for which innovative and unprecedented solutions are needed. Biosecurity is a challenging biocomplexity problem involving multifaceted processes such as interactions between humans and nonhuman biota, anthropogenic environmental and ecological factors, and socioeconomic and political pressures. Key to an effective biosecurity strategy will be fundamental understanding of evolutionary, anthropogenic and environmental driving forces at play in transmission and perpetuation of infectious diseases. Biosecurity solutions will depend on increased support of basic biomedical research and public education, enhanced healthcare preparedness, alternative strategies for ensuringsafety, and improved interagency cooperation regarding global health policy. © 2008 Wiley Periodicals, Inc. Complexity, 2008. url: https://www.ncbi.nlm.nih.gov/pubmed/32313416/ doi: 10.1002/cplx.20246 id: cord-338594-wft7yy6j author: Winkler, Michael title: Rhesus macaque IFITM3 gene polymorphisms and SIV infection date: 2017-03-03 words: 4633.0 sentences: 277.0 pages: flesch: 48.0 cache: ./cache/cord-338594-wft7yy6j.txt txt: ./txt/cord-338594-wft7yy6j.txt summary: In particular, polymorphisms of the human IFITM3 gene have been shown to affect disease severity and progression in influenza A virus (FLUAV) and human immunodeficiency virus (HIV) infection, respectively. Employing previously characterized samples from two cohorts of SIV-infected rhesus macaques, we investigated the relationship between these rhIFITM3 polymorphisms and both AIDS-free survival time and virus load. Polymorphisms in several immune-relevant gene loci such as MHC or KIR are associated with the transmission and course of disease in SIV infected rhesus macaques and HIV-1 infected humans [36, 37] . Immune-related IFITM proteins have been established as important antiviral effectors of the interferon response, and a polymorphism in the human IFITM3 gene has been found to be associated with disease severity and progression in FLUAV and HIV-1 infection [27, 33] . Notably, all polymorphism in the coding region were silent and strong evidence for an association of rhIFITM3 polymorphisms with disease progression and viral load in SIV infected animals was not obtained. abstract: Interferon-induced transmembrane proteins (IFITMs) have been recognized as important antiviral effectors of the innate immune system, both in cell culture and in infected humans. In particular, polymorphisms of the human IFITM3 gene have been shown to affect disease severity and progression in influenza A virus (FLUAV) and human immunodeficiency virus (HIV) infection, respectively. Rhesus macaques (Macaca mulatta) are commonly used to model human infections and the experimental inoculation of these animals with simian immunodeficiency virus (SIV) is one of the best models for HIV/AIDS in humans. However, information on the role of IFITM3 in SIV infection of rhesus macaques is currently lacking. We show that rhesus macaque (rh) IFITM3 inhibits SIV and FLUAV entry in cell culture, although with moderately reduced efficiency as compared to its human counterpart. We further report the identification of 16 polymorphisms in the rhIFITM3 gene, three of which were exonic and synonymous while the remainder was located in non-coding regions. Employing previously characterized samples from two cohorts of SIV-infected rhesus macaques, we investigated the relationship between these rhIFITM3 polymorphisms and both AIDS-free survival time and virus load. In cohort 1, several intronic polymorphisms were significantly associated with virus load or survival. However, an association with both parameters was not observed and significance was lost in most cases when animals were stratified for the presence of MHC allele Mamu-A1*001. Moreover, no significant genotype-phenotype associations were detected in cohort 2. These results suggest that, although IFITM3 can inhibit SIV infection in cell culture, genetic variation in rhIFITM3 might have only a minor impact on the course of SIV infection in experimentally infected animals. url: https://www.ncbi.nlm.nih.gov/pubmed/28257482/ doi: 10.1371/journal.pone.0172847 id: cord-010175-p2py9wau author: Winter, Harland title: GASTROINTESTINAL AND NUTRITIONAL PROBLEMS IN CHILDREN WITH IMMUNODEFICIENCY AND AIDS date: 1996-04-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172360/ doi: 10.1016/s0031-3955(05)70421-1 id: cord-330698-9t24jo8s author: Wurdinger, Thomas title: Extracellular Vesicles and Their Convergence with Viral Pathways date: 2012-07-25 words: 7445.0 sentences: 365.0 pages: flesch: 39.0 cache: ./cache/cord-330698-9t24jo8s.txt txt: ./txt/cord-330698-9t24jo8s.txt summary: Finally, endogenous retrovirus and retrotransposon elements deposited in our genomes millions of years ago can be released from cells within microvesicles, suggestive of a viral origin of the microvesicle system or perhaps of an evolutionary conserved system of virus-vesicle codependence. Microvesicles released by infected cells contain specific components of the cell and the virus, many of which facilitate the ability of virions to persist in a hostile antiviral immune environment [44, 55, 56, 58] . During HSV-1 infection the release of microvesicles, formerly known as L-particles containing viral tegument proteins and glycoproteins, can prime surrounding cells for productive infection and reduce immune rejection [48] [49] [50] . In the case of the human CMV, microvesicles released by infected cells present the C-type lectin family molecule expressed on dendritic cells-used in capture and internalization of pathogens-in complex with the CMV glycoprotein B. Also, the convergence of these pathways may explain the observations of virus-like particles, which can be exosomes or shed microvesicles containing viral proteins or nucleic acids. abstract: Extracellular vesicles (microvesicles), such as exosomes and shed microvesicles, contain a variety of molecules including proteins, lipids, and nucleic acids. Microvesicles appear mostly to originate from multivesicular bodies or to bud from the plasma membrane. Here, we review the convergence of microvesicle biogenesis and aspects of viral assembly and release pathways. Herpesviruses and retroviruses, amongst others, recruit several elements from the microvesicle biogenesis pathways for functional virus release. In addition, noninfectious pleiotropic virus-like vesicles can be released, containing viral and cellular components. We highlight the heterogeneity of microvesicle function during viral infection, addressing microvesicles that can either block or enhance infection, or cause immune dysregulation through bystander action in the immune system. Finally, endogenous retrovirus and retrotransposon elements deposited in our genomes millions of years ago can be released from cells within microvesicles, suggestive of a viral origin of the microvesicle system or perhaps of an evolutionary conserved system of virus-vesicle codependence. More research is needed to further elucidate the complex function of the various microvesicles produced during viral infection, possibly revealing new therapeutic intervention strategies. url: https://doi.org/10.1155/2012/767694 doi: 10.1155/2012/767694 id: cord-318570-wj7r6953 author: Xiao, Yinzong title: Point-of-Care Tests for Hepatitis B: An Overview date: 2020-10-02 words: 8331.0 sentences: 350.0 pages: flesch: 40.0 cache: ./cache/cord-318570-wj7r6953.txt txt: ./txt/cord-318570-wj7r6953.txt summary: If active infection is confirmed, subsequent blood tests are performed to determine the stage of disease and need for treatment, including a hepatitis B virus (HBV) polymerase chain reaction (PCR)-based quantitative DNA level or viral load, a hepatitis B eAg and eAb assay and liver function tests to determine whether an elevated aminotransferase (ALT) indicative of liver inflammation or other signs of impaired liver function are present. POCs usually require small amounts of body fluids (for example, a finger-prick blood sample or oral swab), short turn-around time, and are generally easy to use with minimal required training and therefore can be provided to people in a variety of community and outreach settings by a broad range of trained workers [22] and are scalable to rapidly reach large populations as has been seen with the highly successful Egyptian national hepatitis C screening program [23] . abstract: Despite the heavy disease burden posed by hepatitis B, around 90% of people living with hepatitis B are not diagnosed globally. Many of the affected populations still have limited or no access to essential blood tests for hepatitis B. Compared to conventional blood tests which heavily rely on centralised laboratory facilities, point-of-care testing for hepatitis B has the potential to broaden testing access in low-resource settings and to engage hard-to-reach populations. Few hepatitis B point-of-care tests have been ratified for clinical use by international and regional regulatory bodies, and countries have been slow to adopt point-of-care testing into hepatitis B programs. This review presents currently available point-of-care tests for hepatitis B and their roles in the care cascade, reviewing evidence for testing performance, utility, acceptability, costs and cost-effectiveness when integrated into hepatitis B diagnosis and monitoring programs. We further discuss challenges and future directions in aspects of technology, implementation, and regulation when adopting point-of-care testing in hepatitis B programs. url: https://doi.org/10.3390/cells9102233 doi: 10.3390/cells9102233 id: cord-005033-voi9gu0l author: Xuan, Huiyu title: A CA-based epidemic model for HIV/AIDS transmission with heterogeneity date: 2008-06-07 words: 6567.0 sentences: 395.0 pages: flesch: 57.0 cache: ./cache/cord-005033-voi9gu0l.txt txt: ./txt/cord-005033-voi9gu0l.txt summary: In this paper, we develop an extended CA simulation model to study the dynamical behaviors of HIV/AIDS transmission. Additional, we divide the post-infection process of AIDS disease into several sub-stages in order to facilitate the study of the dynamics in different development stages of epidemics. Higher population density, higher mobility, higher number of infection source, and greater neighborhood are more likely to result in high levels of infections and in persistence. Ahmed and Agiza (1998) develop a CA model that takes into consideration the latency and incubation period of epidemics and allow each individual (agent) to have distinctive susceptibility. We also define four types of agents that are characterized by different infectivity (and susceptibility) and various forms of neighborhood to represent four types of people in real life. To capture this, we extend classical CA models by allowing each agent to have its own attributes such as mobility, infectivity, resistibility (susceptibility) 2 and different extent of neighborhood. abstract: The complex dynamics of HIV transmission and subsequent progression to AIDS make the mathematical analysis untraceable and problematic. In this paper, we develop an extended CA simulation model to study the dynamical behaviors of HIV/AIDS transmission. The model incorporates heterogeneity into agents’ behaviors. Agents have various attributes such as infectivity and susceptibility, varying degrees of influence on their neighbors and different mobilities. Additional, we divide the post-infection process of AIDS disease into several sub-stages in order to facilitate the study of the dynamics in different development stages of epidemics. These features make the dynamics more complicated. We find that the epidemic in our model can generally end up in one of the two states: extinction and persistence, which is consistent with other researchers’ work. Higher population density, higher mobility, higher number of infection source, and greater neighborhood are more likely to result in high levels of infections and in persistence. Finally, we show in four-class agent scenario, variation in susceptibility (or infectivity) and various fractions of four classes also complicates the dynamics, and some of the results are contradictory and needed for further research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088085/ doi: 10.1007/s10479-008-0369-3 id: cord-342719-bdxb45us author: Yamamoto, Shinya title: Antibody Response to SARS-CoV-2 in people living with HIV date: 2020-10-02 words: 408.0 sentences: 39.0 pages: flesch: 62.0 cache: ./cache/cord-342719-bdxb45us.txt txt: ./txt/cord-342719-bdxb45us.txt summary: All five patients received consecutive serological test, and four of five patients had seroconversion by one month after the symptom onset, which were similar to non-HIV-infected patients. 1 Ample studies have demonstrated that PLWH generally show poor serological response to other viruses or viral antigens such as hepatitis B vaccine, 2 especially for PLWH with a high HIV viral load and decreased CD4+ T-cell. 2 One previous report described that an untreated HIV case had seroconversion of SARS-CoV-2 two months after symptoms appeared. ART occurred similarly to that in COVID-19 patients without HIV infection. Absence of seroconversion, as was observed in our Case 2, has been reported particularly in mild 1 or asymptomatic patients. 5 We highlighted that seroconversion of SARS-CoV-2 was similar between well-controlled PLWH and patients without HIV. One case of coronavirus disease 2019 (COVID-19) in a patient co-infected by HIV with a low CD4(+) T-cell count Antibody Responses to SARS-CoV-2 at 8 weeks postinfection in asymptomatic patients. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/33046418/ doi: 10.1016/j.jmii.2020.09.005 id: cord-350221-8u6q3wfa author: Yang, Sung-Tae title: HIV virions sense plasma membrane heterogeneity for cell entry date: 2017-06-28 words: 7788.0 sentences: 413.0 pages: flesch: 55.0 cache: ./cache/cord-350221-8u6q3wfa.txt txt: ./txt/cord-350221-8u6q3wfa.txt summary: We used giant plasma membrane vesicles (GPMVs) derived from HeLa cells that stably express the CD4 receptor and CCR5 co-receptor (CD4 + /CCR5 + ), investigated the lateral partitioning of both receptors in these membranes, and imaged the preferred regions of HIV binding and fusion at the single-particle level (Fig. 1A) . Recognition of Lo/Ld membrane boundaries by HIV Next, we examined whether and how HIV envelope (Env) particles interact with GPMVs. Murine leukemia viruses (MLVs) pseudotyped with HIV gp120/gp41 and fluorescently labeled with mKO-Gag were incubated with CD4 + /CCR5 + GPMVs. We visualized bound particles by epifluorescence microscopy and found that they migrate along The preparation of large-scale phase-separated GPMVs facilitates the study of the lateral distribution of CD4 and CCR5 and the role of ordered lipid domains in HIV entry. abstract: It has been proposed that cholesterol in host cell membranes plays a pivotal role for cell entry of HIV. However, it remains largely unknown why virions prefer cholesterol-rich heterogeneous membranes to uniformly fluid membranes for membrane fusion. Using giant plasma membrane vesicles containing cholesterol-rich ordered and cholesterol-poor fluid lipid domains, we demonstrate that the HIV receptor CD4 is substantially sequestered into ordered domains, whereas the co-receptor CCR5 localizes preferentially at ordered/disordered domain boundaries. We also show that HIV does not fuse from within ordered regions of the plasma membrane but rather at their boundaries. Ordered/disordered lipid domain coexistence is not required for HIV attachment but is a prerequisite for successful fusion. We propose that HIV virions sense and exploit membrane discontinuities to gain entry into cells. This study provides surprising answers to the long-standing question about the roles of cholesterol and ordered lipid domains in cell entry of HIV and perhaps other enveloped viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/28782011/ doi: 10.1126/sciadv.1700338 id: cord-011485-15wtv6bt author: Yang, Wenbo title: An immunoassay cassette with a handheld reader for HIV urine testing in point-of-care diagnostics date: 2020-05-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Currently, most HIV tests are performed with blood samples, or alternatively saliva samples are used for HIV testing. Simple HIV tests need to be performed in hospitals or other medical agencies instead of more invasive HIV blood tests. To enable point-of-care (POC) HIV diagnostics, based on a recently developed lateral flow strip for HIV urine testing, a microfluidic immunoassay cassette with a handheld optical reader is developed. Based on lateral flow strip with gold colloid reporter, the integrated immunoassay cassette can perform sample introduction, metering, discharging, applying and detection which simplifies HIV testing. An indicator is incorporated into the cassette to guide sample introduction based on color change, and further, the excess test sample is stored inside the sealed cassette to avoid any contamination. The low-cost handheld optical reader can provide a test result within a few seconds, which is useful for simple, sensitive and affordable HIV onsite detection. Instead of using normal white LEDs, a customized back light module embedded with green LEDs is adopted to illuminate the lateral flow strip with an appropriate working current to achieve optimal performance. Compared to the standard lateral flow strips using a benchtop reader, with the disposable immunoassay cassette assisted by the handheld optical reader, more convenient, easier-to-operate, and more affordable HIV urine testing can be achieved in POC diagnostics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239691/ doi: 10.1007/s10544-020-00494-4 id: cord-337897-hkvll3xh author: Yang, Zheng Rong title: Peptide Bioinformatics- Peptide Classification Using Peptide Machines date: 2009 words: 7631.0 sentences: 495.0 pages: flesch: 54.0 cache: ./cache/cord-337897-hkvll3xh.txt txt: ./txt/cord-337897-hkvll3xh.txt summary: The earlier work was to investigate a set of experimentally determined (synthesized) functional peptides to find some conserved amino acids, referred In protease cleavage site prediction, we commonly use peptides with a fixed length. The bio-basis function method has been successfully applied to various peptide classification tasks, for instance, the prediction of trypsin cleavage sites [ 9 ] , the prediction of HIV cleavage sites [ 10 ] , the prediction of hepatitis C virus protease cleavage sites [ 16 ] , the prediction of the disorder segments in proteins [ 7 , 17 ] , the prediction of protein phosphorylation sites [ 18 , 19 ] , the prediction of the O-linkage sites in glycoproteins [ 20 ] , the prediction of signal peptides [ 21 ] , the prediction of factor Xa protease cleavage sites [ 22 ] , the analysis of mutation patterns of HIV-1 Fig. 9 . abstract: Peptides scanned from whole protein sequences are the core information for many peptide bioinformatics research subjects, such as functional site prediction, protein structure identification, and protein function recognition. In these applications, we normally need to assign a peptide to one of the given categories using a computer model. They are therefore referred to as peptide classification applications. Among various machine learning approaches, including neural networks, peptide machines have demonstrated excellent performance compared with various conventional machine learning approaches in many applications. This chapter discusses the basic concepts of peptide classification, commonly used feature extraction methods, three peptide machines, and some important issues in peptide classification. url: https://www.ncbi.nlm.nih.gov/pubmed/19065810/ doi: 10.1007/978-1-60327-101-1_9 id: cord-010499-yefxrj30 author: Yelverton, Elizabeth title: The function of a ribosomal frameshifting signal from human immunodeficiency virus‐1 in Escherichia coli date: 2006-10-27 words: 5883.0 sentences: 330.0 pages: flesch: 60.0 cache: ./cache/cord-010499-yefxrj30.txt txt: ./txt/cord-010499-yefxrj30.txt summary: Ribosomal frameshifting in both rightward and leftward directions has also been shown to occur at certain ''hungry'' codons whose cognate aminoacyi-tRNAs are in short supply (Gallant and Foley, 1980; Weiss and Gailant, 1983; 1986; Gallant et ai, 1985; Kurland and Gallant, 1986) . Not all hungry codons are equally prone to shift: in a survey of 21 frameshift mutations of the rllB gene of phage T4, Weiss and Gallant (1986) found that oniy a minority were phenotypicaily suppressible when challenged by limitation for any of several aminoacyl-tRNAs. The context njies governing ribosome frameshifting at hungry sites are under investigation, and have been defined in a few cases (Weiss et al., 1988; Gallant and Lindsiey, 1992; Peter et ai. coli the rate of ribosomal frameshifting on that sequence can be increased by limitation for leucine, the amino acid encoded at the frameshift site. abstract: A 15‐17 nucleotide sequence from the gag‐pol ribosome frameshift site of HIV‐1 directs analogous ribosomal frameshifting in Escherichia coli. Limitation for leucine, which is encoded precisely at the frameshift site, dramatically increased the frequency of leftward frameshifting. Limitation for phenylaianine or arginine, which are encoded just before and just after the frameshift, did not significantly affect frameshifting. Protein sequence analysis demonstrated the occurrence of two closeiy related frameshift mechanisms. In the first, ribosomes appear to bind leucyl‐tRNA at the frameshift site and then slip leftward. This is the 'simultaneous slippage’mechanism. In the second, ribosomes appear to slip before binding amlnoacyl‐tRNA, and then bind phenylaianyl‐tRNA, which is encoded in the left‐shifted reading frame. This mechanism is identicai to the‘overlapping reading’we have demonstrated at other bacterial frameshift sites. The HIV‐1 sequence is prone to frame‐shifting by both mechanisms in E. coli. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192232/ doi: 10.1111/j.1365-2958.1994.tb00310.x id: cord-009269-6fs0f4b7 author: Youde, Jeremy title: Is universal access to antiretroviral drugs an emerging international norm? date: 2008-12-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The international community appears to have embraced a new norm — that of universal access to antiretroviral drugs. The process by which this norm has found acceptance raises interesting questions about how norm entrepreneurs frame their arguments, the role of non-state actors in realizing a norm, and the importance of existent complementary norms. To understand the success of the norm of universal antiretroviral access, I examine the failure of an earlier health-related norm — that of universal primary health care. The campaign for universal antiretroviral access points to a need for a more nuanced understanding of norm evolution within the international community and a more holistic vision of which actors can facilitate the realization of a norm. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140236/ doi: 10.1057/jird.2008.10 id: cord-338438-q5fis2v8 author: Young, Sean D. title: Clinical Care, Research, and Telehealth Services in the Era of Social Distancing to Mitigate COVID-19 date: 2020-05-21 words: 1442.0 sentences: 63.0 pages: flesch: 40.0 cache: ./cache/cord-338438-q5fis2v8.txt txt: ./txt/cord-338438-q5fis2v8.txt summary: In this Note, we describe considerations for integrating technologies, such as telemedicine; social media, mobile applications (apps), and chatbots; and biosensors/wearables into clinical HIV care delivery and research, as well as case examples of current uses of these technologies in adapting to the changing clinical and research needs among populations at risk for and/living with HIV as a result of the COVID-19 pandemic. Social media, chatbots, and mobile apps have been studied across a number of clinical and public health settings, including patient outreach, screening and monitoring; intervention delivery; remote vital sign assessment; as well for providing treatment recommendations and retaining patients in care. COVID-19 will continue to impact the way that technologies are integrated into HIV clinical care and research long after the removal of social distancing policies, making it important to begin investing in the knowledge, infrastructure, and implementation of these technologies now to be prepared for the future. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32440971/ doi: 10.1007/s10461-020-02924-z id: cord-034036-1wigu3i3 author: Yu, Changhao title: Current epidemiological and etiological characteristics and treatment of seizures or epilepsy in patients with HIV infection date: 2020-10-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Seizures or epilepsy is one of the common serious complications in patients with advanced human immunodeficiency virus (HIV) infection or diagnosed with immune deficiency syndrome, with higher incidence and prevalence than in the general population. Generalized seizures are the most common type in the patients. Opportunistic infections are a stereotypical predisposing factor for seizures in HIV patients, but a variety of pathogenic factors can also be found in these patients, such as metabolic perturbation and drug-drug interactions. The diagnostic criteria for seizures in these patients are the same as those in the general population. As HIV patients with seizures need to take both antivirals and antiepileptic drugs, the risk of drug-drug interactions is greatly increased, and the side effects of drugs may also become more prominent. At present, most experience in antiepileptic drug usage has come from the general population, and there is still a lack of guidance of antiepileptic drug use in special groups such as the HIV-infected people. Unlike the old-generation drugs that involve metabolisms through CYP450, the first-line antiepileptic drugs usually bypass CYP450, thus having less drug-drug interactions. In this review, we summarize the recent research progress on the above-mentioned widely discussed topics and make a prospect on future research direction. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575336/ doi: 10.1186/s42494-020-00028-8 id: cord-292286-ygomb3oi author: Zakaryan, Hovakim title: Flavonoids: promising natural compounds against viral infections date: 2017-05-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Flavonoids are widely distributed as secondary metabolites produced by plants and play important roles in plant physiology, having a variety of potential biological benefits such as antioxidant, anti-inflammatory, anticancer, antibacterial, antifungal and antiviral activity. Different flavonoids have been investigated for their potential antiviral activities and several of them exhibited significant antiviral properties in in vitro and even in vivo studies. This review summarizes the evidence for antiviral activity of different flavonoids, highlighting, where investigated, the cellular and molecular mechanisms of action on viruses. We also present future perspectives on therapeutic applications of flavonoids against viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/28547385/ doi: 10.1007/s00705-017-3417-y id: cord-027860-s97hdhh6 author: Zeimet, Anthony title: Infectious Diseases date: 2020-06-22 words: 28925.0 sentences: 1728.0 pages: flesch: 45.0 cache: ./cache/cord-027860-s97hdhh6.txt txt: ./txt/cord-027860-s97hdhh6.txt summary: Although common upper respiratory bacterial pathogens, such as Moraxella (Branhamella) catarrhalis, Streptococcus pneumoniae, and Haemophilus influenzae, may be isolated from patients with acute bronchitis, their relevance is questionable because these bacteria can be present in the respiratory tract of healthy individuals. In the treatment of Bordetella pertussis, early administration of a macrolide antibiotic and patient isolation will likely decrease coughing paroxysms and limit spread of disease (Braman, 2006) (SOR: A). Risk factors for Pseudomonas infection include severe structural lung disease (e.g., bronchiectasis) and recent antibiotic therapy, health care-associated exposures or stay in hospital (especially in the ICU). Patients who present with severe infection or whose infection is progressing despite empiric antibiotic therapy should be treated more aggressively; the treatment strategy should be based on results of appropriate Gram stain, culture, and drug susceptibility analysis. For suspected MRSA skin infections, oral treatment options include trimethoprim-sulfamethoxazole, clindamycin, and doxycycline of purulent material when performing incision and drainage in the event that the patient fails to improve and antibiotic coverage becomes necessary. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315328/ doi: 10.1016/b978-1-4377-1160-8.10016-8 id: cord-104162-fe51v2pt author: Zhang, Chiyu title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Base order, not composition, best reflects local evolutionary pressure for folding of single-stranded nucleic acids. The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 “Achilles heel,” the signal can be targeted by a recently described antiviral compound (NSC 260594) or by synthetic oligonucleotides. Thus, a conserved base-order-rich region of HIV-1 may facilitate therapeutic attack. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential “Achilles heels” for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The region of the FSE scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein. url: https://doi.org/10.1101/2020.10.22.343673 doi: 10.1101/2020.10.22.343673 id: cord-000077-d441jam3 author: Zhang, Hao-Jie title: The Y271 and I274 Amino Acids in Reverse Transcriptase of Human Immunodeficiency Virus-1 Are Critical to Protein Stability date: 2009-07-03 words: 5426.0 sentences: 267.0 pages: flesch: 54.0 cache: ./cache/cord-000077-d441jam3.txt txt: ./txt/cord-000077-d441jam3.txt summary: Reverse transcriptase (RT) of human immunodeficiency virus (HIV)-1 plays a key role in initiating viral replication and is an important target for developing anti-HIV drugs. Our native gel analysis indicated that the mutations at 271 and 274 amino acids might cause conformational changes, leading to the formation of higher order oligomers instead of dimers, resulting in increased protein instability and susceptibility to viral protease. As shown in Fig. 3A , similar levels of Pr160 gag-pol , Gag protein (Pr55 Gag ) and capsid protein p24 (CA p24) were found in cells transfected with the wild type or mutant constructs, indicating that the expression and stability of RT precursor protein were not affected by the mutations. To study if the RTs in the viral particles of Y271A and I274A mutants were degraded by proteolysis that made them undetectable, pseudoviruses of wild type and mutants were generated in the presence or absence of indinavir, a highly specific inhibitor of HIV-1 protease. abstract: Reverse transcriptase (RT) of human immunodeficiency virus (HIV)-1 plays a key role in initiating viral replication and is an important target for developing anti-HIV drugs. Our previous study showed that two mutations (Y271A and I274A) in the turn RT (Gln(269)-Arg(277)) abrogated viral replication, but the replication capacity and RT activity was discordant. In this study, we further investigated why alanine substitutions at these two sites would affect viral replication. We found that both RT activity and RT protein were almost undetectable in viral particles of these two mutants, although the Pr160(gag-pol) mutants were properly expressed, transported and incorporated. Using protease inhibition assay, we demonstrated a correlation between the degradation of the RT mutants and the activity of viral protease. Our native gel analysis indicated that the mutations at 271 and 274 amino acids might cause conformational changes, leading to the formation of higher order oligomers instead of dimers, resulting in increased protein instability and susceptibility to viral protease. Thus, residues 271 and 274 are critical to RT stability and resistance to viral protease. The conservation of the two amino acid residues among different strains of HIV-1 lent further support to this conclusion. The knowledge gained here may prove useful in drug design. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701634/ doi: 10.1371/journal.pone.0006108 id: cord-342076-3a6aky7i author: Zhang, Lei title: Describing the Chinese HIV Surveillance System and the Influences of Political Structures and Social Stigma date: 2012-09-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: China’s public health surveillance system for HIV was established in late 1980s and has evolved significantly during the past three decades. With the gradually changing mode of HIV transmission from sharing of intravenous injecting equipment to sexual exposure and the rapid spread of HIV infection among Chinese homosexual men in recent years, an efficient and comprehensive population-level surveillance system for describing epidemics trends and risk behaviours associated with HIV acquisition are essential for effective public health interventions for HIV. The current review describes the overall strength of the Chinese HIV surveillance system and its structural weaknesses from a political and social perspective. The HIV surveillance system in China has undergone substantial revamping leading to a comprehensive, timely and efficient reporting system. However, large data gaps and lack of quality control and sharing of information obstruct the full performance of the system. This is largely due to fragmented authoritarianism brought about by the underlying political structure. Social stigma and discrimination in health institutes are also key barriers for further improvements of HIV diagnosis and surveillance in China. url: https://doi.org/10.2174/1874613601206010163 doi: 10.2174/1874613601206010163 id: cord-350443-ca5avyjf author: Zhang, Lei title: Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy date: 2012-02-16 words: 7958.0 sentences: 383.0 pages: flesch: 49.0 cache: ./cache/cord-350443-ca5avyjf.txt txt: ./txt/cord-350443-ca5avyjf.txt summary: This study reviews trends in notifiable infectious diseases in China, in their historical context, discusses the current epidemiological state of these infections and their implications for disease surveillance and public health interventions. The total number of diagnosed and death cases were estimated by multiplying morbidity and mortality rates by the overall Chinese population in the study years. In 2008, the three most frequently reported disease types included viral hepatitis (38.3%), bacterial infections (33.3%) and STIs and HIV (9.8%), which account for 5.4, 4.8 and 1.4 million diagnosed cases respectively during the period 2005-2008 (Table 1) . Second, the rapid rise in the number of notified cases of STIs, especially HIV infection, and viral hepatitis in China is associated with growth of the sex industry, increasingly frequent risky sexual behaviours and an increasing number of sexual partners in the general Chinese population. abstract: This study aimed to analyse trends in notifiable infectious diseases in China, in their historical context. Both English and Chinese literature was searched and diseases were categorised according to the type of disease or transmission route. Temporal trends of morbidity and mortality rates were calculated for eight major infectious diseases types. Strong government commitment to public health responses and improvements in quality of life has led to the eradication or containment of a wide range of infectious diseases in China. The overall infectious diseases burden experienced a dramatic drop during 1975–1995, but since then, it reverted and maintained a gradual upward trend to date. Most notifiable diseases are contained at a low endemic level; however, local small-scale outbreaks remain common. Tuberculosis, as a bacterial infection, has re-emerged since the 1990s and has become prevalent in the country. Sexually transmitted infections are in a rapid, exponential growth phase, spreading from core groups to the general population. Together human immunodeficiency virus (HIV), they account for 39% of all death cases due to infectious diseases in China in 2008. Zoonotic infections, such as severe acute respiratory syndrome (SARS), rabies and influenza, pose constant threats to Chinese residents and remain the most deadly disease type among the infected individuals. Therefore, second-generation surveillance of behavioural risks or vectors associated with pathogen transmission should be scaled up. It is necessary to implement public health interventions that target HIV and relevant coinfections, address transmission associated with highly mobile populations, and reduce the risk of cross-species transmission of zoonotic pathogens. url: https://doi.org/10.1371/journal.pone.0031076 doi: 10.1371/journal.pone.0031076 id: cord-339796-gccnvh0z author: Zhang, Si Min title: Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins date: 2015-07-31 words: 9073.0 sentences: 403.0 pages: flesch: 45.0 cache: ./cache/cord-339796-gccnvh0z.txt txt: ./txt/cord-339796-gccnvh0z.txt summary: The MPER in the human immunodeficiency virus type I (HIV-1) envelope protein (Env) interacts with the lipid bilayers through a cluster of tryptophan (Trp) residues and a C-terminal cholesterol-interacting motif. We found that elimination of the membrane-active elements in MPER peptides, namely, penta Trp→alanine (Ala) substitutions and the disruption of the C-terminal cholesterol-interacting motif through deletion inhibited the anti-viral effect against the pseudotyped HIV-1. The secondary structure study revealed that the penta-Trp→Ala substitutions also increased the helical content in the MPER sequence, which prompted us to study the biological relevance of such mutations in pre-fusion Env. We observed that Ala mutations of Trp664, Trp668 and Trp670 in MPER moderately lowered the intracellular and intraviral contents of Env while significantly elevating the content of another viral structural protein, p55/Gag and its derivative p24/capsid. Here we describe the roles of the Trp residues in the membrane-active MPER sequence in anti-HIV fusion inhibitor design and a surprising role in the biosynthesis of viral structural proteins. abstract: The membrane proximal external region (MPER) is a highly conserved membrane-active region located at the juxtamembrane positions within class I viral fusion glycoproteins and essential for membrane fusion events during viral entry. The MPER in the human immunodeficiency virus type I (HIV-1) envelope protein (Env) interacts with the lipid bilayers through a cluster of tryptophan (Trp) residues and a C-terminal cholesterol-interacting motif. The inclusion of the MPER N-terminal sequence contributes to the membrane reactivity and anti-viral efficacy of the first two anti-HIV peptidyl fusion inhibitors T20 and T1249. As a type I transmembrane protein, Env also interacts with the cellular membranes during its biosynthesis and trafficking. Here we investigated the roles of MPER membrane-active sequences during both viral entry and assembly, specifically, their roles in the design of peptidyl fusion inhibitors and the biosynthesis of viral structural proteins. We found that elimination of the membrane-active elements in MPER peptides, namely, penta Trp→alanine (Ala) substitutions and the disruption of the C-terminal cholesterol-interacting motif through deletion inhibited the anti-viral effect against the pseudotyped HIV-1. Furthermore, as compared to C-terminal dimerization, N-terminal dimerization of MPER peptides and N-terminal extension with five helix-forming residues enhanced their anti-viral efficacy substantially. The secondary structure study revealed that the penta-Trp→Ala substitutions also increased the helical content in the MPER sequence, which prompted us to study the biological relevance of such mutations in pre-fusion Env. We observed that Ala mutations of Trp664, Trp668 and Trp670 in MPER moderately lowered the intracellular and intraviral contents of Env while significantly elevating the content of another viral structural protein, p55/Gag and its derivative p24/capsid. The data suggest a role of the gp41 MPER in the membrane-reactive events during both viral entry and budding, and provide insights into the future development of anti-viral therapeutics. url: https://doi.org/10.1371/journal.pone.0134851 doi: 10.1371/journal.pone.0134851 id: cord-260071-z29b30sd author: Zhong, Yu title: Highly potent anti-HIV-1 activity isolated from fermented Polygonum tinctorium Aiton date: 2005-03-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A water-soluble extract of fermented Polygonum tinctorium Aiton (Polygonaceae) called Sukumo, exhibited a potent inhibitory activity against HIV type 1 in vitro. The extract potently suppressed acute HIV-1 (III(B)) infection in MT-4 cells with EC(50) values of 0.5 μg/ml but exhibited low cytotoxicity to MT-4 cells even at a high concentration (CC(50) > 1000 μg/ml). It also inhibited giant cell formation in co-cultures of HIV-infected cells and uninfected Molt-4 cells. Sukumo extract was found to interact with both the viral envelope glycoprotein and cellular receptors, thus blocking virus-cell binding and virus-induced syncytium formation. There was a good correlation between the extract's anti-HIV-1 activity and its inhibitory effects on HIV-1 binding. It also suppressed replication of herpes simplex virus type 1 in Vero cells with an EC(50) of 11.56 μg/ml. On the other hand, there was no appreciable activity against influenza A virus, poliovirus or SARS corona virus when tested at concentrations ranging from 3.2–400 μg/ml as shown by microscopic image analysis for cytopathic effect (CPE). Physico-chemical studies revealed that the anti-HIV activity in the extract was essentially maintained after boiling at 100 °C in 1N HCl or 1N NaOH, and after treatment with 100 mM NaIO(4). The inhibitory activity of the extract was also not reduced after pronase digestion. The active factor in the extract is likely to be a novel compound(s) having a polyanionic substructure and a molecular weight of 10,000–50,000. url: https://www.ncbi.nlm.nih.gov/pubmed/15911029/ doi: 10.1016/j.antiviral.2005.02.003 id: cord-281941-97t45w73 author: Zhou, Daijun title: Cyclophilin A and viral infections date: 2012-08-10 words: 3410.0 sentences: 184.0 pages: flesch: 43.0 cache: ./cache/cord-281941-97t45w73.txt txt: ./txt/cord-281941-97t45w73.txt summary: A number of reports have demonstrated that CyPA plays a critical role in the successful replication of viruses such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), etc. Thus, CyPA plays a suppressive role in the development of CD4 + T cell responses through its interaction with Itk. In recent years many studies showed that CyPA was involved in the pathogenesis of viral infection [8] , cardiovascular disease [9] and cancer [10] . The viral protein R (Vpr) of HIV-1 is the major virion-associated accessory protein that affects a number of biological functions in the retroviral life cycle, including promotion of the transport of the pre-integration complex into the nucleus and the induction of G2 host cell cycle arrest [20] . Cyclophilin A regulates HIV-1 infectivity, as demonstrated by gene targeting in human T cells Critical role of cyclophilin A and its prolyl-peptidyl isomerase activity in the structure and function of the hepatitis C virus replication complex abstract: Abstract Cyclophilin A (CyPA) is a peptidyl-prolyl cis/trans isomerase originally identified as the target of the immunosuppressive drug cyclosporine A. A number of reports have demonstrated that CyPA plays a critical role in the successful replication of viruses such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), etc. However, recent studies demonstrated that CyPA also possesses a repressive effect on the replication of some viruses like Influenza A virus and rotavirus. Moreover, CyPA could also regulate host IFN-I response to viral infections. Together, these evidences showed diverse roles of CyPA in viral infection. url: https://doi.org/10.1016/j.bbrc.2012.07.024 doi: 10.1016/j.bbrc.2012.07.024 id: cord-353012-rxhi8wd2 author: Zhou, Nan title: Glycopeptide Antibiotics Potently Inhibit Cathepsin L in the Late Endosome/Lysosome and Block the Entry of Ebola Virus, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) date: 2016-03-07 words: 6412.0 sentences: 334.0 pages: flesch: 53.0 cache: ./cache/cord-353012-rxhi8wd2.txt txt: ./txt/cord-353012-rxhi8wd2.txt summary: Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Considering that the inhibitory dose of teicoplanin on the activity of cathepsin L is higher than that required for Ebola virus infection inhibition, a cell viability assay was performed to confirm that the inhibitory effect is not due to cytotoxicity (Fig. 6C) . Ebola trVLP system (28) , which can simulate the life cycle of wild-type Ebola viruses to a large extent, was applied to investigate whether teicoplanin and its glycopeptide antibiotic homologs dalbavancin, oritavancin, telavancin, and vancomycin can also inhibit the entry of Ebola trVLPs. Accordingly, the p4cis plasmid encoding Renilla luciferase, VP40, GP, and VP24 was transfected into HEK293T cells along with plasmids expressing T7 RNA polymerase, NP, VP35, VP30, and L viral proteins to produce Ebola trVLPs (Fig. 7A) . abstract: Ebola virus infection can cause severe hemorrhagic fever with a high mortality in humans. The outbreaks of Ebola viruses in 2014 represented the most serious Ebola epidemics in history and greatly threatened public health worldwide. The development of additional effective anti-Ebola therapeutic agents is therefore quite urgent. In this study, via high throughput screening of Food and Drug Administration-approved drugs, we identified that teicoplanin, a glycopeptide antibiotic, potently prevents the entry of Ebola envelope pseudotyped viruses into the cytoplasm. Furthermore, teicoplanin also has an inhibitory effect on transcription- and replication-competent virus-like particles, with an IC(50) as low as 330 nm. Comparative analysis further demonstrated that teicoplanin is able to block the entry of Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) envelope pseudotyped viruses as well. Teicoplanin derivatives such as dalbavancin, oritavancin, and telavancin can also inhibit the entry of Ebola, MERS, and SARS viruses. Mechanistic studies showed that teicoplanin blocks Ebola virus entry by specifically inhibiting the activity of cathepsin L, opening a novel avenue for the development of additional glycopeptides as potential inhibitors of cathepsin L-dependent viruses. Notably, given that teicoplanin has routinely been used in the clinic with low toxicity, our work provides a promising prospect for the prophylaxis and treatment of Ebola, MERS, and SARS virus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26953343/ doi: 10.1074/jbc.m116.716100 id: cord-258167-jqm3qyfm author: Zhou, Peng title: Immunogenicity difference between the SARS coronavirus and the bat SARS-like coronavirus spike (S) proteins date: 2009-09-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract SARS-like coronavirus (SL-CoV) in bats have a similar genomic organization to the human SARS-CoV. Their cognate gene products are highly conserved with the exception of the N-terminal region of the S proteins, which have only 63–64% sequence identity. The N-terminal region of coronavirus S protein is responsible for virus–receptor interaction. In this study, the immunogenicity of the SL-CoV S protein (SSL) was studied and compared with that of SARS-CoV (SSARS). DNA immunization in mice with SSL elicited a high titer of antibodies against HIV-pseudotyped SSL. The sera had low cross-reactivity, but no neutralization activity, for the HIV-pseudotyped SSARS. Studies using wild bat sera revealed that it is highly likely that the immunodominant epitopes overlap with the major neutralizing sites of the SL-CoV S protein. These results demonstrated that SL-CoV and SARS-CoV shared only a limited number of immunogenic epitopes in their S proteins and the major neutralization epitopes are substantially different. This work provides useful information for future development of differential serologic diagnosis and vaccines for coronaviruses with different S protein sequences. url: https://www.sciencedirect.com/science/article/pii/S0006291X09013527 doi: 10.1016/j.bbrc.2009.07.025 id: cord-255075-6azu6k3h author: Zhuang, Jianjian title: Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives date: 2020-05-12 words: 3141.0 sentences: 230.0 pages: flesch: 49.0 cache: ./cache/cord-255075-6azu6k3h.txt txt: ./txt/cord-255075-6azu6k3h.txt summary: Multiplexed efficient on-chip sample preparation 613 and sensitive amplification-free detection of Ebola virus A bead-based 689 immunofluorescence-assay on a microfluidic dielectrophoresis platform for rapid dengue virus 690 detection Fast and Parallel Detection of Four Ebola Virus Species on a Microfluidic-Chip-Based Portable 770 An integrated self-driven microfluidic device for rapid 781 detection of the influenza A (H1N1) virus by reverse transcription loop-mediated isothermal 782 amplification Paper-based RNA detection and 785 multiplexed analysis for Ebola virus diagnostics Multiplex microfluidic paper-based 805 immunoassay for the diagnosis of hepatitis C virus infection Simultaneous and automated detection of influenza A virus hemagglutinin H7 and H9 based on 965 magnetism and size mediated microfluidic chip A 1026 point of care platform based on microfluidic chip for nucleic acid extraction in less than 1 minute D: Schematic of a 1149 paper-based chip for the detection of HIV developed by Li et al. abstract: Massive viral outbreaks draw attention to viruses that have not been thoroughly studied or understood. In recent decades, microfluidic chips, known as “lab-on-a-chip”, appears as a promising tool for the detection of viruses. Here, we review the development of microfluidic chips that could be used in response to viral detection, specifically for viruses involved in more recent outbreaks. The advantages as well as the disadvantages of microfluidic systems are discussed and analyzed. We also propose ideas for future development of these microfluidic chips and we expect this advanced technology to be used in the future for viral outbreaks. url: https://doi.org/10.1016/j.bios.2020.112291 doi: 10.1016/j.bios.2020.112291 id: cord-318363-1mv5j4w2 author: Zvolensky, Michael J. title: Psychological, addictive, and health behavior implications of the COVID-19 pandemic date: 2020-08-27 words: 15836.0 sentences: 701.0 pages: flesch: 39.0 cache: ./cache/cord-318363-1mv5j4w2.txt txt: ./txt/cord-318363-1mv5j4w2.txt summary: Additional risk factors for the development or exacerbation of PTSD symptoms include a prior history of trauma or mental health disturbances, depressed or anxious mood, significant concurrent life stressors (e.g., financial problems, job loss, relationship stress), low social connectedness or support, sleep disturbance, substance use, and emotional numbing or detachment (Colvonen, Straus, Acheson, & Gehrman, 2019; Cusack et al., 2019; Germain, McKeon, & Campbell, 2017; Hancock & Bryant, 2018; Shalev et al., 2019; Steenkamp et al., 2017; Vujanovic & Back, 2019) . That is, a specific type of individual difference factor like anxiety sensitivity is linked to a particular type of problem (e.g., anxiety disorder, worsening of a chronic respiratory illness, severity of hazardous drinking) via a specified mediating process (e.g., smoking, sleep disruption) in the context of certain moderating variables (e.g., higher levels of COVID-19 stress burden). abstract: • The public health impact of COVID-19 on psychological symptoms and disorders, addiction, and health behavior is substantial and ongoing. • An integrative COVID-19 stress-based model could be used to guide research focused on the stress-related burden of the pandemic. • This work could provide a theoretical and empirical knowledge base for future pandemics. url: https://doi.org/10.1016/j.brat.2020.103715 doi: 10.1016/j.brat.2020.103715 id: cord-254279-7u6ap4g4 author: Zwick, Michael B title: gp41: HIV's shy protein date: 2004 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The first X-ray crystal structures of gp41, the protein that mediates fusion of HIV-1 to target cells, were solved in the mid-1990s. The structures provide a foundation for understanding viral entry and the mechanism of action of compounds that block fusion. The first fusion inhibitor has recently entered the clinic, and the hope is that more potent and broadly active compounds, based on molecular design, will follow. url: https://www.ncbi.nlm.nih.gov/pubmed/14760422/ doi: 10.1038/nm0204-133 id: cord-284523-lknyehsa author: da Mata, Élida Cleyse Gomes title: Antiviral activity of animal venom peptides and related compounds date: 2017-01-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viruses exhibit rapid mutational capacity to trick and infect host cells, sometimes assisted through virus-coded peptides that counteract host cellular immune defense. Although a large number of compounds have been identified as inhibiting various viral infections and disease progression, it is urgent to achieve the discovery of more effective agents. Furthermore, proportionally to the great variety of diseases caused by viruses, very few viral vaccines are available, and not all are efficient. Thus, new antiviral substances obtained from natural products have been prospected, including those derived from venomous animals. Venoms are complex mixtures of hundreds of molecules, mostly peptides, that present a large array of biological activities and evolved to putatively target the biochemical machinery of different pathogens or host cellular structures. In addition, non-venomous compounds, such as some body fluids of invertebrate organisms, exhibit antiviral activity. This review provides a panorama of peptides described from animal venoms that present antiviral activity, thereby reinforcing them as important tools for the development of new therapeutic drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/28074089/ doi: 10.1186/s40409-016-0089-0 id: cord-259233-smmhhroe author: de Armas‐Rillo, Laura title: Membrane dynamics associated with viral infection date: 2016-01-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Viral replication and spreading are fundamental events in the viral life cycle, accounting for the assembly and egression of nascent virions, events that are directly associated with viral pathogenesis in target hosts. These processes occur in cellular compartments that are modified by specialized viral proteins, causing a rearrangement of different cell membranes in infected cells and affecting the ER, mitochondria, Golgi apparatus, vesicles and endosomes, as well as processes such as autophagic membrane flux. In fact, the activation or inhibition of membrane trafficking and other related activities are fundamental to ensure the adequate replication and spreading of certain viruses. In this review, data will be presented that support the key role of membrane dynamics in the viral cycle, especially in terms of the assembly, egression and infection processes. By defining how viruses orchestrate these events it will be possible to understand how they successfully complete their route of infection, establishing viral pathogenesis and provoking disease. © 2015 The Authors Reviews in Medical Virology Published by John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/26817660/ doi: 10.1002/rmv.1872 id: cord-308916-6p2qutc5 author: le Roux, David M. title: Community-acquired pneumonia in children — a changing spectrum of disease date: 2017-09-21 words: 4936.0 sentences: 213.0 pages: flesch: 33.0 cache: ./cache/cord-308916-6p2qutc5.txt txt: ./txt/cord-308916-6p2qutc5.txt summary: New conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae have contributed to decreases in radiologic, clinical and complicated pneumonia cases and have reduced hospitalization and mortality. In a review of four randomized controlled trials and two case-control studies of Haemophilus influenzae type B conjugate vaccination in high-burden communities, the vaccination was associated with an 18% decrease in radiologic pneumonia [13] . However, given the high mortality from pneumonia in low-and middle-income countries, the lack of easy access to care, and the high prevalence of risk factors for severe disease, revised World Health Organization pneumonia guidelines still recommend antibiotic treatment for all children who meet the WHO pneumonia case definitions [80] . Effectiveness of heptavalent pneumococcal conjugate vaccine in children younger than 5 years of age for prevention of pneumonia: updated analysis using World Health Organization standardized interpretation of chest radiographs abstract: Pneumonia remains the leading cause of death in children outside the neonatal period, despite advances in prevention and management. Over the last 20 years, there has been a substantial decrease in the incidence of childhood pneumonia and pneumonia-associated mortality. New conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae have contributed to decreases in radiologic, clinical and complicated pneumonia cases and have reduced hospitalization and mortality. The importance of co-infections with multiple pathogens and the predominance of viral-associated disease are emerging. Better access to effective preventative and management strategies is needed in low- and middle-income countries, while new strategies are needed to address the residual burden of disease once these have been implemented. url: https://www.ncbi.nlm.nih.gov/pubmed/29043417/ doi: 10.1007/s00247-017-3827-8 id: cord-002774-tpqsjjet author: nan title: Section II: Poster Sessions date: 2017-12-01 words: 83515.0 sentences: 5162.0 pages: flesch: 54.0 cache: ./cache/cord-002774-tpqsjjet.txt txt: ./txt/cord-002774-tpqsjjet.txt summary: Results: The CHIP Framework The CHIP framework aims to improve the health and wellness of the urban communities served by St. Josephs Health Centre through four intersecting pillars: • Raising Community Voices provides an infrastructure and process that supports community stakeholder input into health care service planning, decision-making, and delivery by the hospital and across the continuum of care; • Sharing Reciprocal Capacity promotes healthy communities through the sharing of our intellectual and physical capacity with our community partners; • Cultivating Integration Initiatives facilitates vertical, horizontal, and intersectoral integration initiatives in support of community-identified needs and gaps; and • Facilitating Healthy Exchange develops best practices in community integration through community-based research, and facilitates community voice in informing public policy. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711696/ doi: 10.1093/jurban/jti137 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-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233304.0 sentences: 13171.0 pages: flesch: 54.0 cache: ./cache/cord-010092-uftc8inx.txt txt: ./txt/cord-010092-uftc8inx.txt summary: Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169345/ doi: 10.1111/vox.12792 id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 words: 230193.0 sentences: 13234.0 pages: flesch: 55.0 cache: ./cache/cord-010119-t1x9gknd.txt txt: ./txt/cord-010119-t1x9gknd.txt summary: Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/ doi: 10.1111/trf.14286 id: cord-010310-jqh75340 author: nan title: Next Generation Technology for Epidemic Prevention and Control: Data-Driven Contact Tracking date: 2018-12-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Contact tracking is one of the key technologies in prevention and control of infectious diseases. In the face of a sudden infectious disease outbreak, contact tracking systems can help medical professionals quickly locate and isolate infected persons and high-risk individuals, preventing further spread and a large-scale outbreak of infectious disease. Furthermore, the transmission networks of infectious diseases established using contact tracking technology can aid in the visualization of actual virus transmission paths, which enables simulations and predictions of the transmission process, assessment of the outbreak trend, and further development and deployment of more effective prevention and control strategies. Exploring effective contact tracking methods will be significant. Governments, academics, and industries have all given extensive attention to this goal. In this paper, we review the developments and challenges of current contact tracing technologies regarding individual and group contact from both static and dynamic perspectives, including static individual contact tracing, dynamic individual contact tracing, static group contact tracing, and dynamic group contact tracing. With the purpose of providing useful reference and inspiration for researchers and practitioners in related fields, directions in multi-view contact tracing, multi-scale contact tracing, and AI-based contact tracing are provided for next-generation technologies for epidemic prevention and control. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176034/ doi: 10.1109/access.2018.2882915 id: cord-014608-g3p19coe author: nan title: Pneumococcal colonization and carriage date: 2014-12-01 words: 21648.0 sentences: 1365.0 pages: flesch: 50.0 cache: ./cache/cord-014608-g3p19coe.txt txt: ./txt/cord-014608-g3p19coe.txt summary: Background and Aims: Data on the nasopharyngeal carriage prevalence of Streptococcus pneumoniae across age groups are important to help predict the impact of introducing pneumococcal conjugate vaccines (PCVs) into routine vaccination programmes, given their important indirect effect. Methods: Nasopharyngeal swabs were collected from well children 3 months to 5Y of age from Karachi, Pakistan as part of a pneumococcal carriage study to evaluate PCV-10 impact. Methods: To determine pneumococcal colonization, we recruited a convenience sample of residents of all ages from 8 rural villages and children aged <5 years at 2 urban pediatric clinics annually during 2008-2012; we determined their PCV13 vaccination status and obtained nasopharyngeal swab specimens. No conflict of interest ISPPD-9 / pneumonia 2014 Mar 9-13;3:1-286 Background: Using nasopharyngeal carriage as a marker of vaccine impact, pneumococcal colonisation and its relation to invasive disease and demographic attributes were examined in children, their parents, and older adults in the UK following the introduction of PCV7 and prior to PCV13. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205665/ doi: 10.1007/bf03399438 id: cord-015324-y44sfr0c author: nan title: Scientific Programme date: 2007-09-01 words: 197618.0 sentences: 12774.0 pages: flesch: 53.0 cache: ./cache/cord-015324-y44sfr0c.txt txt: ./txt/cord-015324-y44sfr0c.txt summary: In order to further validate this approach, we performed a prospective randomized open-label multicenter trial in 41 low-risk pediatric renal transplant recipients (12 f, 29 m; mean age 10.1 yrs; range, 3.4 to 17.8) on CsA (target trough level 100-200 ng/ml), MMF (1200 mg/m 2 per day) and methylprednisolone (3) (4) mg/m 2 per day), who were randomly assigned >1 year posttransplant to continue steroids or to withdraw over a period of 3 months. We evaluated MMF in 15 children with LN, 11 F/4 M, mean age: 12.4±3.9 yrs, proteinuria >3 g/day, decreased C3 and increased anti-dsDNA serum levels, normal renal function. Patients and methods: 91 children and adolescents (60 male, 31 female, mean age at transplantation 9.7±5.2 years) with stable renal function and observation period exceeding 6 months were included. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101932/ doi: 10.1007/s00467-007-0558-3 id: cord-015372-76xvzvdg author: nan title: National scientific medical meeting 1996 abstracts date: 1996 words: 36596.0 sentences: 2204.0 pages: flesch: 53.0 cache: ./cache/cord-015372-76xvzvdg.txt txt: ./txt/cord-015372-76xvzvdg.txt summary: One, two and five-year survival rates were examined; age at diagnosis and lesion type were extremely significant factors in relation to patient outcome. Patients'' age, sex, risk group, CDC stage, CD4 count, indication for therapy, complication rate and response to treatment are described. Fifty-eight patients (34 male, 24 female) ranging in age from 15 to 65 years (Mean + SD = 28.4 + 10.8) were included in the study. Among these 48 patients (mean age 68.0+12.7), after controlling for age and for the duration and continuity of subsequent antipsychotic treatment, increasing duration of initially untreated psychosis was associated with greater severity of negative symptoms (p<0.005) and with lower scores on the MMSE (p<0.05) but not with executive dysfunction on the EXIT (p=0.3). Conclusion Although not a population based study, care of IDDM in Ireland is almost totally hospital clinic based Cigarette smoking is identified as the major problem to be addressed Patients with diabetes meltitus (DM) are at a higher risk of developing vascular complications, including coronary artery disease (CAD). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103226/ doi: 10.1007/bf02945204 id: cord-015936-4fwkf8fn author: nan title: SUBJECT INDEX, volumes 123-130 date: 2005-11-04 words: 69.0 sentences: 10.0 pages: flesch: 78.0 cache: ./cache/cord-015936-4fwkf8fn.txt txt: ./txt/cord-015936-4fwkf8fn.txt summary: key: cord-015936-4fwkf8fn authors: nan title: SUBJECT INDEX, volumes 123-130 date: 2005-11-04 journal: J Virol Methods DOI: 10.1016/s0166-0934(05)00346-0 sha: doc_id: 15936 cord_uid: 4fwkf8fn nan HIV; 2 LTR circles; New marker (125) 11 HIV antigen/antibody combined assay; HIV; Serology; HIV-1 p24 antigen assay (127) (127) (128) (128) 67 Yeast expression; Pichia pastoris; SARS-CoV; N protein (130) 83 enzyme analysis; Flaviviruses; RT-PCR abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120062/ doi: 10.1016/s0166-0934(05)00346-0 id: cord-016829-37i1bn9m author: nan title: Bilateral and Multilateral Financing of HIV/AIDS Programs: The World Bank, the International Monetary Fund, the Global Fund, Bilateral Donors and the Private Sector date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter examines the operations of the World Bank (a multilateral development institution), the International Monetary Fund (a multilateral financial institution) and the Global Fund to Fight AIDS, Tuberculosis and Malaria (a multilateral fundraising and financing institution) to fight HIV/AIDS. We also examine the role of bilateral donors and the private sector in financing the fight against HIV/AIDS. We examine the relationships among bilateral donors and international organizations, what distinguishes their roles in the global HIV/AIDS pandemic and the extent to which their activities overlap. In addition, we consider how funding strategies and parameters may affect the effectiveness of AIDS funding in preventing transmission and providing treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121240/ doi: 10.1007/978-3-540-78392-3_7 id: cord-017675-in9r33ww author: nan title: The Way Forward: Prevention, Treatment and Human Rights date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: There now is a considerable body of evidence to support the view that an effective HIV/AIDS strategy integrates prevention, treatment and human rights. In this chapter, we emphasize the importance of each of these aspects and draw upon the conclusions reached in previous chapters to map out the future of HIV/AIDS. While medicine and science have a crucial role to play in addressing pandemics, whether slow-moving (like HIV/AIDS) or fast-moving (like influenza), the social, legal, political, financial and economic ramifications of pandemics can not be ignored. Well-considered social, legal, political and financial strategies are essential in order to address any pandemic effectively. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122313/ doi: 10.1007/978-3-540-78392-3_9 id: cord-018440-qugmnolo author: nan title: When a Diagnosis Is Reportable date: 2008 words: 2202.0 sentences: 113.0 pages: flesch: 57.0 cache: ./cache/cord-018440-qugmnolo.txt txt: ./txt/cord-018440-qugmnolo.txt summary: In many states, once the HHS is notified of a reportable disease such as confirmed HIV infection, a health investigator representing that state''s HHS will become The Law involved in the case. If a patient has not personally notified their partners of their risk for HIV infection, the investigator may then contact all divulged sexual partners for the need to pursue testing and potential treatment for HIV. Anyone who has sexual relations with or engages in other risk behaviors with Scott is at risk for contracting HIV and syphilis, and protecting the health and welfare of those contact persons takes precedent over maintaining Scott''s confidentiality. Once Scott''s diagnosis is reported, he will meet with a health investigator who will record the names of his contacts and notify them of their exposure to syphilis and HIV. Scott should be informed that his diagnosis will be reported to the public health department and that he will be asked to meet with an investigator and give the names of his sexual contacts. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123314/ doi: 10.1007/978-1-60327-246-9_16 id: cord-019347-tj3ye1mx author: nan title: ABSTRACT BOOK date: 2010-02-19 words: 107926.0 sentences: 6940.0 pages: flesch: 53.0 cache: ./cache/cord-019347-tj3ye1mx.txt txt: ./txt/cord-019347-tj3ye1mx.txt summary: Method:Case Report:A 15y/o w/f athlete presented with a two month history of recurrent hives and angioedema which she associated with ingestion of Halloween candy .One week before evaluation she had hives with Coconut as well.Her history was othewise unremarkable except for recurrent UTI''S, annual sinusitis, pneumonia in 1998 as well as migraines.She denied sexual activity.Her physical exam was normal.Results:An evaluation for autoimmune disease revealed normal ESR, ANA, DSDNA, mono and hepatitis serology as well as lyme titers however her CH50 was low17u/ml(normal 26-58U/ml)and evaluation of complement revealed c4 14mg/dl(normal 16-47mg//dl)and c2 <1.3mg/dl(normal 1.6-3.5mg/dl)with normal c3, c5-c9.Her father had nor-malc4 but c2 was 1.4mg/dl (normal 1.6-3.5mg/dl)Her sister had c2 of 1.5mg/dl and normal c4 and her mother had normal c2 and c4.Her workup included positive prick skin test to ragweed, ash and grass and she was started on Rhinocort and Clarinex seasonally.She has been followed for one year with resolution of hives and is asymptomatic.Her diagnosis had been confirmed by a pediatric rheumatologist.Conclusion;We present an atypical case of C2 complement deficiency in an currently asymptomatic individual. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129269/ doi: 10.1016/s1081-1206(10)61294-x id: cord-019964-9leljj8j author: nan title: Recent research in infectious disease date: 2005-01-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133612/ doi: 10.1016/j.jinf.2004.11.005 id: cord-020010-q58x6xb0 author: nan title: 19th ICAR Abstracts: date: 2006-03-13 words: 46663.0 sentences: 2181.0 pages: flesch: 44.0 cache: ./cache/cord-020010-q58x6xb0.txt txt: ./txt/cord-020010-q58x6xb0.txt summary: In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133865/ doi: 10.1016/j.antiviral.2006.02.001 id: cord-020101-5rib7pe8 author: nan title: Cumulative Author Index for 2008 date: 2008-11-17 words: 2140.0 sentences: 126.0 pages: flesch: 29.0 cache: ./cache/cord-020101-5rib7pe8.txt txt: ./txt/cord-020101-5rib7pe8.txt summary: Cauliflower mosaic virus gene VI product N-terminus contains regions involved in resistance-breakage, self-association and interactions with movement protein Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus DC-SIGN enhances infection of cells with glycosylated West Nile virus in vitro and virus replication in human dendritic cells induces production of Increase in proto-oncogene mRNA transcript levels in bovine lymphoid cells infected with a cytopathic type 2 bovine viral diarrhea virus Complete genome sequence analysis of dengue virus type 2 isolated in Modulation of hepatitis B virus replication by expression of polymerasesurface fusion protein through splicing: Implications for viral persistence Induction of apoptosis in Vero cells by Newcastle disease virus requires viral replication, de-novo protein synthesis and caspase activation Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134142/ doi: 10.1016/s0168-1702(08)00367-5 id: cord-022633-fr55uod6 author: nan title: SAEM Abstracts, Plenary Session date: 2012-04-26 words: 147405.0 sentences: 8927.0 pages: flesch: 54.0 cache: ./cache/cord-022633-fr55uod6.txt txt: ./txt/cord-022633-fr55uod6.txt summary: Staff satisfaction was evaluated through pre/ post-shift and study surveys; administrative data (physician initial assessment (PIA), length of stay (LOS), patients leaving without being seen (LWBS) and against medical advice [LAMA] ) were collected from an electronic, real-time ED information system. Communication Background: The link between extended shift lengths, sleepiness, and occupational injury or illness has been shown, in other health care populations, to be an important and preventable public health concern but heretofore has not been fully described in emergency medical services (EMS Objectives: To assess the effect of an ED-based computer screening and referral intervention for IPV victims and to determine what characteristics resulted in a positive change in their safety. Objectives: Using data from longitudinal surveys by the American Board of Emergency Medicine, the primary objective of this study was to evaluate if resident self-assessments of performance in required competencies improve over the course of graduate medical training and in the years following. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159364/ doi: 10.1111/j.1553-2712.2012.01332.x id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 words: 188640.0 sentences: 9313.0 pages: flesch: 45.0 cache: ./cache/cord-022888-dnsdg04n.txt txt: ./txt/cord-022888-dnsdg04n.txt summary: Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. abstract: No Abtract url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163517/ doi: 10.1002/eji.200990224 id: cord-023017-k6edtg58 author: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 words: 65796.0 sentences: 3553.0 pages: flesch: 51.0 cache: ./cache/cord-023017-k6edtg58.txt txt: ./txt/cord-023017-k6edtg58.txt summary: 14/55 (25%) patients in AC who did not discontinue by week 24 received ribavirin dose reduction in comparison to 31/108 ( The clinical outcome in response to combination therapy for treatment of chronic hepatitis C virus (HCV) infection appears to be different for Caucasian versus African American patients. Over the period of combination therapy, most patients in which serum virus titers were reduced to non detectable levels had significant increases in T cell responses to HCV proteins. CHRONIC Background: Recent large prospective trials demonstrated that the combination therapy of interferon (1FN)-alphalribavirin significantly increased the ratio of a sustained virological response in patients with chronic hepatitis C in comparison with IFN monotherapy, especially in patients with high HCV-RNA titer and genotype lb. Results: Patients with chronic HCV infection showed higher MxA gene expression levels than healthy controls, indicating that hepatitis C virus induces IFN production. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165819/ doi: 10.1002/hep.1840380505 id: cord-023143-fcno330z author: nan title: Molecular aspects of viral immunity date: 2004-02-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167094/ doi: 10.1002/jcb.240591009 id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 words: 130043.0 sentences: 7330.0 pages: flesch: 54.0 cache: ./cache/cord-023346-8sqbqjm1.txt txt: ./txt/cord-023346-8sqbqjm1.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169255/ doi: 10.1111/j.1423-0410.2005.00652.x id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 words: 130046.0 sentences: 7333.0 pages: flesch: 54.0 cache: ./cache/cord-023354-f2ciho6o.txt txt: ./txt/cord-023354-f2ciho6o.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169300/ doi: 10.1111/j.1423-0410.2005.00654.x id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 words: 130049.0 sentences: 7334.0 pages: flesch: 54.0 cache: ./cache/cord-023364-ut56gczm.txt txt: ./txt/cord-023364-ut56gczm.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/ doi: 10.1111/j.1423-0410.2005.00651.x id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 words: 200999.0 sentences: 11528.0 pages: flesch: 44.0 cache: ./cache/cord-031907-ilhr3iu5.txt txt: ./txt/cord-031907-ilhr3iu5.txt summary: L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/ doi: 10.1080/20013078.2020.1784511 id: cord-286574-t9z2ynt5 author: nan title: Speaker presentations date: 2017-09-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://api.elsevier.com/content/article/pii/S0924857917303400 doi: 10.1016/s0924-8579(17)30340-0 id: cord-286711-nr6vnl9h author: nan title: Other viruses causing gastroenteritis date: 2003-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Publisher Summary Besides the viruses producing the majority of human viral gastroenteritis, other viruses infect more rarely but are sometimes able to cause epidemics. In particular, they cause chronic infection in the immunocompromised. Some of these viruses discussed in this chapter are toroviruses, picobirnaviruses, enteroviruses, human immunodeficiency virus (HIV), herpesviruses, and coronaviruses. Toroviruses make up a genus of the Coronaviridae family. They are a well-described cause of diarrhea in calves and horses but may also infect sheep, goats, and pigs. Picobirnaviruses are related to members of the Birnaviridae family. They are found in the feces of HIV-infected patients with diarrhea more frequently than in HIV-infected patients without diarrhea, but a virus-specific immune response was not measurable. The genus Enterovirus is of the Picornaviridae family. All enteroviruses infect man via the gastrointestinal tract where they have their first site of replication, probably in lymphoid tissues of the pharynx and gut. HIV, the causative agent of the acquired immunodeficiency syndrome (AIDS), is a member of the Lentivirus genus of the Retroviridae family. Cytomegalovirus (CMV) and herpes simplex viruses, members of the Herpesviridae family, are found as the cause of colitis and esophagitis, mainly in HIV-infected patients. Coronavirus is another genus of the Coronaviridae family. Coronaviruses infect the respiratory and gastrointestinal tracts. They are a recognized cause of the common cold in man. url: https://api.elsevier.com/content/article/pii/S0168706903090372 doi: 10.1016/s0168-7069(03)09037-2 id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 words: 26536.0 sentences: 3917.0 pages: flesch: 45.0 cache: ./cache/cord-340489-yo3cp5vs.txt txt: ./txt/cord-340489-yo3cp5vs.txt summary: Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. abstract: Zur Orientierung Infektionskrankheiten werden durch Pathogene verursacht, die sich im Wirt vermehren: Ektoparasiten, Helminthen, Protozoen, Pilze, Bakterien, Viren, Prionen. Infektionskrankheiten können alle Organe bzw. Organsysteme befallen. Entstehung und Verlauf werden durch Faktoren beeinflusst, die sich grob einteilen lassen in Erreger- und Wirtsfaktoren. Die Kenntnis und richtige Einschätzung dieser Faktoren sind entscheidend für Diagnostik und Therapie dieser Erkrankungen. url: https://api.elsevier.com/content/article/pii/B9783437428319100130 doi: 10.1016/b978-3-437-42831-9.10013-0 id: cord-350571-6tapkjb6 author: nan title: 45th ESCP-NSF international symposium on clinical pharmacy: clinical pharmacy tackling inequalities and access to health care. Oslo, Norway, 5–7 October 2016 date: 2017-01-10 words: 106013.0 sentences: 6203.0 pages: flesch: 48.0 cache: ./cache/cord-350571-6tapkjb6.txt txt: ./txt/cord-350571-6tapkjb6.txt summary: Possible solutions might be to use shared communication tools like Internet based communication programs and to introduce the patient as a participant at the IMRs. Please specify your abstract type: Research abstract Background and objective: International good pharmacy practice guidelines describe how pharmacists should counsel the patients about their medicines, offer additional services where needed, and intervene at drug related problems. Please specify your abstract type: Descriptive abstract (for projects) Background and objective: In order to improve the medication reconciliation and to implement training programs for the medical team in an associated to general hospital nursing (ASNH) home we measured the discrepancies between pharmacy registered treatments (PRT) and medical prescriptions (MP), and we analysed potentially inappropriate prescriptions according to ''''American Geriatrics Society 2015 Beers Criteria'''' and ''''STOPP-START 2014 criteria. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/28074393/ doi: 10.1007/s11096-016-0404-4 id: cord-299754-tgexahwd author: van Tol, Sarah title: The TRIMendous Role of TRIMs in Virus–Host Interactions date: 2017-08-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The innate antiviral response is integral in protecting the host against virus infection. Many proteins regulate these signaling pathways including ubiquitin enzymes. The ubiquitin-activating (E1), -conjugating (E2), and -ligating (E3) enzymes work together to link ubiquitin, a small protein, onto other ubiquitin molecules or target proteins to mediate various effector functions. The tripartite motif (TRIM) protein family is a group of E3 ligases implicated in the regulation of a variety of cellular functions including cell cycle progression, autophagy, and innate immunity. Many antiviral signaling pathways, including type-I interferon and NF-κB, are TRIM-regulated, thus influencing the course of infection. Additionally, several TRIMs directly restrict viral replication either through proteasome-mediated degradation of viral proteins or by interfering with different steps of the viral replication cycle. In addition, new studies suggest that TRIMs can exert their effector functions via the synthesis of unconventional polyubiquitin chains, including unanchored (non-covalently attached) polyubiquitin chains. TRIM-conferred viral inhibition has selected for viruses that encode direct and indirect TRIM antagonists. Furthermore, new evidence suggests that the same antagonists encoded by viruses may hijack TRIM proteins to directly promote virus replication. Here, we describe numerous virus–TRIM interactions and novel roles of TRIMs during virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/28829373/ doi: 10.3390/vaccines5030023 id: cord-016255-kkko1xne author: van der Meer, J.T.M. title: 14 Intravasale infecties en sepsis date: 2011 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infecties in het hart en de bloedbaan worden intravasale of endovasculaire infecties genoemd. De circulatie van bloed door het hart is essentieel voor de aanvoer van zuurstof en voedingstoffen naar weefsel en organen en voor de afvoer van afvalstoffen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120488/ doi: 10.1007/978-90-313-7944-6_14 ==== 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