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Katani, Robab; Memari, Sahar; Cavanaugh, Meredith; Buza, Joram; Radzio-Basu, Jessica; Mpenda, Fulgence N.; Deist, Melissa S.; Lamont, Susan J.; Kapur, Vivek title: Transcriptional Innate Immune Response of the Developing Chicken Embryo to Newcastle Disease Virus Infection date: 2018-02-27 journal: Front Genet DOI: 10.3389/fgene.2018.00061 sha: doc_id: 2895 cord_uid: z82e7z2v file: cache/cord-266750-41gth6o0.json key: cord-266750-41gth6o0 authors: Puzzitiello, Richard N.; Pagani, Nicholas R.; Moverman, Michael A.; Moon, Andrew S.; Menendez, Mariano E.; Ryan, Scott P. title: Inflammatory and Coagulative Considerations for the Management of Orthopaedic Trauma Patients With COVID-19: A Review of the Current Evidence and Our Surgical Experience date: 2020-05-14 journal: J Orthop Trauma DOI: 10.1097/bot.0000000000001842 sha: doc_id: 266750 cord_uid: 41gth6o0 file: cache/cord-126015-zc7u3g34.json key: cord-126015-zc7u3g34 authors: Krieger, Elizabeth; Vissichelli, Nicole; Leichtle, Stefan; Kashioris, Markos; 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Risi, Renata; Gnessi, Lucio; Watanabe, Mikiko; Mariani, Stefania; Lubrano, Carla title: Letter To the Editor: [Our Response to COVID-19 as Endocrinologists and Diabetologists] date: 2020-04-28 journal: J Clin Endocrinol Metab DOI: 10.1210/clinem/dgaa229 sha: doc_id: 278938 cord_uid: bmahwxbn file: cache/cord-264159-e9071tyv.json key: cord-264159-e9071tyv authors: Lin, Weikang Nicholas; Tay, Matthew Zirui; Lu, Ri; Liu, Yi; Chen, Chia-Hung; Cheow, Lih Feng title: The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date: 2020-06-10 journal: Cells DOI: 10.3390/cells9061440 sha: doc_id: 264159 cord_uid: e9071tyv file: cache/cord-280605-2i4gk7et.json key: cord-280605-2i4gk7et authors: Bachmann, María Consuelo; Bellalta, Sofía; Basoalto, Roque; Gómez-Valenzuela, Fernán; Jalil, Yorschua; Lépez, Macarena; Matamoros, Anibal; von Bernhardi, Rommy title: The Challenge by Multiple Environmental and Biological Factors Induce Inflammation in Aging: Their Role in the Promotion of Chronic Disease date: 2020-10-14 journal: Front Immunol DOI: 10.3389/fimmu.2020.570083 sha: doc_id: 280605 cord_uid: 2i4gk7et file: cache/cord-285778-80baxwgc.json key: cord-285778-80baxwgc authors: nan title: Introduction to the Immune Response date: 2014-10-10 journal: Primer to the Immune Response DOI: 10.1016/b978-0-12-385245-8.00001-7 sha: doc_id: 285778 cord_uid: 80baxwgc file: cache/cord-272512-gevrlcvy.json key: cord-272512-gevrlcvy authors: Shewen, P.E.; Carrasco-Medina, L.; McBey, B.A.; Hodgins, D.C. title: Challenges in mucosal vaccination of cattle date: 2009-03-15 journal: Vet Immunol Immunopathol DOI: 10.1016/j.vetimm.2008.10.297 sha: doc_id: 272512 cord_uid: gevrlcvy 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-024571-vlklgd3x.json key: cord-024571-vlklgd3x authors: Kim, Yushim; Kim, Jihong; Oh, Seong Soo; Kim, Sang-Wook; Ku, Minyoung; Cha, Jaehyuk title: Community Analysis of a Crisis Response Network date: 2019-07-28 journal: Soc Sci Comput Rev DOI: 10.1177/0894439319858679 sha: doc_id: 24571 cord_uid: vlklgd3x file: cache/cord-286072-kgpvdb42.json key: cord-286072-kgpvdb42 authors: Sa Ribero, Margarida; Jouvenet, Nolwenn; Dreux, Marlène; Nisole, Sébastien title: Interplay between SARS-CoV-2 and the type I interferon response date: 2020-07-29 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008737 sha: doc_id: 286072 cord_uid: kgpvdb42 file: cache/cord-284845-on97zu6w.json key: cord-284845-on97zu6w authors: Falcinelli, Shane D.; Chertow, Daniel S.; Kindrachuk, Jason title: Integration of Global Analyses of Host Molecular Responses with Clinical Data To Evaluate Pathogenesis and Advance Therapies for Emerging and Re-emerging Viral Infections date: 2016-07-29 journal: ACS Infectious Diseases DOI: 10.1021/acsinfecdis.6b00104 sha: doc_id: 284845 cord_uid: on97zu6w file: cache/cord-263315-g7os15m1.json key: cord-263315-g7os15m1 authors: Martins-da-Silva, Andrea; Telleria, Erich Loza; Batista, Michel; Marchini, Fabricio Klerynton; Traub-Csekö, Yara Maria; Tempone, Antonio Jorge title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 journal: Viruses DOI: 10.3390/v10010043 sha: doc_id: 263315 cord_uid: g7os15m1 file: cache/cord-298525-hhcfrjrn.json key: cord-298525-hhcfrjrn authors: Hall, Charlotte A.; Chilcott, Robert P. title: Eyeing up the Future of the Pupillary Light Reflex in Neurodiagnostics date: 2018-03-13 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics8010019 sha: doc_id: 298525 cord_uid: hhcfrjrn file: cache/cord-255725-7l9lk9x2.json key: cord-255725-7l9lk9x2 authors: Hertzog, Paul J; Mansell, Ashley; van Driel, Ian R; Hartland, Elizabeth L title: Sculpting the immune response to infection date: 2011-06-20 journal: Nat Immunol DOI: 10.1038/ni0711-579 sha: doc_id: 255725 cord_uid: 7l9lk9x2 file: cache/cord-318599-drvjr7gq.json key: cord-318599-drvjr7gq authors: Amankwah-Amoah, Joseph title: Note: Mayday, Mayday, Mayday! Responding to environmental shocks: Insights on global airlines’ responses to COVID-19 date: 2020-09-29 journal: Transp Res E Logist Transp Rev DOI: 10.1016/j.tre.2020.102098 sha: doc_id: 318599 cord_uid: drvjr7gq file: cache/cord-273479-kira7mz6.json key: cord-273479-kira7mz6 authors: Strike, Philip C.; Wardle, Jane; Steptoe, Andrew title: Mild acute inflammatory stimulation induces transient negative mood date: 2004-10-02 journal: J Psychosom Res DOI: 10.1016/s0022-3999(03)00569-5 sha: doc_id: 273479 cord_uid: kira7mz6 file: cache/cord-322913-sq9mq6f1.json key: cord-322913-sq9mq6f1 authors: Ciabattini, Annalisa; Garagnani, Paolo; Santoro, Francesco; Rappuoli, Rino; Franceschi, Claudio; Medaglini, Donata title: Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date: 2020-11-06 journal: Semin Immunopathol DOI: 10.1007/s00281-020-00821-0 sha: doc_id: 322913 cord_uid: sq9mq6f1 file: cache/cord-314104-dkm8396y.json key: cord-314104-dkm8396y authors: Tam, Theresa W. S. title: Preparing for uncertainty during public health emergencies: What Canadian health leaders can do now to optimize future emergency response date: 2020-03-31 journal: Healthc Manage Forum DOI: 10.1177/0840470420917172 sha: doc_id: 314104 cord_uid: dkm8396y file: cache/cord-274027-ovdhnajp.json key: cord-274027-ovdhnajp authors: Gyasi, Razak M.; Anderson, Eugenia A. title: Rethinking the Gendered Dimensions in the Impacts and Response to COVID-19 Pandemic date: 2020-06-11 journal: nan DOI: 10.1016/j.puhip.2020.100019 sha: doc_id: 274027 cord_uid: ovdhnajp file: cache/cord-289961-7q2wkwrf.json key: cord-289961-7q2wkwrf authors: Chattopadhyay, Saborni; Chen, Jui-Yi; Chen, Hui-Wen; Hu, Che-Ming Jack title: Nanoparticle Vaccines Adopting Virus-like Features for Enhanced Immune Potentiation date: 2017-06-09 journal: Nanotheranostics DOI: 10.7150/ntno.19796 sha: doc_id: 289961 cord_uid: 7q2wkwrf file: cache/cord-257722-7rmzaau4.json key: cord-257722-7rmzaau4 authors: Rhee, Joon Haeng title: Current and New Approaches for Mucosal Vaccine Delivery date: 2019-10-25 journal: Mucosal Vaccines DOI: 10.1016/b978-0-12-811924-2.00019-5 sha: doc_id: 257722 cord_uid: 7rmzaau4 file: cache/cord-311811-nrodyagi.json key: cord-311811-nrodyagi authors: Schutzer, Steven E. title: The use of host factors in microbial forensics date: 2019-12-06 journal: Microbial Forensics DOI: 10.1016/b978-0-12-815379-6.00014-3 sha: doc_id: 311811 cord_uid: nrodyagi file: cache/cord-311823-85wj08gr.json key: cord-311823-85wj08gr authors: Katze, Michael G.; Fornek, Jamie L.; Palermo, Robert E.; Walters, Kathie-Anne; Korth, Marcus J. title: Innate immune modulation by RNA viruses: emerging insights from functional genomics date: 2008 journal: Nat Rev Immunol DOI: 10.1038/nri2377 sha: doc_id: 311823 cord_uid: 85wj08gr file: cache/cord-324788-echu0zmf.json key: cord-324788-echu0zmf authors: Aich, Palok; Potter, Andrew A; Griebel, Philip J title: Modern approaches to understanding stress and disease susceptibility: A review with special emphasis on respiratory disease date: 2009-07-30 journal: Int J Gen Med DOI: nan sha: doc_id: 324788 cord_uid: echu0zmf file: cache/cord-023055-ntbvmssh.json key: cord-023055-ntbvmssh authors: nan title: Immunogenicity date: 2004-02-19 journal: J Cell Biochem DOI: 10.1002/jcb.240410506 sha: doc_id: 23055 cord_uid: ntbvmssh file: cache/cord-328935-mn8r972x.json key: cord-328935-mn8r972x authors: Hodgins, Douglas C.; Chattha, Kuldeep; Vlasova, Anastasia; Parreño, Viviana; Corbeil, Lynette B.; Renukaradhya, Gourapura J.; Saif, Linda J. title: Mucosal Veterinary Vaccines: Comparative Vaccinology date: 2015-03-13 journal: Mucosal Immunology DOI: 10.1016/b978-0-12-415847-4.00068-9 sha: doc_id: 328935 cord_uid: mn8r972x 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-324143-ztj6o4ob.json key: cord-324143-ztj6o4ob authors: Harper, Craig A.; Satchell, Liam P.; Fido, Dean; Latzman, Robert D. title: Functional Fear Predicts Public Health Compliance in the COVID-19 Pandemic date: 2020-04-27 journal: Int J Ment Health Addict DOI: 10.1007/s11469-020-00281-5 sha: doc_id: 324143 cord_uid: ztj6o4ob file: cache/cord-320431-0877trhh.json key: cord-320431-0877trhh authors: Frey, Andreas; Lunding, Lars P.; Ehlers, Johanna C.; Weckmann, Markus; Zissler, Ulrich M.; Wegmann, Michael title: More Than Just a Barrier: The Immune Functions of the Airway Epithelium in Asthma Pathogenesis date: 2020-04-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.00761 sha: doc_id: 320431 cord_uid: 0877trhh file: cache/cord-332838-i8fjwzm6.json key: cord-332838-i8fjwzm6 authors: Woodland, David L.; Winslow, Gary M. title: Immunity to emerging pathogens date: 2008-09-19 journal: Immunol Rev DOI: 10.1111/j.1600-065x.2008.00695.x sha: doc_id: 332838 cord_uid: i8fjwzm6 file: cache/cord-330583-ltkpt80u.json key: cord-330583-ltkpt80u authors: Lee, Kyu-Myoung; Jung, Kyujin title: Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date: 2019-04-22 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph16081432 sha: doc_id: 330583 cord_uid: ltkpt80u file: cache/cord-335871-zieuc7vk.json key: cord-335871-zieuc7vk authors: Brazee, Patricia L.; Sznajder, Jacob I. title: Targeting the Linear Ubiquitin Assembly Complex to Modulate the Host Response and Improve Influenza A Virus Induced Lung Injury date: 2020-05-13 journal: Arch Bronconeumol DOI: 10.1016/j.arbres.2020.04.019 sha: doc_id: 335871 cord_uid: zieuc7vk file: cache/cord-343896-c40fry35.json key: cord-343896-c40fry35 authors: Dong, Fen; Tacchi, Luca; Xu, Zhen; LaPatra, Scott E.; Salinas, Irene title: Vaccination Route Determines the Kinetics and Magnitude of Nasal Innate Immune Responses in Rainbow Trout (Oncorhynchus mykiss) date: 2020-10-01 journal: Biology (Basel) DOI: 10.3390/biology9100319 sha: doc_id: 343896 cord_uid: c40fry35 file: cache/cord-339694-sp212tai.json key: cord-339694-sp212tai authors: Jiang, Xinpeng; Hou, Xingyu; Tang, Lijie; Jiang, Yanping; Ma, Guangpeng; Li, Yijing title: A phase trial of the oral Lactobacillus casei vaccine polarizes Th2 cell immunity against transmissible gastroenteritis coronavirus infection date: 2016-03-28 journal: Appl Microbiol Biotechnol DOI: 10.1007/s00253-016-7424-9 sha: doc_id: 339694 cord_uid: sp212tai file: cache/cord-339935-tguhrqvz.json key: cord-339935-tguhrqvz authors: Zavattaro, Staci M.; Hall, Jeremy L.; Battaglio, R. Paul; Hail, Michael W. title: Introduction: COVID‐19 Viewpoint Symposium, Part II date: 2020-08-12 journal: Public Adm Rev DOI: 10.1111/puar.13290 sha: doc_id: 339935 cord_uid: tguhrqvz file: cache/cord-344985-3mu9rrql.json key: cord-344985-3mu9rrql authors: Fakhruddin, Bapon; Blanchard, Kevin; Ragupathy, Durga title: Are we there yet? The transition from response to recovery for the COVID-19 pandemic date: 2020-05-12 journal: nan DOI: 10.1016/j.pdisas.2020.100102 sha: doc_id: 344985 cord_uid: 3mu9rrql file: cache/cord-342317-m6axi18k.json key: cord-342317-m6axi18k authors: Leigh, Laurasona; Taylor, Colleen; Glassman, Tavis; Thompson, Amy; Sheu, Jiunn-Jye title: A Cross-Sectional Examination on the Factors Related to Emergency Nurses’ Motivation to Protect Themselves against an Ebola Infection date: 2020-05-06 journal: J Emerg Nurs DOI: 10.1016/j.jen.2020.05.002 sha: doc_id: 342317 cord_uid: m6axi18k file: cache/cord-344297-qqohijqi.json key: cord-344297-qqohijqi authors: Smith, Jacqueline; Sadeyen, Jean-Remy; Cavanagh, David; Kaiser, Pete; Burt, David W. title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date: 2015-10-09 journal: BMC Vet Res DOI: 10.1186/s12917-015-0575-6 sha: doc_id: 344297 cord_uid: qqohijqi 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-015147-h0o0yqv8.json key: cord-015147-h0o0yqv8 authors: nan title: Oral Communications and Posters date: 2014-09-12 journal: Inflamm Res DOI: 10.1007/bf03353884 sha: doc_id: 15147 cord_uid: h0o0yqv8 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-022888-dnsdg04n.json key: cord-022888-dnsdg04n authors: nan title: Poster Sessions date: 2009-08-19 journal: Eur J Immunol DOI: 10.1002/eji.200990224 sha: doc_id: 22888 cord_uid: dnsdg04n file: cache/cord-015021-pol2qm74.json key: cord-015021-pol2qm74 authors: nan title: Third International Congress on the Immune Consequences of Trauma, Shock and Sepsis —Mechanisms and Therapeutic Approaches date: 1994 journal: Intensive Care Med DOI: 10.1007/bf02258437 sha: doc_id: 15021 cord_uid: pol2qm74 file: cache/cord-257167-rz4r5sj7.json key: cord-257167-rz4r5sj7 authors: nan title: Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date: 2006-12-31 journal: Neuroscience Research DOI: 10.1016/j.neures.2006.04.004 sha: doc_id: 257167 cord_uid: rz4r5sj7 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-response-cord 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. /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 /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 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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: 95346 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95541 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95570 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. 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: 95298 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95354 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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 94. 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 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: 94982 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97678 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /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 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: 97258 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97272 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97381 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.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/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 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: 97996 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 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: 96892 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97602 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97875 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. /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 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 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: 98160 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 735 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 987 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1134 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 98216 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3535 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 2320 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-029598-qwpya4ox author: Adibe, Bryant title: Creating Wellness in a Pandemic: A Practical Framework for Health Systems Responding to Covid-19 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-029598-qwpya4ox.txt cache: ./cache/cord-029598-qwpya4ox.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-029598-qwpya4ox.txt' /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 /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: 4412 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4550 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 2910 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5032 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 96753 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4006 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4030 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4914 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4175 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3068 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4402 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-290264-pv7ijdnx author: Perakslis, Eric title: A Primer on Biodefense Data Science for Pandemic Preparedness date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-290264-pv7ijdnx.txt cache: ./cache/cord-290264-pv7ijdnx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-290264-pv7ijdnx.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: 4612 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4013 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4476 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 97994 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5206 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 6349 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-017838-fbotc479 author: Fagone, Paolo title: Electroporation-Mediated DNA Vaccination date: 2010-12-15 pages: extension: .txt txt: ./txt/cord-017838-fbotc479.txt cache: ./cache/cord-017838-fbotc479.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-017838-fbotc479.txt' === file2bib.sh === id: cord-005607-b1a39hhw author: Bellingan, G title: Leukocytes: friend or foe date: 2000 pages: extension: .txt txt: ./txt/cord-005607-b1a39hhw.txt cache: ./cache/cord-005607-b1a39hhw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-005607-b1a39hhw.txt' === file2bib.sh === id: cord-285982-1a5u7uux author: Moss, Ronald B title: Prospects for control of emerging infectious diseases with plasmid DNA vaccines date: 2009-09-07 pages: extension: .txt txt: ./txt/cord-285982-1a5u7uux.txt cache: ./cache/cord-285982-1a5u7uux.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-285982-1a5u7uux.txt' === file2bib.sh === id: cord-266750-41gth6o0 author: Puzzitiello, Richard N. title: Inflammatory and Coagulative Considerations for the Management of Orthopaedic Trauma Patients With COVID-19: A Review of the Current Evidence and Our Surgical Experience date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-266750-41gth6o0.txt cache: ./cache/cord-266750-41gth6o0.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-266750-41gth6o0.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: 4015 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7443 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 5384 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7042 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7032 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7437 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3693 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7632 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7927 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 6793 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1806 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: 6502 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 7283 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8119 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-257027-q2y7fewk author: Lemaire, D. title: Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology date: 2011-10-28 pages: extension: .txt txt: ./txt/cord-257027-q2y7fewk.txt cache: ./cache/cord-257027-q2y7fewk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-257027-q2y7fewk.txt' === file2bib.sh === id: cord-002895-z82e7z2v author: Schilling, Megan A. title: Transcriptional Innate Immune Response of the Developing Chicken Embryo to Newcastle Disease Virus Infection date: 2018-02-27 pages: extension: .txt txt: ./txt/cord-002895-z82e7z2v.txt cache: ./cache/cord-002895-z82e7z2v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002895-z82e7z2v.txt' === file2bib.sh === id: cord-216972-migs9rxb author: Garaialde, Diego title: Quantifying the Impact of Making and Breaking Interface Habits date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-216972-migs9rxb.txt cache: ./cache/cord-216972-migs9rxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-216972-migs9rxb.txt' === file2bib.sh === id: cord-126015-zc7u3g34 author: Krieger, Elizabeth title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-126015-zc7u3g34.txt cache: ./cache/cord-126015-zc7u3g34.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-126015-zc7u3g34.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: 5045 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-297776-k38jssr0 author: Volk, Aaron title: Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-297776-k38jssr0.txt cache: ./cache/cord-297776-k38jssr0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297776-k38jssr0.txt' === file2bib.sh === id: cord-018937-5yo4rfml author: Bortolin, Michelangelo title: Disaster Medicine date: 2015-04-18 pages: extension: .txt txt: ./txt/cord-018937-5yo4rfml.txt cache: ./cache/cord-018937-5yo4rfml.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-018937-5yo4rfml.txt' === file2bib.sh === id: cord-018254-v8syiwie author: Rotz, Lisa D. title: Case Study – United States of America date: 2012-08-31 pages: extension: .txt txt: ./txt/cord-018254-v8syiwie.txt cache: ./cache/cord-018254-v8syiwie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018254-v8syiwie.txt' === file2bib.sh === id: cord-022435-pztn9075 author: Roach, Jeff title: Bali Bombings: A Whole of Government Response date: 2009-11-16 pages: extension: .txt txt: ./txt/cord-022435-pztn9075.txt cache: ./cache/cord-022435-pztn9075.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022435-pztn9075.txt' === file2bib.sh === id: cord-278397-u33x4jaw author: Abe, Takayuki title: Negative Regulation of Cytosolic Sensing of DNA date: 2018-10-29 pages: extension: .txt txt: ./txt/cord-278397-u33x4jaw.txt cache: ./cache/cord-278397-u33x4jaw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278397-u33x4jaw.txt' === file2bib.sh === id: cord-292983-msuluuuu author: Ballesteros-Briones, María Cristina title: A new generation of vaccines based on alphavirus self-amplifying RNA date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-292983-msuluuuu.txt cache: ./cache/cord-292983-msuluuuu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-292983-msuluuuu.txt' === file2bib.sh === id: cord-297834-me1ajoyb author: Schountz, Tony title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 pages: extension: .txt txt: ./txt/cord-297834-me1ajoyb.txt cache: ./cache/cord-297834-me1ajoyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297834-me1ajoyb.txt' === file2bib.sh === id: cord-311331-l7dehit8 author: Diaz-Arévalo, Diana title: Nanoparticle-based vaccines: opportunities and limitations date: 2020-01-17 pages: extension: .txt txt: ./txt/cord-311331-l7dehit8.txt cache: ./cache/cord-311331-l7dehit8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-311331-l7dehit8.txt' === file2bib.sh === id: cord-032600-lldbjm77 author: Soni, Dheeraj title: The sixth revolution in pediatric vaccinology: immunoengineering and delivery systems date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-032600-lldbjm77.txt cache: ./cache/cord-032600-lldbjm77.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-032600-lldbjm77.txt' === file2bib.sh === id: cord-026960-g844u7xg author: Wang, Disen title: An Adaptive Response Matching Network for Ranking Multi-turn Chatbot Responses date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-026960-g844u7xg.txt cache: ./cache/cord-026960-g844u7xg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026960-g844u7xg.txt' === file2bib.sh === id: cord-021424-kocwsyi7 author: Shannon, M. Frances title: Genomic Approaches to the Host Response to Pathogens date: 2009-01-30 pages: extension: .txt txt: ./txt/cord-021424-kocwsyi7.txt cache: ./cache/cord-021424-kocwsyi7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-021424-kocwsyi7.txt' === file2bib.sh === id: cord-332838-i8fjwzm6 author: Woodland, David L. title: Immunity to emerging pathogens date: 2008-09-19 pages: extension: .txt txt: ./txt/cord-332838-i8fjwzm6.txt cache: ./cache/cord-332838-i8fjwzm6.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-332838-i8fjwzm6.txt' === file2bib.sh === id: cord-003898-y6zpvw84 author: Tan, Kai Sen title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 pages: extension: .txt txt: ./txt/cord-003898-y6zpvw84.txt cache: ./cache/cord-003898-y6zpvw84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-003898-y6zpvw84.txt' === file2bib.sh === id: cord-288868-qfdxri93 author: Wack, Andreas title: Vaccinology at the beginning of the 21st century date: 2005-06-13 pages: extension: .txt txt: ./txt/cord-288868-qfdxri93.txt cache: ./cache/cord-288868-qfdxri93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288868-qfdxri93.txt' === file2bib.sh === id: cord-303674-0xo2fiop author: Criscuolo, E. title: Alternative Methods of Vaccine Delivery: An Overview of Edible and Intradermal Vaccines date: 2019-03-04 pages: extension: .txt txt: ./txt/cord-303674-0xo2fiop.txt cache: ./cache/cord-303674-0xo2fiop.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-303674-0xo2fiop.txt' === file2bib.sh === id: cord-252568-b8sbvy0g author: Marques Neto, Lázaro Moreira title: Role of Metallic Nanoparticles in Vaccinology: Implications for Infectious Disease Vaccine Development date: 2017-03-08 pages: extension: .txt txt: ./txt/cord-252568-b8sbvy0g.txt cache: ./cache/cord-252568-b8sbvy0g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252568-b8sbvy0g.txt' === file2bib.sh === id: cord-033714-rz5unqaz author: Gupte, Jaideep title: COVID-19: what is not being addressed date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-033714-rz5unqaz.txt cache: ./cache/cord-033714-rz5unqaz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-033714-rz5unqaz.txt' === file2bib.sh === id: cord-023935-o2ffxgnn author: Lorts, Angela title: Sepsis date: 2011-12-16 pages: extension: .txt txt: ./txt/cord-023935-o2ffxgnn.txt cache: ./cache/cord-023935-o2ffxgnn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023935-o2ffxgnn.txt' === file2bib.sh === id: cord-276628-uxsjyezo author: Hedges, Jodi F. title: Harnessing γδ T Cells as Natural Immune Modulators date: 2019-10-25 pages: extension: .txt txt: ./txt/cord-276628-uxsjyezo.txt cache: ./cache/cord-276628-uxsjyezo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276628-uxsjyezo.txt' === file2bib.sh === id: cord-285778-80baxwgc author: nan title: Introduction to the Immune Response date: 2014-10-10 pages: extension: .txt txt: ./txt/cord-285778-80baxwgc.txt cache: ./cache/cord-285778-80baxwgc.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-285778-80baxwgc.txt' === file2bib.sh === id: cord-271250-ywb26cq6 author: Sarkar, Indranil title: Selection of adjuvants for vaccines targeting specific pathogens date: 2019-04-22 pages: extension: .txt txt: ./txt/cord-271250-ywb26cq6.txt cache: ./cache/cord-271250-ywb26cq6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271250-ywb26cq6.txt' === file2bib.sh === id: cord-018475-h8qwxdtn author: Speckhard, Anne title: Prevention Strategies and Promoting Psychological Resilience to Bioterrorism Through Communication date: 2007 pages: extension: .txt txt: ./txt/cord-018475-h8qwxdtn.txt cache: ./cache/cord-018475-h8qwxdtn.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-018475-h8qwxdtn.txt' === file2bib.sh === id: cord-344297-qqohijqi author: Smith, Jacqueline title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date: 2015-10-09 pages: extension: .txt txt: ./txt/cord-344297-qqohijqi.txt cache: ./cache/cord-344297-qqohijqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344297-qqohijqi.txt' === file2bib.sh === id: cord-298525-hhcfrjrn author: Hall, Charlotte A. title: Eyeing up the Future of the Pupillary Light Reflex in Neurodiagnostics date: 2018-03-13 pages: extension: .txt txt: ./txt/cord-298525-hhcfrjrn.txt cache: ./cache/cord-298525-hhcfrjrn.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-298525-hhcfrjrn.txt' === file2bib.sh === id: cord-284845-on97zu6w author: Falcinelli, Shane D. title: Integration of Global Analyses of Host Molecular Responses with Clinical Data To Evaluate Pathogenesis and Advance Therapies for Emerging and Re-emerging Viral Infections date: 2016-07-29 pages: extension: .txt txt: ./txt/cord-284845-on97zu6w.txt cache: ./cache/cord-284845-on97zu6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284845-on97zu6w.txt' === file2bib.sh === id: cord-287396-18p171nr author: Schroyen, Martine title: Current transcriptomics in pig immunity research date: 2014-11-15 pages: extension: .txt txt: ./txt/cord-287396-18p171nr.txt cache: ./cache/cord-287396-18p171nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-287396-18p171nr.txt' === file2bib.sh === id: cord-031081-szqrjxq2 author: Campbell, Margaret C title: In Times of Trouble: A Framework for Understanding Consumers’ Responses to Threats date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-031081-szqrjxq2.txt cache: ./cache/cord-031081-szqrjxq2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-031081-szqrjxq2.txt' === file2bib.sh === id: cord-015910-d9gxew91 author: Grimble, Robert F. title: The Interaction Between Nutrition and Inflammatory Stress Throughout the Life Cycle date: 2005 pages: extension: .txt txt: ./txt/cord-015910-d9gxew91.txt cache: ./cache/cord-015910-d9gxew91.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015910-d9gxew91.txt' === file2bib.sh === id: cord-289961-7q2wkwrf author: Chattopadhyay, Saborni title: Nanoparticle Vaccines Adopting Virus-like Features for Enhanced Immune Potentiation date: 2017-06-09 pages: extension: .txt txt: ./txt/cord-289961-7q2wkwrf.txt cache: ./cache/cord-289961-7q2wkwrf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-289961-7q2wkwrf.txt' === file2bib.sh === id: cord-016713-pw4f8asc author: Goyal, Amit K. title: Nanotechnological Approaches for Genetic Immunization date: 2013-05-24 pages: extension: .txt txt: ./txt/cord-016713-pw4f8asc.txt cache: ./cache/cord-016713-pw4f8asc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016713-pw4f8asc.txt' === file2bib.sh === id: cord-017817-ztp7w9yh author: Land, Walter Gottlieb title: Cell-Autonomous (Cell-Intrinsic) Stress Responses date: 2018-03-28 pages: extension: .txt txt: ./txt/cord-017817-ztp7w9yh.txt cache: ./cache/cord-017817-ztp7w9yh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-017817-ztp7w9yh.txt' === file2bib.sh === id: cord-021966-5m21bsrw author: Shaw, Alan R. title: Vaccines date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-021966-5m21bsrw.txt cache: ./cache/cord-021966-5m21bsrw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-021966-5m21bsrw.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 4 resourceName b'cord-318272-spt0oea0.txt' === file2bib.sh === id: cord-320431-0877trhh author: Frey, Andreas title: More Than Just a Barrier: The Immune Functions of the Airway Epithelium in Asthma Pathogenesis date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-320431-0877trhh.txt cache: ./cache/cord-320431-0877trhh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320431-0877trhh.txt' === file2bib.sh === id: cord-328935-mn8r972x author: Hodgins, Douglas C. title: Mucosal Veterinary Vaccines: Comparative Vaccinology date: 2015-03-13 pages: extension: .txt txt: ./txt/cord-328935-mn8r972x.txt cache: ./cache/cord-328935-mn8r972x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328935-mn8r972x.txt' === file2bib.sh === id: cord-307202-iz1bo218 author: Shaw, Dominick title: Asthma date: 2014-05-02 pages: extension: .txt txt: ./txt/cord-307202-iz1bo218.txt cache: ./cache/cord-307202-iz1bo218.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307202-iz1bo218.txt' === file2bib.sh === id: cord-022252-9yiuuye3 author: Mims, Cedric A. title: Mechanisms of Cell and Tissue Damage date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022252-9yiuuye3.txt cache: ./cache/cord-022252-9yiuuye3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022252-9yiuuye3.txt' === file2bib.sh === id: cord-022592-g7rmzsv5 author: Wynn, James L. title: Pathophysiology of Neonatal Sepsis date: 2016-07-06 pages: extension: .txt txt: ./txt/cord-022592-g7rmzsv5.txt cache: ./cache/cord-022592-g7rmzsv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022592-g7rmzsv5.txt' === file2bib.sh === id: cord-023143-fcno330z author: nan title: Molecular aspects of viral immunity date: 2004-02-19 pages: extension: .txt txt: ./txt/cord-023143-fcno330z.txt cache: ./cache/cord-023143-fcno330z.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-023143-fcno330z.txt' === file2bib.sh === id: cord-023055-ntbvmssh author: nan title: Immunogenicity date: 2004-02-19 pages: extension: .txt txt: ./txt/cord-023055-ntbvmssh.txt cache: ./cache/cord-023055-ntbvmssh.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-023055-ntbvmssh.txt' === file2bib.sh === id: cord-015147-h0o0yqv8 author: nan title: Oral Communications and Posters date: 2014-09-12 pages: extension: .txt txt: ./txt/cord-015147-h0o0yqv8.txt cache: ./cache/cord-015147-h0o0yqv8.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 5 resourceName b'cord-015147-h0o0yqv8.txt' === file2bib.sh === id: cord-015021-pol2qm74 author: nan title: Third International Congress on the Immune Consequences of Trauma, Shock and Sepsis —Mechanisms and Therapeutic Approaches date: 1994 pages: extension: .txt txt: ./txt/cord-015021-pol2qm74.txt cache: ./cache/cord-015021-pol2qm74.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-015021-pol2qm74.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 33 resourceName b'cord-022888-dnsdg04n.txt' === file2bib.sh === id: cord-257167-rz4r5sj7 author: nan title: Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date: 2006-12-31 pages: extension: .txt txt: ./txt/cord-257167-rz4r5sj7.txt cache: ./cache/cord-257167-rz4r5sj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 27 resourceName b'cord-257167-rz4r5sj7.txt' Que is empty; done keyword-response-cord === reduce.pl bib === === reduce.pl bib === id = cord-016713-pw4f8asc author = Goyal, Amit K. title = Nanotechnological Approaches for Genetic Immunization date = 2013-05-24 pages = extension = .txt mime = text/plain words = 16034 sentences = 814 flesch = 34 summary = The use of nonviral particulate carriers for DNA-based vaccination could provide better and safe delivery of encapsulated genetic material, circumvent the need for muscle involvement and facilitate instead the uptake of the Fig. 4 Schematic representation of immunological response greeted by novel DNA-loaded nanocarrier DNA by APCs. However, transfection of APCs with encapsulated DNA into particulate carrier systems will be dependent upon choice of carrier surface charge, size, and lipid/polymer composition, or presence of other biological [e.g., interleukin 2 and interferon-γ (IFN-γ)]. Modification of lipid/DNA complexes by the polymer poly(D,L-lactic acid) was found to be consistently and significantly more effective than either unmodified liposomal DNA or naked DNA in eliciting transgene-specific immune responses to plasmid-encoded antigen when administered by the s.c. route (Bramwell et al. cache = ./cache/cord-016713-pw4f8asc.txt txt = ./txt/cord-016713-pw4f8asc.txt === reduce.pl bib === id = cord-257027-q2y7fewk author = Lemaire, D. title = Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology date = 2011-10-28 pages = extension = .txt mime = text/plain words = 5844 sentences = 241 flesch = 33 summary = Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. The publication of the Haemophilus influenzae genome, the first pathogen to have its complete genome sequence published as a result of an approach to genome analysis using new technologies of high-throughput sequencing (5) , has opened the mind of scientists to a range of new possible approaches to the study of microorganisms and has marked the beginning of a new era in vaccine development: the identification of pathogen candidate antigens based on the knowledge of the genome of the pathogen and on the understanding of microbial biology and host-pathogen interactions, an approach called reverse vaccinology (6) . cache = ./cache/cord-257027-q2y7fewk.txt txt = ./txt/cord-257027-q2y7fewk.txt === reduce.pl bib === id = cord-017838-fbotc479 author = Fagone, Paolo title = Electroporation-Mediated DNA Vaccination date = 2010-12-15 pages = extension = .txt mime = text/plain words = 5279 sentences = 221 flesch = 31 summary = Thus, electroporation-mediated DNA vaccination represents a promising new strategy for the elicitation of strong immune responses directed against the expressed antigen(s) and not the vector, and ongoing studies are currently underway to optimize the working parameters of this technique. [26] demonstrated in mice that upon electroporative treatment, the delivery of a weakly immunogenic hepatitis B virus (HBV) surface antigen (Hbs Ag) DNA vaccine resulted in an increased humoral immune response, characterized by rapid onset and higher titers of anti-Hbs Ag antibodies. In addition, the authors observed in the same study that the potency of an HIV gag pDNA vaccine was increased as shown by the lower dosage of DNA required to induce higher antigen-specific antibody levels and increased CD8 + T cell responses. [31] have demonstrated that gene electrotransfer efficiently increased the cellular immune response both in mice and rhesus macaques vaccinated with a plasmid encoding a nonstructural region of hepatitis C virus (HCV). cache = ./cache/cord-017838-fbotc479.txt txt = ./txt/cord-017838-fbotc479.txt === reduce.pl bib === id = cord-271250-ywb26cq6 author = Sarkar, Indranil title = Selection of adjuvants for vaccines targeting specific pathogens date = 2019-04-22 pages = extension = .txt mime = text/plain words = 11394 sentences = 542 flesch = 39 summary = In-depth understanding of the role of adjuvants in activating the innate immune system, combined with systems vaccinology approaches, have led to the development of next-generation, novel adjuvants that can be used in vaccines against challenging pathogens and in specific target populations. Intact MyD88 signaling in each of the three types of APCs (DCs, macrophages and B cells) is essential for robust activity of TLR ligand-based vaccine adjuvants (PorB, a TLR2 ligand and CpG, a TLR9 ligand) such as induction of in vivo cytokine responses, germinal center (GC) formation and antibody production [49] . A combination adjuvant consisting of poly(I:C), a host defense peptide and PCEP when delivered intranasally transiently induces production of chemokines and cytokines in murine respiratory tissues, which promotes infiltration and activation of DCs, macrophages, and neutrophils to generate improved mucosal and systemic immune responses [55] . cache = ./cache/cord-271250-ywb26cq6.txt txt = ./txt/cord-271250-ywb26cq6.txt === reduce.pl bib === === reduce.pl bib === id = cord-018254-v8syiwie author = Rotz, Lisa D. title = Case Study – United States of America date = 2012-08-31 pages = extension = .txt mime = text/plain words = 5139 sentences = 169 flesch = 29 summary = This act authorized more than 1.5 billion US dollars in grants to state and local governments and healthcare facilities to improve planning, training, detection, and response capacity as well as funding to expand the federal Strategic National Stockpile of medications and vaccines and upgrade food inspection capacity and CDC facilities that deal with public health threats. In addition to the central role the LRN played in detecting and responding to the 2001 anthrax letter event, the commitment to infrastructure support and standardized platform testing capacity within the LRN has also proven extremely bene fi cial in assisting with more rapid and broader deployment of tests developed in response to other emerging public health threats such as the 2003 Severe Acute Respiratory Syndrome (SARS) and the 2009 H1N1 avian in fl uenza pandemic. cache = ./cache/cord-018254-v8syiwie.txt txt = ./txt/cord-018254-v8syiwie.txt === reduce.pl bib === id = cord-278397-u33x4jaw author = Abe, Takayuki title = Negative Regulation of Cytosolic Sensing of DNA date = 2018-10-29 pages = extension = .txt mime = text/plain words = 7194 sentences = 377 flesch = 41 summary = Recent efforts have focused on identifying relevant immune surveillance sensors and components of downstream signaling-Toll-like receptors (TLRs) and their cognate ligands, cytosolic sensing of RNA (primary mediated by the RIG-I/IPS-1 axis), cytosolic sensing of DNA (primary mediated by the cGAS/STING axis), and the inflammasome pathway (primary mediated by NOD-like receptors; NLRs) (Broz and Monack, 2013; Kieser and Kagan, 2017; Kumar et al., 2011a ). It has also been suggested that chronic cGAS/STING activation induced by self DNA may be responsible for induction of aberrant inflammatory diseases like systemic lupus erythematosus (SLE), Aicardi-Goutières syndrome (AGS), and polyarthritis (Barber, 2015; Crowl et al., 2017) . Use of DNA damage induced agents like 7,12-dimethylbenz-α-anthracene (DMBA) has helped shed light on the underlying events initiate the DNA damage-induced immune response via cytosolic DNA sensing pathway and implicates nucleosome leakage in eliciting cGAS/STING-dependent signal activation via recognition of self-DNA (Barber, 2015) . cache = ./cache/cord-278397-u33x4jaw.txt txt = ./txt/cord-278397-u33x4jaw.txt === reduce.pl bib === id = cord-216972-migs9rxb author = Garaialde, Diego title = Quantifying the Impact of Making and Breaking Interface Habits date = 2020-05-14 pages = extension = .txt mime = text/plain words = 6289 sentences = 309 flesch = 50 summary = Through a forced choice lab study task (n=19) and in the wild deployment (n=18) of a notificationdialog experiment on smartphones, we show that people become more accurate and faster at option selection as they develop an interface habit. The contribution of the current paper comes from providing quantitative evidence of how the process of forming and disrupting habits affects user performance in a forced choice interaction task, similar to those seen in notification dialogs or alert boxes. The current research contributes key insight on fundamental user behaviours by quantifying how the process of habit formation and disruption through design affect the speed and accuracy of interactions. The experimental evidence of study 1 shows that, like other habits, allowing participants to form interface habits leads to significant gains in performance, as users became both more accurate and quicker at selecting the desired option. cache = ./cache/cord-216972-migs9rxb.txt txt = ./txt/cord-216972-migs9rxb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-002895-z82e7z2v author = Schilling, Megan A. title = Transcriptional Innate Immune Response of the Developing Chicken Embryo to Newcastle Disease Virus Infection date = 2018-02-27 pages = extension = .txt mime = text/plain words = 5996 sentences = 249 flesch = 43 summary = Since the chicken embryo becomes immunocompetent prior to hatch, we here characterized the transcriptional response of selected innate immune genes to Newcastle disease virus (NDV) infection in chicken embryos at days 10, 14, and 18 of embryonic development. Since the chicken embryo becomes immunocompetent prior to hatch, we here characterized the transcriptional response of selected innate immune genes to Newcastle disease virus (NDV) infection in chicken embryos at days 10, 14, and 18 of embryonic development. The comparative transcriptional profile of SPF White Leghorn chicken embryos (one control and one infected at 18 days, harvested 72 hpi) was determined using the Chicken Innate and Adaptive Immune Responses RT 2 Profiler Array (QIAGEN Inc., Germantown, MD, United States) as an initial screen to select for immune genes in the embryo that are differentially expressed during infection since studies have not been performed previously. cache = ./cache/cord-002895-z82e7z2v.txt txt = ./txt/cord-002895-z82e7z2v.txt === reduce.pl bib === id = cord-126015-zc7u3g34 author = Krieger, Elizabeth title = Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date = 2020-05-13 pages = extension = .txt mime = text/plain words = 6421 sentences = 348 flesch = 42 summary = To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. The HLA genes exhibit extreme allelic polymorphisms and present viral peptides on host HLA molecules to T cells to trigger an adaptive immune response. A quantitative approach relating differences in cytokine levels and polymorphisms in the immune response pathways may help identify patients at risk of severe disease. cache = ./cache/cord-126015-zc7u3g34.txt txt = ./txt/cord-126015-zc7u3g34.txt === reduce.pl bib === id = cord-266750-41gth6o0 author = Puzzitiello, Richard N. title = Inflammatory and Coagulative Considerations for the Management of Orthopaedic Trauma Patients With COVID-19: A Review of the Current Evidence and Our Surgical Experience date = 2020-05-14 pages = extension = .txt mime = text/plain words = 3742 sentences = 221 flesch = 39 summary = A better understanding of this relationship can inform the development of evidencebased management strategies in these patients and limit admissions to overcrowded ICUs. To demonstrate and further define these developing theories on the coagulative and inflammatory risks associated with the surgical treatment of trauma patients with COVID-19, we will present an unexpected outcome on such a patient at our institution. In addition, the hypercoagulable state secondary to COVID-19 and the inflammatory load of intramedullary reaming, fat emboli, and pulmonary embolism resulted in a "second hit" that may have cumulatively pushed our patient past a "tipping point" and into respiratory failure (Fig. 4) . The level of cytokine response, hypercoagulability, and pulmonary dysfunction associated with the COVID-19 virus may predispose to a catastrophic "second hit" after even low-energy trauma. Careful consideration and risk/benefit analysis, including preoperative evaluation of systemic inflammation and respiratory status, is paramount in patients with COVID-19 presenting with orthopaedic trauma injuries. cache = ./cache/cord-266750-41gth6o0.txt txt = ./txt/cord-266750-41gth6o0.txt === reduce.pl bib === id = cord-023935-o2ffxgnn author = Lorts, Angela title = Sepsis date = 2011-12-16 pages = extension = .txt mime = text/plain words = 11110 sentences = 510 flesch = 38 summary = SIRS i s a state of infl ammatory/ immune activation and is based on the presence of at least two of the four following clinical criteria: Temperature >38°C or <36°C, heart rate >90th percentile for age, respiratory rate >90th percentile for age, or hyperventilation to PaCO 2 < 32 mm Hg. The defi nition attempts to "capture" all patients at risk for the subsequent development of severe sepsis or septic shock. Among these, the nuclear factor-k B (NF-k b ) and the mitogen activated protein kinase (MAPK) pathways play a prominent role in regulating the expression of a number of infl ammatory gene products key to propagating the sepsis response. Nuclear factork B (NFk b ) and the mitogen activated protein kinase (MAPK) pathways play a prominent role in regulating the expression of a number of infl ammatory gene products key to propagating the sepsis response. cache = ./cache/cord-023935-o2ffxgnn.txt txt = ./txt/cord-023935-o2ffxgnn.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-033714-rz5unqaz author = Gupte, Jaideep title = COVID-19: what is not being addressed date = 2020-10-13 pages = extension = .txt mime = text/plain words = 8226 sentences = 431 flesch = 51 summary = The visualization of informal settlements in many COVID-19 discussions, however, is of homogenous highdensity inner-city shacks, with insufficient attention given to lowerdensity settlements (more likely to have urban agriculture) that may also face health and economic emergencies. (46) The wealth of grassroots responses to COVID-19 is elaborated by the International Institute for Environment and Development (IIED), which has drawn on experiences from across its partners in the global South, who provide evidence of local groups stepping in to reduce health risks and provide emergency access to food and hygiene. Meanwhile, the vast majority of urban poor communities (85%) reported government-provided "palliatives" intended for the vulnerable had not reached them." (68) Similar findings are evident in Brazil where, for example, low-income favela residents in São Paulo are not receiving the monthly emergency basic income payment (worth US$ 115), despite the shutdown by the city authorities of informal trading on 15 April 2020. Local response in health emergencies: key considerations for addressing the COVID-19 pandemic in informal urban settlements cache = ./cache/cord-033714-rz5unqaz.txt txt = ./txt/cord-033714-rz5unqaz.txt === reduce.pl bib === id = cord-290264-pv7ijdnx author = Perakslis, Eric title = A Primer on Biodefense Data Science for Pandemic Preparedness date = 2020-04-10 pages = extension = .txt mime = text/plain words = 2349 sentences = 128 flesch = 57 summary = 1 This piece will dig deeper into biodefense policy as well as suggest specific actions that the data science community can take to contribute to COVID-19 resilience, response, and recovery efforts. Starting at the top and looking more deeply into risk and resilience in the United States, much of the policy stems from the Homeland Security Presidential Directive 21, which outlines the policy and strategy for public health and medical preparedness. This outbreak is past the point of prevention, and the response must now focus on minimizing the effects as people get sick. A toolset that I have personally used over the years for rapid development and deployment is CommCare by Dimagi, and they have already built a toolkit and guide specifically for COVID-19 outbreak response. 8 My last trip during that outbreak focused upon rebuilding local infrastructure to enable the local health systems to get back to full operation, including the possibility of an Ebola-infected patient presenting and seeking care. cache = ./cache/cord-290264-pv7ijdnx.txt txt = ./txt/cord-290264-pv7ijdnx.txt === reduce.pl bib === id = cord-285982-1a5u7uux author = Moss, Ronald B title = Prospects for control of emerging infectious diseases with plasmid DNA vaccines date = 2009-09-07 pages = extension = .txt mime = text/plain words = 4227 sentences = 202 flesch = 42 summary = The rapid manufacturing capabilities of DNA vaccines may be particularly important for emerging infectious diseases including the current novel H1N1 Influenza A pandemic, where pre-existing immunity is limited. Development in this area has greatly advanced over the years and human clinical trials of DNA vaccines have now been conducted against various infectious pathogens including the malaria parasite, dengue viruses, cytomegalovirus (CMV), Ebola virus, seasonal influenza viruses, avian or pandemic influenza viruses, West Nile virus (WMV), SARS coronavirus, hepatitis B virus, and HIV. Because the process of antigen production by host cells after DNA vaccination mimics the production of antigens during a natural infection, the resulting immune response is thought to be similar to the type induced by pathogens. Lastly, the first human clinical trial of a DNA vaccine formulated with Vaxfectin ® has been completed with plasmids that encode pandemic influenza virus antigens (H5N1). cache = ./cache/cord-285982-1a5u7uux.txt txt = ./txt/cord-285982-1a5u7uux.txt === reduce.pl bib === id = cord-029598-qwpya4ox author = Adibe, Bryant title = Creating Wellness in a Pandemic: A Practical Framework for Health Systems Responding to Covid-19 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2333 sentences = 95 flesch = 44 summary = The task force used its collective expertise to develop four key mitigation strategies, described in detail below, to reinforce staff wellness throughout the crisis: Wellness Rounds, a Wellness Consult Service, an advanced mental health intervention program known as Wellness Plus, and a central Wellness Resource Hub with Wellness Rooms on frontline floors. We established a consult service (Figure 1 ) where any clinical unit or individual can connect directly with a member of the Wellness Response Team for evaluation, triage, and recommendations to improve mental health and well-being. When triggered, the individual is escorted to one of the unit-level Wellness Rooms or the central Wellness Resource Hub (see below) where an experienced clinician (typically a physician or other prescriber) completes a thorough mental health assessment, including identifying an immediate therapeutic intervention and appropriate followup. cache = ./cache/cord-029598-qwpya4ox.txt txt = ./txt/cord-029598-qwpya4ox.txt === reduce.pl bib === id = cord-021424-kocwsyi7 author = Shannon, M. Frances title = Genomic Approaches to the Host Response to Pathogens date = 2009-01-30 pages = extension = .txt mime = text/plain words = 7277 sentences = 343 flesch = 43 summary = This activation process includes widespread changes in the gene expression profi le of the cells with hundreds of genes being either switched on or off in response to signals generated from the pathogen-detecting TLRs. The response of individual genes has been studied in minute detail for a handful of genes and while this has produced an understanding of some aspects of host response to infection it by no means gives us the total picture. Studies in both animal models and human populations have shown that infectious disease and the response of the host to a specifi c infection also has a complex genetic component ( Clementi and Di Gianantonio, 2006 ; Lipoldova and Demant, 2006 ; Marquet et al., 1996 ; Mira et al., 2004 ) . Expression profi ling studies have been used to investigate the differences in the host response to pathogenic and nonpathogenic strains of specifi c infectious agents. cache = ./cache/cord-021424-kocwsyi7.txt txt = ./txt/cord-021424-kocwsyi7.txt === reduce.pl bib === id = cord-297834-me1ajoyb author = Schountz, Tony title = Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date = 2014-03-14 pages = extension = .txt mime = text/plain words = 6425 sentences = 334 flesch = 38 summary = The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. cache = ./cache/cord-297834-me1ajoyb.txt txt = ./txt/cord-297834-me1ajoyb.txt === reduce.pl bib === id = cord-031081-szqrjxq2 author = Campbell, Margaret C title = In Times of Trouble: A Framework for Understanding Consumers’ Responses to Threats date = 2020-07-09 pages = extension = .txt mime = text/plain words = 11083 sentences = 560 flesch = 50 summary = In conjunction with these articles, we hope that this conceptual framework will provide a point of departure for researchers seeking to enhance the understanding of how consumers and markets collectively respond over the short term and long term to threats that disrupt consumers' routines, lives, or even the fabric of society. Our goal is not to provide a comprehensive review of existing literature, but rather a guide to researchers seeking to increase our collective understanding of how consumers and markets together respond over short and long durations to threats that disrupt their very being. The findings of this article suggest that economic recessions, pandemics, and terror threats can affect subjective life expectancy for some consumers, leading to different financial and health decisions than they might make otherwise, as well as potentially impacting their mental health. cache = ./cache/cord-031081-szqrjxq2.txt txt = ./txt/cord-031081-szqrjxq2.txt === reduce.pl bib === id = cord-021966-5m21bsrw author = Shaw, Alan R. title = Vaccines date = 2009-05-15 pages = extension = .txt mime = text/plain words = 21170 sentences = 897 flesch = 33 summary = Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination? cache = ./cache/cord-021966-5m21bsrw.txt txt = ./txt/cord-021966-5m21bsrw.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-297776-k38jssr0 author = Volk, Aaron title = Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date = 2020-05-18 pages = extension = .txt mime = text/plain words = 5843 sentences = 293 flesch = 42 summary = gene expression, we report significant transcriptional upregulation of multiple genes associated with activation of ER sensors IRE1, ATF6, and PERK, such as Edem1, Hspa5 (encoding BiP protein), and Ddit3 (encoding CHOP), in response to virus replication, with the most robust response detected in cells infected with the wild-type or DUBmut virus infection (Fig. 5B, C, and D) . Overall, these differential gene expression analyses in macrophages reveal similar host responses to the wild-type and DUBmut viruses that include activation of UPR pathways and proinflammatory genes, whereas a distinct transcriptional profile during infection with the EndoUmut virus is predominately defined by a focused, robust antiviral response. The results presented here, and from studies of the MERS-CoV dORF3-5 mutant virus (26) Upon infection of a BMDM with EndoUmut, host double-stranded RNA (dsRNA) sensors (including MDA5, PKR, and OAS) are activated, resulting in robust transcription of type I IFN genes and rapid induction of apoptosis, the latter of which precludes the development of a potent inflammatory response. cache = ./cache/cord-297776-k38jssr0.txt txt = ./txt/cord-297776-k38jssr0.txt === reduce.pl bib === id = cord-005607-b1a39hhw author = Bellingan, G title = Leukocytes: friend or foe date = 2000 pages = extension = .txt mime = text/plain words = 3827 sentences = 173 flesch = 37 summary = Over the last three decades we have gained significant insights into leukocyte activation, recruitment and mediator secretion and the contribution of these agents to both the onset and resolution of sepsis and inflammation.¶The body relies on the inflammatory response for protection. A direct consequence of this protective strategy is that the inflammatory response may be inadequate, with the risk of overwhelming sepsis, or excessive, leading to rampant systemic inflammation and consequent multiple organ damage.¶It is now becoming apparent however that in addition to leukocytes other cells have important roles both in defence against invading pathogens and in driving malignant inflammation. Endothelial cells, mesothelial cells, fibroblasts and epithelial cells are also all involved not only with their capacity to drive the inflammatory response through mediator generation but also in innate immune defences including through the production of antimicrobial proteins. cache = ./cache/cord-005607-b1a39hhw.txt txt = ./txt/cord-005607-b1a39hhw.txt === reduce.pl bib === id = cord-015910-d9gxew91 author = Grimble, Robert F. title = The Interaction Between Nutrition and Inflammatory Stress Throughout the Life Cycle date = 2005 pages = extension = .txt mime = text/plain words = 15205 sentences = 709 flesch = 40 summary = Binding of the transcription factors is implicated in activation of a wide range of genes associated with inflammation and the immune response, including those encoding cytokines, cytokine receptors, cell adhesion molecules, acute-phase proteins, and growth factors (Schreck, Rieber, & Baeurerle, 1991) (Fig. 4 ) . While inflammation may be exerting deleterious effects most obviously in patients, people on the borderline of health and disease living in the general population Table 4 Nutrients Commonly Used in Immunonutrient Supplements and Their Potential Mode of Action • n-3 polyunsaturated fatty acids: act as anti-inflammatory agents and reverse immunosuppression • Sulfur amino acids and their precursors: enhance antioxidant status via GSH synthesis • Glutamine: nutrient for immune cells, improves gut barrier function, precursor for GSH • Arginine: stimulates nitric oxide and growth hormone production, improves helper T-cell numbers • Nucleotides: RNA and DNA precursors, improve T-cell function may also require nutritional modulation of ongoing inflammatory processes. cache = ./cache/cord-015910-d9gxew91.txt txt = ./txt/cord-015910-d9gxew91.txt === reduce.pl bib === id = cord-003898-y6zpvw84 author = Tan, Kai Sen title = RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date = 2019-08-27 pages = extension = .txt mime = text/plain words = 7671 sentences = 386 flesch = 44 summary = title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications The aim of this study was to utilize RNA sequencing (RNAseq) technology to not only reveal the hNEC responses (from multiple individuals) against influenza infection, but also to identify those genes with high magnitude changes to serve as potential reference markers of the innate responses of influenza infection. After deriving the transcriptomes by RNAseq, we then further investigated whether the changes in expression of genes resulted in alterations in secretory cytokines and chemokines early in the infection of hNECs. Initially, we detected significant reductions in multiple cytokines at 8 hpi, with the exception of IL-15 which was increased ( Figure S2 ). In conclusion, RNAseq technology allowed us to accurately quantify the magnitude of gene expression changes, as well as the relevant enriched pathways during H3N2 influenza virus infection of hNECs, which can serve as a baseline for future clinical studies. cache = ./cache/cord-003898-y6zpvw84.txt txt = ./txt/cord-003898-y6zpvw84.txt === reduce.pl bib === id = cord-032600-lldbjm77 author = Soni, Dheeraj title = The sixth revolution in pediatric vaccinology: immunoengineering and delivery systems date = 2020-09-14 pages = extension = .txt mime = text/plain words = 6655 sentences = 388 flesch = 32 summary = 2 Second-generation efforts employed more characterized materials, such as the biodegradable synthetic polymer poly (D,L-lactic-co-glycolic acid) (PLGA), which is a widely investigated nanoparticle adjuvant for controlled and effective delivery of vaccine antigens, including synthetic peptides. 32 Thus, pathogen-mimicking nanoparticles can be engineered to enhance the immune response by controlling when and where vaccine components are delivered intracellularly to APCs. 15 A plethora of particulate delivery systems for immunoengineering have been developed, which are summarized further in this review. Recently, we have combined such engineering and rational vaccine design approaches to develop a nanoparticle-based adjuvant and antigen-delivery system designed to be active in human newborns and infants. Furthermore, such formulations hold substantial potential for early life immunization by serving as a dual antigen/adjuvant delivery system that mimics the enhanced neonatal innate and adaptive immune responses elicited by the live Bacille Calmette-Guerin (BCG) vaccine. cache = ./cache/cord-032600-lldbjm77.txt txt = ./txt/cord-032600-lldbjm77.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-292983-msuluuuu author = Ballesteros-Briones, María Cristina title = A new generation of vaccines based on alphavirus self-amplifying RNA date = 2020-09-06 pages = extension = .txt mime = text/plain words = 4942 sentences = 277 flesch = 47 summary = In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. This type of LNP-delivered saRNA vaccines, named SAM (for self-amplifying mRNA) platform, have shown great potential to generate immune responses against influenza virus [20] [21] [22] and Toxoplasma gondii [23] . Despite the fact that the ta-RNA system was able to induce good immune responses in vivo against influenza virus HA, it did not outperform vaccination with a single saRNA molecule expressing the same antigen. cache = ./cache/cord-292983-msuluuuu.txt txt = ./txt/cord-292983-msuluuuu.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-018475-h8qwxdtn author = Speckhard, Anne title = Prevention Strategies and Promoting Psychological Resilience to Bioterrorism Through Communication date = 2007 pages = extension = .txt mime = text/plain words = 10540 sentences = 411 flesch = 46 summary = With the erosion of strict borders between countries (particularly in the European Union) and even world regions (since the fall of the Soviet bloc), the advance and portability of high-tech weaponry including biological, chemical, and nuclear hazards, and the ease and speed of communication through the Internet and telephones for purposes of recruitment, training, and planning terror attacks -terrorists now have a global playing field in which even small groups of individuals can motivate, plan, and enact mass terrorist events. Governments and media must work together preparing ahead of time on how to communicate calmly in such crises in a manner that will offer useful preventative measures, minimize the potential negative effects of psychosocial contagions (including citizenry becoming noncompliant and aggressive), prevent mass sociogenic illness from occurring, and prevent overwhelming of the medical systems by those whose emotional state has put them in need of medical care. cache = ./cache/cord-018475-h8qwxdtn.txt txt = ./txt/cord-018475-h8qwxdtn.txt === reduce.pl bib === id = cord-303674-0xo2fiop author = Criscuolo, E. title = Alternative Methods of Vaccine Delivery: An Overview of Edible and Intradermal Vaccines date = 2019-03-04 pages = extension = .txt mime = text/plain words = 7451 sentences = 359 flesch = 32 summary = In particular, novel strategies based on edible or intradermal vaccine formulations have been demonstrated to trigger both a systemic and mucosal immune response. In this review, we discuss current advances and advantages of edible systems based on plants, algae, yeast, insect cells, and lactic acid bacteria and of the intradermal immunization route. Subsequently, the antigen(s) can be incorporated into different edible systems, as plants, algae, insects, or yeasts, or used for intradermal formulations to induce a mucosal protective response. Remarkably, some preclinical studies based on orally administrated Saccharomyces cerevisiae and developed for different infectious agents, such as HPV and Actinobacillus pleuropneumoniae, showed that this delivery system is able to induce a protective mucosal and a systemic immune response [68] [69] [70] . Another vaccine delivery route capable of triggering both systemic and mucosal immunities is the intradermal route, in which the antigen is delivered through the skin using recently developed self-administrable devices. cache = ./cache/cord-303674-0xo2fiop.txt txt = ./txt/cord-303674-0xo2fiop.txt === reduce.pl bib === === reduce.pl bib === id = cord-018937-5yo4rfml author = Bortolin, Michelangelo title = Disaster Medicine date = 2015-04-18 pages = extension = .txt mime = text/plain words = 3722 sentences = 188 flesch = 51 summary = Disaster is defi ned as any event that causes "a serious disruption of the functioning of a community or a society involving widespread human, material, economic or environmental losses and impacts, which exceeds the ability of the affected community or society to cope using its own resources" [ 1 ] . The Incident Command System (ICS) provides a structure to enable agencies with different legal, jurisdictional, and functional responsibilities to coordinate, plan, and interact effectively on scene [ 11 ] . During a disaster, it is extremely important to establish a unifi ed command, because it enables all responsible agencies to manage and coordinate an incident together by establishing a common approach and a single IAP. It is defi ned as second incident caused by the terrorists, following the fi rst event, with the goal of striking the fi rst responders that are on scene. cache = ./cache/cord-018937-5yo4rfml.txt txt = ./txt/cord-018937-5yo4rfml.txt === reduce.pl bib === id = cord-022435-pztn9075 author = Roach, Jeff title = Bali Bombings: A Whole of Government Response date = 2009-11-16 pages = extension = .txt mime = text/plain words = 4728 sentences = 223 flesch = 44 summary = Domestically, the Department of Family and Community Services (FaCS) coordinated government policy and delivery of assistance to Australians and their families affected by the crisis. A clear lesson from Bali was the extent to which overseas events can resonate at the local community level, underlining the importance of domestic and state/territory agencies being activated early in response to a major overseas crisis. • clarify the roles of agencies and non-government organisations in crisis responses; • review links between Australian government and state disaster plans; and • identify and rectify any gaps in interagency coordination arrangements. One of the lessons of the Australian Government's FMD simulation, Exercise Minotaur (see http://www.affa.gov.au/exerciseminotaur), was the need for agencies to look at human resource capacity in a number of key areas, particularly that of skilled and trained technical employees. cache = ./cache/cord-022435-pztn9075.txt txt = ./txt/cord-022435-pztn9075.txt === reduce.pl bib === id = cord-017817-ztp7w9yh author = Land, Walter Gottlieb title = Cell-Autonomous (Cell-Intrinsic) Stress Responses date = 2018-03-28 pages = extension = .txt mime = text/plain words = 17727 sentences = 855 flesch = 40 summary = Autophagy is an evolutionarily highly conserved self-digestive process in response to environmental stress to eukaryotic cells, by which cytoplasmic components such as defective/damaged or redundant organelles or protein aggregates are delivered to the lysosome for recycling and degradation. More recent studies then revealed that these transcription factors, notably Nrf2, are activated by Keap1 as the primary negative regulator of Nrf2, that is, a molecule that simultaneously operates as a sensor protein able to perceive dyshomeostatic Subclass IIC-4 DAMPs, for example, in terms of redox changes reflecting electrophilic stress. Strikingly, a complex relationship reportedly exists between autophagy and DAMPs in cellular adaption to stress and injury and cell death characterized by a crosstalk between autophagy induction and secretion or release of DAMPs. In fact, growing evidence indicates that autophagic mechanisms are involved in regulating release and degradation of DAMPs including CALR, HMGB1, ATP, and DNA in several cell types [37, 148, 175] . cache = ./cache/cord-017817-ztp7w9yh.txt txt = ./txt/cord-017817-ztp7w9yh.txt === reduce.pl bib === id = cord-023143-fcno330z author = nan title = Molecular aspects of viral immunity date = 2004-02-19 pages = extension = .txt mime = text/plain words = 43425 sentences = 2056 flesch = 47 summary = Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. cache = ./cache/cord-023143-fcno330z.txt txt = ./txt/cord-023143-fcno330z.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-276628-uxsjyezo author = Hedges, Jodi F. title = Harnessing γδ T Cells as Natural Immune Modulators date = 2019-10-25 pages = extension = .txt mime = text/plain words = 6808 sentences = 349 flesch = 46 summary = TCR stimulation leads to a variety of functional responses, such as cytolysis, cytokine production, regulatory effects, and even phagocytosis and antigen presentation, that depend on the activation of receptors and coreceptors. γδ T cells also express various cytokine receptors that contribute to their activation (IL-2R, IL-15R, IL-23R, etc.) and-fine tune their functional responses. SLC11A1 is a divalent metal transporter that is thought to be expressed only in myeloid and macrophage cells; it is important in effective responses against intracellular bacterial infections [49À51]. Follow-up functional assays examined their cell type specificity, induced cytokine responses, and benefit in various infectious disease models [110, 112] . Yamoa polysaccharides activate γδ T as well other immune cells, such as monocytes, and, when given in vivo, enhance protection from infection [110] . Porcine γδ T cells: possible roles on the innate and adaptive immune responses following virus infection cache = ./cache/cord-276628-uxsjyezo.txt txt = ./txt/cord-276628-uxsjyezo.txt === reduce.pl bib === id = cord-022592-g7rmzsv5 author = Wynn, James L. title = Pathophysiology of Neonatal Sepsis date = 2016-07-06 pages = extension = .txt mime = text/plain words = 22148 sentences = 1302 flesch = 39 summary = 14, 15, [27] [28] [29] [30] [31] [32] [33] Prematurity, low birth weight (especially infants weighing less than 1,000 g), male sex, a maternal vaginal culture positive for group B streptococcus (GBS), prolonged rupture of membranes, maternal intrapartum fever, and chorioamnionitis are strongly associated with an increased risk for early-onset sepsis. In addition to the initial inflammatory response including complement activation, molecular detection of PAMPs promotes IL-1β and IL-6 production, which in turn increases the production of multiple other innate proteins that possess valuable immune function and serve to reduce pathogen load. Very low birth weight preterm infants with early onset neonatal sepsis: the predominance of gram-negative infections continues in the National Institute of Child Health and Human Development Neonatal Research Network Very low birth weight preterm infants with early onset neonatal sepsis: the predominance of gram-negative infections continues in the National Institute of Child Health and Human Development Neonatal Research Network cache = ./cache/cord-022592-g7rmzsv5.txt txt = ./txt/cord-022592-g7rmzsv5.txt === reduce.pl bib === id = cord-026960-g844u7xg author = Wang, Disen title = An Adaptive Response Matching Network for Ranking Multi-turn Chatbot Responses date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4523 sentences = 237 flesch = 52 summary = To address this limitation, this paper proposes an adaptive response matching network (ARM) to better model the matching relationship in multi-turn conversations. Specifically, the Dual-encoder model [8] used two LSTMs to generate the embeddings for the utterances and candidate response respectively to compute the matching score. Deep attention model (DAM) [20] proposed self-attention and cross-attention to construct semantic representations at different granularity, and the multirepresentation fusion network (MRFN) [13] has further applied multiple representation strategies for utterances and fused them in the final step to compute the matching scores. Few of them studied how to adapt the matching model to different types of utterances and how to incorporate the domain knowledge in a more general way, which is the focus of our paper. Although a few models have been proposed to solve the problem of multi-turn response selection [2, 13, 17, 20] , none of them studied how to directly adapt the matching mechanisms to different utterance types. cache = ./cache/cord-026960-g844u7xg.txt txt = ./txt/cord-026960-g844u7xg.txt === reduce.pl bib === id = cord-287396-18p171nr author = Schroyen, Martine title = Current transcriptomics in pig immunity research date = 2014-11-15 pages = extension = .txt mime = text/plain words = 9824 sentences = 467 flesch = 44 summary = Other meta-analysis studies, examining the immune response to Salmonella typhimurium, combine microarray information with data such as serum cytokine measurements or microbiota differences. typhimurium will be discussed in the section ''Overall value of transcriptomics in important infectious swine diseases.'' In addition, whole genome microarrays were used to study pig response to Haemophilus parasuis infection by Zhao et al. In 2010, Xiao and collaborators performed a 3' tag digital gene expression (DGE) analysis of the porcine lung transcriptome on pigs infected with the PRRS virus (Xiao et al. Most pig immune studies conducted to identify host response to common porcine pathogens or to immune response stimulators such as LPS or PMA/ionomycin described in this review provide gene expression data from a single tissue or isolated cell type, and this at a limited number of times post-infection/stimulation. Recently, such a meta-analysis was performed by combining results of several microarray-based pig immune studies to find PRRS-specific responses (Badaoui et al. cache = ./cache/cord-287396-18p171nr.txt txt = ./txt/cord-287396-18p171nr.txt === reduce.pl bib === === reduce.pl bib === id = cord-307202-iz1bo218 author = Shaw, Dominick title = Asthma date = 2014-05-02 pages = extension = .txt mime = text/plain words = 19168 sentences = 831 flesch = 37 summary = Current asthma management involves a step-up and step-down approach based on asthma control with a large degree of heterogeneity in responses to the main drug classes currently in use: β(2)-adrenergic receptor agonists, corticosteroids, and leukotriene modifiers. Human studies have identified elevated numbers of cells expressing IL13 mRNA in the bronchial tissue of atopic and nonatopic asthmatic subjects [50] ; administration of recombinant IL13 in mouse lungs resulted in an increase in airway mucus secretion, development of subepithelial fibrosis, airway hyper-responsiveness (AHR), and eosinophilic airway inflammation-that is, several key features of the human disease [51] . While methods of stratifying asthma patients to specific treatments based on nongenetic factors such as clinical outcomes, cellular measures, or protein biomarkers have shown some success, a large body of work has investigated the potential of genetic markers as predictors of patient responses to existing therapies, i.e., pharmacogenetics. cache = ./cache/cord-307202-iz1bo218.txt txt = ./txt/cord-307202-iz1bo218.txt === reduce.pl bib === id = cord-311331-l7dehit8 author = Diaz-Arévalo, Diana title = Nanoparticle-based vaccines: opportunities and limitations date = 2020-01-17 pages = extension = .txt mime = text/plain words = 5064 sentences = 266 flesch = 42 summary = The development of subunit vaccines without risk are considered as an essential need in combination with adequate delivery systems to obtain desired cell and humoral immune responses against infectious diseases. The characteristics of the nanoparticles have allowed targeting desired antigen-presenting cells to improve immunization strategies to induce protection. This chapter focuses on the nanoparticle-based vaccine formulations and the approaches used to realize efficient delivery of vaccines in order to induce host protective immunity against infectious diseases. The combination of the vaccine with the adjuvant or delivery system should be safe, stable, and have the ability to induce long-lived memory B and T cell responses, preferably with a single dose and a maximum of two doses and be free from strict storage requirements [9] . NPs have become an alternative to targeting vaccine delivery to immune cells, improving vaccine efficacy with slow release, easy antigen uptake, and induction of humoral and cellular responses [8] . cache = ./cache/cord-311331-l7dehit8.txt txt = ./txt/cord-311331-l7dehit8.txt === reduce.pl bib === === reduce.pl bib === id = cord-022252-9yiuuye3 author = Mims, Cedric A. title = Mechanisms of Cell and Tissue Damage date = 2013-11-17 pages = extension = .txt mime = text/plain words = 28864 sentences = 1432 flesch = 48 summary = A few viruses are remarkable because they cause no pathological changes at all in the cell, even during a productive infection in which infectious virus particles are produced. Primary consideration will be given to those substances which are produced under ecologically significant conditions (i.e. in the natural host or relevant animal model) and cause (also in biologically relevant systems) damage to cells or tissues thereby contributing to disease. Here we consider toxins which act on extracellular substances and are responsible for many of the main features of the diseases caused by the infecting organism. Circulating immune complexes are also deposited in the walls of small blood vessels in the skin and elsewhere, where they may induce inflammatory changes.* The prodromal rashes seen in exanthematous virus infections and in hepatitis B are probably caused in this way. cache = ./cache/cord-022252-9yiuuye3.txt txt = ./txt/cord-022252-9yiuuye3.txt === reduce.pl bib === id = cord-252568-b8sbvy0g author = Marques Neto, Lázaro Moreira title = Role of Metallic Nanoparticles in Vaccinology: Implications for Infectious Disease Vaccine Development date = 2017-03-08 pages = extension = .txt mime = text/plain words = 5317 sentences = 260 flesch = 39 summary = There is evidence that these particles display adjuvant characteristics, promoting cell recruitment, antigen-presenting cell activation, cytokine production, and inducing a humoral immune response. However, many NPs have been shown to stimulate immune responses, including cell recruitment, activation of antigen (Ag)-presenting cells (APCs), and induction of cytokine and chemokine release. Among the vaccines targeting extracellular bacteria and toxin, two were formulated with lipopolysaccharide (LPS) in glycopeptide Ag. The use of glycoantigen and LPS can trigger an intense response through TLR4 and B cell receptor activation; the presence of gold NPs (AuNPs) may have minimal influence on this response. To understand the possible uses of MeNPs as platforms for vaccines against infectious diseases, analysis is needed of the impact of different physicochemical characteristics of NPs on the innate immune response (Figure 1) . cache = ./cache/cord-252568-b8sbvy0g.txt txt = ./txt/cord-252568-b8sbvy0g.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-288868-qfdxri93 author = Wack, Andreas title = Vaccinology at the beginning of the 21st century date = 2005-06-13 pages = extension = .txt mime = text/plain words = 5082 sentences = 224 flesch = 43 summary = Thus, the use of reverse genetics enables rapid production of a reference vaccine virus in response to the emergence of a new influenza variant [15 ,16] . Activation of DCs increases their ability to process and present antigen and to attract and activate T cells through cytokine secretion; consequently, several cytokines are 414 Host-pathogen interactions Table 1 Human TLR agonists used as adjuvants in vaccine formulations in clinical trials or licensed vaccines a . When viral vehicles (vaccinia or adenovirus) were compared with loaded DCs in terms of their ability to overcome established tolerance and induce immune responses in a transgenic mouse model, the viral formulations were able to do so, whereas DCs required repeated administration of TLR agonists or irrelevant virus, or removal of suppressive CD4 + CD25 + Treg cells [54 ] . A CD4(+) T-cell immune response to a conserved epitope in the circumsporozoite protein correlates with protection from natural Plasmodium falciparum infection and disease cache = ./cache/cord-288868-qfdxri93.txt txt = ./txt/cord-288868-qfdxri93.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-285778-80baxwgc author = nan title = Introduction to the Immune Response date = 2014-10-10 pages = extension = .txt mime = text/plain words = 7980 sentences = 388 flesch = 46 summary = Some innate mechanisms require no induction and are completely non-specific, whereas others are inducible and involve broad receptor-mediated recognition of a limited number of pathogen-associated or damage-associated molecular patterns (PAMPs/DAMPs). When invaders breach anatomical and physiological barriers, innate leukocytes start to take action as a result of pattern recognition mediated by the binding of PRMs to PAMPs furnished by pathogens and to DAMPs emanating from damaged host cells. If the pathogen manages to enter the underlying cell layer, mechanisms mediated by complement and innate leukocytes are induced due to relatively broad recognition of PAMPs. If a more targeted, pathogen-specific response becomes necessary, elements of innate immunity then facilitate induction of highly specific adaptive responses initiated by engagement of the antigen receptors of B, Th or Tc lymphocytes. Innate leukocytes activated by the binding of PRRs to PAMPs provided by the attacking pathogen, or to DAMPs present due to host cell injury or death, work quickly to eliminate the invader using the mechanisms of inflammation, phagocytosis and target cell lysis. cache = ./cache/cord-285778-80baxwgc.txt txt = ./txt/cord-285778-80baxwgc.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-284845-on97zu6w author = Falcinelli, Shane D. title = Integration of Global Analyses of Host Molecular Responses with Clinical Data To Evaluate Pathogenesis and Advance Therapies for Emerging and Re-emerging Viral Infections date = 2016-07-29 pages = extension = .txt mime = text/plain words = 8473 sentences = 421 flesch = 35 summary = Here, we will discuss this approach with a focus on the emerging viral pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola virus (EBOV), and monkeypox virus (MPXV) from the context of clinical presentation, immunological and molecular features of the diseases, and OMICS-based analyses of pathogenesis. As emerging viral infections often result in severe illness including respiratory failure [severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza] and multiorgan failure [Ebola virus disease (EVD)], understanding complex pathogenesis of these infections is required for effective vaccine and therapeutic design and for improved patient care. Specifically, detailed natural history studies merging multiple data streams including OMICS approaches (high-throughput gene expression and kinomics) and focused translational investigations utilizing relevant models that can be validated to human disease are needed to clarify disease pathogenesis, advance therapeutic discovery, and facilitate regulatory approval. cache = ./cache/cord-284845-on97zu6w.txt txt = ./txt/cord-284845-on97zu6w.txt === reduce.pl bib === === reduce.pl bib === id = cord-298525-hhcfrjrn author = Hall, Charlotte A. title = Eyeing up the Future of the Pupillary Light Reflex in Neurodiagnostics date = 2018-03-13 pages = extension = .txt mime = text/plain words = 7841 sentences = 383 flesch = 37 summary = The pupillary light reflex (PLR) describes the constriction and subsequent dilation of the pupil in response to light as a result of the antagonistic actions of the iris sphincter and dilator muscles. The pupillary light reflex (PLR) describes the constriction and subsequent dilation of the pupil in response to light, which not only serves as a major determination of retinal image quality [1, 2] , but also provides an important metric of autonomic nervous system function [3] . The response latency, maximum constriction and pupil escape, and the corresponding constriction parameters (MCV, MCA and RCA; relative constriction amplitude) are dependent on the actions of the sphincter muscle and on the function of retinal photoreceptors, as well as the time consumed in the afferent and efferent pathway. The ability of pupillometry to detect subtle changes in pupillary reaction even when pupils are constricted has potential clinical significance and may provide a useful tool in the early detection, monitoring and management of brain injuries [89] . cache = ./cache/cord-298525-hhcfrjrn.txt txt = ./txt/cord-298525-hhcfrjrn.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-289961-7q2wkwrf author = Chattopadhyay, Saborni title = Nanoparticle Vaccines Adopting Virus-like Features for Enhanced Immune Potentiation date = 2017-06-09 pages = extension = .txt mime = text/plain words = 10531 sentences = 581 flesch = 32 summary = Exploiting the same transport mechanisms aimed at detaining viruses, nanoparticle vaccines can effectively target immune cells in lymph nodes, delivering antigens or adjuvants following administration in peripheral tissues [13, 141, 142] (Fig. 3A) . Given the privilege of nanocarriers in lymphatic transport, nanoparticles have been shown to enhance the delivery of target antigens to lymph nodes and resident immune cells for processing and immune activation. In their animal study, strong anti-ovalbumin humoral response was observed [13] , highlighting the benefit of nanoparticle-mediated lymph node delivery on enhancing antigen processing. These virus-like particles showed high immunogenicity in both murine and avian models and enhanced anti-viral IgA and IgG titers and cellular immune responses in comparison to free protein antigens and a commercial WIV vaccine [155] . Not only can nanoparticle vaccines enhance humoral responses against target antigens, they have been shown to promote cell-based immunity as well as immunological memory. cache = ./cache/cord-289961-7q2wkwrf.txt txt = ./txt/cord-289961-7q2wkwrf.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-023055-ntbvmssh author = nan title = Immunogenicity date = 2004-02-19 pages = extension = .txt mime = text/plain words = 64563 sentences = 3952 flesch = 59 summary = Antigen is internalized into acidic vesicles, proteolyzed, and peptides containing T ceU antigenic determinants are transported to the APC surface where they are recognized by the antigen-specific T cell in conjunction with Ia. Most Ia-"pressing cells are competent APC, however, only B cells have antigen-specilic receptors on their surface aUowing bound antigen to be processed and presented at 1/lW the antigen concentration required by nonspecific APC Little is known about B cell antigen processing function during differentiation, or if Ig-mediated APC function is altered at different maturational stages, thus allowing regulation of B cell-helper T cell interactions. These results indicate that the poor response of murine CTL to human class I antigens is not determined by selection in the thymus, but by species-specific constraints on the interaction of MHC antigens with T-cell recognition structures. cache = ./cache/cord-023055-ntbvmssh.txt txt = ./txt/cord-023055-ntbvmssh.txt === reduce.pl bib === id = cord-328935-mn8r972x author = Hodgins, Douglas C. title = Mucosal Veterinary Vaccines: Comparative Vaccinology date = 2015-03-13 pages = extension = .txt mime = text/plain words = 16336 sentences = 785 flesch = 36 summary = Studies of the potential of novel adjuvants to improve vaccine efficacy against genetically unstable, immune-subverting RNA viruses, such as porcine reproductive and respiratory syndrome virus in pigs, should assist in the control of pathogens with similar characteristics in other species. However, a recent study showed that an inactivated reassortant RV strain (CDC-9 strain) formulated with aluminum phosphate and administered systemically in gnotobiotic pigs resulted in induction of serum IgG antibody titers, coinciding with partial protection against shedding and diarrhea, suggesting that adjuvant may have stimulated local specific (gut IgA antibodies) or nonspecific immune responses, which were not assessed in this study (Wang et al., 2010) . Intranasal delivery of whole cell lysate of Mycobacterium tuberculosis induces protective immune responses to a modified live porcine reproductive and respiratory syndrome virus vaccine in pigs cache = ./cache/cord-328935-mn8r972x.txt txt = ./txt/cord-328935-mn8r972x.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 === === reduce.pl bib === id = cord-320431-0877trhh author = Frey, Andreas title = More Than Just a Barrier: The Immune Functions of the Airway Epithelium in Asthma Pathogenesis date = 2020-04-28 pages = extension = .txt mime = text/plain words = 15225 sentences = 762 flesch = 40 summary = In case of asthma, all these functions are impaired by the already existing allergic immune response that per se weakens the barrier integrity and self-cleaning abilities of the airway epithelium making it more vulnerable to penetration of allergens as well as of infection by bacteria and viruses. Besides this innate "rapid response team, " the polarized epithelium of the human airways is also able to transport and apically release immunoglobulins that carry a J-chain (joining chain) by using its poly Ig receptor (pIgR) (145) (146) (147) that is expressed by all non-stratified epithelial cells (Figure 2) . After contact for example with HDM extracts, representing a major source of asthma associated allergens, TLR4 dependent activation of NFκB and protease induced injuries in airway epithelial cells lead to secretion of chemokines and cytokines like thymic stromal lymphopoietin (TSLP), GM-CSF, IL-25, and IL-33 (211) (212) (213) (214) (215) . cache = ./cache/cord-320431-0877trhh.txt txt = ./txt/cord-320431-0877trhh.txt === reduce.pl bib === === reduce.pl bib === id = cord-332838-i8fjwzm6 author = Woodland, David L. title = Immunity to emerging pathogens date = 2008-09-19 pages = extension = .txt mime = text/plain words = 2279 sentences = 117 flesch = 39 summary = Our choice of pathogens and authors has therefore resulted in reviews that cover many different types of infectious disease and a breadth of immune responses. The relationship between innate immune responses and viral success in the host population is also discussed by Drs Jessica Weaver and Stuart Isaacs (University of Pennsylvania School of Medicine) (6) with respect to monkeypox virus. Several of the reviews in this volume discuss the important role of T cells in viral, bacterial, and parasite emerging infections. For example, CD8 1 T cells play a major role in protective immunity during Plasmodium liver stage infection, as described by Dr Fidel Zavala and colleagues (Johns Hopkins University) (16) in their review of malaria immunity. While T cells can play a key role in protective immunity, they can also mediate considerable pathogenic effects. Dr Alan Rothman and colleagues (University of Massachusetts Medical School) (18) discuss the impact of T-cell responses on dengue virus infections. cache = ./cache/cord-332838-i8fjwzm6.txt txt = ./txt/cord-332838-i8fjwzm6.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-344297-qqohijqi author = Smith, Jacqueline title = The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date = 2015-10-09 pages = extension = .txt mime = text/plain words = 5076 sentences = 284 flesch = 52 summary = title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. [18] we used Affymetrix wholegenome chicken microarrays to examine the tracheal gene expression profiles of a line of birds known to be susceptible to IBV infection (line 15I) and a line known to show resistance (line N). Gene expression differences found in the susceptible 15I line between infected and control birds over days 2, 3 and 4 post infection were analysed, with a view to examining the innate host response to infection by IBV. Gene expression seen during the host response to IBV infection in the trachea of susceptible birds. Genes found to be differentially expressed between susceptible and resistant lines in response to IBV infection in the trachea. cache = ./cache/cord-344297-qqohijqi.txt txt = ./txt/cord-344297-qqohijqi.txt === reduce.pl bib === === reduce.pl bib === id = cord-015147-h0o0yqv8 author = nan title = Oral Communications and Posters date = 2014-09-12 pages = extension = .txt mime = text/plain words = 73711 sentences = 3862 flesch = 43 summary = Cyclooxygenases (COX) catalyze the first step in the synthesis of prostaglandins (PG) from arachidonic acid.COX-1 is constitutively expressed.The COX-2 gene is an immediate early-response gene that is induced by variety of mitogenic and inflammatory stimuli.Levels of COX-2 are increased in both inflamed and malignant tissues.In inflamed tissues, there is both pharmacological and genetic evidence that targeting COX-2 can either improve (e.g., osteoarthritis) or exacerbate symptoms (e.g., inflammatory bowel disease).Multiple lines of evidence suggest that COX-2 plays a significant role in carcinogenesis.The most specific data that support a cause-and effect relationship between COX-2 and tumorigenesis come from genetic studies.Overexpression of COX-2 has been observed to drive tumor formation whereas COX-2 deficiency protects against several tumor types.Selective COX-2 inhibitors protect against the formation and growth of experimental tumors.Moreover, selective COX-2 inhibitors are active in preventing colorectal adenomas in humans.Increased amounts of COX-2-derived PGE2 are found in both inflamed and neoplastic tissues.The fact that PGE2 can stimulate cell proliferation, inhibit apoptosis and induce angiogenesis fits with evidence that induction of COX-2 contributes to both wound healing and tumor growth.Taken together, it seems likely that COX-2 induction contributes to wound healing in response to injury but reduces the threshold for carcinogenesis. cache = ./cache/cord-015147-h0o0yqv8.txt txt = ./txt/cord-015147-h0o0yqv8.txt === 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 === id = cord-015021-pol2qm74 author = nan title = Third International Congress on the Immune Consequences of Trauma, Shock and Sepsis —Mechanisms and Therapeutic Approaches date = 1994 pages = extension = .txt mime = text/plain words = 162327 sentences = 9379 flesch = 50 summary = It is our current understanding that LPS is responsible for many of the pathophysiological events observed during gramnegative infections and that one of the major mechanisms leading to shock and death is the LPS-induced activation of macrophages resulting in the production and release of lipid and peptide mediators, among which tumor necrosis factor seems to be the most important. However plasma IL-6 estimation revealed a statistically significant reduction at 6 hours in tanrine-treated animals compared to glycino and TW controls ( Objective: To evaluate the effects of allogeneic blood transfusion, thermal injury and bacterial garage on interteukin 4 (IL-4), tumor necrosis factor alpha (TNF) production and host mortality and to study if the administration of thymopentth (THY) could affect these events. cache = ./cache/cord-015021-pol2qm74.txt txt = ./txt/cord-015021-pol2qm74.txt === reduce.pl bib === id = cord-257167-rz4r5sj7 author = nan title = Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date = 2006-12-31 pages = extension = .txt mime = text/plain words = 240925 sentences = 13617 flesch = 47 summary = SY1-3-11-3 SAD: A novel kinase implicated in phosphoproteome at the presynaptic active zone Toshihisa Ohtsuka Department of Clinical and Molecular Pathology, Faculty of Medicine/Graduate School of Medicine, University of Toyama, Toyama, Japan SAD is a serine/threonine kianse, which has been shown to regulate various neuronal functions during development, including clustering synaptic vesicles, maturation of synapses, and axon/dendrite polarization: these have recently been revealed by genetic studies in C. The results suggest that EAAT4 plays a major role in regulating the concentration of CF transmitters, possibly glutamate, in the route of its extrasynaptic diffusion, and determining the degree of CF-induced inhibition of GABA release from BCs depending on the regional difference of EAAT4 expression in postsynaptic PCs. Chitoshi Takayama 1 , Yoshiro Inoue 1 1 Department of Molecular Neuroanatomy, Hokkaido University School of Medicine, Sapporo, Japan GABA mediates inhibitory transmission in the adult central nervous system (CNS). cache = ./cache/cord-257167-rz4r5sj7.txt txt = ./txt/cord-257167-rz4r5sj7.txt ===== Reducing email addresses cord-024571-vlklgd3x cord-015147-h0o0yqv8 Creating transaction Updating adr table ===== Reducing keywords cord-016713-pw4f8asc cord-026949-nu46ok9w cord-257027-q2y7fewk cord-017838-fbotc479 cord-004518-jd1wxobz cord-018254-v8syiwie cord-216972-migs9rxb cord-271250-ywb26cq6 cord-031885-by4cujyy cord-021175-0ikkl3hk cord-266750-41gth6o0 cord-002895-z82e7z2v cord-266204-ipa017wz cord-278397-u33x4jaw cord-126015-zc7u3g34 cord-023935-o2ffxgnn cord-270469-lle32mha cord-033714-rz5unqaz cord-290264-pv7ijdnx cord-285982-1a5u7uux cord-029598-qwpya4ox cord-031081-szqrjxq2 cord-297834-me1ajoyb cord-021966-5m21bsrw cord-021424-kocwsyi7 cord-269943-g77qe5ml cord-297776-k38jssr0 cord-015910-d9gxew91 cord-296886-0bma2749 cord-003898-y6zpvw84 cord-032600-lldbjm77 cord-005607-b1a39hhw cord-305263-fgwf6wy3 cord-303319-v3iyur78 cord-021980-ddau5fu3 cord-281883-l9yshyc7 cord-003444-dmpoy0b1 cord-298668-ry49o0xj cord-292983-msuluuuu cord-018265-twp33bb6 cord-007375-hqmyund4 cord-293893-ibca88xu cord-018475-h8qwxdtn cord-303674-0xo2fiop cord-009836-7o6htufh cord-018937-5yo4rfml cord-022435-pztn9075 cord-017817-ztp7w9yh cord-023143-fcno330z cord-309161-ceahghs1 cord-319448-gt6uqfrl cord-030999-27wennun cord-022592-g7rmzsv5 cord-276628-uxsjyezo cord-287396-18p171nr cord-018839-yfaji9cv cord-307202-iz1bo218 cord-022252-9yiuuye3 cord-311331-l7dehit8 cord-252568-b8sbvy0g cord-022076-zpn2h9mt cord-307229-wjx90xki cord-281437-cb3u1s7s cord-278938-bmahwxbn cord-264159-e9071tyv cord-280605-2i4gk7et cord-026960-g844u7xg cord-285778-80baxwgc cord-272512-gevrlcvy cord-302082-aaokc182 cord-288868-qfdxri93 cord-024571-vlklgd3x cord-286072-kgpvdb42 cord-284845-on97zu6w cord-298525-hhcfrjrn cord-263315-g7os15m1 cord-255725-7l9lk9x2 cord-318599-drvjr7gq cord-322913-sq9mq6f1 cord-314104-dkm8396y cord-274027-ovdhnajp cord-273479-kira7mz6 cord-289961-7q2wkwrf cord-257722-7rmzaau4 cord-311823-85wj08gr cord-023055-ntbvmssh cord-324788-echu0zmf cord-328935-mn8r972x cord-311811-nrodyagi cord-318272-spt0oea0 cord-320431-0877trhh cord-324143-ztj6o4ob cord-332838-i8fjwzm6 cord-330583-ltkpt80u cord-335871-zieuc7vk cord-343896-c40fry35 cord-339694-sp212tai cord-339935-tguhrqvz cord-344985-3mu9rrql cord-342317-m6axi18k cord-355541-5sctqkwr cord-344297-qqohijqi cord-354790-xx6imhzb cord-022888-dnsdg04n cord-015021-pol2qm74 cord-257167-rz4r5sj7 cord-015147-h0o0yqv8 Creating transaction Updating wrd table ===== Reducing urls cord-018254-v8syiwie cord-216972-migs9rxb cord-266204-ipa017wz cord-002895-z82e7z2v cord-033714-rz5unqaz cord-290264-pv7ijdnx cord-021424-kocwsyi7 cord-003898-y6zpvw84 cord-032600-lldbjm77 cord-305263-fgwf6wy3 cord-281883-l9yshyc7 cord-003444-dmpoy0b1 cord-022435-pztn9075 cord-319448-gt6uqfrl cord-022076-zpn2h9mt cord-281437-cb3u1s7s cord-024571-vlklgd3x cord-288868-qfdxri93 cord-286072-kgpvdb42 cord-284845-on97zu6w cord-263315-g7os15m1 cord-318599-drvjr7gq cord-322913-sq9mq6f1 cord-314104-dkm8396y cord-311811-nrodyagi cord-324143-ztj6o4ob cord-332838-i8fjwzm6 cord-344985-3mu9rrql cord-344297-qqohijqi cord-022888-dnsdg04n cord-257167-rz4r5sj7 Creating transaction Updating url table ===== Reducing named entities cord-026949-nu46ok9w cord-017838-fbotc479 cord-016713-pw4f8asc cord-257027-q2y7fewk cord-018254-v8syiwie cord-004518-jd1wxobz cord-278397-u33x4jaw cord-266204-ipa017wz cord-216972-migs9rxb cord-021175-0ikkl3hk cord-271250-ywb26cq6 cord-031885-by4cujyy cord-002895-z82e7z2v cord-266750-41gth6o0 cord-126015-zc7u3g34 cord-023935-o2ffxgnn cord-270469-lle32mha cord-033714-rz5unqaz cord-285982-1a5u7uux cord-029598-qwpya4ox cord-031081-szqrjxq2 cord-297834-me1ajoyb cord-021966-5m21bsrw cord-290264-pv7ijdnx cord-021424-kocwsyi7 cord-296886-0bma2749 cord-297776-k38jssr0 cord-269943-g77qe5ml cord-005607-b1a39hhw cord-015910-d9gxew91 cord-032600-lldbjm77 cord-003898-y6zpvw84 cord-305263-fgwf6wy3 cord-021980-ddau5fu3 cord-303319-v3iyur78 cord-003444-dmpoy0b1 cord-281883-l9yshyc7 cord-298668-ry49o0xj cord-292983-msuluuuu cord-007375-hqmyund4 cord-293893-ibca88xu cord-018265-twp33bb6 cord-018475-h8qwxdtn cord-303674-0xo2fiop cord-009836-7o6htufh cord-018937-5yo4rfml cord-022435-pztn9075 cord-017817-ztp7w9yh cord-309161-ceahghs1 cord-319448-gt6uqfrl cord-030999-27wennun cord-276628-uxsjyezo cord-026960-g844u7xg cord-287396-18p171nr cord-022592-g7rmzsv5 cord-307202-iz1bo218 cord-018839-yfaji9cv cord-023143-fcno330z cord-022076-zpn2h9mt cord-311331-l7dehit8 cord-252568-b8sbvy0g cord-022252-9yiuuye3 cord-307229-wjx90xki cord-281437-cb3u1s7s cord-278938-bmahwxbn cord-264159-e9071tyv cord-280605-2i4gk7et cord-285778-80baxwgc cord-272512-gevrlcvy cord-302082-aaokc182 cord-024571-vlklgd3x cord-288868-qfdxri93 cord-286072-kgpvdb42 cord-284845-on97zu6w cord-263315-g7os15m1 cord-298525-hhcfrjrn cord-255725-7l9lk9x2 cord-318599-drvjr7gq cord-322913-sq9mq6f1 cord-314104-dkm8396y cord-273479-kira7mz6 cord-289961-7q2wkwrf cord-274027-ovdhnajp cord-257722-7rmzaau4 cord-311811-nrodyagi cord-311823-85wj08gr cord-324788-echu0zmf cord-328935-mn8r972x cord-318272-spt0oea0 cord-324143-ztj6o4ob cord-320431-0877trhh cord-332838-i8fjwzm6 cord-330583-ltkpt80u cord-335871-zieuc7vk cord-343896-c40fry35 cord-023055-ntbvmssh cord-339694-sp212tai cord-339935-tguhrqvz cord-344985-3mu9rrql cord-342317-m6axi18k cord-344297-qqohijqi cord-355541-5sctqkwr cord-354790-xx6imhzb cord-015147-h0o0yqv8 cord-015021-pol2qm74 cord-022888-dnsdg04n cord-257167-rz4r5sj7 Creating transaction Updating ent table ===== Reducing parts of speech cord-026949-nu46ok9w cord-257027-q2y7fewk cord-017838-fbotc479 cord-018254-v8syiwie cord-004518-jd1wxobz cord-216972-migs9rxb cord-266204-ipa017wz cord-002895-z82e7z2v cord-278397-u33x4jaw cord-031885-by4cujyy cord-021175-0ikkl3hk cord-271250-ywb26cq6 cord-126015-zc7u3g34 cord-266750-41gth6o0 cord-033714-rz5unqaz cord-290264-pv7ijdnx cord-016713-pw4f8asc cord-285982-1a5u7uux cord-270469-lle32mha cord-029598-qwpya4ox cord-297834-me1ajoyb cord-021424-kocwsyi7 cord-005607-b1a39hhw cord-031081-szqrjxq2 cord-003898-y6zpvw84 cord-032600-lldbjm77 cord-297776-k38jssr0 cord-023935-o2ffxgnn cord-305263-fgwf6wy3 cord-303319-v3iyur78 cord-021980-ddau5fu3 cord-281883-l9yshyc7 cord-296886-0bma2749 cord-003444-dmpoy0b1 cord-292983-msuluuuu cord-298668-ry49o0xj cord-269943-g77qe5ml cord-007375-hqmyund4 cord-303674-0xo2fiop cord-018937-5yo4rfml cord-015910-d9gxew91 cord-009836-7o6htufh cord-293893-ibca88xu cord-018475-h8qwxdtn cord-022435-pztn9075 cord-309161-ceahghs1 cord-319448-gt6uqfrl cord-021966-5m21bsrw cord-030999-27wennun cord-018265-twp33bb6 cord-276628-uxsjyezo cord-026960-g844u7xg cord-022076-zpn2h9mt cord-311331-l7dehit8 cord-252568-b8sbvy0g cord-287396-18p171nr cord-281437-cb3u1s7s cord-288868-qfdxri93 cord-272512-gevrlcvy cord-278938-bmahwxbn cord-307229-wjx90xki cord-285778-80baxwgc cord-302082-aaokc182 cord-017817-ztp7w9yh cord-024571-vlklgd3x cord-263315-g7os15m1 cord-298525-hhcfrjrn cord-018839-yfaji9cv cord-264159-e9071tyv cord-280605-2i4gk7et cord-284845-on97zu6w cord-307202-iz1bo218 cord-318599-drvjr7gq cord-022592-g7rmzsv5 cord-322913-sq9mq6f1 cord-273479-kira7mz6 cord-286072-kgpvdb42 cord-289961-7q2wkwrf cord-314104-dkm8396y cord-255725-7l9lk9x2 cord-274027-ovdhnajp cord-311811-nrodyagi cord-311823-85wj08gr cord-324788-echu0zmf cord-324143-ztj6o4ob cord-332838-i8fjwzm6 cord-335871-zieuc7vk cord-339935-tguhrqvz cord-343896-c40fry35 cord-344985-3mu9rrql cord-342317-m6axi18k cord-330583-ltkpt80u cord-339694-sp212tai cord-257722-7rmzaau4 cord-344297-qqohijqi cord-318272-spt0oea0 cord-320431-0877trhh cord-355541-5sctqkwr cord-328935-mn8r972x cord-022252-9yiuuye3 cord-354790-xx6imhzb cord-023143-fcno330z cord-023055-ntbvmssh cord-015147-h0o0yqv8 cord-015021-pol2qm74 cord-022888-dnsdg04n cord-257167-rz4r5sj7 Creating transaction Updating pos table Building ./etc/reader.txt cord-257167-rz4r5sj7 cord-022888-dnsdg04n cord-015021-pol2qm74 cord-022888-dnsdg04n cord-021966-5m21bsrw cord-296886-0bma2749 number of items: 107 sum of words: 1,204,534 average size in words: 22,306 average readability score: 41 nouns: cells; response; cell; responses; expression; vaccine; mice; infection; virus; patients; protein; disease; vaccines; antigen; study; activation; results; role; system; levels; activity; studies; gene; production; dna; receptor; development; effects; host; neurons; type; proteins; analysis; genes; effect; data; antibody; immunity; blood; model; treatment; time; antibodies; sepsis; group; vaccination; function; control; antigens; stress verbs: using; induces; show; increased; suggest; include; associated; express; find; followed; based; mediated; activating; compared; develop; involved; identified; produced; lead; demonstrated; reducing; caused; providing; observe; indicates; results; enhanced; investigated; binding; regulating; infected; determining; related; play; occur; stimulate; presented; require; know; decreased; generate; reported; contains; makes; inhibiting; examining; revealed; studies; signaling; derived adjectives: immune; specific; human; inflammatory; viral; different; high; anti; important; clinical; new; innate; significant; cellular; many; several; dependent; non; low; present; higher; early; single; respiratory; multiple; acute; major; first; infectious; severe; molecular; normal; protective; effective; various; similar; functional; mucosal; like; positive; local; large; novel; bacterial; dendritic; systemic; primary; chronic; recent; genetic adverbs: also; however; well; significantly; therefore; highly; recently; even; furthermore; respectively; previously; often; moreover; directly; now; together; still; especially; particularly; currently; specifically; rather; less; interestingly; first; rapidly; mainly; finally; yet; thereby; similarly; prior; alone; already; potentially; long; generally; relatively; indeed; later; much; strongly; far; almost; usually; clearly; widely; probably; largely; early pronouns: we; it; their; i; its; our; they; them; us; itself; he; themselves; his; one; you; her; she; your; my; me; s; pdcs; ourselves; himself; interleukin-15; igg1; iga1; sarna; oneself; mine; imm+; igmcic; iga2; i-; him; esat-6; e2f2-/-mice; crx-527; beta-2-m; anti-(self; ␤; Ϫ238; yourself; y8tcr.s; wi~; trl2x4; tnf~; thei; ta; sm/ proper nouns: T; Japan; IFN; TNF; University; CD4; LPS; CD8; CTL; B; RNA; C; IL-6; Department; MHC; Tokyo; Univ; HIV; SARS; HLA; A; DNA; Institute; II; M; TCR; School; COVID-19; I; Dept; mg; IL-10; IgA; mRNA; Fig; Research; ER; IL; Science; DC; HCV; Medicine; IL-4; HIV-1; kg; PCR; Sch; Medical; TLR; Med keywords: response; cell; vaccine; immune; dna; infection; ifn; antigen; covid-19; virus; rna; sars; hiv; study; university; mouse; lps; hla; gene; effect; tnf; stress; protein; il-6; ebola; delivery; result; mhc; inflammatory; hcv; elisa; disease; disaster; ctl; cd8; cd4; antibody; vaccination; usa; sepsis; patient; pandemic; model; mers; korea; institute; increase; il-4; il-2; health one topic; one dimension: cells file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121080/ titles(s): Nanotechnological Approaches for Genetic Immunization three topics; one dimension: cells; cells; response file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152278/, https://api.elsevier.com/content/article/pii/S016801020600085X, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123823/ titles(s): Vaccines | Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) | Disaster Theory five topics; three dimensions: cells cell il; vaccine immune virus; japan neurons cells; patients il sepsis; response disaster health file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166418/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121080/, https://api.elsevier.com/content/article/pii/S016801020600085X, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095072/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123823/ titles(s): Immunogenicity | Nanotechnological Approaches for Genetic Immunization | Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) | Third International Congress on the Immune Consequences of Trauma, Shock and Sepsis —Mechanisms and Therapeutic Approaches | Disaster Theory Type: cord title: keyword-response-cord date: 2021-05-25 time: 16:15 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:response ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-278397-u33x4jaw author: Abe, Takayuki title: Negative Regulation of Cytosolic Sensing of DNA date: 2018-10-29 words: 7194.0 sentences: 377.0 pages: flesch: 41.0 cache: ./cache/cord-278397-u33x4jaw.txt txt: ./txt/cord-278397-u33x4jaw.txt summary: Recent efforts have focused on identifying relevant immune surveillance sensors and components of downstream signaling-Toll-like receptors (TLRs) and their cognate ligands, cytosolic sensing of RNA (primary mediated by the RIG-I/IPS-1 axis), cytosolic sensing of DNA (primary mediated by the cGAS/STING axis), and the inflammasome pathway (primary mediated by NOD-like receptors; NLRs) (Broz and Monack, 2013; Kieser and Kagan, 2017; Kumar et al., 2011a ). It has also been suggested that chronic cGAS/STING activation induced by self DNA may be responsible for induction of aberrant inflammatory diseases like systemic lupus erythematosus (SLE), Aicardi-Goutières syndrome (AGS), and polyarthritis (Barber, 2015; Crowl et al., 2017) . Use of DNA damage induced agents like 7,12-dimethylbenz-α-anthracene (DMBA) has helped shed light on the underlying events initiate the DNA damage-induced immune response via cytosolic DNA sensing pathway and implicates nucleosome leakage in eliciting cGAS/STING-dependent signal activation via recognition of self-DNA (Barber, 2015) . abstract: In mammals, cytosolic detection of nucleic acids is critical in initiating innate antiviral responses against invading pathogens (like bacteria, viruses, fungi and parasites). These programs are mediated by multiple cytosolic and endosomal sensors and adaptor molecules (c-GAS/STING axis and TLR9/MyD88 axis, respectively) and lead to the production of type I interferons (IFNs), pro-inflammatory cytokines, and chemokines. While the identity and role of multiple pattern recognition receptors (PRRs) have been elucidated, such immune surveillance systems must be tightly regulated to limit collateral damage and prevent aberrant responses to self- and non-self-nucleic acids. In this review, we discuss recent advances in our understanding of how cytosolic sensing of DNA is controlled during inflammatory immune responses. url: https://doi.org/10.1016/bs.ircmb.2018.09.002 doi: 10.1016/bs.ircmb.2018.09.002 id: cord-303319-v3iyur78 author: Abe, Takayuki title: Cytosolic DNA‐sensing immune response and viral infection date: 2019-02-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: How host cells recognize many kinds of RNA and DNA viruses and initiate innate antiviral responses against them has not yet been fully elucidated. Over the past decade, investigations into the mechanisms underlying these antiviral responses have focused extensively on immune surveillance sensors that recognize virus‐derived components (such as lipids, sugars and nucleic acids). The findings of these studies have suggested that antiviral responses are mediated by cytosolic or intracellular compartment sensors and their adaptor molecules (e.g., TLR, myeloid differentiation primary response 88, retinoic acid inducible gene‐I, IFN‐β promoter stimulator‐1, cyclic GMP‐AMP synthase and stimulator of IFN genes axis) for the primary sensing of virus‐derived nucleic acids, leading to production of type I IFNs, pro‐inflammatory cytokines and chemokines by the host cells. Thus, host cells have evolved an elaborate host defense machinery to recognize and eliminate virus infections. In turn, to achieve sustained viral infection and induce pathogenesis, viruses have also evolved several counteracting strategies for achieving immune escape by targeting immune sensors, adaptor molecules, intracellular kinases and transcription factors. In this review, we discuss recent discoveries concerning the role of the cytosolic nucleic acid‐sensing immune response in viral recognition and control of viral infection. In addition, we consider the regulatory machinery of the cytosolic nucleic acid‐sensing immune response because these immune surveillance systems must be tightly regulated to prevent aberrant immune responses to self and non‐self‐nucleic acids. url: https://doi.org/10.1111/1348-0421.12669 doi: 10.1111/1348-0421.12669 id: cord-029598-qwpya4ox author: Adibe, Bryant title: Creating Wellness in a Pandemic: A Practical Framework for Health Systems Responding to Covid-19 date: 2020-06-01 words: 2333.0 sentences: 95.0 pages: flesch: 44.0 cache: ./cache/cord-029598-qwpya4ox.txt txt: ./txt/cord-029598-qwpya4ox.txt summary: The task force used its collective expertise to develop four key mitigation strategies, described in detail below, to reinforce staff wellness throughout the crisis: Wellness Rounds, a Wellness Consult Service, an advanced mental health intervention program known as Wellness Plus, and a central Wellness Resource Hub with Wellness Rooms on frontline floors. We established a consult service (Figure 1 ) where any clinical unit or individual can connect directly with a member of the Wellness Response Team for evaluation, triage, and recommendations to improve mental health and well-being. When triggered, the individual is escorted to one of the unit-level Wellness Rooms or the central Wellness Resource Hub (see below) where an experienced clinician (typically a physician or other prescriber) completes a thorough mental health assessment, including identifying an immediate therapeutic intervention and appropriate followup. abstract: Caring for Covid-19 patients poses a high risk of short- and long-term psychological distress to hospital employees. Rush University System for Health has developed a simple, practical framework for prioritizing their well-being. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371299/ doi: 10.1056/cat.20.0218 id: cord-324788-echu0zmf author: Aich, Palok title: Modern approaches to understanding stress and disease susceptibility: A review with special emphasis on respiratory disease date: 2009-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Studies in animals and humans link both physical and psychological stress with an increased incidence and severity of respiratory infections. For this manuscript we define stress as the physiological responses an individual undergoes while adjusting to a continually changing environment. It is known that stressors of various types (psychological/physical) can alter the physiological levels of certain hormones, chemokines and cytokines. These alterations send information to the central nervous system to take necessary action which then sends messages to appropriate organs/tissues/cells to respond. These messages can either activate or suppress the immune system as needed and failure to compensate for this by the body can lead to serious health-related problems. Little is known how stress affects disease susceptibility, yet understanding this mechanism is important for developing effective treatments, and for improving health and food quality. The current review focuses on (a) the effects of psychological stressors in humans and animals, (b) various methodologies employed to understand stress responses and their outcomes, and (c) the current status of the attempts to correlate stress and disease with respiratory disease as model system. The methodologies included in this review span traditional epidemiological, behavioral and immunological studies to current high throughput genomic, proteomic, metabolomic/metabonomic approaches. With the advent of various newer omics and bioinformatics methodologies we postulate that it will become feasible to understand the mechanisms through which stress can influence disease onset. Although the literature in this area is limited because of the infancy of this research area, the objective of this review is to illustrate the power of new approaches to address complex biological questions. These new approaches will also aid in our understanding how these processes are related to the dynamics and kinetics of changes in expression of multiple genes at various levels. url: https://www.ncbi.nlm.nih.gov/pubmed/20360883/ doi: nan id: cord-355541-5sctqkwr author: Alcamí, José title: Current situation in the development of a preventive HIV vaccine date: 2005-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-281883-l9yshyc7 author: Alekseeva, Ekaterina title: Enhancement of the expression of HCV core gene does not enhance core-specific immune response in DNA immunization: advantages of the heterologous DNA prime, protein boost immunization regimen date: 2009-06-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Hepatitis C core protein is an attractive target for HCV vaccine aimed to exterminate HCV infected cells. However, although highly immunogenic in natural infection, core appears to have low immunogenicity in experimental settings. We aimed to design an HCV vaccine prototype based on core, and devise immunization regimens that would lead to potent anti-core immune responses which circumvent the immunogenicity limitations earlier observed. METHODS: Plasmids encoding core with no translation initiation signal (pCMVcore); with Kozak sequence (pCMVcoreKozak); and with HCV IRES (pCMVcoreIRES) were designed and expressed in a variety of eukaryotic cells. Polyproteins corresponding to HCV 1b amino acids (aa) 1–98 and 1–173 were expressed in E. coli. C57BL/6 mice were immunized with four 25-μg doses of pCMVcoreKozak, or pCMV (I). BALB/c mice were immunized with 100 μg of either pCMVcore, or pCMVcoreKozak, or pCMVcoreIRES, or empty pCMV (II). Lastly, BALB/c mice were immunized with 20 μg of core aa 1–98 in prime and boost, or with 100 μg of pCMVcoreKozak in prime and 20 μg of core aa 1–98 in boost (III). Antibody response, [(3)H]-T-incorporation, and cytokine secretion by core/core peptide-stimulated splenocytes were assessed after each immunization. RESULTS: Plasmids differed in core-expression capacity: mouse fibroblasts transfected with pCMVcore, pCMVcoreIRES and pCMVcoreKozak expressed 0.22 ± 0.18, 0.83 ± 0.5, and 13 ± 5 ng core per cell, respectively. Single immunization with highly expressing pCMVcoreKozak induced specific IFN-γ and IL-2, and weak antibody response. Single immunization with plasmids directing low levels of core expression induced similar levels of cytokines, strong T-cell proliferation (pCMVcoreIRES), and antibodies in titer 10(3)(pCMVcore). Boosting with pCMVcoreKozak induced low antibody response, core-specific T-cell proliferation and IFN-γ secretion that subsided after the 3rd plasmid injection. The latter also led to a decrease in specific IL-2 secretion. The best was the heterologous pCMVcoreKozak prime/protein boost regimen that generated mixed Th1/Th2-cellular response with core-specific antibodies in titer ≥ 3 × 10(3). CONCLUSION: Thus, administration of highly expressed HCV core gene, as one large dose or repeated injections of smaller doses, may suppress core-specific immune response. Instead, the latter is induced by a heterologous DNA prime/protein boost regimen that circumvents the negative effects of intracellular core expression. url: https://www.ncbi.nlm.nih.gov/pubmed/19505299/ doi: 10.1186/1479-0556-7-7 id: cord-030999-27wennun author: Altmann, Daniel M title: Adaptive immunity to SARS-CoV-2 date: 2020-07-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The majority of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 exposed individuals mount an antibody response within around 2-weeks and spike antigen-binding responses correlate well with functional virus neutralization. A minority makes little detectable antibody, generally those with either very mild/asymptomatic disease or those with severe/lethal infection. However, in general, antibody titre correlates with viral load and duration of exposure. There is evidence for cross-reactivity with the other human coronaviruses, though the functional impact of this is as yet unclear. Therapeutic use of neutralizing monoclonal antibodies offers potential for clinical use. While there is evidence for neutralizing antibody as a correlate of protection, some cases indicate the potential for full recovery in the absence of antibody. Studies of T-cell immunity following acute infection show CD4 and CD8 responses to epitopes across diverse viral antigens, possible cross-reactivity with epitopes from the common cold human coronaviruses and large-scale activation. However, in severe cases, there is evidence for T-cell lymphopaenia as well as expression of exhaustion markers. Analysis of serum biomarkers of disease severity implicates a hyperinflammatory contribution to pathogenesis, though this has not been mechanistically delineated beyond a likely role of raised IL-6, considered a therapeutic target. Despite rapid progress, there remain pressing unknowns. It seems likely that immune memory to SARS-CoV-2 may be relatively short lived, but this will need longitudinal investigation. Also, this is a disease of highly variable presentation and time course, with some progressing to protracted, chronic symptoms, which are not understood. The contribution of immunopathological mechanisms to tissue damage, whether in the lung, kidney, heart or blood vessels, is unclear. The immunology underlying the differential susceptibility between the very young and the very old is unresolved, a question with ramifications for vaccine roll-out. The greatest challenge relates to rapid generation, testing and manufacture of vaccines that are immunogenic, protective (at least from symptomatic disease) and safe—a challenge that looks achievable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454881/ doi: 10.1093/oxfimm/iqaa003 id: cord-318599-drvjr7gq author: Amankwah-Amoah, Joseph title: Note: Mayday, Mayday, Mayday! Responding to environmental shocks: Insights on global airlines’ responses to COVID-19 date: 2020-09-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The COVID-19 pandemic in 2019/2020 ushered in a new turbulent and chaotic global environment where governments not only placed temporary restrictions on people’s movements, but also mandated limits on business activities. However, lacking in the contemporary scholarly discourse is a deeper understanding of how businesses respond to such pandemics. In this research note (RN), a conceptual framework of firms’ responses is advanced. Using the global airline industry, the analysis delineates a host of internally generated and externally imposed firms’ strategic and tactical responses to the pandemic including in-flight service changes, flight cancellations, seeking emergency aids and financial supports, and firm closures. The analysis demonstrates that in responding to the crisis, many airlines sought to minimise erosion of long-developed knowledge, market capabilities, route networks, access to airports, customer base and relationships/trust with customers prior to COVID-19 to equip them for recovery. The wider implications for academics, managers and governments are outlined as the effects of COVID-19 continue to unfold. url: https://www.ncbi.nlm.nih.gov/pubmed/33013185/ doi: 10.1016/j.tre.2020.102098 id: cord-280605-2i4gk7et author: Bachmann, María Consuelo title: The Challenge by Multiple Environmental and Biological Factors Induce Inflammation in Aging: Their Role in the Promotion of Chronic Disease date: 2020-10-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The aging process is driven by multiple mechanisms that lead to changes in energy production, oxidative stress, homeostatic dysregulation and eventually to loss of functionality and increased disease susceptibility. Most aged individuals develop chronic low-grade inflammation, which is an important risk factor for morbidity, physical and cognitive impairment, frailty, and death. At any age, chronic inflammatory diseases are major causes of morbimortality, affecting up to 5–8% of the population of industrialized countries. Several environmental factors can play an important role for modifying the inflammatory state. Genetics accounts for only a small fraction of chronic-inflammatory diseases, whereas environmental factors appear to participate, either with a causative or a promotional role in 50% to 75% of patients. Several of those changes depend on epigenetic changes that will further modify the individual response to additional stimuli. The interaction between inflammation and the environment offers important insights on aging and health. These conditions, often depending on the individual’s sex, appear to lead to decreased longevity and physical and cognitive decline. In addition to biological factors, the environment is also involved in the generation of psychological and social context leading to stress. Poor psychological environments and other sources of stress also result in increased inflammation. However, the mechanisms underlying the role of environmental and psychosocial factors and nutrition on the regulation of inflammation, and how the response elicited for those factors interact among them, are poorly understood. Whereas certain deleterious environmental factors result in the generation of oxidative stress driven by an increased production of reactive oxygen and nitrogen species, endoplasmic reticulum stress, and inflammation, other factors, including nutrition (polyunsaturated fatty acids) and behavioral factors (exercise) confer protection against inflammation, oxidative and endoplasmic reticulum stress, and thus ameliorate their deleterious effect. Here, we discuss processes and mechanisms of inflammation associated with environmental factors and behavior, their links to sex and gender, and their overall impact on aging. url: https://www.ncbi.nlm.nih.gov/pubmed/33162985/ doi: 10.3389/fimmu.2020.570083 id: cord-292983-msuluuuu author: Ballesteros-Briones, María Cristina title: A new generation of vaccines based on alphavirus self-amplifying RNA date: 2020-09-06 words: 4942.0 sentences: 277.0 pages: flesch: 47.0 cache: ./cache/cord-292983-msuluuuu.txt txt: ./txt/cord-292983-msuluuuu.txt summary: In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. This type of LNP-delivered saRNA vaccines, named SAM (for self-amplifying mRNA) platform, have shown great potential to generate immune responses against influenza virus [20] [21] [22] and Toxoplasma gondii [23] . Despite the fact that the ta-RNA system was able to induce good immune responses in vivo against influenza virus HA, it did not outperform vaccination with a single saRNA molecule expressing the same antigen. abstract: DNA or mRNA vaccines have potential advantages over conventional vaccines since they are easier to manufacture and have higher safety profiles. In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. This is mainly due to the fact that saRNA can provide very high expression levels and simultaneously induces strong innate responses, potentiating immunity. saRNA can be administered as viral particles or DNA, but direct delivery as RNA represents a safer and more simple approach. Although saRNA can be delivered as naked RNA, in vivo transfection can be enhanced by electroporation or by complexing it with cationic lipids or polymers. Alphavirus saRNA could have broad application to vaccinate against human pathogens, including emerging ones like SARS-CoV-2, for which clinical trials have been recently initiated. url: https://doi.org/10.1016/j.coviro.2020.08.003 doi: 10.1016/j.coviro.2020.08.003 id: cord-018265-twp33bb6 author: Becker, Pablo D. title: Community-acquired pneumonia: paving the way towards new vaccination concepts date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite the availability of antimicrobial agents and vaccines, community-acquired pneumonia remains a serious problem. Severe forms tend to occur in very young children and among the elderly, since their immune competence is eroded by immaturity and immune senescence, respectively. The main etiologic agents differ according to patient age and geographic area. Streptococcus pneumoniae, Haemophilus influenzae, respiratory syncytial virus (RSV) and parainfluenza virus type 3 (PIV-3) are the most important pathogens in children, whereas influenza viruses are the leading cause of fatal pneumonia in the elderly. Effective vaccines are available against some of these organisms. However, there are still many agents against which vaccines are not available or the existent ones are suboptimal. To tackle this problem, empiric approaches are now being systematically replaced by rational vaccine design. This is facilitated by the growing knowledge in the fields of immunology, microbial pathogenesis and host response to infection, as well as by the availability of sophisticated strategies for antigen selection, potent immune modulators and efficient antigen delivery systems. Thus, a new generation of vaccines with improved safety and efficacy profiles compared to old and new agents is emerging. In this chapter, an overview is provided about currently available and new vaccination concepts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123104/ doi: 10.1007/978-3-7643-7563-8_10 id: cord-281437-cb3u1s7s author: Bedford, Juliet title: A new twenty-first century science for effective epidemic response date: 2019-11-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: With rapidly changing ecology, urbanization, climate change, increased travel and fragile public health systems, epidemics will become more frequent, more complex and harder to prevent and contain. Here we argue that our concept of epidemics must evolve from crisis response during discrete outbreaks to an integrated cycle of preparation, response and recovery. This is an opportunity to combine knowledge and skills from all over the world—especially at-risk and affected communities. Many disciplines need to be integrated, including not only epidemiology but also social sciences, research and development, diplomacy, logistics and crisis management. This requires a new approach to training tomorrow’s leaders in epidemic prevention and response. url: https://www.ncbi.nlm.nih.gov/pubmed/31695207/ doi: 10.1038/s41586-019-1717-y id: cord-005607-b1a39hhw author: Bellingan, G title: Leukocytes: friend or foe date: 2000 words: 3827.0 sentences: 173.0 pages: flesch: 37.0 cache: ./cache/cord-005607-b1a39hhw.txt txt: ./txt/cord-005607-b1a39hhw.txt summary: Over the last three decades we have gained significant insights into leukocyte activation, recruitment and mediator secretion and the contribution of these agents to both the onset and resolution of sepsis and inflammation.¶The body relies on the inflammatory response for protection. A direct consequence of this protective strategy is that the inflammatory response may be inadequate, with the risk of overwhelming sepsis, or excessive, leading to rampant systemic inflammation and consequent multiple organ damage.¶It is now becoming apparent however that in addition to leukocytes other cells have important roles both in defence against invading pathogens and in driving malignant inflammation. Endothelial cells, mesothelial cells, fibroblasts and epithelial cells are also all involved not only with their capacity to drive the inflammatory response through mediator generation but also in innate immune defences including through the production of antimicrobial proteins. abstract: Leukocytes have a fundamental role in innate and adaptive immunity, wound healing, tumour surveillance and in tissue remodelling. It is their function in the inflammatory response however that is of most interest to us in the intensive care setting. Over the last three decades we have gained significant insights into leukocyte activation, recruitment and mediator secretion and the contribution of these agents to both the onset and resolution of sepsis and inflammation.¶The body relies on the inflammatory response for protection. Leukocytes occupy a pivotal position in this but to maintain these cells in a state of permanent activation would be unsustainable, with widespread microvascular plugging, uncontrolled free radical release and an excessive metabolic demand. Leukocytes thus circulate in a quiescent state and are rapidly activated by invading pathogens and other stimuli. A direct consequence of this protective strategy is that the inflammatory response may be inadequate, with the risk of overwhelming sepsis, or excessive, leading to rampant systemic inflammation and consequent multiple organ damage.¶It is now becoming apparent however that in addition to leukocytes other cells have important roles both in defence against invading pathogens and in driving malignant inflammation. This review will focus on two new facets of the innate immune system, the Toll family of proteins as the signal transduction element for endotoxin, and the antimicrobial peptides. These exemplify potential damaging and protective response elements but importantly neither are restricted to leukocytes. The capacity of cells and tissues other than the leukocytes to participate and even lead in the inflammatory responses will also be explored. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094984/ doi: 10.1007/s001340051127 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-009836-7o6htufh author: Borrow, Persephone title: Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date: 2006-04-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Summary: Although viral variants which are not recognized by epitope‐specific cytotoxic T lymphocytes (CTL) have been shown lo arise during a number of persistent virus infections, in many cases their significance remains controversial: it has been argued that the immune response is sufficiently plastic to contain their replication. In this review, we describe the mechanisms by which amino acid changes in viral proteins may affect epitope recognition by virus‐specific CTL, and discuss the viral and immunological basis for the emergence of viral variants bearing such amino acid changes during infection. We then consider the impact that viral variation may have on the host CTL response and its ability to contain virus replication. We argue that the emergence of a viral variant demonstrates that it must have an in vivo replicative advantage, and that as such, the variant must tip the balance between virus replication and immune control somewhat in favor of the virus. Further, we suggest that although the immune response can evolve to recognize new viral epitopes, the CTL generated following such evolution frequently have a reduced ability to contain virus replication. We conclude that this escape mechanism likely does make a significant contribution to persistence/pathogenesis during a number of different virus infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165923/ doi: 10.1111/j.1600-065x.1998.tb01206.x id: cord-018937-5yo4rfml author: Bortolin, Michelangelo title: Disaster Medicine date: 2015-04-18 words: 3722.0 sentences: 188.0 pages: flesch: 51.0 cache: ./cache/cord-018937-5yo4rfml.txt txt: ./txt/cord-018937-5yo4rfml.txt summary: Disaster is defi ned as any event that causes "a serious disruption of the functioning of a community or a society involving widespread human, material, economic or environmental losses and impacts, which exceeds the ability of the affected community or society to cope using its own resources" [ 1 ] . The Incident Command System (ICS) provides a structure to enable agencies with different legal, jurisdictional, and functional responsibilities to coordinate, plan, and interact effectively on scene [ 11 ] . During a disaster, it is extremely important to establish a unifi ed command, because it enables all responsible agencies to manage and coordinate an incident together by establishing a common approach and a single IAP. It is defi ned as second incident caused by the terrorists, following the fi rst event, with the goal of striking the fi rst responders that are on scene. abstract: Millions of people every day face disasters, for example, typhoons, terrorist attacks, earthquakes, famine, civil wars, explosions, and tornadoes. Disaster is defined as every event that causes serious disruption which exceeds the ability of the affected community or society to cope using its own resources. Disasters are usually categorized as natural or man-made and are described using a series of steps called the disaster cycle, defined in four phases: mitigation and prevention, preparedness and planning, response, and recovery. Disaster medicine is an emerging specialty that integrates the medical response to disaster with the systems of disaster management. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123951/ doi: 10.1007/978-3-319-16586-8_25 id: cord-335871-zieuc7vk author: Brazee, Patricia L. title: Targeting the Linear Ubiquitin Assembly Complex to Modulate the Host Response and Improve Influenza A Virus Induced Lung Injury date: 2020-05-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Influenza virus infection is characterized by symptoms ranging from mild congestion and body aches to severe pulmonary edema and respiratory failure. While the majority of those exposed have minor symptoms and recover with little morbidity, an estimated 500,000 people succumb to IAV-related complications each year worldwide. In these severe cases, an exaggerated inflammatory response, known as “cytokine storm”, occurs which results in damage to the respiratory epithelial barrier and development of acute respiratory distress syndrome (ARDS). Data from retrospective human studies as well as experimental animal models of influenza virus infection highlight the fine line between an excessive and an inadequate immune response, where the host response must balance viral clearance with exuberant inflammation. Current pharmacological modulators of inflammation, including corticosteroids and statins, have not been successful in improving outcomes during influenza virus infection. We have reported that the amplitude of the inflammatory response is regulated by Linear Ubiquitin Assembly Complex (LUBAC) activity and that dampening of LUBAC activity is protective during severe influenza virus infection. Therapeutic modulation of LUBAC activity may be crucial to improve outcomes during severe influenza virus infection, as it functions as a molecular rheostat of the host response. Here we review the evidence for modulating inflammation to ameliorate influenza virus infection-induced lung injury, data on current anti-inflammatory strategies, and potential new avenues to target viral inflammation and improve outcomes. url: https://api.elsevier.com/content/article/pii/S0300289620301381 doi: 10.1016/j.arbres.2020.04.019 id: cord-004518-jd1wxobz author: Běláková, Jana title: DNA vaccines: are they still just a powerful tool for the future? date: 2007-12-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vaccination is historically one of the most successful strategies for the prevention of infectious diseases. For safety reasons, modern vaccinology tends toward the usage of inactivated or attenuated microorganisms and uses predominantly subunit vaccines. The antigens need to be clearly defined, pure, stable, appropriately composed, and properly presented to the immune system of the host. Differing ratios of various proportions between specific CD4(+) and CD8(+) T cell responses are essential for conferring the required protection in the case of individual vaccines. To stimulate both CD4(+) and CD8(+) T cells, the antigens must be processed and presented to both antigen-presentation pathways, MHC I and MHC II. Protein antigens delivered by vaccination are processed as extracellular antigens. However, extracellularly delivered antigen can be directed towards intracellular presentation pathways in conjugation with molecules involved in antigen cross-presentation, e.g. heat shock proteins, or by genomic-DNA vaccination. In this overview, current knowledge of the host immune response to DNA vaccines is summarized in the introduction. The subsequent sections discuss techniques for enhancing DNA vaccine efficacy, such as DNA delivery to specific tissues, delivery of DNA to the cell cytoplasm or nucleus, and enhancement of the immune response using molecular adjuvants. Finally, the prospects of DNA vaccination and ongoing clinical trials with various DNA vaccines are discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079751/ doi: 10.1007/s00005-007-0044-4 id: cord-031081-szqrjxq2 author: Campbell, Margaret C title: In Times of Trouble: A Framework for Understanding Consumers’ Responses to Threats date: 2020-07-09 words: 11083.0 sentences: 560.0 pages: flesch: 50.0 cache: ./cache/cord-031081-szqrjxq2.txt txt: ./txt/cord-031081-szqrjxq2.txt summary: In conjunction with these articles, we hope that this conceptual framework will provide a point of departure for researchers seeking to enhance the understanding of how consumers and markets collectively respond over the short term and long term to threats that disrupt consumers'' routines, lives, or even the fabric of society. Our goal is not to provide a comprehensive review of existing literature, but rather a guide to researchers seeking to increase our collective understanding of how consumers and markets together respond over short and long durations to threats that disrupt their very being. The findings of this article suggest that economic recessions, pandemics, and terror threats can affect subjective life expectancy for some consumers, leading to different financial and health decisions than they might make otherwise, as well as potentially impacting their mental health. abstract: The COVID-19 pandemic and the accompanying economic downturn have dramatically impacted the lives of consumers around the world. From a conceptual perspective, such health and economic threats can severely disrupt consumers’ sense of ontological security and elicit adaptive responses by both consumers and marketers. Given the opportune timing, this issue of the Journal of Consumer Research is focused on articles that address questions of consumers’ responses to external threats. The purpose of this introduction is to provide an organizing “conceptual tapestry” to connect the articles appearing in the issue. This framework is provided as a tool to help researchers structure their particular projects within the broader landscape of consumer threat response and to present some potential directions for future research. In conjunction with these articles, we hope that this conceptual framework will provide a point of departure for researchers seeking to enhance the understanding of how consumers and markets collectively respond over the short term and long term to threats that disrupt consumers’ routines, lives, or even the fabric of society. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454649/ doi: 10.1093/jcr/ucaa036 id: cord-319448-gt6uqfrl author: Casadevall, Arturo title: The damage-response framework of microbial pathogenesis date: 2003 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The late twentieth century witnessed the emergence of numerous infectious diseases that are caused by microorganisms that rarely cause disease in normal, healthy immunocompetent hosts. The emergence of these diseases shows that the existing concepts of pathogenicity and virulence do not take into account the fact that both the microorganism and the host contribute to microbial pathogenesis. To address this impediment to studies of host–microorganism interactions, we propose a new theoretical approach to understanding microbial pathogenesis, known as the 'damage-response' framework. url: https://www.ncbi.nlm.nih.gov/pubmed/15040176/ doi: 10.1038/nrmicro732 id: cord-022076-zpn2h9mt author: Chaffee, Mary W. title: The Role of Hospitals in Disaster 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/PMC7152438/ doi: 10.1016/b978-0-323-03253-7.50012-1 id: cord-289961-7q2wkwrf author: Chattopadhyay, Saborni title: Nanoparticle Vaccines Adopting Virus-like Features for Enhanced Immune Potentiation date: 2017-06-09 words: 10531.0 sentences: 581.0 pages: flesch: 32.0 cache: ./cache/cord-289961-7q2wkwrf.txt txt: ./txt/cord-289961-7q2wkwrf.txt summary: Exploiting the same transport mechanisms aimed at detaining viruses, nanoparticle vaccines can effectively target immune cells in lymph nodes, delivering antigens or adjuvants following administration in peripheral tissues [13, 141, 142] (Fig. 3A) . Given the privilege of nanocarriers in lymphatic transport, nanoparticles have been shown to enhance the delivery of target antigens to lymph nodes and resident immune cells for processing and immune activation. In their animal study, strong anti-ovalbumin humoral response was observed [13] , highlighting the benefit of nanoparticle-mediated lymph node delivery on enhancing antigen processing. These virus-like particles showed high immunogenicity in both murine and avian models and enhanced anti-viral IgA and IgG titers and cellular immune responses in comparison to free protein antigens and a commercial WIV vaccine [155] . Not only can nanoparticle vaccines enhance humoral responses against target antigens, they have been shown to promote cell-based immunity as well as immunological memory. abstract: Synthetic nanoparticles play an increasingly significant role in vaccine design and development as many nanoparticle vaccines show improved safety and efficacy over conventional formulations. These nanoformulations are structurally similar to viruses, which are nanoscale pathogenic organisms that have served as a key selective pressure driving the evolution of our immune system. As a result, mechanisms behind the benefits of nanoparticle vaccines can often find analogue to the interaction dynamics between the immune system and viruses. This review covers the advances in vaccine nanotechnology with a perspective on the advantages of virus mimicry towards immune potentiation. It provides an overview to the different types of nanomaterials utilized for nanoparticle vaccine development, including functionalization strategies that bestow nanoparticles with virus-like features. As understanding of human immunity and vaccine mechanisms continue to evolve, recognizing the fundamental semblance between synthetic nanoparticles and viruses may offer an explanation for the superiority of nanoparticle vaccines over conventional vaccines and may spur new design rationales for future vaccine research. These nanoformulations are poised to provide solutions towards pressing and emerging human diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/29071191/ doi: 10.7150/ntno.19796 id: cord-322913-sq9mq6f1 author: Ciabattini, Annalisa title: Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population date: 2020-11-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The SARS-CoV-2 pandemic urgently calls for the development of effective preventive tools. COVID-19 hits greatly the elder and more fragile fraction of the population boosting the evergreen issue of the vaccination of older people. The development of a vaccine against SARS-CoV-2 tailored for the elderly population faces the challenge of the poor immune responsiveness of the older population due to immunosenescence, comorbidities, and pharmacological treatments. Moreover, it is likely that the inflammaging phenotype associated with age could both influence vaccination efficacy and exacerbate the risk of COVID-19-related “cytokine storm syndrome” with an overlap between the factors which impact vaccination effectiveness and those that boost virulence and worsen the prognosis of SARS-CoV-2 infection. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. In the ongoing effort in vaccine development, different SARS-CoV-2 vaccine candidates have been developed, tested in pre-clinical and clinical studies and are undergoing clinical testing, but only a small fraction of these are currently being tested in the older fraction of the population. Recent advances in systems biology integrating clinical, immunologic, and omics data can help to identify stable and robust markers of vaccine response and move towards a better understanding of SARS-CoV-2 vaccine responses in the elderly. url: https://doi.org/10.1007/s00281-020-00821-0 doi: 10.1007/s00281-020-00821-0 id: cord-298668-ry49o0xj author: Ciotti, John Robert title: Effects of MS disease-modifying therapies on responses to vaccinations: a review. date: 2020-08-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: : Development of long-term immunologic memory relies upon humoral and cellular immune responses. Vaccinations aim to stimulate these responses against pathogens. Several studies have evaluated the impact of multiple sclerosis disease-modifying therapies on immune response to vaccines. Findings from these studies have important implications for people with multiple sclerosis who require vaccination and are using disease-modifying therapies. METHODS: : Searches using PubMed and other engines were conducted in May 2020 to collect studies evaluating the impact of various disease-modifying therapies on immune responses to vaccination. RESULTS: : Several studies demonstrated preserved immune responses in people treated with beta-interferons to multiple vaccine types. Limited data suggest vaccine responses to be preserved with dimethyl fumarate treatment, as well. Vaccine responses were reduced to varying degrees in those treated with glatiramer acetate, teriflunomide, sphingosine-1-phosphate receptor modulators, and natalizumab. The timing of vaccination played an important role in those treated with alemtuzumab. Humoral vaccine responses were significantly impaired by B cell depleting anti-CD20 monoclonal antibody therapies, particularly to a neoantigen. Data are lacking on vaccine responses in patients with multiple sclerosis taking cladribine and high-dose corticosteroids. Notably, the majority of these studies have focused on humoral responses, with few examining cellular immune responses to vaccination. CONCLUSIONS: : Prior investigations into the effects of individual disease-modifying therapies on immune responses to existing vaccines can serve as a guide to expected responses to a SARS-CoV-2 vaccine. Responses to any vaccination depend on the vaccine type, the type of response (recall versus response to a novel antigen), and the impact of the individual disease-modifying therapy on humoral and cellular immunity in response to that vaccine type. When considering a given therapy, clinicians should weigh its efficacy against MS for the individual patient versus potential impact on responses to vaccinations that may be needed in the future. url: https://api.elsevier.com/content/article/pii/S2211034820305149 doi: 10.1016/j.msard.2020.102439 id: cord-021980-ddau5fu3 author: Ciottone, Gregory R. title: Introduction to Disaster Medicine date: 2015-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152296/ doi: 10.1016/b978-0-323-28665-7.00001-7 id: cord-303674-0xo2fiop author: Criscuolo, E. title: Alternative Methods of Vaccine Delivery: An Overview of Edible and Intradermal Vaccines date: 2019-03-04 words: 7451.0 sentences: 359.0 pages: flesch: 32.0 cache: ./cache/cord-303674-0xo2fiop.txt txt: ./txt/cord-303674-0xo2fiop.txt summary: In particular, novel strategies based on edible or intradermal vaccine formulations have been demonstrated to trigger both a systemic and mucosal immune response. In this review, we discuss current advances and advantages of edible systems based on plants, algae, yeast, insect cells, and lactic acid bacteria and of the intradermal immunization route. Subsequently, the antigen(s) can be incorporated into different edible systems, as plants, algae, insects, or yeasts, or used for intradermal formulations to induce a mucosal protective response. Remarkably, some preclinical studies based on orally administrated Saccharomyces cerevisiae and developed for different infectious agents, such as HPV and Actinobacillus pleuropneumoniae, showed that this delivery system is able to induce a protective mucosal and a systemic immune response [68] [69] [70] . Another vaccine delivery route capable of triggering both systemic and mucosal immunities is the intradermal route, in which the antigen is delivered through the skin using recently developed self-administrable devices. abstract: Vaccines are recognized worldwide as one of the most important tools for combating infectious diseases. Despite the tremendous value conferred by currently available vaccines toward public health, the implementation of additional vaccine platforms is also of key importance. In fact, currently available vaccines possess shortcomings, such as inefficient triggering of a cell-mediated immune response and the lack of protective mucosal immunity. In this regard, recent work has been focused on vaccine delivery systems, as an alternative to injectable vaccines, to increase antigen stability and improve overall immunogenicity. In particular, novel strategies based on edible or intradermal vaccine formulations have been demonstrated to trigger both a systemic and mucosal immune response. These novel vaccination delivery systems offer several advantages over the injectable preparations including self-administration, reduced cost, stability, and elimination of a cold chain. In this review, the latest findings and accomplishments regarding edible and intradermal vaccines are described in the context of the system used for immunogen expression, their molecular features and capacity to induce a protective systemic and mucosal response. url: https://doi.org/10.1155/2019/8303648 doi: 10.1155/2019/8303648 id: cord-269943-g77qe5ml author: Di Sotto, Antonella title: Plant-Derived Nutraceuticals and Immune System Modulation: An Evidence-Based Overview date: 2020-08-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Immunomodulators are agents able to affect the immune system, by boosting the immune defences to improve the body reaction against infectious or exogenous injuries, or suppressing the abnormal immune response occurring in immune disorders. Moreover, immunoadjuvants can support immune system acting on nonimmune targets, thus improving the immune response. The modulation of inflammatory pathways and microbiome can also contribute to control the immune function. Some plant-based nutraceuticals have been studied as possible immunomodulating agents due to their multiple and pleiotropic effects. Being usually more tolerable than pharmacological treatments, their adjuvant contribution is approached as a desirable nutraceutical strategy. In the present review, the up to date knowledge about the immunomodulating properties of polysaccharides, fatty acids and labdane diterpenes have been analyzed, in order to give scientific basic and clinical evidence to support their practical use. Since promising evidence in preclinical studies, limited and sometimes confusing results have been highlighted in clinical trials, likely due to low methodological quality and lacking standardization. More investigations of high quality and specificity are required to describe in depth the usefulness of these plant-derived nutraceuticals in the immune system modulation, for health promoting and disease preventing purposes. url: https://doi.org/10.3390/vaccines8030468 doi: 10.3390/vaccines8030468 id: cord-311331-l7dehit8 author: Diaz-Arévalo, Diana title: Nanoparticle-based vaccines: opportunities and limitations date: 2020-01-17 words: 5064.0 sentences: 266.0 pages: flesch: 42.0 cache: ./cache/cord-311331-l7dehit8.txt txt: ./txt/cord-311331-l7dehit8.txt summary: The development of subunit vaccines without risk are considered as an essential need in combination with adequate delivery systems to obtain desired cell and humoral immune responses against infectious diseases. The characteristics of the nanoparticles have allowed targeting desired antigen-presenting cells to improve immunization strategies to induce protection. This chapter focuses on the nanoparticle-based vaccine formulations and the approaches used to realize efficient delivery of vaccines in order to induce host protective immunity against infectious diseases. The combination of the vaccine with the adjuvant or delivery system should be safe, stable, and have the ability to induce long-lived memory B and T cell responses, preferably with a single dose and a maximum of two doses and be free from strict storage requirements [9] . NPs have become an alternative to targeting vaccine delivery to immune cells, improving vaccine efficacy with slow release, easy antigen uptake, and induction of humoral and cellular responses [8] . abstract: Infectious diseases are the tip of the iceberg in the economic burden of the developing countries, due to the resistance of the pathogens to antibiotics and the lack of vaccines. The vaccines have become a big challenge in the last decades, where the attention has been focused on scientific challenges such as new vaccine development and adjuvants or delivery systems. The classical vaccines were developed from live-attenuated or killed organisms, such as influenza, smallpox, and BCG, as well as subunits such as Hepatitis B. The attenuated vaccines carry the risk of regaining their pathogenicity under immunosuppression conditions. The development of subunit vaccines without risk are considered as an essential need in combination with adequate delivery systems to obtain desired cell and humoral immune responses against infectious diseases. In the last decades, the use of nanoparticles as a delivery system in vaccines has received special attention to improve vaccine efficacy. These nanoparticles could be composed of lipids, metal and nonmetal inorganics, several polymers, and virus-like particles, which have been tested in research; some of them have already been approved for human and animal use. The characteristics of the nanoparticles have allowed targeting desired antigen-presenting cells to improve immunization strategies to induce protection. The main characteristics of the nanoparticles are to protect the antigens from early proteolytic degradation, control antigen release, and help antigen uptake and processing by antigen-presenting cells, and they should be safe for human and veterinary use. In addition, the nanoparticles could be modified in their physicochemical properties to target specific cells and improve vaccine efficacy. This chapter focuses on the nanoparticle-based vaccine formulations and the approaches used to realize efficient delivery of vaccines in order to induce host protective immunity against infectious diseases. url: https://api.elsevier.com/content/article/pii/B9780128177785000075 doi: 10.1016/b978-0-12-817778-5.00007-5 id: cord-343896-c40fry35 author: Dong, Fen title: Vaccination Route Determines the Kinetics and Magnitude of Nasal Innate Immune Responses in Rainbow Trout (Oncorhynchus mykiss) date: 2020-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: SIMPLE SUMMARY: Many pathogens exploit the olfactory route to reach critical organs in the body such as the brain or lungs. Thus, effective onset of an early innate immune response in the nasal epithelium is key to stopping pathogen progression. The stimulation of nasal immunity by vaccines may depend on the type of vaccine and vaccination route. The goal of this study was to evaluate the ability of a live attenuated viral vaccine to stimulate innate immunity in the olfactory organ of rainbow trout, a teleost fish of commercial aquaculture value. The kinetics and magnitude of the innate immune response depended on the route of vaccination, with the strongest and fastest responses recorded in intranasally vaccinated fish. Injection vaccination had an intermediate effect, whereas immersion vaccination resulted in delayed and weak nasal innate immunity. Injection vaccination, even with the vehicle control, induced mortality in fingerlings, whereas nasal and immersion vaccines were safe. Challenge experiments with the live virus revealed that nasal and injected vaccines conferred very high and comparable levels of protection, but immersion vaccination only induced transient protection. In conclusion, the route of vaccination determines the type, magnitude and velocity of the innate immune response in the nasal epithelium of animals. ABSTRACT: Many pathogens infect animal hosts via the nasal route. Thus, understanding how vaccination stimulates early nasal immune responses is critical for animal and human health. Vaccination is the most effective method to prevent disease outbreaks in farmed fish. Nasal vaccination induces strong innate and adaptive immune responses in rainbow trout and was shown to be highly effective against infectious hematopoietic necrosis (IHN). However, direct comparisons between intranasal, injection and immersion vaccination routes have not been conducted in any fish species. Moreover, whether injection or immersion routes induce nasal innate immune responses is unknown. The goal of this study is to compare the effects of three different vaccine delivery routes, including intranasal (IN), intramuscular (i.m.) injection and immersion (imm) routes on the trout nasal innate immune response. Expression analyses of 13 immune-related genes in trout nasopharynx-associated lymphoid tissue (NALT), detected significant changes in immune expression in all genes analyzed in response to the three vaccination routes. However, nasal vaccination induced the strongest and fastest changes in innate immune gene expression compared to the other two routes. Challenge experiments 7 days post-vaccination (dpv) show the highest survival rates in the IN- and imm-vaccinated groups. However, survival rates in the imm group were significantly lower than the IN- and i.m.-vaccinated groups 28 dpv. Our results confirm that nasal vaccination of rainbow trout with live attenuated IHNV is highly effective and that the protection conferred by immersion vaccination is transient. These results also demonstrate for the first time that immersion vaccines stimulate NALT immune responses in salmonids. url: https://www.ncbi.nlm.nih.gov/pubmed/33019693/ doi: 10.3390/biology9100319 id: cord-309161-ceahghs1 author: Epel, Elissa S. title: The geroscience agenda: What does stress have to do with it? date: 2020-09-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Geroscience offers a counterpoint to the challenged pursuit of curing diseases of aging by focusing on slowing the biological aging process for extended healthspan earlier in life. Remarkable progress has led this field toward animal trials and the next challenge lies with translation to humans. There is an emerging number of small human trials that can take advantage of new models integrating behavioral and social factors. Understanding dynamic aging mechanisms, given the powerful social determinants of aging (Crimmins, 2019) and human variability and environmental contexts (Moffitt, 2019), will be critical. Behavioral and social factors are intrinsic to aging. Toxic stressors broadly defined can lead to stress-acceleration of aging, either directly impacting aging processes or by shaping poor behavioral health, and underlie the socioeconomic disparities of aging. In contrast, hormetic stressors, acute intermittent stressors of moderate intensity, can produce stress resilience, the ability for quick recovery and possibly rejuvenation of cells and tissues. Although health research usually examines static biomarkers, aging is reflected in ability to recover from challenges pointing to new interventions and targets for examining mechanisms. A fuller model incorporating stress resilience provides innovative biobehavioral interventions, both for bolstering response to challenges, such as COVID-19, and for improving healthspan. url: https://api.elsevier.com/content/article/pii/S1568163720303020 doi: 10.1016/j.arr.2020.101167 id: cord-017838-fbotc479 author: Fagone, Paolo title: Electroporation-Mediated DNA Vaccination date: 2010-12-15 words: 5279.0 sentences: 221.0 pages: flesch: 31.0 cache: ./cache/cord-017838-fbotc479.txt txt: ./txt/cord-017838-fbotc479.txt summary: Thus, electroporation-mediated DNA vaccination represents a promising new strategy for the elicitation of strong immune responses directed against the expressed antigen(s) and not the vector, and ongoing studies are currently underway to optimize the working parameters of this technique. [26] demonstrated in mice that upon electroporative treatment, the delivery of a weakly immunogenic hepatitis B virus (HBV) surface antigen (Hbs Ag) DNA vaccine resulted in an increased humoral immune response, characterized by rapid onset and higher titers of anti-Hbs Ag antibodies. In addition, the authors observed in the same study that the potency of an HIV gag pDNA vaccine was increased as shown by the lower dosage of DNA required to induce higher antigen-specific antibody levels and increased CD8 + T cell responses. [31] have demonstrated that gene electrotransfer efficiently increased the cellular immune response both in mice and rhesus macaques vaccinated with a plasmid encoding a nonstructural region of hepatitis C virus (HCV). abstract: There are many positive attributes to DNA vaccination that make it a conceptually desirable platform. In clinical studies, however, standard DNA injection alone generally induces low levels of transgene-specific immunity when compared to other vaccine approaches. In order to boost the immunogenicity of this platform, next-generation DNA vaccines require additional techniques such as the administration of electroporation. This new method involves the generation of a brief electric field in tissue around a local injection site that results in the transient poration, or permeabilization, of the cellular membranes. As a result, antigen-specific immune responses are greatly enhanced and are likely due to increased DNA uptake and antigen expression. Thus, electroporation-mediated DNA vaccination represents a promising new strategy for the elicitation of strong immune responses directed against the expressed antigen(s) and not the vector, and ongoing studies are currently underway to optimize the working parameters of this technique. Here, we review the uses of this technology in conjunction with vaccination and suggest future directions for its further exploration. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122510/ doi: 10.1007/978-1-4419-8363-3_18 id: cord-344985-3mu9rrql author: Fakhruddin, Bapon title: Are we there yet? The transition from response to recovery for the COVID-19 pandemic date: 2020-05-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract There is no corner of the planet that has not been impacted by the rapid spread of the novel coronavirus, COVID-19. While the COVID-19 pandemic has already had far-reaching socioeconomic consequences commonly associated with natural hazards (such as disruption to society, economic damage, and loss of lives), the response of governments around the world has been unparalleled and unlike anything seen before. Governments are faced with a myriad of multi-dimensional effects of the pandemic, including direct impacts on public health systems and population health and indirect socioeconomic effects including disruption to every single sector of the economy and mass unemployment. There is, additionally, the growing realisation that the timescale associated with this crisis may permanently change the very foundations of societies ‘normal’ day-to-day life. As the world transitions to recovering from COVID-19, those developing that recovery need support in adjusting and improving their policies and measures. The situation seems dire, the stakes are high. Literature about the transition between the response and recovery phase in relation to pandemics is scarce. Further complication is that the pandemic will not allow countries to simply transition to the full-scale recovery, instead, a rebound from recovery to response phase is expected for a certain period until the immunization is in place. Pandemics indeed force us to think beyond typical emergency management structures; the cycles of the disaster risk management in the case of biological and other natural hazards are not exactly the same and no one-size-fits-all approach may be used. Still, some parallels may be drawn with the efforts to combat natural hazards and some lessons may be used from previous and the current pandemic. Based on these experiences and reflections, this paper provides a set of policy directions to be considered during the transition towards, as well as throughout, this transition phase. It is suggested that meeting this global, multi-dimensional, and complex challenge will require considerable international collaboration (even convention) and macro-scale changes to global and national policies. The recovery issues are mainly going to be dominated by politics, economics and social science. Necessary for an effective recovery, the pandemic response needs to be a holistic response, combined with an improved data ecosystem between the public health system and the community. We should also view this outbreak and our response to it as an opportunity to learn lessons and reaffirm our universal commitment to sustainable development and enhancing wellbeing around the world. url: https://api.elsevier.com/content/article/pii/S2590061720300399 doi: 10.1016/j.pdisas.2020.100102 id: cord-284845-on97zu6w author: Falcinelli, Shane D. title: Integration of Global Analyses of Host Molecular Responses with Clinical Data To Evaluate Pathogenesis and Advance Therapies for Emerging and Re-emerging Viral Infections date: 2016-07-29 words: 8473.0 sentences: 421.0 pages: flesch: 35.0 cache: ./cache/cord-284845-on97zu6w.txt txt: ./txt/cord-284845-on97zu6w.txt summary: Here, we will discuss this approach with a focus on the emerging viral pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola virus (EBOV), and monkeypox virus (MPXV) from the context of clinical presentation, immunological and molecular features of the diseases, and OMICS-based analyses of pathogenesis. As emerging viral infections often result in severe illness including respiratory failure [severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and influenza] and multiorgan failure [Ebola virus disease (EVD)], understanding complex pathogenesis of these infections is required for effective vaccine and therapeutic design and for improved patient care. Specifically, detailed natural history studies merging multiple data streams including OMICS approaches (high-throughput gene expression and kinomics) and focused translational investigations utilizing relevant models that can be validated to human disease are needed to clarify disease pathogenesis, advance therapeutic discovery, and facilitate regulatory approval. abstract: [Image: see text] Outbreaks associated with emerging and re-emerging viral pathogens continue to increase in frequency and are associated with an increasing burden to global health. In light of this, there is a need to integrate basic and clinical research for investigating the connections between molecular and clinical pathogenesis and for therapeutic development strategies. Here, we will discuss this approach with a focus on the emerging viral pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola virus (EBOV), and monkeypox virus (MPXV) from the context of clinical presentation, immunological and molecular features of the diseases, and OMICS-based analyses of pathogenesis. Furthermore, we will highlight the role of global investigations of host kinases, the kinome, for investigating emerging and re-emerging viral pathogens from the context of characterizing cellular responses and identifying novel therapeutic targets. Lastly, we will address how increased integration of clinical and basic research will assist treatment and prevention efforts for emerging pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/27933782/ doi: 10.1021/acsinfecdis.6b00104 id: cord-320431-0877trhh author: Frey, Andreas title: More Than Just a Barrier: The Immune Functions of the Airway Epithelium in Asthma Pathogenesis date: 2020-04-28 words: 15225.0 sentences: 762.0 pages: flesch: 40.0 cache: ./cache/cord-320431-0877trhh.txt txt: ./txt/cord-320431-0877trhh.txt summary: In case of asthma, all these functions are impaired by the already existing allergic immune response that per se weakens the barrier integrity and self-cleaning abilities of the airway epithelium making it more vulnerable to penetration of allergens as well as of infection by bacteria and viruses. Besides this innate "rapid response team, " the polarized epithelium of the human airways is also able to transport and apically release immunoglobulins that carry a J-chain (joining chain) by using its poly Ig receptor (pIgR) (145) (146) (147) that is expressed by all non-stratified epithelial cells (Figure 2) . After contact for example with HDM extracts, representing a major source of asthma associated allergens, TLR4 dependent activation of NFκB and protease induced injuries in airway epithelial cells lead to secretion of chemokines and cytokines like thymic stromal lymphopoietin (TSLP), GM-CSF, IL-25, and IL-33 (211) (212) (213) (214) (215) . abstract: Allergic bronchial asthma is a chronic disease of the airways that is characterized by symptoms like respiratory distress, chest tightness, wheezing, productive cough, and acute episodes of broncho-obstruction. This symptom-complex arises on the basis of chronic allergic inflammation of the airway wall. Consequently, the airway epithelium is central to the pathogenesis of this disease, because its multiple abilities directly have an impact on the inflammatory response and thus the formation of the disease. In turn, its structure and functions are markedly impaired by the inflammation. Hence, the airway epithelium represents a sealed, self-cleaning barrier, that prohibits penetration of inhaled allergens, pathogens, and other noxious agents into the body. This barrier is covered with mucus that further contains antimicrobial peptides and antibodies that are either produced or specifically transported by the airway epithelium in order to trap these particles and to remove them from the body by a process called mucociliary clearance. Once this first line of defense of the lung is overcome, airway epithelial cells are the first cells to get in contact with pathogens, to be damaged or infected. Therefore, these cells release a plethora of chemokines and cytokines that not only induce an acute inflammatory reaction but also have an impact on the alignment of the following immune reaction. In case of asthma, all these functions are impaired by the already existing allergic immune response that per se weakens the barrier integrity and self-cleaning abilities of the airway epithelium making it more vulnerable to penetration of allergens as well as of infection by bacteria and viruses. Recent studies indicate that the history of allergy- and pathogen-derived insults can leave some kind of memory in these cells that can be described as imprinting or trained immunity. Thus, the airway epithelium is in the center of processes that lead to formation, progression and acute exacerbation of asthma. url: https://doi.org/10.3389/fimmu.2020.00761 doi: 10.3389/fimmu.2020.00761 id: cord-216972-migs9rxb author: Garaialde, Diego title: Quantifying the Impact of Making and Breaking Interface Habits date: 2020-05-14 words: 6289.0 sentences: 309.0 pages: flesch: 50.0 cache: ./cache/cord-216972-migs9rxb.txt txt: ./txt/cord-216972-migs9rxb.txt summary: Through a forced choice lab study task (n=19) and in the wild deployment (n=18) of a notificationdialog experiment on smartphones, we show that people become more accurate and faster at option selection as they develop an interface habit. The contribution of the current paper comes from providing quantitative evidence of how the process of forming and disrupting habits affects user performance in a forced choice interaction task, similar to those seen in notification dialogs or alert boxes. The current research contributes key insight on fundamental user behaviours by quantifying how the process of habit formation and disruption through design affect the speed and accuracy of interactions. The experimental evidence of study 1 shows that, like other habits, allowing participants to form interface habits leads to significant gains in performance, as users became both more accurate and quicker at selecting the desired option. abstract: The frequency with which people interact with technology means that users may develop interface habits, i.e. fast, automatic responses to stable interface cues. Design guidelines often assume that interface habits are beneficial. However, we lack quantitative evidence of how the development of habits actually affect user performance and an understanding of how changes in the interface design may affect habit development. Our work quantifies the effect of habit formation and disruption on user performance in interaction. Through a forced choice lab study task (n=19) and in the wild deployment (n=18) of a notificationdialog experiment on smartphones, we show that people become more accurate and faster at option selection as they develop an interface habit. Crucially this performance gain is entirely eliminated once the habit is disrupted. We discuss reasons for this performance shift and analyse some disadvantages of interface habits, outlining general design patterns on how to both support and disrupt them.Keywords: Interface habits, user behaviour, breaking habit, interaction science, quantitative research. url: https://arxiv.org/pdf/2005.06842v1.pdf doi: nan id: cord-016713-pw4f8asc author: Goyal, Amit K. title: Nanotechnological Approaches for Genetic Immunization date: 2013-05-24 words: 16034.0 sentences: 814.0 pages: flesch: 34.0 cache: ./cache/cord-016713-pw4f8asc.txt txt: ./txt/cord-016713-pw4f8asc.txt summary: The use of nonviral particulate carriers for DNA-based vaccination could provide better and safe delivery of encapsulated genetic material, circumvent the need for muscle involvement and facilitate instead the uptake of the Fig. 4 Schematic representation of immunological response greeted by novel DNA-loaded nanocarrier DNA by APCs. However, transfection of APCs with encapsulated DNA into particulate carrier systems will be dependent upon choice of carrier surface charge, size, and lipid/polymer composition, or presence of other biological [e.g., interleukin 2 and interferon-γ (IFN-γ)]. Modification of lipid/DNA complexes by the polymer poly(D,L-lactic acid) was found to be consistently and significantly more effective than either unmodified liposomal DNA or naked DNA in eliciting transgene-specific immune responses to plasmid-encoded antigen when administered by the s.c. route (Bramwell et al. abstract: Genetic immunization is one of the important findings that provide multifaceted immunological response against infectious diseases. With the advent of r-DNA technology, it is possible to construct vector with immunologically active genes against specific pathogens. Nevertheless, site-specific delivery of constructed genetic material is an important contributory factor for eliciting specific cellular and humoral immune response. Nanotechnology has demonstrated immense potential for the site-specific delivery of biomolecules. Several polymeric and lipidic nanocarriers have been utilized for the delivery of genetic materials. These systems seem to have better compatibility, low toxicity, economical and capable to delivering biomolecules to intracellular site for the better expression of desired antigens. Further, surface engineering of nanocarriers and targeting approaches have an ability to offer better presentation of antigenic material to immunological cells. This chapter gives an overview of existing and emerging nanotechnological approaches for the delivery of genetic materials. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121080/ doi: 10.1007/978-3-642-36853-0_4 id: cord-015910-d9gxew91 author: Grimble, Robert F. title: The Interaction Between Nutrition and Inflammatory Stress Throughout the Life Cycle date: 2005 words: 15205.0 sentences: 709.0 pages: flesch: 40.0 cache: ./cache/cord-015910-d9gxew91.txt txt: ./txt/cord-015910-d9gxew91.txt summary: Binding of the transcription factors is implicated in activation of a wide range of genes associated with inflammation and the immune response, including those encoding cytokines, cytokine receptors, cell adhesion molecules, acute-phase proteins, and growth factors (Schreck, Rieber, & Baeurerle, 1991) (Fig. 4 ) . While inflammation may be exerting deleterious effects most obviously in patients, people on the borderline of health and disease living in the general population Table 4 Nutrients Commonly Used in Immunonutrient Supplements and Their Potential Mode of Action • n-3 polyunsaturated fatty acids: act as anti-inflammatory agents and reverse immunosuppression • Sulfur amino acids and their precursors: enhance antioxidant status via GSH synthesis • Glutamine: nutrient for immune cells, improves gut barrier function, precursor for GSH • Arginine: stimulates nitric oxide and growth hormone production, improves helper T-cell numbers • Nucleotides: RNA and DNA precursors, improve T-cell function may also require nutritional modulation of ongoing inflammatory processes. abstract: The human race inhabits a world in which it is surrounded by a myriad of different microorganisms—yeasts, bacteria, protozoa, and viruses. Most of these are benign, and some, such as the normal gut flora, play an important part in promoting health via the synthesis of vitamins and stimulation of normal function of gut epithelia. Approximately 0.1% of microbes in our environment have catastrophic effects if they penetrate the epithelial surfaces of the body (Bryson, 2003). History reveals many instances in which armies have been defeated and civilizations have collapsed because of encounters between humans and such microorganisms (Diamond, 1999). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120013/ doi: 10.1385/1-59259-952-4:387 id: cord-031885-by4cujyy author: Guo, Hai title: The digitalization and public crisis responses of small and medium enterprises: Implications from a COVID-19 survey date: 2020-09-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The COVID-19 outbreak is a global crisis that has placed small and medium enterprises (SMEs) under huge pressure to survive, requiring them to respond effectively to the crisis. SMEs have adopted various digital technologies to cope with this crisis. Using a data set from a survey with 518 Chinese SMEs, the study examines the relationship between SMEs’ digitalization and their public crisis responses. The empirical results show that digitalization has enabled SMEs to respond effectively to the public crisis by making use of their dynamic capabilities. In addition, digitalization can help improve SMEs’ performance. We propose a theoretical framework of digitalization and crisis responses for SMEs and present three avenues for future research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490323/ doi: 10.1186/s11782-020-00087-1 id: cord-033714-rz5unqaz author: Gupte, Jaideep title: COVID-19: what is not being addressed date: 2020-10-13 words: 8226.0 sentences: 431.0 pages: flesch: 51.0 cache: ./cache/cord-033714-rz5unqaz.txt txt: ./txt/cord-033714-rz5unqaz.txt summary: The visualization of informal settlements in many COVID-19 discussions, however, is of homogenous highdensity inner-city shacks, with insufficient attention given to lowerdensity settlements (more likely to have urban agriculture) that may also face health and economic emergencies. (46) The wealth of grassroots responses to COVID-19 is elaborated by the International Institute for Environment and Development (IIED), which has drawn on experiences from across its partners in the global South, who provide evidence of local groups stepping in to reduce health risks and provide emergency access to food and hygiene. Meanwhile, the vast majority of urban poor communities (85%) reported government-provided "palliatives" intended for the vulnerable had not reached them." (68) Similar findings are evident in Brazil where, for example, low-income favela residents in São Paulo are not receiving the monthly emergency basic income payment (worth US$ 115), despite the shutdown by the city authorities of informal trading on 15 April 2020. Local response in health emergencies: key considerations for addressing the COVID-19 pandemic in informal urban settlements abstract: As the number of confirmed COVID-19 cases nears 27 million, there is a rush to answer (what next) and a rush to act (to solve the immediate problems of COVID-19). This paper discusses, with a specific focus on urban areas in the global South, what is missing to date from this response. That includes an identification of things that there are too much of, things that are not being done at all, and things that are unbalanced. There has been an enormous upsurge of academic research papers and opinions on COVID-19. “Technological” and “scientific” solutions tend to overshadow other approaches, even if people know that “social is important”. Based on our analysis to date, our primary concern is that there is too little understanding about the importance of building dialogue, exploring collaboration and co-producing solutions. There is too little understanding as to why social and cultural responses are important, and how the recognition that they are important can be actioned. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7554414/ doi: 10.1177/0956247820963961 id: cord-274027-ovdhnajp author: Gyasi, Razak M. title: Rethinking the Gendered Dimensions in the Impacts and Response to COVID-19 Pandemic date: 2020-06-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract The outbreak of the novel coronavirus disease 2019 (COVID-19) has demonstrated the urgency to rethink the health system quality to efficiently support and improve global health. Whilst efforts are now gathering pace in response to the deleterious impacts of COVID-19, gendered analysis of these impacts and response to the pandemic has been far too little. A critical consideration of gendered lenses and the respective brunt of health crises of the pandemic on men and women can improve our understanding and direction of efforts toward building robust and equitable public health response. Strategic plans for preparedness must be fully grounded in strong gender analysis in the remit of gender roles and norms, and strengthen the leadership and resourceful participation of women in the decision-making process toward addressing COVID-19 outbreak. url: https://api.elsevier.com/content/article/pii/S2666535220300185 doi: 10.1016/j.puhip.2020.100019 id: cord-298525-hhcfrjrn author: Hall, Charlotte A. title: Eyeing up the Future of the Pupillary Light Reflex in Neurodiagnostics date: 2018-03-13 words: 7841.0 sentences: 383.0 pages: flesch: 37.0 cache: ./cache/cord-298525-hhcfrjrn.txt txt: ./txt/cord-298525-hhcfrjrn.txt summary: The pupillary light reflex (PLR) describes the constriction and subsequent dilation of the pupil in response to light as a result of the antagonistic actions of the iris sphincter and dilator muscles. The pupillary light reflex (PLR) describes the constriction and subsequent dilation of the pupil in response to light, which not only serves as a major determination of retinal image quality [1, 2] , but also provides an important metric of autonomic nervous system function [3] . The response latency, maximum constriction and pupil escape, and the corresponding constriction parameters (MCV, MCA and RCA; relative constriction amplitude) are dependent on the actions of the sphincter muscle and on the function of retinal photoreceptors, as well as the time consumed in the afferent and efferent pathway. The ability of pupillometry to detect subtle changes in pupillary reaction even when pupils are constricted has potential clinical significance and may provide a useful tool in the early detection, monitoring and management of brain injuries [89] . abstract: The pupillary light reflex (PLR) describes the constriction and subsequent dilation of the pupil in response to light as a result of the antagonistic actions of the iris sphincter and dilator muscles. Since these muscles are innervated by the parasympathetic and sympathetic nervous systems, respectively, different parameters of the PLR can be used as indicators for either sympathetic or parasympathetic modulation. Thus, the PLR provides an important metric of autonomic nervous system function that has been exploited for a wide range of clinical applications. Measurement of the PLR using dynamic pupillometry is now an established quantitative, non-invasive tool in assessment of traumatic head injuries. This review examines the more recent application of dynamic pupillometry as a diagnostic tool for a wide range of clinical conditions, varying from neurodegenerative disease to exposure to toxic chemicals, as well as its potential in the non-invasive diagnosis of infectious disease. url: https://doi.org/10.3390/diagnostics8010019 doi: 10.3390/diagnostics8010019 id: cord-324143-ztj6o4ob author: Harper, Craig A. title: Functional Fear Predicts Public Health Compliance in the COVID-19 Pandemic date: 2020-04-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the current context of the global pandemic of coronavirus disease-2019 (COVID-19), health professionals are working with social scientists to inform government policy on how to slow the spread of the virus. An increasing amount of social scientific research has looked at the role of public message framing, for instance, but few studies have thus far examined the role of individual differences in emotional and personality-based variables in predicting virus-mitigating behaviors. In this study, we recruited a large international community sample (N = 324) to complete measures of self-perceived risk of contracting COVID-19, fear of the virus, moral foundations, political orientation, and behavior change in response to the pandemic. Consistently, the only predictor of positive behavior change (e.g., social distancing, improved hand hygiene) was fear of COVID-19, with no effect of politically relevant variables. We discuss these data in relation to the potentially functional nature of fear in global health crises. url: https://www.ncbi.nlm.nih.gov/pubmed/32346359/ doi: 10.1007/s11469-020-00281-5 id: cord-276628-uxsjyezo author: Hedges, Jodi F. title: Harnessing γδ T Cells as Natural Immune Modulators date: 2019-10-25 words: 6808.0 sentences: 349.0 pages: flesch: 46.0 cache: ./cache/cord-276628-uxsjyezo.txt txt: ./txt/cord-276628-uxsjyezo.txt summary: TCR stimulation leads to a variety of functional responses, such as cytolysis, cytokine production, regulatory effects, and even phagocytosis and antigen presentation, that depend on the activation of receptors and coreceptors. γδ T cells also express various cytokine receptors that contribute to their activation (IL-2R, IL-15R, IL-23R, etc.) and-fine tune their functional responses. SLC11A1 is a divalent metal transporter that is thought to be expressed only in myeloid and macrophage cells; it is important in effective responses against intracellular bacterial infections [49À51]. Follow-up functional assays examined their cell type specificity, induced cytokine responses, and benefit in various infectious disease models [110, 112] . Yamoa polysaccharides activate γδ T as well other immune cells, such as monocytes, and, when given in vivo, enhance protection from infection [110] . Porcine γδ T cells: possible roles on the innate and adaptive immune responses following virus infection abstract: There has been renewed interest in harnessing the power of the immune system as a countermeasure against infectious pathogens and cancers. One immune cell target in the development of these approaches is the γδ T cell. These cells are involved in innate and adaptive immune responses against infectious agents and cancers, and they migrate to, and reside in, mucosal tissues. γδ T cells exhibit a broad array of natural (or constitutive) and induced effector functions, including antigen presentation, that can be fine-tuned depending on their stimulation. They express unique antigen receptors as well as nonantigen, innate immune type surface receptors that can be targeted. In this chapter, we will review the biology and the basis for use of γδ T cells as a therapeutic target. We will then summarize novel plant- and microbe-derived materials that enhance γδ T cell activity in animal models and humans that can be used as a new strategy for mucosal vaccine development. url: https://www.sciencedirect.com/science/article/pii/B9780128119242000468 doi: 10.1016/b978-0-12-811924-2.00046-8 id: cord-255725-7l9lk9x2 author: Hertzog, Paul J title: Sculpting the immune response to infection date: 2011-06-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This report describes advances in the understanding of how microbes elicit and evade immune responses and the sensing of pathogens by host cells that leads to the activation and production of intra- and extracellular signaling molecules. url: https://www.ncbi.nlm.nih.gov/pubmed/21685948/ doi: 10.1038/ni0711-579 id: cord-328935-mn8r972x author: Hodgins, Douglas C. title: Mucosal Veterinary Vaccines: Comparative Vaccinology date: 2015-03-13 words: 16336.0 sentences: 785.0 pages: flesch: 36.0 cache: ./cache/cord-328935-mn8r972x.txt txt: ./txt/cord-328935-mn8r972x.txt summary: Studies of the potential of novel adjuvants to improve vaccine efficacy against genetically unstable, immune-subverting RNA viruses, such as porcine reproductive and respiratory syndrome virus in pigs, should assist in the control of pathogens with similar characteristics in other species. However, a recent study showed that an inactivated reassortant RV strain (CDC-9 strain) formulated with aluminum phosphate and administered systemically in gnotobiotic pigs resulted in induction of serum IgG antibody titers, coinciding with partial protection against shedding and diarrhea, suggesting that adjuvant may have stimulated local specific (gut IgA antibodies) or nonspecific immune responses, which were not assessed in this study (Wang et al., 2010) . Intranasal delivery of whole cell lysate of Mycobacterium tuberculosis induces protective immune responses to a modified live porcine reproductive and respiratory syndrome virus vaccine in pigs abstract: Infections of mucosal surfaces are major causes of morbidity, mortality, and economic loss in species of veterinary interest, and a concern for animal welfare. Vaccines are used extensively in veterinary medicine, and innovative vaccine technologies such as recombinant DNA-vectored and distinguishing infected from vaccinated animals (DIVA) vaccines and automated in ovo vaccination (of embryonated chicken eggs) have been rapidly adopted commercially. Immunological research using outbred, nonrodent animal models has contributed to a broader understanding of mucosal defenses, and has provided the initial impetus for investigation of the common mucosal immune system. Studies of the potential of novel adjuvants to improve vaccine efficacy against genetically unstable, immune-subverting RNA viruses, such as porcine reproductive and respiratory syndrome virus in pigs, should assist in the control of pathogens with similar characteristics in other species. Successful development of vaccines to prevent and treat ascending infections of the reproductive tract of cattle set a precedent for applications in other species including humans. Studies of mucosal adjuvants and delivery systems continue at the interface between passive and active immunity, with the goal of inducing the earliest possible protection against enteric and respiratory pathogens of neonates. url: https://api.elsevier.com/content/article/pii/B9780124158474000689 doi: 10.1016/b978-0-12-415847-4.00068-9 id: cord-339694-sp212tai author: Jiang, Xinpeng title: A phase trial of the oral Lactobacillus casei vaccine polarizes Th2 cell immunity against transmissible gastroenteritis coronavirus infection date: 2016-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Transmissible gastroenteritis coronavirus (TGEV) is a member of the genus Coronavirus, family Coronaviridae, order Nidovirales. TGEV is an enteropathogenic coronavirus that causes highly fatal acute diarrhoea in newborn pigs. An oral Lactobacillus casei (L. casei) vaccine against anti-transmissible gastroenteritis virus developed in our laboratory was used to study mucosal immune responses. In this L. casei vaccine, repetitive peptides expressed by L. casei (specifically the MDP and tuftsin fusion protein (MT)) were repeated 20 times and the D antigenic site of the TGEV spike (S) protein was repeated 6 times. Immunization with recombinant Lactobacillus is crucial for investigations of the effect of immunization, such as the first immunization time and dose. The first immunization is more important than the last immunization in the series. The recombinant Lactobacillus elicited specific systemic and mucosal immune responses. Recombinant L. casei had a strong potentiating effect on the cellular immunity induced by the oral L. casei vaccine. However, during TGEV infection, the systemic and local immune responses switched from Th1 to Th2-based immune responses. The systemic humoral immune response was stronger than the cellular immune response after TGEV infection. We found that the recombinant Lactobacillus stimulated IL-17 expression in both the systemic and mucosal immune responses against TGEV infection. Furthermore, the Lactobacillus vaccine stimulated an anti-TGEV infection Th17 pathway. The histopathological examination showed tremendous potential for recombinant Lactobacillus to enable rapid and effective treatment for TGEV with an intestinal tropism in piglets. The TGEV immune protection was primarily dependent on mucosal immunity. url: https://www.ncbi.nlm.nih.gov/pubmed/27020282/ doi: 10.1007/s00253-016-7424-9 id: cord-311823-85wj08gr author: Katze, Michael G. title: Innate immune modulation by RNA viruses: emerging insights from functional genomics date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although often encoding fewer than a dozen genes, RNA viruses can overcome host antiviral responses and wreak havoc on the cells they infect. Some manage to evade host antiviral defences, whereas others elicit an aberrant or disproportional immune response. Both scenarios can result in the disruption of intracellular signalling pathways and significant pathology in the host. Systems-biology approaches are increasingly being used to study the processes of viral triggering and regulation of host immune responses. By providing a global and integrated view of cellular events, these approaches are beginning to unravel some of the complexities of virus–host interactions and provide new insights into how RNA viruses cause disease. url: https://doi.org/10.1038/nri2377 doi: 10.1038/nri2377 id: cord-018839-yfaji9cv author: Kim, Yong-kyun title: Disaster Theory date: 2017-07-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: To find a conclusive definition for contemporary purposes and uses, we look at many of the various definitions of disasters through cataclysmic events, historical records, public policies, laws, and organizational usage. Our natural progression leads us to modern theories of disaster and Disaster Risk Management (DRM) that have had to tackle new types of disasters that are being brought about by the interconnectivity of societies, people, diseases, technology, etc., increasing in magnitude and complexity like what was seen in Fukushima, Japan, in 2011 and on-setting disasters like climate change. After looking at all the historical evidence, we come to a definition for the term disaster for modern usage and what it means for policy implications. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123823/ doi: 10.1007/978-981-10-4789-3_2 id: cord-024571-vlklgd3x author: Kim, Yushim title: Community Analysis of a Crisis Response Network date: 2019-07-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This article distinguishes between clique family subgroups and communities in a crisis response network. Then, we examine the way organizations interacted to achieve a common goal by employing community analysis of an epidemic response network in Korea in 2015. The results indicate that the network split into two groups: core response communities in one group and supportive functional communities in the other. The core response communities include organizations across government jurisdictions, sectors, and geographic locations. Other communities are confined geographically, homogenous functionally, or both. We also find that whenever intergovernmental relations were present in communities, the member connectivity was low, even if intersectoral relations appeared together within them. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206567/ doi: 10.1177/0894439319858679 id: cord-126015-zc7u3g34 author: Krieger, Elizabeth title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date: 2020-05-13 words: 6421.0 sentences: 348.0 pages: flesch: 42.0 cache: ./cache/cord-126015-zc7u3g34.txt txt: ./txt/cord-126015-zc7u3g34.txt summary: To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. The HLA genes exhibit extreme allelic polymorphisms and present viral peptides on host HLA molecules to T cells to trigger an adaptive immune response. A quantitative approach relating differences in cytokine levels and polymorphisms in the immune response pathways may help identify patients at risk of severe disease. abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a variable clinical presentation that ranges from asymptomatic, to severe disease with cytokine storm. The mortality rates also differ across the globe, ranging from 0.5-13%. This variation is likely due to both pathogen and host factors. Host factors may include genetic differences in the immune response genes as well as variation in HLA and KIR allotypes. To better understand what impact these genetic variants in immune response genes may have in the differences observed in the immune response to SARS-CoV-2, a quantitative analysis of a dynamical systems model that considers both, the magnitude of viral growth, and the subsequent innate and adaptive response required to achieve control of infection is considered. Based on this broad quantitative framework it may be posited that the spectrum of symptomatic to severely symptomatic presentations of COVID19 represents the balance between innate and adaptive immune responses. In asymptomatic patients, prompt and adequate adaptive immune response quells infection, whereas in those with severe symptoms a slower inadequate adaptive response leads to a runaway cytokine cascade fueled by ongoing viral replication. Polymorphisms in the various components of the innate and adaptive immune response may cause altered immune response kinetics that would result in variable severity of illness. Understanding how this genetic variation may alter the response to SARS-CoV-2 infection is critical to develop successful treatment strategies. url: https://arxiv.org/pdf/2005.06541v2.pdf doi: nan 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: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-017817-ztp7w9yh author: Land, Walter Gottlieb title: Cell-Autonomous (Cell-Intrinsic) Stress Responses date: 2018-03-28 words: 17727.0 sentences: 855.0 pages: flesch: 40.0 cache: ./cache/cord-017817-ztp7w9yh.txt txt: ./txt/cord-017817-ztp7w9yh.txt summary: Autophagy is an evolutionarily highly conserved self-digestive process in response to environmental stress to eukaryotic cells, by which cytoplasmic components such as defective/damaged or redundant organelles or protein aggregates are delivered to the lysosome for recycling and degradation. More recent studies then revealed that these transcription factors, notably Nrf2, are activated by Keap1 as the primary negative regulator of Nrf2, that is, a molecule that simultaneously operates as a sensor protein able to perceive dyshomeostatic Subclass IIC-4 DAMPs, for example, in terms of redox changes reflecting electrophilic stress. Strikingly, a complex relationship reportedly exists between autophagy and DAMPs in cellular adaption to stress and injury and cell death characterized by a crosstalk between autophagy induction and secretion or release of DAMPs. In fact, growing evidence indicates that autophagic mechanisms are involved in regulating release and degradation of DAMPs including CALR, HMGB1, ATP, and DNA in several cell types [37, 148, 175] . abstract: In this chapter, the role of cell-intrinsic stress responses is examined which include autophagic processes, the oxidative stress response, the heat shock response, the unfolded proteins response, and the DNA damage response. Autophagy (macroautophagy, microautophagy, and chaperone-mediated autophagy) is a self-digestive process in response to environmental stress to eukaryotic cells, by which cytoplasmic components are delivered to the lysosome for recycling and degradation. The oxidative stress response is directed against any oxidative stress and is mediated by antioxidative defense systems including antioxidant enzymes such as superoxide dismutase, detoxifying enzymes such as glutathione peroxidase, and energy-dependent efflux pumps. The heat shock response is induced upon exposure of cells to any stress condition and characterized by emission of heat shock proteins which operate as DAMPs to maintain and restore homeostasis. The unfolded protein response is induced by any stress of the endoplasmic reticulum that is perceived by three sensor molecules. Under remediable endoplasmic reticulum stress conditions, the sensors trigger signalling pathways to resolve this stress. However, in severe irremediable endoplasmic reticulum stress, the unfolded protein response may lead to pro-inflammatory and pro-apoptotic responses resulting in regulated cell death. Finally, the DNA damage response is induced by any DNA damage that occurs in a variety of exogenous and endogenous conditions. When successful, this stress response leads to DNA repair and is associated with the emission of various DAMPs which contribute to restoration of homeostasis. When unsuccessful, the DNA damage response, like the unsuccessful unfolded protein response, can result in regulated cell death, either in form of apoptosis or necrosis. Together, the ultimate goal of all the stress responses is to maintain cellular homeostasis and ensure cell integrity. When they fail, the incidence of regulated cell death is frequently observed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122488/ doi: 10.1007/978-3-319-78655-1_18 id: cord-330583-ltkpt80u author: Lee, Kyu-Myoung title: Factors Influencing the Response to Infectious Diseases: Focusing on the Case of SARS and MERS in South Korea date: 2019-04-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Following the 2003 the severe acute respiratory syndrome (SARS) and the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to explore and examine the factors influencing the response to infectious diseases, which encompasses both communicable and non-communicable diseases. Through a qualitative research method, this research categorizes the factors as inputs, processes and outputs and applies them into the 2003 SARS and MERS outbreak in South Korea. As the results conducted meta-analyses to comprehensively analyze the correlations of factors influencing disaster response from a Korean context, the findings show that the legislative factor had direct and indirect influence on the overall process of infectious disease response and that Leadership of the central government, establishment of an intergovernmental response system, the need for communication, information sharing and disclosure and onsite response were identified as key factors influencing effective infectious disease response. url: https://www.ncbi.nlm.nih.gov/pubmed/31013648/ doi: 10.3390/ijerph16081432 id: cord-342317-m6axi18k author: Leigh, Laurasona title: A Cross-Sectional Examination on the Factors Related to Emergency Nurses’ Motivation to Protect Themselves against an Ebola Infection date: 2020-05-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: The 2014-2016 West African Ebola outbreak impacted the United States. Due to the sporadic occurrence of the Ebola infection, there is insufficient research regarding how the United States emergency nurses provide care to patients potentially infected with the Ebola virus and the nurses’ motivation to protect themselves when providing care to these patients. This study was aimed to investigate the predictors of emergency room nurse’s protection motivation. METHOD: A cross-sectional design was employed in the study. A survey developed based on a modified Protection Motivation Theory was administered to randomly selected emergency room nurses who are members of the Emergency Nurses Association. Descriptive statistics, nonparametric Kruskal-Wallis H-Test (as well as post hoc Dunn-Bonferroni test), Spearman Rho correlation, and Stepwise Multiple Linear regression were conducted for data analysis. RESULT: Protection motivation was found in two components: proactive and passive protection motivation. The regression analysis indicated that response efficacy (β=.27, p<.001) and self-efficacy (β=.17, p<.01) significantly predict emergency nurses’ proactive protection motivation, while perceived vulnerability (β=.26, p<.001), response cost (β=.19, p=.001) and knowledge (β=-.15, p<.01) significantly predict emergency nurses’ passive protection motivation. CONCLUSION: Results indicate the need for interventions to improve emergency nurses’ response efficacy, self-efficacy, and knowledge, while simultaneously reducing the nurses’ perceived vulnerability and response cost. Such interventions would be expected to proactively motivate nurses to protect themselves when providing care to patients that exhibit the signs and symptoms of an Ebola infection and reduce their passive protection motivation. url: https://www.ncbi.nlm.nih.gov/pubmed/32800328/ doi: 10.1016/j.jen.2020.05.002 id: cord-257027-q2y7fewk author: Lemaire, D. title: Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology date: 2011-10-28 words: 5844.0 sentences: 241.0 pages: flesch: 33.0 cache: ./cache/cord-257027-q2y7fewk.txt txt: ./txt/cord-257027-q2y7fewk.txt summary: Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. The publication of the Haemophilus influenzae genome, the first pathogen to have its complete genome sequence published as a result of an approach to genome analysis using new technologies of high-throughput sequencing (5) , has opened the mind of scientists to a range of new possible approaches to the study of microorganisms and has marked the beginning of a new era in vaccine development: the identification of pathogen candidate antigens based on the knowledge of the genome of the pathogen and on the understanding of microbial biology and host-pathogen interactions, an approach called reverse vaccinology (6) . abstract: Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data. url: https://www.ncbi.nlm.nih.gov/pubmed/22030866/ doi: 10.1590/s0100-879x2011007500142 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-023935-o2ffxgnn author: Lorts, Angela title: Sepsis date: 2011-12-16 words: 11110.0 sentences: 510.0 pages: flesch: 38.0 cache: ./cache/cord-023935-o2ffxgnn.txt txt: ./txt/cord-023935-o2ffxgnn.txt summary: SIRS i s a state of infl ammatory/ immune activation and is based on the presence of at least two of the four following clinical criteria: Temperature >38°C or <36°C, heart rate >90th percentile for age, respiratory rate >90th percentile for age, or hyperventilation to PaCO 2 < 32 mm Hg. The defi nition attempts to "capture" all patients at risk for the subsequent development of severe sepsis or septic shock. Among these, the nuclear factor-k B (NF-k b ) and the mitogen activated protein kinase (MAPK) pathways play a prominent role in regulating the expression of a number of infl ammatory gene products key to propagating the sepsis response. Nuclear factork B (NFk b ) and the mitogen activated protein kinase (MAPK) pathways play a prominent role in regulating the expression of a number of infl ammatory gene products key to propagating the sepsis response. abstract: The health care provider faced with the management of a child with septic shock relies on a comprehensive understanding of the numerous disciplines embodied in the practice of pediatric critical care medicine. The child with septic shock may have simultaneous derangements in the function of virtually every system of the body including: cardiovascular, respiratory, immune, renal, coagulation, hepatic, metabolic and neurologic. The degree to which physiologic alterations are manifest in a given patient is variable and influenced by multiple host and non-host factors including: the developmental stage, the presence of co-morbidities, pathogen-related factors, and genetic influences on both the host inflammatory response as well as the response to pharmacologic agents, all combining to have a profound influence on outcome. The clinician must possess a systematic and multifaceted approach to these critically ill patients. The goal of this chapter is to provide a comprehensive description of the epidemiology, biology and pathophysiology (at both the cellular and organ level) of sepsis, as well as outlining the current principles of managing septic shock. It will be apparent that optimal management requires a strong working knowledge of cardiovascular physiology, infectious diseases, multiple organ interactions, immunity, coagulation, pharmacology, and the molecular biology of inflammation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178851/ doi: 10.1007/978-0-85729-923-9_27 id: cord-252568-b8sbvy0g author: Marques Neto, Lázaro Moreira title: Role of Metallic Nanoparticles in Vaccinology: Implications for Infectious Disease Vaccine Development date: 2017-03-08 words: 5317.0 sentences: 260.0 pages: flesch: 39.0 cache: ./cache/cord-252568-b8sbvy0g.txt txt: ./txt/cord-252568-b8sbvy0g.txt summary: There is evidence that these particles display adjuvant characteristics, promoting cell recruitment, antigen-presenting cell activation, cytokine production, and inducing a humoral immune response. However, many NPs have been shown to stimulate immune responses, including cell recruitment, activation of antigen (Ag)-presenting cells (APCs), and induction of cytokine and chemokine release. Among the vaccines targeting extracellular bacteria and toxin, two were formulated with lipopolysaccharide (LPS) in glycopeptide Ag. The use of glycoantigen and LPS can trigger an intense response through TLR4 and B cell receptor activation; the presence of gold NPs (AuNPs) may have minimal influence on this response. To understand the possible uses of MeNPs as platforms for vaccines against infectious diseases, analysis is needed of the impact of different physicochemical characteristics of NPs on the innate immune response (Figure 1) . abstract: Subunit vaccines are safer but less immunogenic than live-attenuated vaccines or whole cell inactivated vaccines. Adjuvants are used to enhance and modulate antigen (Ag) immunogenicity, aiming to induce a protective and long-lasting immune response. Several molecules and formulations have been studied for their adjuvanticity, but only seven have been approved to formulate human vaccines. Metallic nanoparticles (MeNPs), particularly those containing gold and iron oxides, are widely used in medicine for diagnosis and therapy and have been used as carriers for drugs and vaccines. However, little is known about the immune response elicited by MeNPs or about their importance in the development of new vaccines. There is evidence that these particles display adjuvant characteristics, promoting cell recruitment, antigen-presenting cell activation, cytokine production, and inducing a humoral immune response. This review focuses on the characteristics of MeNPs that could facilitate the induction of a cellular immune response, particularly T-helper 1 and T-helper 17, and their potential functions as adjuvants for subunit vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/28337198/ doi: 10.3389/fimmu.2017.00239 id: cord-270469-lle32mha author: Martinon, Fabio title: The endoplasmic reticulum: a sensor of cellular stress that modulates immune responses date: 2012-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Many inflammatory and infectious diseases are characterized by the activation of signaling pathways steaming from the endoplasmic reticulum (ER). These pathways, primarily associated with loss of ER homeostasis, are emerging as key regulators of inflammation and infection. Recent advances shed light on the mechanisms linking ER-stress and immune responses. url: https://www.sciencedirect.com/science/article/pii/S1286457912001827 doi: 10.1016/j.micinf.2012.07.005 id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Hematophagous insects transmit infectious diseases. Sand flies are vectors of leishmaniasis, but can also transmit viruses. We have been studying immune responses of Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas. We identified a non-specific antiviral response in L. longipalpis LL5 embryonic cells when treated with non-specific double-stranded RNAs (dsRNAs). This response is reminiscent of interferon response in mammals. We are investigating putative effectors for this antiviral response. Secreted molecules have been implicated in immune responses, including interferon-related responses. We conducted a mass spectrometry analysis of conditioned medium from LL5 cells 24 and 48 h after dsRNA or mock treatment. We identified 304 proteins. At 24 h, 19 proteins had an abundance equal or greater than 2-fold change, while the levels of 17 proteins were reduced when compared to control cells. At the 48 h time point, these numbers were 33 and 71, respectively. The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. The transcription profile of most candidates did not follow the pattern of secreted protein abundance. url: https://www.ncbi.nlm.nih.gov/pubmed/29346269/ doi: 10.3390/v10010043 id: cord-278938-bmahwxbn author: Masi, Davide title: Letter To the Editor: [Our Response to COVID-19 as Endocrinologists and Diabetologists] date: 2020-04-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32343815/ doi: 10.1210/clinem/dgaa229 id: cord-022252-9yiuuye3 author: Mims, Cedric A. title: Mechanisms of Cell and Tissue Damage date: 2013-11-17 words: 28864.0 sentences: 1432.0 pages: flesch: 48.0 cache: ./cache/cord-022252-9yiuuye3.txt txt: ./txt/cord-022252-9yiuuye3.txt summary: A few viruses are remarkable because they cause no pathological changes at all in the cell, even during a productive infection in which infectious virus particles are produced. Primary consideration will be given to those substances which are produced under ecologically significant conditions (i.e. in the natural host or relevant animal model) and cause (also in biologically relevant systems) damage to cells or tissues thereby contributing to disease. Here we consider toxins which act on extracellular substances and are responsible for many of the main features of the diseases caused by the infecting organism. Circulating immune complexes are also deposited in the walls of small blood vessels in the skin and elsewhere, where they may induce inflammatory changes.* The prodromal rashes seen in exanthematous virus infections and in hepatitis B are probably caused in this way. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155491/ doi: 10.1016/b978-0-12-498262-8.50015-1 id: cord-285982-1a5u7uux author: Moss, Ronald B title: Prospects for control of emerging infectious diseases with plasmid DNA vaccines date: 2009-09-07 words: 4227.0 sentences: 202.0 pages: flesch: 42.0 cache: ./cache/cord-285982-1a5u7uux.txt txt: ./txt/cord-285982-1a5u7uux.txt summary: The rapid manufacturing capabilities of DNA vaccines may be particularly important for emerging infectious diseases including the current novel H1N1 Influenza A pandemic, where pre-existing immunity is limited. Development in this area has greatly advanced over the years and human clinical trials of DNA vaccines have now been conducted against various infectious pathogens including the malaria parasite, dengue viruses, cytomegalovirus (CMV), Ebola virus, seasonal influenza viruses, avian or pandemic influenza viruses, West Nile virus (WMV), SARS coronavirus, hepatitis B virus, and HIV. Because the process of antigen production by host cells after DNA vaccination mimics the production of antigens during a natural infection, the resulting immune response is thought to be similar to the type induced by pathogens. Lastly, the first human clinical trial of a DNA vaccine formulated with Vaxfectin ® has been completed with plasmids that encode pandemic influenza virus antigens (H5N1). abstract: Experiments almost 20 years ago demonstrated that injections of a sequence of DNA encoding part of a pathogen could stimulate immunity. It was soon realized that "DNA vaccination" had numerous potential advantages over conventional vaccine approaches including inherent safety and a more rapid production time. These and other attributes make DNA vaccines ideal for development against emerging pathogens. Recent advances in optimizing various aspects of DNA vaccination have accelerated this approach from concept to reality in contemporary human trials. Although not yet licensed for human use, several DNA vaccines have now been approved for animal health indications. The rapid manufacturing capabilities of DNA vaccines may be particularly important for emerging infectious diseases including the current novel H1N1 Influenza A pandemic, where pre-existing immunity is limited. Because of recent advances in DNA vaccination, this approach has the potential to be a powerful new weapon in protecting against emerging and potentially pandemic human pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/19735569/ doi: 10.1186/1476-8518-7-3 id: cord-290264-pv7ijdnx author: Perakslis, Eric title: A Primer on Biodefense Data Science for Pandemic Preparedness date: 2020-04-10 words: 2349.0 sentences: 128.0 pages: flesch: 57.0 cache: ./cache/cord-290264-pv7ijdnx.txt txt: ./txt/cord-290264-pv7ijdnx.txt summary: 1 This piece will dig deeper into biodefense policy as well as suggest specific actions that the data science community can take to contribute to COVID-19 resilience, response, and recovery efforts. Starting at the top and looking more deeply into risk and resilience in the United States, much of the policy stems from the Homeland Security Presidential Directive 21, which outlines the policy and strategy for public health and medical preparedness. This outbreak is past the point of prevention, and the response must now focus on minimizing the effects as people get sick. A toolset that I have personally used over the years for rapid development and deployment is CommCare by Dimagi, and they have already built a toolkit and guide specifically for COVID-19 outbreak response. 8 My last trip during that outbreak focused upon rebuilding local infrastructure to enable the local health systems to get back to full operation, including the possibility of an Ebola-infected patient presenting and seeking care. abstract: The coronavirus outbreak is sweeping the globe with outbreaks reported on every continent except Antarctica as of March 2020. Data scientists are uniquely and diversely skilled in ways that can be highly effective in minimizing, combatting, and recovering from the impacts of the COVID-19 outbreak. In this Opinion, the basics of biodefense as well as specific opportunities for the data science community to contribute are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/32572397/ doi: 10.1016/j.patter.2020.100018 id: cord-266204-ipa017wz author: Poland, G. A. title: Personalized vaccinology: A review date: 2018-08-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract At the current time, the field of vaccinology remains empirical in many respects. Vaccine development, vaccine immunogenicity, and vaccine efficacy have, for the most part, historically been driven by an empiric “isolate-inactivate-inject” paradigm. In turn, a population-level public health paradigm of “the same dose for everyone for every disease” model has been the normative thinking in regard to prevention of vaccine-preventable infectious diseases. In addition, up until recently, no vaccines had been designed specifically to overcome the immunosenescence of aging, consistent with a post-WWII mentality of developing vaccines and vaccine programs for children. It is now recognized that the current lack of knowledge concerning how immune responses to vaccines are generated is a critical barrier to understanding poor vaccine responses in the elderly and in immunoimmaturity, discovery of new correlates of vaccine immunogenicity (vaccine response biomarkers), and a directed approach to new vaccine development. The new fields of vaccinomics and adversomics provide models that permit global profiling of the innate, humoral, and cellular immune responses integrated at a systems biology level. This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing “downstream” adaptive humoral and cellular responses to infectious pathogens and vaccines. Others have applied systems level approaches to the study of antibody responses (a.k.a. “systems serology”), [1] high-dimensional cell subset immunophenotyping through CyTOF, [2,3] and vaccine induced metabolic changes [4]. In turn, this knowledge is being utilized to better understand the following: identifying who is at risk for which infections; the level of risk that exists regarding poor immunogenicity and/or serious adverse events; and the type or dose of vaccine needed to fully protect an individual. In toto, such approaches allow for a personalized approach to the practice of vaccinology, analogous to the substantial inroads that individualized medicine is playing in other fields of human health and medicine. Herein we briefly review the field of vaccinomics, adversomics, and personalized vaccinology. url: https://www.ncbi.nlm.nih.gov/pubmed/28774561/ doi: 10.1016/j.vaccine.2017.07.062 id: cord-266750-41gth6o0 author: Puzzitiello, Richard N. title: Inflammatory and Coagulative Considerations for the Management of Orthopaedic Trauma Patients With COVID-19: A Review of the Current Evidence and Our Surgical Experience date: 2020-05-14 words: 3742.0 sentences: 221.0 pages: flesch: 39.0 cache: ./cache/cord-266750-41gth6o0.txt txt: ./txt/cord-266750-41gth6o0.txt summary: A better understanding of this relationship can inform the development of evidencebased management strategies in these patients and limit admissions to overcrowded ICUs. To demonstrate and further define these developing theories on the coagulative and inflammatory risks associated with the surgical treatment of trauma patients with COVID-19, we will present an unexpected outcome on such a patient at our institution. In addition, the hypercoagulable state secondary to COVID-19 and the inflammatory load of intramedullary reaming, fat emboli, and pulmonary embolism resulted in a "second hit" that may have cumulatively pushed our patient past a "tipping point" and into respiratory failure (Fig. 4) . The level of cytokine response, hypercoagulability, and pulmonary dysfunction associated with the COVID-19 virus may predispose to a catastrophic "second hit" after even low-energy trauma. Careful consideration and risk/benefit analysis, including preoperative evaluation of systemic inflammation and respiratory status, is paramount in patients with COVID-19 presenting with orthopaedic trauma injuries. abstract: Mounting evidence suggests that the pathogenesis of coronavirus disease 2019 (COVID-19) involves a hyperinflammatory response predisposing patients to thromboembolic disease and acute respiratory distress. In the setting of severe blunt trauma, damaged tissues induce a local and systemic inflammatory response through similar pathways to COVID-19. As such, patients with COVID-19 sustaining orthopaedic trauma injuries may have an amplified response to the traumatic insult because of their baseline hyperinflammatory and hypercoagulable states. These patients may have compromised physiological reserve to withstand the insult of surgical intervention before reaching clinical instability. In this article, we review the current evidence regarding pathogenesis of COVID-19 and its implications on the management of orthopaedic trauma patients by discussing a case and the most recent literature. url: https://doi.org/10.1097/bot.0000000000001842 doi: 10.1097/bot.0000000000001842 id: cord-257722-7rmzaau4 author: Rhee, Joon Haeng title: Current and New Approaches for Mucosal Vaccine Delivery date: 2019-10-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Mucosal surfaces are the interface between the host’s internal milieu and the external environment, and they have dual functions, serving as physical barriers to foreign antigens and as accepting sites for vital materials. Mucosal vaccines are more favored to prevent mucosal infections from the portal of entry. Although mucosal vaccination has many advantages, licensed mucosal vaccines are scarce. The most widely studied mucosal routes are oral and intranasal. Licensed oral and intranasal vaccines are composed mostly of whole cell killed or live attenuated microorganisms serving as both delivery systems and built-in adjuvants. Future mucosal vaccines should be made with more purified antigen components, which will be relatively less immunogenic. To induce robust protective immune responses against well-purified vaccine antigens, an effective mucosal delivery system is an essential requisite. Recent developments in biomaterials and nanotechnology have enabled many innovative mucosal vaccine trials. For oral vaccination, the vaccine delivery system should be able to stably carry antigens and adjuvants and resist harsh physicochemical conditions in the stomach and intestinal tract. Besides many nano/microcarrier tools generated by using natural and chemical materials, the development of oral vaccine delivery systems using food materials should be more robustly researched to expand vaccine coverage of gastrointestinal infections in developing countries. For intranasal vaccination, the vaccine delivery system should survive the very active mucociliary clearance mechanisms and prove safety because of the anatomical location of nasal cavity separated by a thin barrier. Future mucosal vaccine carriers, regardless of administration routes, should have certain common characteristics. They should maintain stability in given environments, be mucoadhesive, and have the ability to target specific tissues and cells. url: https://api.elsevier.com/content/article/pii/B9780128119242000195 doi: 10.1016/b978-0-12-811924-2.00019-5 id: cord-022435-pztn9075 author: Roach, Jeff title: Bali Bombings: A Whole of Government Response date: 2009-11-16 words: 4728.0 sentences: 223.0 pages: flesch: 44.0 cache: ./cache/cord-022435-pztn9075.txt txt: ./txt/cord-022435-pztn9075.txt summary: Domestically, the Department of Family and Community Services (FaCS) coordinated government policy and delivery of assistance to Australians and their families affected by the crisis. A clear lesson from Bali was the extent to which overseas events can resonate at the local community level, underlining the importance of domestic and state/territory agencies being activated early in response to a major overseas crisis. • clarify the roles of agencies and non-government organisations in crisis responses; • review links between Australian government and state disaster plans; and • identify and rectify any gaps in interagency coordination arrangements. One of the lessons of the Australian Government''s FMD simulation, Exercise Minotaur (see http://www.affa.gov.au/exerciseminotaur), was the need for agencies to look at human resource capacity in a number of key areas, particularly that of skilled and trained technical employees. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155689/ doi: 10.1016/b978-0-08-044666-0.50027-0 id: cord-018254-v8syiwie author: Rotz, Lisa D. title: Case Study – United States of America date: 2012-08-31 words: 5139.0 sentences: 169.0 pages: flesch: 29.0 cache: ./cache/cord-018254-v8syiwie.txt txt: ./txt/cord-018254-v8syiwie.txt summary: This act authorized more than 1.5 billion US dollars in grants to state and local governments and healthcare facilities to improve planning, training, detection, and response capacity as well as funding to expand the federal Strategic National Stockpile of medications and vaccines and upgrade food inspection capacity and CDC facilities that deal with public health threats. In addition to the central role the LRN played in detecting and responding to the 2001 anthrax letter event, the commitment to infrastructure support and standardized platform testing capacity within the LRN has also proven extremely bene fi cial in assisting with more rapid and broader deployment of tests developed in response to other emerging public health threats such as the 2003 Severe Acute Respiratory Syndrome (SARS) and the 2009 H1N1 avian in fl uenza pandemic. abstract: The United States (US) considers the intentional use of a biological agent a serious national security threat. Over the last decade, federal, state, and local governments in the US have made concerted efforts to enhance preparedness within the public health, medical, and emergency response systems to address this threat. These activities span a wide range of areas from the enactment of new legal authorities and legislative changes to significant financial investments to enhance multiple detection and response system capabilities and the adoption of a national command and control structure for response. Many of these investments, although prompted by the concern for bioterrorism, have served to strengthen public health, medical, and emergency response systems overall and have proven invaluable in responses to other large-scale emergencies, such as the 2009 H1N1 influenza pandemic. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123088/ doi: 10.1007/978-94-007-5273-3_18 id: cord-003444-dmpoy0b1 author: Rowe, John C. title: A Novel Supplementation Approach to Enhance Host Response to Sublingual Vaccination date: 2019-01-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Sublingual immunization is emerging as an alternative to nasal immunization and induction of mucosal IgA responses. Using Bacillus anthracis edema toxin (EdTx) as an adjuvant, we previously showed that innate responses triggered after sublingual immunization could limit generation of IgA responses. We tested whether co-administration of a neutrophil elastase inhibitor (NEI) could rescue the ability of EdTx to induce broad antibody responses, including mucosal IgA. NEI supplementation of sublingual vaccines containing EdTx promoted antigen-specific serum IgA responses but also enhanced serum IgG1, and IgG2b responses. This enhancing effect of NEI did not extend to all antibody isotypes and IgG sublclasses, since NEI reduced serum IgE responses and did not affect IgG2a/c and IgG3 responses. NEI supplementation also promoted anti-Bacillus anthracis protective antigen (PA) neutralizing antibodies and enhanced high affinity IgG1 and IgA antibodies. In addition to serum IgA, NEI supplementation stimulated antigen-specific mucosal IgA responses in the GI tract, and enhanced antigen-specific IgG responses in vaginal washes. Analysis of CD4(+) T helper cell responses revealed that co-administration of NEI broadened the profile of cytokine responses, by stimulating Th1, Th2, Th17, and Tfh cytokines. We also noted that NEI had a higher stimulatory effect on IL-5, IL-10, IL-17 responses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346055/ doi: 10.1038/s41598-018-36370-8 id: cord-286072-kgpvdb42 author: Sa Ribero, Margarida title: Interplay between SARS-CoV-2 and the type I interferon response date: 2020-07-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. An unbalanced immune response, characterized by a weak production of type I interferons (IFN-Is) and an exacerbated release of proinflammatory cytokines, contributes to the severe forms of the disease. SARS-CoV-2 is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2003 and 2013, respectively. Although IFN treatment gave some encouraging results against SARS-CoV and MERS-CoV in animal models, its potential as a therapeutic against COVID-19 awaits validation. Here, we describe our current knowledge of the complex interplay between SARS-CoV-2 infection and the IFN system, highlighting some of the gaps that need to be filled for a better understanding of the underlying molecular mechanisms. In addition to the conserved IFN evasion strategies that are likely shared with SARS-CoV and MERS-CoV, novel counteraction mechanisms are being discovered in SARS-CoV-2–infected cells. Since the last coronavirus epidemic, we have made considerable progress in understanding the IFN-I response, including its spatiotemporal regulation and the prominent role of plasmacytoid dendritic cells (pDCs), which are the main IFN-I–producing cells. While awaiting the results of the many clinical trials that are evaluating the efficacy of IFN-I alone or in combination with antiviral molecules, we discuss the potential benefits of a well-timed IFN-I treatment and propose strategies to boost pDC-mediated IFN responses during the early stages of viral infection. url: https://doi.org/10.1371/journal.ppat.1008737 doi: 10.1371/journal.ppat.1008737 id: cord-271250-ywb26cq6 author: Sarkar, Indranil title: Selection of adjuvants for vaccines targeting specific pathogens date: 2019-04-22 words: 11394.0 sentences: 542.0 pages: flesch: 39.0 cache: ./cache/cord-271250-ywb26cq6.txt txt: ./txt/cord-271250-ywb26cq6.txt summary: In-depth understanding of the role of adjuvants in activating the innate immune system, combined with systems vaccinology approaches, have led to the development of next-generation, novel adjuvants that can be used in vaccines against challenging pathogens and in specific target populations. Intact MyD88 signaling in each of the three types of APCs (DCs, macrophages and B cells) is essential for robust activity of TLR ligand-based vaccine adjuvants (PorB, a TLR2 ligand and CpG, a TLR9 ligand) such as induction of in vivo cytokine responses, germinal center (GC) formation and antibody production [49] . A combination adjuvant consisting of poly(I:C), a host defense peptide and PCEP when delivered intranasally transiently induces production of chemokines and cytokines in murine respiratory tissues, which promotes infiltration and activation of DCs, macrophages, and neutrophils to generate improved mucosal and systemic immune responses [55] . abstract: Introduction: Adjuvants form an integral component in most of the inactivated and subunit vaccine formulations. Careful and proper selection of adjuvants helps in promoting appropriate immune responses against target pathogens at both innate and adaptive levels such that protective immunity can be elicited. Areas covered: Herein, we describe the recent progress in our understanding of the mode of action of adjuvants that are licensed for use in human vaccines or in clinical or pre-clinical stages at both innate and adaptive levels. Different pathogens have distinct characteristics, which require the host to mount an appropriate immune response against them. Adjuvants can be selected to elicit a tailor-made immune response to specific pathogens based on their unique properties. Identification of biomarkers of adjuvanticity for several candidate vaccines using omics-based technologies can unravel the mechanism of action of modern and experimental adjuvants. Expert opinion: Adjuvant technology has been revolutionized over the last two decades. In-depth understanding of the role of adjuvants in activating the innate immune system, combined with systems vaccinology approaches, have led to the development of next-generation, novel adjuvants that can be used in vaccines against challenging pathogens and in specific target populations. url: https://www.ncbi.nlm.nih.gov/pubmed/31009255/ doi: 10.1080/14760584.2019.1604231 id: cord-002895-z82e7z2v author: Schilling, Megan A. title: Transcriptional Innate Immune Response of the Developing Chicken Embryo to Newcastle Disease Virus Infection date: 2018-02-27 words: 5996.0 sentences: 249.0 pages: flesch: 43.0 cache: ./cache/cord-002895-z82e7z2v.txt txt: ./txt/cord-002895-z82e7z2v.txt summary: Since the chicken embryo becomes immunocompetent prior to hatch, we here characterized the transcriptional response of selected innate immune genes to Newcastle disease virus (NDV) infection in chicken embryos at days 10, 14, and 18 of embryonic development. Since the chicken embryo becomes immunocompetent prior to hatch, we here characterized the transcriptional response of selected innate immune genes to Newcastle disease virus (NDV) infection in chicken embryos at days 10, 14, and 18 of embryonic development. The comparative transcriptional profile of SPF White Leghorn chicken embryos (one control and one infected at 18 days, harvested 72 hpi) was determined using the Chicken Innate and Adaptive Immune Responses RT 2 Profiler Array (QIAGEN Inc., Germantown, MD, United States) as an initial screen to select for immune genes in the embryo that are differentially expressed during infection since studies have not been performed previously. abstract: Traditional approaches to assess the immune response of chickens to infection are through animal trials, which are expensive, require enhanced biosecurity, compromise welfare, and are frequently influenced by confounding variables. Since the chicken embryo becomes immunocompetent prior to hatch, we here characterized the transcriptional response of selected innate immune genes to Newcastle disease virus (NDV) infection in chicken embryos at days 10, 14, and 18 of embryonic development. The results suggest that the innate immune response 72 h after challenge of 18-day chicken embryo is both consistent and robust. The expression of CCL5, Mx1, and TLR3 in lung tissues of NDV challenged chicken embryos from the outbred Kuroiler and Tanzanian local ecotype lines showed that their expression was several orders of magnitude higher in the Kuroiler than in the local ecotypes. Next, the expression patterns of three additional innate-immunity related genes, IL-8, IRF-1, and STAT1, were examined in the highly congenic Fayoumi (M5.1 and M15.2) and Leghorn (Ghs6 and Ghs13) sublines that differ only at the microchromosome bearing the major histocompatibility locus. The results show that the Ghs13 Leghorn subline had a consistently higher expression of all genes except IL-8 and expression seemed to be subline-dependent rather than breed-dependent, suggesting that the innate immune response of chicken embryos to NDV infection may be genetically controlled by the MHC-locus. Taken together, the results suggest that the chicken embryo may represent a promising model to studying the patterns and sources of variation of the avian innate immune response to infection with NDV and related pathogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5835104/ doi: 10.3389/fgene.2018.00061 id: cord-297834-me1ajoyb author: Schountz, Tony title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 words: 6425.0 sentences: 334.0 pages: flesch: 38.0 cache: ./cache/cord-297834-me1ajoyb.txt txt: ./txt/cord-297834-me1ajoyb.txt summary: The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. abstract: Hantaviruses are hosted by rodents, insectivores and bats. Several rodent-borne hantaviruses cause two diseases that share many features in humans, hemorrhagic fever with renal syndrome in Eurasia or hantavirus cardiopulmonary syndrome in the Americas. It is thought that the immune response plays a significant contributory role in these diseases. However, in reservoir hosts that have been closely examined, little or no pathology occurs and infection is persistent despite evidence of adaptive immune responses. Because most hantavirus reservoirs are not model organisms, it is difficult to conduct meaningful experiments that might shed light on how the viruses evade sterilizing immune responses and why immunopathology does not occur. Despite these limitations, recent advances in instrumentation and bioinformatics will have a dramatic impact on understanding reservoir host responses to hantaviruses by employing a systems biology approach to identify important pathways that mediate virus/reservoir relationships. url: https://www.ncbi.nlm.nih.gov/pubmed/24638205/ doi: 10.3390/v6031317 id: cord-287396-18p171nr author: Schroyen, Martine title: Current transcriptomics in pig immunity research date: 2014-11-15 words: 9824.0 sentences: 467.0 pages: flesch: 44.0 cache: ./cache/cord-287396-18p171nr.txt txt: ./txt/cord-287396-18p171nr.txt summary: Other meta-analysis studies, examining the immune response to Salmonella typhimurium, combine microarray information with data such as serum cytokine measurements or microbiota differences. typhimurium will be discussed in the section ''''Overall value of transcriptomics in important infectious swine diseases.'''' In addition, whole genome microarrays were used to study pig response to Haemophilus parasuis infection by Zhao et al. In 2010, Xiao and collaborators performed a 3'' tag digital gene expression (DGE) analysis of the porcine lung transcriptome on pigs infected with the PRRS virus (Xiao et al. Most pig immune studies conducted to identify host response to common porcine pathogens or to immune response stimulators such as LPS or PMA/ionomycin described in this review provide gene expression data from a single tissue or isolated cell type, and this at a limited number of times post-infection/stimulation. Recently, such a meta-analysis was performed by combining results of several microarray-based pig immune studies to find PRRS-specific responses (Badaoui et al. abstract: Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig’s robustness and resilience against pathogens through selection, a better understanding of the genetic and epigenetic factors in the immune response is required. This review highlights results from the most recent transcriptome research, and the meta-analyses performed, in the context of pig immunity. A technological overview is given including wholegenome microarrays, immune-specific arrays, small-scale high-throughput expression methods, high-density tiling arrays, and next generation sequencing (NGS). Although whole genome microarray techniques will remain complementary to NGS for some time in domestic species, research will transition to sequencing-based methods due to cost-effectiveness and the extra information that such methods provide. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review. With emphasis on the insights obtained from transcriptomic analyses for porcine immunity, we also discuss the experimental design in pig immunity research and the value of the newly published porcine genome assembly in using the pig as a model for human immune response. We conclude by discussing the importance of establishing community standards to maximize the possibility of integrative computational analyses, such as was clearly beneficial for the human ENCODE project. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00335-014-9549-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00335-014-9549-4 doi: 10.1007/s00335-014-9549-4 id: cord-311811-nrodyagi author: Schutzer, Steven E. title: The use of host factors in microbial forensics date: 2019-12-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Advances have been made in the forensic analysis of microbes and toxins. An underdeveloped and underutilized area in microbial forensics is how the host interacts with microorganisms in a way that provides unique signatures for forensic use. For forensic purposes, an immediate goal is to distinguish a potential victim and innocent person from a perpetrator, and to distinguish between a naturally acquired or intentional infection. Principal methods that are sufficiently developed are characterization of the humoral immune response to microbial antigens including vaccine-induced immunity and detection of antibiotics that may be present in a possible perpetrator. This chapter presents central elements of the host response in a simplified fashion and describes a representative example, which, in the appropriate context, has a high potential of providing evidence that may aid an investigation to distinguish a perpetrator from a victim. This chapter also presents information about the immune system so that the interested reader can have a fuller understanding of the immune response in general. url: https://www.sciencedirect.com/science/article/pii/B9780128153796000143 doi: 10.1016/b978-0-12-815379-6.00014-3 id: cord-021424-kocwsyi7 author: Shannon, M. Frances title: Genomic Approaches to the Host Response to Pathogens date: 2009-01-30 words: 7277.0 sentences: 343.0 pages: flesch: 43.0 cache: ./cache/cord-021424-kocwsyi7.txt txt: ./txt/cord-021424-kocwsyi7.txt summary: This activation process includes widespread changes in the gene expression profi le of the cells with hundreds of genes being either switched on or off in response to signals generated from the pathogen-detecting TLRs. The response of individual genes has been studied in minute detail for a handful of genes and while this has produced an understanding of some aspects of host response to infection it by no means gives us the total picture. Studies in both animal models and human populations have shown that infectious disease and the response of the host to a specifi c infection also has a complex genetic component ( Clementi and Di Gianantonio, 2006 ; Lipoldova and Demant, 2006 ; Marquet et al., 1996 ; Mira et al., 2004 ) . Expression profi ling studies have been used to investigate the differences in the host response to pathogenic and nonpathogenic strains of specifi c infectious agents. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149680/ doi: 10.1016/b978-0-12-369420-1.00107-4 id: cord-021966-5m21bsrw author: Shaw, Alan R. title: Vaccines date: 2009-05-15 words: 21170.0 sentences: 897.0 pages: flesch: 33.0 cache: ./cache/cord-021966-5m21bsrw.txt txt: ./txt/cord-021966-5m21bsrw.txt summary: Because a number of proteins produced in isolation by recombinant methods have been observed to elicit lower immune responses than do natural infections or live attenuated vaccines, the development and use of adjuvants to optimize recombinant vaccine immunogenicity represent an important parallel area for future exploration. Modern molecular biology and biochemistry have provided numerous options for vaccine immunogen presentation, including recombinant proteins (and recombinant virus-like particles (VLPs)), synthetic proteins, protein-polysaccharide conjugates, and gene delivery systems (recombinant viral vectors, or DNA vaccines) >> Is the antigen of interest sufficiently immunogenic on its own, or is augmentation of the desired immune response by conjugation to a specific carrier or addition of an adjuvant necessary to elicit a sufficient and sufficiently durable immune response in individuals in the target population for vaccination? abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152278/ doi: 10.1016/b978-0-323-04404-2.10092-2 id: cord-307202-iz1bo218 author: Shaw, Dominick title: Asthma date: 2014-05-02 words: 19168.0 sentences: 831.0 pages: flesch: 37.0 cache: ./cache/cord-307202-iz1bo218.txt txt: ./txt/cord-307202-iz1bo218.txt summary: Current asthma management involves a step-up and step-down approach based on asthma control with a large degree of heterogeneity in responses to the main drug classes currently in use: β(2)-adrenergic receptor agonists, corticosteroids, and leukotriene modifiers. Human studies have identified elevated numbers of cells expressing IL13 mRNA in the bronchial tissue of atopic and nonatopic asthmatic subjects [50] ; administration of recombinant IL13 in mouse lungs resulted in an increase in airway mucus secretion, development of subepithelial fibrosis, airway hyper-responsiveness (AHR), and eosinophilic airway inflammation-that is, several key features of the human disease [51] . While methods of stratifying asthma patients to specific treatments based on nongenetic factors such as clinical outcomes, cellular measures, or protein biomarkers have shown some success, a large body of work has investigated the potential of genetic markers as predictors of patient responses to existing therapies, i.e., pharmacogenetics. abstract: Asthma is a common respiratory disease with a complex etiology involving a combination of genetic and environmental components. Current asthma management involves a step-up and step-down approach based on asthma control with a large degree of heterogeneity in responses to the main drug classes currently in use: β(2)-adrenergic receptor agonists, corticosteroids, and leukotriene modifiers. Importantly, asthma is heterogeneous with respect to clinical presentation and the inflammatory mechanisms that underlie it. This heterogeneity likely contributes to variable results in clinical trials, particularly when targeting specific inflammatory mediators. These factors have motivated a drive toward stratified medicine in asthma based on clinical/cellular outcomes or genetics (i.e., pharmacogenetics). Significant progress has been made in identifying genetic polymorphisms that influence the efficacy and potential for adverse effects of all main classes of asthma drugs. Importantly an emerging role for genetics in phase II development of newer therapies has been demonstrated (e.g., anti-IL4). Similarly, the stratification of patients based on clinical characteristics (e.g., blood and sputum eosinophil levels) has been critical in evaluating newer therapies (e.g., anti-IL5). As a proof of concept, anti-IgE is the latest therapy to be introduced into clinical practice, although only for severe, allergic patients (i.e., in a stratified manner). As new asthma genes are identified using genome-wide association, among other technologies, new targets (e.g., IL33/IL33 receptor (IL1RL1)) will emerge and pharmacogenetics in these development programs will be essential. In this chapter we review the current understanding of asthma pathobiology and its clinical presentation, as well as the use of stratified medicine, which holds great promise for maximizing clinical outcomes and minimizing adverse effects in existing and new therapies. url: https://www.sciencedirect.com/science/article/pii/B9780123868824000281 doi: 10.1016/b978-0-12-386882-4.00028-1 id: cord-272512-gevrlcvy author: Shewen, P.E. title: Challenges in mucosal vaccination of cattle date: 2009-03-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recognition of the mucosal portal of entry for many infectious diseases and of the relevance of mucosal immune response to protection has encouraged the development of vaccines administered by mucosal routes, principally oral and intranasal, for stimulation of intestinal and nasopharyngeal lymphoid tissues respectively. The oral route is problematic in cattle and other ruminants where antigen degradation in the rumen is likely, prior to transit to the intestine. On the other hand, rumination can be exploited for exposure of nasopharyngeal tissues during cudding if vaccine antigen is expressed by a fibrous feed like alfalfa. An increase in anti-leukotoxin (Lkt) IgA was demonstrated in nasal secretions of calves following feeding of alfalfa expressing a truncated Lkt50 from Mannheimia haemolytica, and there is evidence suggesting that such vaccination may protect against experimentally induced pneumonia. Intranasal vaccination is an alternative approach for use in pre-ruminating calves. Intranasal administration of ISCOMs carrying soluble antigens of M. haemolytica, including native Lkt, induced Lkt specific IgA in nasal secretions after vaccination at 4 and 6 weeks of age. Subcutaneous (s.c.) administration of the same vaccine induced Lkt specific IgG in both serum and nasal secretions, whereas s.c. administration of a commercial M. haemolytica vaccine did not. Regardless of the vaccination strategy employed it is difficult to assess the immunogenicity of mucosally administered vaccines because production of secreted antibodies tends to be transient, and they do not persist on the mucosal surface in the absence of ongoing antigenic stimulation. An additional challenge is demonstration of vaccine efficacy in response to experimental infection. Protection of the mucosally vaccinated animal will most probably result from recall response, which may not amplify sufficiently to counter the effects of experimental pulmonary delivery of a large bolus of virulent bacteria, even though the response would suffice over the more prolonged and gradual infection that occurs in natural induction of pneumonia. url: https://www.sciencedirect.com/science/article/pii/S0165242708004030 doi: 10.1016/j.vetimm.2008.10.297 id: cord-344297-qqohijqi author: Smith, Jacqueline title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date: 2015-10-09 words: 5076.0 sentences: 284.0 pages: flesch: 52.0 cache: ./cache/cord-344297-qqohijqi.txt txt: ./txt/cord-344297-qqohijqi.txt summary: title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. [18] we used Affymetrix wholegenome chicken microarrays to examine the tracheal gene expression profiles of a line of birds known to be susceptible to IBV infection (line 15I) and a line known to show resistance (line N). Gene expression differences found in the susceptible 15I line between infected and control birds over days 2, 3 and 4 post infection were analysed, with a view to examining the innate host response to infection by IBV. Gene expression seen during the host response to IBV infection in the trachea of susceptible birds. Genes found to be differentially expressed between susceptible and resistant lines in response to IBV infection in the trachea. abstract: BACKGROUND: Infectious Bronchitis is a highly contagious respiratory disease which causes tracheal lesions and also affects the reproductive tract and is responsible for large economic losses to the poultry industry every year. This is due to both mortality (either directly provoked by IBV itself or due to subsequent bacterial infection) and lost egg production. The virus is difficult to control by vaccination, so new methods to curb the impact of the disease need to be sought. Here, we seek to identify genes conferring resistance to this coronavirus, which could help in selective breeding programs to rear chickens which do not succumb to the effects of this disease. METHODS: Whole genome gene expression microarrays were used to analyse the gene expression differences, which occur upon infection of birds with Infectious Bronchitis Virus (IBV). Tracheal tissue was examined from control and infected birds at 2, 3 and 4 days post-infection in birds known to be either susceptible or resistant to the virus. The host innate immune response was evaluated over these 3 days and differences between the susceptible and resistant lines examined. RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. Potential candidate genes for resistance to IBV are highlighted. CONCLUSIONS: The early host response to IBV is analysed and potential candidate genes for disease resistance are identified. These putative resistance genes can be used as targets for future genetic and functional studies to prove a causative link with resistance to IBV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0575-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12917-015-0575-6 doi: 10.1186/s12917-015-0575-6 id: cord-032600-lldbjm77 author: Soni, Dheeraj title: The sixth revolution in pediatric vaccinology: immunoengineering and delivery systems date: 2020-09-14 words: 6655.0 sentences: 388.0 pages: flesch: 32.0 cache: ./cache/cord-032600-lldbjm77.txt txt: ./txt/cord-032600-lldbjm77.txt summary: 2 Second-generation efforts employed more characterized materials, such as the biodegradable synthetic polymer poly (D,L-lactic-co-glycolic acid) (PLGA), which is a widely investigated nanoparticle adjuvant for controlled and effective delivery of vaccine antigens, including synthetic peptides. 32 Thus, pathogen-mimicking nanoparticles can be engineered to enhance the immune response by controlling when and where vaccine components are delivered intracellularly to APCs. 15 A plethora of particulate delivery systems for immunoengineering have been developed, which are summarized further in this review. Recently, we have combined such engineering and rational vaccine design approaches to develop a nanoparticle-based adjuvant and antigen-delivery system designed to be active in human newborns and infants. Furthermore, such formulations hold substantial potential for early life immunization by serving as a dual antigen/adjuvant delivery system that mimics the enhanced neonatal innate and adaptive immune responses elicited by the live Bacille Calmette-Guerin (BCG) vaccine. abstract: ABSTRACT: Infection is the predominant cause of mortality in early life, and immunization is the most promising biomedical intervention to reduce this burden. However, very young infants fail to respond optimally to most vaccines currently in use, especially neonates. In 2005, Stanley Plotkin proposed that new delivery systems would spur a new revolution in pediatric vaccinology, just as attenuation, inactivation, cell culture of viruses, genetic engineering, and adjuvantation had done in preceding decades. Recent advances in the field of immunoengineering, which is evolving alongside vaccinology, have begun to increasingly influence vaccine formulation design. Historically, the particulate nature of materials used in many vaccine formulations was empiric, often because of the need to stabilize antigens or reduce endotoxin levels. However, present vaccine delivery systems are rationally engineered to mimic the size, shape, and surface chemistry of pathogens, and are therefore often referred to as “pathogen-like particles”. More than a decade from his original assessment, we re-assess Plotkin’s prediction. In addition, we highlight how immunoengineering and advanced delivery systems may be uniquely capable of enhancing vaccine responses in vulnerable populations, such as infants. IMPACT: Immunoengineering and advanced delivery systems are leading to new developments in pediatric vaccinology. Summarizes delivery systems currently in use and development, and prospects for the future. Broad overview of immunoengineering’s impact on vaccinology, catering to Pediatric Clinicians and Immunologists. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7511675/ doi: 10.1038/s41390-020-01112-y id: cord-018475-h8qwxdtn author: Speckhard, Anne title: Prevention Strategies and Promoting Psychological Resilience to Bioterrorism Through Communication date: 2007 words: 10540.0 sentences: 411.0 pages: flesch: 46.0 cache: ./cache/cord-018475-h8qwxdtn.txt txt: ./txt/cord-018475-h8qwxdtn.txt summary: With the erosion of strict borders between countries (particularly in the European Union) and even world regions (since the fall of the Soviet bloc), the advance and portability of high-tech weaponry including biological, chemical, and nuclear hazards, and the ease and speed of communication through the Internet and telephones for purposes of recruitment, training, and planning terror attacks -terrorists now have a global playing field in which even small groups of individuals can motivate, plan, and enact mass terrorist events. Governments and media must work together preparing ahead of time on how to communicate calmly in such crises in a manner that will offer useful preventative measures, minimize the potential negative effects of psychosocial contagions (including citizenry becoming noncompliant and aggressive), prevent mass sociogenic illness from occurring, and prevent overwhelming of the medical systems by those whose emotional state has put them in need of medical care. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123356/ doi: 10.1007/978-1-4020-5808-0_13 id: cord-302082-aaokc182 author: Stanberry, Lawrence R. title: Vaccines of the future date: 2011-08-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://api.elsevier.com/content/article/pii/S2210762211000076 doi: 10.1016/j.pervac.2011.05.006 id: cord-273479-kira7mz6 author: Strike, Philip C. title: Mild acute inflammatory stimulation induces transient negative mood date: 2004-10-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: This study aims to assess the mood changes induced by mild acute inflammatory stimulation (typhoid vaccination). METHODS: Using a double blind study design, 26 healthy volunteers underwent baseline assessments of mood, financial strain and work stress and were randomised to injection of Salmonella typhi vaccine or placebo injection. Mood, symptoms and body temperature was assessed by a modified version of the Profile of Mood States at 1, 2, 3, 4, 6 and 8 h post injection. RESULTS: Typhoid vaccination induces no increases in physical symptoms or temperature. Mood improved over the day in the placebo but not in the vaccine condition. Negative changes in mood following injection were correlated with chronic stress (financial strain) in the vaccination condition (r=−.65, P<.025). CONCLUSION: A mild acute inflammatory stimulus induces transient negative mood, and responses were modulated by chronic stress. Implications for depressed mood in physical illness are discussed. url: https://api.elsevier.com/content/article/pii/S0022399903005695 doi: 10.1016/s0022-3999(03)00569-5 id: cord-314104-dkm8396y author: Tam, Theresa W. S. title: Preparing for uncertainty during public health emergencies: What Canadian health leaders can do now to optimize future emergency response date: 2020-03-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: It is clear that the risk for epidemics with high health and socio-economic impacts remains but there will be many unknowns at the start of future responses to these events. This article highlights principles and practices to assist health leaders in preparing for uncertainty, including integrating scalability to ensure response activities can be more easily adapted to suit evolving needs; assessing risk and capabilities to inform planning for appropriate response measures; and considering overall flexibility and adaptability of plans, systems, and resources. Ultimately, being prepared for “Disease X” is about applying the approaches that we have learned from previous events, using evidence-based practices to develop and strengthen foundational capacities, so that we are able to respond to the unanticipated in proportionate and appropriate ways. url: https://www.ncbi.nlm.nih.gov/pubmed/32228317/ doi: 10.1177/0840470420917172 id: cord-003898-y6zpvw84 author: Tan, Kai Sen title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 words: 7671.0 sentences: 386.0 pages: flesch: 44.0 cache: ./cache/cord-003898-y6zpvw84.txt txt: ./txt/cord-003898-y6zpvw84.txt summary: title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications The aim of this study was to utilize RNA sequencing (RNAseq) technology to not only reveal the hNEC responses (from multiple individuals) against influenza infection, but also to identify those genes with high magnitude changes to serve as potential reference markers of the innate responses of influenza infection. After deriving the transcriptomes by RNAseq, we then further investigated whether the changes in expression of genes resulted in alterations in secretory cytokines and chemokines early in the infection of hNECs. Initially, we detected significant reductions in multiple cytokines at 8 hpi, with the exception of IL-15 which was increased ( Figure S2 ). In conclusion, RNAseq technology allowed us to accurately quantify the magnitude of gene expression changes, as well as the relevant enriched pathways during H3N2 influenza virus infection of hNECs, which can serve as a baseline for future clinical studies. abstract: The human nasal epithelium is the primary site of exposure to influenza virus, the initiator of host responses to influenza and the resultant pathologies. Influenza virus may cause serious respiratory infection resulting in major complications, as well as severe impairment of the airways. Here, we elucidated the global transcriptomic changes during H3N2 infection of human nasal epithelial cells from multiple individuals. Using RNA sequencing, we characterized the differentially-expressed genes and pathways associated with changes occurring at the nasal epithelium following infection. We used in vitro differentiated human nasal epithelial cell culture model derived from seven different donors who had no concurrent history of viral infections. Statistical analysis highlighted strong transcriptomic signatures significantly associated with 24 and 48 h after infection, but not at the earlier 8-h time point. In particular, we found that the influenza infection induced in the nasal epithelium early and altered responses in interferon gamma signaling, B-cell signaling, apoptosis, necrosis, smooth muscle proliferation, and metabolic alterations. These molecular events initiated at the infected nasal epithelium may potentially adversely impact the airway, and thus the genes we identified could serve as potential diagnostic biomarkers or therapeutic targets for influenza infection and associated disease management. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770044/ doi: 10.3390/cells8090986 id: cord-007375-hqmyund4 author: Tang, Yi-Wei title: Host Single-Nucleotide Polymorphisms and Altered Responses to Inactivated Influenza Vaccine date: 2007-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We analyzed the relationship between host gene polymorphisms and responses in recipients of inactivated influenza vaccine, who were classified into poor, normal, or adverse response groups. The frequency of the mannose-binding lectin-2 codon 54 allele was significantly different among the 3 types of responders, with a decreased odds ratio for the development of poor or adverse responses (P = .033). There was no statistical relationship between responses and either tumor necrosis factor-α or interleukin (IL)-10 promoter polymorphisms among the 3 response groups. When poor and normal responses were combined, the -1082 A allele in the IL-10 promoter conferred a significantly decreased risk of the development of adverse responses (P = .041). These data indicate that host polymorphisms play a role in determining responses to influenza vaccine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7111848/ doi: 10.1086/521370 id: cord-026949-nu46ok9w author: Varshney, Deeksha title: Natural Language Generation Using Transformer Network in an Open-Domain Setting date: 2020-05-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Prior works on dialog generation focus on task-oriented setting and utilize multi-turn conversational utterance-response pairs. However, natural language generation (NLG) in the open-domain environment is more challenging. The conversations in an open-domain chit-chat model are mostly single-turn in nature. Current methods used for modeling single-turn conversations often fail to generate contextually relevant responses for a large dataset. In our work, we develop a transformer-based method for natural language generation (NLG) in an open-domain setting. Experiments on the utterance-response pairs show improvement over the baselines, both in terms of quantitative measures like BLEU and ROUGE and human evaluation metrics like fluency and adequacy. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298179/ doi: 10.1007/978-3-030-51310-8_8 id: cord-297776-k38jssr0 author: Volk, Aaron title: Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date: 2020-05-18 words: 5843.0 sentences: 293.0 pages: flesch: 42.0 cache: ./cache/cord-297776-k38jssr0.txt txt: ./txt/cord-297776-k38jssr0.txt summary: gene expression, we report significant transcriptional upregulation of multiple genes associated with activation of ER sensors IRE1, ATF6, and PERK, such as Edem1, Hspa5 (encoding BiP protein), and Ddit3 (encoding CHOP), in response to virus replication, with the most robust response detected in cells infected with the wild-type or DUBmut virus infection (Fig. 5B, C, and D) . Overall, these differential gene expression analyses in macrophages reveal similar host responses to the wild-type and DUBmut viruses that include activation of UPR pathways and proinflammatory genes, whereas a distinct transcriptional profile during infection with the EndoUmut virus is predominately defined by a focused, robust antiviral response. The results presented here, and from studies of the MERS-CoV dORF3-5 mutant virus (26) Upon infection of a BMDM with EndoUmut, host double-stranded RNA (dsRNA) sensors (including MDA5, PKR, and OAS) are activated, resulting in robust transcription of type I IFN genes and rapid induction of apoptosis, the latter of which precludes the development of a potent inflammatory response. abstract: Coronaviruses (CoVs) encode multiple interferon (IFN) antagonists that modulate the host response to virus replication. Here, we evaluated the host transcriptional response to infection with murine coronaviruses encoding independent mutations in one of two different viral antagonists, the deubiquitinase (DUB) within nonstructural protein 3 or the endoribonuclease (EndoU) within nonstructural protein 15. We used transcriptomics approaches to compare the scope and kinetics of the host response to the wild-type (WT), DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response that predominantly involves type I interferons and interferon-related genes, whereas the WT and DUBmut viruses more broadly stimulate upregulation of over 2,800 genes, including networks associated with activating the unfolded protein response (UPR) and the proinflammatory response associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in shaping the kinetics and magnitude of the host response during virus infection and demonstrates that inactivating a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages. IMPORTANCE Macrophages are an important cell type during coronavirus infections because they “notice” the infection and respond by inducing type I interferons, which limits virus replication. In turn, coronaviruses encode proteins that mitigate the cell’s ability to signal an interferon response. Here, we evaluated the host macrophage response to two independent mutant coronaviruses, one with reduced deubiquitinating activity (DUBmut) and the other containing an inactivated endoribonuclease (EndoUmut). We observed a rapid, robust, and focused response to the EndoUmut virus, which was characterized by enhanced expression of interferon and interferon-related genes. In contrast, wild-type virus and the DUBmut virus elicited a more limited interferon response and ultimately activated over 2,800 genes, including players in the unfolded protein response and proinflammatory pathways associated with progression of significant disease. This study reveals that EndoU activity substantially contributes to the ability of coronaviruses to evade the host innate response and to replicate in macrophages. url: https://www.ncbi.nlm.nih.gov/pubmed/32188729/ doi: 10.1128/jvi.00178-20 id: cord-288868-qfdxri93 author: Wack, Andreas title: Vaccinology at the beginning of the 21st century date: 2005-06-13 words: 5082.0 sentences: 224.0 pages: flesch: 43.0 cache: ./cache/cord-288868-qfdxri93.txt txt: ./txt/cord-288868-qfdxri93.txt summary: Thus, the use of reverse genetics enables rapid production of a reference vaccine virus in response to the emergence of a new influenza variant [15 ,16] . Activation of DCs increases their ability to process and present antigen and to attract and activate T cells through cytokine secretion; consequently, several cytokines are 414 Host-pathogen interactions Table 1 Human TLR agonists used as adjuvants in vaccine formulations in clinical trials or licensed vaccines a . When viral vehicles (vaccinia or adenovirus) were compared with loaded DCs in terms of their ability to overcome established tolerance and induce immune responses in a transgenic mouse model, the viral formulations were able to do so, whereas DCs required repeated administration of TLR agonists or irrelevant virus, or removal of suppressive CD4 + CD25 + Treg cells [54 ] . A CD4(+) T-cell immune response to a conserved epitope in the circumsporozoite protein correlates with protection from natural Plasmodium falciparum infection and disease abstract: Today, the main challenges for vaccinologists include improving vaccines against as yet undefeated pathogens, rapid identification and response to emerging diseases and successful intervention in chronic diseases in which ongoing immune responses are insufficient. Reverse genetics and reverse vaccinology are now used to generate rapidly new vaccine strains and to mine whole genomes in the search for promising antigens. The rational design of adjuvants has become possible as a result of the discovery of the receptors that recognize microbial patterns and lead to dendritic cell activation. Antigen-loaded dendritic cells, DNA in naked, formulated or viral form, and other delivery systems are used to maximize immune responses. Although work on the ‘easy’ vaccines has already been completed, it is hoped that a combination of conceptual and technical innovation will enable the development of more complex and sophisticated vaccines in the future. url: https://www.ncbi.nlm.nih.gov/pubmed/15950445/ doi: 10.1016/j.coi.2005.05.005 id: cord-305263-fgwf6wy3 author: Wang, Ben X. title: The yin and yang of viruses and interferons date: 2012-02-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Interferons (IFNs)-α/β are critical effectors of the innate immune response to virus infections. Through activation of the IFN-α/β receptor (IFNAR), they induce expression of IFN-stimulated genes (ISGs) that encode antiviral proteins capable of suppressing viral replication and promoting viral clearance. Many highly pathogenic viruses have evolved mechanisms to evade an IFN response and the balance between the robustness of the host immune response and viral antagonistic mechanisms determines whether or not the virus is cleared. Here, we discuss IFNs as broad-spectrum antivirals for treatment of acute virus infections. In particular, they are useful for treatment of re-emerging virus infections, where direct-acting antivirals (DAAs) have limited utility due to DAA-resistant mutations, and for newly emerging virus strains in which the time to vaccine availability precludes vaccination at the onset of an outbreak. url: https://doi.org/10.1016/j.it.2012.01.004 doi: 10.1016/j.it.2012.01.004 id: cord-026960-g844u7xg author: Wang, Disen title: An Adaptive Response Matching Network for Ranking Multi-turn Chatbot Responses date: 2020-05-26 words: 4523.0 sentences: 237.0 pages: flesch: 52.0 cache: ./cache/cord-026960-g844u7xg.txt txt: ./txt/cord-026960-g844u7xg.txt summary: To address this limitation, this paper proposes an adaptive response matching network (ARM) to better model the matching relationship in multi-turn conversations. Specifically, the Dual-encoder model [8] used two LSTMs to generate the embeddings for the utterances and candidate response respectively to compute the matching score. Deep attention model (DAM) [20] proposed self-attention and cross-attention to construct semantic representations at different granularity, and the multirepresentation fusion network (MRFN) [13] has further applied multiple representation strategies for utterances and fused them in the final step to compute the matching scores. Few of them studied how to adapt the matching model to different types of utterances and how to incorporate the domain knowledge in a more general way, which is the focus of our paper. Although a few models have been proposed to solve the problem of multi-turn response selection [2, 13, 17, 20] , none of them studied how to directly adapt the matching mechanisms to different utterance types. abstract: With the increasing popularity of personal assistant systems, it is crucial to build a chatbot that can communicate with humans and assist them to complete different tasks. A fundamental problem that any chatbots need to address is how to rank candidate responses based on previous utterances in a multi-turn conversation. A previous utterance could be either a past input from the user or a past response from the chatbot. Intuitively, a correct response needs to match well with both past responses and past inputs, but in a different way. Moreover, the matching process should depend on not only the content of the utterances but also domain knowledge. Although various models have been proposed for response matching, few of them studied how to adapt the matching mechanism to utterance types and domain knowledge. To address this limitation, this paper proposes an adaptive response matching network (ARM) to better model the matching relationship in multi-turn conversations. Specifically, the ARM model has separate response matching encoders to adapt to different matching patterns required by different utterance types. It also has a knowledge embedding component to inject domain-specific knowledge in the matching process. Experiments over two public data sets show that the proposed ARM model can significantly outperform the state of the art methods with much fewer parameters. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298192/ doi: 10.1007/978-3-030-51310-8_22 id: cord-021175-0ikkl3hk author: Wilson, Christopher title: The new informatics of pandemic response: humanitarian technology, efficiency, and the subtle retreat of national agency date: 2018-05-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Digital communication technologies play an increasingly prominent role in humanitarian operations and in response to international pandemics specifically. A burgeoning body of scholarship on the topic displays high expectations for such tools to increase the efficiency of pandemic response. This article reviews empirical uses of communications technology in humanitarian and pandemic response, and the 2014 Ebola response in particular, in order to propose a three-part conceptual model for the new informatics of pandemic response. This model distinguishes between the use of digital communication tools for diagnostic, risk communication, and coordination activities and highlights how the influx of novel actors and tendencies towards digital and operational convergence risks focusing humanitarian action and decision-making outside national authorities’ spheres of influence in pandemic response. This risk exacerbates a fundamental tension between the humanitarian promise of new technologies and the fundamental norm that international humanitarian response should complement and give primacy to the role of national authorities when possible. The article closes with recommendations for ensuring the inclusion of roles and agency for national authorities in technology-supported communication processes for pandemic response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149122/ doi: 10.1186/s41018-018-0036-5 id: cord-332838-i8fjwzm6 author: Woodland, David L. title: Immunity to emerging pathogens date: 2008-09-19 words: 2279.0 sentences: 117.0 pages: flesch: 39.0 cache: ./cache/cord-332838-i8fjwzm6.txt txt: ./txt/cord-332838-i8fjwzm6.txt summary: Our choice of pathogens and authors has therefore resulted in reviews that cover many different types of infectious disease and a breadth of immune responses. The relationship between innate immune responses and viral success in the host population is also discussed by Drs Jessica Weaver and Stuart Isaacs (University of Pennsylvania School of Medicine) (6) with respect to monkeypox virus. Several of the reviews in this volume discuss the important role of T cells in viral, bacterial, and parasite emerging infections. For example, CD8 1 T cells play a major role in protective immunity during Plasmodium liver stage infection, as described by Dr Fidel Zavala and colleagues (Johns Hopkins University) (16) in their review of malaria immunity. While T cells can play a key role in protective immunity, they can also mediate considerable pathogenic effects. Dr Alan Rothman and colleagues (University of Massachusetts Medical School) (18) discuss the impact of T-cell responses on dengue virus infections. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/18837772/ doi: 10.1111/j.1600-065x.2008.00695.x id: cord-022592-g7rmzsv5 author: Wynn, James L. title: Pathophysiology of Neonatal Sepsis date: 2016-07-06 words: 22148.0 sentences: 1302.0 pages: flesch: 39.0 cache: ./cache/cord-022592-g7rmzsv5.txt txt: ./txt/cord-022592-g7rmzsv5.txt summary: 14, 15, [27] [28] [29] [30] [31] [32] [33] Prematurity, low birth weight (especially infants weighing less than 1,000 g), male sex, a maternal vaginal culture positive for group B streptococcus (GBS), prolonged rupture of membranes, maternal intrapartum fever, and chorioamnionitis are strongly associated with an increased risk for early-onset sepsis. In addition to the initial inflammatory response including complement activation, molecular detection of PAMPs promotes IL-1β and IL-6 production, which in turn increases the production of multiple other innate proteins that possess valuable immune function and serve to reduce pathogen load. Very low birth weight preterm infants with early onset neonatal sepsis: the predominance of gram-negative infections continues in the National Institute of Child Health and Human Development Neonatal Research Network Very low birth weight preterm infants with early onset neonatal sepsis: the predominance of gram-negative infections continues in the National Institute of Child Health and Human Development Neonatal Research Network abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7158364/ doi: 10.1016/b978-0-323-35214-7.00152-9 id: cord-293893-ibca88xu author: Xie, Tian title: Parallel Evolution and Response Decision Method for Public Sentiment based on System Dynamics date: 2020-05-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract Governments face difficulties in policy making in many areas such as health, food safety, and large-scale projects where public perceptions can be misplaced. For example, the adoption of the MMR vaccine has been opposed due to the publicity indicating an erroneous link between the vaccine and autism. This research proposes the “Parallel Evolution and Response Decision Framework for Public Sentiments” as a real-time decision-making method to simulate and control the public sentiment evolution mechanisms. This framework is based on the theories of Parallel Control and Management (PCM) and System Dynamics (SD) and includes four iterative steps: namely, SD modelling, simulating, optimizing, and controlling. A concrete case of an anti-nuclear mass incident that sparked public sentiment in China is introduced as a study sample to test the effectiveness of the proposed method. In addition, the results indicate the effects by adjusting the key control variables of response strategies. These variables include response time, response capacity, and transparency of the government regarding public sentiment. Furthermore, the advantages and disadvantages of the proposed method will be analyzed to determine how it can be used by policy makers in predicting public opinion and offering effective response strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/32834432/ doi: 10.1016/j.ejor.2020.05.025 id: cord-296886-0bma2749 author: Xu, Yingying title: Intranasal DNA Vaccine for Protection against Respiratory Infectious Diseases: The Delivery Perspectives date: 2014-07-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Intranasal delivery of DNA vaccines has become a popular research area recently. It offers some distinguished advantages over parenteral and other routes of vaccine administration. Nasal mucosa as site of vaccine administration can stimulate respiratory mucosal immunity by interacting with the nasopharyngeal-associated lymphoid tissues (NALT). Different kinds of DNA vaccines are investigated to provide protection against respiratory infectious diseases including tuberculosis, coronavirus, influenza and respiratory syncytial virus (RSV) etc. DNA vaccines have several attractive development potential, such as producing cross-protection towards different virus subtypes, enabling the possibility of mass manufacture in a relatively short time and a better safety profile. The biggest obstacle to DNA vaccines is low immunogenicity. One of the approaches to enhance the efficacy of DNA vaccine is to improve DNA delivery efficiency. This review provides insight on the development of intranasal DNA vaccine for respiratory infections, with special attention paid to the strategies to improve the delivery of DNA vaccines using non-viral delivery agents. url: https://www.ncbi.nlm.nih.gov/pubmed/25014738/ doi: 10.3390/pharmaceutics6030378 id: cord-339935-tguhrqvz author: Zavattaro, Staci M. title: Introduction: COVID‐19 Viewpoint Symposium, Part II date: 2020-08-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32836466/ doi: 10.1111/puar.13290 id: cord-307229-wjx90xki author: da Silveira, Matheus Pelinski title: Physical exercise as a tool to help the immune system against COVID-19: an integrative review of the current literature date: 2020-07-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acute viral respiratory infections are the main infectious disease in the world. In 2020, a new disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coronavirus disease 2019 (COVID-19), became a global pandemic. The immune response to the virus depends on factors such as genetics, age and physical state, and its main input receptor is the angiotensin-converting enzyme 2. The practice of physical exercises acts as a modulator of the immune system. During and after physical exercise, pro- and anti-inflammatory cytokines are released, lymphocyte circulation increases, as well as cell recruitment. Such practice has an effect on the lower incidence, intensity of symptoms and mortality in viral infections observed in people who practice physical activity regularly, and its correct execution must be considered to avoid damage. The initial response is given mainly by type I interferons (IFN-I), which drive the action macrophages and lymphocytes, followed by lymphocyte action. A suppression of the IFN-I response has been noted in COVID-19. Severe conditions have been associated with storms of pro-inflammatory cytokines and lymphopenia, as well as circulatory changes and virus dispersion to other organs. The practice of physical activities strengthens the immune system, suggesting a benefit in the response to viral communicable diseases. Thus, regular practice of adequate intensity is suggested as an auxiliary tool in strengthening and preparing the immune system for COVID-19. Further studies are needed to associate physical exercise with SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32728975/ doi: 10.1007/s10238-020-00650-3 id: cord-015021-pol2qm74 author: nan title: Third International Congress on the Immune Consequences of Trauma, Shock and Sepsis —Mechanisms and Therapeutic Approaches date: 1994 words: 162327.0 sentences: 9379.0 pages: flesch: 50.0 cache: ./cache/cord-015021-pol2qm74.txt txt: ./txt/cord-015021-pol2qm74.txt summary: It is our current understanding that LPS is responsible for many of the pathophysiological events observed during gramnegative infections and that one of the major mechanisms leading to shock and death is the LPS-induced activation of macrophages resulting in the production and release of lipid and peptide mediators, among which tumor necrosis factor seems to be the most important. However plasma IL-6 estimation revealed a statistically significant reduction at 6 hours in tanrine-treated animals compared to glycino and TW controls ( Objective: To evaluate the effects of allogeneic blood transfusion, thermal injury and bacterial garage on interteukin 4 (IL-4), tumor necrosis factor alpha (TNF) production and host mortality and to study if the administration of thymopentth (THY) could affect these events. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095072/ doi: 10.1007/bf02258437 id: cord-015147-h0o0yqv8 author: nan title: Oral Communications and Posters date: 2014-09-12 words: 73711.0 sentences: 3862.0 pages: flesch: 43.0 cache: ./cache/cord-015147-h0o0yqv8.txt txt: ./txt/cord-015147-h0o0yqv8.txt summary: Cyclooxygenases (COX) catalyze the first step in the synthesis of prostaglandins (PG) from arachidonic acid.COX-1 is constitutively expressed.The COX-2 gene is an immediate early-response gene that is induced by variety of mitogenic and inflammatory stimuli.Levels of COX-2 are increased in both inflamed and malignant tissues.In inflamed tissues, there is both pharmacological and genetic evidence that targeting COX-2 can either improve (e.g., osteoarthritis) or exacerbate symptoms (e.g., inflammatory bowel disease).Multiple lines of evidence suggest that COX-2 plays a significant role in carcinogenesis.The most specific data that support a cause-and effect relationship between COX-2 and tumorigenesis come from genetic studies.Overexpression of COX-2 has been observed to drive tumor formation whereas COX-2 deficiency protects against several tumor types.Selective COX-2 inhibitors protect against the formation and growth of experimental tumors.Moreover, selective COX-2 inhibitors are active in preventing colorectal adenomas in humans.Increased amounts of COX-2-derived PGE2 are found in both inflamed and neoplastic tissues.The fact that PGE2 can stimulate cell proliferation, inhibit apoptosis and induce angiogenesis fits with evidence that induction of COX-2 contributes to both wound healing and tumor growth.Taken together, it seems likely that COX-2 induction contributes to wound healing in response to injury but reduces the threshold for carcinogenesis. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095932/ doi: 10.1007/bf03353884 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-023055-ntbvmssh author: nan title: Immunogenicity date: 2004-02-19 words: 64563.0 sentences: 3952.0 pages: flesch: 59.0 cache: ./cache/cord-023055-ntbvmssh.txt txt: ./txt/cord-023055-ntbvmssh.txt summary: Antigen is internalized into acidic vesicles, proteolyzed, and peptides containing T ceU antigenic determinants are transported to the APC surface where they are recognized by the antigen-specific T cell in conjunction with Ia. Most Ia-"pressing cells are competent APC, however, only B cells have antigen-specilic receptors on their surface aUowing bound antigen to be processed and presented at 1/lW the antigen concentration required by nonspecific APC Little is known about B cell antigen processing function during differentiation, or if Ig-mediated APC function is altered at different maturational stages, thus allowing regulation of B cell-helper T cell interactions. These results indicate that the poor response of murine CTL to human class I antigens is not determined by selection in the thymus, but by species-specific constraints on the interaction of MHC antigens with T-cell recognition structures. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166418/ doi: 10.1002/jcb.240410506 id: cord-023143-fcno330z author: nan title: Molecular aspects of viral immunity date: 2004-02-19 words: 43425.0 sentences: 2056.0 pages: flesch: 47.0 cache: ./cache/cord-023143-fcno330z.txt txt: ./txt/cord-023143-fcno330z.txt summary: Based on a variety of experimental evidence, it is clear that demyelination induced in SJUJ mice by infection with the BeAn strain of TMEV is a Thl-mediated event: (a) disease induction is suppressed in T cell-deprived mice and by in vivo treatment with anti-I-A and anti-CD4 antibodies; (b) disease susceptibility correlates temporally with the development of TMEV-specific, MHC-class Il-restricted DTH responses and with a predominance of anti-viral lgG2a antibody; (c) activated (Le., lL-2RC) T cells infiltrating the CNS are exclusively of the CD4+ phenotype, and (d) proinflammatory cytokines (IFNq and TNF-p) are predominantly produced in the CNS. These results have important implications for a possible viral trigger in MS as they indicate that chronic demyelination in TMEV-infected mice is initiated in the absence of demonstrable neuroantigen-specific autoimmune responses and are consistent with a model wherein early myelin damage is mediated via primarily by mononuclear phagocytes recruited to the CNS and activated by pro-inflammatory cytokines produced by TMEV-specific Thl cells. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167094/ doi: 10.1002/jcb.240591009 id: cord-257167-rz4r5sj7 author: nan title: Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006) date: 2006-12-31 words: 240925.0 sentences: 13617.0 pages: flesch: 47.0 cache: ./cache/cord-257167-rz4r5sj7.txt txt: ./txt/cord-257167-rz4r5sj7.txt summary: SY1-3-11-3 SAD: A novel kinase implicated in phosphoproteome at the presynaptic active zone Toshihisa Ohtsuka Department of Clinical and Molecular Pathology, Faculty of Medicine/Graduate School of Medicine, University of Toyama, Toyama, Japan SAD is a serine/threonine kianse, which has been shown to regulate various neuronal functions during development, including clustering synaptic vesicles, maturation of synapses, and axon/dendrite polarization: these have recently been revealed by genetic studies in C. The results suggest that EAAT4 plays a major role in regulating the concentration of CF transmitters, possibly glutamate, in the route of its extrasynaptic diffusion, and determining the degree of CF-induced inhibition of GABA release from BCs depending on the regional difference of EAAT4 expression in postsynaptic PCs. Chitoshi Takayama 1 , Yoshiro Inoue 1 1 Department of Molecular Neuroanatomy, Hokkaido University School of Medicine, Sapporo, Japan GABA mediates inhibitory transmission in the adult central nervous system (CNS). abstract: nan url: https://api.elsevier.com/content/article/pii/S016801020600085X doi: 10.1016/j.neures.2006.04.004 id: cord-285778-80baxwgc author: nan title: Introduction to the Immune Response date: 2014-10-10 words: 7980.0 sentences: 388.0 pages: flesch: 46.0 cache: ./cache/cord-285778-80baxwgc.txt txt: ./txt/cord-285778-80baxwgc.txt summary: Some innate mechanisms require no induction and are completely non-specific, whereas others are inducible and involve broad receptor-mediated recognition of a limited number of pathogen-associated or damage-associated molecular patterns (PAMPs/DAMPs). When invaders breach anatomical and physiological barriers, innate leukocytes start to take action as a result of pattern recognition mediated by the binding of PRMs to PAMPs furnished by pathogens and to DAMPs emanating from damaged host cells. If the pathogen manages to enter the underlying cell layer, mechanisms mediated by complement and innate leukocytes are induced due to relatively broad recognition of PAMPs. If a more targeted, pathogen-specific response becomes necessary, elements of innate immunity then facilitate induction of highly specific adaptive responses initiated by engagement of the antigen receptors of B, Th or Tc lymphocytes. Innate leukocytes activated by the binding of PRRs to PAMPs provided by the attacking pathogen, or to DAMPs present due to host cell injury or death, work quickly to eliminate the invader using the mechanisms of inflammation, phagocytosis and target cell lysis. abstract: In this chapter we provide an overview of the immune system and its vital role maintaining human health. Immune responses require the coordinated action of leukocytes that travel the body to eliminate threats posed by trauma, infection, toxins, and cancer. Leukocytes communicate via direct contact and via production and receipt of soluble proteins and intercellular messenger proteins called cytokines. Complete clearance of unwanted entities may involve both innate and adaptive leukocyte responses, which influence each other. Some innate mechanisms require no induction and are completely non-specific, whereas others are inducible and involve broad receptor-mediated recognition of a limited number of pathogen-associated or damage-associated molecular patterns (PAMPs/DAMPs). Adaptive responses involve the selective activation of lymphocytes via engagement of their antigen receptors by a specific foreign antigen. The three major subsets of lymphocytes are T helper cells (Th), cytotoxic T cells (Tc) and B cells, which use distinct mechanisms to recognize antigen and carry out different effector functions. Immune system malfunction can contribute to many clinical illnesses including autoimmune disorders, allergies, immunodeficiencies, chronic inflammation and cancer. url: https://www.sciencedirect.com/science/article/pii/B9780123852458000017 doi: 10.1016/b978-0-12-385245-8.00001-7 ==== 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