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M. Kaderi title: Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA date: 2017-09-07 journal: J Immunol Res DOI: 10.1155/2017/6412353 sha: doc_id: 2686 cord_uid: zzongyfa file: cache/cord-002704-cpa2sl50.json key: cord-002704-cpa2sl50 authors: El Bissati, Kamal; Zhou, Ying; Paulillo, Sara Maria; Raman, Senthil Kumar; Karch, Christopher P.; Roberts, Craig W.; Lanar, David E.; Reed, Steve; Fox, Chris; Carter, Darrick; Alexander, Jeff; Sette, Alessandro; Sidney, John; Lorenzi, Hernan; Begeman, Ian J.; Burkhard, Peter; McLeod, Rima title: Protein nanovaccine confers robust immunity against Toxoplasma date: 2017-09-05 journal: NPJ Vaccines DOI: 10.1038/s41541-017-0024-6 sha: doc_id: 2704 cord_uid: cpa2sl50 file: cache/cord-004435-l66ost6q.json key: cord-004435-l66ost6q authors: Oli, Angus Nnamdi; Obialor, Wilson Okechukwu; Ifeanyichukwu, Martins Ositadimma; Odimegwu, Damian Chukwu; Okoyeh, Jude Nnaemeka; Emechebe, George Ogonna; Adejumo, Samson Adedeji; Ibeanu, Gordon C title: Immunoinformatics and Vaccine Development: An Overview date: 2020-02-26 journal: Immunotargets Ther DOI: 10.2147/itt.s241064 sha: doc_id: 4435 cord_uid: l66ost6q file: cache/cord-003143-n6b0r92e.json key: cord-003143-n6b0r92e authors: Zhao, Min; Liu, Kefang; Luo, Jiejian; Tan, Shuguang; Quan, Chuansong; Zhang, Shuijun; Chai, Yan; Qi, Jianxun; Li, Yan; Bi, Yuhai; Xiao, Haixia; Wong, Gary; Zhou, Jianfang; Jiang, Taijiao; Liu, Wenjun; Yu, Hongjie; Yan, Jinghua; Liu, Yingxia; Shu, Yuelong; Wu, Guizhen; Wu, Aiping; Gao, George F.; Liu, William J. title: Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses date: 2018-08-07 journal: mBio DOI: 10.1128/mbio.01408-18 sha: doc_id: 3143 cord_uid: n6b0r92e file: cache/cord-004395-erqmbi2b.json key: cord-004395-erqmbi2b authors: Bugembe, Daniel Lule; Ekii, Andrew Obuku; Ndembi, Nicaise; Serwanga, Jennifer; Kaleebu, Pontiano; Pala, Pietro title: Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort date: 2020-02-22 journal: BMC Infect Dis DOI: 10.1186/s12879-020-4876-4 sha: doc_id: 4395 cord_uid: erqmbi2b file: cache/cord-006273-xcw0kxjg.json key: cord-006273-xcw0kxjg authors: Willemze, R; Rodrigues, C A; Labopin, M; Sanz, G; Michel, G; Socié, G; Rio, B; Sirvent, A; Renaud, M; Madero, L; Mohty, M; Ferra, C; Garnier, F; Loiseau, P; Garcia, J; Lecchi, L; Kögler, G; Beguin, Y; Navarrete, C; Devos, T; Ionescu, I; Boudjedir, K; Herr, A-L; Gluckman, E; Rocha, V title: KIR-ligand incompatibility in the graft-versus-host direction improves outcomes after umbilical cord blood transplantation for acute leukemia date: 2009-01-08 journal: Leukemia DOI: 10.1038/leu.2008.365 sha: doc_id: 6273 cord_uid: xcw0kxjg file: cache/cord-007301-5m269nzi.json key: cord-007301-5m269nzi authors: Lundegaard, Claus; Lund, Ole; Keşmir, Can; Brunak, Søren; Nielsen, Morten title: Modeling the adaptive immune system: predictions and simulations date: 2007-12-15 journal: Bioinformatics DOI: 10.1093/bioinformatics/btm471 sha: doc_id: 7301 cord_uid: 5m269nzi file: cache/cord-007626-n51v4ior.json key: cord-007626-n51v4ior authors: Dhib-Jalbut, Suhayl; Kufta, Conrad V.; Flerlage, Marjorie; Shimojo, Naoki; McFarland, Henry F. title: Adult human glial cells can present target antigens to HLA-restricted cytotoxic T-cells date: 2002-11-11 journal: J Neuroimmunol DOI: 10.1016/0165-5728(90)90163-h sha: doc_id: 7626 cord_uid: n51v4ior file: cache/cord-007664-c5snhymz.json key: cord-007664-c5snhymz authors: Mauerhoff, Thekla; Pujol-Borrell, Ricardo; Mirakian, Rita; Bottazzo, Gian Franco title: Differential expression and regulation of major histocompatibility complex (MHC) products in neural and glial cells of the human fetal brain date: 2002-11-13 journal: J Neuroimmunol DOI: 10.1016/0165-5728(88)90049-5 sha: doc_id: 7664 cord_uid: c5snhymz file: cache/cord-007851-v6h1yro7.json key: cord-007851-v6h1yro7 authors: Han, Ki-Cheol; Park, Daechan; Ju, Shinyeong; Lee, Young Eun; Heo, Sun-Hee; Kim, Young-Ae; Lee, Ji Eun; Lee, Yuna; Park, Kyong Hwa; Park, Se-Ho; Lee, Hee Jin; Lee, Cheolju; Jang, Mihue title: Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging date: 2020-04-03 journal: Sci Rep DOI: 10.1038/s41598-020-62244-z sha: doc_id: 7851 cord_uid: v6h1yro7 file: cache/cord-007719-3ypv9k9p.json key: cord-007719-3ypv9k9p authors: Wang, Mingjun; Claesson, Mogens H. title: Classification of Human Leukocyte Antigen (HLA) Supertypes date: 2014-05-06 journal: Immunoinformatics DOI: 10.1007/978-1-4939-1115-8_17 sha: doc_id: 7719 cord_uid: 3ypv9k9p file: cache/cord-009323-sfxpchma.json key: cord-009323-sfxpchma authors: Link, Hartmut; Kolb, Hans-Jochem; Ebell, Wolfram; Hossfeld, Dieter Kurt; Zander, Axel; Niethammer, Dietrich; Wandt, Hannes; Grosse-Wilde, Hans; Schaefer, Ulrich W. title: Die Transplantation hämatopoetischer Stammzellen: Teil I: Definitionen, prinzipielle Anwendungsmöglichkeiten, Komplikationen date: 1997 journal: Med Klin (Munich) DOI: 10.1007/bf03044917 sha: doc_id: 9323 cord_uid: sfxpchma file: cache/cord-005487-vac061r8.json key: cord-005487-vac061r8 authors: nan title: Physicians Abstracts: EBMT 2010 date: 2010-04-07 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2010.40 sha: doc_id: 5487 cord_uid: vac061r8 file: cache/cord-009836-7o6htufh.json key: cord-009836-7o6htufh authors: Borrow, Persephone; Shaw, George M. title: Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date: 2006-04-28 journal: Immunol Rev DOI: 10.1111/j.1600-065x.1998.tb01206.x sha: doc_id: 9836 cord_uid: 7o6htufh file: cache/cord-005480-yg7salqt.json key: cord-005480-yg7salqt authors: nan title: Oral Sessions and Working Party date: 2008-03-26 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2008.30 sha: doc_id: 5480 cord_uid: yg7salqt file: cache/cord-010222-5oxie0zc.json key: cord-010222-5oxie0zc authors: Oldstone, Michael B.A. title: Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date: 2004-04-11 journal: J Autoimmun DOI: 10.1016/0896-8411(89)90130-3 sha: doc_id: 10222 cord_uid: 5oxie0zc file: cache/cord-005478-5iu38pr6.json key: cord-005478-5iu38pr6 authors: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date: 2019-07-03 journal: Bone Marrow Transplant DOI: 10.1038/s41409-019-0562-9 sha: doc_id: 5478 cord_uid: 5iu38pr6 file: cache/cord-009571-mygj2nd4.json key: cord-009571-mygj2nd4 authors: nan title: Proceedings of the 42nd annual meeting of the american rheumatism association a section of the arthritis foundation june 1 & 2, 1978 new york city abstracts of papers presented date: 2005-11-23 journal: Arthritis Rheum DOI: 10.1002/art.1780210508 sha: doc_id: 9571 cord_uid: mygj2nd4 file: cache/cord-010088-s9tfvtao.json key: cord-010088-s9tfvtao authors: nan title: Oral Abstracts date: 2013-11-01 journal: Vox Sang DOI: 10.1111/vox.12100_1 sha: doc_id: 10088 cord_uid: s9tfvtao file: cache/cord-013093-aa4cf44u.json key: cord-013093-aa4cf44u authors: Cassotta, Antonino; Paparoditis, Philipp; Geiger, Roger; Mettu, Ramgopal R.; Landry, Samuel J.; Donati, Alessia; Benevento, Marco; Foglierini, Mathilde; Lewis, David J.M.; Lanzavecchia, Antonio; Sallusto, Federica title: Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin date: 2020-07-09 journal: J Exp Med DOI: 10.1084/jem.20200206 sha: doc_id: 13093 cord_uid: aa4cf44u file: cache/cord-013894-1bgvj62a.json key: cord-013894-1bgvj62a authors: Wang, Qihui; Song, Hao; Cheng, Hao; Qi, Jianxun; Nam, Gol; Tan, Shuguang; Wang, Junzhi; Fang, Min; Shi, Yi; Tian, Zhigang; Cao, Xuetao; An, Zhiqiang; Yan, Jinghua; Gao, George F. title: Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex date: 2019-07-04 journal: Cell Mol Immunol DOI: 10.1038/s41423-019-0258-5 sha: doc_id: 13894 cord_uid: 1bgvj62a file: cache/cord-015389-vwgai4k9.json key: cord-015389-vwgai4k9 authors: nan title: Publication only date: 2009-03-25 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2009.50 sha: doc_id: 15389 cord_uid: vwgai4k9 file: cache/cord-016235-2lhrkmrv.json key: cord-016235-2lhrkmrv authors: Roden, Anja C.; Tazelaar, Henry D. title: Lung date: 2010-05-17 journal: Pathology of Solid Organ Transplantation DOI: 10.1007/978-3-540-79343-4_7 sha: doc_id: 16235 cord_uid: 2lhrkmrv file: cache/cord-016413-lvb79oxo.json key: cord-016413-lvb79oxo authors: Efthimiou, Petros; Yadlapati, Sujani title: Adult-Onset Still’s Disease date: 2018-07-14 journal: Auto-Inflammatory Syndromes DOI: 10.1007/978-3-319-96929-9_19 sha: doc_id: 16413 cord_uid: lvb79oxo file: cache/cord-016998-6n662amh.json key: cord-016998-6n662amh authors: nan title: Nierentransplantation date: 2007 journal: Praxis der Nephrologie DOI: 10.1007/978-3-540-48556-8_13 sha: doc_id: 16998 cord_uid: 6n662amh file: cache/cord-014976-546zaoxn.json key: cord-014976-546zaoxn authors: nan title: Publication only date: 2006-03-08 journal: Bone Marrow Transplant DOI: 10.1038/sj.bmt.1705327 sha: doc_id: 14976 cord_uid: 546zaoxn file: cache/cord-017184-1ewi3dka.json key: cord-017184-1ewi3dka authors: nan title: Primary Immunodeficiencies date: 2008 journal: Pediatric Allergy, Asthma and Immunology DOI: 10.1007/978-3-540-33395-1_22 sha: doc_id: 17184 cord_uid: 1ewi3dka file: cache/cord-017629-fuv157f1.json key: cord-017629-fuv157f1 authors: De Groot, Anne S.; Moise, Leonard; McMurry, Julie A.; Martin, William title: Epitope-Based Immunome-Derived Vaccines: A Strategy for Improved Design and Safety date: 2008-07-31 journal: Clinical Applications of Immunomics DOI: 10.1007/978-0-387-79208-8_3 sha: doc_id: 17629 cord_uid: fuv157f1 file: cache/cord-017702-v46ye328.json key: cord-017702-v46ye328 authors: Ganguly, Nirmal Kumar; Saha, Gautam Kumar title: Pharmacogenomics and Personalized Medicine for Infectious Diseases date: 2013-06-11 journal: Omics for Personalized Medicine DOI: 10.1007/978-81-322-1184-6_27 sha: doc_id: 17702 cord_uid: v46ye328 file: cache/cord-017856-4fccnygg.json key: cord-017856-4fccnygg authors: Roden, Anja C.; Tazelaar, Henry D. title: Pathology of Lung Rejection: Cellular and Humoral Mediated date: 2018-04-24 journal: Lung Transplantation DOI: 10.1007/978-3-319-91184-7_13 sha: doc_id: 17856 cord_uid: 4fccnygg file: cache/cord-018595-x3tleomb.json key: cord-018595-x3tleomb authors: Dodiuk-Gad, Roni P.; Chung, Wen-Hung; Shear, Neil H. title: Adverse Medication Reactions date: 2017-04-25 journal: Clinical and Basic Immunodermatology DOI: 10.1007/978-3-319-29785-9_25 sha: doc_id: 18595 cord_uid: x3tleomb file: cache/cord-018714-i291z2ju.json key: cord-018714-i291z2ju authors: Criado, Paulo Ricardo title: Adverse Drug Reactions date: 2016-12-31 journal: Dermatology in Public Health Environments DOI: 10.1007/978-3-319-33919-1_26 sha: doc_id: 18714 cord_uid: i291z2ju file: cache/cord-022474-xxy83c6u.json key: cord-022474-xxy83c6u authors: Tenorio, Grace C.; Gupte, Snehalata C.; Munker, Reinhold title: Transfusion Medicine and Immunohematology date: 2007 journal: Modern Hematology DOI: 10.1007/978-1-59745-149-9_22 sha: doc_id: 22474 cord_uid: xxy83c6u file: cache/cord-034402-64xz1j9i.json key: cord-034402-64xz1j9i authors: Srivastava, Shivani; Sharma, Suraj Kumar; Srivastava, Vivek; Kumar, Ajay title: Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach date: 2020-10-29 journal: Int J Pept Res Ther DOI: 10.1007/s10989-020-10128-1 sha: doc_id: 34402 cord_uid: 64xz1j9i file: cache/cord-103662-a4ok5wqc.json key: cord-103662-a4ok5wqc authors: Tarek, M.; Elhefnawi, M.; Maricato, J. T.; Diaz, R. S.; Shytaj, I. L.; Savarino, A. title: Custommune: a web tool to design personalized and population-targeted vaccine epitopes date: 2020-04-29 journal: nan DOI: 10.1101/2020.04.25.20079426 sha: doc_id: 103662 cord_uid: a4ok5wqc file: cache/cord-023675-sidvbzqy.json key: cord-023675-sidvbzqy authors: Oldstone, Michael B.A. title: Virus-induced Autoimmunity: Molecular Mimicry as a Route to Autoimmune Disease date: 2013-11-17 journal: T-Cell Activation in Health and Disease DOI: 10.1016/b978-0-12-252682-4.50023-8 sha: doc_id: 23675 cord_uid: sidvbzqy file: cache/cord-031937-qhlatg84.json key: cord-031937-qhlatg84 authors: Verma, Anukriti; Sharda, Shivani; Rathi, Bhawna; Somvanshi, Pallavi; Pandey, Bimlesh Dhar title: Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date: 2020-09-15 journal: Sci Rep DOI: 10.1038/s41598-020-71674-8 sha: doc_id: 31937 cord_uid: qhlatg84 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-103837-iuvigqdx.json key: cord-103837-iuvigqdx authors: Knierman, Michael D.; Lannan, Megan B.; Spindler, Laura J.; McMillian, Carl L.; Konrad, Robert J.; Siegel, Robert W. title: The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date: 2020-11-13 journal: nan DOI: 10.1016/j.celrep.2020.108454 sha: doc_id: 103837 cord_uid: iuvigqdx file: cache/cord-104099-xhi0oxtr.json key: cord-104099-xhi0oxtr authors: Hensen, L.; Illing, P. T.; Clemens, E. B.; Nguyen, T. H. O.; Koutsakos, M.; van de Sandt, C. E.; Mifsud, N. A.; Nguyen, A.; Szeto, C.; Chua, B.; Halim, H.; Rizzetto, S.; Luciani, F.; Loh, L.; Grant, E. J.; Saunders, P.; Brooks, A.; Rockman, S.; Kotsimbos, T. C.; Cheng, A. C.; Richards, M.; Westall, G. P.; Wakim, L. M.; Loudovaris, T.; Mannering, S. I.; Elliott, M.; Tangye, S. G.; Jackson, D.; Flanagan, K. L.; Rossjohn, J.; Gras, S.; Davies, J.; Miller, A.; Tong, S.; Purcell, A. 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Moise, Leonard; Martin, Rebecca F; Torres, Melissa; Pilotte, Nils; Williams, Steven A; De Groot, Anne S title: Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases date: 2015-01-02 journal: Expert Rev Vaccines DOI: 10.1586/14760584.2015.955478 sha: doc_id: 319993 cord_uid: er3sm4u8 file: cache/cord-342942-1s32o9m8.json key: cord-342942-1s32o9m8 authors: Stamatakis, George; Samiotaki, Martina; Mpakali, Anastasia; Panayotou, George; Stratikos, Efstratios title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 journal: bioRxiv DOI: 10.1101/2020.06.22.164681 sha: doc_id: 342942 cord_uid: 1s32o9m8 file: cache/cord-346957-bmajkabp.json key: cord-346957-bmajkabp authors: Lv, Yanbo; Ruan, Zhihua; Wang, Li; Ni, Bing; Wu, Yuzhang title: Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date: 2009-12-03 journal: BMC Immunol DOI: 10.1186/1471-2172-10-61 sha: doc_id: 346957 cord_uid: bmajkabp file: cache/cord-355374-e8k72955.json key: cord-355374-e8k72955 authors: Clemens, E. Bridie; van de Sandt, Carolien; Wong, Sook San; Wakim, Linda M.; Valkenburg, Sophie A. title: Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine date: 2018-03-26 journal: Vaccines (Basel) DOI: 10.3390/vaccines6020018 sha: doc_id: 355374 cord_uid: e8k72955 file: cache/cord-346032-188gnf8j.json key: cord-346032-188gnf8j authors: Cheung, Ying-Kit; Cheng, Samuel Chak-Sum; Sin, Fion Wan-Yee; Chan, Kin-Tak; Xie, Yong title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date: 2007-08-10 journal: Vaccine DOI: 10.1016/j.vaccine.2007.05.025 sha: doc_id: 346032 cord_uid: 188gnf8j file: cache/cord-329669-z3t7plvh.json key: cord-329669-z3t7plvh authors: Poulton, Kay; Wright, Paul; Hughes, Pamela; Savic, Sinisa; Welberry Smith, Matthew; Guiver, Malcolm; Morton, Muir; van Dellen, David; Tholouli, Eleni; Wynn, Robert; Clark, Brendan title: A role for human leucocyte antigens in the susceptibility to SARS‐Cov‐2 infection observed in transplant patients date: 2020-07-05 journal: Int J Immunogenet DOI: 10.1111/iji.12505 sha: doc_id: 329669 cord_uid: z3t7plvh file: cache/cord-320490-3jmo35jc.json key: cord-320490-3jmo35jc authors: Ismail, Saba; Ahmad, Sajjad; Azam, Syed Sikander title: Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date: 2020-04-12 journal: bioRxiv DOI: 10.1101/2020.04.05.026005 sha: doc_id: 320490 cord_uid: 3jmo35jc file: cache/cord-326983-h6gdck2u.json key: cord-326983-h6gdck2u authors: Ferretti, Andrew P.; Kula, Tomasz; Wang, Yifan; Nguyen, Dalena M.V.; Weinheimer, Adam; Dunlap, Garrett S.; Xu, Qikai; Nabilsi, Nancy; Perullo, Candace R.; Cristofaro, Alexander W.; Whitton, Holly J.; Virbasius, Amy; Olivier, Kenneth J.; Buckner, Lyndsey R.; Alistar, Angela T.; Whitman, Eric D.; Bertino, Sarah A.; Chattopadhyay, Shrikanta; MacBeath, Gavin title: Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date: 2020-10-20 journal: Immunity DOI: 10.1016/j.immuni.2020.10.006 sha: doc_id: 326983 cord_uid: h6gdck2u file: cache/cord-333670-qv1orlv5.json key: cord-333670-qv1orlv5 authors: Mutti, Luciano; Pentimalli, Francesca; Baglio, Giovanni; Maiorano, Patrizia; Saladino, Rita Emilena; Correale, Pierpaolo; Giordano, Antonio title: Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date: 2020-05-28 journal: Front Immunol DOI: 10.3389/fimmu.2020.01208 sha: doc_id: 333670 cord_uid: qv1orlv5 file: cache/cord-344364-vu389d88.json key: cord-344364-vu389d88 authors: Wang, Wei; Zhang, Wei; Zhang, Jingjing; He, Ji; Zhu, Faming title: Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date: 2020-06-02 journal: HLA DOI: 10.1111/tan.13941 sha: doc_id: 344364 cord_uid: vu389d88 file: cache/cord-346445-hgqohdct.json key: cord-346445-hgqohdct authors: Toyoshima, Yujiro; Nemoto, Kensaku; Matsumoto, Saki; Nakamura, Yusuke; Kiyotani, Kazuma title: SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date: 2020-07-22 journal: J Hum Genet DOI: 10.1038/s10038-020-0808-9 sha: doc_id: 346445 cord_uid: hgqohdct file: cache/cord-344933-k23kzqxl.json key: cord-344933-k23kzqxl authors: Flahou, Charlotte; Sugimoto, Naoshi; Eto, Koji title: Innovations dans la culture de plaquettes à partir de cellules souches pluripotentes induites* date: 2020-09-28 journal: Bull Acad Natl Med DOI: 10.1016/j.banm.2020.09.040 sha: doc_id: 344933 cord_uid: k23kzqxl file: cache/cord-333966-st6gyozv.json key: cord-333966-st6gyozv authors: Taherkhani, Reza; Farshadpour, Fatemeh; Makvandi, Manoochehr title: Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date: 2015-03-17 journal: J Med Virol DOI: 10.1002/jmv.24171 sha: doc_id: 333966 cord_uid: st6gyozv file: cache/cord-333391-6l0cpvgr.json key: cord-333391-6l0cpvgr authors: Bortolotti, Daria; Gentili, Valentina; Rizzo, Sabrina; Rotola, Antonella; Rizzo, Roberta title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date: 2020-08-26 journal: Cells DOI: 10.3390/cells9091975 sha: doc_id: 333391 cord_uid: 6l0cpvgr file: cache/cord-344691-vmc0rrrk.json key: cord-344691-vmc0rrrk authors: Srinivasan, K.N.; Zhang, G.L.; Khan, A.M.; August, J.T.; Brusic, V. title: Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens date: 2004-08-04 journal: Bioinformatics DOI: 10.1093/bioinformatics/bth943 sha: doc_id: 344691 cord_uid: vmc0rrrk file: cache/cord-347647-m9vk9m7h.json key: cord-347647-m9vk9m7h authors: Eapen, Mary; Zhang, Mei-Jie; Tang, Xiao-Ying; Lee, Stephanie J.; Fei, Ming-Wei; Wang, Hai-lin; Hebert, Kyle M.; Arora, Mukta; Chhabra, Saurabh; Devine, Steven M.; Hamadani, Mehdi; D'Souza, Anita; Pasquini, Marcelo C.; Phelan, Rachel; Rizzo, J. Douglas; Saber, Wael; Shaw, Bronwen E.; Weisdorf, Daniel J; Horowitz, Mary M. title: Hematopoietic cell transplantation with cryopreserved grafts for severe aplastic anemia date: 2020-05-08 journal: Biol Blood Marrow Transplant DOI: 10.1016/j.bbmt.2020.04.027 sha: doc_id: 347647 cord_uid: m9vk9m7h file: cache/cord-352150-ey9kc7zj.json key: cord-352150-ey9kc7zj authors: Degauque, Nicolas; Brouard, Sophie; Soulillou, Jean-Paul title: Cross-Reactivity of TCR Repertoire: Current Concepts, Challenges, and Implication for Allotransplantation date: 2016-03-24 journal: Front Immunol DOI: 10.3389/fimmu.2016.00089 sha: doc_id: 352150 cord_uid: ey9kc7zj file: cache/cord-353877-wzndpcq3.json key: cord-353877-wzndpcq3 authors: Albagi, Sahar Obi Abd; Al-Nour, Mosab Yahya; Elhag, Mustafa; Abdelihalim, Asaad Tageldein Idris; Haroun, Esraa Musa; Essa, Mohammed Elmujtba Adam; Abubaker, Mustafa; Hassan, Mohammed A. title: A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date: 2020-05-20 journal: bioRxiv DOI: 10.1101/2020.05.20.106351 sha: doc_id: 353877 cord_uid: wzndpcq3 file: cache/cord-349451-vak2p7ac.json key: cord-349451-vak2p7ac authors: Rocha, Francisco Airton Castro; Duarte-Monteiro, Ana Margarida; da Mota, Licia Maria Henrique; Pinto, Ana Carolina Matias Dinelly; Fonseca, João Eurico title: Microbes, Helminths and Rheumatic Diseases date: 2020-05-07 journal: Best Pract Res Clin Rheumatol DOI: 10.1016/j.berh.2020.101528 sha: doc_id: 349451 cord_uid: vak2p7ac file: cache/cord-313474-1gux1gsi.json key: cord-313474-1gux1gsi authors: nan title: Physicians Abstracts date: 2015-03-20 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2015.27 sha: doc_id: 313474 cord_uid: 1gux1gsi 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-010092-uftc8inx.json key: cord-010092-uftc8inx authors: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 journal: Vox Sang DOI: 10.1111/vox.12792 sha: doc_id: 10092 cord_uid: uftc8inx file: cache/cord-005460-ezrn8cva.json key: cord-005460-ezrn8cva authors: nan title: Physicians – Poster Session date: 2017-07-28 journal: Bone Marrow Transplant DOI: 10.1038/bmt.2017.134 sha: doc_id: 5460 cord_uid: ezrn8cva file: cache/cord-010119-t1x9gknd.json key: cord-010119-t1x9gknd authors: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 journal: Transfusion DOI: 10.1111/trf.14286 sha: doc_id: 10119 cord_uid: t1x9gknd file: cache/cord-005453-4057qib7.json key: cord-005453-4057qib7 authors: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 journal: Bone Marrow Transplant DOI: 10.1038/s41409-019-0559-4 sha: doc_id: 5453 cord_uid: 4057qib7 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-hla-cord parallel: Warning: Only enough available processes to run 8 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 28 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 4 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 24 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 58 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 37 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: No more processes: Decreasing number of running jobs to 57. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 23. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 7. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 3. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 36. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 2. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 56. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 22. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/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/cordent2carrel.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/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 35. 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/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /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 27. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 34. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 55. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 33. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/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: 26938 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26205 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26371 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26844 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26136 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26808 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 27623 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26751 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26375 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 26837 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: 28394 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 27103 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes === file2bib.sh === id: cord-007719-3ypv9k9p author: Wang, Mingjun title: Classification of Human Leukocyte Antigen (HLA) Supertypes date: 2014-05-06 pages: extension: .txt txt: ./txt/cord-007719-3ypv9k9p.txt cache: ./cache/cord-007719-3ypv9k9p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007719-3ypv9k9p.txt' === file2bib.sh === id: cord-002686-zzongyfa author: Oany, Arafat Rahman title: Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA date: 2017-09-07 pages: extension: .txt txt: ./txt/cord-002686-zzongyfa.txt cache: ./cache/cord-002686-zzongyfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002686-zzongyfa.txt' === file2bib.sh === id: cord-007664-c5snhymz author: Mauerhoff, Thekla title: Differential expression and regulation of major histocompatibility complex (MHC) products in neural and glial cells of the human fetal brain date: 2002-11-13 pages: extension: .txt txt: ./txt/cord-007664-c5snhymz.txt cache: ./cache/cord-007664-c5snhymz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007664-c5snhymz.txt' === file2bib.sh === id: cord-001247-pxzbirqd author: Sun, Lu title: A new unconventional HLA-A2-restricted epitope from HBV core protein elicits antiviral cytotoxic T lymphocytes date: 2014-03-22 pages: extension: .txt txt: ./txt/cord-001247-pxzbirqd.txt cache: ./cache/cord-001247-pxzbirqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001247-pxzbirqd.txt' === file2bib.sh === id: cord-007851-v6h1yro7 author: Han, Ki-Cheol title: Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-007851-v6h1yro7.txt cache: ./cache/cord-007851-v6h1yro7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007851-v6h1yro7.txt' === file2bib.sh === id: cord-002463-qhtj1pef author: Dash, Raju title: In silico-based vaccine design against Ebola virus glycoprotein date: 2017-03-21 pages: extension: .txt txt: ./txt/cord-002463-qhtj1pef.txt cache: ./cache/cord-002463-qhtj1pef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002463-qhtj1pef.txt' === file2bib.sh === id: cord-000488-x5ardo5j author: Pedersen, Lasse Eggers title: Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities date: 2011-07-08 pages: extension: .txt txt: ./txt/cord-000488-x5ardo5j.txt cache: ./cache/cord-000488-x5ardo5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000488-x5ardo5j.txt' === file2bib.sh === 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 pages: extension: .txt txt: ./txt/cord-009836-7o6htufh.txt cache: ./cache/cord-009836-7o6htufh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009836-7o6htufh.txt' === file2bib.sh === id: cord-004435-l66ost6q author: Oli, Angus Nnamdi title: Immunoinformatics and Vaccine Development: An Overview date: 2020-02-26 pages: extension: .txt txt: ./txt/cord-004435-l66ost6q.txt cache: ./cache/cord-004435-l66ost6q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004435-l66ost6q.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: 46522 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49134 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50056 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49618 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-016413-lvb79oxo author: Efthimiou, Petros title: Adult-Onset Still’s Disease date: 2018-07-14 pages: extension: .txt txt: ./txt/cord-016413-lvb79oxo.txt cache: ./cache/cord-016413-lvb79oxo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016413-lvb79oxo.txt' === file2bib.sh === id: cord-013894-1bgvj62a author: Wang, Qihui title: Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex date: 2019-07-04 pages: extension: .txt txt: ./txt/cord-013894-1bgvj62a.txt cache: ./cache/cord-013894-1bgvj62a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013894-1bgvj62a.txt' === file2bib.sh === id: cord-013093-aa4cf44u author: Cassotta, Antonino title: Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-013093-aa4cf44u.txt cache: ./cache/cord-013093-aa4cf44u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-013093-aa4cf44u.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: 58479 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 58384 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-255069-9xueqdri author: Leary, Shay title: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-255069-9xueqdri.txt cache: ./cache/cord-255069-9xueqdri.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255069-9xueqdri.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: 59870 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50136 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-016235-2lhrkmrv author: Roden, Anja C. title: Lung date: 2010-05-17 pages: extension: .txt txt: ./txt/cord-016235-2lhrkmrv.txt cache: ./cache/cord-016235-2lhrkmrv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016235-2lhrkmrv.txt' === file2bib.sh === id: cord-034402-64xz1j9i author: Srivastava, Shivani title: Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-034402-64xz1j9i.txt cache: ./cache/cord-034402-64xz1j9i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-034402-64xz1j9i.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: 63613 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 67435 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-017702-v46ye328 author: Ganguly, Nirmal Kumar title: Pharmacogenomics and Personalized Medicine for Infectious Diseases date: 2013-06-11 pages: extension: .txt txt: ./txt/cord-017702-v46ye328.txt cache: ./cache/cord-017702-v46ye328.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017702-v46ye328.txt' === file2bib.sh === id: cord-103662-a4ok5wqc author: Tarek, M. title: Custommune: a web tool to design personalized and population-targeted vaccine epitopes date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-103662-a4ok5wqc.txt cache: ./cache/cord-103662-a4ok5wqc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103662-a4ok5wqc.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: 71422 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38720 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38095 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38523 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-031937-qhlatg84 author: Verma, Anukriti title: Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-031937-qhlatg84.txt cache: ./cache/cord-031937-qhlatg84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-031937-qhlatg84.txt' === file2bib.sh === id: cord-018595-x3tleomb author: Dodiuk-Gad, Roni P. title: Adverse Medication Reactions date: 2017-04-25 pages: extension: .txt txt: ./txt/cord-018595-x3tleomb.txt cache: ./cache/cord-018595-x3tleomb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018595-x3tleomb.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: 73810 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 75644 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-104099-xhi0oxtr author: Hensen, L. title: CD8+ T-cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-104099-xhi0oxtr.txt cache: ./cache/cord-104099-xhi0oxtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-104099-xhi0oxtr.txt' === file2bib.sh === id: cord-265277-ymvrserl author: Crooke, Stephen N. title: Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-265277-ymvrserl.txt cache: ./cache/cord-265277-ymvrserl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265277-ymvrserl.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: 77904 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 78255 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-254190-bxfne94u author: Tu, Wenwei title: Application of Humanized Mice in Immunological Research date: 2015-07-07 pages: extension: .txt txt: ./txt/cord-254190-bxfne94u.txt cache: ./cache/cord-254190-bxfne94u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254190-bxfne94u.txt' parallel: Warning: No more processes: Decreasing number of running jobs to 21. 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: 78154 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 81853 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 83319 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 83702 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 84377 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-015389-vwgai4k9 author: nan title: Publication only date: 2009-03-25 pages: extension: .txt txt: ./txt/cord-015389-vwgai4k9.txt cache: ./cache/cord-015389-vwgai4k9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015389-vwgai4k9.txt' === file2bib.sh === id: cord-266204-ipa017wz author: Poland, G. A. title: Personalized vaccinology: A review date: 2018-08-28 pages: extension: .txt txt: ./txt/cord-266204-ipa017wz.txt cache: ./cache/cord-266204-ipa017wz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-266204-ipa017wz.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: 88215 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-280641-zqdrzyzl author: Fernández Fabrellas, Estrella title: Epidemiología de la sarcoidosis date: 2007-02-28 pages: extension: .txt txt: ./txt/cord-280641-zqdrzyzl.txt cache: ./cache/cord-280641-zqdrzyzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280641-zqdrzyzl.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: 89624 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-275608-joyan7ij author: Sewell, Andrew K. title: Why must T cells be cross-reactive? date: 2012-08-24 pages: extension: .txt txt: ./txt/cord-275608-joyan7ij.txt cache: ./cache/cord-275608-joyan7ij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275608-joyan7ij.txt' === file2bib.sh === id: cord-289711-4ab3d00h author: Yarmarkovich, Mark title: Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-289711-4ab3d00h.txt cache: ./cache/cord-289711-4ab3d00h.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-289711-4ab3d00h.txt' === file2bib.sh === id: cord-281141-ouno4jpl author: Mahajan, Swapnil title: Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-281141-ouno4jpl.txt cache: ./cache/cord-281141-ouno4jpl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281141-ouno4jpl.txt' === file2bib.sh === id: cord-271032-imc6woht author: Schulte-Schrepping, Jonas title: Severe COVID-19 is marked by a dysregulated myeloid cell compartment date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-271032-imc6woht.txt cache: ./cache/cord-271032-imc6woht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271032-imc6woht.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: 95070 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 94571 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 95051 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-326554-iphe3rni author: Joshi, Amit title: In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple’s Disease date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-326554-iphe3rni.txt cache: ./cache/cord-326554-iphe3rni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326554-iphe3rni.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: 96376 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 68017 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-288916-i8ukefp8 author: Gómez-Herranz, Maria title: The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis date: 2019-04-02 pages: extension: .txt txt: ./txt/cord-288916-i8ukefp8.txt cache: ./cache/cord-288916-i8ukefp8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288916-i8ukefp8.txt' === file2bib.sh === id: cord-275677-hbv49e01 author: Ramana, Lakshmi Narashimhan title: Targeting strategies for delivery of anti-HIV drugs date: 2014-10-28 pages: extension: .txt txt: ./txt/cord-275677-hbv49e01.txt cache: ./cache/cord-275677-hbv49e01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275677-hbv49e01.txt' === file2bib.sh === id: cord-299279-v0vznri2 author: Røder, Gustav title: Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501 date: 2008-05-17 pages: extension: .txt txt: ./txt/cord-299279-v0vznri2.txt cache: ./cache/cord-299279-v0vznri2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299279-v0vznri2.txt' === file2bib.sh === id: cord-312865-nno2yjae author: Sylvester‐Hvid, C. title: SARS CTL vaccine candidates; HLA supertype‐, genome‐wide scanning and biochemical validation date: 2004-04-23 pages: extension: .txt txt: ./txt/cord-312865-nno2yjae.txt cache: ./cache/cord-312865-nno2yjae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-312865-nno2yjae.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: 1669 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-334603-yt2pmxi3 author: de Sousa, Eric title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-334603-yt2pmxi3.txt cache: ./cache/cord-334603-yt2pmxi3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334603-yt2pmxi3.txt' === file2bib.sh === id: cord-306308-zjq6cscm author: de Moura, Ronald Rodrigues title: Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-306308-zjq6cscm.txt cache: ./cache/cord-306308-zjq6cscm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306308-zjq6cscm.txt' === file2bib.sh === id: cord-343262-zopxdw1d author: Srinivasan, Raghuraman C. title: Effects of Cryogenic Storage on Human Amnion Epithelial Cells date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-343262-zopxdw1d.txt cache: ./cache/cord-343262-zopxdw1d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343262-zopxdw1d.txt' === file2bib.sh === id: cord-288496-7rrh2gg6 author: Stryhn, Anette title: A Systematic, Unbiased Mapping of CD8(+) and CD4(+) T Cell Epitopes in Yellow Fever Vaccinees date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-288496-7rrh2gg6.txt cache: ./cache/cord-288496-7rrh2gg6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288496-7rrh2gg6.txt' === file2bib.sh === id: cord-347714-vxxhglx7 author: Abitogun, Folagbade title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-347714-vxxhglx7.txt cache: ./cache/cord-347714-vxxhglx7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347714-vxxhglx7.txt' === file2bib.sh === id: cord-342942-1s32o9m8 author: Stamatakis, George title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-342942-1s32o9m8.txt cache: ./cache/cord-342942-1s32o9m8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342942-1s32o9m8.txt' === file2bib.sh === id: cord-330615-h8sktgo6 author: Jabri, ‡ § Bana title: Selective expansion of intraepithelial lymphocytes expressing the HLA-E–specific natural killer receptor CD94 in celiac disease date: 2000-05-31 pages: extension: .txt txt: ./txt/cord-330615-h8sktgo6.txt cache: ./cache/cord-330615-h8sktgo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-330615-h8sktgo6.txt' === file2bib.sh === id: cord-348283-7xorq5ce author: Naz, Anam title: Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-348283-7xorq5ce.txt cache: ./cache/cord-348283-7xorq5ce.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348283-7xorq5ce.txt' === file2bib.sh === id: cord-329669-z3t7plvh author: Poulton, Kay title: A role for human leucocyte antigens in the susceptibility to SARS‐Cov‐2 infection observed in transplant patients date: 2020-07-05 pages: extension: .txt txt: ./txt/cord-329669-z3t7plvh.txt cache: ./cache/cord-329669-z3t7plvh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-329669-z3t7plvh.txt' === file2bib.sh === id: cord-346957-bmajkabp author: Lv, Yanbo title: Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date: 2009-12-03 pages: extension: .txt txt: ./txt/cord-346957-bmajkabp.txt cache: ./cache/cord-346957-bmajkabp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346957-bmajkabp.txt' === file2bib.sh === id: cord-346032-188gnf8j author: Cheung, Ying-Kit title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date: 2007-08-10 pages: extension: .txt txt: ./txt/cord-346032-188gnf8j.txt cache: ./cache/cord-346032-188gnf8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346032-188gnf8j.txt' === file2bib.sh === id: cord-333670-qv1orlv5 author: Mutti, Luciano title: Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date: 2020-05-28 pages: extension: .txt txt: ./txt/cord-333670-qv1orlv5.txt cache: ./cache/cord-333670-qv1orlv5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333670-qv1orlv5.txt' === file2bib.sh === id: cord-326983-h6gdck2u author: Ferretti, Andrew P. title: Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-326983-h6gdck2u.txt cache: ./cache/cord-326983-h6gdck2u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326983-h6gdck2u.txt' === file2bib.sh === id: cord-344364-vu389d88 author: Wang, Wei title: Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-344364-vu389d88.txt cache: ./cache/cord-344364-vu389d88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344364-vu389d88.txt' === file2bib.sh === id: cord-320490-3jmo35jc author: Ismail, Saba title: Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date: 2020-04-12 pages: extension: .txt txt: ./txt/cord-320490-3jmo35jc.txt cache: ./cache/cord-320490-3jmo35jc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320490-3jmo35jc.txt' === file2bib.sh === id: cord-346445-hgqohdct author: Toyoshima, Yujiro title: SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-346445-hgqohdct.txt cache: ./cache/cord-346445-hgqohdct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346445-hgqohdct.txt' === file2bib.sh === id: cord-333966-st6gyozv author: Taherkhani, Reza title: Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date: 2015-03-17 pages: extension: .txt txt: ./txt/cord-333966-st6gyozv.txt cache: ./cache/cord-333966-st6gyozv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333966-st6gyozv.txt' === file2bib.sh === id: cord-355374-e8k72955 author: Clemens, E. Bridie title: Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine date: 2018-03-26 pages: extension: .txt txt: ./txt/cord-355374-e8k72955.txt cache: ./cache/cord-355374-e8k72955.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355374-e8k72955.txt' === file2bib.sh === id: cord-344691-vmc0rrrk author: Srinivasan, K.N. title: Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens date: 2004-08-04 pages: extension: .txt txt: ./txt/cord-344691-vmc0rrrk.txt cache: ./cache/cord-344691-vmc0rrrk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344691-vmc0rrrk.txt' === file2bib.sh === id: cord-347647-m9vk9m7h author: Eapen, Mary title: Hematopoietic cell transplantation with cryopreserved grafts for severe aplastic anemia date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-347647-m9vk9m7h.txt cache: ./cache/cord-347647-m9vk9m7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347647-m9vk9m7h.txt' === file2bib.sh === id: cord-344933-k23kzqxl author: Flahou, Charlotte title: Innovations dans la culture de plaquettes à partir de cellules souches pluripotentes induites* date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-344933-k23kzqxl.txt cache: ./cache/cord-344933-k23kzqxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344933-k23kzqxl.txt' === file2bib.sh === id: cord-333391-6l0cpvgr author: Bortolotti, Daria title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-333391-6l0cpvgr.txt cache: ./cache/cord-333391-6l0cpvgr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333391-6l0cpvgr.txt' === file2bib.sh === id: cord-353877-wzndpcq3 author: Albagi, Sahar Obi Abd title: A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-353877-wzndpcq3.txt cache: ./cache/cord-353877-wzndpcq3.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-353877-wzndpcq3.txt' === file2bib.sh === id: cord-352150-ey9kc7zj author: Degauque, Nicolas title: Cross-Reactivity of TCR Repertoire: Current Concepts, Challenges, and Implication for Allotransplantation date: 2016-03-24 pages: extension: .txt txt: ./txt/cord-352150-ey9kc7zj.txt cache: ./cache/cord-352150-ey9kc7zj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352150-ey9kc7zj.txt' === file2bib.sh === id: cord-349451-vak2p7ac author: Rocha, Francisco Airton Castro title: Microbes, Helminths and Rheumatic Diseases date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-349451-vak2p7ac.txt cache: ./cache/cord-349451-vak2p7ac.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-349451-vak2p7ac.txt' === file2bib.sh === id: cord-014976-546zaoxn author: nan title: Publication only date: 2006-03-08 pages: extension: .txt txt: ./txt/cord-014976-546zaoxn.txt cache: ./cache/cord-014976-546zaoxn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-014976-546zaoxn.txt' === file2bib.sh === id: cord-005487-vac061r8 author: nan title: Physicians Abstracts: EBMT 2010 date: 2010-04-07 pages: extension: .txt txt: ./txt/cord-005487-vac061r8.txt cache: ./cache/cord-005487-vac061r8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-005487-vac061r8.txt' === file2bib.sh === id: cord-005478-5iu38pr6 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-005478-5iu38pr6.txt cache: ./cache/cord-005478-5iu38pr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-005478-5iu38pr6.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 4 resourceName b'cord-023055-ntbvmssh.txt' === file2bib.sh === id: cord-005480-yg7salqt author: nan title: Oral Sessions and Working Party date: 2008-03-26 pages: extension: .txt txt: ./txt/cord-005480-yg7salqt.txt cache: ./cache/cord-005480-yg7salqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-005480-yg7salqt.txt' === file2bib.sh === id: cord-313474-1gux1gsi author: nan title: Physicians Abstracts date: 2015-03-20 pages: extension: .txt txt: ./txt/cord-313474-1gux1gsi.txt cache: ./cache/cord-313474-1gux1gsi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-313474-1gux1gsi.txt' === file2bib.sh === id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023364-ut56gczm.txt cache: ./cache/cord-023364-ut56gczm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-023364-ut56gczm.txt' === file2bib.sh === id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023354-f2ciho6o.txt cache: ./cache/cord-023354-f2ciho6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-023354-f2ciho6o.txt' === file2bib.sh === id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023346-8sqbqjm1.txt cache: ./cache/cord-023346-8sqbqjm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-023346-8sqbqjm1.txt' === file2bib.sh === id: cord-009567-osstpum6 author: nan title: Abstracts Oral date: 2008-04-23 pages: extension: .txt txt: ./txt/cord-009567-osstpum6.txt cache: ./cache/cord-009567-osstpum6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-009567-osstpum6.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 20 resourceName b'cord-022888-dnsdg04n.txt' === file2bib.sh === id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 pages: extension: .txt txt: ./txt/cord-010119-t1x9gknd.txt cache: ./cache/cord-010119-t1x9gknd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-010119-t1x9gknd.txt' === file2bib.sh === id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 pages: extension: .txt txt: ./txt/cord-010092-uftc8inx.txt cache: ./cache/cord-010092-uftc8inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 13 resourceName b'cord-010092-uftc8inx.txt' === file2bib.sh === id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 pages: extension: .txt txt: ./txt/cord-005460-ezrn8cva.txt cache: ./cache/cord-005460-ezrn8cva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 23 resourceName b'cord-005460-ezrn8cva.txt' === file2bib.sh === id: cord-005453-4057qib7 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 pages: extension: .txt txt: ./txt/cord-005453-4057qib7.txt cache: ./cache/cord-005453-4057qib7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 40 resourceName b'cord-005453-4057qib7.txt' Que is empty; done keyword-hla-cord === reduce.pl bib === id = cord-000488-x5ardo5j author = Pedersen, Lasse Eggers title = Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities date = 2011-07-08 pages = extension = .txt mime = text/plain words = 7264 sentences = 371 flesch = 53 summary = We have recently developed efficient methods to generate recombinant human MHC-I (also known as human leukocyte antigen class I, HLA-I) molecules, accompanying peptide-binding assays and predictors, and HLA tetramers for specific CTL staining and manipulation. Recombinant constructs encoding chimeric and SLA-1*0401 molecules A synthetic gene encoding a transmembrane-truncated fragment encompassing residues 1 to 275 of human HLA-A*11:01 alpha chain followed by a FXa-BSP-HAT tag (FXa = factor Xa cleavage site comprised of the amino acid sequence IEGR, BSP = biotinylation signal peptide, HAT = histidine affinity tag for purification purposes; see Online Resource 1) had previously been generated and inserted into the pET28 expression plasmid (Novagen) (Ferre et al. cache = ./cache/cord-000488-x5ardo5j.txt txt = ./txt/cord-000488-x5ardo5j.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-001247-pxzbirqd author = Sun, Lu title = A new unconventional HLA-A2-restricted epitope from HBV core protein elicits antiviral cytotoxic T lymphocytes date = 2014-03-22 pages = extension = .txt mime = text/plain words = 4630 sentences = 259 flesch = 55 summary = Our data therefore provide insights into the structure characteristics of this unconventional epitope binding to MHC-I molecules, as well as epitope specific CTL activity that orchestrate T cell response and immune evasion in HBV infected patients. To identify immune-dominant HBV-specific CTL epitopes, especially epitopes from HBc protein, is therefore necessary for monitoring T cell responses during disease progression, as well as for developing epitope-based therapeutic vaccines against CHB (Inchauspe and Michel, 2007; Gordon et al., 2013; Liu et al., 2013a, b) . To further determine the epitope-specific CTLs, fresh PBMCs from HLA-A2 + AHB patients were stimulated with HBc141-149 peptide and detected by ex vivo IFN-γ ELISPOT assays. In this study, we identified a new HLA-A2-restricted CD8 + T cell epitope HBc141-149 by screening an overlapping 9-mer peptide pool covering HBV core protein. cache = ./cache/cord-001247-pxzbirqd.txt txt = ./txt/cord-001247-pxzbirqd.txt === reduce.pl bib === id = cord-002463-qhtj1pef author = Dash, Raju title = In silico-based vaccine design against Ebola virus glycoprotein date = 2017-03-21 pages = extension = .txt mime = text/plain words = 5830 sentences = 358 flesch = 50 summary = Top scored eiptope subjected to 100 ns MD simulation **RMSF **RMSD **Hydrogen bond occupency analysis Secquence, having highest vaxijen score Prediction of B cell epitope, using-**T cell epitope prediction by proteasomal C terminal cleavage, TAP transport efficiency and MHC class 1 binding **Epitopes with IC50 value less than 50 for their binding to MHC class 1 molecule from IEDB analysis along with binding to highest number of alleles in both analyses were chosen **Epitope conservancy analysis **Population coverage analysis **Kolaskar and Tongaonkar antigenicity scale 48 **Emini surface accessibility prediction 47 **Karplus and Schulz flexibility prediction 49 **Bepipred linear epitope prediction 50 **Chou and Fasman beta turn prediction 52 Vaxijen analysis with a threshold score of >0. We also validated each epitope by molecular docking simulation and MM-GBSA/MM-PBSA studies with HLA-A*32:15 protein, as it was found common in the results from MHC-I binding interaction analysis. cache = ./cache/cord-002463-qhtj1pef.txt txt = ./txt/cord-002463-qhtj1pef.txt === reduce.pl bib === id = cord-002686-zzongyfa author = Oany, Arafat Rahman title = Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA date = 2017-09-07 pages = extension = .txt mime = text/plain words = 4966 sentences = 265 flesch = 47 summary = In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. The generalized modules of membrane antigen-(GMMA-) based outer membrane proteins including SigA were also shown to be highly immunogenic [12] , which prompted us to target SigA as one of the best vaccine candidates and to design potential peptide vaccine covering all the Shigella spp. The SigA protein sequences of different strains of Shigella species were retrieved from the NCBI GenBank [22] database and analysed in the VaxiJen v2.0 [23] server for the determination of the most potent antigenic protein. IEDB analysis resource predicted both MHC class I-and MHC class II-based coverage of the selected epitopes for the world population to assess the feasibility of being a potential vaccine candidate. cache = ./cache/cord-002686-zzongyfa.txt txt = ./txt/cord-002686-zzongyfa.txt === reduce.pl bib === === reduce.pl bib === id = cord-004435-l66ost6q author = Oli, Angus Nnamdi title = Immunoinformatics and Vaccine Development: An Overview date = 2020-02-26 pages = extension = .txt mime = text/plain words = 8946 sentences = 534 flesch = 39 summary = Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/re-emerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. 13 An approach that must accommodate many factors affecting vaccine development like pathogen antigenic variability, the emergence of infectious disease, human genetic variation is the goal of immunoinformatics [ Figure 1 ]. 110 The surface glycoprotein can be regarded as antigen and hence can serve as a target for the immune system which if sequenced, using the new immunoinformatics approach and a common site for the varying proteins identified, a potent vaccine can be developed which can accommodate the antigenic drift/shifts of the virus. cache = ./cache/cord-004435-l66ost6q.txt txt = ./txt/cord-004435-l66ost6q.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-007664-c5snhymz author = Mauerhoff, Thekla title = Differential expression and regulation of major histocompatibility complex (MHC) products in neural and glial cells of the human fetal brain date = 2002-11-13 pages = extension = .txt mime = text/plain words = 4673 sentences = 212 flesch = 51 summary = To gain an insight into the regulation of HLA in the different cell types in the CNS and to compare it to that observed in the endocrine organs, we have studied the effect of the lympho/monokines interferon (IFN)-α and -γ, tumour necrosis factor (TNF)-α, and interleukin (IL)-2 and other agents on this aspect of the biology of human fetal brain cells in culture. It has previously been reported that primary cultures of human fetal brain tissue can be a useful substrate for studying the expression of cell type-specific antigens, e.g. gangliosides, tetanus toxin receptors (Dickson et al., 1982 (Dickson et al., , 1985 , and the present data confirm that they can also be successfully employed to investigate the expression and modulation of HLA molecules. cache = ./cache/cord-007664-c5snhymz.txt txt = ./txt/cord-007664-c5snhymz.txt === reduce.pl bib === === reduce.pl bib === id = cord-007851-v6h1yro7 author = Han, Ki-Cheol title = Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging date = 2020-04-03 pages = extension = .txt mime = text/plain words = 4886 sentences = 260 flesch = 41 summary = We used a combined application of this method involving immune-specific signature analysis and HLA-associated peptidomics using samples from six patients with triple-negative breast cancer (TNBC) in order to select immunogenic HLA epitopes for in vitro testing. Integrated WTS data revealed a higher priority to select promising HLA-peptides via high-resolution bioinformatics analysis, showing immune-cell-specific signatures and TCR-repertoire diversity in tumors. We then found a positive correlation between TCR diversity, reflecting clonal composition, and the expression of MHC-class І molecules, suggesting that active tumor-antigen presentation promotes the generation of antigen-specific TILs. Additionally, immune-specific signature analysis can discriminate specific immune-cell types in each patient and thus enhance the efficiency of selective HLA-peptidomic approaches. In this study, the HLA-peptidomics approach combined with comprehensive analysis of immune-specific signatures and TCR repertories showed high selectivity to determine the immunogenic T-cell epitopes. Identification of potential vaccine epitopes coupled with immune-specific signature analysis, HLA-peptidomics, and single-cell-based immunogenicity testing offers a discriminative and powerful tool for cancer-vaccine development. cache = ./cache/cord-007851-v6h1yro7.txt txt = ./txt/cord-007851-v6h1yro7.txt === reduce.pl bib === === reduce.pl bib === id = cord-007719-3ypv9k9p author = Wang, Mingjun title = Classification of Human Leukocyte Antigen (HLA) Supertypes date = 2014-05-06 pages = extension = .txt mime = text/plain words = 3649 sentences = 158 flesch = 51 summary = Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of importance for the development of new effective vaccines capable of activating the cellular arm of the immune response. Thus, identifi cation of new antigenic peptides, derived from infectious agents or tumor antigens, which may bind to HLA-I or HLA-II molecules in exchange with self-peptides normally occupying the HLA-binding site ( see below), is important for developing new effective vaccines capable of activating the cellular arm of the immune responses. To reduce this complexity, one option is to group thousands of different HLA molecules into clusters of several so-called HLA supertypes: a classifi cation that refers to a group of HLA alleles with largely overlapping peptide binding specifi cities. cache = ./cache/cord-007719-3ypv9k9p.txt txt = ./txt/cord-007719-3ypv9k9p.txt === reduce.pl bib === id = cord-005487-vac061r8 author = nan title = Physicians Abstracts: EBMT 2010 date = 2010-04-07 pages = extension = .txt mime = text/plain words = 58975 sentences = 3128 flesch = 58 summary = We retrospectively analyzed 1257 patients (pts), 755 children (age≤18) and 502 adults, receiving fi rst single (n = 1080) or double UCBT (n = 177) in EBMT centers, between 1995 and 2009 , for malignant and non-malignant diseases, who survived at least 100 days from transplantation with neutrophils recovery and without relapse or autologous reconstitution. Prochymal® improves response rates in patients with steroid-refractory acute graft-versus-host disease involving the liver and gut: results of a randomized, placebo-controlled, multicentre phase III trial in GvHD P.J. Martin (1) , J.P. Uberti (2) Background and methods: Steroid-refractory acute GVHD (SR-GVHD) remains a signifi cant and life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). A. Nagler (1) Background: Allogeneic transplantation of hematopoietic stem cells (allo-SCT) from an HLA-matched related (MRD) or unrelated donor (URD) is a curative option for patients (pts) with high-risk hematological disease (HRHD). cache = ./cache/cord-005487-vac061r8.txt txt = ./txt/cord-005487-vac061r8.txt === reduce.pl bib === 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 pages = extension = .txt mime = text/plain words = 10041 sentences = 299 flesch = 34 summary = Epitope mapping performed using the Gpl 60 sequence of the patient's autologous early HIV-1 population indicated that this response was in fact extremely focused on a single epitope encompassing Gpl60 amino acids 30-38(9), recognized in association with HLA-B44, The frequency of epitope-specific CTL was extremely high: at the earhest timepoint available for study, which may have been shghtly after the peak of the primary immune response, 1 in 1 7 peripheral blood mononuclear cells (EBMCs) were found to score as virus-specific CTL precursors by limiting dilution analysis, a technique which has recently been shown to greatly underestimate the total numher of epitope-specific T cells (55, 56) , As shown in Fig, 1 , viral variants bearing mutations in the epitopic sequence which conferred escape from recognition by epitope-specific CTL rapidly appeared in this patienc, and then increased in frequency until 164/1998 they had cotnpieteiy repiaced the transmitted virai strain. cache = ./cache/cord-009836-7o6htufh.txt txt = ./txt/cord-009836-7o6htufh.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-005480-yg7salqt author = nan title = Oral Sessions and Working Party date = 2008-03-26 pages = extension = .txt mime = text/plain words = 72626 sentences = 3873 flesch = 55 summary = Standard NIH or Eurolupus cyclophosphamide (CY) protocols and mycophenolate Mofetil (MMF) as induction therapy in severe BILAG A SLE is still associated with 20 % failure, 50% relapse and 10% to 15 % death at 10 years In the absence of a single standard treatment worldwide for refractory SLE, phase I-II studies analysed the use of: a) rituximab (anti CD20 mAb) in more than 1 000 patients showing complete to partial early response around 100% with relapse in 50 to 60% of the cases; b) autologous Hematopoietic Stem Cell Transplantation (HSCT) since 1997 under the auspices of the joined EBMT-EULAR working party, reporting durable remission with reduced or no immunosuppressive drug requirement in 66%, one-third of whom later relapsed to some degree with a 74 ± 7% (n= 62/79) overall survival at 5 years for SLE among the 863 HSCT procedures registered: in 2007 in the EBMT data base. cache = ./cache/cord-005480-yg7salqt.txt txt = ./txt/cord-005480-yg7salqt.txt === reduce.pl bib === id = cord-005478-5iu38pr6 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date = 2019-07-03 pages = extension = .txt mime = text/plain words = 63350 sentences = 3869 flesch = 58 summary = There were some differences among groups: patients in group-1 were younger (median age 46 years, p< 0.02) were transplanted in more recent year (2015, p< 0.001), received more frequently a regimen based on TBF (thiotepa, fludarabine and busulfan) (83%, p< 0.001) and bone marrow (BM) as source of stem cells (77%, p< 0.001), with no ATG (100%, p< 0.001). Clinical Trial Registry: NCT01217723 Disclosure: None of the Authors have any conflicts of interest to declare O105 Immune reconstitution -based score at diagnosis of CGVHD predicts GVHD severity and overall-survival: A novel prognostication tool for GVHD treatment tailoring Background: Allogeneic stem cell transplantation (HSCT) survivors are at a relevant risk of developing chronic GvHD (cGvHD), which importantly affects quality of life and increases morbidity and mortality. cache = ./cache/cord-005478-5iu38pr6.txt txt = ./txt/cord-005478-5iu38pr6.txt === reduce.pl bib === id = cord-013093-aa4cf44u author = Cassotta, Antonino title = Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin date = 2020-07-09 pages = extension = .txt mime = text/plain words = 10936 sentences = 470 flesch = 50 summary = The detailed and unbiased characterization of HA-reactive memory and naive CD4 + T cell repertoires, paralleled by a deep analysis of the naturally presented repertoire of MHC-II-binding HA peptides by mass spectrometry (MS)-based immunopeptidomics, allowed us to shed new light on the factors governing CD4 + T cell clonal selection and immunodominance to influenza HA in humans. We then selected a large number of H1-HA-specific T cell clones derived from naive or memory T cells of donor HD1 and determined their functional avidity by measuring the proliferative response to autologous monocytes pulsed with different concentrations of the H1-HA peptides or H1-HA protein, which need processing for presentation on MHC-II molecules. cache = ./cache/cord-013093-aa4cf44u.txt txt = ./txt/cord-013093-aa4cf44u.txt === reduce.pl bib === === reduce.pl bib === id = cord-015389-vwgai4k9 author = nan title = Publication only date = 2009-03-25 pages = extension = .txt mime = text/plain words = 23868 sentences = 1465 flesch = 57 summary = This study evaluates the safety of this approach, in terms of infusion-related toxicity and hematopoietic reconstitution, in 385 consecutive autologous transplantations performed from 4/97 to 9/08 in 348 patients (median age 46; underlying disease: lymphoma in 178, myeloma in 131, acute leukaemia in 17, breast cancer in 22). Patients and methods: Eight pts after allogeneic hematopoetic stem cell transplantation (HSCT) underwent MSCs infusions (median age of pts was 11 years, male/female: 6/2) between 2006 and 2009. Akiyama Tokyo Metropolitan Komagome Hospital (Tokyo, JP) Acute graft-versus-host disease (GVHD) is one of the major factors that have infl uence on the outcomes of allogeneic hematopoietic stem cell transplantation (HSCT). Material and methods: during a 8 years period we have performed 144 stem cells transplantation in 134 patients with different hematological malignancies(AML: 74; ALL: 6; CML: 7; CLL: 1, NHL: 13; Hodgkin Diseases: 16; Multiple myelomas: 24; Aplastic anaemia: 1;Myelofi brosis:1 Ewing Sarcoma: 1; Male:78 Female 66. cache = ./cache/cord-015389-vwgai4k9.txt txt = ./txt/cord-015389-vwgai4k9.txt === reduce.pl bib === id = cord-016235-2lhrkmrv author = Roden, Anja C. title = Lung date = 2010-05-17 pages = extension = .txt mime = text/plain words = 12865 sentences = 674 flesch = 35 summary = Unlike the situation with heart transplant recipients, chronic vascular rejection in lung transplants has not resulted in graft loss; however, some patients develop pulmonary hypertension particularly those with BOS [92, 111] . However, based on the link between acute rejection and development of BOS, surveillance transbronchial biopsies in asymptomatic lung transplant recipients has become common practice in many large lung transplantation centers because evidence suggests that patients who have multiple episodes of low grade (A1) lesions within the first 12 months posttransplantation develop early onset BOS. A study [49] in which surveillance transbronchial biopsies were performed at 3, 6, 9, and 12 weeks posttransplantation, at the time of symptoms, and for follow-up of acute rejection or CMV pneumonia showed that patients who develop acute small airways rejection within the first year after transplantation are at risk of development of BOS at 1.76, 3.3, and 5.5 years after detection of B3/ B4 lesion (by 1996 ISHLT criteria, see Table 7 .2), B2 lesion or B0/B1 lesion, respectively. cache = ./cache/cord-016235-2lhrkmrv.txt txt = ./txt/cord-016235-2lhrkmrv.txt === reduce.pl bib === id = cord-016413-lvb79oxo author = Efthimiou, Petros title = Adult-Onset Still’s Disease date = 2018-07-14 pages = extension = .txt mime = text/plain words = 6126 sentences = 315 flesch = 40 summary = Adult-onset Still's disease (AOSD) is a rare systemic, autoinflammatory disorder that often presents in adolescence and early adulthood with fever, rash, and polyarthritis. Mutation of perforin and the MUNC13-4 genes have been seen in patients with macrophage activation syndrome (MAS), a known severe, life-threatening complication of AOSD [3] . Patients who have the chronic articular disease pattern can present with joint erosions making the differential diagnosis from RA problematic, especially in the absence of systemic signs and symptoms. Interleukin-1 receptor antagonist (anakinra) treatment in patients with systemic-onset juvenile idiopathic arthritis or adult onset Still disease: preliminary experience in France Effectiveness of first-line treatment with recombinant interleukin-1 receptor antagonist in steroid-naive patients with new-onset systemic juvenile idiopathic arthritis: results of a prospective cohort study Clinical manifestations of adult-onset Still's disease presenting with erosive arthritis: association with low levels of ferritin and Interleukin-18 cache = ./cache/cord-016413-lvb79oxo.txt txt = ./txt/cord-016413-lvb79oxo.txt === reduce.pl bib === id = cord-017702-v46ye328 author = Ganguly, Nirmal Kumar title = Pharmacogenomics and Personalized Medicine for Infectious Diseases date = 2013-06-11 pages = extension = .txt mime = text/plain words = 16564 sentences = 798 flesch = 43 summary = Deciphering the pathogen virulence factors, host susceptibility genes, and the molecular programs involved in the pathogenesis of disease has paved the way for discovery of new molecular targets for drugs, diagnostic markers, and vaccines. The pathogen genome on one hand gives us the information about the important genes conferring disease pathogenesis as well as drug resistance, while the genome of the host on the other hand will reveal the susceptibility genes, and the further knowledge of polymorphisms in genes of the host metabolic and immune system will lead to the new vaccine strategies, drugs targets, and also their treatment outcomes. Several fi eld studies have further suggested that there is a need for calibration of isoniazid dosage as per the individual tuberculosis patient's age, acetylator status, and disease process for an effective antimicrobial outcome of drug treatment (Jeena et al. cache = ./cache/cord-017702-v46ye328.txt txt = ./txt/cord-017702-v46ye328.txt === reduce.pl bib === id = cord-013894-1bgvj62a author = Wang, Qihui title = Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex date = 2019-07-04 pages = extension = .txt mime = text/plain words = 6883 sentences = 408 flesch = 65 summary = Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Structural comparisons of LILRB1/2 binding to different HLA alleles Similar to previous reports, 14,17 D1 interacts with the HLA-G1 α3 domain. As assessed by the SPR assay, dimeric HLA-G1 presenting variable peptides displayed similar binding strengths for LILRB1 and LILRB2 (with four Ig-like domains or D1D2), indicating that the peptides seem to have no effect on the interactions. Structural data in this study indicate that through trans interaction, one HLA-G1 monomer binds to one LILRB1/2 molecule. The complex structure reported here provides the first direct evidence that D1D2 is responsible for all of the interactions with HLA-Is, while D3D4 is not the reason to explain why HLA-Is that carry a single residue substitution in their α1α2 domains or in the presented peptides display variable binding affinities to LILRB2. cache = ./cache/cord-013894-1bgvj62a.txt txt = ./txt/cord-013894-1bgvj62a.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-018595-x3tleomb author = Dodiuk-Gad, Roni P. title = Adverse Medication Reactions date = 2017-04-25 pages = extension = .txt mime = text/plain words = 16304 sentences = 910 flesch = 39 summary = 2. Delayed-type drug hypersensitivity: Delayed-type drug hypersensitivity reactions usually take several days to weeks following drug exposure, with variable clinical presentations that may include Maculopapular Eruption (MPE), Fixed Drug Eruption (FDE), Acute Generalized Exanthematous Pustulosis (AGEP), Stevens-Johnson Syndrome (SJS), Toxic Epidermal Necrolysis (TEN) and Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS). Examples of strong associations of HLA alleles with specific drug-induced hypersensitivity reactions include abacavir, nevirapine, carbamazepine, and allopurinol (Table 25. [61] , who reported the weak associations of HLA-A29, B12, and MPE maculopapular drug eruption, DRESS drug reaction with eosinophilia and systemic symptoms, SJS/TEN Stevens-Johnson syndrome/toxic epidermal necrolysis DR7 in sulfonamide-related TEN, and HLA-A2, B12 in oxicam-related TEN in Europeans [61] . Drug specific cytotoxic T-cells in the skin lesions of a patient with toxic epidermal necrolysis cache = ./cache/cord-018595-x3tleomb.txt txt = ./txt/cord-018595-x3tleomb.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-014976-546zaoxn author = nan title = Publication only date = 2006-03-08 pages = extension = .txt mime = text/plain words = 51926 sentences = 2983 flesch = 53 summary = In order to evaluate if malignant and non malignant hematological diseases quantitatively and qualitatively affect BM derived MSCs, bone marrow from children with acute lymphoblastic leukemia (ALL diagnosis n=9, different phases of treatment n=29, end of therapy n=10), idiopathic thrombocytopenic purpura (n=16), autoimmune neutropenia (n=12) and control patients (solid tumors without BM involvement, n=30) was harvested and the mononuclear cell (MNC) fraction isolated. Case: In our hospital a total of 3 patients with relapsed Hodgkin's disease underwent reduced-intensity conditioning (RIC) allogeneic stem cell transplantation (allo-SCT) from an HLA-identical sibling. We report a case of a young male patient of 19 years old with aggressive MS who was treated with a high-dose immunosuppressive regimen (HDIS) using myeloablation followed by autologous blood stem cell transplantation (ASCT) that has induced a dramatic and long-lasting remission of the disease. cache = ./cache/cord-014976-546zaoxn.txt txt = ./txt/cord-014976-546zaoxn.txt === reduce.pl bib === id = cord-255069-9xueqdri author = Leary, Shay title = Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date = 2020-04-11 pages = extension = .txt mime = text/plain words = 1821 sentences = 77 flesch = 43 summary = The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . cache = ./cache/cord-255069-9xueqdri.txt txt = ./txt/cord-255069-9xueqdri.txt === reduce.pl bib === id = cord-103662-a4ok5wqc author = Tarek, M. title = Custommune: a web tool to design personalized and population-targeted vaccine epitopes date = 2020-04-29 pages = extension = .txt mime = text/plain words = 8116 sentences = 454 flesch = 45 summary = When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this aim, by intersecting input data from patient-specific viral sequences and HLA alleles, Custommune provides an output of epitopes of desired length filtered for their predicted specificity, immunogenicity and mutation potential. Class I and Class II HLA alleles which were predicted by Custommune to bind RBDp and RBDg epitopes of SARS-CoV-2 were used to estimate potential vaccine coverage in the populations of interest. cache = ./cache/cord-103662-a4ok5wqc.txt txt = ./txt/cord-103662-a4ok5wqc.txt === reduce.pl bib === id = cord-034402-64xz1j9i author = Srivastava, Shivani title = Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4517 sentences = 286 flesch = 52 summary = This present study aims at the prediction of B cell epitopes for subunit vaccine designing against Listeria monocytogenes using a reverse vaccinology approach. For computational identification and characterization of epitopes for the preparation of subunit vaccine designing, complete proteome analysis of Listeria monocytogenes F2365 strain (GenBank accession number AE017262.2) was performed using the UniProtKB database. The first requirement in the reverse vaccinology approach of vaccine designing is to eliminate all non-allergic proteins from a complete proteome set of bacteria, Listeria monocytogenes. In this exploration and investigation, the prediction of B cell epitopes has been performed by the authors for the designing of the vaccine against listeriosis by using a reverse vaccinology approach. Tertiary structure modeling of alleles was generated with the help of HLA alleles were performed Based on low binding energy, 4 peptides were selected viz., CEETFGIRL, MKFLFPLKL, FLKIDPPIL, and VRH-HGGGHK. cache = ./cache/cord-034402-64xz1j9i.txt txt = ./txt/cord-034402-64xz1j9i.txt === reduce.pl bib === id = cord-104099-xhi0oxtr author = Hensen, L. title = CD8+ T-cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph date = 2020-10-05 pages = extension = .txt mime = text/plain words = 9678 sentences = 568 flesch = 55 summary = We defined CD8+ T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. Our data present the first evidence of influenza-specific CD8+ T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8+ T-cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease. 10 .02.20206086 doi: medRxiv preprint immunogenicity of novel peptides in HLA-A24-expressing mice, peripheral blood of Indigenous and non-Indigenous HLA-A24 + healthy and influenza-infected individuals, and human tissues. To determine the immunogenicity of novel IAV-and IBV-derived peptides during primary and secondary influenza virus infection in vivo, we utilized HLA-A24-expressing transgenic (HHD-A24) mice 45 Table 2 ). . https://doi.org/10.1101/2020.10.02.20206086 doi: medRxiv preprint across virus strains circulating in South-East Asia and Australia suggests that the prominent HLA-A24-restricted CD8 + T-cell responses are likely to confer broad cross-reactive immunity to IAV. cache = ./cache/cord-104099-xhi0oxtr.txt txt = ./txt/cord-104099-xhi0oxtr.txt === reduce.pl bib === id = cord-031937-qhlatg84 author = Verma, Anukriti title = Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date = 2020-09-15 pages = extension = .txt mime = text/plain words = 6760 sentences = 326 flesch = 31 summary = In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. The contributions of the microorganisms in the co-evolved IBD and ReA as part of the disease network was created through the interactive maps of the essential host interaction proteins (verified using literature survey) and the information processed through gene expression data analysis 64 . The pathways of the above host interacting proteins were found out using KEGG database that provides ontologies for proteins related to biological processes 67 www.nature.com/scientificreports/ Subsequently, the role of drugs or inhibitors used to suppress the effect of IBD and ReA such as indomethacin, prednisone, ciprofloxacin, sulfasalazine, azathioprine, methotrexate and hydroxychloroquine was scored in the disease network through their docking studies against the potential targets (both host as well microbial targets) as per published methodologies 68, 69 . cache = ./cache/cord-031937-qhlatg84.txt txt = ./txt/cord-031937-qhlatg84.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 === === reduce.pl bib === === reduce.pl bib === id = cord-254190-bxfne94u author = Tu, Wenwei title = Application of Humanized Mice in Immunological Research date = 2015-07-07 pages = extension = .txt mime = text/plain words = 6246 sentences = 254 flesch = 34 summary = On the contrary, humanized mice established by peripheral blood cells provide a ready platform for studying the functions of mature immune cells but the length of window appropriate for research is still limited by chronic GVHD and ongoing reduced engraftment. Distinct from their T cell companion, reconstitution of functional B lymphocytes is generally poor in humanized mice and needed to improve in the future although their primary repertoire were principally unaltered by the differences between mouse and human stromal environments [ 53 ] and their ability to produce antigen-specifi c antibody was partly developed [ 54 ] . In above three studies, investigators planted solid grafts into immunodefi cient mice before reconstitution of human immune system and induced rejection by infusion of mature human cells. Humanized immune system (HIS) mice as a tool to study human NK cell development Humanized mice as a model to study human hematopoietic stem cell transplantation cache = ./cache/cord-254190-bxfne94u.txt txt = ./txt/cord-254190-bxfne94u.txt === reduce.pl bib === id = cord-265277-ymvrserl author = Crooke, Stephen N. title = Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date = 2020-05-14 pages = extension = .txt mime = text/plain words = 4620 sentences = 249 flesch = 52 summary = A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. cache = ./cache/cord-265277-ymvrserl.txt txt = ./txt/cord-265277-ymvrserl.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-266204-ipa017wz author = Poland, G. A. title = Personalized vaccinology: A review date = 2018-08-28 pages = extension = .txt mime = text/plain words = 7232 sentences = 331 flesch = 36 summary = 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. A decade ago, we described the idea of vaccinomics and adversomics, based on the immune response network theory [5, 6] , which utilizes immunogenetics/imunogenomics and systems biology approaches to understand the basis for inter-individual variations in vaccineinduced immune responses in humans, as well as the basis for adverse side effects from vaccines [7] . Published data reveal that innate and adaptive immunity is decreased with age, but the systems-level mechanisms for these findings are unclear [66, 68] , particularly in regard to influenza and other viral vaccine responses where the morbidity, mortality, and associated healthcare costs are greater in older individuals [11] . cache = ./cache/cord-266204-ipa017wz.txt txt = ./txt/cord-266204-ipa017wz.txt === reduce.pl bib === === reduce.pl bib === id = cord-271032-imc6woht author = Schulte-Schrepping, Jonas title = Severe COVID-19 is marked by a dysregulated myeloid cell compartment date = 2020-08-05 pages = extension = .txt mime = text/plain words = 9740 sentences = 692 flesch = 58 summary = Given the dramatic changes in various immune cell populations (Fig. 1C+D) , we next 171 assessed their composition and activation state by droplet-based scRNA-seq in 27 samples 172 from 18 COVID-19 patients (8 mild & 10 severe, cohort 1, Table S1 ) collected between day 173 3 and day 20 after symptom onset. All LDNs also expressed high levels of alarmins S100A8 and S100A9 (Fig. 5D) , whereas 343 other S100 genes (e.g. S100A4, S100A12) were strongly induced in selected neutrophil 344 Alterations of the neutrophil compartment were further interrogated by mass cytometry of 362 whole blood samples of COVID-19 patients (n=8 mild + 9 severe, cohort 1), FLI patients 363 (n=8), and age-and gender-matched controls (n=9) (Table S1), using a panel designed to 364 detect myeloid cell maturation and activation states as well as markers of 365 immunosuppression or dysfunction (Table S2) . cache = ./cache/cord-271032-imc6woht.txt txt = ./txt/cord-271032-imc6woht.txt === reduce.pl bib === === reduce.pl bib === id = cord-275677-hbv49e01 author = Ramana, Lakshmi Narashimhan title = Targeting strategies for delivery of anti-HIV drugs date = 2014-10-28 pages = extension = .txt mime = text/plain words = 12944 sentences = 571 flesch = 42 summary = Immunoliposomes loaded with the protease inhibitor indinavir and surface modified with anti-HLA-DR were found to effectively bind to HIV infected cells and deliver the antiretroviral drug leading to a significant reduction in the viral load [44] . In a recent work, lipid nanoparticles conjugated with two peptide sequences that were derived from the binding domains of CD4 designated as CD4-BP2 and CD4-BP4 were used for targeted delivery of the protease inhibitor indinavir to HIV infected CD4 + cells with high specificity [54] . The lectin actinohivin isolated from the actinomycete Longisporum albida has also been identified as an important targeting moiety that binds to the mannose residues present in the gp120 at lower concentrations with an affinity greater than anti-gp120 antibodies thereby preventing the interaction of the viral glycoprotein with CXCR4 and CCR5 chemokine receptors [13] . cache = ./cache/cord-275677-hbv49e01.txt txt = ./txt/cord-275677-hbv49e01.txt === reduce.pl bib === === reduce.pl bib === id = cord-275608-joyan7ij author = Sewell, Andrew K. title = Why must T cells be cross-reactive? date = 2012-08-24 pages = extension = .txt mime = text/plain words = 7748 sentences = 347 flesch = 47 summary = However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide–MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide-MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. Box 1 | Extensive T cell cross-reactivity and apparent specificity are not incongruous From the 20 proteinogenic amino acids, it is possible to generate vast numbers of peptides of a length that can be presented by MHC molecules (see the table). First, a cross-reactive T cell repertoire generates a near perfect solution to the huge challenge of providing effective immune cover by allowing a limited number of T cells to provide immunity against virtually all foreign peptides that can bind to self MHC molecules. cache = ./cache/cord-275608-joyan7ij.txt txt = ./txt/cord-275608-joyan7ij.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-280641-zqdrzyzl author = Fernández Fabrellas, Estrella title = Epidemiología de la sarcoidosis date = 2007-02-28 pages = extension = .txt mime = text/plain words = 6760 sentences = 547 flesch = 51 summary = Además de investigar la posible etiología de la enfermedad, este estudio examina el situación psicosocial 15 y el curso clínico de 736 pacientes incluidos en los 6 primeros meses desde el diagnóstico histológico de sarcoidosis, y los compara con otros tantos controles pareados por edad, sexo y raza, con un seguimiento de los primeros 215 casos durante los 2 años siguientes a la inclusión 16 . Tanto la piel como los pulmones -órganos más comúnmente afectados-están siempre en contacto con estos antígenos; los estudios sobre la inmunopatogenia de la sarcoidosis apoyan que la enfermedad es el resultado de una superrespuesta inmunitaria y que hay un gran número de potenciales antígenos ambientales que pueden inducir la sensibilización y la consiguiente respuesta mediada por células responsable del desarrollo de granulomas 43 . cache = ./cache/cord-280641-zqdrzyzl.txt txt = ./txt/cord-280641-zqdrzyzl.txt === reduce.pl bib === id = cord-288916-i8ukefp8 author = Gómez-Herranz, Maria title = The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis date = 2019-04-02 pages = extension = .txt mime = text/plain words = 11700 sentences = 702 flesch = 52 summary = A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The HPV16+ and IFITM1/3 positive cervical cancer cell line SiHa [38] [39] exhibit IFNγ inducible STAT1, IRF1, and IFITM1/3 proteins (Fig. 1G ). Also of note is attenuation of HLA-A, HLA-B, HLA-C, and ISG15 protein synthesis 24 h post-IFNγ treatment in the IFITM1/IFITM3 double null cells compared to parental SiHa (Fig. 5F vs 5B). By contrast, basal HLA-B protein expression was attenuated in the IFITM1/IFITM3 double null cells after IFNγ treatment (Fig. 6F vs 6E) . cache = ./cache/cord-288916-i8ukefp8.txt txt = ./txt/cord-288916-i8ukefp8.txt === reduce.pl bib === id = cord-281141-ouno4jpl author = Mahajan, Swapnil title = Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date = 2020-11-05 pages = extension = .txt mime = text/plain words = 6208 sentences = 307 flesch = 52 summary = A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . cache = ./cache/cord-281141-ouno4jpl.txt txt = ./txt/cord-281141-ouno4jpl.txt === reduce.pl bib === === reduce.pl bib === id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130049 sentences = 7334 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023364-ut56gczm.txt txt = ./txt/cord-023364-ut56gczm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-289711-4ab3d00h author = Yarmarkovich, Mark title = Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date = 2020-06-08 pages = extension = .txt mime = text/plain words = 5290 sentences = 252 flesch = 46 summary = Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. Here we describe an approach for prioritizing viral epitopes derived 105 from a prioritized list of 33mer peptides predicted to safely target the vulnerabilities of 106 SARS-CoV-2, generate highly immunogenic epitopes on both MHC class I and II in the 107 vast majority of the population, and maximize the likelihood that these peptides will drive 108 an adaptive memory response. Here we present a comprehensive immunogenicity map of the SARS-CoV-2 248 virus (Table S1) , and propose sixty-five 33mer peptide sequences predicted to generate 249 B and T cell epitopes from a diverse sampling of viral domains across all 10 SARS-250 cache = ./cache/cord-289711-4ab3d00h.txt txt = ./txt/cord-289711-4ab3d00h.txt === reduce.pl bib === === reduce.pl bib === id = cord-288496-7rrh2gg6 author = Stryhn, Anette title = A Systematic, Unbiased Mapping of CD8(+) and CD4(+) T Cell Epitopes in Yellow Fever Vaccinees date = 2020-08-31 pages = extension = .txt mime = text/plain words = 15229 sentences = 676 flesch = 50 summary = Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. cache = ./cache/cord-288496-7rrh2gg6.txt txt = ./txt/cord-288496-7rrh2gg6.txt === reduce.pl bib === id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130046 sentences = 7333 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023354-f2ciho6o.txt txt = ./txt/cord-023354-f2ciho6o.txt === reduce.pl bib === id = cord-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130043 sentences = 7330 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023346-8sqbqjm1.txt txt = ./txt/cord-023346-8sqbqjm1.txt === reduce.pl bib === === reduce.pl bib === id = cord-009567-osstpum6 author = nan title = Abstracts Oral date = 2008-04-23 pages = extension = .txt mime = text/plain words = 131214 sentences = 7728 flesch = 53 summary = Introduction: Previously, it has been demonstrated that FOXP3, a gene required for the development and function of regulatory T cells, was highly expressed in the graft during cardiac rejection, suggesting infiltration of regulatory T cells in the transplanted organ during an allogeneic response. Efficacy and safety parameters assessed at follow-up included: acute rejection; patient and graft survival; renal function, vital signs, basic lab results and immunosuppressive regimen for the patients 10 years after completion of the original study. We analyzed, for the first time, the expression of TLR4 in PBMC from kidney recipients with contrasted situations: operational tolerance and chronic immune-mediated rejection (Banff 2005), compared to patients with normal histology and stable graft function, non transplant patients with renal failure and healthy volunteers. cache = ./cache/cord-009567-osstpum6.txt txt = ./txt/cord-009567-osstpum6.txt === reduce.pl bib === id = cord-326554-iphe3rni author = Joshi, Amit title = In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple’s Disease date = 2020-05-18 pages = extension = .txt mime = text/plain words = 3216 sentences = 189 flesch = 49 summary = This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. Nowadays epitope based vaccines provide better options in search of good treatment strategy for such type of harmful and rare malady, even if the individuals are genetically predisposed as in case of classical Whipple's disease (Trotta et al. Immune Epitope Database (IEDB) analysis Resource tool of population coverage was used to predict population coverage of the putative epitopes that are exhibiting interaction to HLA alleles and based on MHC-II restriction data (Bui et al. PatchDock tool was deployed for interaction between selected structures of epitopes and HLA DRB1 proteins. Still no one has used vaccine based treatments for Whipple's disease, as it is thought to be rare and possess reduced genome but considered one of the harmful pathogen of human ( Raoult et al. cache = ./cache/cord-326554-iphe3rni.txt txt = ./txt/cord-326554-iphe3rni.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-299279-v0vznri2 author = Røder, Gustav title = Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501 date = 2008-05-17 pages = extension = .txt mime = text/plain words = 2815 sentences = 178 flesch = 68 summary = The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making it available for interactions with a potential T-cell receptor. The overall structure of the present HLA-B*1501 peptide-binding groove is similar to the previously two determined HLA-B*1501 structures (Røder et al., 2006) and to other MHC-I molecules (see Fig. 1 ). The pGln2 peptide residue is located in the B pocket in the same orientation as the pGlu2 in the previously described HLA-B*1501-LEKARGSTY structure (Røder et al., 2006) . The pGlu4 peptide residue points away from the peptide-binding groove and the side chain does not interact with any HLA-B*1501 residues. The conformation observed does not interact with any HLA-B*1501 residues, but makes a hydrogen bond to two water molecules (HOH67 and HOH348) present between the peptide and the floor of the peptide-binding groove, thereby forming water-mediated contacts with the HLA-B*1501 protein. cache = ./cache/cord-299279-v0vznri2.txt txt = ./txt/cord-299279-v0vznri2.txt === reduce.pl bib === id = cord-312865-nno2yjae author = Sylvester‐Hvid, C. title = SARS CTL vaccine candidates; HLA supertype‐, genome‐wide scanning and biochemical validation date = 2004-04-23 pages = extension = .txt mime = text/plain words = 2118 sentences = 114 flesch = 45 summary = One would therefore expect that an effective vaccine should induce mucosal immunity such as that effected by secretory immunoglobulin A (IgA), which specifically prevents an infectious agent from penetrating the mucosal epithelium, and by cytotoxic T lymphocytes (CTLs), which specifically eradicate infected cells (5) . Human CTLs are specific for peptides presented in the context of human leukocyte antigen (HLA) molecules [generically known as ''major histocompatibility complex (MHC) molecules'']. Thus, 13 of the 15 peptides predicted to be good binders to A*0301 were found to bind to another member of the A3 supertype, HLA-A*1101. Similarly, nine of the 15 peptides predicted to be good binders to A*1101 were found to bind to HLA-A*0301 (Table 1) Once all nine supertypes have been tested, we would project to have found well over 100 different vaccine candidates. Immunogenicity of a human immunodeficiency virus (HIV) polytope vaccine containing multiple HLA A2 HIV CD8(þ) cytotoxic T-cell epitopes cache = ./cache/cord-312865-nno2yjae.txt txt = ./txt/cord-312865-nno2yjae.txt === reduce.pl bib === === reduce.pl bib === id = cord-306308-zjq6cscm author = de Moura, Ronald Rodrigues title = Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date = 2020-08-05 pages = extension = .txt mime = text/plain words = 2514 sentences = 175 flesch = 54 summary = Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. cache = ./cache/cord-306308-zjq6cscm.txt txt = ./txt/cord-306308-zjq6cscm.txt === reduce.pl bib === id = cord-343262-zopxdw1d author = Srinivasan, Raghuraman C. title = Effects of Cryogenic Storage on Human Amnion Epithelial Cells date = 2020-07-15 pages = extension = .txt mime = text/plain words = 5436 sentences = 283 flesch = 42 summary = In this study, hAEC were isolated from full-term human placenta from 14 different donors, cryopreserved using a protocol and reagents commonly adopted for epithelial cell preservation. In anticipation that the transplant product used in any future clinical trial will be previously cryopreserved cells, the current study was undertaken to determine if there are any significant differences between the populations initially isolated from the amnion membranes, and the cells recovered following the cryopreservation procedure. The presence of CD45, a receptor linked to protein tyrosine phosphatase present in cells of the hematopoietic lineage, was detected in 9/12 of hAEC preparations immediately after isolation at an average level of 1.2% ± 1.4% cells, but greatly reduced after cryopreservation and washing steps, where only four preparations still contained an extremely low number of CD45 positive cells (0.3% ± 0.4%; p = 0.0146) ( Figure 2D ). The presence of HLA-G on hAEC after isolation was confirmed using a specific antibody, and HLA-G Amnion epithelial cells have been reported to express characteristic immunomodulatory molecules, such as HLA class Ib [21, 22] . cache = ./cache/cord-343262-zopxdw1d.txt txt = ./txt/cord-343262-zopxdw1d.txt === reduce.pl bib === id = cord-334603-yt2pmxi3 author = de Sousa, Eric title = Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date = 2020-07-18 pages = extension = .txt mime = text/plain words = 1791 sentences = 101 flesch = 41 summary = title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave's disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. cache = ./cache/cord-334603-yt2pmxi3.txt txt = ./txt/cord-334603-yt2pmxi3.txt === reduce.pl bib === id = cord-347714-vxxhglx7 author = Abitogun, Folagbade title = COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date = 2020-10-14 pages = extension = .txt mime = text/plain words = 3707 sentences = 191 flesch = 44 summary = (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach cache = ./cache/cord-347714-vxxhglx7.txt txt = ./txt/cord-347714-vxxhglx7.txt === reduce.pl bib === id = cord-348283-7xorq5ce author = Naz, Anam title = Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date = 2020-07-10 pages = extension = .txt mime = text/plain words = 8183 sentences = 482 flesch = 56 summary = The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Designed vaccines were then tested with different epitopes, including Truncated Ov-ASP-1 Protein (residues 10-153) and Beta defensin (45 residues long), and constructs having higher antigenicity and that are predicted to produce high antibody titers were added with the multi epitope vaccine construct to the enhance immune response (30) . For the interaction analysis of vaccine 3 and BCR (CD79), the HADDOCK server clustered 140 probable structures into 13 different clusters, which represented a total of 70% of the water-refined models. cache = ./cache/cord-348283-7xorq5ce.txt txt = ./txt/cord-348283-7xorq5ce.txt === reduce.pl bib === id = cord-330615-h8sktgo6 author = Jabri, ‡ § Bana title = Selective expansion of intraepithelial lymphocytes expressing the HLA-E–specific natural killer receptor CD94 in celiac disease date = 2000-05-31 pages = extension = .txt mime = text/plain words = 7980 sentences = 417 flesch = 51 summary = Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. In preliminary immunohistochemical studies of intestinal frozen tissue sections, the pattern of staining of IELs with anti-CD56, -Pen5, -p46, -p58, and -CD94 antibodies was compared in 4 adult patients with active celiac disease and in 4 normal controls. Cytolytic T lymphocytes displaying natural killer (NK)-like activity: expression of NK-related functional receptors for HLA class I molecules (p58 and CD94) and inhibitory effect on the TCR-mediated target cell lysis or lymphokine production cache = ./cache/cord-330615-h8sktgo6.txt txt = ./txt/cord-330615-h8sktgo6.txt === reduce.pl bib === === reduce.pl bib === id = cord-342942-1s32o9m8 author = Stamatakis, George title = Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date = 2020-06-22 pages = extension = .txt mime = text/plain words = 4074 sentences = 209 flesch = 47 summary = Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. cache = ./cache/cord-342942-1s32o9m8.txt txt = ./txt/cord-342942-1s32o9m8.txt === reduce.pl bib === id = cord-355374-e8k72955 author = Clemens, E. Bridie title = Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine date = 2018-03-26 pages = extension = .txt mime = text/plain words = 14155 sentences = 614 flesch = 38 summary = Influenza virus-specific CD8 + Trm in human lung tissue also maintain diverse TCR profiles-a feature important for effective T cell function and protection against the generation of viral-escape mutants [128] . HLA-I allele expression is an important predictor of cross-reactive influenza-specific CD8 + T cell immunity, with a recent study identifying five alleles (A*02:01, A*03:01, B*57:01, B*18:01, and B*08:01) capable of eliciting robust CD8 + T cell responses against immunogenic NP and M1 peptides that are conserved across all human influenza A virus, including the novel avian-derived H7N9 virus [18] . Thus, upon infection with H7N9, individuals with these HLA alleles will need time to activate and amplify new primary CD8 + T cell responses to distinct H7N9 peptide variants rather than recalling T cell responses generated against seasonal influenza viruses, potentially resulting in longer time to recovery and greater risk of severe disease compared to individuals with pre-existing cross-protective CD8 + T cell memory. cache = ./cache/cord-355374-e8k72955.txt txt = ./txt/cord-355374-e8k72955.txt === reduce.pl bib === id = cord-346957-bmajkabp author = Lv, Yanbo title = Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date = 2009-12-03 pages = extension = .txt mime = text/plain words = 4933 sentences = 261 flesch = 57 summary = RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. To investigate the capacity of candidate peptides to mobilize a human CTL repertoire, HLA-A2 + PBLs from ten HLA-A2 + donors were stimulated in vitro by DCs loaded with Alignment of the putative amino acid sequences of S proteins from eighteen SARS-CoV strains A dot among the individual sequences denoted nucleotides that are the same as the consensus. Furthermore, SARS-CoV/S-derived peptides Sp6, Sp7 and Sp8 could not only induce the increased S protein specific IFN-γ secreting T cell frequency but also the enhanced cytolytic capacity of these CTLs. To further address whether the immunogenic candidate peptide is naturally processed and presented, HLA-A2.1/ K b transgenic mice were immunized with S/pVAX1 plasmid containing a full-length cDNA encoding the SARS-CoV/S protein. cache = ./cache/cord-346957-bmajkabp.txt txt = ./txt/cord-346957-bmajkabp.txt === reduce.pl bib === id = cord-346032-188gnf8j author = Cheung, Ying-Kit title = Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date = 2007-08-10 pages = extension = .txt mime = text/plain words = 4754 sentences = 228 flesch = 53 summary = title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. The results of the T-cell stimulation assay demonstrated that the novel N-protein peptide revealed in the present study is able to trigger specific cytotoxic T-cell response in human PBMCs. The four most immunogenic peptides (N220, N223, N227 and N317) selected in the T2-cell binding assay and the human T-cell stimulation assay were further tested for their potency in triggering immune response against the SARS N-protein expressing cells in an animal model. A peptide sequence useful for inducing the cytotoxic T-cell response should be presented as endogenous peptide epitope through proteasome digestion and have a high binding affinity towards the human MHC class I molecules. cache = ./cache/cord-346032-188gnf8j.txt txt = ./txt/cord-346032-188gnf8j.txt === reduce.pl bib === id = cord-329669-z3t7plvh author = Poulton, Kay title = A role for human leucocyte antigens in the susceptibility to SARS‐Cov‐2 infection observed in transplant patients date = 2020-07-05 pages = extension = .txt mime = text/plain words = 2270 sentences = 124 flesch = 50 summary = HLA frequencies observed were compared against two control populations: first, against published frequencies in a UK deceased donor population (n = 10,000) representing the target population of the virus, and second, using a cohort of individuals from the combined transplant waiting lists of both centres (n = 308), representing a comparator group of unaffected individuals of the same demographic. This study investigated HLA profiles of patients admitted with PCR-confirmed SARS-CoV-2 infection to identify any potential HLA bias which might indicate an impaired capacity to mount an effective immune response to the infection. All patients included in the study had previously been HLA typed to support transplantation and required hospital treatment for COVID-19 disease, indicating that their symptoms were severe, requiring clinical support or intervention. Statistical analysis was performed using MedCalc v19.3 (MedCalc Software) to compare frequencies of allele group carriage between the patient and control populations using Fisher's exact test. cache = ./cache/cord-329669-z3t7plvh.txt txt = ./txt/cord-329669-z3t7plvh.txt === reduce.pl bib === id = cord-326983-h6gdck2u author = Ferretti, Andrew P. title = Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date = 2020-10-20 pages = extension = .txt mime = text/plain words = 5634 sentences = 274 flesch = 56 summary = We focused on memory cells to identify epitopes that are functionally recognized during the course of SARS-CoV-2 infection and included patients with a J o u r n a l P r e -p r o o f range of symptoms to determine if any obvious associations are observed between CD8 + T cell response and disease severity. To determine the global landscape of CD8 + T cell recognition in an unbiased fashion, we built upon a genome-wide screening technology, termed T-Scan (Kula et al., 2019) , that enabled us to simultaneously screen all the memory CD8 + T cells in a patient, one HLA allele at a time, against every possible viral epitope in SARS-CoV-2, as well as the four seasonal coronaviruses that cause the common cold ( Figure 1A ). cache = ./cache/cord-326983-h6gdck2u.txt txt = ./txt/cord-326983-h6gdck2u.txt === reduce.pl bib === id = cord-320490-3jmo35jc author = Ismail, Saba title = Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date = 2020-04-12 pages = extension = .txt mime = text/plain words = 6688 sentences = 412 flesch = 52 summary = In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . cache = ./cache/cord-320490-3jmo35jc.txt txt = ./txt/cord-320490-3jmo35jc.txt === reduce.pl bib === id = cord-333670-qv1orlv5 author = Mutti, Luciano title = Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date = 2020-05-28 pages = extension = .txt mime = text/plain words = 2500 sentences = 123 flesch = 40 summary = In Italy, the possibility of performing autopsies or post-mortem diagnostic studies on suspect, probable, or confirmed COVID-19 cases has been intensively debated (5, 6) ; however, postmortem pathological analysis of COVID-19 patients in China has shown findings consistent with Acute Respiratory Distress Syndrome (ARDS) (7-9) (Figure 1 ). Consistently, recent results indicate that a systemic immune dysregulation that triggers auto-sustaining inflammatory lung damage, causing fatal respiratory-failure and consequent multiorgan-failure, is the main virus-related-death cause in patients who develop SARS-CoV-2 (10). Overall, understanding the role of pro-inflammatory cytokines certainly unravels a new battleground against the lethal clinical effect of CODIV-19 infection; this, along with the identification of a high-risk autoimmune profile, including the genotyping of Class I and II HLA, which have a key role in shaping the anti-viral immune response and Th1/Th2 lymphocyte subset response (Figure 1) , and immune-profiling, could also help to prevent these dangerous evolutions of the disease (29) . cache = ./cache/cord-333670-qv1orlv5.txt txt = ./txt/cord-333670-qv1orlv5.txt === reduce.pl bib === id = cord-344364-vu389d88 author = Wang, Wei title = Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1754 sentences = 115 flesch = 61 summary = Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing (NGS). Frequencies of the HLA-C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID-19 patients than in the control population, with uncorrected statistical significance. The allele distributions of HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1 loci were compared between COVID-19 patients and control individuals. HLA-C*07:29, C*08:01G (including C*08:01 and C*08:22), B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 frequencies were higher in COVID-19 patients than in the control population, with uncorrected statistical significance (P < .05). 8 In the present study, HLA-C*07:29 was found in one COVID-19 patient, but in no individuals in the control group. 15, 16 In the present study, these SARS-susceptibility alleles were not found to occur at a significantly different frequency in COVID-19 patients after P-value correction. cache = ./cache/cord-344364-vu389d88.txt txt = ./txt/cord-344364-vu389d88.txt === reduce.pl bib === id = cord-346445-hgqohdct author = Toyoshima, Yujiro title = SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date = 2020-07-22 pages = extension = .txt mime = text/plain words = 3553 sentences = 187 flesch = 53 summary = Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. In this study, we comprehensively analyzed 12,343 SARS-CoV-2 genome sequences isolated from patients/ individuals in six geographic areas, including Asia, North America, South America, Europe, Oceania, and Africa, and investigated their correlations to the fatality rates in 28 different countries. In this study, we investigated the SARS-CoV-2 virus mutations and found that the frequencies of S protein 614G variant and its highly linked variant, ORF1ab 4715L, were significantly correlated with fatality rates in the 28 countries and 17 states of the United States. In summary, we comprehensively investigated SARS-CoV-2 genome mutations, BCG-vaccination status, and HLA genotypes in the 28 different countries and identified significant associations of some virus genome variants with the fatality rates. cache = ./cache/cord-346445-hgqohdct.txt txt = ./txt/cord-346445-hgqohdct.txt === reduce.pl bib === id = cord-333966-st6gyozv author = Taherkhani, Reza title = Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date = 2015-03-17 pages = extension = .txt mime = text/plain words = 5199 sentences = 255 flesch = 51 summary = The aim of this study was to design a high density multiepitope protein, which can be a promising multiepitope vaccine candidate against Hepatitis E virus (HEV). Therefore, the present study was undertaken to design a high density multiepitope protein compromising four HTL epitopes with high-affinity binding to the HLA molecules using the in silico analysis, and to evaluate the immunological properties of this protein in vitro. In brief, approximately 1  10 5 cells/well of PBMCs of each sample in RPMI 1640 and 10% FCS were added to four wells of round-bottom 96-well plates in total volume of 180 ml/well, stimulated with 20 ml/well of truncated ORF2 protein (10 mg/ml), high density multiepitope (10 mg/ml) and Phytohemagglutinin (PHA) (5 mg/ml) (Sigma-Aldrich) separately, and incubated at 37˚C for 4 days. IFN-g ELISPOT responses to high density multiepitope protein and truncated ORF2 protein were found significantly higher in HEV-recovered individuals than control group (P < 0.001). cache = ./cache/cord-333966-st6gyozv.txt txt = ./txt/cord-333966-st6gyozv.txt === reduce.pl bib === id = cord-344933-k23kzqxl author = Flahou, Charlotte title = Innovations dans la culture de plaquettes à partir de cellules souches pluripotentes induites* date = 2020-09-28 pages = extension = .txt mime = text/plain words = 5589 sentences = 537 flesch = 60 summary = Dans cette revue, nous souhaitons apporter une vue d'ensemble de la production in vitro de plaquettes à partir de cellules iPS, et de son possible potentiel transformatif, d'importance capitale dans le domaine de la transfusion des produits sanguins. De plus, contrairement aux réponses allo-immunitaires (par exemple la maladie du greffon contre l'hôte), qui sont évitables par la déplétion des leucocytes ou l'irradiation des produits dérivés du sang, être les cas réfractaires aux transfusions de plaquettes nonconcordantes pour les Antigènes des Leucocytes Humains (HLA) et des Antigènes Plaquettaires Humains (HPA) n'ont pour l'instant pas de solution [6] . La production de plaquettes ex-vivo à partir de cellules souches pluripotentes induites (iPSC) est une solution pour résoudre les problèmes liés à la transfusion allogénique. D'une part, il est possible de produire des plaquettes dérivées d'iPSC produite à partir des cellules du patient, qui dans ce cas n'éliciteront pas de réponse immunitaire. Ex vivo megakaryocyte expansion and platelet production from human cord blood stem cells cache = ./cache/cord-344933-k23kzqxl.txt txt = ./txt/cord-344933-k23kzqxl.txt === reduce.pl bib === id = cord-333391-6l0cpvgr author = Bortolotti, Daria title = SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5689 sentences = 309 flesch = 57 summary = title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway When we stained the cells with anticlassical HLA class I molecules (HLA-A, HLA-B, HLA-C) antibody, we recognized a significant decrease in their membrane expression when lung epithelial cells were transfected with SP1 protein (p < 0.001; Student t test) ( Figure 3D ,E). To be sure that the increase in HLA-E expression in lung epithelial cells transfected with SP1 protein is controlled by GATA3 transcription factor, we treated the cells with pyrrothiogatain. When NK cells were co-cultured with SP1-transfected Beas-2B cells, we observed an increase in the protein (p < 0.001; Student t test) ( Figure 6A ,B) and mRNA (p < 0.01; Student t test) ( Figure 6C ) expression of the inhibitory receptor NKG2A/CD94. On the contrary, lung cells, which express HLA-E molecules in the presence of SARS-CoV spike 1 protein, are able to inhibit IFN-gamma secretion and NK cell activation. cache = ./cache/cord-333391-6l0cpvgr.txt txt = ./txt/cord-333391-6l0cpvgr.txt === reduce.pl bib === id = cord-344691-vmc0rrrk author = Srinivasan, K.N. title = Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens date = 2004-08-04 pages = extension = .txt mime = text/plain words = 3654 sentences = 184 flesch = 52 summary = Results: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. A number of predictive methods for MHC classes I and II binding peptides are available, including those based on binding motifs (Rammensee et al., 1995) , quantitative matrices (Parker et al., 1994) , artificial neural networks (ANNs) , hidden Markov models (HMMs) (Mamitsuka, 1998) , multivariate statistical approaches (Guan et al., 2003) , support vector machines (Zhao et al., 2003) and decision trees (Savoie et al., 1999) . In our prediction of promiscuous class I T-cell epitopes, we made predictions of T-cell epitope hot spots in nucleocapsid protein of the severe acute respiratory syndrome coronavirus (SARS-CoV). MULTIPRED, a computational system developed for human leukocyte antigen (HLA) classes I-A2 and I-A3 binding, predicts individual 9-mer T-cell epitopes and also promiscuous class I regions as immunological hot spots, based on HMM and ANN models (Zhang et al., 2003) . cache = ./cache/cord-344691-vmc0rrrk.txt txt = ./txt/cord-344691-vmc0rrrk.txt === reduce.pl bib === id = cord-347647-m9vk9m7h author = Eapen, Mary title = Hematopoietic cell transplantation with cryopreserved grafts for severe aplastic anemia date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2800 sentences = 176 flesch = 55 summary = We recorded higher 1-year rates of graft failure (HR 2.26, 95% CI 1.17 – 4.35, p=0.01) and of 1-year overall mortality (HR 3.13, 95% CI 1.60 – 6.11, p=0.0008) after transplantation of cryopreserved compared to non-cryopreserved grafts with adjustment for sex, performance score, comorbidity, cytomegalovirus serostatus, and ABO blood group match). To study the effect of cryopreserved compared to non-cryopreserved grafts, (matched-pairs) marginal Cox regression models were built and adjusted for sex, cytomegalovirus serostatus, performance score, comorbidity score, and donor-recipient ABO blood group match. The current analysis was undertaken to examine whether there are differences in survival or other transplant outcomes after transplantation of cryopreserved bone marrow or peripheral blood for severe aplastic anemia. 21 An analysis of non-cryopreserved bone marrow cellular subsets for unrelated donor transplantations failed to show an effect of graft composition on hematopoietic recovery or survival although that report included only 7 patients with aplastic anemia. cache = ./cache/cord-347647-m9vk9m7h.txt txt = ./txt/cord-347647-m9vk9m7h.txt === reduce.pl bib === id = cord-352150-ey9kc7zj author = Degauque, Nicolas title = Cross-Reactivity of TCR Repertoire: Current Concepts, Challenges, and Implication for Allotransplantation date = 2016-03-24 pages = extension = .txt mime = text/plain words = 7844 sentences = 367 flesch = 46 summary = Keywords: TCR repertoire, transplantation, cross-reactivity, alloreactivity, TCR, MHC, T cell UNDeRSTANDiNG THe CROSS-ReACTiviTY Shaping the T Lymphocyte Receptor Repertoire Through evolution, numerous processes have been selected to generate a diverse repertoire of TCRαβ able to protect mammalian from pathogenic insults (Figure 1) . Despite the high diversity of the TCR repertoire, a high degree of cross-reactivity has been reported that could be explained by the "natural" ability of TCR to interact with MHC molecules (MHC focus model) as well as the interaction of TCR to a limited number of amino acids of the peptide bound to the MHC peptide groove. Cross-reactivity can be defined by the ability of a given TCR to interact with more than one pMHC complex with different presented peptides or MHC molecules. Before presenting the experimental approach aiming to quantify the number of peptides recognized by a single TCR, we would like to present clear evidences of the cross-reactivity involving memory T cells without previous antigen encounter. cache = ./cache/cord-352150-ey9kc7zj.txt txt = ./txt/cord-352150-ey9kc7zj.txt === reduce.pl bib === id = cord-353877-wzndpcq3 author = Albagi, Sahar Obi Abd title = A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date = 2020-05-20 pages = extension = .txt mime = text/plain words = 3747 sentences = 264 flesch = 58 summary = Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. Consistent with global efforts, this study aims to predict potential COVID-19 Peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. The molecular docking results showed that the Spike peptide FTISVTTEI has the lowest docking energy score with the MHC I HLA-B1503 allele, hence it is predicted to have the highest binding affinity. Regarding the interaction with the MHC II molecule, the Spike peptide EVFNATRFASVYAWN showed the lowest docking energy score with the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1*06:02, and HLA-DRB1, hence it is predicted to have the highest binding affinity to the three alleles. cache = ./cache/cord-353877-wzndpcq3.txt txt = ./txt/cord-353877-wzndpcq3.txt === reduce.pl bib === id = cord-349451-vak2p7ac author = Rocha, Francisco Airton Castro title = Microbes, Helminths and Rheumatic Diseases date = 2020-05-07 pages = extension = .txt mime = text/plain words = 7465 sentences = 355 flesch = 33 summary = Studies suggest the billions of germs that compose the gut microbiota influence one's innate and adaptive immune responses at the intestinal level, but these microorganisms may also impact rheumatic diseases. Evidence indicates that changes in the gut microbiome alter the pathogenesis of immune-mediated diseases such as rheumatoid arthritis and ankylosing spondylitis but also of other disorders like atherosclerosis and osteoarthritis. The pathogenesis of Chlamydia-related arthritis can be considered distinct from that associated with enteric bacteria since it involves metabolically active organisms residing long-term within monocytic cells in synovial tissues, after resolution of the primary genital infection and migration of the cells to the joint, a process that is known as persistence [56, [61] [62] [63] . Studies indicate inflammatory bowel disease, or, at least, intestinal inflammation, is more prevalent in SpA patients (AS or others) and some genes associated with AS are also associated with IBD [83, 85] , including genes related to gut physiology and immunology. cache = ./cache/cord-349451-vak2p7ac.txt txt = ./txt/cord-349451-vak2p7ac.txt === reduce.pl bib === id = cord-313474-1gux1gsi author = nan title = Physicians Abstracts date = 2015-03-20 pages = extension = .txt mime = text/plain words = 51420 sentences = 2890 flesch = 57 summary = Materials (or patients) and methods: We performed a multicenter, multinational, open-label, randomized study comparing anti-lymphocyte globulin (ATG-Fresenius s ) 10 mg/kg on day -3, -2 and -1 with no ATG in patients with AML (n ¼ 110) or ALL (n ¼ 45) in 1 st complete remission (CR; n ¼ 139) or 2 nd CR (n ¼ 16) who received peripheral blood stem cells from their HLA-identical sibling after standard TBI (12 Gy)/Ccclophosphamide (120 mg/kg) or busulfan (16 mg/ kg)/Cy (120 mg/kg) based myeloablative conditioning regimen. After allo-HSCT, detection of positive WT1 was followed by immunomodulatory therapeutic interventions according to the time from transplant, the presence of active graft-versus-host disease (GvHD) and the general clinical conditions: tapering and/or discontinuation of immunosuppressive drugs (IS), donor lymphocytes infusions (DLI), administration of hypomethylating agents. Introduction: Haploidentical hematopoietic stem cell transplantation(Haplo-HSCT)is feasible option for patients with acute leukemia(AL)at high risk of relapse who do not have HLA-matched related or unrelated donors. cache = ./cache/cord-313474-1gux1gsi.txt txt = ./txt/cord-313474-1gux1gsi.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 === id = cord-010092-uftc8inx author = nan title = Abstract of 29th Regional Congress of the ISBT date = 2019-06-07 pages = extension = .txt mime = text/plain words = 233304 sentences = 13171 flesch = 54 summary = Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. cache = ./cache/cord-010092-uftc8inx.txt txt = ./txt/cord-010092-uftc8inx.txt === reduce.pl bib === id = cord-005460-ezrn8cva author = nan title = Physicians – Poster Session date = 2017-07-28 pages = extension = .txt mime = text/plain words = 287105 sentences = 15681 flesch = 56 summary = Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . cache = ./cache/cord-005460-ezrn8cva.txt txt = ./txt/cord-005460-ezrn8cva.txt === reduce.pl bib === id = cord-010119-t1x9gknd author = nan title = Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date = 2017-09-04 pages = extension = .txt mime = text/plain words = 230193 sentences = 13234 flesch = 55 summary = Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). cache = ./cache/cord-010119-t1x9gknd.txt txt = ./txt/cord-010119-t1x9gknd.txt === reduce.pl bib === id = cord-005453-4057qib7 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date = 2019-07-03 pages = extension = .txt mime = text/plain words = 275771 sentences = 16876 flesch = 56 summary = To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. cache = ./cache/cord-005453-4057qib7.txt txt = ./txt/cord-005453-4057qib7.txt ===== Reducing email addresses cord-007301-5m269nzi cord-103837-iuvigqdx cord-288916-i8ukefp8 cord-275608-joyan7ij cord-289711-4ab3d00h cord-287709-y247lan1 cord-284944-hcgfe9wv cord-330615-h8sktgo6 cord-349451-vak2p7ac Creating transaction Updating adr table ===== Reducing keywords cord-000488-x5ardo5j cord-003270-vu9b5a14 cord-002724-gtv9syzi cord-001247-pxzbirqd cord-003472-ml4pbewf cord-000224-2lz03oqb cord-002463-qhtj1pef cord-002704-cpa2sl50 cord-002686-zzongyfa cord-004435-l66ost6q cord-003143-n6b0r92e cord-006273-xcw0kxjg cord-007664-c5snhymz cord-004395-erqmbi2b cord-007851-v6h1yro7 cord-007626-n51v4ior cord-009323-sfxpchma cord-007301-5m269nzi cord-007719-3ypv9k9p cord-005487-vac061r8 cord-009836-7o6htufh cord-010222-5oxie0zc cord-016413-lvb79oxo cord-005478-5iu38pr6 cord-005480-yg7salqt cord-009571-mygj2nd4 cord-013093-aa4cf44u cord-016235-2lhrkmrv cord-015389-vwgai4k9 cord-013894-1bgvj62a cord-010088-s9tfvtao cord-017702-v46ye328 cord-018595-x3tleomb cord-017184-1ewi3dka cord-022474-xxy83c6u cord-017856-4fccnygg cord-017629-fuv157f1 cord-018714-i291z2ju cord-016998-6n662amh cord-014976-546zaoxn cord-255069-9xueqdri cord-103662-a4ok5wqc cord-034402-64xz1j9i cord-031937-qhlatg84 cord-104099-xhi0oxtr cord-103837-iuvigqdx cord-023675-sidvbzqy cord-028275-szb45jm2 cord-126015-zc7u3g34 cord-023055-ntbvmssh cord-254190-bxfne94u cord-261392-dw56h8vj cord-265277-ymvrserl cord-023143-fcno330z cord-266902-wuty839o cord-273906-s7l0yxc0 cord-275677-hbv49e01 cord-280172-6o1gqe8v cord-280979-0vaarrji cord-275608-joyan7ij cord-286858-zbhtl2yn cord-284944-hcgfe9wv cord-280641-zqdrzyzl cord-288916-i8ukefp8 cord-281141-ouno4jpl cord-298169-2133gahl cord-023364-ut56gczm cord-287709-y247lan1 cord-266204-ipa017wz cord-288496-7rrh2gg6 cord-289711-4ab3d00h cord-288146-xqxznv1r cord-271032-imc6woht cord-286968-ud1uerc8 cord-023354-f2ciho6o cord-023346-8sqbqjm1 cord-304635-z5vmhopa cord-009567-osstpum6 cord-326554-iphe3rni cord-296007-1gsgd22t cord-310252-0cdqhrcw cord-316330-55nd3pwe cord-329825-e9mepqvn cord-299279-v0vznri2 cord-294212-nlekz39f cord-334603-yt2pmxi3 cord-343262-zopxdw1d cord-330615-h8sktgo6 cord-348283-7xorq5ce cord-306308-zjq6cscm cord-319993-er3sm4u8 cord-342942-1s32o9m8 cord-355374-e8k72955 cord-346957-bmajkabp cord-346032-188gnf8j cord-320490-3jmo35jc cord-329669-z3t7plvh cord-326983-h6gdck2u cord-333670-qv1orlv5 cord-346445-hgqohdct cord-344364-vu389d88 cord-333966-st6gyozv cord-344933-k23kzqxl cord-333391-6l0cpvgr cord-344691-vmc0rrrk cord-347647-m9vk9m7h cord-347714-vxxhglx7 cord-312865-nno2yjae cord-022888-dnsdg04n cord-313474-1gux1gsi cord-352150-ey9kc7zj cord-349451-vak2p7ac cord-010092-uftc8inx cord-353877-wzndpcq3 cord-010119-t1x9gknd cord-005453-4057qib7 cord-005460-ezrn8cva Creating transaction Updating wrd table ===== Reducing urls cord-000488-x5ardo5j cord-003270-vu9b5a14 cord-001247-pxzbirqd cord-002463-qhtj1pef cord-002686-zzongyfa cord-004395-erqmbi2b cord-002704-cpa2sl50 cord-003143-n6b0r92e cord-006273-xcw0kxjg cord-007851-v6h1yro7 cord-007301-5m269nzi cord-007719-3ypv9k9p cord-005480-yg7salqt cord-005478-5iu38pr6 cord-013093-aa4cf44u cord-013894-1bgvj62a cord-018595-x3tleomb cord-017702-v46ye328 cord-010088-s9tfvtao cord-017629-fuv157f1 cord-103662-a4ok5wqc cord-104099-xhi0oxtr cord-031937-qhlatg84 cord-103837-iuvigqdx cord-028275-szb45jm2 cord-273906-s7l0yxc0 cord-266204-ipa017wz cord-280172-6o1gqe8v cord-275608-joyan7ij cord-271032-imc6woht cord-280979-0vaarrji cord-281141-ouno4jpl cord-023364-ut56gczm cord-286968-ud1uerc8 cord-289711-4ab3d00h cord-287709-y247lan1 cord-023354-f2ciho6o cord-288496-7rrh2gg6 cord-023346-8sqbqjm1 cord-304635-z5vmhopa cord-296007-1gsgd22t cord-316330-55nd3pwe cord-329825-e9mepqvn cord-288146-xqxznv1r cord-294212-nlekz39f cord-334603-yt2pmxi3 cord-348283-7xorq5ce cord-346957-bmajkabp cord-329669-z3t7plvh cord-320490-3jmo35jc cord-346032-188gnf8j cord-344364-vu389d88 cord-346445-hgqohdct cord-333966-st6gyozv cord-333391-6l0cpvgr cord-349451-vak2p7ac cord-022888-dnsdg04n cord-010119-t1x9gknd cord-005453-4057qib7 cord-010092-uftc8inx cord-005460-ezrn8cva Creating transaction Updating url table ===== Reducing named entities cord-000488-x5ardo5j cord-002724-gtv9syzi cord-003270-vu9b5a14 cord-000224-2lz03oqb cord-003472-ml4pbewf cord-001247-pxzbirqd cord-002463-qhtj1pef cord-002686-zzongyfa cord-004395-erqmbi2b cord-003143-n6b0r92e cord-002704-cpa2sl50 cord-007664-c5snhymz cord-004435-l66ost6q cord-006273-xcw0kxjg cord-007626-n51v4ior 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score: 49 nouns: patients; cells; blood; cell; results; donors; donor; disease; study; group; transfusion; treatment; transplantation; days; time; risk; years; data; patient; response; analysis; methods; day; expression; transplant; infection; months; stem; age; platelet; cases; number; antigen; survival; protein; system; antibodies; mice; samples; therapy; levels; virus; epitopes; graft; plasma; pts; antibody; peptides; use; peptide verbs: used; shown; including; received; compared; associated; increasing; performed; followed; based; found; identified; developed; induce; observed; reducing; reported; treated; evaluated; relates; binding; suggest; determines; tested; detected; presenting; provide; expressed; analyze; occurring; requiring; undergo; give; demonstrate; remains; obtaining; indicate; resulting; improve; predict; leads; collected; matched; aim; considered; caused; assess; derived; contains; decreased adjectives: high; anti; specific; immune; clinical; median; positive; acute; human; significant; non; different; severe; higher; first; low; negative; viral; chronic; red; single; new; autologous; important; peripheral; post; overall; normal; major; lower; pre; hematopoietic; similar; unrelated; primary; total; available; effective; early; common; multiple; whole; free; present; molecular; second; several; potential; possible; long adverbs: also; respectively; however; well; significantly; therefore; previously; still; even; highly; prior; often; especially; recently; currently; furthermore; clinically; now; mainly; statistically; moreover; less; finally; particularly; usually; potentially; alone; later; least; together; retrospectively; frequently; approximately; successfully; fully; interestingly; relatively; generally; subsequently; first; directly; already; rapidly; almost; commonly; additionally; rather; strongly; specifically; yet pronouns: we; our; it; their; i; its; they; them; he; she; her; us; his; one; itself; you; your; themselves; my; himself; him; ourselves; haec; me; p210bcr; netmhcpan4.0; itma; s; r348; p24ag; mg; igg4; ifitm3; yourself; u; ours; interleukin-15; imm+; igmcic; esat-6; e2f2-/-mice; crx-527; c5-derived; beta-2-m; anti-(self; +; ≥65; ≥10×; αat; ya proper nouns: HLA; T; HSCT; GVHD; MHC; CD8; CD4; II; SARS; C; CMV; mg; RBC; SCT; B; HIV; OS; CD34; AML; A; IFN; HCV; NK; GvHD; TCR; PCR; G; Blood; CTL; CoV-2; University; Fig; CI; ATG; S; Background; D; ABO; ASCT; HBV; M; I; Hospital; IV; Table; Hb; kg; RNA; Study; CR keywords: hla; cell; sars; mhc; patient; cd8; cd4; hiv; cmv; pcr; result; hsct; hcv; gvhd; donor; dna; cd34; aml; transplantation; transfusion; study; ric; hospital; hbv; group; blood; university; response; protein; platelet; nrm; nat; method; ifn; disease; day; ctl; abo; test; tcr; table; system; rna; rhd; rbc; hct; epitope; dat; atg; asct one topic; one dimension: patients file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214623/ titles(s): Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities three topics; one dimension: patients; cells; hla file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163517/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121448/ titles(s): Physicians – Poster Session | Poster Sessions | Nierentransplantation five topics; three dimensions: blood transfusion patients; patients cell cells; cells cell mice; hla cell epitopes; patients cells rejection file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166418/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110254/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120462/ titles(s): EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS | Physicians – Poster Session | Immunogenicity | Modeling the adaptive immune system: predictions and simulations | Lung Type: cord title: keyword-hla-cord date: 2021-05-25 time: 00:10 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:hla ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-347714-vxxhglx7 author: Abitogun, Folagbade title: COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date: 2020-10-14 words: 3707.0 sentences: 191.0 pages: flesch: 44.0 cache: ./cache/cord-347714-vxxhglx7.txt txt: ./txt/cord-347714-vxxhglx7.txt summary: (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach abstract: The COVID19 pandemic has resulted in 1,092,342 deaths as of 14th October 2020, indicating the urgent need for a vaccine. This study highlights novel protein sequences generated by shot gun sequencing protocols that could serve as potential antigens in the development of novel subunit vaccines and through a stringent inclusion criterion, we characterized these protein sequences and predicted their 3D structures. We found distinctly antigenic sequences from the SARS-CoV-2 that have led to identification of 4 proteins that demonstrate an advantageous binding with Human leukocyte antigen-1 molecules. Results show how previously unexplored proteins may serve as better candidates for subunit vaccine development due to their high stability and immunogenicity, reinforce by their HLA-1 binding propensities and low global binding energies. This study thus takes a unique approach towards furthering the development of vaccines by employing multiple consensus strategies involved in immuno-informatics technique. url: https://doi.org/10.1101/2020.10.14.339689 doi: 10.1101/2020.10.14.339689 id: cord-353877-wzndpcq3 author: Albagi, Sahar Obi Abd title: A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date: 2020-05-20 words: 3747.0 sentences: 264.0 pages: flesch: 58.0 cache: ./cache/cord-353877-wzndpcq3.txt txt: ./txt/cord-353877-wzndpcq3.txt summary: Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. Consistent with global efforts, this study aims to predict potential COVID-19 Peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. The molecular docking results showed that the Spike peptide FTISVTTEI has the lowest docking energy score with the MHC I HLA-B1503 allele, hence it is predicted to have the highest binding affinity. Regarding the interaction with the MHC II molecule, the Spike peptide EVFNATRFASVYAWN showed the lowest docking energy score with the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1*06:02, and HLA-DRB1, hence it is predicted to have the highest binding affinity to the three alleles. abstract: Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. To achieve this goal, several Immune Epitope Database (IEDB) tools, molecular docking, and safety prediction servers were used. According to the results, The Spike peptide peptides SQCVNLTTRTQLPPAYTNSFTRGVY is predicted to have the highest binding affinity to the B-Cells. The Spike peptide FTISVTTEI has the highest binding affinity to the MHC I HLA-B1503 allele. The Nucleocapsid peptides KTFPPTEPK and RWYFYYLGTGPEAGL have the highest binding affinity to the MHC I HLA-A0202 allele and the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1- *06:02, HLA-DRB1, respectively. Furthermore, those peptides were predicted as non-toxic and non-allergen. Therefore, the combination of those peptides is predicted to stimulate better immunological responses with respectable safety. url: https://doi.org/10.1101/2020.05.20.106351 doi: 10.1101/2020.05.20.106351 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: 10041.0 sentences: 299.0 pages: flesch: 34.0 cache: ./cache/cord-009836-7o6htufh.txt txt: ./txt/cord-009836-7o6htufh.txt summary: Epitope mapping performed using the Gpl 60 sequence of the patient''s autologous early HIV-1 population indicated that this response was in fact extremely focused on a single epitope encompassing Gpl60 amino acids 30-38(9), recognized in association with HLA-B44, The frequency of epitope-specific CTL was extremely high: at the earhest timepoint available for study, which may have been shghtly after the peak of the primary immune response, 1 in 1 7 peripheral blood mononuclear cells (EBMCs) were found to score as virus-specific CTL precursors by limiting dilution analysis, a technique which has recently been shown to greatly underestimate the total numher of epitope-specific T cells (55, 56) , As shown in Fig, 1 , viral variants bearing mutations in the epitopic sequence which conferred escape from recognition by epitope-specific CTL rapidly appeared in this patienc, and then increased in frequency until 164/1998 they had cotnpieteiy repiaced the transmitted virai strain. 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-333391-6l0cpvgr author: Bortolotti, Daria title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date: 2020-08-26 words: 5689.0 sentences: 309.0 pages: flesch: 57.0 cache: ./cache/cord-333391-6l0cpvgr.txt txt: ./txt/cord-333391-6l0cpvgr.txt summary: title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway When we stained the cells with anticlassical HLA class I molecules (HLA-A, HLA-B, HLA-C) antibody, we recognized a significant decrease in their membrane expression when lung epithelial cells were transfected with SP1 protein (p < 0.001; Student t test) ( Figure 3D ,E). To be sure that the increase in HLA-E expression in lung epithelial cells transfected with SP1 protein is controlled by GATA3 transcription factor, we treated the cells with pyrrothiogatain. When NK cells were co-cultured with SP1-transfected Beas-2B cells, we observed an increase in the protein (p < 0.001; Student t test) ( Figure 6A ,B) and mRNA (p < 0.01; Student t test) ( Figure 6C ) expression of the inhibitory receptor NKG2A/CD94. On the contrary, lung cells, which express HLA-E molecules in the presence of SARS-CoV spike 1 protein, are able to inhibit IFN-gamma secretion and NK cell activation. abstract: Natural killer cells are important in the control of viral infections. However, the role of NK cells during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has previously not been identified. Peripheral blood NK cells from SARS-CoV and SARS-CoV-2 naïve subjects were evaluated for their activation, degranulation, and interferon-gamma expression in the presence of SARS-CoV and SARS-CoV-2 spike proteins. K562 and lung epithelial cells were transfected with spike proteins and co-cultured with NK cells. The analysis was performed by flow cytometry and immune fluorescence. SARS-CoV and SARS-CoV-2 spike proteins did not alter NK cell activation in a K562 in vitro model. On the contrary, SARS-CoV-2 spike 1 protein (SP1) intracellular expression by lung epithelial cells resulted in NK cell-reduced degranulation. Further experiments revealed a concomitant induction of HLA-E expression on the surface of lung epithelial cells and the recognition of an SP1-derived HLA-E-binding peptide. Simultaneously, there was increased modulation of the inhibitory receptor NKG2A/CD94 on NK cells when SP1 was expressed in lung epithelial cells. We ruled out the GATA3 transcription factor as being responsible for HLA-E increased levels and HLA-E/NKG2A interaction as implicated in NK cell exhaustion. We show for the first time that NK cells are affected by SP1 expression in lung epithelial cells via HLA-E/NKG2A interaction. The resulting NK cells’ exhaustion might contribute to immunopathogenesis in SARS-CoV-2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/32859121/ doi: 10.3390/cells9091975 id: cord-004395-erqmbi2b author: Bugembe, Daniel Lule title: Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort date: 2020-02-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Identifying immunogens that induce HIV-1-specific immune responses is a lengthy process that can benefit from computational methods, which predict T-cell epitopes for various HLA types. METHODS: We tested the performance of the NetMHCpan4.0 computational neural network in re-identifying 93 T-cell epitopes that had been previously independently mapped using the whole proteome IFN-γ ELISPOT assays in 6 HLA class I typed Ugandan individuals infected with HIV-1 subtypes A1 and D. To provide a benchmark we compared the predictions for NetMHCpan4.0 to MHCflurry1.2.0 and NetCTL1.2. RESULTS: NetMHCpan4.0 performed best correctly predicting 88 of the 93 experimentally mapped epitopes for a set length of 9-mer and matched HLA class I alleles. Receiver Operator Characteristic (ROC) analysis gave an area under the curve (AUC) of 0.928. Setting NetMHCpan4.0 to predict 11-14mer length did not improve the prediction (37–79 of 93 peptides) with an inverse correlation between the number of predictions and length set. Late time point peptides were significantly stronger binders than early peptides (Wilcoxon signed rank test: p = 0.0000005). MHCflurry1.2.0 similarly predicted all but 2 of the peptides that NetMHCpan4.0 predicted and NetCTL1.2 predicted only 14 of the 93 experimental peptides. CONCLUSION: NetMHCpan4.0 class I epitope predictions covered 95% of the epitope responses identified in six HIV-1 infected individuals, and would have reduced the number of experimental confirmatory tests by > 80%. Algorithmic epitope prediction in conjunction with HLA allele frequency information can cost-effectively assist immunogen design through minimizing the experimental effort. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036183/ doi: 10.1186/s12879-020-4876-4 id: cord-013093-aa4cf44u author: Cassotta, Antonino title: Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin date: 2020-07-09 words: 10936.0 sentences: 470.0 pages: flesch: 50.0 cache: ./cache/cord-013093-aa4cf44u.txt txt: ./txt/cord-013093-aa4cf44u.txt summary: The detailed and unbiased characterization of HA-reactive memory and naive CD4 + T cell repertoires, paralleled by a deep analysis of the naturally presented repertoire of MHC-II-binding HA peptides by mass spectrometry (MS)-based immunopeptidomics, allowed us to shed new light on the factors governing CD4 + T cell clonal selection and immunodominance to influenza HA in humans. We then selected a large number of H1-HA-specific T cell clones derived from naive or memory T cells of donor HD1 and determined their functional avidity by measuring the proliferative response to autologous monocytes pulsed with different concentrations of the H1-HA peptides or H1-HA protein, which need processing for presentation on MHC-II molecules. abstract: The importance of CD4(+) T helper (Th) cells is well appreciated in view of their essential role in the elicitation of antibody and cytotoxic T cell responses. However, the mechanisms that determine the selection of immunodominant epitopes within complex protein antigens remain elusive. Here, we used ex vivo stimulation of memory T cells and screening of naive and memory T cell libraries, combined with T cell cloning and TCR sequencing, to dissect the human naive and memory CD4(+) T cell repertoire against the influenza pandemic H1 hemagglutinin (H1-HA). We found that naive CD4(+) T cells have a broad repertoire, being able to recognize naturally processed as well as cryptic peptides spanning the whole H1-HA sequence. In contrast, memory Th cells were primarily directed against just a few immunodominant peptides that were readily detected by mass spectrometry–based MHC-II peptidomics and predicted by structural accessibility analysis. Collectively, these findings reveal the presence of a broad repertoire of naive T cells specific for cryptic H1-HA peptides and demonstrate that antigen processing represents a major constraint determining immunodominance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7537397/ doi: 10.1084/jem.20200206 id: cord-346032-188gnf8j author: Cheung, Ying-Kit title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date: 2007-08-10 words: 4754.0 sentences: 228.0 pages: flesch: 53.0 cache: ./cache/cord-346032-188gnf8j.txt txt: ./txt/cord-346032-188gnf8j.txt summary: title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. The results of the T-cell stimulation assay demonstrated that the novel N-protein peptide revealed in the present study is able to trigger specific cytotoxic T-cell response in human PBMCs. The four most immunogenic peptides (N220, N223, N227 and N317) selected in the T2-cell binding assay and the human T-cell stimulation assay were further tested for their potency in triggering immune response against the SARS N-protein expressing cells in an animal model. A peptide sequence useful for inducing the cytotoxic T-cell response should be presented as endogenous peptide epitope through proteasome digestion and have a high binding affinity towards the human MHC class I molecules. abstract: The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. In this study, we have identified a novel HLA-A*0201 restricted epitope, N220 (LALLLLDRL), of the SARS-CoV N-protein through bioinformatics analysis. The N-protein peptide N220 shows a high binding affinity towards human MHC class I in T2-cells, and is capable of activating cytotoxic T-cells in human peripheral blood mononuclear cells (PBMCs). The application of using the N220 peptide sequence with a single-chain-trimer (SCT) approach to produce a potential DNA vaccine candidate was investigated in HLA-A2.1K(b) transgenic mice. Cytotoxicity assay clearly showed that the T-cells obtained from the vaccinated animals were able to kill the N-protein expressing cells with a cytotoxicity level of 86% in an effector cells/target cells ratio of 81:1 one week after the last vaccination, which is significantly higher than other N-protein peptides previously described. The novel immunogenic N-protein peptide revealed in the present study provides valuable information for therapeutic SARS vaccine design. url: https://api.elsevier.com/content/article/pii/S0264410X07005932 doi: 10.1016/j.vaccine.2007.05.025 id: cord-355374-e8k72955 author: Clemens, E. Bridie title: Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine date: 2018-03-26 words: 14155.0 sentences: 614.0 pages: flesch: 38.0 cache: ./cache/cord-355374-e8k72955.txt txt: ./txt/cord-355374-e8k72955.txt summary: Influenza virus-specific CD8 + Trm in human lung tissue also maintain diverse TCR profiles-a feature important for effective T cell function and protection against the generation of viral-escape mutants [128] . HLA-I allele expression is an important predictor of cross-reactive influenza-specific CD8 + T cell immunity, with a recent study identifying five alleles (A*02:01, A*03:01, B*57:01, B*18:01, and B*08:01) capable of eliciting robust CD8 + T cell responses against immunogenic NP and M1 peptides that are conserved across all human influenza A virus, including the novel avian-derived H7N9 virus [18] . Thus, upon infection with H7N9, individuals with these HLA alleles will need time to activate and amplify new primary CD8 + T cell responses to distinct H7N9 peptide variants rather than recalling T cell responses generated against seasonal influenza viruses, potentially resulting in longer time to recovery and greater risk of severe disease compared to individuals with pre-existing cross-protective CD8 + T cell memory. abstract: Next-generation vaccines that utilize T cells could potentially overcome the limitations of current influenza vaccines that rely on antibodies to provide narrow subtype-specific protection and are prone to antigenic mismatch with circulating strains. Evidence from animal models shows that T cells can provide heterosubtypic protection and are crucial for immune control of influenza virus infections. This has provided hope for the design of a universal vaccine able to prime against diverse influenza virus strains and subtypes. However, multiple hurdles exist for the realisation of a universal T cell vaccine. Overall primary concerns are: extrapolating human clinical studies, seeding durable effective T cell resident memory (Trm), population human leucocyte antigen (HLA) coverage, and the potential for T cell-mediated immune escape. Further comprehensive human clinical data is needed during natural infection to validate the protective role T cells play during infection in the absence of antibodies. Furthermore, fundamental questions still exist regarding the site, longevity and duration, quantity, and phenotype of T cells needed for optimal protection. Standardised experimental methods, and eventually simplified commercial assays, to assess peripheral influenza-specific T cell responses are needed for larger-scale clinical studies of T cells as a correlate of protection against influenza infection. The design and implementation of a T cell-inducing vaccine will require a consensus on the level of protection acceptable in the community, which may not provide sterilizing immunity but could protect the individual from severe disease, reduce the length of infection, and potentially reduce transmission in the community. Therefore, increasing the standard of care potentially offered by T cell vaccines should be considered in the context of pandemic preparedness and zoonotic infections, and in combination with improved antibody vaccine targeting methods. Current pandemic vaccine preparedness measures and ongoing clinical trials under-utilise T cell-inducing vaccines, reflecting the myriad questions that remain about how, when, where, and which T cells are needed to fight influenza virus infection. This review aims to bring together basic fundamentals of T cell biology with human clinical data, which need to be considered for the implementation of a universal vaccine against influenza that harnesses the power of T cells. url: https://www.ncbi.nlm.nih.gov/pubmed/29587436/ doi: 10.3390/vaccines6020018 id: cord-018714-i291z2ju author: Criado, Paulo Ricardo title: Adverse Drug Reactions date: 2016-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Adverse events and adverse drug reactions are common in clinical practice. Side effects range from the common to the rare and may be confused with other mucocutaneous manifestations resulting from several medications to treat infections, other medical conditions, and in the clinical setting of oncologic treatment. The objective of this chapter to review current data on adverse drug reactions, here classified as (i) severe adverse drug reactions, (ii) uncomplicated cutaneous adverse drug reactions, and (iii) adverse drug reactions caused by chemotherapy drugs, particularly those cases whereby the dermatologist is requested to issue a report and asked to comment on the safety and viability of readministration of a specific drug. We describe aspects associated with these events, presenting a detailed analysis of each of them. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123670/ doi: 10.1007/978-3-319-33919-1_26 id: cord-265277-ymvrserl author: Crooke, Stephen N. title: Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date: 2020-05-14 words: 4620.0 sentences: 249.0 pages: flesch: 52.0 cache: ./cache/cord-265277-ymvrserl.txt txt: ./txt/cord-265277-ymvrserl.txt summary: A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. abstract: A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spread of SARS-CoV-2; yet, rational vaccine design efforts are currently hampered by the lack of knowledge regarding viral epitopes targeted during an immune response, and the need for more in-depth knowledge on betacoronavirus immunology. To that end, we developed a computational workflow using a series of open-source algorithms and webtools to analyze the proteome of SARS-CoV-2 and identify putative T cell and B cell epitopes. Using increasingly stringent selection criteria to select peptides with significant HLA promiscuity and predicted antigenicity, we identified 41 potential T cell epitopes (5 HLA class I, 36 HLA class II) and 6 potential B cell epitopes, respectively. Docking analysis and binding predictions demonstrated enrichment for peptide binding to HLA-B (class I) and HLA-DRB1 (class II) molecules. Overlays of predicted B cell epitopes with the structure of the viral spike (S) glycoprotein revealed that 4 of 6 epitopes were located in the receptor-binding domain of the S protein. To our knowledge, this is the first study to comprehensively analyze all 10 (structural, non-structural and accessory) proteins from SARS-CoV-2 using predictive algorithms to identify potential targets for vaccine development. Significance Statement The novel coronavirus SARS-CoV-2 recently emerged from China, rapidly spreading and ushering in a global pandemic. Despite intensive research efforts, our knowledge of SARS-CoV-2 immunology and the proteins targeted by the immune response remains relatively limited, making it difficult to rationally design candidate vaccines. We employed a suite of bioinformatic tools, computational algorithms, and structural modeling to comprehensively analyze the entire SARS-CoV-2 proteome for potential T cell and B cell epitopes. Utilizing a set of stringent selection criteria to filter peptide epitopes, we identified 41 T cell epitopes (5 HLA class I, 36 HLA class II) and 6 B cell epitopes that could serve as promising targets for peptide-based vaccine development against this emerging global pathogen. url: https://doi.org/10.1101/2020.05.14.093757 doi: 10.1101/2020.05.14.093757 id: cord-002463-qhtj1pef author: Dash, Raju title: In silico-based vaccine design against Ebola virus glycoprotein date: 2017-03-21 words: 5830.0 sentences: 358.0 pages: flesch: 50.0 cache: ./cache/cord-002463-qhtj1pef.txt txt: ./txt/cord-002463-qhtj1pef.txt summary: Top scored eiptope subjected to 100 ns MD simulation **RMSF **RMSD **Hydrogen bond occupency analysis Secquence, having highest vaxijen score Prediction of B cell epitope, using-**T cell epitope prediction by proteasomal C terminal cleavage, TAP transport efficiency and MHC class 1 binding **Epitopes with IC50 value less than 50 for their binding to MHC class 1 molecule from IEDB analysis along with binding to highest number of alleles in both analyses were chosen **Epitope conservancy analysis **Population coverage analysis **Kolaskar and Tongaonkar antigenicity scale 48 **Emini surface accessibility prediction 47 **Karplus and Schulz flexibility prediction 49 **Bepipred linear epitope prediction 50 **Chou and Fasman beta turn prediction 52 Vaxijen analysis with a threshold score of >0. We also validated each epitope by molecular docking simulation and MM-GBSA/MM-PBSA studies with HLA-A*32:15 protein, as it was found common in the results from MHC-I binding interaction analysis. abstract: Ebola virus (EBOV) is one of the lethal viruses, causing more than 24 epidemic outbreaks to date. Despite having available molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet for the management and avoidance of EBOV infections in humans. Disclosing this, the present study described an epitope-based peptide vaccine against EBOV, using a combination of B-cell and T-cell epitope predictions, followed by molecular docking and molecular dynamics simulation approach. Here, protein sequences of all glycoproteins of EBOV were collected and examined via in silico methods to determine the most immunogenic protein. From the identified antigenic protein, the peptide region ranging from 186 to 220 and the sequence HKEGAFFLY from the positions of 154–162 were considered the most potential B-cell and T-cell epitopes, correspondingly. Moreover, this peptide (HKEGAFFLY) interacted with HLA-A*32:15 with the highest binding energy and stability, and also a good conservancy of 83.85% with maximum population coverage. The results imply that the designed epitopes could manifest vigorous enduring defensive immunity against EBOV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367765/ doi: 10.2147/aabc.s115859 id: cord-017629-fuv157f1 author: De Groot, Anne S. title: Epitope-Based Immunome-Derived Vaccines: A Strategy for Improved Design and Safety date: 2008-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vaccine science has extended beyond genomics to proteomics and has come to also encompass ‘immunomics,’ the study of the universe of pathogen-derived or neoplasm-derived peptides that interface with B and T cells of the host immune system. It has been theorized that effective vaccines can be developed using the minimum essential subset of T cell and B cell epitopes that comprise the ‘immunome.’ Researchers are therefore using bioinformatics sequence analysis tools, epitope-mapping tools, microarrays, and high-throughput immunology assays to discover the minimal essential components of the immunome. When these minimal components, or epitopes, are packaged with adjuvants in an appropriate delivery vehicle, the complete package comprises an epitope-based immunome-derived vaccine. Such vaccines may have a significant advantage over conventional vaccines, as the careful selection of the components may diminish undesired side effects such as have been observed with whole pathogen and protein subunit vaccines. This chapter will review the pre-clinical and anticipated clinical development of computer-driven vaccine design and the validation of epitope-based immunome-derived vaccines in animal models; it will also include an overview of heterologous immunity and other emerging issues that will need to be addressed by vaccines of all types in the future. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122239/ doi: 10.1007/978-0-387-79208-8_3 id: cord-352150-ey9kc7zj author: Degauque, Nicolas title: Cross-Reactivity of TCR Repertoire: Current Concepts, Challenges, and Implication for Allotransplantation date: 2016-03-24 words: 7844.0 sentences: 367.0 pages: flesch: 46.0 cache: ./cache/cord-352150-ey9kc7zj.txt txt: ./txt/cord-352150-ey9kc7zj.txt summary: Keywords: TCR repertoire, transplantation, cross-reactivity, alloreactivity, TCR, MHC, T cell UNDeRSTANDiNG THe CROSS-ReACTiviTY Shaping the T Lymphocyte Receptor Repertoire Through evolution, numerous processes have been selected to generate a diverse repertoire of TCRαβ able to protect mammalian from pathogenic insults (Figure 1) . Despite the high diversity of the TCR repertoire, a high degree of cross-reactivity has been reported that could be explained by the "natural" ability of TCR to interact with MHC molecules (MHC focus model) as well as the interaction of TCR to a limited number of amino acids of the peptide bound to the MHC peptide groove. Cross-reactivity can be defined by the ability of a given TCR to interact with more than one pMHC complex with different presented peptides or MHC molecules. Before presenting the experimental approach aiming to quantify the number of peptides recognized by a single TCR, we would like to present clear evidences of the cross-reactivity involving memory T cells without previous antigen encounter. abstract: Being able to track donor reactive T cells during the course of organ transplantation is a key to improve the graft survival, to prevent graft dysfunction, and to adapt the immunosuppressive regimen. The attempts of transplant immunologists have been for long hampered by the large size of the alloreactive T cell repertoire. Understanding how self-TCR can interact with allogeneic MHC is a key to critically appraise the different assays available to analyze the TCR Vβ repertoire usage. In this report, we will review conceptually and experimentally the process of cross-reactivity. We will then highlight what can be learned from allotransplantation, a situation of artificial cross-reactivity. Finally, the low- and high-resolution techniques to characterize the TCR Vβ repertoire usage in transplantation will be critically discussed. url: https://doi.org/10.3389/fimmu.2016.00089 doi: 10.3389/fimmu.2016.00089 id: cord-007626-n51v4ior author: Dhib-Jalbut, Suhayl title: Adult human glial cells can present target antigens to HLA-restricted cytotoxic T-cells date: 2002-11-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: T-lymphocyte recognition of antigen either on antigen-presenting cells (APC) necessary for the generation of an immune response or on target cells during the effector phase of a cellular immune response requires expression of HLA molecules. Although immune mechanisms operate in many disease processes of the central nervous system (CNS), cells of the CNS generally express low levels of HLA molecules. In this study, the potential for upregulation of HLA molecules on adult human glial cells was examined. Moreover, the functional implication of this upregulation was assessed by the capacity of glial cells to process and present target antigens to HLA class I-restricted influenza-specific and class II-restrict myelin basic protein (MBP)-specific CTL lines. Glial cells cultured from adult human surgical brain specimens or cells from established glioblastoma multiforme cell lines were studied. Lysis by antigen-specific CTLs was dependent on treatment of the target cell with interferon-γ. The lysis was HLA restricted and antigen specific. The results indicate that adult human glial cells can process and present antigen to HLA-restricted CTLs but require the upregulation of HLA molecules. These findings have implications for infectious and autoimmune diseases of the CNS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119691/ doi: 10.1016/0165-5728(90)90163-h id: cord-018595-x3tleomb author: Dodiuk-Gad, Roni P. title: Adverse Medication Reactions date: 2017-04-25 words: 16304.0 sentences: 910.0 pages: flesch: 39.0 cache: ./cache/cord-018595-x3tleomb.txt txt: ./txt/cord-018595-x3tleomb.txt summary: 2. Delayed-type drug hypersensitivity: Delayed-type drug hypersensitivity reactions usually take several days to weeks following drug exposure, with variable clinical presentations that may include Maculopapular Eruption (MPE), Fixed Drug Eruption (FDE), Acute Generalized Exanthematous Pustulosis (AGEP), Stevens-Johnson Syndrome (SJS), Toxic Epidermal Necrolysis (TEN) and Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS). Examples of strong associations of HLA alleles with specific drug-induced hypersensitivity reactions include abacavir, nevirapine, carbamazepine, and allopurinol (Table 25. [61] , who reported the weak associations of HLA-A29, B12, and MPE maculopapular drug eruption, DRESS drug reaction with eosinophilia and systemic symptoms, SJS/TEN Stevens-Johnson syndrome/toxic epidermal necrolysis DR7 in sulfonamide-related TEN, and HLA-A2, B12 in oxicam-related TEN in Europeans [61] . Drug specific cytotoxic T-cells in the skin lesions of a patient with toxic epidermal necrolysis abstract: Cutaneous adverse drug reactions (ADRs) are among the most frequent adverse reactions in patients receiving drug therapy. They have a broad spectrum of clinical manifestations, are caused by various drugs, and result from different pathophysiological mechanisms. Hence, their diagnosis and management is challenging. Severe cutaneous ADRs comprise a group of diseases with major morbidity and mortality, reaching 30 % mortality rate in cases of Toxic Epidermal Necrolysis. This chapter covers the terminology, epidemiology, pathogenesis and classification of cutaneous ADR, describes the severe cutaneous ADRs and the clinical and laboratory approach to the patient with cutaneous ADR and presents the translation of laboratory-based discoveries on the genetic predisposition and pathogenesis of cutaneous ADRs to clinical management guidelines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123512/ doi: 10.1007/978-3-319-29785-9_25 id: cord-347647-m9vk9m7h author: Eapen, Mary title: Hematopoietic cell transplantation with cryopreserved grafts for severe aplastic anemia date: 2020-05-08 words: 2800.0 sentences: 176.0 pages: flesch: 55.0 cache: ./cache/cord-347647-m9vk9m7h.txt txt: ./txt/cord-347647-m9vk9m7h.txt summary: We recorded higher 1-year rates of graft failure (HR 2.26, 95% CI 1.17 – 4.35, p=0.01) and of 1-year overall mortality (HR 3.13, 95% CI 1.60 – 6.11, p=0.0008) after transplantation of cryopreserved compared to non-cryopreserved grafts with adjustment for sex, performance score, comorbidity, cytomegalovirus serostatus, and ABO blood group match). To study the effect of cryopreserved compared to non-cryopreserved grafts, (matched-pairs) marginal Cox regression models were built and adjusted for sex, cytomegalovirus serostatus, performance score, comorbidity score, and donor-recipient ABO blood group match. The current analysis was undertaken to examine whether there are differences in survival or other transplant outcomes after transplantation of cryopreserved bone marrow or peripheral blood for severe aplastic anemia. 21 An analysis of non-cryopreserved bone marrow cellular subsets for unrelated donor transplantations failed to show an effect of graft composition on hematopoietic recovery or survival although that report included only 7 patients with aplastic anemia. abstract: The COVID-19 pandemic and the ensuing barriers to the collection and transport of donor cells, it is often necessary to collect and cryopreserve grafts before initiation of transplant conditioning. The effect on transplant outcomes in non-malignant disease is unknown. This analysis examined the effect of cryopreservation of related and unrelated donor grafts for transplantation for severe aplastic anemia in the US during 2013-2019. Included are 52 recipients of cryopreserved grafts who were matched for age, donor type, and graft type to 194 recipients who received non-cryopreserved grafts. Marginal Cox regression models were built to study the effect of cryopreservation and other risk factors associated with outcomes. We recorded higher 1-year rates of graft failure (HR 2.26, 95% CI 1.17 – 4.35, p=0.01) and of 1-year overall mortality (HR 3.13, 95% CI 1.60 – 6.11, p=0.0008) after transplantation of cryopreserved compared to non-cryopreserved grafts with adjustment for sex, performance score, comorbidity, cytomegalovirus serostatus, and ABO blood group match). Acute and chronic GVHD did not differ between groups. Adjusted probabilities of 1-year survival were 73% (95% 60 – 84) and 91% (95% CI 86 – 94) with cryopreserved and non-cryopreserved grafts, respectively. These data support the use of non-cryopreserved grafts, when possible, for severe aplastic anemia. url: https://api.elsevier.com/content/article/pii/S1083879120302822 doi: 10.1016/j.bbmt.2020.04.027 id: cord-016413-lvb79oxo author: Efthimiou, Petros title: Adult-Onset Still’s Disease date: 2018-07-14 words: 6126.0 sentences: 315.0 pages: flesch: 40.0 cache: ./cache/cord-016413-lvb79oxo.txt txt: ./txt/cord-016413-lvb79oxo.txt summary: Adult-onset Still''s disease (AOSD) is a rare systemic, autoinflammatory disorder that often presents in adolescence and early adulthood with fever, rash, and polyarthritis. Mutation of perforin and the MUNC13-4 genes have been seen in patients with macrophage activation syndrome (MAS), a known severe, life-threatening complication of AOSD [3] . Patients who have the chronic articular disease pattern can present with joint erosions making the differential diagnosis from RA problematic, especially in the absence of systemic signs and symptoms. Interleukin-1 receptor antagonist (anakinra) treatment in patients with systemic-onset juvenile idiopathic arthritis or adult onset Still disease: preliminary experience in France Effectiveness of first-line treatment with recombinant interleukin-1 receptor antagonist in steroid-naive patients with new-onset systemic juvenile idiopathic arthritis: results of a prospective cohort study Clinical manifestations of adult-onset Still''s disease presenting with erosive arthritis: association with low levels of ferritin and Interleukin-18 abstract: Adult-onset Still’s disease (AOSD) is a rare systemic, autoinflammatory disorder that often presents in adolescence and early adulthood with fever, rash, and polyarthritis. There are significant genetic and clinical similarities with systemic juvenile idiopathic arthritis (sJIA) with a different chronological disease onset. The disease can have many protean characteristics leading to delays in diagnosis. Treatment includes corticosteroids; traditional immunomodulators, such as methotrexate; and targeted biologic treatments that include IL-1 and IL-6 inhibitors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120682/ doi: 10.1007/978-3-319-96929-9_19 id: cord-002704-cpa2sl50 author: El Bissati, Kamal title: Protein nanovaccine confers robust immunity against Toxoplasma date: 2017-09-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We designed and produced a self-assembling protein nanoparticle. This self-assembling protein nanoparticle contains five CD8(+) HLA-A03-11 supertypes-restricted epitopes from antigens expressed during Toxoplasma gondii’s lifecycle, the universal CD4(+) T cell epitope PADRE, and flagellin as a scaffold and TLR5 agonist. These CD8(+) T cell epitopes were separated by N/KAAA spacers and optimized for proteasomal cleavage. Self-assembling protein nanoparticle adjuvanted with TLR4 ligand-emulsion GLA-SE were evaluated for their efficacy in inducing IFN-γ responses and protection of HLA-A*1101 transgenic mice against T. gondii. Immunization, using self-assembling protein nanoparticle-GLA-SE, activated CD8(+) T cells to produce IFN-γ. Self-assembling protein nanoparticle-GLA-SE also protected HLA-A*1101 transgenic mice against subsequent challenge with Type II parasites. Hence, combining CD8(+) T cell-eliciting peptides and PADRE into a multi-epitope protein that forms a nanoparticle, administered with GLA-SE, leads to efficient presentation by major histocompatibility complex Class I and II molecules. Furthermore, these results suggest that activation of TLR4 and TLR5 could be useful for development of vaccines that elicit T cells to prevent toxoplasmosis in humans. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627305/ doi: 10.1038/s41541-017-0024-6 id: cord-280641-zqdrzyzl author: Fernández Fabrellas, Estrella title: Epidemiología de la sarcoidosis date: 2007-02-28 words: 6760.0 sentences: 547.0 pages: flesch: 51.0 cache: ./cache/cord-280641-zqdrzyzl.txt txt: ./txt/cord-280641-zqdrzyzl.txt summary: Además de investigar la posible etiología de la enfermedad, este estudio examina el situación psicosocial 15 y el curso clínico de 736 pacientes incluidos en los 6 primeros meses desde el diagnóstico histológico de sarcoidosis, y los compara con otros tantos controles pareados por edad, sexo y raza, con un seguimiento de los primeros 215 casos durante los 2 años siguientes a la inclusión 16 . Tanto la piel como los pulmones -órganos más comúnmente afectados-están siempre en contacto con estos antígenos; los estudios sobre la inmunopatogenia de la sarcoidosis apoyan que la enfermedad es el resultado de una superrespuesta inmunitaria y que hay un gran número de potenciales antígenos ambientales que pueden inducir la sensibilización y la consiguiente respuesta mediada por células responsable del desarrollo de granulomas 43 . abstract: La sarcoidosis es una enfermedad multisistémica que afecta frecuentemente al pulmón. Su incidencia y prevalencia han sido ampliamente estudiadas, pero la falta de estandarización del diagnóstico, los diferentes métodos de detección de casos y la escasa sensibilidad y especificidad de las pruebas diagnósticas explican los datos discordantes. El pronóstico es generalmente favorable. Gran parte de las personas afectadas no manifestarán nunca síntomas y muchas tienen remisión espontánea. El curso es crónico en el 10-30% de los casos, con un deterioro permanente de la función pulmonar. La enfermedad es el resultado de la acción de un agente externo que desencadena la respuesta inmunitaria característica en individuos genéticamente susceptibles. Se han implicado factores ambientales, ocupacionales y genéticos, pero las investigaciones están todavía en los inicios. Estudios de casos y controles, así como los avances en biología molecular, ayudarán a definir los factores de susceptibilidad genética y a entender los distintos fenotipos de la sarcoidosis. Sarcoidosis is a multisystemic disease in which lung involvement is common. Its incidence and prevalence have been extensively studied, but with contradictory results because of the lack of standard diagnostic criteria, variations in the methods for detecting cases, and the low sensitivity and specificity of diagnostic tests. Prognosis is generally favorable. Many of those affected remain asymptomatic and remission often occurs spontaneously, although between 10% and 30% of the patients have chronic disease and permanent deterioration in lung function. Sarcoidosis is caused by an external agent that triggers a characteristic immune response in genetically susceptible individuals. Environmental, occupational, and genetic factors have all been implicated, but research is still in the early stages. Case-control studies, as well as advances in molecular biology, will help to identify genetic susceptibility factors and to understand the different phenotypes of sarcoidosis. url: https://api.elsevier.com/content/article/pii/S0300289607710347 doi: 10.1157/13098420 id: cord-326983-h6gdck2u author: Ferretti, Andrew P. title: Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date: 2020-10-20 words: 5634.0 sentences: 274.0 pages: flesch: 56.0 cache: ./cache/cord-326983-h6gdck2u.txt txt: ./txt/cord-326983-h6gdck2u.txt summary: We focused on memory cells to identify epitopes that are functionally recognized during the course of SARS-CoV-2 infection and included patients with a J o u r n a l P r e -p r o o f range of symptoms to determine if any obvious associations are observed between CD8 + T cell response and disease severity. To determine the global landscape of CD8 + T cell recognition in an unbiased fashion, we built upon a genome-wide screening technology, termed T-Scan (Kula et al., 2019) , that enabled us to simultaneously screen all the memory CD8 + T cells in a patient, one HLA allele at a time, against every possible viral epitope in SARS-CoV-2, as well as the four seasonal coronaviruses that cause the common cold ( Figure 1A ). abstract: Developing effective strategies to prevent or treat COVID-19 requires understanding the natural immune response to SARS-CoV-2. We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8+ T cells of COVID-19 patients. In total, we identified 3–8 epitopes for each of the six most prevalent human leukocyte antigen (HLA) types. These epitopes were broadly shared across patients and located in regions of the virus that are not subject to mutational variation. Notably, only 3 of the 29 shared epitopes were located in the spike protein, whereas most epitopes were located in ORF1ab or the nucleocapsid protein. We also found that CD8+ T cells generally do not cross-react with epitopes in the four seasonal coronaviruses that cause the common cold. Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8+ T cell immunity to SARS-CoV-2. url: https://api.elsevier.com/content/article/pii/S1074761320304477 doi: 10.1016/j.immuni.2020.10.006 id: cord-344933-k23kzqxl author: Flahou, Charlotte title: Innovations dans la culture de plaquettes à partir de cellules souches pluripotentes induites* date: 2020-09-28 words: 5589.0 sentences: 537.0 pages: flesch: 60.0 cache: ./cache/cord-344933-k23kzqxl.txt txt: ./txt/cord-344933-k23kzqxl.txt summary: Dans cette revue, nous souhaitons apporter une vue d''ensemble de la production in vitro de plaquettes à partir de cellules iPS, et de son possible potentiel transformatif, d''importance capitale dans le domaine de la transfusion des produits sanguins. De plus, contrairement aux réponses allo-immunitaires (par exemple la maladie du greffon contre l''hôte), qui sont évitables par la déplétion des leucocytes ou l''irradiation des produits dérivés du sang, être les cas réfractaires aux transfusions de plaquettes nonconcordantes pour les Antigènes des Leucocytes Humains (HLA) et des Antigènes Plaquettaires Humains (HPA) n''ont pour l''instant pas de solution [6] . La production de plaquettes ex-vivo à partir de cellules souches pluripotentes induites (iPSC) est une solution pour résoudre les problèmes liés à la transfusion allogénique. D''une part, il est possible de produire des plaquettes dérivées d''iPSC produite à partir des cellules du patient, qui dans ce cas n''éliciteront pas de réponse immunitaire. Ex vivo megakaryocyte expansion and platelet production from human cord blood stem cells abstract: La production in vitro de plaquettes offre une opportunité de résoudre les problèmes liés aux limitations d’approvisionnement et à la sécurité des dons de produits dérivés du sang. Les cellules souches pluripotentes induites – ou iPSC – sont une source idéale pour la production de cellules à des fins de thérapies régénératives. Nous avons précédemment établi avec succès une lignée mégacaryocytaire immortalisée à partir d’iPSC. Celle-ci possède une capacité de prolifération fiable. Par ailleurs, il est possible de les cryoconserver. Elle est donc une source adaptée de cellules primaires pour la production de plaquettes suivant les Bonnes Pratiques de Fabrication (BPF). Dans le même temps, la capacité améliorée des bioréacteurs à reproduire certaines conditions physiologiques, telle que la turbulence, de pair avec la découverte de molécules favorisant la thrombopoïèse, a contribué à l’accomplissement de la production de plaquettes en quantité et qualité suffisantes pour répondre aux besoins cliniques. La production de plaquettes à partir de cellules iPS s’étend aussi aux patients en état de réfraction allo-immune, par la production de plaquettes autologues ou dont on a génétiquement manipulé l’expression des Antigènes des Leucocytes Humains (HLA) et des Antigènes Plaquettaires Humain (HPA). Considérant ces avancées fondamentales, les plaquettes iPSC avec expression des HLA modifiées se présentent comme un potentiel produit de transfusion universel. Dans cette revue, nous souhaitons apporter une vue d’ensemble de la production in vitro de plaquettes à partir de cellules iPS, et de son possible potentiel transformatif, d’importance capitale dans le domaine de la transfusion des produits sanguins. Ex vivo production of human platelets have been pursued as an alternative measure to resolve limitations in the supply and safety of current platelet transfusion products. To this end, induced pluripotent stem cells (iPSCs) are considered an ideal global source, since they are not only pluripotent and self-renewing, but also are available from basically any person, have relatively few ethical issues, and are easy to manipulate. From human iPSCs, megakaryocyte (MK) lines with robust proliferation capacity have been established by the introduction of specified sets of genes. These expandable MKs are also cryopreservable and thus would be suitable as master cells for good manufacturing practice (GMP) grade production of platelets, assuring availability on demand and safety against blood-borne infections. Meanwhile, developments in bioreactors that physically mimic the in vivo environment and discovery of substances that promote thrombopoiesis have yielded competent platelets with improved efficiency. The derivation of platelets from iPSCs could further resolve transfusion-related alloimmune complications through the manufacturing of autologous products and human leukocyte antigen (HLA)-compatible platelets by manipulation of HLAs and human platelet antigens (HPAs). Considering these key advances in the field, HLA-deleted platelets could become a universal product that is manufactured at industrial level to safely fulfill almost all demands. In this review, we overview the ex vivo production of iPSC-derived platelets towards clinical applications, a production that would revolutionize the blood transfusion system. url: https://api.elsevier.com/content/article/pii/S0001407920305161 doi: 10.1016/j.banm.2020.09.040 id: cord-017702-v46ye328 author: Ganguly, Nirmal Kumar title: Pharmacogenomics and Personalized Medicine for Infectious Diseases date: 2013-06-11 words: 16564.0 sentences: 798.0 pages: flesch: 43.0 cache: ./cache/cord-017702-v46ye328.txt txt: ./txt/cord-017702-v46ye328.txt summary: Deciphering the pathogen virulence factors, host susceptibility genes, and the molecular programs involved in the pathogenesis of disease has paved the way for discovery of new molecular targets for drugs, diagnostic markers, and vaccines. The pathogen genome on one hand gives us the information about the important genes conferring disease pathogenesis as well as drug resistance, while the genome of the host on the other hand will reveal the susceptibility genes, and the further knowledge of polymorphisms in genes of the host metabolic and immune system will lead to the new vaccine strategies, drugs targets, and also their treatment outcomes. Several fi eld studies have further suggested that there is a need for calibration of isoniazid dosage as per the individual tuberculosis patient''s age, acetylator status, and disease process for an effective antimicrobial outcome of drug treatment (Jeena et al. abstract: Humans have been plagued by the scourge of invasion by pathogens leading to infectious diseases from the time in memoriam and are still the cause of morbidity and mortality among millions of individuals. Trying to understand the disease mechanisms and finding the remedial measures have been the quest of humankind. The susceptibility to disease of an individual in a given population is determined by ones genetic buildup. Response to treatment and the disease prognosis also depends upon individual’s genetic predisposition. The environmental stress induces mutations and is leading to the emergence of ever-increasing more dreaded infectious pathogens, and now we are in the era of increasing antibiotic resistance that has thrown up a challenge to find new treatment regimes. Discoveries in the science of high-throughput sequencing and array technologies have shown new hope and are bringing a revolution in human health. The information gained from sequencing of both human and pathogen genomes is a way forward in deciphering host-pathogen interactions. Deciphering the pathogen virulence factors, host susceptibility genes, and the molecular programs involved in the pathogenesis of disease has paved the way for discovery of new molecular targets for drugs, diagnostic markers, and vaccines. The genomic diversity in the human population leads to differences in host responses to drugs and vaccines and is the cause of poor response to treatment as well as adverse reactions. The study of pharmacogenomics of infectious diseases is still at an early stage of development, and many intricacies of the host-pathogen interaction are yet to be understood in full measure. However, progress has been made over the decades of research in some of the important infectious diseases revealing how the host genetic polymorphisms of drug-metabolizing enzymes and transporters affect the bioavailability of the drugs which further determine the efficacy and toxicology of the drugs used for treatment. Further, the field of structural biology and chemistry has intertwined to give rise to medical structural genomics leading the way to the discovery of new drug targets against infectious diseases. This chapter explores how the advent of “omics” technologies is making a beginning in bringing about a change in the prevention, diagnosis, and treatments of the infectious diseases and hence paving way for personalized medicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122342/ doi: 10.1007/978-81-322-1184-6_27 id: cord-280979-0vaarrji author: Gauttier, V. title: Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date: 2020-08-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which enters the body principally through the nasal and larynx mucosa and progress to the lungs through the respiratory tract. SARS-CoV-2 replicates efficiently in respiratory epithelial cells motivating the development of alternative and rapidly scalable vaccine inducing mucosal protective and long-lasting immunity. We have previously developed an immunologically optimized multi-neoepitopes-based peptide vaccine platform which has already demonstrated tolerance and efficacy in hundreds of lung cancer patients. Here, we present a multi-target CD8 T cell peptide COVID-19 vaccine design targeting several structural (S, M, N) and non-structural (NSPs) SARS-CoV-2 proteins with selected epitopes in conserved regions of the SARS-CoV-2 genome. We observed that a single subcutaneous injection of a serie of epitopes induces a robust immunogenicity in-vivo as measured by IFNγ ELIspot. Upon tetramer characterization we found that this serie of epitopes induces a strong proportion of virus-specific CD8 T cells expressing CD103, CD44, CXCR3 and CD49a, the specific phenotype of tissue-resident memory T lymphocytes (Trm). Finally, we observed broad cellular responses, as characterized by IFNγ production, upon restimulation with structural and non-structural protein-derived epitopes using blood T cells isolated from convalescent asymptomatic, moderate and severe COVID-19 patients. These data provide insights for further development of a second generation of COVID-19 vaccine focused on inducing lasting Th1-biased memory CD8 T cell sentinels protection using immunodominant epitopes naturally observed after SARS-CoV-2 infection resolution. Statement of Significance Humoral and cellular adaptive immunity are different and complementary immune defenses engaged by the body to clear viral infection. While neutralizing antibodies have the capacity to block virus binding to its entry receptor expressed on human cells, memory T lymphocytes have the capacity to eliminate infected cells and are required for viral clearance. However, viruses evolve quickly, and their antigens are prone to mutations to avoid recognition by the antibodies (phenomenon named ‘antigenic drift’). This limitation of the antibody-mediated immunity could be addressed by the T-cell mediated immunity, which is able to recognize conserved viral peptides from any viral proteins presented by virus-infected cells. Thus, by targeting several proteins and conserved regions on the genome of a virus, T-cell epitope-based vaccines are less subjected to mutations and may work effectively on different strains of the virus. We designed a multi-target T cell-based vaccine containing epitope regions optimized for CD8+ T cell stimulation that would drive long-lasting cellular immunity with high specificity, avoiding undesired effects such as antibody-dependent enhancement (ADE) and antibody-induced macrophages hyperinflammation that could be observed in subjects with severe COVID-19. Our in-vivo results showed that a single injection of selected CD8 T cell epitopes induces memory viral-specific T-cell responses with a phenotype of tissue-resident memory T cells (Trm). Trm has attracted a growing interest for developing vaccination strategies since they act as immune sentinels in barrier tissue such as the respiratory tract and the lung. Because of their localization in tissues, they are able to immediately recognize infected cells and, because of their memory phenotypes, they rapidly respond to viral infection by orchestrating local protective immune responses to eliminate pathogens. Lastly, such multiepitope-based vaccination platform uses robust and well-validated synthetic peptide production technologies that can be rapidly manufactured in a distributed manner. url: https://doi.org/10.1101/2020.08.14.240093 doi: 10.1101/2020.08.14.240093 id: cord-329825-e9mepqvn author: Giamarellos-Bourboulis, Evangelos J. title: Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date: 2020-04-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Proper management of COVID-19 mandates better understanding of disease pathogenesis. The sudden clinical deterioration 7–8 days after initial symptom onset suggests that severe respiratory failure (SRF) in COVID-19 is driven by a unique pattern of immune dysfunction. We studied immune responses of 54 COVID-19 patients, 28 of whom had SRF. All patients with SRF displayed either macrophage activation syndrome (MAS) or very low human leukocyte antigen D related (HLA-DR) expression accompanied by profound depletion of CD4 lymphocytes, CD19 lymphocytes, and natural killer (NK) cells. Tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) production by circulating monocytes was sustained, a pattern distinct from bacterial sepsis or influenza. SARS-CoV-2 patient plasma inhibited HLA-DR expression, and this was partially restored by the IL-6 blocker Tocilizumab; off-label Tocilizumab treatment of patients was accompanied by increase in circulating lymphocytes. Thus, the unique pattern of immune dysregulation in severe COVID-19 is characterized by IL-6-mediated low HLA-DR expression and lymphopenia, associated with sustained cytokine production and hyper-inflammation. url: https://api.elsevier.com/content/article/pii/S1931312820302365 doi: 10.1016/j.chom.2020.04.009 id: cord-288916-i8ukefp8 author: Gómez-Herranz, Maria title: The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis date: 2019-04-02 words: 11700.0 sentences: 702.0 pages: flesch: 52.0 cache: ./cache/cord-288916-i8ukefp8.txt txt: ./txt/cord-288916-i8ukefp8.txt summary: A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The HPV16+ and IFITM1/3 positive cervical cancer cell line SiHa [38] [39] exhibit IFNγ inducible STAT1, IRF1, and IFITM1/3 proteins (Fig. 1G ). Also of note is attenuation of HLA-A, HLA-B, HLA-C, and ISG15 protein synthesis 24 h post-IFNγ treatment in the IFITM1/IFITM3 double null cells compared to parental SiHa (Fig. 5F vs 5B). By contrast, basal HLA-B protein expression was attenuated in the IFITM1/IFITM3 double null cells after IFNγ treatment (Fig. 6F vs 6E) . abstract: Interferon-induced transmembrane proteins IFITM1 and IFITM3 (IFITM1/3) play a role in both RNA viral restriction and in human cancer progression. Using immunohistochemical staining of FFPE tissue, we identified subgroups of cervical cancer patients where IFITM1/3 protein expression is inversely related to metastasis. Guide RNA-CAS9 methods were used to develop an isogenic IFITM1/IFITM3 double null cervical cancer model in order to define dominant pathways triggered by presence or absence of IFITM1/3 signalling. A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. Conversely, SWATH-IP mass spectrometry of ectopically expressed SBP-tagged IFITM1 identified ISG15 and HLA-B as dominant co-associated proteins. ISG15ylation was attenuated in IFNγ treated IFITM1/IFITM3 double-null cells. Proximity ligation assays indicated that HLA-B can interact with IFITM1/3 proteins in parental SiHa cells. Cell surface expression of HLA-B was attenuated in IFNγ treated IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The data together suggest that pro-metastatic growth associated with IFITM1/3 negative cervical cancers relates to attenuated expression of MHC Class I molecules that would support tumor immune escape. url: https://doi.org/10.1016/j.cellsig.2019.03.024 doi: 10.1016/j.cellsig.2019.03.024 id: cord-007851-v6h1yro7 author: Han, Ki-Cheol title: Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging date: 2020-04-03 words: 4886.0 sentences: 260.0 pages: flesch: 41.0 cache: ./cache/cord-007851-v6h1yro7.txt txt: ./txt/cord-007851-v6h1yro7.txt summary: We used a combined application of this method involving immune-specific signature analysis and HLA-associated peptidomics using samples from six patients with triple-negative breast cancer (TNBC) in order to select immunogenic HLA epitopes for in vitro testing. Integrated WTS data revealed a higher priority to select promising HLA-peptides via high-resolution bioinformatics analysis, showing immune-cell-specific signatures and TCR-repertoire diversity in tumors. We then found a positive correlation between TCR diversity, reflecting clonal composition, and the expression of MHC-class І molecules, suggesting that active tumor-antigen presentation promotes the generation of antigen-specific TILs. Additionally, immune-specific signature analysis can discriminate specific immune-cell types in each patient and thus enhance the efficiency of selective HLA-peptidomic approaches. In this study, the HLA-peptidomics approach combined with comprehensive analysis of immune-specific signatures and TCR repertories showed high selectivity to determine the immunogenic T-cell epitopes. Identification of potential vaccine epitopes coupled with immune-specific signature analysis, HLA-peptidomics, and single-cell-based immunogenicity testing offers a discriminative and powerful tool for cancer-vaccine development. abstract: Identification of tumor antigens that induce cytotoxic T lymphocytes (CTLs) is crucial for cancer-vaccine development. Despite their predictive ability, current algorithmic approaches and human leukocyte antigen (HLA)-peptidomic analysis allow limited selectivity. Here, we optimized a method to rapidly screen and identify highly immunogenic epitopes that trigger CTL responses. We used a combined application of this method involving immune-specific signature analysis and HLA-associated peptidomics using samples from six patients with triple-negative breast cancer (TNBC) in order to select immunogenic HLA epitopes for in vitro testing. Additionally, we applied high-throughput imaging at the single-cell level in order to confirm the immunoreactivity of the selected peptides. The results indicated that this method enabled identification of promising CTL peptides capable of inducing antitumor immunity. This platform combining high-resolution computational analysis, HLA-peptidomics, and high-throughput immunogenicity testing allowed rapid and robust identification of highly immunogenic epitopes and represents a powerful technique for cancer-vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125174/ doi: 10.1038/s41598-020-62244-z id: cord-104099-xhi0oxtr author: Hensen, L. title: CD8+ T-cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph date: 2020-10-05 words: 9678.0 sentences: 568.0 pages: flesch: 55.0 cache: ./cache/cord-104099-xhi0oxtr.txt txt: ./txt/cord-104099-xhi0oxtr.txt summary: We defined CD8+ T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. Our data present the first evidence of influenza-specific CD8+ T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8+ T-cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease. 10 .02.20206086 doi: medRxiv preprint immunogenicity of novel peptides in HLA-A24-expressing mice, peripheral blood of Indigenous and non-Indigenous HLA-A24 + healthy and influenza-infected individuals, and human tissues. To determine the immunogenicity of novel IAV-and IBV-derived peptides during primary and secondary influenza virus infection in vivo, we utilized HLA-A24-expressing transgenic (HHD-A24) mice 45 Table 2 ). . https://doi.org/10.1101/2020.10.02.20206086 doi: medRxiv preprint across virus strains circulating in South-East Asia and Australia suggests that the prominent HLA-A24-restricted CD8 + T-cell responses are likely to confer broad cross-reactive immunity to IAV. abstract: Indigenous people worldwide are at high-risk of developing severe influenza disease. HLA-A*24:02 allele, highly prevalent in Indigenous populations, is associated with influenza-induced mortality, although the basis for this association is unclear. We defined CD8+ T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. We identified immunodominant protective CD8+ T-cell epitopes, one towards IAV and six towards IBV, with A24/PB2550-558-specific CD8+ T-cells cells being cross-reactive between IAV and IBV. Memory CD8+ T-cells towards these specificities were present in blood (CD27+CD45RA- phenotype) and tissues (CD103+CD69+ phenotype) of healthy subjects, and effector CD27-CD45RA-PD-1+CD38+CD8+ T-cells in IAV/IBV patients. Our data present the first evidence of influenza-specific CD8+ T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8+ T-cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease. url: http://medrxiv.org/cgi/content/short/2020.10.02.20206086v1?rss=1 doi: 10.1101/2020.10.02.20206086 id: cord-320490-3jmo35jc author: Ismail, Saba title: Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date: 2020-04-12 words: 6688.0 sentences: 412.0 pages: flesch: 52.0 cache: ./cache/cord-320490-3jmo35jc.txt txt: ./txt/cord-320490-3jmo35jc.txt summary: In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . abstract: The COVID-19 pandemic caused by SARS-CoV-2 is a public-health emergency of international concern and thus calling for the development of safe and effective therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for vaccine, antibodies and inhibitor development because of many roles it plays in attachment, fusion and entry into the host cell. In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in solution aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel analytical tool axial frequency distribution (AFD). Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus has the potential to be considered in experimental studies. url: https://doi.org/10.1101/2020.04.05.026005 doi: 10.1101/2020.04.05.026005 id: cord-330615-h8sktgo6 author: Jabri, ‡ § Bana title: Selective expansion of intraepithelial lymphocytes expressing the HLA-E–specific natural killer receptor CD94 in celiac disease date: 2000-05-31 words: 7980.0 sentences: 417.0 pages: flesch: 51.0 cache: ./cache/cord-330615-h8sktgo6.txt txt: ./txt/cord-330615-h8sktgo6.txt summary: Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. In preliminary immunohistochemical studies of intestinal frozen tissue sections, the pattern of staining of IELs with anti-CD56, -Pen5, -p46, -p58, and -CD94 antibodies was compared in 4 adult patients with active celiac disease and in 4 normal controls. Cytolytic T lymphocytes displaying natural killer (NK)-like activity: expression of NK-related functional receptors for HLA class I molecules (p58 and CD94) and inhibitory effect on the TCR-mediated target cell lysis or lymphokine production abstract: Abstract Background & Aims: Celiac disease is a gluten-induced enteropathy characterized by the presence of gliadin-specific CD4+ T cells in the lamina propria and by a prominent intraepithelial T-cell infiltration of unknown mechanism. The aim of this study was to characterize the subset(s) of intraepithelial lymphocytes (IELs) expanding during active celiac disease to provide insights into the mechanisms involved in their expansion. Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. In addition, in vitro studies were performed to identify candidate stimuli for NK receptor expression. Results: In normal intestine, different proportions of IELs, which were mainly T cells, expressed the NK receptors CD94/NKG2, NKR-P1A, KIR2D/3D, NKp46, Pen5, or CD56. During the active phase of celiac disease, the frequency of CD94+ IELs, which were mostly αβ T cells, was conspicuously increased over controls. In contrast, the expression of other NK markers was not modified. Furthermore, expression of CD94 could be selectively induced in vitro by T-cell receptor activation and/or interleukin 15, a cytokine produced by intestinal epithelial cells. Conclusions: The gut epithelium favors the development of T cells that express NK receptors. In active celiac disease, there is a specific and selective increase of IELs expressing CD94, the HLA-E–specific NK receptor that may be related to T-cell receptor activation and/or interleukin 15 secretion. GASTROENTEROLOGY 2000;118:867-879 url: https://www.sciencedirect.com/science/article/pii/S0016508500701739 doi: 10.1016/s0016-5085(00)70173-9 id: cord-304635-z5vmhopa author: Ji, Wei title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner date: 2019-06-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The viral peptides presentation by major histocompatibility complex class I (MHC I) molecules play a pivotal role in T-cell recognition and the subsequent virus clearance. This process is delicately adjusted by the variant residues of MHC I, especially the residues in the peptide binding groove (PBG). In a series of MHC I molecules, a salt bridge is formed above the N-terminus of the peptides. However, the potential impact of the salt bridge on peptide binding and T-cell receptor (TCR) recognition of MHC I, as well as the corresponding molecular basis, are still largely unknown. Herein, we determined the structures of HLA-B*4001 and H-2K(d) in which two different types of salt bridges (Arg62-Glu163 or Arg66-Glu163) across the PBG were observed. Although the two salt bridges led to different conformation shifts of both the MHC I α helix and the peptides, binding of the peptides with the salt bridge residues was relatively conserved. Furthermore, through a series of in vitro and in vivo investigations, we found that MHC I mutations that disrupt the salt bridge alleviate peptide binding and can weaken the TCR recognition of MHC I-peptide complexes. Our study may provide key references for understanding MHC I-restricted peptide recognition by T-cells. url: https://doi.org/10.1016/j.molimm.2019.06.005 doi: 10.1016/j.molimm.2019.06.005 id: cord-326554-iphe3rni author: Joshi, Amit title: In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple’s Disease date: 2020-05-18 words: 3216.0 sentences: 189.0 pages: flesch: 49.0 cache: ./cache/cord-326554-iphe3rni.txt txt: ./txt/cord-326554-iphe3rni.txt summary: This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. Nowadays epitope based vaccines provide better options in search of good treatment strategy for such type of harmful and rare malady, even if the individuals are genetically predisposed as in case of classical Whipple''s disease (Trotta et al. Immune Epitope Database (IEDB) analysis Resource tool of population coverage was used to predict population coverage of the putative epitopes that are exhibiting interaction to HLA alleles and based on MHC-II restriction data (Bui et al. PatchDock tool was deployed for interaction between selected structures of epitopes and HLA DRB1 proteins. Still no one has used vaccine based treatments for Whipple''s disease, as it is thought to be rare and possess reduced genome but considered one of the harmful pathogen of human ( Raoult et al. abstract: Whipple’s disease is one of the rare maladies in terms of spread but very fatal one as it is linked with many disorders (like Gastroenteritis, Endocarditis etc.). Also, current regimens include less effective drugs which require long duration follows up. This exploratory study was conducted to commence the investigation for crafting multi target epitope vaccine against its bacterial pathogen Tropheryma whipplei. The modern bioinformatics tools like VaxiJen, NETMHCII PAN 3.2, ALLERGEN-FP, PATCH-DOCK, TOXIC-PRED, MHCPRED and IEDB were deployed, which makes the study more intensive in analyzing proteome of T. whipplei as these methods are based on robust result generating statistical algorithms ANN, HMM, and ML. This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. VLMVSAFPL epitope is a part of DNA-directed RNA polymerase subunit beta, and IRYLAALHL epitope is a part of membranous protein insertase YidC of this bacterium. Molecular-Docking and Molecular-Simulation analysis yields the perfect interaction based on Atomic contact energy, binding scores along with RMSD values (0 to 1.5 Ǻ) in selection zone. The IEDB (Immune epitope database) population coverage analysis exhibits satisfactory relevance with respect to world population. url: https://www.ncbi.nlm.nih.gov/pubmed/32427224/ doi: 10.1007/s10989-020-10077-9 id: cord-103837-iuvigqdx author: Knierman, Michael D. title: The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date: 2020-11-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The precise elucidation of the antigen sequences for T-cell immunosurveillance greatly enhances our ability to both understand and modulate humoral responses to viral infection or active immunization. Mass spectrometry is used to identify 526 unique sequences from SARS-CoV-2 spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The identified sequences span the entire spike protein and several sequences are isolated from a majority of the donors sampled indicating promiscuous binding. Importantly, many peptides derived from the receptor binding domain used for cell entry are identified. This work represents a precise and comprehensive immunopeptidomic investigation with SARS-CoV-2 spike glycoprotein and allows detailed analysis of features which may aid vaccine development to end the current COVID-19 pandemic. url: https://api.elsevier.com/content/article/pii/S2211124720314431 doi: 10.1016/j.celrep.2020.108454 id: cord-288146-xqxznv1r author: Kohyama, Shunsuke title: Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date: 2009-09-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Spike and nucleocapsid are structural proteins of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) and major targets for cytotoxic T lymphocytes (CTLs). In contrast, non-structural proteins encoded by two-thirds of viral genome are poorly characterized for cell-mediated immunity. We previously demonstrated that nucleocapsid-derived peptides chemically coupled to the surface of liposomes effectively elicited SARS-CoV-specific CTLs in mice. Here, we attempted to identify HLA-A*0201-restricted CTL epitopes derived from a non-structural polyprotein 1a (pp1a) of SARS-CoV, and investigated whether liposomal peptides derived from pp1a were effective for CTL induction. Out of 30 peptides predicted on computational algorithms, nine peptides could significantly induce interferon gamma (IFN-γ)-producing CD8(+) T cells in mice. These peptides were coupled to the surface of liposomes, and inoculated into mice. Six liposomal peptides effectively induced IFN-γ-producing CD8(+) T cells and seven liposomal peptides including the six peptides primed CTLs showing in vivo killing activities. Further, CTLs induced by the seven liposomal peptides lysed an HLA-A*0201 positive cell line expressing naturally processed, pp1a-derived peptides. Of note, one of the liposomal peptides induced high numbers of long-lasting memory CTLs. These data suggest that surface-linked liposomal peptides derived from pp1a might offer an efficient CTL-based vaccine against SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/19748524/ doi: 10.1016/j.antiviral.2009.09.004 id: cord-126015-zc7u3g34 author: Krieger, Elizabeth title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date: 2020-05-13 words: nan sentences: nan pages: flesch: nan cache: txt: summary: 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-255069-9xueqdri author: Leary, Shay title: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date: 2020-04-11 words: 1821.0 sentences: 77.0 pages: flesch: 43.0 cache: ./cache/cord-255069-9xueqdri.txt txt: ./txt/cord-255069-9xueqdri.txt summary: The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . abstract: The COVID-19 pandemic is caused by the single-stranded RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a virus of zoonotic origin that was first detected in Wuhan, China in December 2019. There is evidence that homologous recombination contributed to this cross-species transmission. Since that time the virus has demonstrated a high propensity for human-to-human transmission. Here we report two newly identified adjacent amino acid polymorphisms in the nucleocapsid at positions 203 and 204 (R203K/G204R) due to three adjacent nucleotide changes across the two codons (i.e. AGG GGA to AAA CGA). This new strain within the LGG clade may have arisen by a form of homologous recombination from the core sequence (CS-B) of the transcription-regulating sequences of SAS-CoV-2 itself and has rapidly increased to approximately one third of reported sequences from Europe during the month of March 2020. We note that these polymorphisms are predicted to reduce the binding of an overlying putative HLA-C*07-restricted epitope and that HLA-C*07 is prevalent in Caucasians being carried by >40% of the population. The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. url: https://doi.org/10.1101/2020.04.10.029454 doi: 10.1101/2020.04.10.029454 id: cord-009323-sfxpchma author: Link, Hartmut title: Die Transplantation hämatopoetischer Stammzellen: Teil I: Definitionen, prinzipielle Anwendungsmöglichkeiten, Komplikationen date: 1997 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The transplantation of hematopoietic and lymphopoetic stem and progenitor cells has become a standard procedure for the treatment of many malignant diseases. Autologous stem cells are derived from the patient himself, allogeneic cells from an HLA-identical or HLA-compatible family or unrelated donor. Hematopoetic stem cells can be obtained from bone marrow, blood and fetal cord blood. After 3 to 5 days treatment, the granulocyte-colony stimulating factor (G-CSF) mobilizes stem- and progenitor cells from the marrow into the blood. This method is now standard in autologous transplantation and is increasingly preferred in allogeneic transplantation. The time to hematopoietic recovery is shorter with blood stem cells than with bone marrow cells. With myeloablative high dose therapy followed by stem cell transplantation, long term disease free survival is possible in many cases and great proportions of patients can be cured (see part II). Improvements of supportive care have reduced toxicity of treatment substantially, however severe complications still occur at oropharynx, gastrointestinal tract, liver, lung, skin, kidney, urinary tract and nervous system. After allogeneic transplantation immunocompetent donor cells can react with the recipients tissue. In HLA-identical donor and recipients differences in the minor histocompatibility antigens account for this graft-versus-host-reaction (GvH), which is mainly mediated by transplanted T-cells. The GvH-reaction can affect skin, liver, gut and other organs and cause clinically relevant GvH-disease (GvHD). The GvHD is more severe in HLA-mis-matched or unrelated transplantations. Immunodeficiency and organ dysfunction due to GvHD may predispose to life threatening infections and impair the outcome of transplantion. Unrelated cord blood stem cells may have a minor risk of inducing acute GvHD, as stem and T-cells are immature. After allogeneic stem cell transplantation, the relapse rate of leukemia or lymphoma is significantly reduced by immunoreactive cells: graft-versus-tumor (GvT) or graftversus-leukemia effect (GvL). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146030/ doi: 10.1007/bf03044917 id: cord-007301-5m269nzi author: Lundegaard, Claus title: Modeling the adaptive immune system: predictions and simulations date: 2007-12-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Motivation: Immunological bioinformatics methods are applicable to a broad range of scientific areas. The specifics of how and where they might be implemented have recently been reviewed in the literature. However, the background and concerns for selecting between the different available methods have so far not been adequately covered. Summary: Before using predictions systems, it is necessary to not only understand how the methods are constructed but also their strength and limitations. The prediction systems in humoral epitope discovery are still in their infancy, but have reached a reasonable level of predictive strength. In cellular immunology, MHC class I binding predictions are now very strong and cover most of the known HLA specificities. These systems work well for epitope discovery, and predictions of the MHC class I pathway have been further improved by integration with state-of-the-art prediction tools for proteasomal cleavage and TAP binding. By comparison, class II MHC binding predictions have not developed to a comparable accuracy level, but new tools have emerged that deliver significantly improved predictions not only in terms of accuracy, but also in MHC specificity coverage. Simulation systems and mathematical modeling are also now beginning to reach a level where these methods will be able to answer more complex immunological questions. Contact: lunde@cbs.dtu.dk Supplementary information: Supplementary data are available at Bioinformatics online. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110254/ doi: 10.1093/bioinformatics/btm471 id: cord-346957-bmajkabp author: Lv, Yanbo title: Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date: 2009-12-03 words: 4933.0 sentences: 261.0 pages: flesch: 57.0 cache: ./cache/cord-346957-bmajkabp.txt txt: ./txt/cord-346957-bmajkabp.txt summary: RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. To investigate the capacity of candidate peptides to mobilize a human CTL repertoire, HLA-A2 + PBLs from ten HLA-A2 + donors were stimulated in vitro by DCs loaded with Alignment of the putative amino acid sequences of S proteins from eighteen SARS-CoV strains A dot among the individual sequences denoted nucleotides that are the same as the consensus. Furthermore, SARS-CoV/S-derived peptides Sp6, Sp7 and Sp8 could not only induce the increased S protein specific IFN-γ secreting T cell frequency but also the enhanced cytolytic capacity of these CTLs. To further address whether the immunogenic candidate peptide is naturally processed and presented, HLA-A2.1/ K b transgenic mice were immunized with S/pVAX1 plasmid containing a full-length cDNA encoding the SARS-CoV/S protein. abstract: BACKGROUND: The spike (S) protein is a major structural glycoprotein of coronavirus (CoV), the causal agent of severe acute respiratory syndrome (SARS). The S protein is a potent target for SARS-specific cell-mediated immune responses. However, the mechanism CoV pathogenesis in SARS and the role of special CTLs in virus clearance are still largely uncharacterized. Here, we describe a study that leads to the identification of a novel HLA-A*0201-restricted epitope from conserved regions of S protein. RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. Four of eight candidate peptides were tested by HLA-A*0201 binding assays. Among the four candidate peptides, Sp8 (S(958-966), VLNDILSRL) induced specific CTLs both ex vivo in PBLs of healthy HLA-A2(+ )donors and in HLA-A2.1/K(b )transgenic mice immunized with a plasmid encoding full-length S protein. The immunized mice released IFN-γ and lysed target cells upon stimulation with Sp8 peptide-pulsed autologous dendritic cells in comparison to other candidates. CONCLUSION: These results suggest that Sp8 is a naturally processed epitope. We propose that Sp8 epitope should help in the characterization of mechanisms of virus control and immunopathology in SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/19958537/ doi: 10.1186/1471-2172-10-61 id: cord-281141-ouno4jpl author: Mahajan, Swapnil title: Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date: 2020-11-05 words: 6208.0 sentences: 307.0 pages: flesch: 52.0 cache: ./cache/cord-281141-ouno4jpl.txt txt: ./txt/cord-281141-ouno4jpl.txt summary: A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . abstract: The COVID-19 pandemic has revealed a range of disease phenotypes in infected patients with asymptomatic, mild or severe clinical outcomes, but the mechanisms that determine such variable outcomes remain unresolved. In this study, we identified immunodominant CD8 T-cell epitopes in the RBD and the non-RBD domain of the spike antigen using a novel TCR-binding algorithm. A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. The T-cell reactivity to the predicted epitopes was higher than the Spike-S1 and S2 peptide pools containing 157 and 158 peptides both in unexposed donors and in convalescent patients suggesting that strong T-cell epitopes are likely to be missed when larger peptide pools are used in assays. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. This finding is in contrast to multiple published studies in which pre-existing T-cell immunity is suggested to arise from shared epitopes between SARS-CoV-2 and other common cold-causing coronaviruses. Whether the presence of pre-existing T-cell immunity provides protection against COVID-19 or contributes to severe disease phenotype remains to be determined in a larger cohort. However, our findings raise the expectation that a significant majority of the global population is likely to have SARS-CoV-2 reactive T-cells because of prior exposure to flu and CMV viruses, in addition to common cold-causing coronaviruses. url: https://doi.org/10.1101/2020.11.03.367375 doi: 10.1101/2020.11.03.367375 id: cord-003472-ml4pbewf author: Manczinger, Máté title: Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations date: 2019-01-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Central players of the adaptive immune system are the groups of proteins encoded in the major histocompatibility complex (MHC), which shape the immune response against pathogens and tolerance to self-peptides. The corresponding genomic region is of particular interest, as it harbors more disease associations than any other region in the human genome, including associations with infectious diseases, autoimmune disorders, cancers, and neuropsychiatric diseases. Certain MHC molecules can bind to a much wider range of epitopes than others, but the functional implication of such an elevated epitope-binding repertoire has remained largely unclear. It has been suggested that by recognizing more peptide segments, such promiscuous MHC molecules promote immune response against a broader range of pathogens. If so, the geographical distribution of MHC promiscuity level should be shaped by pathogen diversity. Three lines of evidence support the hypothesis. First, we found that in pathogen-rich geographical regions, humans are more likely to carry highly promiscuous MHC class II DRB1 alleles. Second, the switch between specialist and generalist antigen presentation has occurred repeatedly and in a rapid manner during human evolution. Third, molecular positions that define promiscuity level of MHC class II molecules are especially diverse and are under positive selection in human populations. Taken together, our work indicates that pathogen load maintains generalist adaptive immune recognition, with implications for medical genetics and epidemiology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372212/ doi: 10.1371/journal.pbio.3000131 id: cord-261392-dw56h8vj author: Matijevic, Mark title: Immunization with a poly (lactide co-glycolide) encapsulated plasmid DNA expressing antigenic regions of HPV 16 and 18 results in an increase in the precursor frequency of T cells that respond to epitopes from HPV 16, 18, 6 and 11 date: 2011-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract A phase II trial was conducted in subjects with human papillomavirus (HPV) associated high-grade cervical dysplasia testing the safety and efficacy of a microparticle encapsulated pDNA vaccine. Amolimogene expresses T cell epitopes from E6 and E7 proteins of HPV types 16 and 18. An analysis was performed on a subset of HLA-A2+ subjects to test whether CD8+ T cells specific to HPV 16, 18, 6 and 11 were increased in response to amolimogene immunization. Of the 21 subjects receiving amolimogene, 11 had elevated CD8+ T cell responses to HPV 16 and/or 18 peptides and seven of these also had increases to corresponding HPV 6 and/or 11 peptides. In addition, T cells primed and expanded in vitro with an HPV 18 peptide demonstrated cross-reactivity to the corresponding HPV 11 peptide. These data demonstrate that treatment with amolimogene elicits T cell responses to HPV 16, 18, 6 and 11. url: https://api.elsevier.com/content/article/pii/S000887491100092X doi: 10.1016/j.cellimm.2011.04.005 id: cord-007664-c5snhymz author: Mauerhoff, Thekla title: Differential expression and regulation of major histocompatibility complex (MHC) products in neural and glial cells of the human fetal brain date: 2002-11-13 words: 4673.0 sentences: 212.0 pages: flesch: 51.0 cache: ./cache/cord-007664-c5snhymz.txt txt: ./txt/cord-007664-c5snhymz.txt summary: To gain an insight into the regulation of HLA in the different cell types in the CNS and to compare it to that observed in the endocrine organs, we have studied the effect of the lympho/monokines interferon (IFN)-α and -γ, tumour necrosis factor (TNF)-α, and interleukin (IL)-2 and other agents on this aspect of the biology of human fetal brain cells in culture. It has previously been reported that primary cultures of human fetal brain tissue can be a useful substrate for studying the expression of cell type-specific antigens, e.g. gangliosides, tetanus toxin receptors (Dickson et al., 1982 (Dickson et al., , 1985 , and the present data confirm that they can also be successfully employed to investigate the expression and modulation of HLA molecules. abstract: The cells of the central nervous system (CNS) have the peculiarity of physiologically expressing very low levels of HLA molecules. In multiple sclerosis (MS), however, as in endocrine autoimmune diseases, there is a marked increase of HLA expression in the tissue (i.e. the plaques) and this is attributable not only to infiltrating cells but also to the astrocytes. To gain an insight into the regulation of HLA in the different cell types in the CNS and to compare it to that observed in the endocrine organs, we have studied the effect of the lympho/monokines interferon (IFN)-α and -γ, tumour necrosis factor (TNF)-α, and interleukin (IL)-2 and other agents on this aspect of the biology of human fetal brain cells in culture. A two-colour immunofluorescence technique which combines antibodies to diverse CNS cell markers and monoclonal antibodies (MoAbs) to the non-polymorphic region of HLA molecules was used throughout this study. In control cultures, only astrocytes expressed MHC class I, but after incubation with either IFN-γ or TNF-α oligodendrocytes acquired class I expression. Surprisingly, astrocytes became spontaneously class II positive in culture and this was greatly enhanced by IFN-γ. Other agents such as IL-2, epidermal growth factor, phorbolmyristate acetate and lectins had no effect. The expression of HLA molecules in the cells of the CNS both in basal conditions and in response to lymphokines is therefore selective and highly heterogenous, thus reflecting their intrinsic biological diversity. These findings may help to explain the features of the immunopathology of MS and also of latent viral infections of neural cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119889/ doi: 10.1016/0165-5728(88)90049-5 id: cord-286858-zbhtl2yn author: Mishra, B. title: tamasomā jyotirgamaya: Seeking the Self Amidst Covids’ Cytokine Cyclones date: 2020-10-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Pondering on pandemics and the promise of purification from the plethora of problems that it has spawned, the paper builds on a game-theoretic model of host–pathogen interaction, and... moves beyond. It highlights how quickly this ‘wicked’ problem has led to deceptive Nash equilibria of certain information-asymmetric games as well as their sequels of more complex intertwined games at human scale but without an exit strategy in sight. In the absence of clarity (e.g., access to complete information) and yet facing a capricious and complex conspirator, we overview an exemplary solution, created by RxCovea, and examine how it might help. url: https://doi.org/10.1007/s41745-020-00186-1 doi: 10.1007/s41745-020-00186-1 id: cord-296007-1gsgd22t author: Mohseni, Amir Hossein title: Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date: 2020-09-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The coronavirus disease 2019 (COVID-19) is triggered by severe acute respiratory syndrome mediated by coronavirus 2 (SARS-CoV-2) infection and was declared by WHO as a major international public health concern. While worldwide efforts are being advanced towards vaccine development, the structural modeling of TCR-pMHC (T Cell Receptor-peptide-bound Major Histocompatibility Complex) regarding SARS-CoV-2 epitopes and the design of effective T cell vaccine based on these antigens are still unresolved. Here, we present both pMHC and TCR-pMHC interfaces to infer peptide epitopes of the SARS-CoV-2 proteins. Accordingly, significant TCR-pMHC templates (Z-value cutoff > 4) along with interatomic interactions within the SARS-CoV-2-derived hit peptides were clarified. Also, we applied the structural analysis of the hit peptides from different coronaviruses to highlight a feature of evolution in SARS-CoV-2, SARS-CoV, bat-CoV, and MERS-CoV. Peptide-protein flexible docking between each of the hit peptides and their corresponding MHC molecules were performed, and a multi-hit peptides vaccine against the S and N glycoprotein of SARS-CoV-2 was designed. Filtering pipelines including antigenicity, and also physiochemical properties of designed vaccine were then evaluated by different immunoinformatics tools. Finally, vaccine-structure modeling and immune simulation of the desired vaccine were performed aiming to create robust T cell immune responses. We anticipate that our design based on the T cell antigen epitopes and the frame of the immunoinformatics analysis could serve as valuable supports for the development of COVID-19 vaccine. url: https://doi.org/10.1101/2020.09.12.294413 doi: 10.1101/2020.09.12.294413 id: cord-333670-qv1orlv5 author: Mutti, Luciano title: Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date: 2020-05-28 words: 2500.0 sentences: 123.0 pages: flesch: 40.0 cache: ./cache/cord-333670-qv1orlv5.txt txt: ./txt/cord-333670-qv1orlv5.txt summary: In Italy, the possibility of performing autopsies or post-mortem diagnostic studies on suspect, probable, or confirmed COVID-19 cases has been intensively debated (5, 6) ; however, postmortem pathological analysis of COVID-19 patients in China has shown findings consistent with Acute Respiratory Distress Syndrome (ARDS) (7-9) (Figure 1 ). Consistently, recent results indicate that a systemic immune dysregulation that triggers auto-sustaining inflammatory lung damage, causing fatal respiratory-failure and consequent multiorgan-failure, is the main virus-related-death cause in patients who develop SARS-CoV-2 (10). Overall, understanding the role of pro-inflammatory cytokines certainly unravels a new battleground against the lethal clinical effect of CODIV-19 infection; this, along with the identification of a high-risk autoimmune profile, including the genotyping of Class I and II HLA, which have a key role in shaping the anti-viral immune response and Th1/Th2 lymphocyte subset response (Figure 1) , and immune-profiling, could also help to prevent these dangerous evolutions of the disease (29) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32574270/ doi: 10.3389/fimmu.2020.01208 id: cord-287709-y247lan1 author: Navarrete, Cristina title: Cord Blood Banking: Operational and Regulatory Aspects date: 2014-12-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Umbilical cord blood (UCB) is an alternative source of hematopoietic stem cells for transplantation in patients with hematological malignancies, bone marrow failures, immunodeficiencies, and inherited metabolic disorders. In order to facilitate these transplants, large repositories of frozen UCB units collected from altruistic unrelated donations have been established and to date there are more than 600,000 units stored in cord blood banks all over the world. These products have been collected, stored, and released for transplantation under stringent quality conditions in order to ensure their safety and efficacy. The development and evolution of the policies and procedures currently in use in cord blood banking have been largely influenced by the clinical outcome of the transplants performed using these units. This review will describe some of the main steps and procedures involved in the clinical banking of unrelated UCB donations starting from the recruitment and selection of the potential donor (the mother) to the final distribution of the unit to the transplant program and its clinical outcome follow-up. url: https://api.elsevier.com/content/article/pii/B9780124077850000153 doi: 10.1016/b978-0-12-407785-0.00015-3 id: cord-348283-7xorq5ce author: Naz, Anam title: Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date: 2020-07-10 words: 8183.0 sentences: 482.0 pages: flesch: 56.0 cache: ./cache/cord-348283-7xorq5ce.txt txt: ./txt/cord-348283-7xorq5ce.txt summary: The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Designed vaccines were then tested with different epitopes, including Truncated Ov-ASP-1 Protein (residues 10-153) and Beta defensin (45 residues long), and constructs having higher antigenicity and that are predicted to produce high antibody titers were added with the multi epitope vaccine construct to the enhance immune response (30) . For the interaction analysis of vaccine 3 and BCR (CD79), the HADDOCK server clustered 140 probable structures into 13 different clusters, which represented a total of 70% of the water-refined models. abstract: A recent pandemic caused by a single-stranded RNA virus, COVID-19, initially discovered in China, is now spreading globally. This poses a serious threat that needs to be addressed immediately. Genome analysis of SARS-CoV-2 has revealed its close relation to SARS-coronavirus along with few changes in its spike protein. The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. The S1 and S2 domains of spike proteins were analyzed, and two vaccine constructs were prioritized with T-cell and B-cell epitopes. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Prioritized epitopes were then modeled using linkers and adjuvants, and respective 3D models were constructed to evaluate their physiochemical properties and their possible interactions with ACE2, HLA Superfamily alleles, TLR2, and TLR4. url: https://www.ncbi.nlm.nih.gov/pubmed/32754160/ doi: 10.3389/fimmu.2020.01663 id: cord-286968-ud1uerc8 author: Nienhold, R. title: Two distinct immunopathological profiles in lungs of lethal COVID-19 date: 2020-06-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Immune responses in lungs of Coronavirus Disease 2019 (COVID-19) are poorly characterized. We conducted transcriptomic, histologic and cellular profiling of post mortem COVID-19 and normal lung tissues. Two distinct immunopathological reaction patterns were identified. One pattern showed high expression of interferon stimulated genes (ISGs) and cytokines, high viral loads and limited pulmonary damage, the other pattern showed severely damaged lungs, low ISGs, low viral loads and abundant immune infiltrates. Distinct patterns of pulmonary COVID-19 immune responses correlated to hospitalization time and may guide treatment and vaccination approaches. url: http://medrxiv.org/cgi/content/short/2020.06.17.20133637v1?rss=1 doi: 10.1101/2020.06.17.20133637 id: cord-002686-zzongyfa author: Oany, Arafat Rahman title: Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA date: 2017-09-07 words: 4966.0 sentences: 265.0 pages: flesch: 47.0 cache: ./cache/cord-002686-zzongyfa.txt txt: ./txt/cord-002686-zzongyfa.txt summary: In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. The generalized modules of membrane antigen-(GMMA-) based outer membrane proteins including SigA were also shown to be highly immunogenic [12] , which prompted us to target SigA as one of the best vaccine candidates and to design potential peptide vaccine covering all the Shigella spp. The SigA protein sequences of different strains of Shigella species were retrieved from the NCBI GenBank [22] database and analysed in the VaxiJen v2.0 [23] server for the determination of the most potent antigenic protein. IEDB analysis resource predicted both MHC class I-and MHC class II-based coverage of the selected epitopes for the world population to assess the feasibility of being a potential vaccine candidate. abstract: Shigellosis, a bacillary dysentery, is closely associated with diarrhoea in human and causes infection of 165 million people worldwide per year. Casein-degrading serine protease autotransporter of enterobacteriaceae (SPATE) subfamily protein SigA, an outer membrane protein, exerts both cytopathic and enterotoxic effects especially cytopathic to human epithelial cell type-2 (HEp-2) and is shown to be highly immunogenic. In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. At first, 44 SigA proteins from different variants of S. flexneri, S. dysenteriae, S. boydii, and S. sonnei were assessed to find the most antigenic protein. We retrieved 12 peptides based on the highest score for human leukocyte antigen (HLA) supertypes analysed by NetCTL. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. From these, FHTVTVNTL and IELAGTLTL peptides were shown to have 100% conservancy. Finally, IELAGTLTL was shown to have the highest population coverage (83.86%) among the whole world population. In vivo study of the proposed epitope might contribute to the development of functional and unique widespread vaccine, which might be an operative alleyway to thwart dysentery from the world. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5610819/ doi: 10.1155/2017/6412353 id: cord-010222-5oxie0zc author: Oldstone, Michael B.A. title: Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date: 2004-04-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172880/ doi: 10.1016/0896-8411(89)90130-3 id: cord-023675-sidvbzqy author: Oldstone, Michael B.A. title: Virus-induced Autoimmunity: Molecular Mimicry as a Route to Autoimmune Disease date: 2013-11-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173430/ doi: 10.1016/b978-0-12-252682-4.50023-8 id: cord-004435-l66ost6q author: Oli, Angus Nnamdi title: Immunoinformatics and Vaccine Development: An Overview date: 2020-02-26 words: 8946.0 sentences: 534.0 pages: flesch: 39.0 cache: ./cache/cord-004435-l66ost6q.txt txt: ./txt/cord-004435-l66ost6q.txt summary: Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/re-emerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines'' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. 13 An approach that must accommodate many factors affecting vaccine development like pathogen antigenic variability, the emergence of infectious disease, human genetic variation is the goal of immunoinformatics [ Figure 1 ]. 110 The surface glycoprotein can be regarded as antigen and hence can serve as a target for the immune system which if sequenced, using the new immunoinformatics approach and a common site for the varying proteins identified, a potent vaccine can be developed which can accommodate the antigenic drift/shifts of the virus. abstract: The use of vaccines have resulted in a remarkable improvement in global health. It has saved several lives, reduced treatment costs and raised the quality of animal and human lives. Current traditional vaccines came empirically with either vague or completely no knowledge of how they modulate our immune system. Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/re-emerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. And these concerns have driven immunologists toward research for a better approach to vaccine design that will consider these challenges. Currently, immunoinformatics has paved the way for a better understanding of some infectious disease pathogenesis, diagnosis, immune system response and computational vaccinology. The importance of this immunoinformatics in the study of infectious diseases is diverse in terms of computational approaches used, but is united by common qualities related to host–pathogen relationship. Bioinformatics methods are also used to assign functions to uncharacterized genes which can be targeted as a candidate in vaccine design and can be a better approach toward the inclusion of women that are pregnant into vaccine trials and programs. The essence of this review is to give insight into the need to focus on novel computational, experimental and computation-driven experimental approaches for studying of host–pathogen interactions and thus making a case for its use in vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049754/ doi: 10.2147/itt.s241064 id: cord-003270-vu9b5a14 author: Panahi, Heidar Ali title: A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins date: 2018-10-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Human papillomaviruses (HPVs) are a group of circular double-stranded DNA viruses, showing severe tropism to mucosal tissues. A subset of HPVs, especially HPV16 and 18, are the primary etiological cause for several epithelial cell malignancies, causing about 5.2% of all cancers worldwide. Due to the high prevalence and mortality, HPV-associated cancers have remained as a significant health problem in human society, making an urgent need to develop an effective therapeutic vaccine against them. Achieving this goal is primarily dependent on the identification of efficient tumor-associated epitopes, inducing a robust cell-mediated immune response. Previous information has shown that E5, E6, and E7 early proteins are responsible for the induction and maintenance of HPV-associated cancers. Therefore, the prediction of major histocompatibility complex (MHC) class I T cell epitopes of HPV16, 18, 31 and 45 oncoproteins was targeted in this study. For this purpose, a two-step plan was designed to identify the most probable CD8+ T cell epitopes. In the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and in the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens’ analyses were carried out successively by different tools. Finally, we introduced five probable CD8+ T cell epitopes for each oncoprotein of the HPV genotypes (60 epitopes in total), which obtained better scores by an integrated approach. These predicted epitopes are valuable candidates for in vitro or in vivo therapeutic vaccine studies against the HPV-associated cancers. Additionally, this two-step plan that each step includes several analyses to find appropriate epitopes provides a rational basis for DNA- or peptide-based vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6200245/ doi: 10.1371/journal.pone.0205933 id: cord-000488-x5ardo5j author: Pedersen, Lasse Eggers title: Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities date: 2011-07-08 words: 7264.0 sentences: 371.0 pages: flesch: 53.0 cache: ./cache/cord-000488-x5ardo5j.txt txt: ./txt/cord-000488-x5ardo5j.txt summary: We have recently developed efficient methods to generate recombinant human MHC-I (also known as human leukocyte antigen class I, HLA-I) molecules, accompanying peptide-binding assays and predictors, and HLA tetramers for specific CTL staining and manipulation. Recombinant constructs encoding chimeric and SLA-1*0401 molecules A synthetic gene encoding a transmembrane-truncated fragment encompassing residues 1 to 275 of human HLA-A*11:01 alpha chain followed by a FXa-BSP-HAT tag (FXa = factor Xa cleavage site comprised of the amino acid sequence IEGR, BSP = biotinylation signal peptide, HAT = histidine affinity tag for purification purposes; see Online Resource 1) had previously been generated and inserted into the pET28 expression plasmid (Novagen) (Ferre et al. abstract: In all vertebrate animals, CD8(+) cytotoxic T lymphocytes (CTLs) are controlled by major histocompatibility complex class I (MHC-I) molecules. These are highly polymorphic peptide receptors selecting and presenting endogenously derived epitopes to circulating CTLs. The polymorphism of the MHC effectively individualizes the immune response of each member of the species. We have recently developed efficient methods to generate recombinant human MHC-I (also known as human leukocyte antigen class I, HLA-I) molecules, accompanying peptide-binding assays and predictors, and HLA tetramers for specific CTL staining and manipulation. This has enabled a complete mapping of all HLA-I specificities (“the Human MHC Project”). Here, we demonstrate that these approaches can be applied to other species. We systematically transferred domains of the frequently expressed swine MHC-I molecule, SLA-1*0401, onto a HLA-I molecule (HLA-A*11:01), thereby generating recombinant human/swine chimeric MHC-I molecules as well as the intact SLA-1*0401 molecule. Biochemical peptide-binding assays and positional scanning combinatorial peptide libraries were used to analyze the peptide-binding motifs of these molecules. A pan-specific predictor of peptide–MHC-I binding, NetMHCpan, which was originally developed to cover the binding specificities of all known HLA-I molecules, was successfully used to predict the specificities of the SLA-1*0401 molecule as well as the porcine/human chimeric MHC-I molecules. These data indicate that it is possible to extend the biochemical and bioinformatics tools of the Human MHC Project to other vertebrate species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00251-011-0555-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214623/ doi: 10.1007/s00251-011-0555-3 id: cord-002724-gtv9syzi author: Pfortmueller, Carmen Andrea title: Assessment of immune organ dysfunction in critical illness: utility of innate immune response markers date: 2017-10-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In critically ill patients, organ dysfunctions are routinely assessed, monitored, and treated. Mounting data show that substantial critical illness-induced changes in the immune system can be observed in most ICU patients and that not only “hyper-inflammation” but also persistence of an anti-inflammatory phenotype (as in sepsis-associated immunosuppression) is associated with increased morbidity and mortality. Despite common perception, changes in functional immunity cannot be adequately assessed by routine inflammatory biomarkers such as C-reactive protein, procalcitonin, or numerical analysis of leukocyte (sub)-counts. Cytokines appear also not suited due to their short half-life and pleiotropy, their unexclusive origin from immune cells, and their potential to undergo antagonization by circulating inactivating molecules. Thus, beyond leukocyte quantification and use of routine biomarkers, direct assessment of immune cell function seems required to characterize the immune systems’ status. This may include determination of, e.g., ex vivo cellular cytokine release, phagocytosis activity, and/or antigen-presenting capacity. In this regard, standardized flow-cytometric assessment of the major histocompatibility-II complex human leukocyte antigen (-D related) (HLA-DR) has gained particular interest. Monocytic HLA-DR (mHLA-DR) controls the interplay between innate and adaptive immunity and may serve as a “global” biomarker of injury-associated immunosuppression, and its decreased expression is associated with adverse clinical outcomes (e.g., secondary infection risk, mortality). Importantly, recent data demonstrate that injury-associated immunosuppression can be reversed—opening up new therapeutic avenues in affected patients. Here we discuss the potential scientific and clinical value of assessment of functional immunity with a focus on monocytes/macrophages and review the current state of knowledge and potential perspectives for affected critically ill patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653680/ doi: 10.1186/s40635-017-0163-0 id: cord-266204-ipa017wz author: Poland, G. A. title: Personalized vaccinology: A review date: 2018-08-28 words: 7232.0 sentences: 331.0 pages: flesch: 36.0 cache: ./cache/cord-266204-ipa017wz.txt txt: ./txt/cord-266204-ipa017wz.txt summary: 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. A decade ago, we described the idea of vaccinomics and adversomics, based on the immune response network theory [5, 6] , which utilizes immunogenetics/imunogenomics and systems biology approaches to understand the basis for inter-individual variations in vaccineinduced immune responses in humans, as well as the basis for adverse side effects from vaccines [7] . Published data reveal that innate and adaptive immunity is decreased with age, but the systems-level mechanisms for these findings are unclear [66, 68] , particularly in regard to influenza and other viral vaccine responses where the morbidity, mortality, and associated healthcare costs are greater in older individuals [11] . 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-000224-2lz03oqb author: Porter, Kristen A. title: Class II Transactivator (CIITA) Enhances Cytoplasmic Processing of HIV-1 Pr55Gag date: 2010-06-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The Pr55(gag) (Gag) polyprotein of HIV serves as a scaffold for virion assembly and is thus essential for progeny virion budding and maturation. Gag localizes to the plasma membrane (PM) and membranes of late endosomes, allowing for release of infectious virus directly from the cell membrane and/or upon exocytosis. The host factors involved in Gag trafficking to these sites are largely unknown. Upon activation, CD4+ T cells, the primary target of HIV infection, express the class II transcriptional activator (CIITA) and therefore the MHC class II isotype, HLA-DR. Similar to Gag, HLA-DR localizes to the PM and at the membranes of endosomes and specialized vesicular MHC class II compartments (MIICs). In HIV producer cells, transient HLA-DR expression induces intracellular Gag accumulation and impairs virus release. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that both stable and transient expression of CIITA in HIV producer cells does not induce HLA-DR-associated intracellular retention of Gag, but does increase the infectivity of virions. However, neither of these phenomena is due to recapitulation of the class II antigen presentation pathway or CIITA-mediated transcriptional activation of virus genes. Interestingly, we demonstrate that CIITA, apart from its transcriptional effects, acts cytoplasmically to enhance Pr160(gag-pol) (Gag-Pol) levels and thereby the viral protease and Gag processing, accounting for the increased infectivity of virions from CIITA-expressing cells. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that CIITA enhances HIV Gag processing, and provides the first evidence of a novel, post-transcriptional, cytoplasmic function for a well-known transactivator. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892040/ doi: 10.1371/journal.pone.0011304 id: cord-329669-z3t7plvh author: Poulton, Kay title: A role for human leucocyte antigens in the susceptibility to SARS‐Cov‐2 infection observed in transplant patients date: 2020-07-05 words: 2270.0 sentences: 124.0 pages: flesch: 50.0 cache: ./cache/cord-329669-z3t7plvh.txt txt: ./txt/cord-329669-z3t7plvh.txt summary: HLA frequencies observed were compared against two control populations: first, against published frequencies in a UK deceased donor population (n = 10,000) representing the target population of the virus, and second, using a cohort of individuals from the combined transplant waiting lists of both centres (n = 308), representing a comparator group of unaffected individuals of the same demographic. This study investigated HLA profiles of patients admitted with PCR-confirmed SARS-CoV-2 infection to identify any potential HLA bias which might indicate an impaired capacity to mount an effective immune response to the infection. All patients included in the study had previously been HLA typed to support transplantation and required hospital treatment for COVID-19 disease, indicating that their symptoms were severe, requiring clinical support or intervention. Statistical analysis was performed using MedCalc v19.3 (MedCalc Software) to compare frequencies of allele group carriage between the patient and control populations using Fisher''s exact test. abstract: We analysed data from 80 patients who tested positive for SARS‐CoV‐2 RNA who had previously been HLA typed to support transplantation. Data were combined from two adjacent centres in Manchester and Leeds to achieve a sufficient number for early analysis. HLA frequencies observed were compared against two control populations: first, against published frequencies in a UK deceased donor population (n = 10,000) representing the target population of the virus, and second, using a cohort of individuals from the combined transplant waiting lists of both centres (n = 308), representing a comparator group of unaffected individuals of the same demographic. We report a significant HLA association with HLA‐ DQB1*06 (53% vs. 36%; p < .012; OR 1.96; 95% CI 1.94–3.22) and infection. A bias towards an increased representation of HLA‐A*26, HLA‐DRB1*15, HLA‐DRB1*10 and DRB1*11 was also noted but these were either only significant using the UK donor controls, or did not remain significant after correction for multiple tests. Likewise, HLA‐A*02, HLA‐B*44 and HLA‐C*05 may exert a protective effect, but these associations did not remain significant after correction for multiple tests. This is relevant information for the clinical management of patients in the setting of the current SARS‐CoV‐2 pandemic and potentially in risk‐assessing staff interactions with infected patients. url: https://doi.org/10.1111/iji.12505 doi: 10.1111/iji.12505 id: cord-275677-hbv49e01 author: Ramana, Lakshmi Narashimhan title: Targeting strategies for delivery of anti-HIV drugs date: 2014-10-28 words: 12944.0 sentences: 571.0 pages: flesch: 42.0 cache: ./cache/cord-275677-hbv49e01.txt txt: ./txt/cord-275677-hbv49e01.txt summary: Immunoliposomes loaded with the protease inhibitor indinavir and surface modified with anti-HLA-DR were found to effectively bind to HIV infected cells and deliver the antiretroviral drug leading to a significant reduction in the viral load [44] . In a recent work, lipid nanoparticles conjugated with two peptide sequences that were derived from the binding domains of CD4 designated as CD4-BP2 and CD4-BP4 were used for targeted delivery of the protease inhibitor indinavir to HIV infected CD4 + cells with high specificity [54] . The lectin actinohivin isolated from the actinomycete Longisporum albida has also been identified as an important targeting moiety that binds to the mannose residues present in the gp120 at lower concentrations with an affinity greater than anti-gp120 antibodies thereby preventing the interaction of the viral glycoprotein with CXCR4 and CCR5 chemokine receptors [13] . abstract: Human Immunodeficiency Virus (HIV) infection remains a significant cause of mortality globally. Though antiretroviral therapy has significantly reduced AIDS-related morbidity and mortality, there are several drawbacks in the current therapy, including toxicity, drug–drug interactions, development of drug resistance, necessity for long-term drug therapy, poor bio-availability and lack of access to tissues and reservoirs. To circumvent these problems, recent anti-HIV therapeutic research has focused on improving drug delivery systems through drug delivery targeted specifically to host cells infected with HIV or could potentially get infected with HIV. In this regard, several surface molecules of both viral and host cell origin have been described in recent years, that would enable targeted drug delivery in HIV infection. In the present review, we provide a comprehensive overview of the need for novel drug delivery systems, and the successes and challenges in the identification of novel viral and host-cell molecules for the targeted drug delivery of anti-HIV drugs. Such targeted anti-retroviral drug delivery approaches could pave the way for effective treatment and eradication of HIV from the body. url: https://api.elsevier.com/content/article/pii/S0168365914005835 doi: 10.1016/j.jconrel.2014.08.003 id: cord-316330-55nd3pwe author: Ramos-Lopez, Omar title: Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date: 2020-10-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: OBJECTIVE: To systematically explore genetic polymorphisms associated with the clinical outcomes in SARS-CoV infection in humans. METHODS: This comprehensive literature search comprised available English papers published in PubMed/Medline and SCOPUS databases following the PRISMA-P guidelines and PICO/AXIS criteria. RESULTS: Twenty-nine polymorphisms located in 21 genes were identified as associated with SARS-CoV susceptibility/resistance, disease severity, and clinical outcomes predominantly in Asian populations. Thus, genes implicated in key pathophysiological processes such as the mechanisms related to the entry of the virus into the cell and the antiviral immune/inflammatory responses were identified. CONCLUSIONS: Although caution must be taken, the results of this systematic review suggest that multiple genetic polymorphisms are associated with SARS-CoV infection features by affecting virus pathogenesis and host immune response, which could have important applications for the study and understanding of genetics in SARS-CoV-2/COVID-19 and for personalized translational clinical practice depending on the population studied and associated environments. url: https://www.ncbi.nlm.nih.gov/pubmed/33110916/ doi: 10.1155/2020/6901217 id: cord-273906-s7l0yxc0 author: Ranga, Vipin title: Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date: 2020-07-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The emergence of the COVID-19 outbreak at the end of 2019, caused by the novel coronavirus SARS-CoV-2, has, to date, led to over 13.6 million infections and nearly 600,000 deaths. Consequently, there is an urgent need to better understand the molecular factors triggering immune defense against the virus and to develop countermeasures to hinder its spread. Using in silico analyses, we showed that human major histocompatibility complex (MHC) class I cell-surface molecules vary in their capacity for binding different SARS-CoV-2-derived epitopes, i.e., short sequences of 8-11 amino acids, and pinpointed five specific SARS-CoV-2 epitopes that are likely to be presented to cytotoxic T-cells and hence activate immune responses. The identified epitopes, each one of nine amino acids, have high sequence similarity to the equivalent epitopes of SARS-CoV virus, which are known to elicit an effective T cell response in vitro. Moreover, we give a structural explanation for the binding of SARS-CoV-2-epitopes to MHC molecules. Our data can help us to better understand the differences in outcomes of COVID-19 patients and may aid the development of vaccines against SARS-CoV-2 and possible future outbreaks of novel coronaviruses. url: https://doi.org/10.3390/vaccines8030408 doi: 10.3390/vaccines8030408 id: cord-028275-szb45jm2 author: Reza Khorramizadeh, M. title: Animal models for human disease date: 2020-06-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: This chapter introduces some types of animal models which are used for better understanding the disease mechanisms and its treatment. These experimental models fall into two categories: spontaneous models and induced models. Among the diseases, rheumatoid arthritis (RA) as an autoimmune disease was considered. To study the pathogenesis of RA, we explained collagen-induced arthritis as an animal model that reflects a characteristic feature of RA patients. In addition, experimental allergic encephalomyelitis (EAE) as an experimental model for multiple sclerosis (MS) was explained in detail to represent a standard method to investigate in its mechanism, finding the way for the amelioration of this incurable neurological disorder. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329115/ doi: 10.1016/b978-0-12-811710-1.00008-2 id: cord-349451-vak2p7ac author: Rocha, Francisco Airton Castro title: Microbes, Helminths and Rheumatic Diseases date: 2020-05-07 words: 7465.0 sentences: 355.0 pages: flesch: 33.0 cache: ./cache/cord-349451-vak2p7ac.txt txt: ./txt/cord-349451-vak2p7ac.txt summary: Studies suggest the billions of germs that compose the gut microbiota influence one''s innate and adaptive immune responses at the intestinal level, but these microorganisms may also impact rheumatic diseases. Evidence indicates that changes in the gut microbiome alter the pathogenesis of immune-mediated diseases such as rheumatoid arthritis and ankylosing spondylitis but also of other disorders like atherosclerosis and osteoarthritis. The pathogenesis of Chlamydia-related arthritis can be considered distinct from that associated with enteric bacteria since it involves metabolically active organisms residing long-term within monocytic cells in synovial tissues, after resolution of the primary genital infection and migration of the cells to the joint, a process that is known as persistence [56, [61] [62] [63] . Studies indicate inflammatory bowel disease, or, at least, intestinal inflammation, is more prevalent in SpA patients (AS or others) and some genes associated with AS are also associated with IBD [83, 85] , including genes related to gut physiology and immunology. abstract: There has been a progressive interest on the modifications of the human defense system following insults occurring in the interface between our body and the external environment, as they may provoke or worsen disease states. Studies suggest the billions of germs that compose the gut microbiota influence one’s innate and adaptive immune responses at the intestinal level, but these microorganisms may also impact rheumatic diseases. The microbiota of the skin, respiratory and urinary tracts may also be relevant in rheumatology. Evidence indicates that changes in the gut microbiome alter the pathogenesis of immune-mediated diseases such as rheumatoid arthritis and ankylosing spondylitis but also of other disorders like atherosclerosis and osteoarthritis. Therapeutic strategies to modify the microbiota, including probiotics and fecal microbiota transplantation, have been received with skepticism, which, in turn, has drawn attention back to previously developed interventions such as antibiotics. Helminths adapted to humans over the evolution process, but their role in disease modulation, particularly immune-mediated diseases, remains to be understood. The present review focuses on data concerning modifications of the immune system induced by interactions with microbes and pluricellular organisms, namely helminths, and their impact on rheumatic diseases. Practical aspects, including specific microbiota-targeted therapies, are also discussed. url: https://api.elsevier.com/content/article/pii/S1521694220300450 doi: 10.1016/j.berh.2020.101528 id: cord-016235-2lhrkmrv author: Roden, Anja C. title: Lung date: 2010-05-17 words: 12865.0 sentences: 674.0 pages: flesch: 35.0 cache: ./cache/cord-016235-2lhrkmrv.txt txt: ./txt/cord-016235-2lhrkmrv.txt summary: Unlike the situation with heart transplant recipients, chronic vascular rejection in lung transplants has not resulted in graft loss; however, some patients develop pulmonary hypertension particularly those with BOS [92, 111] . However, based on the link between acute rejection and development of BOS, surveillance transbronchial biopsies in asymptomatic lung transplant recipients has become common practice in many large lung transplantation centers because evidence suggests that patients who have multiple episodes of low grade (A1) lesions within the first 12 months posttransplantation develop early onset BOS. A study [49] in which surveillance transbronchial biopsies were performed at 3, 6, 9, and 12 weeks posttransplantation, at the time of symptoms, and for follow-up of acute rejection or CMV pneumonia showed that patients who develop acute small airways rejection within the first year after transplantation are at risk of development of BOS at 1.76, 3.3, and 5.5 years after detection of B3/ B4 lesion (by 1996 ISHLT criteria, see Table 7 .2), B2 lesion or B0/B1 lesion, respectively. abstract: Experiments with animals in the 1940 and 1950s demonstrated that lung transplantation was technically possible [33]. In 1963, Dr. James Hardy performed the first human lung transplantation. The recipient survived 18 days, ultimately succumbing to renal failure and malnutrition [58]. From 1963 through 1978, multiple attempts at lung transplantation failed because of rejection and complications at the bronchial anastomosis. In the 1980s, improvements in immunosuppression, especially the introduction of cyclosporin A, and enhanced surgical techniques led to renewed interest in organ transplantation. In 1981, a 45-year-old-woman received the first successful heart–lung transplantation for idiopathic pulmonary arterial hypertension (IPAH) [106]. She survived 5 years after the procedure. Two years later the first successful single lung transplantation for idiopathic pulmonary fibrosis (IPF) [128] was reported, and in 1986 the first double lung transplantation for emphysema [25] was performed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120462/ doi: 10.1007/978-3-540-79343-4_7 id: cord-017856-4fccnygg author: Roden, Anja C. title: Pathology of Lung Rejection: Cellular and Humoral Mediated date: 2018-04-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Acute rejection is an important risk factor for bronchiolitis obliterans syndrome, the clinical manifestation of chronic airway rejection in lung allograft recipients. Patients with acute rejection might be asymptomatic or present with symptoms that are not specific and can be also seen in other conditions. Clinical tests such as pulmonary function tests and imaging studies among others usually are abnormal; however, their results are also not specific for acute rejection. Histopathologic features of acute rejection in adequate samples of transbronchial lung biopsy of the lung allograft are currently the gold standard to assess for acute rejection in lung transplant recipients. Acute alloreactive injury can affect both the vasculature and the airways. Currently, the guidelines of the 2007 International Society of Heart and Lung Transplantation consensus conference are recommended for the histopathologic assessment of rejection. There are no specific morphologic features recognized to diagnose antibody-mediated rejection (AMR) in lung allografts. Therefore, the diagnosis of AMR currently requires a “triple test” including clinical features, serologic evidence of donor-specific antibodies, and pathologic findings supportive of AMR. Complement 4d deposition is used to support a diagnosis of AMR in many solid organ transplants; however, its significance for the diagnosis of AMR in lung allografts is not entirely clear. This chapter discusses the currently recommended guidelines for the assessment of cellular rejection of lung allografts and summarizes our knowledge about morphologic features and immunophenotypic tests that might help in the diagnosis of AMR. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122533/ doi: 10.1007/978-3-319-91184-7_13 id: cord-299279-v0vznri2 author: Røder, Gustav title: Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501 date: 2008-05-17 words: 2815.0 sentences: 178.0 pages: flesch: 68.0 cache: ./cache/cord-299279-v0vznri2.txt txt: ./txt/cord-299279-v0vznri2.txt summary: The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making it available for interactions with a potential T-cell receptor. The overall structure of the present HLA-B*1501 peptide-binding groove is similar to the previously two determined HLA-B*1501 structures (Røder et al., 2006) and to other MHC-I molecules (see Fig. 1 ). The pGln2 peptide residue is located in the B pocket in the same orientation as the pGlu2 in the previously described HLA-B*1501-LEKARGSTY structure (Røder et al., 2006) . The pGlu4 peptide residue points away from the peptide-binding groove and the side chain does not interact with any HLA-B*1501 residues. The conformation observed does not interact with any HLA-B*1501 residues, but makes a hydrogen bond to two water molecules (HOH67 and HOH348) present between the peptide and the floor of the peptide-binding groove, thereby forming water-mediated contacts with the HLA-B*1501 protein. abstract: The human leukocyte antigen (HLA) class I system comprises a highly polymorphic set of molecules that specifically bind and present peptides to cytotoxic T cells. HLA-B*1501 is a prototypical member of the HLA-B62 supertype and only two peptide–HLA-B*1501 structures have been determined. Here, the crystal structure of HLA-B*1501 in complex with a SARS coronavirus-derived nonapeptide (VQQESSFVM) has been determined at high resolution (1.87 Å). The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making it available for interactions with a potential T-cell receptor. url: https://www.ncbi.nlm.nih.gov/pubmed/18540051/ doi: 10.1107/s1744309108012396 id: cord-280172-6o1gqe8v author: Sanami, Samira title: Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date: 2020-07-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused COVID-19 disease in China. So far, no vaccine has licensed to protect against infection with COVID-19, therefore an effective COVID-19 vaccine needed. The aim of this study was to predict antigenic peptides of SARS-CoV-2 for designing the COVID-19 vaccine using immunoinformatic analysis. In this study, T and B-cell epitopes of S protein were predicted and screened based on the antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. The epitopes were joined by the appropriate linker. LT-IIc as an adjuvant was attached to the end of the structure. The secondary and 3D structure of the vaccine was predicted. The refinement process was performed to improve the quality of the 3D model structure; the validation process is performed using the Ramachandran plot and ProSA z-score. The proposed vaccine's binding affinity to the HLA-A11: 01 and HLA-DRB1_01: 01 molecule was evaluated by molecular docking. Using molecular dynamics, the stability of vaccine-HLA complexes was also evaluated. Finally, in silico gene cloning was performed in the pET30a (+) vector. The findings suggest that the current vaccine may be a promising vaccine to prevent SARS-CoV-2 infection. url: https://doi.org/10.1016/j.ijbiomac.2020.07.117 doi: 10.1016/j.ijbiomac.2020.07.117 id: cord-271032-imc6woht author: Schulte-Schrepping, Jonas title: Severe COVID-19 is marked by a dysregulated myeloid cell compartment date: 2020-08-05 words: 9740.0 sentences: 692.0 pages: flesch: 58.0 cache: ./cache/cord-271032-imc6woht.txt txt: ./txt/cord-271032-imc6woht.txt summary: Given the dramatic changes in various immune cell populations (Fig. 1C+D) , we next 171 assessed their composition and activation state by droplet-based scRNA-seq in 27 samples 172 from 18 COVID-19 patients (8 mild & 10 severe, cohort 1, Table S1 ) collected between day 173 3 and day 20 after symptom onset. All LDNs also expressed high levels of alarmins S100A8 and S100A9 (Fig. 5D) , whereas 343 other S100 genes (e.g. S100A4, S100A12) were strongly induced in selected neutrophil 344 Alterations of the neutrophil compartment were further interrogated by mass cytometry of 362 whole blood samples of COVID-19 patients (n=8 mild + 9 severe, cohort 1), FLI patients 363 (n=8), and age-and gender-matched controls (n=9) (Table S1), using a panel designed to 364 detect myeloid cell maturation and activation states as well as markers of 365 immunosuppression or dysfunction (Table S2) . abstract: Summary Coronavirus Disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progresses to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19, associated with increased neutrophil counts and dysregulated immune responses, remains unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole blood and peripheral blood mononuclear cells to determine changes in immune cell composition and activation in mild vs. severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and it reveals profound alterations in the myeloid cell compartment associated with severe COVID-19. url: https://doi.org/10.1016/j.cell.2020.08.001 doi: 10.1016/j.cell.2020.08.001 id: cord-310252-0cdqhrcw author: Seliger, Barbara title: Chapter 7 IFN Inducibility of Major Histocompatibility Antigens in Tumors date: 2008-12-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Interferons represent a protein family with pleiotropic functions including immunomodulatory, cytostatic, and cytotoxic activities. Based on these effects, interferons are involved in innate as well as adaptive immunity, thereby shaping the tumor host immune responses. These cytokines, alone or in combination, have been successfully implemented for the treatment of some malignancies. However, it has been recently demonstrated that tumor cells could be resistant to interferon treatment, which may be associated with an escape of tumor cells from immune surveillance. Therefore, the aim of this chapter is to summarize the frequency of impaired interferon signal transduction, their underlying molecular mechanisms, and their clinical relevance. url: https://www.ncbi.nlm.nih.gov/pubmed/19055946/ doi: 10.1016/s0065-230x(08)00407-7 id: cord-275608-joyan7ij author: Sewell, Andrew K. title: Why must T cells be cross-reactive? date: 2012-08-24 words: 7748.0 sentences: 347.0 pages: flesch: 47.0 cache: ./cache/cord-275608-joyan7ij.txt txt: ./txt/cord-275608-joyan7ij.txt summary: However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide–MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide-MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. Box 1 | Extensive T cell cross-reactivity and apparent specificity are not incongruous From the 20 proteinogenic amino acids, it is possible to generate vast numbers of peptides of a length that can be presented by MHC molecules (see the table). First, a cross-reactive T cell repertoire generates a near perfect solution to the huge challenge of providing effective immune cover by allowing a limited number of T cells to provide immunity against virtually all foreign peptides that can bind to self MHC molecules. abstract: Clonal selection theory proposed that individual T cells are specific for a single peptide–MHC antigen. However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide–MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. This compromise on specificity has profound implications because the chance of any natural peptide–MHC ligand being an optimal fit for its cognate TCR is small, as there will almost always be more-potent agonists. Furthermore, any TCR raised against a specific peptide–MHC complex in vivo can only be the best available solution from the naive T cell pool and is unlikely to be the best possible solution from the substantially greater number of TCRs that could theoretically be produced. This 'systems view' of TCR recognition provides a plausible cause for autoimmune disease and substantial scope for multiple therapeutic interventions. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nri3279) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/22918468/ doi: 10.1038/nri3279 id: cord-284944-hcgfe9wv author: Silvin, Aymeric title: Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19 date: 2020-08-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Summary Blood myeloid cells are known to be dysregulated in the coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2. It is unknown whether the innate myeloid response differs with disease severity, and whether markers of innate immunity discriminate high risk patients. Thus, we performed high dimensional flow cytometry and single cell RNA sequencing of COVID-19 patient peripheral blood cells and detected the disappearance of non-classical CD14LowCD16High monocytes, the accumulation of HLA-DRLow classical monocytes, and the release of massive amounts of calprotectin (S100A8/S100A9) in severe cases. Immature CD10LowCD101-CXCR4+/- neutrophils with an immuno-suppressive profile accumulated as well in blood and lungs, suggesting emergency myelopoiesis. We finally showed that calprotectin plasma level and a routine flow cytometry assay detecting decreased frequencies of non-classical monocytes could discriminate patients who develop a severe COVID-19 form, suggesting a predictive value that deserves prospective evaluation. url: https://www.sciencedirect.com/science/article/pii/S0092867420309934?v=s5 doi: 10.1016/j.cell.2020.08.002 id: cord-344691-vmc0rrrk author: Srinivasan, K.N. title: Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens date: 2004-08-04 words: 3654.0 sentences: 184.0 pages: flesch: 52.0 cache: ./cache/cord-344691-vmc0rrrk.txt txt: ./txt/cord-344691-vmc0rrrk.txt summary: Results: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. A number of predictive methods for MHC classes I and II binding peptides are available, including those based on binding motifs (Rammensee et al., 1995) , quantitative matrices (Parker et al., 1994) , artificial neural networks (ANNs) , hidden Markov models (HMMs) (Mamitsuka, 1998) , multivariate statistical approaches (Guan et al., 2003) , support vector machines (Zhao et al., 2003) and decision trees (Savoie et al., 1999) . In our prediction of promiscuous class I T-cell epitopes, we made predictions of T-cell epitope hot spots in nucleocapsid protein of the severe acute respiratory syndrome coronavirus (SARS-CoV). MULTIPRED, a computational system developed for human leukocyte antigen (HLA) classes I-A2 and I-A3 binding, predicts individual 9-mer T-cell epitopes and also promiscuous class I regions as immunological hot spots, based on HMM and ANN models (Zhang et al., 2003) . abstract: Motivation: Processing and presentation of major histocompatibility complex class I antigens to cytotoxic T-lymphocytes is crucial for immune surveillance against intracellular bacteria, parasites, viruses and tumors. Identification of antigenic regions on pathogen proteins will play a pivotal role in designer vaccine immunotherapy. We have developed a system that not only identifies high binding T-cell antigenic epitopes, but also class I T-cell antigenic clusters termed immunological hot spots. Methods: MULTIPRED, a computational system for promiscuous prediction of HLA class I binders, uses artificial neural networks (ANN) and hidden Markov models (HMM) as predictive engines. The models were rigorously trained, tested and validated using experimentally identified HLA class I T-cell epitopes from human melanoma related proteins and human papillomavirus proteins E6 and E7. We have developed a scoring scheme for identification of immunological hot spots for HLA class I molecules, which is the sum of the highest four predictions within a window of 30 amino acids. Results: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. The analysis of proteins E6 and E7 showed that ANN models appear to be more accurate for prediction of HLA-A3 hot spots and HMM models for HLA-A2 predictions. For illustration of its utility we applied MULTIPRED for prediction of promiscuous T-cell epitopes in all four SARS coronavirus structural proteins. MULTIPRED predicted HLA-A2 and HLA-A3 hot spots in each of these proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/15262812/ doi: 10.1093/bioinformatics/bth943 id: cord-343262-zopxdw1d author: Srinivasan, Raghuraman C. title: Effects of Cryogenic Storage on Human Amnion Epithelial Cells date: 2020-07-15 words: 5436.0 sentences: 283.0 pages: flesch: 42.0 cache: ./cache/cord-343262-zopxdw1d.txt txt: ./txt/cord-343262-zopxdw1d.txt summary: In this study, hAEC were isolated from full-term human placenta from 14 different donors, cryopreserved using a protocol and reagents commonly adopted for epithelial cell preservation. In anticipation that the transplant product used in any future clinical trial will be previously cryopreserved cells, the current study was undertaken to determine if there are any significant differences between the populations initially isolated from the amnion membranes, and the cells recovered following the cryopreservation procedure. The presence of CD45, a receptor linked to protein tyrosine phosphatase present in cells of the hematopoietic lineage, was detected in 9/12 of hAEC preparations immediately after isolation at an average level of 1.2% ± 1.4% cells, but greatly reduced after cryopreservation and washing steps, where only four preparations still contained an extremely low number of CD45 positive cells (0.3% ± 0.4%; p = 0.0146) ( Figure 2D ). The presence of HLA-G on hAEC after isolation was confirmed using a specific antibody, and HLA-G Amnion epithelial cells have been reported to express characteristic immunomodulatory molecules, such as HLA class Ib [21, 22] . abstract: Perinatal stem cells and epithelial cells isolated from full term amnion membrane, in particular, have attracted interest over the last decade, as a promising source of multipotent cells for cellular therapies. Human amnion epithelial cells (hAEC) have been used to treat monogenetic liver disease such as maple syrup urine disease or fibrosis of the liver in preclinical studies. In most studies xeno-transplants of hAEC were conducted without providing immunosuppression to recipients, reflecting the tolerogenic properties of hAEC. For many cell types, successful cryopreservation is critical for providing a readily available, off-the-shelf product. In this study, hAEC were isolated from full-term human placenta from 14 different donors, cryopreserved using a protocol and reagents commonly adopted for epithelial cell preservation. The cells were analyzed in terms of survival, recovery, and homogeneity, profiled for surface markers characteristic of epithelial, mesenchymal, endothelial, or hematopoietic cells. There were no significant differences observed in the percentage of cells with epithelial cell markers before and after cryopreservation. The relative proportion of stromal and hematopoietic cells was significantly reduced in hAEC preparations after cryopreservation. The expression of stem cell and immunomodulatory molecules were confirmed in the final product. Since multipotent cells are readily available from full-term placenta, this novel cell source might significantly increase the number of patients eligible to receive cellular therapies for liver and other diseases. url: https://doi.org/10.3390/cells9071696 doi: 10.3390/cells9071696 id: cord-034402-64xz1j9i author: Srivastava, Shivani title: Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach date: 2020-10-29 words: 4517.0 sentences: 286.0 pages: flesch: 52.0 cache: ./cache/cord-034402-64xz1j9i.txt txt: ./txt/cord-034402-64xz1j9i.txt summary: This present study aims at the prediction of B cell epitopes for subunit vaccine designing against Listeria monocytogenes using a reverse vaccinology approach. For computational identification and characterization of epitopes for the preparation of subunit vaccine designing, complete proteome analysis of Listeria monocytogenes F2365 strain (GenBank accession number AE017262.2) was performed using the UniProtKB database. The first requirement in the reverse vaccinology approach of vaccine designing is to eliminate all non-allergic proteins from a complete proteome set of bacteria, Listeria monocytogenes. In this exploration and investigation, the prediction of B cell epitopes has been performed by the authors for the designing of the vaccine against listeriosis by using a reverse vaccinology approach. Tertiary structure modeling of alleles was generated with the help of HLA alleles were performed Based on low binding energy, 4 peptides were selected viz., CEETFGIRL, MKFLFPLKL, FLKIDPPIL, and VRH-HGGGHK. abstract: Listeriosis is a major foodborne infection provoked by a bacterium known as Listeria monocytogenes. It is one of the predominant causes of death in pregnant women, infants, and immunocompromised persons. Despite such fatal effects, until now there is no proper medication or drug available for such a serious foodborne infection. One of the most promising ways to deal with this challenge is vaccination. This present study aims at the prediction of B cell epitopes for subunit vaccine designing against Listeria monocytogenes using a reverse vaccinology approach. Among screened out 299 epitopes of strain F2365 of Listeria monocytogenes, based on the VaxiJen score, the top 20 epitopes were selected. 3D modeling of epitopes and alleles was generated by PEPstrMOD and Swiss Model respectively. Molecular docking reveals 4 epitopes viz., MKFLFPLKL, CEETFGIRL, FLKIDPPIL, and VRHHGGGHK based on binding energy. All 4 epitopes were investigated for non-toxicity, binding affinity, and population coverage. After vigorous investigation, epitope FLKIDPPIL was anticipated as the best vaccine contender. The stability of the FLKIDPPIL-HLA DRB1 _0101 complex was proved by performing the simulation. Here, predicted peptide through the Insilico approach may become a potential remedy against listeriosis, after the wet-lab approach and clinical trials. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7595573/ doi: 10.1007/s10989-020-10128-1 id: cord-342942-1s32o9m8 author: Stamatakis, George title: Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date: 2020-06-22 words: 4074.0 sentences: 209.0 pages: flesch: 47.0 cache: ./cache/cord-342942-1s32o9m8.txt txt: ./txt/cord-342942-1s32o9m8.txt summary: Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. abstract: Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 greatly limited the variability of peptide sequences produced. Less than 7% of computationally predicted epitopes were found to be produced experimentally, suggesting that aminopeptidase processing may constitute a significant filter to epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness for viral antigenic epitopes. url: https://doi.org/10.1101/2020.06.22.164681 doi: 10.1101/2020.06.22.164681 id: cord-288496-7rrh2gg6 author: Stryhn, Anette title: A Systematic, Unbiased Mapping of CD8(+) and CD4(+) T Cell Epitopes in Yellow Fever Vaccinees date: 2020-08-31 words: 15229.0 sentences: 676.0 pages: flesch: 50.0 cache: ./cache/cord-288496-7rrh2gg6.txt txt: ./txt/cord-288496-7rrh2gg6.txt summary: Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. abstract: Examining CD8(+) and CD4(+) T cell responses after primary Yellow Fever vaccination in a cohort of 210 volunteers, we have identified and tetramer-validated 92 CD8(+) and 50 CD4(+) T cell epitopes, many inducing strong and prevalent (i.e., immunodominant) T cell responses. Restricted by 40 and 14 HLA-class I and II allotypes, respectively, these responses have wide population coverage and might be of considerable academic, diagnostic and therapeutic interest. The broad coverage of epitopes and HLA overcame the otherwise confounding effects of HLA diversity and non-HLA background providing the first evidence of T cell immunodomination in humans. Also, double-staining of CD4(+) T cells with tetramers representing the same HLA-binding core, albeit with different flanking regions, demonstrated an extensive diversification of the specificities of many CD4(+) T cell responses. We suggest that this could reduce the risk of pathogen escape, and that multi-tetramer staining is required to reveal the true magnitude and diversity of CD4(+) T cell responses. Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4(+) and/or CD8(+) T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. This approach is systematic, exhaustive, and can be done in any individual of any HLA haplotype. It is all-inclusive in the sense that it includes all protein antigens and peptide epitopes, and encompasses both CD4(+) and CD8(+) T cell epitopes. It is efficient and, importantly, reduces the false discovery rate. The unbiased nature of the T cell epitope discovery approach presented here should support the refinement of future peptide-HLA class I and II predictors and tetramer technologies, which eventually should cover all HLA class I and II isotypes. We believe that future investigations of emerging pathogens (e.g., SARS-CoV-2) should include population-wide T cell epitope discovery using blood samples from patients, convalescents and/or long-term survivors, who might all hold important information on T cell epitopes and responses. url: https://www.ncbi.nlm.nih.gov/pubmed/32983097/ doi: 10.3389/fimmu.2020.01836 id: cord-001247-pxzbirqd author: Sun, Lu title: A new unconventional HLA-A2-restricted epitope from HBV core protein elicits antiviral cytotoxic T lymphocytes date: 2014-03-22 words: 4630.0 sentences: 259.0 pages: flesch: 55.0 cache: ./cache/cord-001247-pxzbirqd.txt txt: ./txt/cord-001247-pxzbirqd.txt summary: Our data therefore provide insights into the structure characteristics of this unconventional epitope binding to MHC-I molecules, as well as epitope specific CTL activity that orchestrate T cell response and immune evasion in HBV infected patients. To identify immune-dominant HBV-specific CTL epitopes, especially epitopes from HBc protein, is therefore necessary for monitoring T cell responses during disease progression, as well as for developing epitope-based therapeutic vaccines against CHB (Inchauspe and Michel, 2007; Gordon et al., 2013; Liu et al., 2013a, b) . To further determine the epitope-specific CTLs, fresh PBMCs from HLA-A2 + AHB patients were stimulated with HBc141-149 peptide and detected by ex vivo IFN-γ ELISPOT assays. In this study, we identified a new HLA-A2-restricted CD8 + T cell epitope HBc141-149 by screening an overlapping 9-mer peptide pool covering HBV core protein. abstract: Cytotoxic T cells (CTLs) play a key role in the control of Hepatitis B virus (HBV) infection and viral clearance. However, most of identified CTL epitopes are derived from HBV of genotypes A and D, and few have been defined in virus of genotypes B and C which are more prevalent in Asia. As HBV core protein (HBc) is the most conservative and immunogenic component, in this study we used an overlapping 9-mer peptide pool covering HBc to screen and identify specific CTL epitopes. An unconventional HLA-A2-restricted epitope HBc141–149 was discovered and structurally characterized by crystallization analysis. The immunogenicity and anti-HBV activity were further determined in HBV and HLA-A2 transgenic mice. Finally, we show that mutations in HBc141–149 epitope are associated with viral parameters and disease progression in HBV infected patients. Our data therefore provide insights into the structure characteristics of this unconventional epitope binding to MHC-I molecules, as well as epitope specific CTL activity that orchestrate T cell response and immune evasion in HBV infected patients. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978166/ doi: 10.1007/s13238-014-0041-4 id: cord-312865-nno2yjae author: Sylvester‐Hvid, C. title: SARS CTL vaccine candidates; HLA supertype‐, genome‐wide scanning and biochemical validation date: 2004-04-23 words: 2118.0 sentences: 114.0 pages: flesch: 45.0 cache: ./cache/cord-312865-nno2yjae.txt txt: ./txt/cord-312865-nno2yjae.txt summary: One would therefore expect that an effective vaccine should induce mucosal immunity such as that effected by secretory immunoglobulin A (IgA), which specifically prevents an infectious agent from penetrating the mucosal epithelium, and by cytotoxic T lymphocytes (CTLs), which specifically eradicate infected cells (5) . Human CTLs are specific for peptides presented in the context of human leukocyte antigen (HLA) molecules [generically known as ''''major histocompatibility complex (MHC) molecules'''']. Thus, 13 of the 15 peptides predicted to be good binders to A*0301 were found to bind to another member of the A3 supertype, HLA-A*1101. Similarly, nine of the 15 peptides predicted to be good binders to A*1101 were found to bind to HLA-A*0301 (Table 1) Once all nine supertypes have been tested, we would project to have found well over 100 different vaccine candidates. Immunogenicity of a human immunodeficiency virus (HIV) polytope vaccine containing multiple HLA A2 HIV CD8(þ) cytotoxic T-cell epitopes abstract: Abstract: An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T‐lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)‐restricted presentation of SARS‐derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477–91). The latter was recently established when a causative coronavirus (SARS‐CoV) was isolated and full‐length sequenced (Marra et al., Science 2003: 300: 1399–404). Here, we have combined advanced bioinformatics and high‐throughput immunology to perform an HLA supertype‐, genome‐wide scan for SARS‐specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201–12). For each HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design. url: https://www.ncbi.nlm.nih.gov/pubmed/15104671/ doi: 10.1111/j.0001-2815.2004.00221.x id: cord-333966-st6gyozv author: Taherkhani, Reza title: Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date: 2015-03-17 words: 5199.0 sentences: 255.0 pages: flesch: 51.0 cache: ./cache/cord-333966-st6gyozv.txt txt: ./txt/cord-333966-st6gyozv.txt summary: The aim of this study was to design a high density multiepitope protein, which can be a promising multiepitope vaccine candidate against Hepatitis E virus (HEV). Therefore, the present study was undertaken to design a high density multiepitope protein compromising four HTL epitopes with high-affinity binding to the HLA molecules using the in silico analysis, and to evaluate the immunological properties of this protein in vitro. In brief, approximately 1  10 5 cells/well of PBMCs of each sample in RPMI 1640 and 10% FCS were added to four wells of round-bottom 96-well plates in total volume of 180 ml/well, stimulated with 20 ml/well of truncated ORF2 protein (10 mg/ml), high density multiepitope (10 mg/ml) and Phytohemagglutinin (PHA) (5 mg/ml) (Sigma-Aldrich) separately, and incubated at 37˚C for 4 days. IFN-g ELISPOT responses to high density multiepitope protein and truncated ORF2 protein were found significantly higher in HEV-recovered individuals than control group (P < 0.001). abstract: The aim of this study was to design a high density multiepitope protein, which can be a promising multiepitope vaccine candidate against Hepatitis E virus (HEV). Initially, conserved and antigenic helper T‐lymphocyte (HTL) epitopes in the HEV capsid protein were predicted by in silico analysis. Subsequently, a multiepitope comprising four HTL epitopes with high‐affinity binding to the HLA molecules was designed, and repeated four times as high density multiepitope construct. This construct was synthesized and cloned into pET‐30a (+) vector. Then, it was transformed and expressed in Escherichia coli BL21 cells. The high density multiepitope protein was purified by Ni‐NTA agarose and concentrated using Amicon filters. Finally, the immunological properties of this high density multiepitope protein were evaluated in vitro. The results showed that the high density multiepitope construct was successfully expressed and purified. SDS‐PAGE and Western blot analyses showed the presence of a high density multiepitope protein band of approximately 33 kDa. Approximately 1 mg of the purified protein was obtained from each liter of the culture media. Moreover, the purified multiepitope protein was capable of induction of proliferation responses, IFN‐γ ELISPOT responses and IFN‐γ and IL‐12 cytokines production in a significant level in peripheral blood mononuclear cells (PBMCs) isolated from HEV‐recovered individuals compared to the control group. In conclusion, the newly produced multiepitope protein can induce significant T helper type 1 responses in vitro, and can be considered as a novel strategy for the development of HEV vaccines in the future. J. Med. Virol. 87:1225–1234, 2015. © 2015 Wiley Periodicals, Inc. url: https://doi.org/10.1002/jmv.24171 doi: 10.1002/jmv.24171 id: cord-298169-2133gahl author: Tamouza, Ryad title: Understanding the genetic contribution of the Human Leukocyte Antigen system to common major psychiatric disorders in a world pandemic context date: 2020-10-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The human leukocyte antigen (HLA) is a complex genetic system that encodes proteins which predominantly regulate immune/inflammatory processes. It can be involved in a variety of immuno-inflammatory disorders ranging from infections to autoimmunity and cancers. The HLA system is also suggested to be involved in neurodevelopment and neuroplasticity, especially through microglia regulation and synaptic pruning. Consequently, this highly polymorphic gene region has recently emerged as a major player in the etiology of several major psychiatric disorders, such as schizophrenia, autism spectrum disorder and bipolar disorder and with less evidence for major depressive disorders and attention deficit hyperactivity disorder. We thus review here the role of HLA genes in particular subgroups of psychiatric disorders and foresee their potential implication in future research. In particular, given the prominent role that the HLA system plays in the regulation of viral infection, this review is particularly timely in the context of the Covid-19 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/33031918/ doi: 10.1016/j.bbi.2020.09.033 id: cord-103662-a4ok5wqc author: Tarek, M. title: Custommune: a web tool to design personalized and population-targeted vaccine epitopes date: 2020-04-29 words: 8116.0 sentences: 454.0 pages: flesch: 45.0 cache: ./cache/cord-103662-a4ok5wqc.txt txt: ./txt/cord-103662-a4ok5wqc.txt summary: When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this aim, by intersecting input data from patient-specific viral sequences and HLA alleles, Custommune provides an output of epitopes of desired length filtered for their predicted specificity, immunogenicity and mutation potential. Class I and Class II HLA alleles which were predicted by Custommune to bind RBDp and RBDg epitopes of SARS-CoV-2 were used to estimate potential vaccine coverage in the populations of interest. abstract: Computational prediction of immunogenic epitopes is a promising platform for therapeutic and preventive vaccine design. A potential target for this strategy is human immunodeficiency virus (HIV-1), for which, despite decades of efforts, no vaccine is available. In particular, a therapeutic vaccine devised to eliminate infected cells would represent a key component of cure strategies. HIV peptides designed based on individual viro-immunological data from people living with HIV/AIDS have recently shown able to induce post-therapy viral set point abatement. However, the reproducibility and scalability of this method is curtailed by the errors and arbitrariness associated with manual peptide design as well as by the time-consuming process. We herein introduce Custommune, a user-friendly web tool to design personalized and population-targeted vaccines. When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. Of note, Custommune predictions compared favorably with manually designed peptides administered in a recent phase II clinical trial (NCT02961829). Furthermore, we utilized Custommune to design preventive vaccines targeted for populations highly affected by COVID-19. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Overall, our data describe a new tool for rapid development of personalized or population-based immunotherapy against chronic and acute viral infections. url: http://medrxiv.org/cgi/content/short/2020.04.25.20079426v1?rss=1 doi: 10.1101/2020.04.25.20079426 id: cord-022474-xxy83c6u author: Tenorio, Grace C. title: Transfusion Medicine and Immunohematology date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Blood transfusion is essential and vital in the successful treatment of many malignant and nonmalignant hematological disorders. Children with thalassemia, adults with myelodysplastic syndromes, and patients with autoimmune hemolytic anemias, leukemias, or aplastic anemias become chronically dependent on blood transfusions. Modern treatment procedures such as high-dose chemotherapy and progenitor cell transplantation require intensive support with blood components and products. The serological basis of blood transfusion, the available blood components and products, and adverse effects of blood transfusion with special emphasis on infectious disease transmission are discussed in this chapter. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155745/ doi: 10.1007/978-1-59745-149-9_22 id: cord-319993-er3sm4u8 author: Terry, Frances E title: Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases date: 2015-01-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Vaccines have been invaluable for global health, saving lives and reducing healthcare costs, while also raising the quality of human life. However, newly emerging infectious diseases (EID) and more well-established tropical disease pathogens present complex challenges to vaccine developers; in particular, neglected tropical diseases, which are most prevalent among the world’s poorest, include many pathogens with large sizes, multistage life cycles and a variety of nonhuman vectors. EID such as MERS-CoV and H7N9 are highly pathogenic for humans. For many of these pathogens, while their genomes are available, immune correlates of protection are currently unknown. These complexities make developing vaccines for EID and neglected tropical diseases all the more difficult. In this review, we describe the implementation of an immunoinformatics-driven approach to systematically search for key determinants of immunity in newly available genome sequence data and design vaccines. This approach holds promise for the development of 21st century vaccines, improving human health everywhere. url: https://doi.org/10.1586/14760584.2015.955478 doi: 10.1586/14760584.2015.955478 id: cord-346445-hgqohdct author: Toyoshima, Yujiro title: SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date: 2020-07-22 words: 3553.0 sentences: 187.0 pages: flesch: 53.0 cache: ./cache/cord-346445-hgqohdct.txt txt: ./txt/cord-346445-hgqohdct.txt summary: Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. In this study, we comprehensively analyzed 12,343 SARS-CoV-2 genome sequences isolated from patients/ individuals in six geographic areas, including Asia, North America, South America, Europe, Oceania, and Africa, and investigated their correlations to the fatality rates in 28 different countries. In this study, we investigated the SARS-CoV-2 virus mutations and found that the frequencies of S protein 614G variant and its highly linked variant, ORF1ab 4715L, were significantly correlated with fatality rates in the 28 countries and 17 states of the United States. In summary, we comprehensively investigated SARS-CoV-2 genome mutations, BCG-vaccination status, and HLA genotypes in the 28 different countries and identified significant associations of some virus genome variants with the fatality rates. abstract: The coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, has rapidly expanded to a global pandemic. However, numbers of infected cases, deaths, and mortality rates related to COVID-19 vary from country to country. Although many studies were conducted, the reasons of these differences have not been clarified. In this study, we comprehensively investigated 12,343 SARS-CoV-2 genome sequences isolated from patients/individuals in six geographic areas and identified a total of 1234 mutations by comparing with the reference SARS-CoV-2 sequence. Through a hierarchical clustering based on the mutant frequencies, we classified the 28 countries into three clusters showing different fatality rates of COVID-19. In correlation analyses, we identified that ORF1ab 4715L and S protein 614G variants, which are in a strong linkage disequilibrium, showed significant positive correlations with fatality rates (r = 0.41, P = 0.029 and r = 0.43, P = 0.022, respectively). We found that BCG-vaccination status significantly associated with the fatality rates as well as number of infected cases. In BCG-vaccinated countries, the frequency of the S 614G variant had a trend of association with the higher fatality rate. We also found that the frequency of several HLA alleles, including HLA-A*11:01, were significantly associated with the fatality rates, although these factors were associated with number of infected cases and not an independent factor to affect fatality rate in each country. Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. url: https://doi.org/10.1038/s10038-020-0808-9 doi: 10.1038/s10038-020-0808-9 id: cord-254190-bxfne94u author: Tu, Wenwei title: Application of Humanized Mice in Immunological Research date: 2015-07-07 words: 6246.0 sentences: 254.0 pages: flesch: 34.0 cache: ./cache/cord-254190-bxfne94u.txt txt: ./txt/cord-254190-bxfne94u.txt summary: On the contrary, humanized mice established by peripheral blood cells provide a ready platform for studying the functions of mature immune cells but the length of window appropriate for research is still limited by chronic GVHD and ongoing reduced engraftment. Distinct from their T cell companion, reconstitution of functional B lymphocytes is generally poor in humanized mice and needed to improve in the future although their primary repertoire were principally unaltered by the differences between mouse and human stromal environments [ 53 ] and their ability to produce antigen-specifi c antibody was partly developed [ 54 ] . In above three studies, investigators planted solid grafts into immunodefi cient mice before reconstitution of human immune system and induced rejection by infusion of mature human cells. Humanized immune system (HIS) mice as a tool to study human NK cell development Humanized mice as a model to study human hematopoietic stem cell transplantation abstract: During the past decade, the development of humanized mouse models and their general applications in biomedical research greatly accelerated the translation of outcomes obtained from basic research into potential diagnostic and therapeutic strategies in clinic. In this chapter, we firstly present an overview on the history and current progress of diverse humanized mouse models and then focus on those equipped with reconstituted human immune system. The update advancement in the establishment of humanized immune system mice and their applications in the studies of the development of human immune system and the pathogenesis of multiple human immune-related diseases are intensively reviewed here, while the shortcoming and perspective of these potent tools are discussed as well. As a valuable bridge across the gap between bench work and clinical trial, progressive humanized mouse models will undoubtedly continue to play an indispensable role in the wide area of biomedical research. url: https://doi.org/10.1007/978-1-4939-3139-2_10 doi: 10.1007/978-1-4939-3139-2_10 id: cord-031937-qhlatg84 author: Verma, Anukriti title: Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date: 2020-09-15 words: 6760.0 sentences: 326.0 pages: flesch: 31.0 cache: ./cache/cord-031937-qhlatg84.txt txt: ./txt/cord-031937-qhlatg84.txt summary: In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. The contributions of the microorganisms in the co-evolved IBD and ReA as part of the disease network was created through the interactive maps of the essential host interaction proteins (verified using literature survey) and the information processed through gene expression data analysis 64 . The pathways of the above host interacting proteins were found out using KEGG database that provides ontologies for proteins related to biological processes 67 www.nature.com/scientificreports/ Subsequently, the role of drugs or inhibitors used to suppress the effect of IBD and ReA such as indomethacin, prednisone, ciprofloxacin, sulfasalazine, azathioprine, methotrexate and hydroxychloroquine was scored in the disease network through their docking studies against the potential targets (both host as well microbial targets) as per published methodologies 68, 69 . abstract: Reactive Arthritis (ReA), a rare seronegative inflammatory arthritis, lacks exquisite classification under rheumatic autoimmunity. ReA is solely established using differential clinical diagnosis of the patient cohorts, where pathogenic triggers linked to enteric and urogenital microorganisms e.g. Salmonella, Shigella, Yersinia, Campylobacter, Chlamydia have been reported. Inflammatory Bowel Disease (IBD), an idiopathic enteric disorder co-evolved and attuned to present gut microbiome dysbiosis, can be correlated to the genesis of enteropathic arthropathies like ReA. Gut microbes symbolically modulate immune system homeostasis and are elementary for varied disease patterns in autoimmune disorders. The gut-microbiota axis structured on the core host-microbe interactions execute an imperative role in discerning the etiopathogenesis of ReA and IBD. This study predicts the molecular signatures for ReA with co-evolved IBD through the enveloped host-microbe interactions and microbe-microbe ‘interspecies communication’, using synonymous gene expression data for selective microbes. We have utilized a combinatorial approach that have concomitant in-silico work-pipeline and experimental validation to corroborate the findings. In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. Cross validation of the target/s or biomarker/s was done by targeted gene expression analysis following a non-probabilistic convenience sampling. Studies were performed to substantiate the host-microbe disease network consisting of protein-marker-symptom/disease-pathway-drug associations resulting in possible identification of vital drug targets, biomarkers, pathways and inhibitors for IBD and ReA. Our study identified Na((+))/H((+)) anti-porter (NHAA) and Kynureninase (KYNU) to be robust early and essential host-microbe interacting targets for IBD co-evolved ReA. Other vital host-microbe interacting genes, proteins, pathways and drugs include Adenosine Deaminase (ADA), Superoxide Dismutase 2 (SOD2), Catalase (CAT), Angiotensin I Converting Enzyme (ACE), carbon metabolism (folate biosynthesis) and methotrexate. These can serve as potential prognostic/theranostic biomarkers and signatures that can be extrapolated to stratify ReA and related autoimmunity patient cohorts for further pilot studies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7492238/ doi: 10.1038/s41598-020-71674-8 id: cord-294212-nlekz39f author: Wang, Dongliang title: Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date: 2020-07-03 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Currently, there is limited knowledge about the immunological profiles of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). We used computer-based immunoinformatic analysis and the newly resolved 3-dimensional (3D) structures of the SARS-CoV-2 S trimeric protein, together with analyses of the immunogenic profiles of SARS-CoV, to anticipate potential B-cell and T-cell epitopes of the SARS-CoV-2 S protein for vaccine design, particularly for peptide-driven vaccine design and serological diagnosis. Nine conserved linear B-cell epitopes and multiple discontinuous B-cell epitopes composed of 69 residues on the surface of the SARS-CoV-2 trimeric S protein were predicted to be highly antigenic. We found that the SARS-CoV-2 S protein has a different antigenic profile than that of the SARS-CoV S protein due to the variations in their primary and 3D structures. Importantly, SARS-CoV-2 may exploit an immune evasion mechanism through two point mutations in the critical and conserved linear neutralization epitope (overlap with fusion peptide) around a sparsely glycosylated area. These mutations lead to a significant decrease in the antigenicity of this epitope in the SARS-CoV-2 S protein. In addition, 62 T-cell epitopes in the SARS-CoV-2 S protein were predicted in our study. The structure-based immunoinformatic analysis for the SARS-CoV-2 S protein in this study may improve vaccine design, diagnosis, and immunotherapy against the pandemic of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32635180/ doi: 10.3390/vaccines8030355 id: cord-007719-3ypv9k9p author: Wang, Mingjun title: Classification of Human Leukocyte Antigen (HLA) Supertypes date: 2014-05-06 words: 3649.0 sentences: 158.0 pages: flesch: 51.0 cache: ./cache/cord-007719-3ypv9k9p.txt txt: ./txt/cord-007719-3ypv9k9p.txt summary: Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of importance for the development of new effective vaccines capable of activating the cellular arm of the immune response. Thus, identifi cation of new antigenic peptides, derived from infectious agents or tumor antigens, which may bind to HLA-I or HLA-II molecules in exchange with self-peptides normally occupying the HLA-binding site ( see below), is important for developing new effective vaccines capable of activating the cellular arm of the immune responses. To reduce this complexity, one option is to group thousands of different HLA molecules into clusters of several so-called HLA supertypes: a classifi cation that refers to a group of HLA alleles with largely overlapping peptide binding specifi cities. abstract: Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of importance for the development of new effective vaccines capable of activating the cellular arm of the immune response. However, the barrier to the development of peptide-based vaccines with maximum population coverage is that the restricting HLA genes are extremely polymorphic resulting in a vast diversity of peptide-binding HLA specificities and a low population coverage for any given peptide–HLA specificity. One way to reduce this complexity is to group thousands of different HLA molecules into several so-called HLA supertypes: a classification that refers to a group of HLA alleles with largely overlapping peptide binding specificities. In this chapter, we focus on the state-of-the-art classification of HLA supertypes including HLA-I supertypes and HLA-II supertypes and their application in development of peptide-based vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121184/ doi: 10.1007/978-1-4939-1115-8_17 id: cord-013894-1bgvj62a author: Wang, Qihui title: Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex date: 2019-07-04 words: 6883.0 sentences: 408.0 pages: flesch: 65.0 cache: ./cache/cord-013894-1bgvj62a.txt txt: ./txt/cord-013894-1bgvj62a.txt summary: Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Structural comparisons of LILRB1/2 binding to different HLA alleles Similar to previous reports, 14,17 D1 interacts with the HLA-G1 α3 domain. As assessed by the SPR assay, dimeric HLA-G1 presenting variable peptides displayed similar binding strengths for LILRB1 and LILRB2 (with four Ig-like domains or D1D2), indicating that the peptides seem to have no effect on the interactions. Structural data in this study indicate that through trans interaction, one HLA-G1 monomer binds to one LILRB1/2 molecule. The complex structure reported here provides the first direct evidence that D1D2 is responsible for all of the interactions with HLA-Is, while D3D4 is not the reason to explain why HLA-Is that carry a single residue substitution in their α1α2 domains or in the presented peptides display variable binding affinities to LILRB2. abstract: Leukocyte immunoglobulin (Ig)-like receptors (LILRs), also known as CD85 and immunoglobulin-like transcripts (ILTs), play pivotal roles in regulating immune responses. These receptors define an immune checkpoint that immune therapy can target. Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Although the discrete domains of LILRB1/2 are clear, the assembly mode of the four extracellular Ig-like domains (D1, D2, D3, and D4) remains unknown. Previous data indicate that D1D2 is responsible for binding to HLA class I (HLA-I), but the roles of D3D4 are still unclear. Here, we determined the crystal structure of the four Ig-like domain LILRB2 and four-domain LILRB1 in complex with HLA-G1. The angles between adjacent domains and the staggered assembly of the four domains suggest limited flexibility and limited plasticity of the receptors during ligand binding. The complex structure of four-domain LILRB1 and HLA-G1 supports the model that D1D2 is responsible for HLA-I binding, while D3D4 acts as a scaffold. Accordingly, cis and trans binding models for HLA-I binding to LILRB1/2 are proposed. The geometries of LILRB1/2 in complex with dimeric and monomeric HLA-G1 suggest the accessibility of the dimeric receptor, which in turn, transduces more inhibitory signals. The assembly of LILRB1/2 and its binding to HLA-G1 could aid in the design of immune regulators and benefit immune interference. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7609294/ doi: 10.1038/s41423-019-0258-5 id: cord-344364-vu389d88 author: Wang, Wei title: Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date: 2020-06-02 words: 1754.0 sentences: 115.0 pages: flesch: 61.0 cache: ./cache/cord-344364-vu389d88.txt txt: ./txt/cord-344364-vu389d88.txt summary: Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing (NGS). Frequencies of the HLA-C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID-19 patients than in the control population, with uncorrected statistical significance. The allele distributions of HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1 loci were compared between COVID-19 patients and control individuals. HLA-C*07:29, C*08:01G (including C*08:01 and C*08:22), B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 frequencies were higher in COVID-19 patients than in the control population, with uncorrected statistical significance (P < .05). 8 In the present study, HLA-C*07:29 was found in one COVID-19 patient, but in no individuals in the control group. 15, 16 In the present study, these SARS-susceptibility alleles were not found to occur at a significantly different frequency in COVID-19 patients after P-value correction. abstract: COVID‐19 is a respiratory disease caused by a novel coronavirus and is currently a global pandemic. HLA variation is associated with COVID‐19 because HLA plays a pivotal role in the immune response to pathogens. Here, 82 individuals with COVID‐19 were genotyped for HLA‐A, ‐B, ‐C, ‐DRB1, ‐DRB3/4/5, ‐DQA1, ‐DQB1, ‐DPA1, and ‐DPB1 loci using next‐generation sequencing (NGS). Frequencies of the HLA‐C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID‐19 patients than in the control population, with uncorrected statistical significance. Only HLA‐C*07:29 and B*15:27 were significant when the corrected P‐value was considered. These data suggested that some HLA alleles may be associated with the occurrence of COVID‐19. url: https://doi.org/10.1111/tan.13941 doi: 10.1111/tan.13941 id: cord-266902-wuty839o author: Wang, Yan title: Weak binder for MHC molecule is a potent Mycobacterium tuberculosis-specific CTL epitope in the context of HLA-A24 allele date: 2012-10-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstracts Tuberculosis causes serious health problem for the world population. Antigenic peptides selected by pathogen-specific cytotoxic T lymphocytes (CTLs) are presented by major histocompatibility complex (MHC; or human leukocyte antigen [HLA] in humans) molecules, and HLA-A restricted responses may be of interest for vaccine development and the understanding of cellular immunity. A series of peptides derived from the 10-KDa culture filtrate protein (CFP10) and the 6 kDa early secretory antigenic target (ESAT-6) in the Mycobacterium tuberculosis (Mtb) have been screened and a CTL epitope restricted by the human leukocyte antigen HLA-A24, a common HLA allele in Asian people, has been identified. In this study, we studied a panel of CFP10 and ESAT-6-derived peptides to identify those with binding motifs for HLA-A24 molecules. The antigenicity of candidate peptides was assessed with in vitro refolding tests and an enzyme-linked immunospot (ELISPOT) assay, and by tetramer staining to determine the capacity to stimulate CTLs from peripheral blood mononuclear cells (PBMCs) of HLA-A24-positive TB Patients. We report that one novel candidate peptide at positions 5–14 of ESAT-6 of Mtb could induce peptide-specific CTLs from PBMCs of HLA-A24-positive patients, but not from HLA-A24-negative patients and HLA-A24-positive healthy controls. Identified epitope is a weak binder for HLA-A24 molecule in a mini MHC refolding assay. Since the peptide is presented by a common HLA class I molecule, it may be useful for immunotherapy against Mtb infection and vaccine development in the large population of Mtb-infected patients. url: https://api.elsevier.com/content/article/pii/S0882401012001349 doi: 10.1016/j.micpath.2012.07.002 id: cord-006273-xcw0kxjg author: Willemze, R title: KIR-ligand incompatibility in the graft-versus-host direction improves outcomes after umbilical cord blood transplantation for acute leukemia date: 2009-01-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Donor killer cell immunoglobulin-like receptor (KIR)-ligand incompatibility is associated with decreased relapse incidence (RI) and improved leukemia-free survival (LFS) after haploidentical and HLA-mismatched unrelated hematopoietic stem cell transplantation. We assessed outcomes of 218 patients with acute myeloid leukemia (AML n=94) or acute lymphoblastic leukemia (n=124) in complete remission (CR) who had received a single-unit unrelated cord blood transplant (UCBT) from a KIR-ligand-compatible or -incompatible donor. Grafts were HLA-A, -B or -DRB1 matched (n=21) or mismatched (n=197). Patients and donors were categorized according to their degree of KIR-ligand compatibility in the graft-versus-host direction by determining whether or not they expressed HLA-C group 1 or 2, HLA-Bw4 or HLA-A3/-A11. Both HLA-C/-B KIR-ligand- and HLA-A-A3/-A11 KIR-ligand-incompatible UCBT showed a trend to improved LFS (P=0.09 and P=0.13, respectively). Sixty-nine donor–patient pairs were HLA-A, -B or -C KIR-ligand incompatible and 149 compatible. KIR-ligand-incompatible UCBT showed improved LFS (hazards ratio=2.05, P=0.0016) and overall survival (OS) (hazards ratio=2.0, P=0.004) and decreased RI (hazards ratio=0.53, P=0.05). These results were more evident for AML transplant recipients (2-year LFS and RI with or without KIR-ligand incompatibility 73 versus 38% (P=0.012), and 5 versus 36% (P=0.005), respectively). UCBT for acute leukemia in CR from KIR-ligand-incompatible donors is associated with decreased RI and improved LFS and OS. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/leu.2008.365) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101531/ doi: 10.1038/leu.2008.365 id: cord-289711-4ab3d00h author: Yarmarkovich, Mark title: Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date: 2020-06-08 words: 5290.0 sentences: 252.0 pages: flesch: 46.0 cache: ./cache/cord-289711-4ab3d00h.txt txt: ./txt/cord-289711-4ab3d00h.txt summary: Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. Here we describe an approach for prioritizing viral epitopes derived 105 from a prioritized list of 33mer peptides predicted to safely target the vulnerabilities of 106 SARS-CoV-2, generate highly immunogenic epitopes on both MHC class I and II in the 107 vast majority of the population, and maximize the likelihood that these peptides will drive 108 an adaptive memory response. Here we present a comprehensive immunogenicity map of the SARS-CoV-2 248 virus (Table S1) , and propose sixty-five 33mer peptide sequences predicted to generate 249 B and T cell epitopes from a diverse sampling of viral domains across all 10 SARS-250 abstract: Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. We further prioritize genomic regions that generate highly dissimilar peptides from the human proteome, and are also predicted to produce B cell epitopes. We propose sixty-five 33mer peptide sequences, a subset of which can be tested using DNA or mRNA delivery strategies. These include peptides that are contained within evolutionarily divergent regions of the spike protein reported to increase infectivity through increased binding to the ACE2 receptor and within a newly evolved furin cleavage site thought to increase membrane fusion. Validation and implementation of this vaccine concept could specifically target specific vulnerabilities of SARS-CoV-2 and should engage a robust adaptive immune response in the vast majority of the population. url: https://doi.org/10.1016/j.xcrm.2020.100036 doi: 10.1016/j.xcrm.2020.100036 id: cord-003143-n6b0r92e author: Zhao, Min title: Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses date: 2018-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Against a backdrop of seasonal influenza virus epidemics, emerging avian influenza viruses (AIVs) occasionally jump from birds to humans, posing a public health risk, especially with the recent sharp increase in H7N9 infections. Evaluations of cross-reactive T-cell immunity to seasonal influenza viruses and human-infecting AIVs have been reported previously. However, the roles of influenza A virus-derived epitopes in the cross-reactive T-cell responses and heterosubtypic protections are not well understood; understanding those roles is important for preventing and controlling new emerging AIVs. Here, among the members of a healthy population presumed to have previously been infected by pandemic H1N1 (pH1N1), we found that pH1N1-specific T cells showed cross- but biased reactivity to human-infecting AIVs, i.e., H5N1, H6N1, H7N9, and H9N2, which correlates with distinct protections. Through a T-cell epitope-based phylogenetic analysis, the cellular immunogenic clustering expanded the relevant conclusions to a broader range of virus strains. We defined the potential key conserved epitopes required for cross-protection and revealed the molecular basis for the immunogenic variations. Our study elucidated an overall profile of cross-reactivity to AIVs and provided useful recommendations for broad-spectrum vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083907/ doi: 10.1128/mbio.01408-18 id: cord-306308-zjq6cscm author: de Moura, Ronald Rodrigues title: Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date: 2020-08-05 words: 2514.0 sentences: 175.0 pages: flesch: 54.0 cache: ./cache/cord-306308-zjq6cscm.txt txt: ./txt/cord-306308-zjq6cscm.txt summary: Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. abstract: AIMS: Brazil is nowadays one of the epicentres of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and new therapies are needed to face it. In the context of specific immune response against the virus, a correlation between Major Histocompatibility Complex Class I (MHC-I) and the severity of the disease in patients with COVID-19 has been suggested. Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. RESULTS: We identified 24 immunogenic epitopes in the SARS-CoV-2 protein S that could interact with 17 different MHC-I alleles (namely, HLA-A*01:01; HLA-A*02:01; HLA-A*11:01; HLA-A*24:02; HLA-A*68:01; HLA-A*23:01; HLA-A*26:01; HLA-A*30:02; HLA-A*31:01; HLA-B*07:02; HLA-B*51:01; HLA-B*35:01; HLA-B*44:02; HLA-B*35:03; HLA-C*05:01; HLA-C*07:01 and HLA-C*15:02) in the Brazilian population. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. url: https://doi.org/10.1136/jclinpath-2020-206946 doi: 10.1136/jclinpath-2020-206946 id: cord-334603-yt2pmxi3 author: de Sousa, Eric title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date: 2020-07-18 words: 1791.0 sentences: 101.0 pages: flesch: 41.0 cache: ./cache/cord-334603-yt2pmxi3.txt txt: ./txt/cord-334603-yt2pmxi3.txt summary: title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave''s disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. abstract: Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. Ethnicity has been the focus of attention after data from the United Kingdom showed a disproportionate number of deaths among healthcare workers from black, Asian and other ethnic minority backgrounds (1). In addition to ethnicity, socio-economic factors, prior vaccinations and exposure to other coronaviruses, other factors need to be considered to explain geographical and regional variations in susceptibility, severity of clinical expression of COVID-19 disease and outcomes. In the United States there have been disproportionate COVID-19 death rates among African Americans at around 2.6 times higher than that of other groups. Although these data could be due to multiple cultural and socioeconomic factors an underlying genetic susceptibility to SARS-CoV-2 infection may be a factor. url: https://doi.org/10.1016/j.ijid.2020.07.016 doi: 10.1016/j.ijid.2020.07.016 id: cord-005453-4057qib7 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date: 2019-07-03 words: 275771.0 sentences: 16876.0 pages: flesch: 56.0 cache: ./cache/cord-005453-4057qib7.txt txt: ./txt/cord-005453-4057qib7.txt summary: To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091813/ doi: 10.1038/s41409-019-0559-4 id: cord-005460-ezrn8cva author: nan title: Physicians – Poster Session date: 2017-07-28 words: 287105.0 sentences: 15681.0 pages: flesch: 56.0 cache: ./cache/cord-005460-ezrn8cva.txt txt: ./txt/cord-005460-ezrn8cva.txt summary: Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091844/ doi: 10.1038/bmt.2017.134 id: cord-005478-5iu38pr6 author: nan title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date: 2019-07-03 words: 63350.0 sentences: 3869.0 pages: flesch: 58.0 cache: ./cache/cord-005478-5iu38pr6.txt txt: ./txt/cord-005478-5iu38pr6.txt summary: There were some differences among groups: patients in group-1 were younger (median age 46 years, p< 0.02) were transplanted in more recent year (2015, p< 0.001), received more frequently a regimen based on TBF (thiotepa, fludarabine and busulfan) (83%, p< 0.001) and bone marrow (BM) as source of stem cells (77%, p< 0.001), with no ATG (100%, p< 0.001). Clinical Trial Registry: NCT01217723 Disclosure: None of the Authors have any conflicts of interest to declare O105 Immune reconstitution -based score at diagnosis of CGVHD predicts GVHD severity and overall-survival: A novel prognostication tool for GVHD treatment tailoring Background: Allogeneic stem cell transplantation (HSCT) survivors are at a relevant risk of developing chronic GvHD (cGvHD), which importantly affects quality of life and increases morbidity and mortality. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092200/ doi: 10.1038/s41409-019-0562-9 id: cord-005480-yg7salqt author: nan title: Oral Sessions and Working Party date: 2008-03-26 words: 72626.0 sentences: 3873.0 pages: flesch: 55.0 cache: ./cache/cord-005480-yg7salqt.txt txt: ./txt/cord-005480-yg7salqt.txt summary: Standard NIH or Eurolupus cyclophosphamide (CY) protocols and mycophenolate Mofetil (MMF) as induction therapy in severe BILAG A SLE is still associated with 20 % failure, 50% relapse and 10% to 15 % death at 10 years In the absence of a single standard treatment worldwide for refractory SLE, phase I-II studies analysed the use of: a) rituximab (anti CD20 mAb) in more than 1 000 patients showing complete to partial early response around 100% with relapse in 50 to 60% of the cases; b) autologous Hematopoietic Stem Cell Transplantation (HSCT) since 1997 under the auspices of the joined EBMT-EULAR working party, reporting durable remission with reduced or no immunosuppressive drug requirement in 66%, one-third of whom later relapsed to some degree with a 74 ± 7% (n= 62/79) overall survival at 5 years for SLE among the 863 HSCT procedures registered: in 2007 in the EBMT data base. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092258/ doi: 10.1038/bmt.2008.30 id: cord-005487-vac061r8 author: nan title: Physicians Abstracts: EBMT 2010 date: 2010-04-07 words: 58975.0 sentences: 3128.0 pages: flesch: 58.0 cache: ./cache/cord-005487-vac061r8.txt txt: ./txt/cord-005487-vac061r8.txt summary: We retrospectively analyzed 1257 patients (pts), 755 children (age≤18) and 502 adults, receiving fi rst single (n = 1080) or double UCBT (n = 177) in EBMT centers, between 1995 and 2009 , for malignant and non-malignant diseases, who survived at least 100 days from transplantation with neutrophils recovery and without relapse or autologous reconstitution. Prochymal® improves response rates in patients with steroid-refractory acute graft-versus-host disease involving the liver and gut: results of a randomized, placebo-controlled, multicentre phase III trial in GvHD P.J. Martin (1) , J.P. Uberti (2) Background and methods: Steroid-refractory acute GVHD (SR-GVHD) remains a signifi cant and life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). A. Nagler (1) Background: Allogeneic transplantation of hematopoietic stem cells (allo-SCT) from an HLA-matched related (MRD) or unrelated donor (URD) is a curative option for patients (pts) with high-risk hematological disease (HRHD). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092333/ doi: 10.1038/bmt.2010.40 id: cord-009567-osstpum6 author: nan title: Abstracts Oral date: 2008-04-23 words: 131214.0 sentences: 7728.0 pages: flesch: 53.0 cache: ./cache/cord-009567-osstpum6.txt txt: ./txt/cord-009567-osstpum6.txt summary: Introduction: Previously, it has been demonstrated that FOXP3, a gene required for the development and function of regulatory T cells, was highly expressed in the graft during cardiac rejection, suggesting infiltration of regulatory T cells in the transplanted organ during an allogeneic response. Efficacy and safety parameters assessed at follow-up included: acute rejection; patient and graft survival; renal function, vital signs, basic lab results and immunosuppressive regimen for the patients 10 years after completion of the original study. We analyzed, for the first time, the expression of TLR4 in PBMC from kidney recipients with contrasted situations: operational tolerance and chronic immune-mediated rejection (Banff 2005), compared to patients with normal histology and stable graft function, non transplant patients with renal failure and healthy volunteers. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159651/ doi: 10.1111/j.1600-6143.2008.02254.x id: cord-009571-mygj2nd4 author: nan title: Proceedings of the 42nd annual meeting of the american rheumatism association a section of the arthritis foundation june 1 & 2, 1978 new york city abstracts of papers presented date: 2005-11-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159665/ doi: 10.1002/art.1780210508 id: cord-010088-s9tfvtao author: nan title: Oral Abstracts date: 2013-11-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169312/ doi: 10.1111/vox.12100_1 id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233304.0 sentences: 13171.0 pages: flesch: 54.0 cache: ./cache/cord-010092-uftc8inx.txt txt: ./txt/cord-010092-uftc8inx.txt summary: Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169345/ doi: 10.1111/vox.12792 id: cord-010119-t1x9gknd author: nan title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 words: 230193.0 sentences: 13234.0 pages: flesch: 55.0 cache: ./cache/cord-010119-t1x9gknd.txt txt: ./txt/cord-010119-t1x9gknd.txt summary: Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/ doi: 10.1111/trf.14286 id: cord-014976-546zaoxn author: nan title: Publication only date: 2006-03-08 words: 51926.0 sentences: 2983.0 pages: flesch: 53.0 cache: ./cache/cord-014976-546zaoxn.txt txt: ./txt/cord-014976-546zaoxn.txt summary: In order to evaluate if malignant and non malignant hematological diseases quantitatively and qualitatively affect BM derived MSCs, bone marrow from children with acute lymphoblastic leukemia (ALL diagnosis n=9, different phases of treatment n=29, end of therapy n=10), idiopathic thrombocytopenic purpura (n=16), autoimmune neutropenia (n=12) and control patients (solid tumors without BM involvement, n=30) was harvested and the mononuclear cell (MNC) fraction isolated. Case: In our hospital a total of 3 patients with relapsed Hodgkin''s disease underwent reduced-intensity conditioning (RIC) allogeneic stem cell transplantation (allo-SCT) from an HLA-identical sibling. We report a case of a young male patient of 19 years old with aggressive MS who was treated with a high-dose immunosuppressive regimen (HDIS) using myeloablation followed by autologous blood stem cell transplantation (ASCT) that has induced a dramatic and long-lasting remission of the disease. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092326/ doi: 10.1038/sj.bmt.1705327 id: cord-015389-vwgai4k9 author: nan title: Publication only date: 2009-03-25 words: 23868.0 sentences: 1465.0 pages: flesch: 57.0 cache: ./cache/cord-015389-vwgai4k9.txt txt: ./txt/cord-015389-vwgai4k9.txt summary: This study evaluates the safety of this approach, in terms of infusion-related toxicity and hematopoietic reconstitution, in 385 consecutive autologous transplantations performed from 4/97 to 9/08 in 348 patients (median age 46; underlying disease: lymphoma in 178, myeloma in 131, acute leukaemia in 17, breast cancer in 22). Patients and methods: Eight pts after allogeneic hematopoetic stem cell transplantation (HSCT) underwent MSCs infusions (median age of pts was 11 years, male/female: 6/2) between 2006 and 2009. Akiyama Tokyo Metropolitan Komagome Hospital (Tokyo, JP) Acute graft-versus-host disease (GVHD) is one of the major factors that have infl uence on the outcomes of allogeneic hematopoietic stem cell transplantation (HSCT). Material and methods: during a 8 years period we have performed 144 stem cells transplantation in 134 patients with different hematological malignancies(AML: 74; ALL: 6; CML: 7; CLL: 1, NHL: 13; Hodgkin Diseases: 16; Multiple myelomas: 24; Aplastic anaemia: 1;Myelofi brosis:1 Ewing Sarcoma: 1; Male:78 Female 66. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104434/ doi: 10.1038/bmt.2009.50 id: cord-016998-6n662amh author: nan title: Nierentransplantation date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Die Nierentransplantation ist die effektivste Behandlungsmethode der chronischen terminalen Niereninsuffizienz. Seit den 1960er Jahren entwickelte sie sich zu einer Standardtherapie. Wichtige Voraussetzungen waren die Entdeckung des HLA-Systems, die Entwicklung der Immunsuppressiva sowie die technische Perfektionierung des Organerhaltes außerhalb eines lebenden Körpers. Die 5-Jahres-Überlebensrate für Allotransplantate beträgt etwa 65%, diejenige von Lebendspenden 79%. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121448/ doi: 10.1007/978-3-540-48556-8_13 id: cord-017184-1ewi3dka author: nan title: Primary Immunodeficiencies date: 2008 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Primary immunodeficiencies (PIDs), once considered to be very rare, are now increasingly recognized because of growing knowledge in the immunological field and the availability of more sophisticated diagnostic techniques and therapeutic modalities [161]. However in a database of >120,000 inpatients of a general hospital for conditions suggestive of ID 59 patients were tested, and an undiagnosed PID was found in 17 (29%) of the subjects tested [107]. The publication of the first case of agammaglobulinemia by Bruton in 1952 [60] demonstrated that the PID diagnosis is first done in the laboratory. However, PIDs require specialized immunological centers for diagnosis and management [33]. A large body of epidemiological evidence supports the hypothesis of the existence of a close etiopathogenetic relation between PID and atopy [73]. In particular, an elevated frequency of asthma, food allergy (FA), atopic dermatitis and enteric pathologies can be found in various PIDs. In addition we will discuss another subject that is certainly of interest: the pseudo-immunodepressed child with recurrent respiratory infections (RRIs), an event that often requires medical intervention and that very often leads to the suspicion that it involves antibody deficiencies [149]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121684/ doi: 10.1007/978-3-540-33395-1_22 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: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167094/ doi: 10.1002/jcb.240591009 id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 words: 130043.0 sentences: 7330.0 pages: flesch: 54.0 cache: ./cache/cord-023346-8sqbqjm1.txt txt: ./txt/cord-023346-8sqbqjm1.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169255/ doi: 10.1111/j.1423-0410.2005.00652.x id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 words: 130046.0 sentences: 7333.0 pages: flesch: 54.0 cache: ./cache/cord-023354-f2ciho6o.txt txt: ./txt/cord-023354-f2ciho6o.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169300/ doi: 10.1111/j.1423-0410.2005.00654.x id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 words: 130049.0 sentences: 7334.0 pages: flesch: 54.0 cache: ./cache/cord-023364-ut56gczm.txt txt: ./txt/cord-023364-ut56gczm.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/ doi: 10.1111/j.1423-0410.2005.00651.x id: cord-313474-1gux1gsi author: nan title: Physicians Abstracts date: 2015-03-20 words: 51420.0 sentences: 2890.0 pages: flesch: 57.0 cache: ./cache/cord-313474-1gux1gsi.txt txt: ./txt/cord-313474-1gux1gsi.txt summary: Materials (or patients) and methods: We performed a multicenter, multinational, open-label, randomized study comparing anti-lymphocyte globulin (ATG-Fresenius s ) 10 mg/kg on day -3, -2 and -1 with no ATG in patients with AML (n ¼ 110) or ALL (n ¼ 45) in 1 st complete remission (CR; n ¼ 139) or 2 nd CR (n ¼ 16) who received peripheral blood stem cells from their HLA-identical sibling after standard TBI (12 Gy)/Ccclophosphamide (120 mg/kg) or busulfan (16 mg/ kg)/Cy (120 mg/kg) based myeloablative conditioning regimen. After allo-HSCT, detection of positive WT1 was followed by immunomodulatory therapeutic interventions according to the time from transplant, the presence of active graft-versus-host disease (GvHD) and the general clinical conditions: tapering and/or discontinuation of immunosuppressive drugs (IS), donor lymphocytes infusions (DLI), administration of hypomethylating agents. Introduction: Haploidentical hematopoietic stem cell transplantation(Haplo-HSCT)is feasible option for patients with acute leukemia(AL)at high risk of relapse who do not have HLA-matched related or unrelated donors. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/25794251/ doi: 10.1038/bmt.2015.27 ==== 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