item: #1 of 117
          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: 6993
      flesch: 36
     summary: Curiously, CIITA expressing cells produced virus that was significantly more infectious than CIITA deficient cells, and this was independent of the class II antigen presentation pathway. Not only was processing to capsid p24 more complete in CIITA expressing cells, but vector-only control cells and those only expressing HLA-DR contained increased levels of processing intermediates.
    keywords: cells; ciita; class; expression; figure; gag; hiv; hla; mhc; processing; release; retention; virus
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        item: #2 of 117
          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: 7279
      flesch: 43
     summary: A high efficiency and high throughput size separation method Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach Purification of correctly oxidized MHC class I heavy-chain molecules under denaturing conditions: a novel strategy exploiting disulfide assisted protein folding High-throughput polymerase chain reaction cleanup in microtiter format Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays NetMHCpan, a method for MHC class I binding prediction beyond humans Preparation of iodine-131 labelled human growth hormone of high specific activity Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins The peptide-binding specificity of HLA-A*3001 demonstrates membership of the HLA-A3 supertype An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions Identifying cytotoxic T cell epitopes from genomic and proteomic information: the human MHC project One-pot, mix-and-read peptide-MHC tetramers Definition of supertypes for HLA molecules using clustering of specificity matrices NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11 Reliable prediction of T-cell epitopes using neural networks with novel sequence representations Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence Efficient assembly of recombinant major histocompatibility complex class I molecules with preformed disulfide bonds Induction of footand-mouth disease virus-specific cytotoxic T cell killing by vaccination The interaction of beta 2-microglobulin (beta 2m) with mouse class I major histocompatibility antigens and its ability to support peptide binding. We have previously demonstrated that denatured MHC molecules can de novo fold efficiently, however, only in the presence of appropriate peptide.
    keywords: 0401; amino; binding; hla; human; mhc; molecules; peptide; porcine; position; sla-1
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        item: #3 of 117
          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: 4671
      flesch: 45
     summary: Meanwhile, currently the mostly used methods to predict and identify T cell epitopes are either by computer algorithms based on the mode of peptide binding to MHC molecules, or measurement of T cell responses of PBMCs simulated with panels of overlapping peptides (Liu et al., 2011) . Our work may therefore provide a comprehensive evaluation of the impact of the newly defined epitope on viral specific T cell response and suggests a possible immune evasion for maintenance of viral persistence in patients with HBV infection.
    keywords: cell; epitope; fig; hbc141; hbv; hla; mice; patients; peptide
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        item: #4 of 117
          id: cord-002463-qhtj1pef
      author: Dash, Raju
       title: In silico-based vaccine design against Ebola virus glycoprotein
        date: 2017-03-21
       words: 5837
      flesch: 42
     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. In silico prediction of B-and T-cell epitope on Lassa virus proteins for peptide based subunit vaccine design An in silico approach predicted potential therapeutics that can confer protection from maximum pathogenic Hantaviruses Development of a DNA vaccine designed to induce cytotoxic T lymphocyte responses to multiple conserved epitopes in HIV-1 A combined immuno-informatics and structure-based modeling approach for prediction of T cell epitopes of secretory proteins of Mycobacterium tuberculosis The Phyre2 web portal for protein modeling, prediction and analysis The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities Computations of Standard Binding Free Energies with Molecular Dynamics Simulations Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach Computational elucidation of potential antigenic CTL epitopes in Ebola virus Epitope-based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study A highly conserved GEQYQQLR epitope has been identified in the nucleoprotein of Ebola virus by using an in silico approach Conformational flexibility in designing peptides for immunology: the molecular dynamics approach Managing protein flexibility in docking and its applications Protein flexibility: Multiple molecular dynamics simulations of insulin chain B Toward an atomistic understanding of the immune synapse: Large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex MHC-peptide binding is assisted by bound water molecules
    keywords: analysis; binding; cell; design; ebola; ebov; energy; epitope; hla; prediction; protein; sequence; simulation; vaccine; virus
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        item: #5 of 117
          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: 4980
      flesch: 43
     summary: 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. Implications for vaccination strategies GenBank VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines Basic local alignment search tool OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Genome-wide prediction of vaccine candidates for Leishmania major: an integrated approach Design of an epitope-based peptide vaccine against spike protein of human coronavirus: an in silico approach Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach Peptide binding predictions for HLA DR, DP and DQ molecules MHCcluster, a method for functional clustering of MHC molecules Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery Predicting population coverage of T-cell epitope-based diagnostics and vaccines Evaluation of comparative protein modeling by MODEL-LER AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling The DISOPRED server for the prediction of protein disorder Protein frustratometer: a tool to localize energetic frustration in protein molecules AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading The Protein Data Bank PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides
    keywords: analysis; cell; class; epitope; hla; mhc; mhc class; peptide; prediction; protein; shigella; siga; vaccine
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        item: #6 of 117
          id: cord-002704-cpa2sl50
      author: El Bissati, Kamal
       title: Protein nanovaccine confers robust immunity against Toxoplasma
        date: 2017-09-05
       words: 7821
      flesch: 54
     summary: Why prevent, diagnose and treat congenital toxoplasmosis? Early and longitudinal evaluations of treated infants and children and untreated historical patients with congenital toxoplasmosis: the chicago collaborative treatment trial Identification of T. gondii epitopes, adjuvants, and host genetic factors that influence protection of mice and humans Toxoplasma gondii HLA-B*0702-restricted GRA7(20-28) peptide with adjuvants and a universal helper T cell epitope elicits CD8(+) T cells producing interferon-gamma and reduces parasite burden in HLA-B*0702 mice Human immunome, bioinformatic analyses using HLA supermotifs and the parasite genome, binding assays, studies of human T cell responses, and immunization of HLA-A*1101 transgenic mice including novel adjuvants provide a foundation for HLA-A03 restricted CD8+ T cell epitope based, adjuvanted vaccine protective against Toxoplasma gondii Towards an immunosense vaccine to prevent toxoplasmosis: protective Toxoplasma gondii epitopes restricted by HLA-A*0201 Peptidic nanoparticles as drug delivery and antigen display systems Self-assembling peptide nanoparticles useful as vaccines. Earlier studies provide support for using GLA-SE as an adjuvant for a wide variety of protein vaccines, including our own.
    keywords: cd8; cell; epitopes; flagellin; gla; hla; human; mice; peptides; protein; sapn; studies; vaccine; work
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        item: #7 of 117
          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: 6203
      flesch: 29
     summary: Diagnostic and predictive value of circulating activated T cells Reduced monocyte HLA-DR expression: a novel biomarker of disease severity and outcome in acetaminophen-induced acute liver failure Predictive value of interleukins 6, 8 and 10, and low HLA-DR expression in acute renal failure Predicting post-stroke infections and outcome with blood-based immune and stress markers Decreased monocyte HLA-DR expression in patients after non-shockable out-of-hospital cardiac arrest Immune responses after acute ischemic stroke or myocardial infarction Heart failure and kidney dysfunction: epidemiology, mechanisms and management Leukocyte redistribution: effects of beta blockers in patients with chronic heart failure The ins and outs of MHC class II-mediated antigen processing and presentation Monocyte human leukocyte antigen-DR transcriptional downregulation by cortisol during septic shock Phenotype changes and impaired function of dendritic cell subsets in patients with sepsis: a prospective observational analysis Monocyte deactivation in septic patients: restoration by IFN-gamma treatment Neutrophils with myeloid derived suppressor function deplete arginine and constrain T cell function in septic shock patients A high frequency of MDSCs in sepsis patients, with the granulocytic subtype dominating in gram-positive cases Early expansion of circulating granulocytic myeloid-derived suppressor cells predicts development of nosocomial infections in patients with sepsis Human myeloid-derived suppressor cells are associated with chronic immune suppression after severe sepsis/septic shock Apoptosis-induced lymphopenia in sepsis and other severe injuries Interleukin-6: an overview Point-of-care testing for interleukin-6 in cerebro spinal fluid (CSF) after subarachnoid haemorrhage Interleukin-6 serum level assessment using a new qualitative point-of-care test in sepsis: a comparison with ELISA measurements However, it should be noted that they do not reflect immune cell functionality as cytokines are mostly pleiotropic, derived from different cells including non-immune cells, may be counteracted by natural inhibitors (e.g., gp130 for IL-6), and have variable clearance rates [4, 6, 11, 12] .
    keywords: antigen; cells; dr expression; expression; immune; immunosuppression; injury; mhla; mortality; patients; sepsis
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        item: #8 of 117
          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: 8029
      flesch: 47
     summary: In intracellular cytokine staining (ICS) assays, both the cross-CD8 ϩ T cells (4.37% gamma interferon positive [IFN-␥ ϩ ] CD8 ϩ CD8 ϩ ) and CD4 ϩ T cells (0.27% IFN-␥ ϩ CD4 ϩ CD4 ϩ ) displayed a bias with respect to H5N1; in contrast, H7N9 presented the lowest cross-T-cell reactivity level, with 1.08% IFN-␥-secreting cells in CD8 ϩ T cells and 0.14% IFN-␥secreting cells in CD4 ϩ T cells (Fig. The results showed that for all the antigens, the effector memory (CD45RA Ϫ CD62L Ϫ ) T-cell subset dominated the IFN-␥-secreting cells both among CD8 ϩ and CD4 ϩ T cells.
    keywords: a*2402; aivs; cell; cross; epitopes; fig; h5n1; h7n9; hla; influenza; p25; peptide; ph1n1; responses; virus
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        item: #9 of 117
          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: 7034
      flesch: 46
     summary: Regarding the fundamental importance of epitope prediction in vaccine development, we investigated the best potential CD8+ T cell epitopes from the E5, E6, and E7 oncoproteins of four prevalent hrHPV genotypes (16, 18, 31 and 45) in the world and Iran There are several limitations for epitope prediction: 1) The major drawback of peptidebased vaccines is low immunogenicity [92, 93] .
    keywords: binding; cell; epitopes; hla; hpv; human; mhc; molecules; papillomavirus; peptide; prediction; step
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        item: #10 of 117
          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: 7062
      flesch: 42
     summary: In sum, we conclude that HLA promiscuity level is a human trait with paramount importance during adaptation to local pathogens. Under the assumption that local pathogen diversity drives the evolution of epitope recognition of HLA class II alleles, promiscuity as a molecular trait should have evolved rapidly as human populations expanded into new territories.
    keywords: alleles; binding; class; data; diversity; drb1; epitope; hla; human; mhc; populations; promiscuity
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        item: #11 of 117
          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: 4415
      flesch: 37
     summary: In this analysis we showed that the computational method NetMHCpan4.0 predicted 95% of previously experimentally mapped HIV-1 epitopes in 6 HIV-1 infected individuals expressing a total of 22 different HLA class I alleles. A community resource benchmarking predictions of peptide binding to MHC-I molecules Efficient peptide-MHC-I binding prediction for alleles with few known binders MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides Automated benchmarking of peptide-MHC class I binding predictions An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions Largescale validation of methods for cytotoxic T-lymphocyte epitope prediction Reliable prediction of T-cell epitopes using neural networks with novel sequence representations MHCflurry: open-source class I MHC binding affinity prediction T-cell antigenic sites tend to be amphipathic structures Emerging vaccine informatics Prediction of peptide-MHC binding using profiles Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection Macrophage inflammatory Protein-1
    keywords: binders; binding; cell; class; computational; data; epitopes; hla; netmhcpan4.0; peptides; predictions
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        item: #12 of 117
          id: cord-004435-l66ost6q
      author: Oli, Angus Nnamdi
       title: Immunoinformatics and Vaccine Development: An Overview
        date: 2020-02-26
       words: 8948
      flesch: 30
     summary: mSphere An overview of bioinformatics tools for epitope prediction: implications on vaccine development Bioinformatics tools for identifying class I-restricted epitopes In silico-accelerated identification of conserved and immunogenic variola/vaccinia T-cell epitopes NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies iVAX: an integrated toolkit for the selection and optimization of antigens and the design of epitope-driven vaccines From genome to vaccine: in silico predictions, ex vivo verification Designing string-of-beads vaccines with optimal spacers HIV vaccine development by computer assisted design: the GAIA vaccine NERVE: new Enhanced reverse vaccinology environment Jennerpredict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions Genome-wide prediction of vaccine target of human herpes simplex viruses using Vaxign RV VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology PanRV: pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome Understanding Emerging and Re-Emerging Infectious Diseases. Current conventional vaccines came empirically when there were vague or no knowledge of vaccine immune system activation.
    keywords: antigenic; antigens; approach; cell; data; design; development; diseases; epitope; hla; host; human; immune; immunoinformatics; infection; pathogens; protein; responses; system; vaccine; virus
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        item: #13 of 117
          id: cord-005453-4057qib7
      author: None
       title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session
        date: 2019-07-03
       words: 276280
      flesch: 51
     summary: Goals: In the present study, we describe the frequencies of CRE colonization and analyzed its relationship with development of CRE bacteremia and mortality in two different scenarios: stem cell transplant patients (HSCT) and Leukemia patients. The aim of this study was to analyse a single centre experience with HSCT patients requiring ICU admission and the factors affecting outcome.
    keywords: /kg; acute gvhd; administration; adult patients; age; agvhd; aim; allogeneic hsct; allosct; aml; analysis; anti; asct; associated; atg; autologous; b cells; based; blood; blood cells; blood stem; bone; busulfan; car; cases; cause; cd19; cd34; cd4; cell count; cell depletion; cell disease; cell dose; cell graft; cell lymphoma; cell source; cell therapy; cell transplantation; cells; center; chemotherapy; children; chimerism; chronic gvhd; clinical; cmv; cmv disease; cohort; combination; common; complications; conclusions; conditioning; conditioning regimen; control; count; criteria; csa; csf; cyclophosphamide; data; days; days post; death; declare; development; diagnosis; difference; disclosure; disease; disease patients; disease relapse; dli; donor; donor age; donor chimerism; donor t; donor transplant; dose; early; ebv; ecp; effect; efficacy; engraftment; experience; expression; factors; failure; female; figure; flow; fludarabine; follow; following; free; function; grade; graft; group; group patients; gvhd grade; gvhd patients; gvhd prophylaxis; haploidentical; haploidentical hsct; hct; hematopoietic; high; hla; hospital; host disease; hsct group; hsct patients; hsct recipients; iii; immune; impact; incidence; increase; induction; infection; infusion; intensity; leukemia patients; levels; lymphocyte; lymphoma patients; major; male; marrow; marrow transplantation; matched; mds; mean; median; median os; medical; methods; mm patients; mobilization; months; mortality; mrd; msd; mud; multiple; myeloid; myeloma patients; n=1; negative; neutrophil; nhl patients; nk cells; non; nrm; number; option; outcome; overall; patients; patients age; patients background; patients characteristics; pbsc; pcr; pediatric; period; pfs; pgf patients; phase; platelet; population; positive; post; post transplant; potential; pre; present; previous; primary; prior; procedure; progression; protocol; ptcy; pts; range; rate; ratio; reactivation; received; reconstitution; recovery; reduced; refractory; regimen; relapse; remission; response; results; retrospectively; risk patients; safety; samples; sc patients; second; secondary; serum; severe; sibling; specific; standard; status; stem cell; steroid; studies; study; study patients; survival; syndrome; system; t cells; table; term; test; therapy; time; total; toxicity; transplant patients; transplantation background; transplanted; treatment; tumor; type; underwent; unrelated; use; versus; vod; years
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        item: #14 of 117
          id: cord-005460-ezrn8cva
      author: None
       title: Physicians – Poster Session
        date: 2017-07-28
       words: 287532
      flesch: 53
     summary: After three months of treatment patient showed an increase in T cells count (CD3, 411/mmc), and a decrease of toxic metabolites: AXP, 1.652 micromol/ml RBC; dAXP, 0.011 micromol/ml RBC; %dAXP, 0.7 maternal T-cell engraftment persists, despite a good response to the PEG-ADA therapy. Moreover, caspases pathway was significantly activated in thawing CD3+, CD56+ and CD14 + cells: FLICA+ cells % in thawing cells were, respectively, 16.8%, 31.1% and 6.2% vs 3%, 9.7% and o1% in fresh cells.
    keywords: acute gvhd; adult patients; age; aim; allogeneic; allogeneic hsct; aml patients; analysis; anti; asct; associated; atg; autologous; based; beam; blood; blood cell; blood stem; bone; busulfan; cases; cause; cd34; cell count; cell disease; cell dose; cell lymphoma; cell source; cell therapy; cell transplantation; cells; center; chemotherapy; children; chimerism; chronic gvhd; clinical; cmv; cohort; collection; complete; complications; conditioning; conditioning regimen; conflict; consecutive; control; cord; count; cr patients; criteria; csf; cyclophosphamide; data; days; death; development; diagnosis; difference; disclosure; disease; disease relapse; disease risk; dli; donor; donor cell; donor hsct; dose; early; ebv; ecp; effect; efficacy; engraftment; experience; factors; failure; female; figure; fludarabine; follow; following; free; function; grade; graft; group; group patients; gvhd; gvhd grade; gvhd patients; gvhd prophylaxis; haploidentical; hct; hematology; hematopoietic; high; hla; hospital; host disease; hr =; hsct patients; hsct recipients; iii; immune; impact; incidence; increase; induction; infection; infusion; intensity; interest; leukemia patients; levels; line; lymphoma patients; major; male; malignancies; marrow; marrow transplantation; matched; mds patients; mean; median; median follow; median os; melphalan; mobilization; months; mortality; mrd; mud; myeloablative; myeloid; myeloma patients; n =; negative; neutrophil; nk cell; non; nrm; number; outcome; overall; p =; patients; patients characteristics; patients relapse; pbsc; pediatric; period; pfs; platelet; population; positive; post; post hsct; post transplant; potential; pre; primary; prior; procedure; progression; pts; range; rate; reactivation; receiving; recipients; recovery; refractory; regimen; relapse; related; remission; report; respectively; response; results; ric; risk group; risk patients; score; second; secondary; setting; severe; sibling; significant; specific; standard; status; stem cell; steroid; studies; study; survival; syndrome; t cell; table; tbi; term; therapy; time; tma patients; total; toxicity; transplant patients; transplanted; treatment; trm; type; underwent; university; unrelated; use; versus; vod; years
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        item: #15 of 117
          id: cord-005478-5iu38pr6
      author: None
       title: The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session
        date: 2019-07-03
       words: 63536
      flesch: 53
     summary: Commonly reported AEs (≥20% patients) were URTI, AST/ALT elevations, fatigue, nausea and diarrhea. %]) attributed to injection site-related TEAEs.
    keywords: acute; age; allogeneic; aml; analysis; atg; background; blood; car; cases; cell; cell transplantation; chronic; cmv; cohort; conclusions; conditioning; data; days; disclosure; disease; donor; dose; figure; follow; free; grade; graft; group; gvhd; haplo; hct; hla; hsct; immune; incidence; leukemia; median; methods; months; mortality; mrd; non; nrm; outcome; patients; post; primary; pts; range; rate; regimen; relapse; response; results; ric; risk; score; severe; stem; stem cell; study; survival; t cell; therapy; time; transplant; transplantation; treatment; trial; years
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        item: #16 of 117
          id: cord-005480-yg7salqt
      author: None
       title: Oral Sessions and Working Party
        date: 2008-03-26
       words: 72763
      flesch: 51
     summary: Therefore, we compared BM versus PB in patients patients transplanted after 1994: 1226 patients received BM and 4605 PB. Since transplantation patients were treated only with symptomatic therapy.
    keywords: acute; age; allogeneic; aml; aml patients; analysis; asct; associated; autologous; blood; bone; cases; cell; cell transplantation; chemotherapy; children; chronic; cmv; conclusion; conditioning; cord; data; days; diagnosis; disease; donor; dose; ebmt; effect; engraftment; factors; failure; follow; grade; graft; group; gvhd; hct; high; hla; host; hsct; iii; impact; incidence; intensity; leukemia; marrow; median; months; mortality; msc; non; number; outcome; patients; phase; positive; post; pre; pts; range; recipients; regimen; relapse; remission; response; results; ric; risk; risk patients; source; stem cell; studies; study; survival; t cells; tbi; term; therapy; time; total; transplantation; transplanted; treatment; trm; unrelated; use; versus; vs.; years
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        item: #17 of 117
          id: cord-005487-vac061r8
      author: None
       title: Physicians Abstracts: EBMT 2010
        date: 2010-04-07
       words: 59087
      flesch: 53
     summary: Introduction: Development of leukemia or myelodysplasia derived from donor cells termed donor cell leukemia (DCL) is a rare but severe complication following allogeneic hematopoietic transplantation. Conclusion: The answers to these questions will help to further characterize donor cell derived leukemia and provide new insights into leukemogenesis in general.
    keywords: acute; age; allogeneic; aml; analysis; asct; autologous; blood; cases; cell transplantation; cells; children; chronic; cmv; conclusion; conditioning; data; days; disease; donor; donor t; dose; ebmt; factors; follow; grade; graft; group; gvhd; hct; high; hla; hsct; incidence; infl; leukemia; median; methods; months; mortality; n =; non; number; outcome; p =; patients; pts; range; regimen; relapse; response; results; ric; risk; rst; severe; signifi; specifi; stem; stem cell; study; survival; t cells; therapy; time; transplantation; treatment; unrelated; vs.; years
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        item: #18 of 117
          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: 5883
      flesch: 41
     summary: Mismatches between donor KIR ligand and recipient KIR ligand in the GvH direction (the donor-recipient KIR-ligand model) have been used by the Perugia group and Hsu et al., [7] [8] [9] 12, 22 between donor KIR and recipient KIR by Gagne et al. 28 and between donor KIR and recipient KIR ligand by Leung et al. 29, 30 Criticizing the donor-recipient KIR-ligand model one could argue that, as some donors might not have possessed the relevant KIR gene, a minority of donor-recipient pairs might have been misclassified in this study. Minor histocompatibility antigens as target of graft-versus-leukemia reactions Graft-versus-leukemia effect of donor lymphocyte transfusions in marrow grafted patients Natural killer cell receptors: new biology and insights into the graft-versus-leukemia effect Killer immunoglobulin-like receptors MHC class I molecules and KIRs in human history, health and survival Recognition of HLA-A3 and HLA-A11 by KIR3DL2 is peptide-specific Role of natural killer cell alloreactivity in HLA-mismatched hematopoietic stem cell transplantation Effectiveness of donor natural killer alloreactivity in mismatched haematopoietic transplants Donor natural killer cell allorecognition of missing self in haploidentical hematopoieitc transplantation for acute myeloid leukemia: challenging its predictive value Survival advantage with KIR ligand incompatibility in hematopoietic stem cell transplantation from unrelated donors Genotypic inhibitory killer immunoglobulin-like receptor ligand incompatibility enhances the long-term antileukemic effect of unmodified allogeneic hematopoietic stem cell transplantation in patients with myeloid leukemias Improved outcome in HLA-identical sibling hematopoietic stem-cell transplantation for acute myelogenous leukemia predicted by KIR and HLA genotypes Evaluation of KIR ligand incompatibility in mismatched unrelated donor hematopoietic transplants The effect of KIR ligand incompatibility on the outcome of unrelated donor transplantation: a report from the center for international blood and bone marrow transplant research, the European blood and bone marrow transplant registry, and the Dutch registry Role of KIR ligand incompatibility in hematopoietic stem cell transplantation using unrelated donors The impact of donor KIR and patient HLA-C genotypes on outcome following HLA-identical sibling hematopoietic stem cell transplantation for myeloid leukemia Detrimental effect of natural killer cell alloreactivity in T-replete hematopoietic stem cell transplantation for leukaemia patients History of the clinical use of umbilical cord blood hematopoietic cells Transplants of umbilical-cord blood or bone marrow from unrelated donors in adults with acute leukemia Donor selection for unrelated cord blood transplants Outcomes of transplantation of unrelated donor umbilical cord blood and bone marrow in children with acute leukaemia: a comparison study Alloreactive natural killer cells in mismatched hematopoietic stem cell transplantation Consensus Conference on Acute GvHD Grading Chronic graft-versus-host syndrome in man.
    keywords: blood; cell; cord; donor; group; hla; incompatibility; kir; ligand; patients; transplantation
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        item: #19 of 117
          id: cord-007301-5m269nzi
      author: Lundegaard, Claus
       title: Modeling the adaptive immune system: predictions and simulations
        date: 2007-12-15
       words: 10033
      flesch: 35
     summary: However, there are other issues affecting the predictive performance of most MHC class II binding prediction methods. 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.
    keywords: alleles; amino; antigen; binding; cell; class; cleavage; data; epitopes; et al; hla; linear; methods; mhc; mhc class; molecules; peptide; prediction; system; tap
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        item: #20 of 117
          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: 3597
      flesch: 45
     summary: 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 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. These lines were used 6 days after stimulation to examine presentation of class II-restricted antigen by glial cell targets.
    keywords: antigen; cells; class; hla; molecules; targets
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        item: #21 of 117
          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: 4676
      flesch: 40
     summary: Our previous work has clearly indicated that human endocrine cells have different sensitivities to the in vitro effect of lympho/monokines with regard to the induction of HLA class II expression. Referring to class II molecules, our results agree with the generally accepted concept that cells of the neuronal lineage are refractory to the effect of available modulators, alone or in combinations, on the levels of HLA class II expression regardless of the species employed (Wong et ai., 1985) .
    keywords: astrocytes; brain; cells; class; expression; hla; human
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        item: #22 of 117
          id: cord-007719-3ypv9k9p
      author: Wang, Mingjun
       title: Classification of Human Leukocyte Antigen (HLA) Supertypes
        date: 2014-05-06
       words: 3654
      flesch: 35
     summary: As mentioned above, one way to reduce this complexity is to group HLA molecules into HLA supertypes; a classifi cation that as mentioned above refers to a group of HLA alleles with largely overlapping peptide binding specifi cities [ 24 , 25 , 30 ] . 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.
    keywords: binding; cells; class; hla; molecules; peptide; supertypes
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        item: #23 of 117
          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: 4903
      flesch: 30
     summary: Furthermore, our results indicated a positive correlation between the number of peptides identified via HLA-peptidomics and the amount of HLA molecules expressed on the surface of cancer cells. Immunopeptidomes Using Mass Spectrometry The prognostic influence of tumour-infiltrating lymphocytes in cancer: a systematic review with meta-analysis Prognostic value of tumor-infiltrating lymphocytes in triple-negative breast cancers from two phase III randomized adjuvant breast cancer trials: ECOG 2197 and ECOG 1199 T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences T-cell antigen receptor genes and T-cell recognition Prognostic value, localization and correlation of PD-1/PD-L1, CD8 and FOXP3 with the desmoplastic stroma in pancreatic ductal adenocarcinoma Leukocyte complexity predicts breast cancer survival and functionally regulates response to chemotherapy Robust enumeration of cell subsets from tissue expression profiles Measuring multiple parameters of CD8+ tumor-infiltrating lymphocytes in human cancers by image analysis Prioritization of cancer antigens: keeping the target in sight Post-proteasomal antigen processing for major histocompatibility complex class I presentation NetMHCpan, a method for MHC class I binding prediction beyond humans MHC class I/peptide stability: implications for immunodominance, in vitro proliferation, and diversity of responding CTL High-throughput imaging: Focusing in on drug discovery in 3D Enabling 1536-Well High-Throughput Cell-Based Screening through the Application of Novel Centrifugal Plate Washing Decreased proliferation of human melanoma cell lines caused by antisense RNA against translation factor eIF-4A1 Two members of the TRiC chaperonin complex, CCT2 and TCP1 are essential for survival of breast cancer cells and are linked to driving oncogenes A Prognostic Model for Patients with Triple-Negative Breast Cancer: Importance of the Modified Nottingham Prognostic Index and Age Triple negative breast cancer: the kiss of death Immunotherapeutic approaches in triple-negative breast cancer: latest research and clinical prospects Comprehensive molecular portraits of human breast tumours The immune contexture in human tumours: impact on clinical outcome Squalene emulsion potentiates the adjuvant activity of the TLR4 agonist, GLA, via inflammatory caspases, IL-18, and IFN-gamma Assessment of Antigen-Specific Cellular Immunogenicity Using Intracellular Cytokine Staining, ELISpot, and Culture Supernatants The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Trimmomatic: a flexible trimmer for Illumina sequence data STAR: ultrafast universal RNA-seq aligner RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants MiXCR: software for comprehensive adaptive immunity profiling Comprehensive analysis of human protein N-termini enables assessment of various protein forms Soluble plasma HLA peptidome as a potential source for cancer biomarkers MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification Seq 2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion We would like to express my special appreciation and thank Dr. Supplementary information is available for this paper at https://doi.org/10.1038/s41598-020-62244-z.Correspondence and requests for materials should be addressed to K.-C.H., C.L. or M.J.Reprints and permissions information is available at www.nature.com/reprints.Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
    keywords: analysis; antigen; cancer; cd8; cells; class; data; epitopes; expression; fig; genes; hla; mhc; peptides
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        item: #24 of 117
          id: cord-009323-sfxpchma
      author: Link, Hartmut
       title: Die Transplantation hämatopoetischer Stammzellen: Teil I: Definitionen, prinzipielle Anwendungsmöglichkeiten, Komplikationen
        date: 1997
       words: 5209
      flesch: 33
     summary: Clift: Veno-occlusive disease of the liver and multiorgan failure after bone marrow transplantadon: a cohort study of 355 patients Autologous tramptants for chronic rnyelogenous leukaemia: Resutts from eight transplant ~oups lnfection in bone marrow transplant recipients Risk factors for cytomegalovirus infection after human marrow transplantation WeisdorE Myelodysplastic syndrome after autologous bone marrow transplantation: an additional late complication of curative cancer therapy Forman: The outcome of matched unrelated donor bone marrow transplantation in patients with hematolo~c malignancies using molecular typing for donor selection and graft-versus-host disease prophylaxis regfimen of cyclosporine, methotrexate, and prednisone Acute g'raft-versus-host disease: analysis of¡ factors after allogeneic marrow transplantation and prophylaxis with cyclospo¡ and methotrexate Selecuve depletion of CD8+ cells for prevention ofgraft-versus-host disease after bone marrow transplantation: A randomized controlled t¡ al Weisdorfi Late infections after allogeneic bone marrow transplantation: Comparison of incidence in related and unrelated donor transplant recipients Weisdo~ Predictive factors for chronic gxaftversus-host disease after histocompatible sibling donor bone marrow transplantadon Immunogenedc marrow donor search for 1012 patients: a retrospec¡ analysis ofstrategies, outcome and costs Progress ofunrehted bone marrow donor search at the University Hospital of Essen (1991-1994) Transplantation potential of hematopoietic cells released into the circulation during routine chemotherapy for non-Hodgkin's lymphoma Meeting report: Consensus conference on acute GVHD grading Knochenmarktransplantation bei akuter Leuk~mie: Prophylaktische Antiserumbehandlung des Knochenmarkes zur Unterdrª einer Transplantat-gegen-Wirt-Reaktion Eastera Cooperative Oncology Group: Recommended guidelines for the management ofautologous and allogeneic bone rnarrow tramplantafion: The time to hematopoietic recovery is shorter with blood stem cells than with bone marrow cells.
    keywords: auch; auf; bei; bis; blood; bone; cells; das; der; des; die; disease; donor; durch; eine; graft; gvhd; hla; host; ist; leukemia; marrow; mit; nach; oder; patienten; patients; recipients; stammzelltransplantation; stem; transplantation; treatment; und; versus; von; werden; zellen
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        item: #25 of 117
          id: cord-009567-osstpum6
      author: None
       title: Abstracts Oral
        date: 2008-04-23
       words: 131515
      flesch: 49
     summary: This graft infiltration by recipient cells was more pronounced with vascularized skin grafts, and to a higher degree in heart transplants. Recipient cells similarly infiltrated allogeneic grafts early on and in larger numbers than for syngeneic grafts by day 4/5 post-transplantation.
    keywords: activation; activity; acute; age; allogeneic; allograft; allograft rejection; allograft survival; amr; analysis; anti; antibodies; antibody; antigen; b cells; background; balb; biopsies; biopsy; blood; c4d; cardiac; cd25; cd4; cd4 t; cd8; center; chronic; clinical; cmv; cni; conclusion; control; creatinine; criteria; data; days; death; development; disease; donor; donor cells; donor kidney; dose; dsa; effect; expression; factors; failure; flow; follow; foxp3; function; gene; gfr; graft; graft function; graft loss; graft rejection; graft survival; group; heart; high; hla; human; immune; immunosuppression; incidence; increase; induction; infection; injury; ischemia; islet; kidney; kidney recipients; kidney transplant; levels; liver; liver graft; liver transplantation; loss; low; mean; median; meld; methods; mice; mmf; model; months; mrna; negative; nk cells; non; number; organ; outcomes; patients; period; population; positive; post; post transplant; potential; presence; primary; production; proliferation; pts; rates; recipients; regulatory; rejection; renal; response; results; risk; role; serum; specific; study; survival; t cells; tacrolimus; term; therapy; time; tlr4; tolerance; total; transplant; transplant patients; transplant recipients; transplantation; treatment; treg; treg cells; type; university; use; vitro; vivo; vs.; year
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        item: #26 of 117
          id: cord-009571-mygj2nd4
      author: None
       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: 46205
      flesch: 47
     summary: Ten of 11 boys had disease onset prior to sexual maturation, whereas disease began after menarche in ADCC activity between patient cells and control cells when either the mixed mononuclear population or monocyte-depleted population were studied as effectors. Urate clear-ance appears to be the major determinant of serum uric acid concentration even in sickle cell patients with urate overproduction.
    keywords: acid; activity; anti; antibodies; antibody; antigen; arthritis; assay; binding; blood; bone; cartilage; cells; changes; complement; complexes; control; disease; dna; erythematosus; fluid; group; high; human; igg; igm; immune; joint; levels; lupus; lymphocytes; mean; mice; months; negative; normal; patients; positive; presence; present; renal; response; results; rheumatoid; sera; serum; sle; sle patients; studies; study; synovial; tissue; treatment; type; urate; years
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        item: #27 of 117
          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: 10062
      flesch: 19
     summary: Amino acid mutations in flanking sequences may thus affect the recognition of viral CTL epitopes, as was originally demonstrated in experiments using cytomegalovirus and influenza virus-specific CTL (13, 14), The precise mechanism by which antigen processing was affected was not defmed in these studies or a subsequent paper describing mutations in the Nef protein of human immunodeficiency virus type 1 (HIV-1) which also affected presentation of a nearby CTL epitope (15), However, in a more recent report, alteration of proteasome-mediated degradation due to a single amino acid difference within a CTL epitope was shown to form the basis of lack of presentation of this epitope by infected cells (16). Firstly, as a mutation will only be selected for if it confers a fitness advantage on the virus hearing it, CTL escape virus variants will only grow out in infections where CTL pressure exerts significant control over virus replication.
    keywords: cells; ctl; ctl escape; ctl response; cytotoxic; epitope; escape; hla; host; infection; mutations; replication; response; specific; variants; virus
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        item: #28 of 117
          id: cord-010088-s9tfvtao
      author: None
       title: Oral Abstracts
        date: 2013-11-01
       words: 43554
      flesch: 46
     summary: The information of blood donors with rare blood types is registered into the National Registering System for Blood Donors with Rare Blood Types by professional technician from organizations join the program. Present methods to recruit blood donors based on age, gender and occupation groups for a stable blood supply.
    keywords: aims; anti; antibodies; antibody; antigens; background; blood; blood components; blood donation; blood donors; blood group; blood products; blood transfusion; cases; cells; collection; data; day; development; events; group; haemovigilance; hbv; hcv; health; hit; hla; identification; immune; infection; international; inventory; management; methods; national; non; patients; plasma; platelet; platelet transfusion; population; positive; process; production; products; quality; reactions; red; results; risk; safety; samples; study; system; testing; therapy; time; transfusion; treatment; use; years
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        item: #29 of 117
          id: cord-010092-uftc8inx
      author: None
       title: Abstract of 29th Regional Congress of the ISBT
        date: 2019-06-07
       words: 233543
      flesch: 50
     summary: One central question is the need of individual NAT screening (ID) versus minipool NAT screening (MP) approaches to identify all relevant viremias in blood donors. 3A-S02-03 Background: The screening of blood donors and returning travelers from active transmission areas have highlighted the importance of diagnosis of acute arboviral infections.
    keywords: abo blood; addition; aims; allele; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; available; average; background; bacterial; bleeding; blood bank; blood cells; blood center; blood chimerism; blood collection; blood components; blood count; blood culture; blood demand; blood donation; blood donors; blood establishments; blood flow; blood group; blood grouping; blood loss; blood management; blood plasma; blood platelet; blood pressure; blood processing; blood products; blood results; blood safety; blood samples; blood services; blood supply; blood system; blood test; blood transfusion; blood type; blood units; blood volume; care; cases; cause; cell donors; cell transfusion; clinical; concentrates; concentration; conclusions; confirmed; content; control; cord blood; countries; criteria; cross; current; data; day; days; deferral; detection; difference; disease; dna; donations; donor samples; effect; events; evidence; exon; expression; factors; female; ferritin; flow; following; frequency; gel; gene; genotyping; group system; groups; hbv; hcv; health; hemoglobin; hev; history; hiv; hla; hospital; hospital blood; human; identification; igg; impact; incidence; increase; individuals; infection; information; international; iron; laboratory; levels; life; low; major; mean; median; medical; methods; min; ml blood; model; molecular; months; n =; national; need; negative; new; non; number; order; overall; p =; patients; pcr; pcs; period; phenotype; plasma; plasma donors; plasma transfusion; platelet; platelet donors; platelet transfusion; population; positive; post; potential; practice; presence; present; prevalence; procedure; process; production; quality; quality blood; range; rate; rbc blood; rbc transfusion; rbcs; reactive; red; reduced; repeat donors; research; results; rhd; rhd blood; risk; routine; screening; selection; sequencing; serum; significant; specific; staff; standard; status; storage; studies; study; summary; surgery; systems; tested; testing; tests; therapy; time donors; total; transfusion medicine; transfusion reactions; transfusion safety; transfusion service; transfusion therapy; transfusions; treated; treatment; typing; use; value; variant; versus; weak; women; years
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        item: #30 of 117
          id: cord-010119-t1x9gknd
      author: None
       title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017
        date: 2017-09-04
       words: 230433
      flesch: 50
     summary: Probability of occurrence of cannabis metabolites in blood donor samples is likely to be highly variable across donor centers and is largely dependent on blood donor demographics. OBRR, CBER, FDA Background/Case Studies: Extended molecular typing of a large number of blood donors can increase the likelihood of identifying donor red blood cells (RBCs) that match those of the recipient.
    keywords: abo; abo blood; acute; addition; alleles; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; average; background; bacterial; blood; blood bank; blood cells; blood center; blood collection; blood components; blood count; blood donation; blood donors; blood group; blood loss; blood management; blood order; blood ordering; blood products; blood safety; blood samples; blood screening; blood services; blood specimens; blood supplier; blood supply; blood system; blood testing; blood transfusion; blood type; blood units; blood volume; care; case studies; case study; cases; cd36; cell transfusion; center background; centers; change; clinical; collections; concentration; conclusion; control; cord blood; cost; count; cross; culture; current; data; days; decreased; detection; difference; disease; dna; donations; donor samples; dose; dtt; effect; emergency blood; evaluation; events; evidence; expression; factors; fda; female; ffp; finding; flow; following; frequency; fresh; gel; gene; genotyping; given; groups; hbv; hcv; health; hemoglobin; hemolysis; high; history; hiv; hla; hospital; hospital blood; hospital transfusion; hours; human; identification; igg; immucor; impact; implementation; improvement; incidence; increase; infection; information; initial; institution; inventory; iron; laboratory; levels; low; manual; mean; median; medical; method; mice; minutes; model; molecular; months; mtp; need; negative; new; non; normal; number; order; partial; pathogen; patients; pcr; performance; period; phase; phenotype; plasma; plasma samples; plasma transfusion; plasma units; platelet; platelet blood; platelet transfusion; platelet units; plt; plts; population; positive; post; post transfusion; potential; practice; pre; presence; present; prevalence; procedure; process; processing; program; protocol; quality; r blood; range; rate; rbc; rbc blood; rbc transfusion; rbc units; rbcs; reactive; reactivity; reagent; recipients; recovery; red; reduced; reduction; reference; report; response; results; review; rhd; risk; routine; screening; second; sensitivity; sequencing; serum; set; small; solution; specific; specificity; staff; standard; storage; study design; study period; survey; systems; table; technology; test results; testing; tests; therapy; time; titer; total; tpe; training; transfused; transfusion medicine; transfusion practice; transfusion protocol; transfusion reactions; transfusion results; transfusion service; transfusions; trauma; treatment; tube; typing; units; university; use; values; virus; wastage; wbc; weak; weeks; women; year; zika; zikv
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        item: #31 of 117
          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: 2754
      flesch: 33
     summary: The effect of induced chronic viral infections on the immunologic diseases of New Zealand mice Host IgG and C3 deposits in the choroid plexus during spontaneous immune complex disease Molecular mimicry and autoimmune disease Viruses perturb lymphocyte functions: Selected principles characterizing virus-induced immunosuppression Virus-induced immunosuppression: Infections with measles virus and human immunodeficiency virus Serologic relatedness between 2 and actin revealed by monoclonal antibody SV40 large T shares an antigenic determinant with cellular protein of molecular weight 68,000 Molecular mimicry in virus infection: Cross-reaction of measles phosphoprotein or of herpes simplex virus protein with human intermediate filaments Molecular mimicry: Frequency of reactivity of monoclonal antiviral anitbodies with normal tissues Amino acid homology and immune responses between the encephalitogenic site of myelin basic protein and virus: A mechanism for autoimmunity Autoantibodies to HLA-B27 in the sera of HLA-B27 patients with ankylosing spondylitis and Reiter's syndrome: Molecular mimicry with Klebsiella pneumoniae as potential mechanism of atuoimmune disease HLA-B27 related antigens in articular tissues of patients with ankylosing spondylitis Autoimmune pathogenesis for ankylosing spondylitis (AS) and Reiter's syndrome (RS): Autoantibodies against an epitope shared by HLA-B27 and Klebsiella pneumoniae nitrogenase in sera of HLA-B27 patients with AS and RS Peptides as probes to study molecular mimicry and virus induced autoimmunity Molecular mimicry and myasthenia gravis: Uncovering a novel site of the acetylcholine receptor that has biologic activity and reacts immunochemically with herpes simplex virus Examples of molecular mimicry were first described as such in the early 1980s by investigators who found that monoclonal antibodies against SV40 T antigens crossreacted with host cell proteins [8] .
    keywords: achr; antibodies; cross; hla; mimicry; protein; virus
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        item: #32 of 117
          id: cord-013093-aa4cf44u
      author: Cassotta, Antonino
       title: Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin
        date: 2020-07-09
       words: 11129
      flesch: 43
     summary: Cell culture T cells were cultured in RPMI 1640 supplemented with 2 mM glutamine, 1% (vol/vol) nonessential amino acids, 1% (vol/vol) sodium pyruvate, penicillin (50 U/ml), streptomycin (50 µg/ml; all from Invitrogen), and 5% human serum (Swiss Red Cross). We can only speculate that by stabilizing a protein domain or by locking HA in the prefusion conformation, certain antibodies might change processing of HA by endosomal cathepsins, leading to decreased production of relevant T cell peptides (Corti et al., 2011; Lee and Wilson, 2015) .
    keywords: antigen; binding; cd4; cell; cell clones; clones; donor; fig; hla; memory; mhc; peptides; specific; t cell
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        item: #33 of 117
          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: 6889
      flesch: 57
     summary: Similarly, LILRB1/2 likely adopts the same binding mode to interact with other HLA-Is (Fig. S7) , and D3D4 does not contact HLA-Is. Cis and trans interactions between LILRB1/2 and HLA-G1 Previous data indicate that D1D2 is responsible for binding to HLA class I (HLA-I), but the roles of D3D4 are still unclear.
    keywords: binding; cells; complex; d1d2; d3d4; domains; fig; hla; interaction; lilrb1; lilrb1/2; loop; structure
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        item: #34 of 117
          id: cord-014976-546zaoxn
      author: None
       title: Publication only
        date: 2006-03-08
       words: 51973
      flesch: 49
     summary: On admission before transplantation patient was presented with massive lymphadenopathy, anemia (Hb 76 g/L), WBC 24.8 x 109/L with absolute lymphocytosis (lymphocytes 98%) and thrombocytopenia 23 x 109/L. Pre-transplant conditioning consisted of high-dose cyclophosphamide and total body irradiation. There are publications about hyperkalemia in patients after renal transplantation but only few reports devote this phenomen in bone marrow transplantation patients.
    keywords: acute; age; allogeneic; aml; analysis; asct; autologous; blood; blood stem; bone; bone marrow; case; cd34; cell dose; cell transplantation; cells; chemotherapy; children; chimerism; chronic; clinical; complete; conclusion; conditioning; count; csf; cyclophosphamide; day; days; diagnosis; disease; donor; dose; engraftment; follow; grade; graft; group; gvhd; high; hla; host; hsct; levels; lymphoma; marrow; marrow transplantation; median; methods; months; non; number; patients; pbsc; post; prophylaxis; pts; range; recovery; regimen; relapse; remission; results; risk; sct; second; severe; skin; stem cell; study; therapy; time; total; transplanted; treatment; years
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        item: #35 of 117
          id: cord-015389-vwgai4k9
      author: None
       title: Publication only
        date: 2009-03-25
       words: 23906
      flesch: 53
     summary: Two years overall survival and disease free survival of AML patients were 70% and 67% respectively. The use of this AMD3100 in combination with G-CSF in patients unable to collect adequate CD34+ cells with G-CSF alone was recently reported in 280 patients with lymphoma and multiple myeloma (MM) .
    keywords: acute; age; allogeneic; aml; blood; cases; cd34; cell; cell transplantation; conclusion; conditioning; cord; days; disease; donor; dose; engraftment; graft; group; gvhd; hsct; median; methods; months; patients; post; pts; range; regimen; relapse; remission; results; risk; second; stem; stem cell; survival; therapy; time; transplantation; treatment; years
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        item: #36 of 117
          id: cord-016235-2lhrkmrv
      author: Roden, Anja C.
       title: Lung
        date: 2010-05-17
       words: 12880
      flesch: 33
     summary: The effect of recipient's age on lung transplant outcome Pretransplant panel reactive antibody in lung transplant recipients is associated with significantly worse post-transplant survival in a multicenter study Gastroesophageal reflux disease in lung transplant recipients Lung homotransplantation in man Association of minimal rejection in lung transplant recipients with obliterative bronchiolitis Prospective analysis of 1, 235 transbronchial lung biopsies in lung transplant recipients Rejection is reduced in thoracic organ recipients when transplanted in the first year of life C4d deposition in lung allografts is associated with circulating anti-HLA alloantibody Acute and chronic onset of bronchiolitis obliterans syndrome (BOS): are they different entities? Anti-HLA class I antibody binding to airway epithelial cells induces production of fibrogenic growth factors and apoptotic cell death: a possible mechanism for bronchiolitis obliterans syndrome Pleural effusion from acute lung rejection Refining the identification of discriminatory genes for rejection in lung transplantation: the largo study Significance of a solitary perivascular mononuclear infiltrate in lung allograft recipients with mild acute cellular rejection Native lung complications in single-lung transplant recipients and the role of pneumonectomy Immunodeficiency-associated lymphoproliferative disorders Correlative morphologic and molecular genetic analysis demonstrates three distinct categories of posttransplantation lymphoproliferative disorders The US experience with lung transplantation for pulmonary lymphangioleiomyomatosis The diagnosis of obliterative bronchiolitis after heart-lung and lung transplantation: low yield of transbronchial lung biopsy Clinical impact of community-acquired respiratory viruses on bronchiolitis obliterans after lung transplant Lung transplantation at Duke University Medical Center Pulmonary inflammation after lung transplantation The incidence of cancer in patients with idiopathic pulmonary fibrosis and sarcoidosis in the UK Posttransplant lymphoproliferative disorders not associated with Epstein-Barr virus: a distinct entity? Identification of prognostic factors in 61 patients with posttransplantation lymphoproliferative disorders Chronic aspiration of gastric fluid induces the development of obliterative bronchiolitis in rat lung transplants GI complications after orthotopic lung transplantation B-cell posttransplant lymphoproliferative disorders in heart and/or lungs recipients: clinical and molecular-histogenetic study of 17 cases from a single institution C3d and the septal microvasculature as a predictor of chronic lung allograft dysfunction Selection and evaluation of recipients for heart-lung and lung transplantation Outcomes of lung transplantation in patients with scleroderma Complications (excluding hyperinflation) involving the native lung after single-lung transplantation: incidence, radiologic features, and clinical importance Evolving strategies in lung transplantation for emphysema Surveillance bronchoscopy in lung transplant recipients: risk versus benefit Clinical implications and longitudinal alteration of peripheral blood transcriptional signals indicative of future cardiac allograft rejection Lung transplantation: a decade of experience Acute humoral rejection of human lung allografts and elevation of C4d in bronchoalveolar lavage fluid Lung transplantation for end-stage pulmonary sarcoidosis: outcome in a series of seven consecutive patients Pulmonary hypertension in patients with bronchiolitis obliterans syndrome listed for retransplantation Epstein-Barr virus-negative post-transplant lymphoproliferative disorders: a distinct entity? Lymphomas after solid organ transplantation: a collaborative transplant study report General overview of lung transplantation and review of organ allocation Development of an antibody specific to major histocompatibility antigens detectable by flow cytometry after lung transplant is associated with bronchiolitis obliterans syndrome Gastroesophageal reflux as a reversible cause of allograft dysfunction after lung transplantation Bronchoalveolar lavage cell gene expression in acute lung rejection: development of a diagnostic classifier Lung transplantation for lymphangioleiomyomatosis The changing pattern of posttransplant malignancies Does human leukocyte antigen matching influence the outcome of lung transplantation? Several host genetic characteristics have been suggested to modulate acute lung rejection.
    keywords: acute; allograft; bronchiolitis; chronic; diagnosis; disease; grade; heart; hla; infection; injury; lung; lung transplantation; patients; posttransplantation; pulmonary; recipients; rejection; risk; study; transplantation; years
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        item: #37 of 117
          id: cord-016413-lvb79oxo
      author: Efthimiou, Petros
       title: Adult-Onset Still’s Disease
        date: 2018-07-14
       words: 6129
      flesch: 38
     summary: Myocarditis, pericarditis, and pleural effusions have also been observed in AOSD patients, and they seem to respond to anti-inflammatory treatment. Several retrospective case series and one open-labeled prospective randomized trial have evaluated the use of anakinra in AOSD patients [41, 42] .
    keywords: adult; anakinra; aosd; arthritis; cases; disease; fever; macrophage; onset; patients; symptoms; syndrome; treatment
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        item: #38 of 117
          id: cord-016998-6n662amh
      author: None
       title: Nierentransplantation
        date: 2007
       words: 6873
      flesch: 35
     summary: Im Schnitt lag die 1-Jahres-Transplantatüberlebensrate Ende der 1970er Jahre bei etwa 55%, in der ersten Hälfte der 1980er Jahre bei etwa 75% und in der zweiten Hälfte bei fast 90%. Die Plasmaspiegel von Phosphat, AP, β 2 -Mikroglo-bulin und Parathormon fallen, die Kalzifikationen nehmen ab.
    keywords: abstoßung; als; antigene; antikörper; auch; auf; aus; azathioprin; bei; beim; bis; ciclosporin; cmv; das; dem; der; des; die; diese; durch; ebv; eine; empfänger; etwa; führt; für; gabe; gegen; hla; immunsuppression; infektion; ist; jahren; jedoch; kann; können; man; mit; mycophenolat; nach; nicht; nierentransplantation; noch; nur; oder; okt; patienten; rezidiv; sich; sie; sind; sowie; transplantation; und; unter; von; vor; werden; wird; zur; über
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        item: #39 of 117
          id: cord-017184-1ewi3dka
      author: None
       title: Primary Immunodeficiencies
        date: 2008
       words: 44590
      flesch: 43
     summary: Therefore defects in BM prethymic T cell development can contribute to T cell deficiency in nu/nu mice [90] . T-cell proliferative responses to mitogens were defective and IL 2 R expression was deficient on his T lymphocytes, and B cells did not differentiate into antibodysecreting cells when provided with the help of normal T cells [245] .
    keywords: absence; age; b cells; bmt; bone; cases; cd8; cells; children; chromosome; chronic; class; clinical; combined; common; defect; deficiencies; deficiency; development; diagnosis; disease; expression; fig; function; gene; hla; ifn; iga; ige; igg; igm; immunodeficiency; infections; levels; life; lymphocyte; marrow; months; mutations; normal; patients; pid; present; primary; production; protein; recurrent; rris; scid; serum; severe; study; symptoms; syndrome; t cells; table; transplantation; treatment; years
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        item: #40 of 117
          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: 11196
      flesch: 36
     summary: The immunome Computational immunology: The coming of age Fitness costs limit viral escape from cytotoxic T lymphocytes at a structurally constrained epitope Design of peptide-based vaccines for cancer Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing The immunodominant influenza matrix T cell epitope recognized in human induces influenza protection in HLA-A2/K(b) transgenic mice A repetitive sequence of Ebstein-Barr virus nuclear antigen 6 comprises overlapping T cell epitopes which induce HLA-DR restricted CD4+ T lymphocytes Reverse vaccinology and genomics Enhancing DNA immunization Exact prediction of natural T cell epitope T cells primed by influenza virion internal components can cooperate in the antibody response to haemagglutinin Prior vaccination increases the epitopic breadth of the cytotoxic T-lymphocyte response that evolves in rhesus monkeys following a simian-human immunodeficiency virus infection CTL epitopes identified with a defective recombinant adenovirus expressing measles virus nucleoprotein and evaluation of their protective capacity in mice Functional analysis of influenza-specific helper T cell clones in vivo. In its minimal form, an IDV would contain only adjuvanated B cell and T cell epitopes in delivery vehicles such as liposomes.
    keywords: antigens; approach; cell; class; development; epitopes; et al; hiv; hla; human; mhc; mice; peptide; protein; response; sequences; t cell; tools; vaccine
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        item: #41 of 117
          id: cord-017702-v46ye328
      author: Ganguly, Nirmal Kumar
       title: Pharmacogenomics and Personalized Medicine for Infectious Diseases
        date: 2013-06-11
       words: 16571
      flesch: 34
     summary: From the several RNAi screenings in human and in fruit fl y cells, only 300 host factors were validated from about 10,000 and 20,000 targets identifi ed in the initial screen (Agaisse et al. 2005 ; Brass et al. 2008 ; Konig et al. 2008 ; Krishnan et al. 2008 ; Zhou et al. 2008 ) . It has been observed in the case of measles vaccination that only 10 % of the population was seronegative and clustered in family (Poland 1999a , b ; Poland et al. 1999c ).
    keywords: acetylators; activity; discovery; disease; drug; enzymes; et al; gene; genome; hepatotoxicity; hla; host; human; infection; isoniazid; leishmaniasis; major; malaria; nat2; pathogen; patients; polymorphism; population; protein; resistance; response; risk; slow; studies; study; susceptibility; technologies; treatment; tuberculosis
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        item: #42 of 117
          id: cord-017856-4fccnygg
      author: Roden, Anja C.
       title: Pathology of Lung Rejection: Cellular and Humoral Mediated
        date: 2018-04-24
       words: 7788
      flesch: 31
     summary: For instance, the recipient alloimmune response is thought to be related to the recognition of differences to donor antigens leading to acute lung allograft rejection. Several host genetic characteristics have been studied that may modulate acute lung rejection.
    keywords: acute; allograft; amr; antibodies; biopsies; bronchiolitis; hla; lung; patients; rejection; study; transbronchial; transplantation
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        item: #43 of 117
          id: cord-018595-x3tleomb
      author: Dodiuk-Gad, Roni P.
       title: Adverse Medication Reactions
        date: 2017-04-25
       words: 16329
      flesch: 37
     summary: In view of the large diversity of cutaneous drug reactions, it is helpful to approach them as clinicopathologic entities and to base the diagnosis on a combination of clinical, histo- logical and disease course data [89] . Heightened awareness of the possible mimicry of other skin diseases and of the suspicious histopathological clues pointing to drug etiology are key elements to the appropriate histological diagnosis of drug reactions in the skin [85, 88, 89] .
    keywords: acute; adrs; carbamazepine; cases; cells; diagnosis; dress; drug; drug hypersensitivity; drug reactions; epidermal; eruption; hla; hypersensitivity; involvement; johnson; lesions; necrolysis; patients; reactions; sjs; skin; specific; stevens; study; symptoms; syndrome; treatment; type; urticaria
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        item: #44 of 117
          id: cord-018714-i291z2ju
      author: Criado, Paulo Ricardo
       title: Adverse Drug Reactions
        date: 2016-12-31
       words: 23933
      flesch: 36
     summary: This group of drug reactions includes anaphylaxis, Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), and, depending on the systemic involvement, erythroderma. This group of drug reactions includes anaphylaxis, SJS, TEN, drug hypersensitivity, and, depending on the systemic involvement, erythroderma, acute generalized exanthematous pustulosis (AGEP), cutaneous necrosis induced by anticoagulants, druginduced vasculitis, and reactions such as serum disease [4] .
    keywords: acute; agents; cases; cells; chemotherapeutic; chemotherapy; corticosteroids; days; diagnosis; dihs; disease; dress; drug; drug reactions; eccrine; edema; epidermal; eruption; erythema; fig; hla; immune; involvement; lesions; necrosis; onset; patients; reactions; reactivation; sjs; skin; symptoms; syndrome; treatment; type; use; vasculitis; weeks
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        item: #45 of 117
          id: cord-022474-xxy83c6u
      author: Tenorio, Grace C.
       title: Transfusion Medicine and Immunohematology
        date: 2007
       words: 12096
      flesch: 42
     summary: Scientific Basis of Transfusion Medicine Estimated risk of transmission of the West Nile virus through blood transfusion in the US American Association of Blood Banks Current and emerging infectious risks of blood transfusions Current prevalence and incidence of infectious disease markers and estimated window-period risk in the American Red Cross blood donor population Modern Blood Banking and Transfusion Medicine Blood Banking and Transfusion Medicine Standards for Blood Banks and Transfusion Services Transfusion Medicine Transfusion Therapy: Clinical Principles and Practice The HLA System: Basic Biology and Clinical Applications Clinical Practice of Transfusion Medicine Risks of transfusion-transmitted infection Rossi's Principles of Transfusion Medicine Principles of Transfusion Medicine Request for an exception under 21 CFR (Code of Federal Regulation) 640.120, Alternative Procedures, to 610.53 (d), Dating Periods, to use the Gambro 7-day ELP Platelet Storage System Using Apheresis Platelets Collected with the Cobe Spectra Apheresis System and Gambro Trima Automated Blood Component Collection System US Food and Drug Administration approves Gambro BCT's 7-day platelet Post-Market Surveillance Plan. Children with thalassemia, adults with myelodysplastic syndromes, and patients with autoimmune hemolytic anemias, leukemias, or aplastic anemias become chronically dependent on blood transfusions.
    keywords: antibodies; antigens; blood; cell; class; components; disease; donors; group; hla; individuals; infection; patients; plasma; platelet; products; reactions; red; risk; system; testing; transfusion; transmission; virus
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        item: #46 of 117
          id: cord-022888-dnsdg04n
      author: None
       title: Poster Sessions
        date: 2009-08-19
       words: 189173
      flesch: 41
     summary: Our aim is to describe how B cell lymphoma cells respond to TGF-b compared to normal peripheral B cells, to create an overview of the different signaling pathways involved, and to characterize the mechanisms behind the loss of sensitivity to TGF-b. Methods: Proliferation assays were performed on 11 different B-cell lymphoma cell lines and normal peripheral B cells to screen for TGF-b-induced effects. Using a CD3 and CD28 activation model system -TLR4 presence on CD4+ cells is found in mouse T cells, human T cells and Jurkat cell lines.
    keywords: + cells; ability; absence; activity; addition; analysis; antibodies; antibody; antigen; apoptosis; apoptotic; assay; associated; autoimmune; b cells; b t; binding; blood; bone; c mice; cancer cells; capacity; cd4; cd8 +; cd8 cells; cd8 t; cell activation; cell activity; cell culture; cell cycle; cell death; cell development; cell differentiation; cell epitopes; cell function; cell level; cell lines; cell membrane; cell population; cell proliferation; cell receptor; cell responses; cell subsets; cell surface; cell tolerance; cell types; cells cells; changes; chronic; class; clinical; colitis; complex; conclusion; contrast; control; control cells; cross; ctl; cytokine; cytokine production; cytometry; cytotoxic t; data; day; days; dcs; deficient; delta t; dendritic; disease; dna; early; effector cells; effector t; effects; elisa; expansion; experiments; expression; expression levels; factor; family; findings; flow; following; formation; function; gamma; gd cells; gd t; gene; gene expression; group; high; hiv; hla; host; human; ifn; ifng; igg; il-10; il-2; il-4; il-6; immune; immunity; increase; independent; induction; infected; infection; inflammation; inflammatory; inhibition; inkt; interaction; intracellular; levels; lps; macrophages; major; marrow cells; mast cells; mechanisms; membrane; memory t; methods; mhc; mice; model; molecules; monocytes; mouse; mouse t; mrna; murine; negative; neutrophils; new; nkt cells; non; normal; novel; number; objectives; pathway; patients; pcr; peptide; peripheral; plasma cells; play; positive; potential; presence; presentation; primary; production; promoter; protein; protein expression; receptors; regulation; regulatory; release; results; role; secretion; serum; signaling; skin; sle; specific; spleen; stem cells; stimulation; studies; study; surface expression; system; t cells; t em; t h; t helper; t lymphocytes; target cells; tcr; test; th1 cells; time; tissue; tlr; tnf; tolerance; transcription; treatment; tumor cells; type; university; vaccination; vaccine; vg9vd2 t; virus; vitro; vivo; work
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        item: #47 of 117
          id: cord-023055-ntbvmssh
      author: None
       title: Immunogenicity
        date: 2004-02-19
       words: 64788
      flesch: 56
     summary: o present fragments of that antigen very efficiently t o T cells. 10. carrier (KLH) primed T cells were transferred in the presence or absence of antigen into irradiated, K-allotype distinct adoptive host.
    keywords: ability; activity; amino; analysis; antibodies; antibody; antigen; b cells; binding; c e; c r; c t; cd3; cd4; cd8; cell activation; cell antigen; cell clones; cell epitopes; cell line; cell proliferation; cell receptor; cell response; cell surface; cells; chain; class; ctl; cytotoxic t; data; e l; e n; e s; epitopes; expression; f e; f t; gene; h e; hla; human; induced; l l; l s; l t; l y; levels; lines; mab; mhc; mice; molecules; monoclonal; mouse; mrna; murine; murine t; n g; n s; n t; non; o l; o n; p e; p l; p t; peptide; presence; present; production; proliferation; protein; r e; r l; recognition; region; residues; response; results; s c; s p; s s; sequence; specific; spleen cells; studies; t antigen; t cell; t e; t h; t helper; t lymphocytes; t o; t r; t s; t t; t u; t y; tcr; u l; w e
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        item: #48 of 117
          id: cord-023143-fcno330z
      author: None
       title: Molecular aspects of viral immunity
        date: 2004-02-19
       words: 43520
      flesch: 44
     summary: The immunohistological analysis suggests that CD8+ T cell dependent disappearence of marginal zone macrophages of follicular dendritic cells and of virus infected cells in general correlates with immunosuppression. Our studies indicate that MHC class I resmcted CD8+ cytotoxic T lymphocytes (CTLs) are activated in response to viral antigens leading to destruction of virus infected cells and loss of transgene expression.
    keywords: activity; amino; analysis; animals; antibodies; antibody; antigen; b cells; binding; cd4; cd8; cell responses; challenge; class; clones; cns; ctl; ctl response; cytokines; cytotoxic t; days; different; disease; dna; epitopes; expression; gene; hiv; hla; host; human; ifn; immune; immunity; infected; infection; influenza; lcmv; levels; lymphocytes; memory; mhc; mice; model; molecules; mouse; murine; peptides; primary; production; protein; recognition; recombinant; replication; response; results; role; sequence; specific; spleen; strains; studies; t cells; type; vaccine; vaccinia; viral; virus; virus infection; viruses; vivo
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        item: #49 of 117
          id: cord-023346-8sqbqjm1
      author: None
       title: MONDAY: POSTERS
        date: 2005-06-08
       words: 130150
      flesch: 50
     summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion.
    keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years
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        item: #50 of 117
          id: cord-023354-f2ciho6o
      author: None
       title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS
        date: 2005-06-08
       words: 130154
      flesch: 50
     summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion.
    keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years
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        item: #51 of 117
          id: cord-023364-ut56gczm
      author: None
       title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS
        date: 2005-06-08
       words: 130157
      flesch: 50
     summary: The Polish Blood Transfusion Act of 22nd August 1997, in force since January 1st 1999, has been supplemented by 8 Decrees: 1. procedures for external BTS audits; 2. requirements for donor selection; 3. requirements and procedures for organization and safe management of blood transfusion in hospitals; 4. requirements for implementing of national and regional donor registers; 5. employment criteria for BTS personnel; 6. training requirements for hospital personnel involved in blood and blood product administration; 7. national, uniform price list for blood and blood products; 8. organization requirements for setting up of a National Committee for Blood and Blood Transfusion. Introduction: TRALI is a life threatening adverse reaction of blood transfusion.
    keywords: aim; analysis; anti; antibodies; antibody; antigens; apheresis; assay; associated; background; blood banking; blood banks; blood cells; blood center; blood collection; blood components; blood donation; blood donors; blood establishments; blood group; blood loss; blood plasma; blood pressure; blood products; blood safety; blood samples; blood service; blood supply; blood system; blood transfusion; blood units; blood volume; cases; clinical; complications; concentrates; conclusion; control; cord blood; count; data; day; days; detection; disease; dna; donations; effect; events; factor; ffp; following; frequency; general; groups; hbsag; hbv; hcv; health; high; hla; hospital; hospital blood; identification; important; increase; infections; information; introduction; iron; laboratory; level; low; major; management; mean; medical; methods; national; negative; new; non; number; order; patients; pcr; period; plasma; platelet; platelet transfusion; population; positive; post; practice; presence; present; procedure; process; quality; range; rbc; rbc transfusion; rbcs; red; results; rhd; risk; routine; screening; serum; specific; standard; storage; studies; study; surgery; system; table; test; tested; testing; therapy; time blood; total; transfusion medicine; transfusion reactions; transfusion service; transfusion therapy; transfusions; treatment; type; use; weak; women; years
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        item: #52 of 117
          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: 2388
      flesch: 34
     summary: The effect of induced chronic viral infections on the immunologic diseases of New Zealand mice Host IgG and C3 deposits in the choroid plexus during spontaneous immune complex disease Molecular mimicry and autoimmune disease Viruses perturb lymphocyte functions: Selected principles characterizing virus-induced immunosuppression Virus-induced immunosuppression: Infections with measles virus and human immunodeficiency virus Serologic relatedness between Thyl.2 and actin revealed by monoclonal antibody SV40 large T shares an antigenic determinant with cellular protein of molecular weight 68,000 Molecular mimicry in virus infection: Cross-reaction of measles phosphoprotein or Oldstone of herpes simplex virus protein with human intermediate filaments Molecular mimicry: Frequency of reactivity of monoclonal antiviral anitbodies with normal tissues Amino acid homology and immune responses between the encephalitogenic site of myelin basic protein and virus: A mechanism for autoimmunity Autoantibodies to HLA-B27 in the sera of HLA-B27 patients with ankylosing spondylitis and Reiter's syndrome: Molecular mimicry with Klebsiella pneumoniae as potential mechanism of atuoimmune disease HLA-B27 related antigens in articular tissues of patients with ankylosing spondylitis Autoimmune pathogenesis for ankylosing spondylitis (AS) and Reiter's syndrome (RS): Autoantibodies against an epitope shared by HLA-B27 and Klebsiella pneumoniae nitrogenase in sera of HLA-B27 patients with AS and RS Peptides as probes to study molecular mimicry and virus induced autoimmunity Molecular mimicry and myasthenia gravis: Uncovering a novel site of the acetylcholine receptor that has biologic activity and reacts immunochemically with herpes simplex virus Examples of molecular mimicry were first described as such in the early 1980s by investigators who found that monoclonal antibodies against SV40 T antigens crossreacted with host cell proteins [8] .
    keywords: achr; cross; hla; mimicry; protein; virus
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        item: #53 of 117
          id: cord-028275-szb45jm2
      author: Reza Khorramizadeh, M.
       title: Animal models for human disease
        date: 2020-06-26
       words: 11618
      flesch: 42
     summary: The sublining also undergoes alterations for its cellularity, both in cell type and in cell numbers, with prominent infiltration of mononuclear cells, including T cells, B cells, macrophages, and plasma cells. T cells are also important for CIA development during early stages of disease progression.
    keywords: animal; arthritis; cells; collagen; cytokines; disease; et al; human; inflammatory; mice; models; myelin; patients; rheumatoid; rheumatoid arthritis; sclerosis; synovial; system; t cells; treatment; type
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        item: #54 of 117
          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: 6766
      flesch: 19
     summary: KYNU was further mapped with host proteins (direct and indirect) resulting in 1994 interactions. It is suggested that in host-microbe interactions, bacterial proteins entering host cells interact with host proteins and inject their effector components, but has not been proven in ReA and IBD.
    keywords: analysis; arthritis; associated; disease; expression; genes; hla; host; human; ibd; metabolic; microbe; microorganisms; network; protein; rea; target
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        item: #55 of 117
          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
      flesch: 47
     summary: This present study aims at the prediction of B cell epitopes for subunit vaccine designing against Listeria monocytogenes using a reverse vaccinology approach. This study is mainly based on the anticipation of B cell epitopes for the utility of vaccine designing against listeriosis.
    keywords: epitopes; listeria; listeriosis; monocytogenes; non; server; vaccine
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        item: #56 of 117
          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: 8122
      flesch: 40
     summary: Therapeutic conserved elements (CE) DNA vaccine induces strong T-cell responses against highly conserved viral sequences during simian-human immunodeficiency virus infection HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity Post-therapy viral set-point abatement following combined antiproliferative and immune-boosting interventions: results from a randomised clinical trial The COVID-19 epidemic Evaluation of the establishment of herd immunity in the population by means of serological surveys and vaccination coverage NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics Mechanisms of viral mutation BepiPred-2.0: improving sequencebased B-cell epitope prediction using conformational epitopes Chloroquine is a potent inhibitor of SARS coronavirus infection and spread New insights into the antiviral effects of chloroquine Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro Hydroxychloroquine and Azithromycin as a treatment of COVID-19: preliminary results of an open-label non-randomized clinical trial Substrate-based design of the first class of angiotensin-converting enzyme-related carboxypeptidase (ACE2) inhibitors ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2 Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes Screening and Identification of Severe Acute Respiratory Syndrome-Associated Coronavirus-Specific CTL Epitopes The $1,000 Genome: The Revolution in DNA Sequencing and the New Era of Personalized Medicine The epidemiological transition: the current status of infectious diseases in the developed world versus the developing world Therapeutic HIV Peptide Vaccine OpenVax: An Open-Source Computational Pipeline for Cancer Neoantigen Prediction How will country-based mitigation measures influence the course of the COVID-19 epidemic? Moreover, the choice of a highly conserved viral target as a source of vaccine epitopes should ensure a broadly effective response in those individuals for whom the vaccine should prove immunogenic.
    keywords: ace2; alleles; class; cov-2; custommune; design; epitopes; gag; hla; license; population; preprint; sars; sequences; vaccine
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        item: #57 of 117
          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: 8585
      flesch: 46
     summary: The donor ID is listed on X-axis and the total number of spike protein peptides from that particular donor denoted on the Y-axis. (A) Prevalence of peptide clusters across donors.
    keywords: cell; class; clusters; cov-2; donors; et al; glycoprotein; hla; human; peptides; protein; sars; sequence; spike; table
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        item: #58 of 117
          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: 9758
      flesch: 47
     summary: Thus, CD8 + T cells directed at our novel HLA-A24-restricted IBV-specific epitopes provide a substantial level of protection against influenza disease, as they can markedly decrease body weight loss, accelerate viral clearance and reduce the cytokine storm at the site of infection. A virus varies across ethnicities Multimorbidity among Aboriginal people in New South Wales contributes significantly to their higher mortality Risk factors and mitigation of influenza among Indigenous children in Australia, Canada, United States, and New Zealand: a scoping review Recalling the Future: Immunological Memory Toward Unpredictable Influenza Viruses Cytotoxic T-Cell Immunity to Influenza Cross-Recognition of Avian H5N1 Influenza Virus by Human Cytotoxic T-Lymphocyte Populations Directed to Human Influenza A Virus Cellular immune correlates of protection against symptomatic pandemic influenza Recovery from severe H7N9 disease is associated with diverse response mechanisms dominated by CD8+ T cells Innate and adaptive T cells in influenza disease Human Cytotoxic T Lymphocytes Directed to Seasonal Influenza
    keywords: a24; cd8; cell; fig; hla; iav; ibv; influenza; license; medrxiv; medrxiv preprint; pb2; peptides; preprint; responses; supplementary
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        item: #59 of 117
          id: cord-126015-zc7u3g34
      author: Krieger, Elizabeth
       title: Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective
        date: 2020-05-13
       words: 6427
      flesch: 28
     summary: H1N1) 2009 Pandemic: A Case-Control Study Cytomegalovirus Infection in Ireland: Seroprevalence, HLA Class I Alleles, and Implications Mathematical modeling provides kinetic details of the human immune response to vaccination A qualitatively validated mathematical-computational model of the immune response to the yellow fever vaccine Modeling Influenza Virus Infection: A Roadmap for Influenza Research Dynamical System Modeling of Immune Reconstitution after Allogeneic Stem Cell Transplantation Identifies Patients at Risk for Adverse Outcomes Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential in HLA-Matched and -Mismatched Donor-Recipient Pairs Killer Immunoglobulin-Like Receptor-Ligand Interactions Predict Clinical Outcomes following Unrelated Donor Transplantations Stem cell transplantation as a dynamical system: are clinical outcomes deterministic? Understanding how combinations of HLA and KIR genes influence disease Direct Recognition of Cytomegalovirus by Activating and Inhibitory NK Cell Receptors Determining the Quantitative Principles of T Cell Response to Antigenic Disparity in Stem Cell Transplantation 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.
    keywords: cell; cov-2; cytokine; disease; hla; infection; kir; patients; polymorphism; receptor; response; sars; toll; virus
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        item: #60 of 117
          id: cord-254190-bxfne94u
      author: Tu, Wenwei
       title: Application of Humanized Mice in Immunological Research
        date: 2015-07-07
       words: 6266
      flesch: 17
     summary: Scientists are still improving the humanized mouse model but are optimistic about its future role in evaluating AIDS vaccine candidates Humanized mice as a preclinical tool for infectious disease and biomedical research HLA transgenic mice as humanized mouse models of disease and immunity Prevention of Humanized diabetogenic CD8 T-cell responses in HLA-transgenic NOD mice by a multipeptide coupled-cell approach CD8 T cell responses to myelin oligodendrocyte glycoprotein-derived peptides in humanized HLA-A*0201 Humanized mice for studying human leukocyte integrins in vivo Full reconstitution of human platelets in humanized mice after macrophage depletion Human T cell development in the liver of humanized NOD/SCID/ IL-2Rgamma(null)(NSG) mice generated by intrahepatic injection of CD34(+) human (h) cord blood (CB) cells Systemic human T cell developmental processes in humanized mice cotransplanted with human fetal thymus/ liver tissue and hematopoietic stem cells Expression of HLA class II molecules in humanized NOD. Rapid evolution of HIV-1 to functional CD8(+) T cell responses in humanized BLT mice Effi cient infection, activation, and impairment of pDCs in the BM and peripheral lymphoid organs during early HIV-1 infection in humanized rag2(-)/(-) gamma C(-)/(-) mice in vivo Plasmacytoid dendritic cells suppress HIV-1 replication but contribute to HIV-1 induced immunopathogenesis in humanized mice In vivo blockade of the PD-1 receptor suppresses HIV-1 viral loads and improves CD4+ T cell levels in humanized mice PD-1 blockade in chronically HIV-1-infected humanized mice suppresses viral loads Engineering HIV-1-resistant T-cells from short-hairpin RNAexpressing hematopoietic stem/progenitor cells in humanized BLT mice An aptamer-siRNA chimera suppresses HIV-1 viral loads and protects from helper CD4(+) T cell decline in humanized mice HLA-B*57 elite suppressor and chronic progressor HIV-1 isolates replicate vigorously and cause CD4+ T cell depletion in humanized BLT mice Intravital microscopy in BLT-humanized mice to study cellular dynamics in HIV infection Gene therapy strategies for HIV/AIDS: preclinical modeling in humanized mice Humanized mice for modeling human infectious disease: challenges, progress, and outlook Mosquito bite delivery of dengue virus enhances immunogenicity and pathogenesis in humanized mice Utility of humanized BLT mice for analysis of dengue virus infection and antiviral drug testing Enhanced humoral and HLA-A2-restricted dengue virus-specifi c T-cell responses in humanized BLT NSG mice Dengue virus infection induces broadly cross-reactive human IgM antibodies that recognize intact virions in humanized BLT-NSG mice Dengue virus tropism in humanized mice recapitulates human dengue fever EBNA3B-defi cient EBV promotes B cell lymphomagenesis in humanized mice and is found in human tumors A novel animal model of Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis in humanized mice Epstein-Barr virus induces erosive arthritis in humanized mice T cells modulate Epstein-Barr virus latency phenotypes during infection of humanized mice Reproduction of Epstein-Barr virus infection and pathogenesis in humanized mice Adoptive transfer of EBV Specifi c CD8+ T cell clones can transiently control EBV infection in humanized mice HCMV infection of humanized mice after transplantation of G-CSF-mobilized peripheral blood stem cells from HCMV-seropositive donors Adult T-cell leukemia/lymphoma development in HTLV-1-infected humanized SCID mice Of men in mice: the success and promise of humanized mouse models for human malaria parasite infections Leishmania major infection in humanized mice induces systemic infection and provokes a nonprotective human immune response Humanized nonobese diabetic-scid IL2rgammanull mice are susceptible to lethal Salmonella Typhi infection Humanized mice for Salmonella typhi infection: new tools for an old problem Modeling of human herpesvirus infections in humanized mice Human herpesvirus 6A infection and immunopathogenesis in humanized Rag2(-)/(-) gammac(-)/(-) mice Engrafted human cells generate adaptive immune responses to Mycobacterium bovis BCG infection in humanized mice CD4+ cell-dependent granuloma formation in humanized mice infected with mycobacteria Humanized mice, a new model to study the infl uence of drug treatment on neonatal sepsis Humanized mice for the study of infectious diseases Development of a transgenic mouse model susceptible to human coronavirus 229E New generation humanized mice for virus research: comparative aspects and future prospects Infectious diseases in humanized mice Use of humanized severe combined immunodeficient mice for human vaccine development Human immune responses and potential for vaccine assessment in humanized mice Broad infl uenza-specifi c CD8+ T-cell responses in humanized mice vaccinated with infl uenza virus vaccines Humanized mice: are we there yet? Humanized mice: current states and perspectives Humanized mice for immune system investigation: progress, promise and challenges This work was supported in part by the Area of Excellence program supported by the University Grants Committee of the Hong Kong SAR, China (AoE/M-12/06 and AoE/M-06/08).
    keywords: cells; development; diseases; hla; human; immune; infection; mice; model; mouse; specifi; system; transgenic; virus
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        item: #61 of 117
          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: 1824
      flesch: 33
     summary: Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA HIV evolution: CTL escape mutation and reversion after transmission Molecular footprints reveal the impact of the protective HLA-A*03 allele in hepatitis C virus infection Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level Cross-species transmission of the newly identified coronavirus 2019-nCoV Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission HIV protease resistance and viral fitness Selection of viral adaptations to polymorphic host responses mediated by T cells, NKcells, antibodies and antiviral drugs are well described for other RNA viruses such as HIV and HCV 4, 11 .
    keywords: cov-2; nucleocapsid; polymorphisms; sars; strains
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        item: #62 of 117
          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: 5798
      flesch: 52
     summary: Our analysis on this small number of trial subjects was not designed to further explore this observation but rather to study the induction of HPV T cell responses and their cross reactive properties following immunization with amolimogene. The frequency of HPV peptide responses in the placebo control group was low however, it should be noted that one subject (#22) had a response to the HPV 16 E7, LLMGTLGIV and HPV 18 E7, LFLNTLSFV peptides that was low in overall magnitude, but met the criteria for an enhanced response.
    keywords: amolimogene; cd8; cells; hla; hpv; human; peptide; responses; specific; subjects
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        item: #63 of 117
          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: 4637
      flesch: 38
     summary: Prior immunization with severe acute respiratory syndrome (SARS)-434 associated coronavirus (SARS-CoV) nucleocapsid protein causes severe pneumonia in mice 435 infected with SARS-CoV Characterization of the receptor-binding domain (RBD) of 2019 novel 537 coronavirus: implication for development of RBD protein as a viral attachment inhibitor and 538 vaccine Quantitative comparison of the efficiency of antibodies against S1 and S2 540 subunit of SARS coronavirus spike protein in virus neutralization and blocking of receptor 541 binding: implications for the functional roles of S2 subunit Neutralizing epitopes of the SARS-CoV S-protein cluster independent of 543 repertoire, antigen structure or mAb technology Identification and characterization of novel neutralizing epitopes in the 545 receptor-binding domain of SARS-CoV spike protein: revealing the critical antigenic 546 determinants in inactivated SARS-CoV vaccine Discovery of 548 naturally processed and HLA-presented class I peptides from vaccinia virus infection using mass 549 spectrometry for vaccine development Development of Autologous C5 Vaccine Nanoparticles to Reduce 551 Intravascular Hemolysis in Vivo Plug-and-Display: decoration of Virus-Like Particles via isopeptide 553 bonds for modular immunization A novel candidate HPV vaccine: MS2 phage VLP displaying a tandem HPV 555 L2 peptide offers similar protection in mice to Gardasil-9 Targeted 557 immunomodulation using antigen-conjugated nanoparticles Scoring function for automated assessment of protein structure 560 template quality GalaxyPepDock: a protein-peptide docking tool based 562 on interaction similarity and energy optimization World Health Organization (2020) Draft landscape of COVID-19 candidate vaccines Tortoises, hares, and vaccines: A cautionary note for SARS-CoV-2 vaccine 428 development Immunization with SARS coronavirus vaccines leads to pulmonary 430 immunopathology on challenge with the SARS virus Vaccine efficacy in senescent mice challenged with recombinant SARS-432 CoV bearing epidemic and zoonotic spike variants
    keywords: cell; class; cov-2; epitopes; hla; peptides; protein; sars; vaccine
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        item: #64 of 117
          id: cord-266204-ipa017wz
      author: Poland, G. A.
       title: Personalized vaccinology: A review
        date: 2018-08-28
       words: 7241
      flesch: 27
     summary: Dissecting polyclonal vaccine-induced humoral immunity against HIV using systems serology Cytometry by time-offlight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8 + T cell phenotypes Highresolution myogenic lineage mapping by single-cell mass cytometry Metabolic phenotypes of response to vaccination in humans Heterogeneity in vaccine immune response: the role of immunogenetics and the emerging field of vaccinomics Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century Pharmacology, vaccinomics, and the second golden age of vaccinology A systems biology approach to the effect of aging, immunosenescence and vaccine response Genetics and vaccines in the era of personalized medicine The weight of obesity on the human immune response to vaccination Understanding immunosenescence to improve responses to vaccines Vaccine immunogenetics: bedside to bench to population Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology Vaccine discovery and translation of new vaccine technology Systems vaccinology: learning to compute the behavior of vaccine induced immunity Additive effects of HLA alleles and innate immune genes determine viral outcome in HCV infection Role of HLA, KIR, MICA, and cytokines genes in leprosy Association of variants in BAT1-LTA-TNF-BTNL2 genes within 6p21.3 region show graded risk to leprosy in unrelated cohorts of Indian population Immunogenetics of HIV disease Vaccinomics provides the opportunity to examine not only immune response genes likely to be involved in vaccine response, but also the possibility of identifying the influence of new (uncharacterized) genes on vaccine-induced immunity.
    keywords: age; cell; development; genes; immunity; immunogenicity; influenza; responses; sex; systems; vaccination; vaccine; vaccinology; vaccinomics; virus
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        item: #65 of 117
          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: 3553
      flesch: 45
     summary: Our study demonstrates that, although in vitro refolding is an effective approach to identify HLA class I-restricted T cell epitopes, the peptides which have refolding capacity with the corresponding HLA allele, for example P4, may not react well with T cells in further assays, such as the ELISPOT assay and tetramer staining. Moreover, the cytokine interferon gamma (IFN-g) produced by T cells has a critical role in the protective immunological response against primary infection.
    keywords: a24; cells; hla; patients; pbmcs; peptides; specific; tuberculosis
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        item: #66 of 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: 9745
      flesch: 42
     summary: Interestingly, immature cell clusters in severe COVID-19 showed signs of recent activation 390 like upregulation of CD64 (Mortaz et al., 2018) , RANK and RANKL (Riegel et al., 2012) , as 391 well as reduced CD62L expression (Mortaz et al., 2018) . Plotting cell cluster-specific surface marker expression onto 384 the UMAPs (Fig. 6C ) as well as statistical analyses of cell cluster distribution and surface 385 marker expression among different patient groups supported these observations (Fig. 386 6D+E) .
    keywords: analysis; cell; cluster; cohort; covid-19; data; disease; expression; fig; genes; hla; marker; monocytes; neutrophils; patients; pbmc; samples; scrna; seq; table
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        item: #67 of 117
          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: 7109
      flesch: 41
     summary: Furthermore, the latest experimental reports suggest that the S glycoprotein of SARS-CoV-2 is both O-and N-glycosylated, especially on the RDB domain, which could mask immunogenic epitopes and may play an important role in SARS-CoV-2 immune evasion [61] MHC-I allotypes are known to bind epitopes with lengths of 8 to 11 amino acids.
    keywords: a*02:01; allotypes; binding; cell; class; complex; cov-2; epitopes; hla; iedb; mhc; protein; sars; table
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        item: #68 of 117
          id: cord-275608-joyan7ij
      author: Sewell, Andrew K.
       title: Why must T cells be cross-reactive?
        date: 2012-08-24
       words: 7781
      flesch: 38
     summary: No one is naive: the significance of heterologous T-cell immunity The history of the smallpox vaccine The role of BCG in prevention of leprosy: a metaanalysis CD4 T-cell-mediated heterologous immunity between mycobacteria and poxviruses Human papillomavirus type 16 E7 peptide-directed CD8 + T cells from patients with cervical cancer are cross-reactive with the coronavirus NS2 protein Broad cross-reactive TCR repertoires recognizing dissimilar Epstein-Barr and influenza A virus epitopes Cross-reactivity between HLA-A2-restricted FLU-M1:58-66 and HIV p17 GAG:77-85 epitopes in HIV-infected and uninfected individuals Cross-reactive influenza virus-specific CD8 + T cells contribute to lymphoproliferation in Epstein-Barr virus-associated infectious mononucleosis Cross-reactivity between hepatitis C virus and influenza A virus determinantspecific cytotoxic T cells Heterologous T cell immunity in severe hepatitis C virus infection Molecular mimicry in T cell-mediated autoimmunity: viral peptides activate human T cell clones specific for myelin basic protein Molecular mimicry and immunemediated diseases Molecular mimicry by herpes simplex virustype 1: autoimmune disease after viral infection Molecular mimicry and autoimmunity Infection, mimics, and autoimmune disease Selection of functional T cell receptor mutants from a yeast surface-display library Directed evolution of human T-cell receptors with picomolar affinities by phage display Cutting edge: evidence for a dynamically driven T cell signaling mechanism Interplay between T cell receptor binding kinetics and the level of cognate peptide presented by major histocompatibility complexes governs CD8 + T cell responsiveness Human TCR-binding affinity is governed by MHC class restriction Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor Kinetic proofreading in T-cell receptor signal transduction Adoptive immunotherapy for cancer: harnessing the T cell response Cancer regression in patients after transfer of genetically engineered lymphocytes Monoclonal TCR-redirected tumor cell killing Modification of MHC anchor residues generates heteroclitic peptides that alter TCR binding and T cell recognition Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination Quantitating T cell cross-reactivity for unrelated peptide antigens Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection Structure of a TCR with high affinity for selfantigen reveals basis for escape from negative selection Germ line-governed recognition of a cancer epitope by an immunodominant human T-cell receptor The shaping of T cell receptor recognition by self-tolerance We thank S. Smith and N. Watson for editing the manuscript. key: cord-275608-joyan7ij authors: Sewell, Andrew K. title: Why must T cells be cross-reactive? date: 2012-08-24 journal:
    keywords: antigen; binding; cell; class; cross; hla; mhc; molecules; peptide; receptor; recognition; tcr; tcrs
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        item: #69 of 117
          id: cord-275677-hbv49e01
      author: Ramana, Lakshmi Narashimhan
       title: Targeting strategies for delivery of anti-HIV drugs
        date: 2014-10-28
       words: 12986
      flesch: 38
     summary: An immunoliposomal carrier encapsulating the protease inhibitor P11 and surface modified with anti-gp120 was reported to exhibit excellent specificity towards HIV infected cells due to binding of the anti-gp120 to the exposed domains of gp120 present on the surface of HIV infected cells [12] . Actinohivin, a prokaryotic lectin found in actinomycetes was identified to possess anti-HIV activity and was found to specifically target HIV infected cells.
    keywords: affinity; anti; binding; ccr5; cd4; cells; cxcr4; delivery; drug; gp120; high; hiv; hiv infection; hla; infected; infection; macrophages; nanoparticles; receptor; surface; t cells; targeting; virus
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        item: #70 of 117
          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: 5871
      flesch: 50
     summary: The study of vaccine structure in this complex showed high RMSF in most of its amino acids. KK and GPGPG linkers joined the screened T and B-cell epitopes in a structure of multi-epitope vaccine, respectively.
    keywords: amino; cell; epitopes; fig; hla; model; protein; sars; server; simulation; structure; vaccine
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        item: #71 of 117
          id: cord-280641-zqdrzyzl
      author: Fernández Fabrellas, Estrella
       title: Epidemiología de la sarcoidosis
        date: 2007-02-28
       words: 6762
      flesch: 33
     summary: Si se da por sentado que la latencia entre la exposición al agente causal y el desarrollo de síntomas de sarcoidosis es del orden de unas pocas semanas a pocos meses, como se ha visto en modelos animales experimentales, la exposición tendría que ocurrir en muchos casos durante los meses previos a las manifestaciones clínicas. La evidencia epidemiológica de estos trabajos indica que hay que considerar factores de riesgo tanto ambientales como genéticos en la etiología de la sarcoidosis, porque probablemente la interacción entre ellos producirá la enfermedad 20 .
    keywords: access; agentes; ambientales; años; casos; como; con; de la; de los; del; durante; enfermedad; entre; esta; este; estos; estudio; exposición; factores; han; hla; incidencia; la enfermedad; la sarcoidosis; las; los; más; pacientes; para; patients; pero; población; por; pulmonar; que; raza; riesgo; sarcoidosis; sin; sobre; son; study; una
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        item: #72 of 117
          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: 4320
      flesch: 18
     summary: 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). Th1-biasing immunization using CD8 T cells optimized peptide vaccination may offer an important alternative and complementary approach with a history of safe administration, may be developed and updated rapidly, and should avoid safety pitfalls in the pursuit of a COVID-19 vaccine 8, 13, 14 .
    keywords: cd8; cell; covid-19; epitopes; hla; memory; peptide; responses; sars; vaccine; virus
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        item: #73 of 117
          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: 6239
      flesch: 46
     summary: Stained cells were analyzed in BD Accuri C6 Plus to detect the expression of activation markers IFN- and CD137 (4-1BB) on CD4 and CD8 T cells. medRxiv Revealing factors determining immunodominant responses against dominant epitopes Identifying specificity groups in the T cell receptor repertoire Clonally diverse CTL response to a dominant viral epitope recognizes potential epitope variants Narrowed TCR repertoire and viral escape as a consequence of heterologous immunity Limited T cell receptor repertoire diversity in tuberculosis patients correlates with clinical severity A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells Direct link between mhc polymorphism, T cell avidity, and diversity in immune defense SARS-CoV-2 T cell immunity: Specificity, function, durability, and role in protection Convergent antibody responses to SARS-CoV-2 in convalescent individuals Altered cytokine levels and immune responses in patients with SARS-CoV-2 infection and related conditions Disease severity dictates SARS-CoV-2-specific neutralizing antibody responses in COVID-19 High neutralizing antibody titer in intensive care unit patients with COVID-19 The Immune Epitope Database (IEDB): 2018 update NetMHCpan, a method for MHC class I binding prediction beyond humans Reliable prediction of T-cell epitopes using neural networks with novel sequence representations A simple method for displaying the hydropathic character of a protein NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data
    keywords: cd8; cd8 t; cell; cov-2; donors; epitopes; figure; hla; peptide; response; sars; spike
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        item: #74 of 117
          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: 10810
      flesch: 35
     summary: Severe patients exhibited an expansion in the proportion of circulating neutrophils within the peripheral blood cell population (Figure 1E) , which was associated with an increase in their absolute number (Table S2) , as already reported . Focusing on neutrophil subsets, we noticed a slight increase in the fraction of CD10 Low CD101 + neutrophils in mild COVID-19 patients (Figure 1F) , whereas the fraction of CD10 Low CD101neutrophils was remarkably amplified in severe patients, suggesting an accumulation of immature subsets of neutrophils (Ng et al., 2019) in the peripheral blood of these patients ( Figure 1G and S1C-E).
    keywords: analysis; blood; calprotectin; cd14; cd16; cells; controls; covid-19; covid-19 patients; disease; et al; expression; figure; fraction; hla; levels; low; monocytes; neutrophils; patients; plasma
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        item: #75 of 117
          id: cord-286858-zbhtl2yn
      author: Mishra, B.
       title: tamasomā jyotirgamaya: Seeking the Self Amidst Covids’ Cytokine Cyclones
        date: 2020-10-22
       words: 5822
      flesch: 39
     summary: Interferons: A family of proteins (lymphokines), secreted by infected host cells to protect uninfected cells from viral infections. Since, many pathogens (e.g., SARS-CoV-2) can engage in deception (e.g., entering a host cell by targeting host ACE2 receptorby binding to a site somewhat distant from the ACE2 canonical binding site), innate immune system may need other auxiliary adaptive agents to be educated ex tempore, replicate dynamically and retain memory.
    keywords: adaptive; cells; game; group; hla; host; immune; information; model; problem; receiver; self; sender; signaling; system; utility
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        item: #76 of 117
          id: cord-286968-ud1uerc8
      author: Nienhold, R.
       title: Two distinct immunopathological profiles in lungs of lethal COVID-19
        date: 2020-06-19
       words: 2621
      flesch: 48
     summary: Histological analysis of COVID-19 lung tissues revealed striking pulmonary damage exclusively in ISG low samples, with distinct peri-alveolar foci of infiltrating CD68+ macrophages and CD8+ T cells (Figure 1e) . Expression of ISGs was tightly correlated with pulmonary viral load (Figure 2a) , and immunohistochemical staining showed SARS-CoV-2 nucleocapsid protein mostly in pneumocytes of ISG high lungs (Figure 2b) .
    keywords: author; covid-19; figure; funder; license; medrxiv; peer; peer review; perpetuity; preprint; review
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        item: #77 of 117
          id: cord-287709-y247lan1
      author: Navarrete, Cristina
       title: Cord Blood Banking: Operational and Regulatory Aspects
        date: 2014-12-12
       words: 9375
      flesch: 40
     summary: International society of hematotherapy and graft engineering The impact of post-thaw colony-forming units-granulocyte/macrophage on engraftment following unrelated cord blood transplantation in pediatric recipients Total colony-forming units are a strong, independent predictor of neutrophil and platelet engraftment after unrelated umbilical cord blood transplantation: a single-centre analysis of 435 cord blood transplants Obstetric predictors of placental/umbilical cord blood volume for transplantation Bigger is better: maternal and neonatal predictors of hematopoietic potential of umbilical cord blood units Association among birth weight, placental weight, gestational period and product quality indicators of umbilical cord blood units The Cord Blood Apgar: a novel scoring system to optimize selection of banked cord blood grafts for transplantation Cord blood banking: volume reduction of cord blood units using a semi-automated closed system Cord blood processing: volume reduction Cord blood banking for clinical transplantation Pre-transplant manipulation processing of umbilical cord blood units: efficacy of Rubinstien's thawing technique used in 40 transplantation procedures Qualitative and quantitative cell recovery in umbilical cord blood processed by two automated devices in routine cord blood banking: a comparative study Comparison of cord blood thawing methods on cell recovery, potency and infusion Methods of freezing cord blood hematopoietic stem cells Successful short-term cryopreservation of volume-reduced cord blood units in a cryogenic mechanical freezer: effects on cell recovery, viability, and clonogenic potential Current thawing and infusion practice of cryopreserved cord blood: the impact on graft quality, recipient safety and transplantation outcomes Reexposure of cord blood to noinherited maternal HLA antigens improves transplant outcome in hematological malignancies Effect of HLA-matching recipients to donor non-inherited maternal antigens on outcomes after mismatched umbilical cord blood transplantation for hematologic malignancy KIR-ligand incompatibility in the graft-versus-host direction improves outcomes after umbilical cord blood transplantation for acute leukemia Negative effect of Kir alloreactivity in recipients of umbilical cord blood transplant depends on transplantation conditioning intensity International exchange of cord blood units: the registry aspects A gift for life. The minimum number of cord blood units needed for Koreans is 51 -DQ in 122 unrelated cord blood/patient pair transplants hardly improves long-term clinical outcome Effect of donor-recipient HLA matching at HLA A, B, C and DRB1 on outcomes after umbilical-cord blood transplantation for leukaemia and myelodysplastic syndrome: a retrospective analysis Estimation of size of cord blood inventory based on high-resolution typing of HLAs Creation of a double chimera after the transplantation of umbilical-cord blood from two partially matched unrelated donors Transplantation of 2 partially HLA-matched umbilical cord blood units to enhance engraftment in adults with hematologic malignancy Single versus double unrelated umbilical cord blood units for allogeneic transplantation in adults with advanced hematological malignancies: a retrospective comparison of outcomes Ex vivo expansion of umbilical cord blood Notch-mediated expansion of human cord blood progenitor cells capable of rapid myeloid reconstitution Direct intrabone transplant of unrelated cord-blood cells in acute leukaemia: a phase I/II study Results of a pilot study on the use of thirdparty donor mesenchymal stromal cells in cord blood transplantation in adults Unrelated umbilical cord blood transplants in adults: early recovery of neutrophils by supportive co-transplantation of a low number of highly purified peripheral blood CD34+ cells from an HLA-haploidentical donor Infectious complications following unrelated cord blood transplantation
    keywords: banking; blood transplantation; blood units; cbb; cd34; cells; collection; cord blood; donor; hla; number; processing; transplantation; ucb; units
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        item: #78 of 117
          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: 6169
      flesch: 49
     summary: 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. In the case of immunization with liposomal peptides, mice were subcutaneously (s.c.) immunized once or several times at one-week intervals with each of (Rammensee et al., 1999) at http://www.syfpeithi.de/. b Peptide binding scores to HLA-A2.1 were determined by the BIMAS database (Parker et al., 1994) at http://www-bimas.cit.nih.gov/molbio/hla bind/. c Data of peptide binding assays are shown as BL50, indicating a concentration of each peptide that yields the half-maximal MFI of T2 cells pulsed with a control peptide, NS3-1585.
    keywords: cd8; cells; fig; hla; liposomal; mice; peptides; pp1a; sars
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        item: #79 of 117
          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: 15253
      flesch: 41
     summary: This suggests that CD4 + T cell epitopes are more numerous than CD8 + T cell epitopes, perhaps as much as 2-3 times greater. 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.
    keywords: 15mer; approach; cd4; cd8; cell epitopes; cell responses; cells; class; discovery; epitopes; hla; peptides; responses; restriction; t cell; tetramer; yfv
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        item: #80 of 117
          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: 11737
      flesch: 45
     summary: However, as the oesophagus squamous epithelium also exhibits IFITM1 protein expression in the basal cells of normal squamous epithelium (Protein Atlas, Supplementary Fig. 4) , and the normal oesophagus is not noted for HPV infection, we would suggest that the expression of IFITM1 protein in basal cells is not related to HPV status. Attenuation of IFITM1 protein expression can inhibit growth, invasion, and/or migration of cancer cells [34] .
    keywords: anti; cancer; cells; data; expression; fig; hla; ifitm1; ifitm1/3; ifnγ; interferon; isg15; min; protein; signalling; siha; silac; sirna; stat1; supplementary; synthesis; treatment
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        item: #81 of 117
          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: 5296
      flesch: 29
     summary: 263 Constructs can be designed to contain a combination of optimal B and/or T cell 264 epitopes, or deployed as a construct consisting of the top scoring T cell epitopes to be 265 used in combination with the vaccines currently being developed targeting spike protein 266 in order to drive the adaptive memory response. We further prioritize genomic regions that generate highly dissimilar peptides from the human proteome, and are also predicted to produce B cell epitopes.
    keywords: 33mer; cell; cov-2; epitopes; hla; peptides; population; sars; spike; table; vaccine
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        item: #82 of 117
          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: 6083
      flesch: 44
     summary: Faster de novo structure prediction for linear peptides in solution and in complex PatchDock and SymmDock: Servers for rigid and symmetric docking Fast Interaction Refinement in molecular docking A web server for fast interaction refinement in molecular docking Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV HLA-A*0201 T-cell epitopes in severe acute respiratory syndrome (SARS) coronavirus nucleocapsid and spike proteins Identification of an HLA-A*0201-restricted CD8+ T-cell epitope Ssp-1 of SARS-CoV spike protein Searching immunodominant epitopes prior to epidemic: HLA class II-restricted SARS-CoV spike protein epitopes in unexposed individuals Structure of SARS coronavirus spike receptor-binding domain complexed with receptor The spike protein of SARS-CoV-A target for vaccine and therapeutic development Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice Evaluation of modified vaccinia virus Ankara based recombinant SARS vaccine in ferrets Identification of immunodominant sites on the spike protein of severe acute respiratory syndrome (SARS) coronavirus: Implication for developing SARS diagnostics and vaccines A study on antigenicity and receptor-binding ability of fragment 450-650 of the spike protein of SARS coronavirus Identification of an Antigenic Determinant on the S2 Domain of the Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein Capable of Inducing Neutralizing Antibodies Screening and Identification of Linear B-Cell Epitopes and Entry-Blocking Peptide of Severe Acute Respiratory Syndrome (SARS)-Associated Coronavirus Using Synthetic Overlapping Peptide Library Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients Structural Basis of Neutralization by a Human Anti-severe Acute Respiratory Syndrome Spike Protein Antibody, 80R Structure of Severe Acute Respiratory Syndrome Coronavirus Receptor-binding Domain Complexed with Neutralizing Antibody Better Epitope Discovery, Precision Immune Engineering, and Accelerated Vaccine Design Using Immunoinformatics Tools. A Novel Coronavirus from Patients with Pneumonia in China A new coronavirus associated with human respiratory disease in China Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus Structure analysis of the receptor binding of 2019-nCoV Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC Receptor usage and cell entry of porcine epidemic diarrhea coronavirus A 193-Amino Acid Fragment of the SARS Coronavirus S Protein Efficiently Binds Angiotensin-converting Enzyme 2 Conformational States of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein Ectodomain Immunological Responses against SARS-Coronavirus Infection in Humans B-Cell Responses in Patients Who Have Recovered from Severe Acute Respiratory Syndrome Target a Dominant Site in the S2 Domain of the Surface Spike Glycoprotein Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor Epitope-based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: An immune-informatics study Structural basis of receptor recognition by SARS-CoV-2 Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 A server for prediction of protective antigens, tumour antigens and subunit vaccines Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8(+) T cells Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes PEP-FOLD3:
    keywords: cell; cell epitopes; cov-2; epitopes; hla; protein; residues; s protein; sars; table; vaccine
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        item: #83 of 117
          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: 2332
      flesch: 43
     summary: Designing of multi-hit peptides vaccine sequence 1 3 7 A set of high immunogenic hit peptides derived from N and S proteins of SARS-CoV-2 with high binding 1 3 8 events to HLA-A0201, HLA-B0801, HLA-B3501, HLA-B3508, HLA-B4405, and HLA-E were selected 1 3 9 on the basis of their solvent exposed residues and hydrophobicity scales. The binding events among hit peptides derived from N proteins related to HLA-A0201 2 1 9 Our TCR-pMHC models predicted that position 2 of the homologous peptide antigens ( Figure 1A ) related 2 2 0 to TCR-pMHC complex of SARS-CoV-2 as well as SARS-CoV and bat-CoV
    keywords: cov; figure; hla; peptide; sars
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        item: #84 of 117
          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: 5960
      flesch: 21
     summary: We thus review here the role of HLA genes in particular subgroups of psychiatric disorders and foresee their potential implication in future research.  HLA is also involved in anti-infections processes including against the coronavirus family Common sequence variants in the major histocompatibility complex region associate with cerebral ventricular size in schizophrenia Expression estimation and eQTL mapping for HLA genes with a personalized pipeline Association of Polygenic Score for Schizophrenia and HLA Antigen and Inflammation Genes With Response to Lithium in Bipolar Affective Disorder: A Genome-Wide Association Study Study of the leukocyte phenotypes in Hodgkin's disease Genetic pleiotropy between multiple sclerosis and schizophrenia but not bipolar disorder: differential involvement of immune-related gene loci Influence of HLA-C expression level on HIV control Infection and inflammation in schizophrenia and bipolar disorder: a genome wide study for interactions with genetic variation HLA-class II haplotypes and Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder Distinct HLA associations of LGI1 and CASPR2-antibody diseases Combining clinical and molecular heterogeneity within CASPR2-antibody mediated diseases: towards the underlying disease biology Immune proteins in brain development and synaptic plasticity Thinning Faster?
    keywords: associated; association; autism; class; disorders; et al; genetic; hla; immune; mhc; risk; schizophrenia; system
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        item: #85 of 117
          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: 2819
      flesch: 63
     summary: To populate the 'structure space' of HLA molecules, we have previously reported two HLA-A*1101 (Blicher et al., 2005 and two HLA-B*1501 structures (Røder et al., 2006) . Peptide residue 1.
    keywords: b*1501; binding; groove; hla; peptide; residue
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        item: #86 of 117
          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: 5542
      flesch: 57
     summary: We further analyzed the structures of H-2L d , H-2D b , and H-2D d , which contain the same residues for salt bridge forming (R62 and E163) as HLA-B*4001 but do not contain salt bridges. 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.
    keywords: b*4001; binding; bridge; cell; h-2k; hla; mhc; mutants; peptide; residues; salt; salt bridge
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        item: #87 of 117
          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: 2520
      flesch: 45
     summary: Emerging novel coronavirus (2019-nCoV)-current scenario, evolutionary perspective based on genome analysis and recent developments Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies Structural basis for the recognition of SARS-CoV-2 by fulllength human ACE2 A novel coronavirus associated with severe acute respiratory syndrome The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade Characterization of the binding profile of peptide to transporter associated with antigen processing (TAP) using Gaussian process regression Total predicted MHC-I epitope load is inversely associated with mortality from SARS-CoV-2 Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools SWISS-MODEL: homology modelling of protein structures and complexes 3Drefine: an interactive web server for efficient protein structure refinement Verification of protein structures: patterns of nonbonded atomic interactions Structure validation by Cα geometry: ϕ,ψ and Cβ deviation NetMHCpan-4.0: improved peptide-MHC class 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.
    keywords: alleles; brazilian; cov-2; epitopes; hla; mhc; protein; sars
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        item: #88 of 117
          id: cord-310252-0cdqhrcw
      author: Seliger, Barbara
       title: Chapter 7 IFN Inducibility of Major Histocompatibility Antigens in Tumors
        date: 2008-12-03
       words: 8551
      flesch: 31
     summary: 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. However, it has been suggested that tumor cells might develop either a transient or a permanent IFN insensitivity.
    keywords: antigen; cells; class; class ii; et al; expression; genes; hla; ifn; interferon; melanoma; mhc; mhc class; stat1; tumor; type
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        item: #89 of 117
          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: 2121
      flesch: 33
     summary: The pep- for the top-ranking peptides, only 22 (or 2-3%) of the 952 combinations involves cross-responses, where a peptide predicted to be a top-ranking binder to one HLA molecule turns out to be a binder to a member of another HLA supertype, i.e. it supports the contention that HLA supertypes effect significant diversification of anti-SARS CTL responses. These would all have been predicted to be successfully processed by the proteasome and biochemically validated for HLA binding.
    keywords: binding; cytotoxic; epitopes; hla; peptide; sars
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        item: #90 of 117
          id: cord-313474-1gux1gsi
      author: None
       title: Physicians Abstracts
        date: 2015-03-20
       words: 51535
      flesch: 53
     summary: TRM at 1 year was 9% in Arm A, and 15% in Arm B and 16% in Arm C. Two year OS and DFS for each arm are: arm A -62.2% and 56%; arm B -68% and 59% and 48% and 48% for arm C. For the 115 pts who received standard risk transplants (i.e., pts with high risk forms of AML, ALL or NHL in 1 o CR, AML in 2 o CR, MDS RA/RCMD, CML in 1 o CP or MM in CR1), 2 year OS and DFS are: arm A -60% and 59%; arm B -74% and 65%; arm C -50% and 50%, with relapse rates at 2 yrs of arm All pts engrafted promptly (median d þ 10, range þ 9 -þ 12).TRM (grade II-IV) at 12mos is 18% (95% CI: 8% -31%).
    keywords: acute; age; allogeneic; aml; analysis; blood; cd34; cells; chronic; cmv; conclusion; conditioning; data; days; disclosure; disease; donor; dose; follow; graft; group; gvhd; hct; high; hla; hsct; incidence; interest; introduction; leukemia; levels; matched; materials; median; methods; months; mortality; n ¼; non; p ¼; patients; post; pts; range; recipients; relapse; response; results; ric; risk; specific; stem; study; survival; t cells; therapy; time; transplantation; treatment; years
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        item: #91 of 117
          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: 3502
      flesch: 26
     summary: For instance, Chinese individuals homozygous for the tandem repeat domain in exon 4 of the CLEC4M gene were less susceptible to SARS infection [17] . International Journal of Genomics SARS and MERS: recent insights into emerging coronaviruses A novel coronavirus associated with severe acute respiratory syndrome Novel coronavirus disease (COVID-19): a pandemic (epidemiology, pathogenesis and potential therapeutics) Coronavirus cis-acting RNA elements Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages The pathogenesis and treatment of the 'Cytokine Storm' in COVID-19 COVID-19 for the cardiologist: basic virology, epidemiology, cardiac manifestations, and potential therapeutic strategies Emerging coronaviruses: genome structure, replication, and pathogenesis Obesity and SARS-CoV-2: a population to safeguard Coronavirus COV-19/SARS-CoV-2 affects women less than men: clinical response to viral infection Evolution, revolution and heresy in the genetics of infectious disease susceptibility The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis Guide for current nutrigenetic, nutrigenomic, and nutriepigenetic approaches for precision nutrition involving the prevention and management of chronic diseases associated with obesity The PRISMA statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration Combining classifiers for robust PICO element detection Development of a critical appraisal tool to assess the quality of cross-sectional studies (AXIS) Homozygous L-SIGN (CLEC4M) plays a protective role in SARS coronavirus infection ACE1 polymorphism and progression of SARS The interferon gamma gene polymorphism +874 A/T is associated with severe acute respiratory syndrome Association of cytokine and chemokine gene polymorphisms with severe acute respiratory syndrome Significance of the myxovirus resistance A (MxA) gene -123C>a singlenucleotide polymorphism in suppressed interferon β induction of severe acute respiratory syndrome coronavirus infection Polymorphisms of interferon-inducible genes OAS-1 and MxA associated with SARS in the Vietnamese population Roles of TNF-α gene polymorphisms in the occurrence and progress of SARS-Cov infection: a case-control study High prevalence of the CD14-159CC genotype in patients infected with severe acute respiratory syndrome-associated coronavirus Association of humanleukocyte-antigen class I (B * 0703) and class II (DRB1 * 0301) genotypes with susceptibility and resistance to the development of severe acute respiratory syndrome Association of HLA class I with severe acute respiratory syndrome coronavirus infection Epidemiological and genetic correlates of severe acute respiratory syndrome coronavirus infection in the hospital with the highest nosocomial infection rate in Taiwan in 2003 Human-leukocyte antigen class I Cw 1502 and class II DR 0301 genotypes are associated with resistance to severe acute respiratory syndrome (SARS) infection Cellular entry of the SARS coronavirus Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus
    keywords: coronavirus; cov; covid-19; disease; genetic; infection; polymorphisms; sars; susceptibility; syndrome
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        item: #92 of 117
          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: 8936
      flesch: 36
     summary: These papers made it possible to design vaccines in silico A comparison of two methods for T cell epitope mapping: cell free in vitro versus immunoinformatics A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus Putting immunoinformatics to the test Elimination of IL-10-inducing T-helper epitopes from an IGFBP-2 vaccine ensures potent antitumor activity The two-faced T cell epitope: examining the host-microbe interface with JanusMatrix Basic local alignment search tool Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage A mathematical exploration of the cross-conservation between human pathogen (viruses) and human host that demonstrated a significant increase in the number of cross-conserved epitopes in viruses that 'hit and stay' (commensals) as compared to 'hit and run' viruses such as ebola Virus-specific CD4(+) memory-phenotype T Cells are abundant in unexposed adults Further evidence that cross-reactive T-cell recognition is discernable Gut immune maturation depends on colonization with a host-specific microbiota Has the microbiota played a critical role in the evolution of the adaptive immune system? Peripheral education of the immune system by colonic commensal microbiota A travel guide to Cytoscape plugins Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection T cell epitope: It also validates the individualized T-cell epitope measure tool for HLA-specific immunogenicity prediction Human immune responses to H. pylori HLA class II epitopes identified by immunoinformatic methods Peptide-pulsed dendritic cells induce the hepatitis C viral epitope-specific responses of naïve human T cells Immunogenic consensus sequence t helper epitopes for a pan-burkholderia biodefense vaccine Analysis of ChimeriVax Japanese Encephalitis (JE) virus sequence for T cell epitopes and comparison to circulating wild type JE Virus strains Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-09 conventional influenza vaccine A study demonstrating that analysis of Hemagglutinin prior to production of vaccine might reveal important insights: in this case, that seasonal influenza might protect against pandemic influenza, a prediction that was later corroborated by other researchers in vitro and in vivo.
    keywords: antigens; approach; cell; class; design; development; epitopes; genome; hla; human; ntd; pathogens; potential; proteins; response; tools; vaccines
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        item: #93 of 117
          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: 6758
      flesch: 46
     summary: The count for other salt bridges from TLR3 to MEPVC is in following order: Asp124-Arg706 (mean, 3, max,7 and min,3), Glu98-Lys679 (mean, 5, max,10 and min,4), Asp402-Arg641 (mean, 12, max, 18 and min, 4), Glu146-Arg706 (mean,7 max,11 and min,3), Glu146-Lys679 (mean,5 max,13 and min,2), Glu272-Lys655 Gln722-Side 0.02% The vital hydrogen bond interactions involved between TLR3 receptor and MEPVC shortlisted by VMD were subjected to a novel AFD analysis to elucidate 3D movements of MEPVC atoms with respect to a reference TLR3 residues atom in simulation time. Residue wise decomposition of net binding energy into TLR3 receptor and MEPVC interacting residues.
    keywords: binding; complex; coronavirus; energy; epitopes; immune; interactions; kcal; mepvc; mol; protein; receptor; residues; sars; spike; structure; system; tlr3; vaccine
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        item: #94 of 117
          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: 3218
      flesch: 34
     summary: .The effectiveness of epitope based vaccines for treatment of endocarditis has already been claimed (Priyadarshini et al. 2014) . paratuberculosis proteins that were upregulated under stress conditions VMD-visual molecular dynamics Improved methods for predicting peptide binding affinity to MHC class II molecules Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach Reverse vaccinology: basics and applications Silico identification of epitope based peptide vaccine for Nipah virus High prevalence of Tropheryma whipplei in Lao kindergarten children Protective enterotoxigenic Escherichia coli antigens in a murine intranasal challenge model Description of Tropheryma whipplei gen. nov., sp. nov., the Whipple's disease bacillus Treatment of classical Whipple's disease: from in vitro results to clinical outcome PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex Tropheryma whipplei infection and Whipple's disease Population coverage analysis of T-Cell epitopes of Neisseria meningitidis serogroup B from iron acquisition proteins for vaccine design Reduced peripheral and mucosal Tropheryma whipplei specific Th1 response in patients with Whipple's disease Impaired immune functions of monocytes and macrophages in Whipple's disease In silico analysis and experimental validation of Mycobacterium tuberculosis-specific proteins and peptides of Mycobacterium tuberculosis for immunological diagnosis and vaccine development Identification of putative drug targets and annotation of unknown proteins in Tropheryma whipplei A case of Whipple's disease (intestinal lipodystrophy)
    keywords: alleles; analysis; bacterium; disease; epitopes; hla; vaccine; whipple
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        item: #95 of 117
          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: 5653
      flesch: 46
     summary: Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8+ T cell immunity to SARS-CoV-2. Identification of CD8 + T cell epitopes in five HLA-A*01:01 patients Coronavirus Disease 2019, or COVID-19, is a global pandemic that has claimed over a million lives world-wide and has affected countless more. 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.
    keywords: cd8; cells; cov-2; epitopes; figure; hla; patients; protein; sars
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        item: #96 of 117
          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: 2275
      flesch: 38
     summary: This is an in silico study in which HLA types have been imputed, but these observations add support to our own observation in regard to HLA-DR15 and DQ6 in this early study of individuals with known HLA types. 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.
    keywords: group; hla; infection; patients; study; transplant
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        item: #97 of 117
          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: 3759
      flesch: 38
     summary: Three main features need to be outlined: (1) patients with COVID-19 and SRF are less severe than those with severe bacterial CAP, on the basis of the traditional severity scores of sequential organ failure assessment (SOFA) and acute physiology and chronic health evaluation (APACHE) II; (2) this leads to the conclusion that COVID-19 patients undergo an acute immune dysregulation with deterioration into SRF before the overall state of severity is advanced; and (3) although the burden of co-morbidities of patients with COVID-19, as expressed by the Charlson's co-morbidity index, is higher among patients with SRF than among patients without SRF, it remains remarkably lower that traditional bacterial CAP and sepsis. The function of PBMCs in patients with SRF caused by 2009H1N1 was also impaired, and there was lower TNF-a production, a pattern different from COVID-19 patients ( Figure 4C) .
    keywords: cd45; cov-2; covid-19; dysregulation; hla; il-6; patients; sars
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        item: #98 of 117
          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: 8010
      flesch: 41
     summary: In CD94 ϩ T cells, signaling via CD94 can modulate, positively or negatively, activation through the TCR, depending on the associated NKG2 molecule. These findings suggest a scenario whereby IELs primed in the celiac disease microenvironment may be locally regulated positively or negatively by IL-15 and HLA-E. Thus, EC injury and the resulting intestinal dysfunction in celiac disease may not only depend on the activation of gliadin-specific, DQ2-, The pathogenesis of celiac disease Evidence for a primary association of celiac disease to a particular HLA-DQ ␣/␤ heterodimer Identification of tissue transglutaminase as the autoantigen of celiac disease Activated T lymphocytes in the celiac lesion: non-proliferative activation (CD25) of CD4 ϩ ␣/␤ cells in the lamina propria but proliferation (Ki-67) of ␣/␤ and ␥/␦ cells in the epithelium Numbers of T cell receptor (TCR) ␣␤ ϩ but not of TcR ␥␦ ϩ intraepithelial lymphocytes correlate with the grade of villous atrophy in coeliac patients on a long term normal diet Tissue transglutaminase selectively modifies gliadin peptides that are recognized by gut-derived T cells in celiac disease Selective deamidation by tissue transglutaminase strongly enhances gliadin-specific T cell reactivity Heterogeneous reactivity patterns of HLA-DQrestricted, small intestinal T-cell clones from patients with celiac disease Gluten specific, HLA-DQ restricted T cells from coeliac mucosa produce cytokines with Th1 or Th0 profile dominated by interferon ␥ Quantitation of intraepithelial lymphocytes in human jejunum Classification of intractable diarrhea in infancy using clinical and immunohistological criteria Time dose responses of celiac mucosae to graded oral challenges with Frazer fraction-III of gliadin Gluten, major histocompatibility complex, and the small intestine.
    keywords: cd94; cells; disease; expression; hla; iels; lymphocytes; receptors; tcr
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        item: #99 of 117
          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: 5712
      flesch: 52
     summary: However, the role of NK cells during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has previously not been identified. K562 and lung epithelial cells were transfected with spike proteins and co-cultured with NK cells.
    keywords: cells; cov-2; expression; figure; hla; lung; nkg2a; protein; sars; sp1; spike; student
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        item: #100 of 117
          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: 2505
      flesch: 30
     summary: Interestingly, another preprint study identified specific SARS-COV-2 neutralizing antibodies (NAbs) in the plasma of patients who had recovered from infection and recorded that 30% of patients failed to develop high titers of NAbs after COVID-19 infection (32) . 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 ).
    keywords: cov-2; covid-19; hla; patients; response; sars; virus
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        item: #101 of 117
          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: 5209
      flesch: 47
     summary: At a concentration of 1 Â 10 5 cells/well, PBMCs of each sample in RPMI 1640 and 10% FCS were added to the four wells of 96-well plates, and stimulated with truncated ORF2 protein (10 mg/ml), high density multiepitope protein (10 mg/ml), and PHA (5 mg/ml) separately at 37˚C. The unstimulated PBMCs of each sample were used to evaluate spontaneous production of cytokines. The cell proliferative responses in HEV-recovered group following stimulation with high density multiepitope protein and truncated ORF2 protein were found higher than control group (P < 0.001); and these responses were observed higher with high density multiepitope protein than truncated ORF2 protein in HEV-recovered group (P ¼ 0.013)
    keywords: cells; density; epitopes; et al; hepatitis; hev; multiepitope; orf2; protein; vaccine; virus
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        item: #102 of 117
          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: 1797
      flesch: 15
     summary: A Systematic review DRB1*03/DRB3*0101, and DRB3*0202 are susceptibility genes for Graves' disease in North American Caucasians, whereas DRB1*07 is protective E6 and E7 Gene Polymorphisms in Human Papillomavirus Types-58 and 33 Identified in Southwest China Multiple sclerosis and autoimmune diseases: epidemiology and HLA-DR association in North-east Italy Analysis of HLA DP, DQ, and DR allesles in adult Italian rheumatoid arthritis patients Genes for insulin-dependent diabetes mellitus (IDDM) in the major histocompatibility complex (MHC) of African-Americans HLA-encoded genetic predisposition in IDDM: DR4 subtypes may be associated with different degrees of protection Identification of LFA-1 as a candidate autoantigen in treatment-resistant Lyme arthritis A variant of childhood-onset myasthenia gravis: HLA typing and clinical characteristics in Japan Association of HLA-DRB3*0202 and serum IgG antibodies to Chlamydia pneumoniae with essential hypertension in a highly homogeneous population from Majorca Molecular analysis of HLA class IIassociated susceptibility to neuroinflammatory diseases in Korean children HLA-DPB1 and HLA class I confer risk of and protection from narcolepsy DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis Professor Ippolito, Sir Zumla and Prof Mohamed Osman are co-investigators investigators of the Pan-African Network on Emerging and Re-emerging Infections (PANDORA-ID-NET) funded by the European and Developing Countries Clinical Trials Partnership the EU Horizon 2020 Framework Programme for Research and Innovation. Is ethnicity linked to incidence or outcomes of covid-19? Association of HLA class I with severe acute respiratory syndrome coronavirus infection Association of human-leukocyteantigen class I (B*0703) and class II (DRB1*0301) genotypes with susceptibility and resistance to the development of severe acute respiratory syndrome Homozygous L-SIGN (CLEC4M) plays a protective role in SARS coronavirus infection Black/white differences in leukocyte subpopulations in men HLA studies in the context of coronavirus outbreaks Guillain-Barre syndrome associated with SARS-CoV-2 infection: causality or coincidence? Association between human leukocyte antigen-DR and demylinating Guillain-Barre syndrome The MHC locus and genetic susceptibility to autoimmune and infectious diseases Genetics of the HLA region in the prediction of type 1 diabetes Crystal structure of HLA-DQ0602 that protects against type 1 diabetes and confers strong susceptibility to narcolepsy HLA class II molecules influence susceptibility versus protection in inflammatory diseases by determining the cytokine profile DQB1*06:02-Associated Pathogenic Anti-Myelin Autoimmunity in Multiple Sclerosis-Like Disease: Potential Function of DQB1*06:02 as a Disease-Predisposing Allele
    keywords: class; cov-2; covid-19; hla; mhc; sars; susceptibility
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        item: #103 of 117
          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: 4077
      flesch: 38
     summary: Only a subset of generated peptides was predicted to bind with sufficient affinity onto at least one HLA: 23% for ERAP1, 22% for ERAP2, 6% for ERAP1/ERAP2 mixture and 21% for IRAP (peptide sequences are listed in Table 1a ). 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 Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens.
    keywords: cov-2; erap1; hla; irap; mixture; peptides; sars; trimming
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        item: #104 of 117
          id: cord-343262-zopxdw1d
      author: Srinivasan, Raghuraman C.
       title: Effects of Cryogenic Storage on Human Amnion Epithelial Cells
        date: 2020-07-15
       words: 5442
      flesch: 40
     summary: Since the amnion is an avascular membrane, vascular endothelial cells would not be expected to be present in isolates of hAEC cells. In immune-competent models and patients, hAEC cells engrafted and survived, without administration of immunosuppressive drugs [13, 16, 33] .
    keywords: amnion; cases; cells; cryopreservation; expression; figure; haec; hla; human; immune; markers
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        item: #105 of 117
          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: 1757
      flesch: 53
     summary: Here, we report HLA allele frequencies in Chinese Han individuals with COVID-19 and a comparison between HLA allele distribution in COVID-19 patients and healthy individuals. Therefore, the association of HLA alleles with COVID-19 warrants further research.
    keywords: alleles; covid-19; hla; individuals; sars
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        item: #106 of 117
          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: 3668
      flesch: 43
     summary: For validation of hot spot predictions, a test dataset for peptides to HLAclass I alleles were taken from a set of 240 9-mer peptides of human papillomavirus type 16 E6 and E7 proteins reported by Kast et al. (1994) . The results of validation of hot spot predictions by MULTIPRED models suggests that the overall performances of were reliable and a single MULTIPRED model could make reasonably accurate predictions of peptides binding to multiple alleles of HLA molecules, and also for variants of HLA supertypes that lack experimental binding data.
    keywords: ann; hla; peptides; prediction
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        item: #107 of 117
          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: 5593
      flesch: 50
     summary: L'hypothèse concernant la trajectoire développementale des érythroblastes et des MK leur attribue un progéniteur commun, les MK-érythroïdes (MEP) 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.
    keywords: aux; cells; cellules; ces; dans; des; est; hla; human; ipsc; les; leur; par; partir; plaquettes; platelet; pour; production; qui; sont; stem; transfusion; une; vivo; être
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        item: #108 of 117
          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: 4776
      flesch: 38
     summary: The N-protein transduced N/E6E7/2.1K b cells were used as target cells. The spontaneous release of LDH by target cells or effector cells The full-length amino acid sequence of the SARS N-protein was subjected to bioinformatic analysis to search for HLA-A*0201 restricted nine-amino acid peptides.
    keywords: cells; class; cytotoxic; dna; hla; human; mhc; peptide; protein; response; sars; vaccine
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        item: #109 of 117
          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: 3555
      flesch: 46
     summary: 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 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.
    keywords: countries; cov-2; fatality; fig; rates; sars
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        item: #110 of 117
          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: 4964
      flesch: 53
     summary: In DNA-immunized mice cytotoxicity assays, the target cells were the J(A2/kb) cells loaded with the candidate peptides, the positive control peptide S 411-420 , the irrelevant peptides HBcAg (131) (132) (133) (134) (135) (136) (137) (138) (139) (140) , and J(A2/kb) cells alone. the eight candidate peptides, positive control peptides S 411-420 , or negative control peptides HBcAg (131) (132) (133) (134) (135) (136) (137) (138) (139) (140) .
    keywords: a*0201; binding; candidate; cells; cov; ctl; hla; peptides; protein; sars
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        item: #111 of 117
          id: cord-347647-m9vk9m7h
      author: Eapen, Mary
       title: Hematopoietic cell transplantation with cryopreserved grafts for severe aplastic anemia
        date: 2020-05-08
       words: 2814
      flesch: 47
     summary: 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. The 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.
    keywords: anemia; aplastic; donor; grafts; transplantation
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        item: #112 of 117
          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: 3709
      flesch: 30
     summary: Obtaining these antigenic epitopes using the immune-informatics approach will help inform which epitopes to use in the construct of protein vaccines against SARS-CoV-2 using proteins other than the spike protein. Homology modelling of protein structures and complexes LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins IntFOLD: An integrated server for modelling protein structures and functions from amino acid sequences The I-TASSER Suite: protein structure and function prediction FALCON:
    keywords: analysis; coronavirus; cov-2; epitopes; hla; proteins; residues; sars; server; structural; vaccine
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        item: #113 of 117
          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: 8223
      flesch: 52
     summary: Conservation analysis revealed the high similarity between the prioritized epitopes of the SARS-CoV-2 spike protein with MERS and SARS spike protein epitopes ( Table 2 ). This step was executed to better understand the structures of predicted vaccines.
    keywords: binding; cell; domain; epitopes; haddock; models; protein; receptor; sars; score; spike; structures; vaccine
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        item: #114 of 117
          id: cord-349451-vak2p7ac
      author: Rocha, Francisco Airton Castro
       title: Microbes, Helminths and Rheumatic Diseases
        date: 2020-05-07
       words: 7470
      flesch: 28
     summary: * Identify causal relationships between microbiome perturbations and human rheumatic disease * Inflammatory bowel diseases, e.g. Crohn's disease, are considered perfect models of the association between changes in dietary habits and less exposure to germs with increased incidence of diseases considered to be immune-mediated.
    keywords: arthritis; b27; cells; development; diseases; gut; hla; human; immune; infection; microbiota; pathogenesis; patients; response; role; spa
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        item: #115 of 117
          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: 7862
      flesch: 33
     summary: Correlation with immune status Molecular detection and in vivo analysis of the specific T cell response to a protein antigen Statistical analysis of CDR3 length distributions for the assessment of T and B cell repertoire biases Expanded CD8 T-cell sharing between periphery and CNS in multiple sclerosis The blood of healthy individuals exhibits CD8 T cells with a highly altered TCR Vb repertoire but with an unmodified phenotype T cell repertoire alterations of vascularized xenografts Direct recognition of foreign MHC determinants by naive T cells mobilizes specific Vbeta families without skewing of the complementarity-determining region 3 length distribution Highly altered V beta repertoire of T cells infiltrating long-term rejected kidney allografts Immune responses elicited in tertiary lymphoid tissues display distinctive features Improved assessment of T-cell receptor (TCR) VB repertoire in clinical specimens: combination of TCR-CDR3 spectratyping with flow cytometry-based TCR VB frequency analysis Blood T-cell Vbeta transcriptome in melanoma patients Serial blood T cell repertoire alterations in multiple sclerosis patients; correlation with clinical and MRI parameters Serial evolution of TCR beta chain transcript mobilization in HIV type-1-infected patients following vaccine immune stimulation and HAART interruption Operationally tolerant and minimally immunosuppressed kidney recipients display strongly altered blood T-cell clonal regulation Analysis of the peripheral T-cell repertoire in kidney transplant patients Expansion of highly differentiated cytotoxic terminally differentiated effector memory CD8+ T cells in a subset of clinically stable kidney transplant recipients: a potential marker for late graft dysfunction Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance The natural history of clinical operational tolerance after kidney transplantation through twenty-seven cases Clinical operational tolerance after kidney transplantation Indirect CD4+ TH1 response, antidonor antibodies and diffuse C4d graft deposits in long-term recipients conditioned by donor antigens priming Functional compartmentalization following induction of long-term graft survival with pregraft donor-specific transfusion Clonal CD8+ T cell persistence and variable gene usage bias in a human transplanted hand TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture Tracking donor-reactive T cells: evidence for clonal deletion in tolerant kidney transplant patients High-resolution characterization of cytokine-producing alloreactivity in naive and allograft-primed mice The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. At the other range of the resolution spectrum, deep-sequencing of TCR Vβ obtains a full picture of the usage of T cell repertoire with deep or ultra-deep resolution.
    keywords: cd8; cells; class; cross; donor; graft; hla; mhc; molecules; peptide; reactivity; repertoire; specific; t cells; tcr
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        item: #116 of 117
          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: 3749
      flesch: 49
     summary: Spike peptide (EVFNATRFASVYAWN) interacts with HLA-DPA1*01:03/DPB1*02:01 allele by forming hydrogen bonds with the amino acids Val2, Ser10, Tyr12, Tyr40A, Glu59A, hydrophobic bonds with the amino acids Val2, Phe8, Tyr40A, Ala41A, Ala42A, Asn93A, Leu101A, Leu104A, Trp14, Tyr174A, and pi-pi bonds with the aromatic amino acid Phe8, Ser10, Tyr12, Trp14, Tyr174A. This finding indicates the higher binding affinity of Spike peptide MIAQYTSAL to the MHC I HLA-C1203 allele and supports the MDockPeP
    keywords: allele; amino; binding; bonds; hla; mhc; nucleocapsid; peptides; spike
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        item: #117 of 117
          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: 14183
      flesch: 32
     summary: The state of current knowledge of influenza T cell responses in humans is still trying to catch up with the lessons we have learned from animal models. 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.
    keywords: cd4; cd8; cell; epitopes; hla; human; immune; immunity; infection; influenza; lung; memory; pandemic; protection; responses; specific; t cell; trm; vaccine; virus; viruses
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