item: #1 of 106 id: cord-000149-dp8971im author: Otting, Nel title: Definition of Mafa-A and -B haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis) date: 2009-11-24 words: 3841 flesch: 50 summary: Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques Genetic divergence of the rhesus macaque major histocompatibility complex Comparative genetics of a highly divergent DRB microsatellite in different macaque species Phylogeny.fr: robust phylogenetic analysis for the non-specialist Evolutionary stability of MHC class II haplotypes in diverse rhesus macaque populations Extensive sharing of MHC class II alleles between rhesus and cynomolgus macaques A highly divergent microsatellite facilitating fast and accurate DRB haplotyping in humans and rhesus macaques Compound evolutionary history of the rhesus macaque MHC class I B region revealed by microsatellite analysis and localization of retroviral sequences ISAG/IUIS-VIC Comparative MHC Nomenclature Committee report MHC class I A loci polymorphism and diversity in three Southeast Asian populations of cynomolgus macaque Nomenclature for the major histocompatibility complexes of different species: a proposal Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques The locus encoding an oligomorphic family of MHC-A alleles (Mane-A*06/Mamu-A*05) is present at high frequency in several macaque species Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys Mhc haplotype H6 is associated with sustained control of SIVmac251 infection in Mauritian cynomolgus macaques Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques Extensive Mhc-DQB variation in humans and non-human primate species Unparalleled complexity of the MHC class I region in rhesus macaques MHC class I A region diversity and polymorphism in macaque species A snapshot of the Mamu-B genes and their allelic repertoire in rhesus macaques of Chinese origin MHC class keywords: alleles; cynomolgus; et al; macaques; mafa; mhc cache: cord-000149-dp8971im.txt plain text: cord-000149-dp8971im.txt item: #2 of 106 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 cache: cord-000224-2lz03oqb.txt plain text: cord-000224-2lz03oqb.txt item: #3 of 106 id: cord-000479-u87eaaj8 author: Stolf, Beatriz S. title: Protein Disulfide Isomerase and Host-Pathogen Interaction date: 2011-10-11 words: 6000 flesch: 36 summary: Here, we summarise examples of the cellular association of host PDI with different pathogens and explore the possible roles of pathogen PDIs in infection. Overall, PDI redox activity modulates the stability of the antigen peptide-MHC class I complex and further determines the transport of the complex to the plasma membrane keywords: antigen; cells; disulfide; endoplasmic; host; infection; isomerase; leishmania; oxidase; pathogen; pdi; phagocytosis; process; protein; redox; reticulum cache: cord-000479-u87eaaj8.txt plain text: cord-000479-u87eaaj8.txt item: #4 of 106 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 cache: cord-000488-x5ardo5j.txt plain text: cord-000488-x5ardo5j.txt item: #5 of 106 id: cord-000695-g5sum116 author: Hou, Yanxia title: Prediction and Identification of T Cell Epitopes in the H5N1 Influenza Virus Nucleoprotein in Chicken date: 2012-06-20 words: 5347 flesch: 52 summary: First, this is the first study to determine the structural characteristics of the peptide-binding domains of chicken MHC class I molecules belonging to the B4, B12, B15, and B19 haplotypes using a combined motif-structure method to predict T cell epitopes in chickens. The results indicate that peptides NP(89–97) (PKKTGGPIY) and NP(198–206) (KRGINDRNF) are NP T cell epitopes in chicken of certain haplotypes. keywords: b19; binding; cell; chicken; class; epitopes; haplotypes; mhc; molecules; peptide; t cell cache: cord-000695-g5sum116.txt plain text: cord-000695-g5sum116.txt item: #6 of 106 id: cord-000871-ej0e1c4d author: Kim, Yohan title: Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation date: 2013-01-24 words: 4352 flesch: 39 summary: The connection between positional epitope biases with protein conservation is reasonable in the context of boosting effects associated with repeated vaccine administrations. This sampling bias in turn may influence from which regions of proteins epitopes are more often detected, resulting in positional bias of epitopes. keywords: bias; conservation; epitopes; fig; mhc; peptides; proteins; virus cache: cord-000871-ej0e1c4d.txt plain text: cord-000871-ej0e1c4d.txt item: #7 of 106 id: cord-001674-tp4o7fxx author: Oliveira, Cláudia C. title: Alternative Antigen Processing for MHC Class I: Multiple Roads Lead to Rome date: 2015-06-05 words: 6641 flesch: 33 summary: Front Immunol DOI: 10.3389/fimmu.2015.00298 sha: doc_id: 1674 cord_uid: tp4o7fxx The well described conventional antigen-processing pathway is accountable for most peptides that end up in MHC class I molecules at the cell surface. Proteasomal cleavage typically creates a peptide's C-terminus compatible with MHC class I binding, and peptides are typically extended at their N-terminus (2, 3) . keywords: antigen; cells; class; mhc; mhc class; molecules; pathway; peptide; presentation; processing; protein; spp; tap cache: cord-001674-tp4o7fxx.txt plain text: cord-001674-tp4o7fxx.txt item: #8 of 106 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 cache: cord-002463-qhtj1pef.txt plain text: cord-002463-qhtj1pef.txt item: #9 of 106 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 cache: cord-002686-zzongyfa.txt plain text: cord-002686-zzongyfa.txt item: #10 of 106 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 cache: cord-003270-vu9b5a14.txt plain text: cord-003270-vu9b5a14.txt item: #11 of 106 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 cache: cord-003472-ml4pbewf.txt plain text: cord-003472-ml4pbewf.txt item: #12 of 106 id: cord-004518-jd1wxobz author: Běláková, Jana title: DNA vaccines: are they still just a powerful tool for the future? date: 2007-12-03 words: 8119 flesch: 34 summary: Efficacious expression of protein from DNA vaccines is dependent on the presence of DNA vaccine in the nucleus. In contrast to plasmid DNA vaccines, virally vectored genetic vaccines induce a specific immune response not only against the expressed transgene, but also against the viral capsid and/or envelope and this response is often effective even after the first immunization. keywords: antigen; cells; delivery; dna; expression; gene; immunization; injection; mhc; mice; plasmid; protein; response; vaccination; vaccines; vectors; virus cache: cord-004518-jd1wxobz.txt plain text: cord-004518-jd1wxobz.txt item: #13 of 106 id: cord-004975-4c23d77d author: Larcher, Clara title: Influence of viral infection on expression of cell surface antigens in human retinal pigment epithelial cells date: 1997 words: 3087 flesch: 41 summary: The cell biology of antigen processing and presentation Modulation and function of intercellular adhesion molecule-1 (CD54) on human retinal pigment epithelial cells Proliferative vitreoretinopathy: an examination of the involvement of lymphocytes, adhesion molecules and HLA-DR antigens Human retinal pigment epithelial cells differentially express MHC class II (HLA, DP, DR and DQ) antigens in response to in vitro stimulation with lymphokine or purified IFN-gamma Interactions between lymphocytes and cells of the blood-retina barrier: mechanisms of T lymphocyte adhesion to human retinal capillary endothelial cells and retinal pigment epithelial cells in vitro Retinal pigment epithelial cells modulate lymphocyte function at the blood-retina barrier by autocrine PGE2 and membrane-bound mechanisms Cell lines producing human T-cell lymphoma virus type 1 show altered HLA expression Modulation of MHC antigen expression by viruses and oncogenes Cytokinemediated activation of a neuronal retinal resident cell provokes antigen presentation EB-virus transformed human iymphocytes from uveitis and retinitis pigmentosa patients secrete antibodies to retinal antigens Murine coronavirus induces an acute and long lasting disease of the retina Redistribution and reduction of interphotoreceptor retinoid-binding protein during ocular coronavirus infection Down modulation of MHC-I in a CD4+ T cell line, CEM-E5, after HIV-1 infection Expression of class I major histocompatibility antigens switched off by highly oncogenic adenovirus 12 in transformed rat cells Protection of mice by an apathogenic strain of HSV 1 against lethal infection by a pathogenic strain of HSV type 1 Santigen: from gene to autoimmune uveitis Molecular mimicry between a uveitopathogenic site of S-antigen and viral peptides. One of the strategies used by viruses to cause persistent infection so as to evade host immunosurveillance is the interference with the expression or function of cell surface molecules [12, 13] . keywords: antigens; cells; class; expression; infection; mhc; rpec; virus cache: cord-004975-4c23d77d.txt plain text: cord-004975-4c23d77d.txt item: #14 of 106 id: cord-005330-4k7hc1ww author: Bien, Christian G. title: T-cells in human encephalitis date: 2005 words: 5425 flesch: 24 summary: Clonal expansions of CD8(+) T cells dominate the T cell infiltrate in active multiple sclerosis lesions as shown by micromanipulation and single cell polymerase chain reaction A survival game of hide and seek: cytomegaloviruses and MHC class I antigen presentation pathways Paraneoplastic disorders of the central nervous system: update on diagnostic criteria and treatment Apoptosis of T lymphocytes in acute disseminated encephalomyelitis Cell-mediated autoimmunity in paraneoplastic neurological syndromes with anti-Hu antibodies Perforinmediated effector function within the central nervous system requires IFN-gamma-mediated MHC up-regulation Perforin and gamma interferon-mediated control of coronavirus central nervous system infection by CD8 T cells in the absence of CD4 T cells Immunohistochemical analysis of anti-Hu-associated paraneoplastic encephalomyelitis Destruction of neurons by cytotoxic T cells: a new pathogenic mechanism in Rasmussen's encephalitis An open study of tacrolimus therapy in Rasmussen encephalitis Pathogenesis, diagnosis and treatment of Rasmussen encephalitis: a European consensus statement The natural history of Rasmussen's encephalitis Viral Encephalitis in Humans Immunohistological analysis of T lymphocyte subsets in the central nervous system in chronic progressive multiple sclerosis Adhesion molecule expression and lymphocyte adhesion to cerebral endothelium: effects of measles virus and herpes simplex 1 virus Subacute encephalitis of later adult life mainly affecting the limbic areas Therapy for paraneoplastic neurologic syndromes in six patients with protein A column immunoadsorption A post-transcriptional regulatory mechanism restricts expression of the paraneoplastic cerebellar degeneration antigen cdr2 to immune privileged tissues Limbic encephalitis and its association with carcinoma Partial characterization of the Purkinje cell antigens in paraneoplastic cerebellar degeneration Detection of the anti-Hu antibody in the serum of patients with small cell lung cancer-a quantitative western blot analysis Detection of the anti-Hu antibody in specific regions of the nervous system and tumor from patients with paraneoplastic encephalomyelitis/sensory neuronopathy Cdr2, a target antigen of naturally occuring human tumor immunity, is widely expressed in gynecological tumors A prospective study demonstrates an association between JC virus-specific cytotoxic T lymphocytes and the early control of progressive multifocal leukoencephalopathy Detection of JC virus-specific cytotoxic T lymphocytes in healthy individuals Chronic encephalitis associated with epilepsy: immunohistochemical and ultrastructural studies Production of B cell stimulatory factor-2 and interferon gamma in the central nervous system during viral meningitis and encephalitis. However, any further attempt to prove this hypothesis failed: Most of the antigens were found to reside mainly within the cytoplasma or even the nuclei of brain cells (thereby being out of reach of antibodies); removal of antibodies from patients' circulation by plasma exchange or immunoabsorption did not consistently improve these patients' clinical symptoms (Graus et al., 1990a; Cher et al., 1995; Gultekin et al., 2000) ; and passive transfer and immunization studies failed to induce disease in animals (Sillevis Smitt et al., 1995; Tanaka et al., 1995) . keywords: anti; brain; cd8; cells; encephalitis; et al; lymphocytes; paraneoplastic; patients; virus cache: cord-005330-4k7hc1ww.txt plain text: cord-005330-4k7hc1ww.txt item: #15 of 106 id: cord-005393-rhji4io9 author: Popko, Brian title: The effects of interferon-γ on the central nervous system date: 1997 words: 7981 flesch: 29 summary: In vivo expression of inducible nitric oxide synthase in experimentally induced neurologic diseases Differential regulation of oligodendrocyte markers by glucocorticoids: post-h-anscriptional regulation of both proteolipid protein and myelin basic protein and transcriptional regulation of glycerol phosphate dehydrogenase Morphological and molecular response of the MOCH-1 oligodendrocyte cell line to serum and Lnterferon-y: possible implications for demyelinating disorders Immunological aspects of experimental allergic encephalomyelitis and multiple sclerosis Immunological aspects of demyelinating diseases Cell type-specific regulation of major histocompatibility complex (MHC) class I gene expression in astrocytes, oligodendrocytes, and neurons Differential expression and regulation of major histocompatibility complex (MHC) products in neural and glial cells of the human fetal brain Selective killing of cholinergic neurons by microglial activation in basal forebrain mixed neuronal/glial cultures Cytokine-regulated adhesion between encephalitogenic T lymphocytes and cerebrovascular endothelial cells Induction of active and adoptive relapsing experimental autoimmune encephalomyelitis (EAE) using an encephalitogenir epitope of proteolipid protein Activation of microglial cells by beta-amyloid protein and interferon-gamma Microglial cell cytotoxicity of oligodendrocytes is mediated through nitric oxide Evdution of the T-cell d~ng the course of experimental imanune-mediated demyelinating disea~s Nitric oxide induces necrotic but not apoptotic cell death in oligodendrocytes Differential expression of Ia and Ia-associated invariant chain in mouse tissue after in vivo treatment with IFN-7 Interferon pretreatment lowers the threshold for maximal heat-shock response in mouse cells Early evidence demonstrating the ability of brain cells, including neurons, to express MHC molecules includes experiments in which IFN-y was either added to mixed brain cultures or i~ected directly into the CNS (Wong et al., 1984 (Wong et al., , 1985 . keywords: astrocytes; brain; cells; class; cns; eae; et al; expression; human; ifn; immune; interferon; mhc; mice; oligodendrocytes; protein cache: cord-005393-rhji4io9.txt plain text: cord-005393-rhji4io9.txt item: #16 of 106 id: cord-005400-50lmj4op author: Ada, Gordon title: Overview of vaccines and vaccination date: 2005 words: 7488 flesch: 45 summary: Combining vaccines so that three or more can be administered simultaneously results in considerable savings, therefore there are determined efforts to add other vaccines to longtime successful combinations (diphtheria, acellular pertussis, tetanus [DaPT] and MMR) such as DaPT-hepatitis B-H aemophilus influenzae type b. Live, attenuated agent vaccines have the potential to stimulate strong humoral and cell-mediated immune responses that can be highly effective in preventing or clearing a later infection in most recipients. keywords: agents; antigen; cells; countries; disease; dna; infection; measles; mhc; new; response; vaccination; vaccine; virus cache: cord-005400-50lmj4op.txt plain text: cord-005400-50lmj4op.txt item: #17 of 106 id: cord-005550-qrrdi667 author: Mayer, F title: Non-neutral evolution of the major histocompatibility complex class II gene DRB1 in the sac-winged bat Saccopteryx bilineata date: 2007-05-23 words: 5006 flesch: 45 summary: The spatial and rapid temporal variation in frequency of MHC alleles and resistance provides evidence for frequency-dependent selection (Hill et al., 1994; Westerdahl et al., 2004; Charbonnel and Pemberton, 2005) . Distinguishing between the frequencydependent selection and the heterozygote advantage hypothesis is difficult, because both models require a correlation between parasites and particular MHC alleles. keywords: alleles; bat; class; diversity; drb; individuals; mhc; sac; selection; sequence; types cache: cord-005550-qrrdi667.txt plain text: cord-005550-qrrdi667.txt item: #18 of 106 id: cord-005953-5z89yeb6 author: None title: Abstracts des 114. Internistenkongresses 2008 date: 2008 words: 16191 flesch: 40 summary: Hohe Prävalenz der ASS-Non-Responder bei ACVB-Patienten in den multiplen Testanalysen Hintergrund und Zielsetzung: In der Therapie der HIV-Infektion sind Wechselwirkungen und Unverträglichkeit der mittlerweile zahlreich zur Verfügung stehenden antiretoviralen Medikamente ein grosses Problem. Auch in der Subgruppe der überlebenden keywords: als; apoptose; auf; baseline; bei; cells; cholesterol; class; clopidogrel; combination; das; dem; der; des; diabetes; die; disease; durch; eine; ergebnisse; expression; fat; für; glucose; group; gruppe; hbv; heart; hzv; ifn; ist; jedoch; ldl; methoden; methods; min; mit; mittels; mmhg; nach; nicht; non; p<0.05; patienten; patients; platelets; protein; reduction; results; schlussfolgerung; sind; studie; study; system; therapie; therapy; tolerance; treatment; type; und; unter; untersucht; vascular; vivo; von; war; werden; wurde; zellen; zur; über cache: cord-005953-5z89yeb6.txt plain text: cord-005953-5z89yeb6.txt item: #19 of 106 id: cord-007275-emmoeuqd author: Cooper, Joanne C. title: An Impaired Breeding Phenotype in Mice with a Genetic Deletion of Beta-2 Microglobulin and Diminished MHC Class I Expression: Role in Reproductive Fitness(1) date: 2007-08-01 words: 4443 flesch: 48 summary: In addition, the litter size and weaning success of B2m deficient mice were lower than the control. Breeding studies from crosses between the transgenic mice and the wild-type parental strain show that B2m deficient mice have a significantly lower frequency of mating than the control B2m(+/+) mice. keywords: b2 m; class; m à; m þ; mhc; mice cache: cord-007275-emmoeuqd.txt plain text: cord-007275-emmoeuqd.txt item: #20 of 106 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 cache: cord-007301-5m269nzi.txt plain text: cord-007301-5m269nzi.txt item: #21 of 106 id: cord-007603-27m9wz0i author: Rall, Glenn F. title: A transgenic mouse model to assess the interaction of cytotoxic T lymphocytes with virally infected, class I MHC-expressing astrocytes date: 2002-11-11 words: 3690 flesch: 39 summary: An increase in mean fluorescence (from 12.26 to 23.24) was found in primary transgenic astrocytes relative to non-transgenic astrocytes (Fig. 4A, arrows) . + RNA was extracted from brains and analyzed by Northern blot and sequential hybridization with different probes (Mucke et al., 1991) . keywords: astrocytes; cells; class; expression; mhc; mice; transgenic cache: cord-007603-27m9wz0i.txt plain text: cord-007603-27m9wz0i.txt item: #22 of 106 id: cord-007621-rapinodd author: Vidovic, Maria title: Induction and regulation of class II major histocompatibility complex mRNA expression in astrocytes by interferon-γ and tumor necrosis factor-α date: 2002-11-13 words: 6691 flesch: 45 summary: Furthermore, astrocyte class II mRNA expression was inhibited when cycloheximide (CHX) was added together with IFN-γ or IFN-γ/TNF-α, and when CHX was added up to 4 h after treatment with IFN-γ or IFN-γ/TNF-α. These results indicate that astrocyte class II mRNA expression is mediated by newly synthesized proteins induced by IFN-γ and/or IFN-γ/TNF-α. keywords: astrocytes; cells; class; class ii; et al; expression; ifn; mhc; mrna; tnf cache: cord-007621-rapinodd.txt plain text: cord-007621-rapinodd.txt item: #23 of 106 id: cord-007636-kfd0wqdx author: Wen, P. title: The effects of irradiation on major histocampatibility complex expression and lymphocytic infiltration in the normal rat brain and the 9L gliosarcoma brain tumor model date: 2002-11-13 words: 1930 flesch: 39 summary: Nominal standard dose and the rat Systemic administration of recombinant interleukin 2 stimulates in vivo lymphoid proliferation in tissues Regression and inhibition of sarcoma growth by interference with a radiosensitive T-cell population Radiation therapy of 9L rat brain tumors Decreased expression of HLA class II antigens on human uveal melanoma cells after in vivo X-ray irradiation An improved rat brain tumor model Therapeutic trials in the management of metastatic brain tumors by different time/dose fraction schemes of radiation therapy Molecular basis of the immune response to neural antigens Monoclonal antibody analysis of MHC expression in human brain biopsies: tissue ranging from 'histologically normal' to that showing different levels of glial tumor involvement Interactions between leucocytes and individual brain tumor cells in the rat brain Radiation immunobiology and immunomodulation Principles and Practice of Radiation Oncology Reactive microglia are positive for HLA-DR in the substantia nigra of Parkinson's and Alzheimer's disease brains y-Irradiation facilitates the expression of adoptive immunity against established tumors by eliminating suppressor T cells Morphological studies of rat brain tumors induced by N-nitrosomethyhirea The immunopathology of experimental allergic encephalomyelitis. Two kinds of evidence suggest that the class II-positive cells were not tumor cells. keywords: brain; cells; class; irradiation; tumor cache: cord-007636-kfd0wqdx.txt plain text: cord-007636-kfd0wqdx.txt item: #24 of 106 id: cord-007654-lchdm4xr author: Liu, Yang title: Flavivirus infection up-regulates the expression of class I and class II major histocompatibility antigens on and enhances T cell recognition of astrocytes in vitro date: 2002-12-11 words: 5042 flesch: 43 summary: major histecompatibility complex antigens on infected cells Antigen-inducible, H-2-restricted interleukin-2-producing T cell hybridomas lack of independent antigen and H-2 re. cognition Relationship between surface H-2 concentration, size of different target cells and lysis by cytotoxic T cells Clones of cytotoxic lymphocytes can recognize uninfected cells in a primary response against influenza virus Immunohistochemical identification of T lyn~lphocytes in the central nervous system of patients with multiple selerosis and subacute sclerusilag panencephalitis An improved assay for interleukin-2 (lymphocyte growth factor) produced by mitogen activated lymphocytes Theiler's virus-induced demyelination: prevention by immunosuppression Preparation of separate astre~lJial and ollgodendroglial cell cultures from rat cerebral tissue Enhanced representation of HL-A antigens on human lymphocytes after mitogenesis induced by phytohemagglutinin of Epstein-Barr virus Antigen presentation in brain: MHC induction on brain end~ thdium and astrocytes compared Viral particles induce la antigen expression on astrocytes Pathobiology of flaviviruses Infection of cultured mnrine brain cells by Semliki Forest virus: effect of interferon-o.~ on viral replication, viral antigen display, major histocompafibility complex antigen display and lysis by cytotoxie T lymphocytes Properties of mo~clonal antibodies to mouse Ig allotypes, H-2 and Ia antigens Hybridoma cell lines secreting monoclonal antibodies to mouse H-2 and la antigens Adenoviruses of subgenera B, C, D, and E modulate cell-surface expression of major histccompatibility complex class I antigens Temporary pr~-~,ence of self-reactive cytotoxic T iymphocytes during murine lymphocytic choriomeningitis Decreased expression of H-2 antigens following acute measles virus infection A simple method of estimating fifty percent end points hlunone response geue products (la antigens) on gliai and endothelial cells in virus induced demyelination Intracellular v-interferon triggers an antiviral state in transformed L cells Immune response (It) gene of the murine major histocompatibility complex Interlenkin 4 (IgGI induction factor): a multifunctional lymphokin acting also on T cells Clonal analysis of cytolytic T lymphocyte-mediated lysis of target cells with inducible antigen expression: correlation between antigen density and requirement for Ly-2/3 function l~e cytotoxic response to murine cytomegalovirus. I. Induction of la antigen expression on astrocytes T cells via in-anune interferon and its effect on antigen presentation Retrovirus induced changes in major histocompatibility complex antigen expression influence susceptibility to lysis by cytotoxic T lymphocytes The endothelium-astrocyte immune control system Cell mediated cytotoxicity against ectromelia virus-infected target cells Conjugation of antibodies with fluorochromes: modrficat!ous to the standard methods Viral induced autoimmnnity: monoclonai antibb.lies that react with endocrine tissues Multiple organ-re.~ctive monoclonal autoantibodies Expression of la antigens by cultured estrocytes treated with y-interferon Quantitative variation in la antigen expression plays a central role in immune regulation Effect of herpes simplex virus type 1 and 2 on surface expression of class ! keywords: antigen; astrocytes; cells; class; expression; ifn; infection; mhc; virus; wnv cache: cord-007654-lchdm4xr.txt plain text: cord-007654-lchdm4xr.txt item: #25 of 106 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 cache: cord-007851-v6h1yro7.txt plain text: cord-007851-v6h1yro7.txt item: #26 of 106 id: cord-008523-avkgldnp author: Perlman, Stanley title: Selection of and evasion from cytotoxic T cell responses in the central nervous system date: 2004-01-07 words: 8877 flesch: 33 summary: The CD4 and CD8 T cell response in maternal antibody-protected mice that develop chronic demyelination is proinflammatory and readily detected (Castro et al., 1994; . The ability of the virus to tolerate mutations in the part of the protein that contains the target CD8 T cell epitope is also important. keywords: cell; class; cns; ctl; epitope; escape; et al; infected; mhc; mice; mutants; response; virus cache: cord-008523-avkgldnp.txt plain text: cord-008523-avkgldnp.txt item: #27 of 106 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 cache: cord-009567-osstpum6.txt plain text: cord-009567-osstpum6.txt item: #28 of 106 id: cord-009570-djxoiytq author: Gran, Bruno title: Molecular mimicry and multiple sclerosis: Degenerate T‐cell recognition and the induction of autoimmunity date: 2001-06-01 words: 5342 flesch: 32 summary: I. Clinical results of a multicenter, randomized, double-blind, placebo-controlled trial Intermittent cyclophosphamide pulse therapy in progressive multiple sclerosis: final report of the Northeast Cooperative Multiple Sclerosis Treatment Group Treatment of multiple sclerosis with gamma interferon: exacerbations associated with activation of the immune system Distinct patterns of multiple sclerosis pathology indicates heterogeneity on pathogenesis The neuropathology of multiple sclerosis The lesion in multiple sclerosis and chronic relapsing experimental allergic encephalomyelitis: a structural comparison Autoaggressive T lymphocyte lines recognize the encephalitogenic region of myelin basic protein in vitro selection from unprimed rat T lymphocyte populations Major histocompatibility complex-linked control of the murine immune response to myelin basic protein Cellular immune reactivity within the CNS Isolation of myelin basic protein-reactive T-cell lines from normal human blood Fine specificity and HLA restriction of myelin basic protein-specific cytotoxic T cell lines from multiple sclerosis patients and healthy individuals Myelin basic protein-specific T lymphocyte lines from MS patients and healthy individuals Increased frequency of interleukin-2-responsive T cells specific for myelin basic protein in peripheral blood and cerebrospinal fluid of patients with multiple sclerosis T-cell recognition of an immunodominant myelin basic protein epitope in multiple sclerosis Clinical viral infections and multiple sclerosis Influence of infection on exacerbations of multiple sclerosis Epidemiologic evidence for multiple sclerosis as an infection Myelin basic protein and human coronavirus 229E cross-reactive T cells in multiple sclerosis Restriction of in vitro T cellmediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation Activation of naive, memory and effector T cells Cytokine-producing cells in experimental autoimmune encephalomyelitis and multiple sclerosis Naive and effector CD4 T cells differ in their requirements for T cell receptor versus costimulatory signals A viral peptide with limited homology to a self peptide can induce clinical signs of experimental autoimmune encephalomyelitis A cartilagemimicking T-cell epitope on a 65K mycobacterial heat-shock protein: adjuvant arthritis as a model for human rheumatoid arthritis Molecular mimicry: can epitope mimicry induce autoimmune disease? Promiscuous and allele-specific anchors in HLA-DR binding peptides Separation of T helper 1 clone cytolysis from proliferation and lymphokine production using analog peptides Structural basis for T cell recognition of altered peptide ligands: a single T cell receptor can productively recognize a large continuum of related ligands Self-nonself discrimination by T cells Ligand motifs of HLA-DRB5*0101 and DRB1*1501 molecules delineated from self-peptides Structural requirements for binding of an immunodominant myelin basic protein peptide to DR2 isotypes and for its recognition by human T cell clones Molecular mimicry in T cell-mediated autoimmunity: viral peptides activate human T cell clones specific for myelin basic protein Differential activation of human autoreactive T cell clones by altered peptide ligands derived from myelin basic protein peptide (87-99) Modifications of peptide ligands enhancing T cell responsiveness imply large numbers of stimulatory ligands for autoreactive T cells Predictable TCR antigen recognition based on peptide scans leads to the identification of agonist ligands with no sequence homology Complementary mutations in an antigenic peptide allow for crossreactivity of autoreactive T-cell clones Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery Decrypting the structure of major histocompatibility complex class I-restricted cytotoxic T lymphocyte epitopes with complex peptide libraries Probing degeneracy in T-cell recognition using combinatorial peptide libraries Identification of high potency microbial and self ligands for a human autoreactive class II-restricted T cell clone A very high level of crossreactivity is an essential feature of the T-cell receptor Separation of IL-4 production from Th cell proliferation by an altered T cell receptor ligand Relationships among TCR ligand potency, thresholds for effector function elicitation, and the quality of early signaling events in human T cells Altered peptide ligand-induced partial T cell activation: molecular mechanisms and role in T cell biology The shaping of the brain-specific T lymphocyte repertoire in the thymus Negative selection of lymphocytes Positive selection of lymphocytes Evidence for a differential avidity model of T cell selection in the thymus A differential-avidity model for T-cell selection T-cell selection Endogenous peptides associated with MHC class II and selection of CD4 T cells Activation of MBP-specific T cells by thymic cells in the absence of exogenous MBP Expression of autoimmune disease-related antigens by cells of the immune system Transcription of a broad range of self-antigens in human thymus suggests a role for central mechanisms in tolerance toward peripheral antigens Thymic expression of autoantigens correlates with resistance to autoimmune disease Intrathymic expression of genes involved in organ specific autoimmune disease AFter recognition of antigen/MHC, T cells become activated, undergo clonal expansion, and acquire effector functions such as cytokine production and cytotoxicity. keywords: amino; antigen; cells; mhc; myelin; peptide; recognition; sclerosis; self; tcr cache: cord-009570-djxoiytq.txt plain text: cord-009570-djxoiytq.txt item: #29 of 106 id: cord-010500-ajmj2hyj author: ELLEGREN, H. title: Limited polymorphism at major histocompatibility complex (MHC) loci in the Swedish moose A. alces date: 2008-06-28 words: 3573 flesch: 45 summary: Preserving MHC polymorphism has in fact been put forward as being a prime objective in all conservation programs (Hughes 1991) . As an illustration of the varying levels of MHC polymorphism in cattle and moose, a blot with bovine PVuII digests hybridized with the same human DQB probe as employed in the present study is shown in Fig. I@) . keywords: class; dna; drb; mhc; moose; polymorphism; swedish; variability cache: cord-010500-ajmj2hyj.txt plain text: cord-010500-ajmj2hyj.txt item: #30 of 106 id: cord-010508-jtbxefm4 author: Mohammed, Arwa A. title: Epitope-Based Peptide Vaccine against Glycoprotein G of Nipah Henipavirus Using Immunoinformatics Approaches date: 2020-04-22 words: 3843 flesch: 43 summary: The distribution of henipaviruses in Southeast Asia and Australasia: is Wallace's line a barrier to Nipah virus? Recombinant nipah virus vaccines protect pigs against challenge Bats and emerging zoonoses: henipaviruses and SARS Recurrent zoonotic transmission of Nipah virus into humans Nipah virus: transmission of a zoonotic paramyxovirus Epidemiology, surveillance, and control of Nipah virus infections in Malaysia Risk factors for Nipah virus infection among pteropid bats, Peninsular Malaysia Pteropid bats are confirmed as the reservoir hosts of henipaviruses: a comprehensive experimental study of virus transmission NIPAH virus: a new threat to South Asia The pandemic potential of Nipah virus The killer virus called Nipah: a review Clinical features of Nipah virus encephalitis among pig farmers in Malaysia Production and characterization of monoclonal antibodies against binary ethylenimine inactivated Nipah virus Enhancing preparation for large Nipah outbreaks beyond Bangladesh: preventing a tragedy like Ebola in West Africa Highly conserved epitopes of ZIKA envelope glycoprotein may act as a novel peptide vaccine with high coverage: immunoinformatics approach Current progress of immunoinformatics approach harnessed for cellular-and antibody-dependent vaccine design Computational vaccinology and epitope vaccine design by immunoinformatics Nipah virus infection: pathology and pathogenesis of an emerging paramyxoviral zoonosis Nipah virus attachment glycoprotein stalk C-terminal region links receptor binding to fusion triggering The promise and challenge of epitope-focused vaccines A brief review of computer-assisted approaches to rational design of peptide vaccines Peptide-based synthetic vaccines A computational approach for designing a universal epitope-based peptide vaccine against Nipah virus A focus on vaccine development Current protocols in microbiology A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases Peptide vaccine: progress and challenges NCBI protein sequence database The immune epitope database (IEDB) 3.0 Design and evaluation of primer pairs for efficient detection of avian rotavirus Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines Improved method for predicting linear B-cell epitopes A semi-empirical method for prediction of antigenic determinants on protein antigens Immune epitope database analysis resource Immune epitope database analysis resource (IEDB-AR) Nipah virus (NiV) is an RNA virus that belongs to the genus Henipavirus within the family Paramyxoviridae and has first emerged in Malaysia in 1998, gaining its name from a village called Sungai Nipah where it was isolated from the cerebrospinal fluid (CSF) of one of the patients [1] [2] [3] [4] . keywords: alleles; binding; class; epitope; glycoprotein; mhc; nipah; peptide; vaccine; virus cache: cord-010508-jtbxefm4.txt plain text: cord-010508-jtbxefm4.txt item: #31 of 106 id: cord-010640-s1oqphvn author: Baral, Prabin title: In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever date: 2020-05-06 words: 4838 flesch: 43 summary: Since the interactions between protein and epitope peptide are mostly influenced by non-covalent interactions, we computed the number of hydrogen bonds and the interaction energy between the allele and epitope as a function of the MD simulation time. The IEDB showed that the E1, E4, E18, E22, E27, E29 epitopes, which bind to solvent exposed regions on the protein (Fig. 3) , have not been previously reported as LASV epitopes or vaccine candidates. keywords: allele; cell; cell epitopes; epitopes; lasv; mhc; prediction; sequence; structure; table cache: cord-010640-s1oqphvn.txt plain text: cord-010640-s1oqphvn.txt item: #32 of 106 id: cord-011173-c1i0a92f author: Moore, Tamson V. title: Improved MHC II epitope prediction — a step towards personalized medicine date: 2019-12-13 words: 1664 flesch: 32 summary: Evidence indicates that CD4 + T cell responses to MHC class II (MHC II)-restricted antigens are required for robust responses to ICIs 3 and that neoantigen vaccines can enhance CD4 + T cell responses 2 . One remaining hurdle, however, is that only a minority of predicted MHC II-binding peptides induced CD4 + T cell responses (8.3% (5 of 60) with MixMHC2pred and 10.8% (20 of 185) with MARIA) 5, 6 . keywords: binding; cd4; mhc cache: cord-011173-c1i0a92f.txt plain text: cord-011173-c1i0a92f.txt item: #33 of 106 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 cache: cord-013093-aa4cf44u.txt plain text: cord-013093-aa4cf44u.txt item: #34 of 106 id: cord-013315-plptulfb author: Tilocca, Bruno title: Immunoinformatic-Based Prediction of Candidate Epitopes for the Diagnosis and Control of Paratuberculosis (Johne’s Disease) date: 2020-08-27 words: 6837 flesch: 36 summary: The list of epitope sequences was further analyzed through the Basic Local Alignment Search Tool for protein sequences (pBLAST) The list of epitope sequences was further analyzed through the Basic Local Alignment Search Tool for protein sequences (pBLAST) keywords: avium; binding; class; disease; epitopes; map; mhc; mycobacterium; paratuberculosis; peptides; prediction; protein; sequences cache: cord-013315-plptulfb.txt plain text: cord-013315-plptulfb.txt item: #35 of 106 id: cord-013590-pkm81fq1 author: Deseke, Malte title: Ligand recognition by the γδ TCR and discrimination between homeostasis and stress conditions date: 2020-07-24 words: 9315 flesch: 38 summary: Recognition of TCR-γδ+ CTL clones is affected by mutations at positions 152 and 156 Generation and molecular recognition of melanomaassociated antigen-specific human γδ T cells Self-recognition of CD1 by γ/δ T cells: implications for innate immunity Recognition of pollen-derived phosphatidyl-ethanolamine by human CD1d-restricted γδ T cells Cardiolipin binds to CD1d and stimulates CD1d-restricted γδ T cells in the normal murine repertoire Molecular analysis of lipid-reactive Vδ1 γδ T cells identified by CD1c tetramers Crystal structure of Vδ1 T cell receptor in complex with CD1d-sulfatide shows MHC-like recognition of a self-lipid by human γδ T cells Cutting edge: CD1d restriction and Th1/Th2/Th17 cytokine secretion by human Vδ3 T cells Qa-1 restricted recognition of foreign antigen by a γδ T-cell hybridoma Infection-induced expansion of a MHC class Ib-dependent intestinal intraepithelial γδ T cell subset A class of γδ T cell receptors recognize the underside of the antigen-presenting molecule MR1 Cell stress-regulated human major histocompatibility complex class I gene expressed in gastrointestinal epithelium T cell antigen receptor engagement and specificity in the recognition of stress-inducible MHC class I-related chains by human epithelial γδ T cells Crystal structure of a T-cell receptor specific for the human MHC class I homolog MICA Recognition of the product of a novel MHC TL region gene (27b) by a mouse γδ T cell receptor The nature of major histocompatibility complex recognition by γδ T cells A population of murine γδ T cells that recognize an inducible MHC class Ib molecule Crystal structure of a γδ T cell receptor ligand T22: a truncated MHC-like fold Recasting human Vδ1 lymphocytes in an adaptive role Vδ2+T cells--two subsets for the price of one Sensing of cell stress by human γδ TCR-dependent recognition of annexin A2 γδ T-cell conference 2012: Close encounters for the fifth time Ectopically expressed human tumor biomarker MutS homologue 2 is a novel endogenous ligand that is recognized by human γδ T cells to induce innate anti-tumor/virus immunity Antigen recognition properties of a Vγ1.3Vδ2-T-cell receptor from a rare variant of polymyositis Target specificity of an autoreactive pathogenic human γδ-T cell receptor in myositis HSV-1 glycoprotein I-reactive TCR gamma delta cells directly recognize the peptide backbone in a conformationally dependent manner Specific recognition of staphylococcal enterotoxin A by human T cells bearing receptors with the Vγ9 region A novel strategy to screen Bacillus Calmette-Guérin protein antigen recognized by γδ TCR Identification of a new tuberculosis antigen recognized by γσ T cell receptor γδ T cells recognize a microbial encoded B cell antigen to initiate a rapid antigen-specific interleukin-17 response Gamma delta T cells recognize haptens and mount a haptenspecific response Gamma delta T cell receptors confer autonomous responsiveness to the insulin-peptide B:9-23 γδ T cells recognize the insulin B:9-23 peptide antigen when it is dimerized through thiol oxidation Isolation of CD4-CD8-mycobacteria-reactive T lymphocyte clones from rheumatoid arthritis synovial fluid Recognition of a peptide antigen by heat shock-reactive γδ T lymphocytes Heat shock protein Hsp60-reactive γδ cells: a large, diversified T-lymphocyte subset with highly focused specificity Human T-cell recognition of Listeria monocytogenes: recognition of listeriolysin O by TcRαβ+ and TcRγδ+ T cells Human TCR-γ+/δ+, CD8+ T lymphocytes recognize tetanus toxoid in an MHC-restricted fashion Dual antigenic recognition by cloned human γδ T cells Cytotoxic T lymphocytes specific for self tumor immunoglobulin express T cell receptor δ chain Gamma delta T cell recognition of tumor Ig peptide Recognition of synthetic polyanionic ligands underlies spontaneous reactivity of Vγ1 γδTCRs CDR3 length in antigen-specific immune receptors Cells: T cells with B-cell-like recognition properties γδ T cells: first line of defense and beyond Restricted diversity of Vγ9-JP rearrangements in unstimulated human γ/δ T lymphocytes Evolution of the V, D, and J gene segments used in the primate T-cell receptor reveals a dichotomy of conservation and diversity Conservation of nonpeptide antigen recognition by Rhesus monkey Vγ2Vδ2 T cells Vγ9 and Vδ2 T cell antigen receptor genes and butyrophilin 3 (BTN3) emerged with placental mammals and are concomitantly preserved in selected species like alpaca (Vicugna pacos) Alpaca (Vicugna pacos), the first nonprimate species with a phosphoantigen-reactive Vγ9Vδ2 T cell subset Nonpeptide antigens, presentation mechanisms, and immunological memory of human Vγ2Vδ2 T cells: discriminating friend from foe through the recognition of prenyl pyrophosphate antigens Early innate responses to pathogens: pattern recognition by unconventional human T-cells Human T cell receptor γδ cells recognize endogenous mevalonate metabolites in tumor cells Alkylamines cause Vγ9Vδ2 T-cell activation and proliferation by inhibiting the mevalonate pathway The promise of γδ T cells and the γδ T cell receptor for cancer immunotherapy Human γδ TCR repertoires in health and disease Direct presentation of nonpeptide prenyl pryophosphate antigens to human gamma delta T cells Key implication of CD277/Butyrophilin-3 (BTN3A) in cellular stress sensing by a major human γ δ T cell subset The molecular basis for modulation of human Vγ9Vδ2 T cell responses by CD277/butyrophilin-3 (BTN3A)-specific antibodies Regulation of immunity by butyrophilins Butyrophilin 3A1 binds phosphorylated antigens and stimulates human γδ T cells The intracellular B30.2 domain of butyrophilin 3A1 binds phosphoantigens to mediate activation of human Vγ9Vδ2T Cells Sensor function for butyrophilin 3A1 in prenyl pyrophosphate stimulation of human Vγ2Vδ2 T cells The butyrophilin 3A1 intracellular domain undergoes a conformational change involving the juxtamembrane region Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation The juxtamembrane domain of butyrophilin BTN3A1 controls phosphoantigen-mediated activation of human Vγ9Vδ2 T cells Activation of human γδ T cells by cytosolic interactions of BTN3A1 with soluble phosphoantigens and the cytoskeletal adaptor periplakin RhoB mediates phosphoantigen recognition by Vγ9Vδ2 T cell receptor Heteromeric interactions regulate butyrophilin (BTN) and BTN-like molecules governing γδ T cell biology Vγ9Vδ2 TCR-activation by phosphorylated antigens requires butyrophilin 3 A1 (BTN3A1) and additional genes on human chromosome 6 Butyrophilin 2A1 is essential for phosphoantigen reactivity by gd T cells Butyrophilin-2A1 directly binds germline-encoded regions of the Vγ9Vδ2 TCR and is essential for phosphoantigen sensing Vγ2Vδ2 T cell receptor recognition of prenyl pyrophosphates is dependent on All CDRs Skint1, the prototype of a newly identified immunoglobulin superfamily gene cluster, positively selects epidermal γδ T cells Skint-1 is a highly specific, unique selecting component for epidermal T cells Skint-1 identifies a common molecular mechanism for the development of interferon-γ-secreting versus interleukin-17-secreting γδ T cells Positive selection of dendritic epidermal γδ T cell precursors in the fetal thymus determines expression of skin-homing receptors Selection of the cutaneous intraepithelial γδ+ T cell repertoire by a thymic stromal determinant Characterization of a putative receptor binding surface on skint-1, a critical determinant of dendritic epidermal t cell selection Epithelia use butyrophilin-like molecules to shape organ-specific γδ T cell compartments The γδTCR combines innate immunity with adaptive immunity by utilizing spatially distinct regions for agonist selection and antigen responsiveness Butyrophilin-like 3 directly binds a human Vγ4+ T cell receptor using a modality distinct from clonally-restricted antigen Ligand recognition by the γδ TCR and discrimination between homeostasis Structure of the superantigen Staphylococcal Enterotoxin B in complex with TCR and peptide-MHC demonstrates absence of TCR-peptide contacts Antigen recognition by gammadelta T cells Recognition of Listeria infection by germline elements of the Vγ1.1 Vδ6.3 TCR Activation of TCR Vδ1 + and Vδ1 − Vδ2 keywords: activation; antigen; binding; btn3a1; cells; human; ligand; mhc; molecules; receptor; recognition; specific; tcr; tcrs; vγ9vδ2; γδ tcr cache: cord-013590-pkm81fq1.txt plain text: cord-013590-pkm81fq1.txt item: #36 of 106 id: cord-016594-lj0us1dq author: Flower, Darren R. title: Identification of Candidate Vaccine Antigens In Silico date: 2012-09-28 words: 12575 flesch: 33 summary: A long, naturally presented immunodominant epitope from NY-ESO-1 tumor antigen: implications for cancer vaccine design Identification and characterization of pathogenicity and other genomic islands using base composition analyses A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands CpGcluster: a distance-based algorithm for CpG-island detection CpGIF: an algorithm for the identification of CpG islands Identifying CpG islands by different computational techniques CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes Evaluation of genomic island predictors using a comparative genomics approach IslandPath: aiding detection of genomic islands in prokaryotes Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models A computational approach for identifying pathogenicity islands in prokaryotic genomes Resolving the structural features of genomic islands: a machine learning approach Detection of genomic islands via segmental genome heterogeneity Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes IslandViewer: an integrated interface for computational identification and visualization of genomic islands Towards pathogenomics: a web-based resource for pathogenicity islands Identification and characterization of a novel family of pneumococcal proteins that are protective against sepsis Functional genomics of pathogenic bacteria SYFPEITHI: database for searching and Tcell epitope prediction SYFPEITHI: database for MHC ligands and peptide motifs HIV sequence databases MHCBN 4.0: a database of MHC/TAP binding peptides and T-cell epitopes MHCBN: a comprehensive database of MHC binding and non-binding peptides EPIMHC: a curated database of MHCbinding peptides for customized computational vaccinology AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data JenPep: a novel computational information resource for immunobiology and vaccinology JenPep: a database of quantitative functional peptide data for immunology The immune epitope database 2.0 AntigenDB: an immunoinformatics database of pathogen antigens VIOLIN: vaccine investigation and online information network Epitopic peptides with low similarity to the host proteome: towards biological therapies without side effects Peptimmunology: immunogenic peptides and sequence redundancy Primer: mechanisms of immunologic tolerance Recent advances in immune modulation Cutting edge: contributions of apoptosis and anergy to systemic T cell tolerance Discriminating antigen and non-antigen using proteome dissimilarity III: tumour and parasite antigens Discriminating antigen and non-antigen using proteome dissimilarity II: viral and fungal antigens Discriminating antigen and non-antigen using proteome dissimilarity: bacterial antigens Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Single proteins might have dual but related functions in intracellular and extracellular microenvironments Locating proteins in the cell using TargetP, SignalP and related tools Improved prediction of signal peptides: SignalP 3.0 A comprehensive assessment of N-terminal signal peptides prediction methods WoLF PSORT: protein localization predictor Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains SubLoc: a server/client suite for protein subcellular location based on SOAP Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins Advantages of combined transmembrane topology and signal peptide prediction-the Phobius web server Prediction of lipoprotein signal peptides in Gram-negative bacteria Prediction of twin-arginine signal peptides Validating subcellular localization prediction tools with mycobacterial proteins Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram-and gram+ compartments Multi-class subcellular location prediction for bacterial proteins Alpha helical trans-membrane proteins: enhanced prediction using a Bayesian approach Beta barrel trans-membrane proteins: enhanced prediction using a Bayesian approach A predictor of membrane class: discriminating alpha-helical and beta-barrel membrane proteins from non-membranous proteins TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences LIPPRED: a web server for accurate prediction of lipoprotein signal sequences and cleavage sites Combining algorithms to predict bacterial protein sub-cellular location: parallel versus concurrent implementations Predicting the subcellular localization of viral proteins within a mammalian host cell Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells Structure and sequence relationships in the lipocalins and related proteins Structural Relationship of Streptavidin to the Calycin Protein Superfamily Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition Adaptation of protein surfaces to subcellular location Hierarchical classification of G-protein-coupled receptors with data-driven selection of attributes and classifiers GPCRTree: online hierarchical classification of GPCR function Optimizing amino acid groupings for GPCR classification On the hierarchical classification of G protein-coupled receptors Proteomic applications of automated GPCR classification VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties DNA and peptide sequences and chemical processes multivariately modeled by principal component analysis and partial least-squares projections to latent structures Principal property-values for 6 nonnatural amino-acids and their application to a structure activity relationship for oxytocin peptide analogs Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates Proteochemometrics analysis of substrate interactions with dengue virus NS3 proteases Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions Improved approach for proteochemometrics modeling: application to organic compound-amine G protein-coupled receptor interactions Melanocortin receptors: ligands and proteochemometrics modeling Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands Peptide quantitative structureactivity-relationships, a multivariate approach Multivariate parametrization of 55 coded and non-coded amino-acids New chemical descriptors relevant for the design of biologically active peptides. Vaccines based on APCs and peptides are new but unproven strategies; most modern vaccine development relies instead on effective searches for vaccine antigens. keywords: analysis; antigens; approach; binding; candidate; cell; data; database; discovery; epitope; genome; genomic; host; immunogenicity; islands; methods; mhc; peptide; prediction; protein; sequence; system; vaccines; vaccinology cache: cord-016594-lj0us1dq.txt plain text: cord-016594-lj0us1dq.txt item: #37 of 106 id: cord-017296-jdp8kgg5 author: Deschler, Barbara title: Particular Treatment Procedures date: 2008 words: 7746 flesch: 32 summary: A sufficient PBSC yield is the prerequisite for high-dose chemotherapy with stem cell transplantation (PBSCT). Four different approaches can be distinguished: • Active specific immunotherapy • Active non-specific immunotherapy • Passive immunotherapy • Adoptive immunotherapy The T-cellular immune response is crucial to recognize and eliminate tumor cells. keywords: blood; bone; cancer; cells; chemotherapy; donor; gene; graft; marrow; patients; pbsc; phase; proteins; stem; studies; therapy; transfer; transfusion; transplantation; treatment; tumor cache: cord-017296-jdp8kgg5.txt plain text: cord-017296-jdp8kgg5.txt item: #38 of 106 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 cache: cord-017629-fuv157f1.txt plain text: cord-017629-fuv157f1.txt item: #39 of 106 id: cord-017819-85x0juiw author: Christe, Philippe title: Biological conservation and parasitism date: 2006 words: 6171 flesch: 34 summary: In contrast, widespread host species that live in high density are exposed to a wide range of parasite species that may affect drastically the population dynamics of these carnivores, suggesting that macroparasites may regulate them at least locally. Parasite species may also be subject to the Allee effects that influence the occurrence and the severity of epidemics as illustrated by patchy distributions of worms in hosts as a result of the necessity for female worms to find a mate in order to reproduce (Cornell et al. 2004 ). keywords: conservation; diversity; effects; et al; host; immune; mhc; parasites; pathogens; population; selection; species; stress cache: cord-017819-85x0juiw.txt plain text: cord-017819-85x0juiw.txt item: #40 of 106 id: cord-018034-gx5c9mk8 author: None title: Cell and Tissue Reactions date: 2006 words: 17149 flesch: 37 summary: Brain cells can also swell without a concomitant increase in brain volume if fluid shifts from an extracellular to an intracellular space. Moderate levels of ICAM-1 and very low levels of VCAM-1, two molecules responsible for the adhesive properties of granulocytes and of T-cells, are expressed by brain endothelial cells. keywords: antigen; apoptosis; astrocytes; bbb; blood; brain; cells; cerebral; cns; csf; damage; death; edema; endothelial; et al; expression; fig; herniation; hydrocephalus; icp; inflammation; injury; intracranial; ischemia; molecules; necrosis; neurons; pressure; swelling; system; tissue cache: cord-018034-gx5c9mk8.txt plain text: cord-018034-gx5c9mk8.txt item: #41 of 106 id: cord-021079-m6nbs2c0 author: Yong, Voon Wee title: Major histocompatibility complex molecules on glial cells date: 2004-11-23 words: 5293 flesch: 29 summary: The consequence of glial cell MHC expression for immune interactions in the CNS is discussed in the context of glial cell antigen presentation capacity and neural cell susceptibility to cell-mediated immune effector mechanisms. 7 Many studies have used frozen sections and often the morphology of cells was suboptimal, leading to possible misidentification of MHC immunoreactive cells . keywords: antigen; astrocytes; cells; class; expression; human; mhc; molecules; oligodendrocytes cache: cord-021079-m6nbs2c0.txt plain text: cord-021079-m6nbs2c0.txt item: #42 of 106 id: cord-021693-odfxkfu7 author: Lim, Dong-Gyun title: Molecular Mimicry in Multiple Sclerosis: Role of MHC-Altered Peptide Ligands (MAPL) date: 2007-05-09 words: 3887 flesch: 36 summary: Cross-linking leads to activation of T cells with particular V[3 families of TCR. The previous concept for the antigen specificity of T cells predicted that the presence of strict sequence homology between the microbial antigens and self-peptide was necessary to induce autoimmunity ( Fig. 1 , top A). keywords: cells; cross; mhc; mimicry; myelin; peptide cache: cord-021693-odfxkfu7.txt plain text: cord-021693-odfxkfu7.txt item: #43 of 106 id: cord-022142-d4yxgv83 author: David, Ayelet title: Polymer-Based DNA Delivery Systems for Cancer Immunotherapy date: 2016-05-28 words: 7791 flesch: 32 summary: immunotherapy Targeting tumor antigens to dendritic cells using particulate carriers Engineering dendritic cells to enhance cancer immunotherapy Combining immunotherapy and targeted therapies in cancer treatment Dendritic cell based PSMA immunotherapy for prostate cancer using a CD40-targeted adenovirus vector Immunobiology of dendritic cells Taking dendritic cells into medicine Presentation of tumour antigens by dendritic cells and challenges faced Intracellular events regulating cross-presentation Spinning molecular immunology into successful immunotherapy Towards a systems understanding of MHC class I and MHC class II antigen presentation Dendritic cell-based cancer gene therapy Multivalent glycopeptide dendrimers for the targeted delivery of antigens to dendritic cells Into the intracellular logistics of cross-presentation Cross-priming in health and disease A modular and combinatorial view of the antigen crosspresentation pathway in dendritic cells Regulation of antigen transport into the cytosol for crosspresentation by ubiquitination of the mannose receptor Cellular vaccine approaches Whole tumor antigen vaccines Improvement of different vaccine delivery systems for cancer therapy Third generation dendritic cell vaccines for tumor immunotherapy Dendritic-cell immunotherapy: from ex vivo loading to in vivo targeting Design and development of polymers for gene delivery RNA-based vaccines Mesenchymal stem cells: a promising targeteddelivery vehicle in cancer gene therapy Cationic polymer based gene delivery systems Biodegradable nanoparticles of mPEG-PLGA-PLL triblock copolymers as novel non-viral vectors for improving siRNA delivery and gene silencing Polymers for intracellular delivery of nucleic acids Synthesis of biodegradable multi-block copolymers of poly( L -lysine) and poly(ethylene glycol) as a non-viral gene carrier Novel vectors for gene delivery formed by self-assembly of DNA with poly( L -lysine) grafted with hydrophilic polymers Stabilization of poly-L -lysine/ DNA polyplexes for in vivo gene delivery to the liver Steric stabilization of poly-L -lysine/DNA complexes by the covalent attachment of semitelechelic poly Polymer-based gene delivery with low cytotoxicity by a unique balance of side-chain termini Role of DNA topology in uptake of polyplex molecules by dendritic cells Poly-L -lysine-coated nanoparticles: a potent delivery system to enhance DNA vaccine effi cacy Mannose-based molecular patterns on stealth microspheres for receptor-specifi c targeting of human antigen-presenting cells Revisit complexation between DNA and polyethylenimine-effect of length of free polycationic chains on gene transfection The proton sponge: a trick to enter cells the viruses did not exploit Polycation gene delivery systems: escape from endosomes to cytosol Different behavior of branched and linear polyethylenimine for gene delivery in vitro and in vivo Polyethylenimine-mediated gene delivery to the lung and therapeutic applications Biodegradable poly(ethylenimine) for plasmid DNA delivery Design of magnetic polyplexes taken up effi ciently by dendritic cell for enhanced DNA vaccine delivery Polyethylenimine-graft-poly(ethylene glycol) copolymers: infl uence of copolymer block structure on DNA complexation and biological activities as gene delivery system The decrease of PAMAM dendrimerinduced cytotoxicity by PEGylation via attenuation of oxidative stress PEGylation signifi cantly affects cellular uptake and intracellular traffi cking of non-viral gene delivery particles Recent developments in cancer vaccines Rapid monoclonal antibody generation via dendritic cell targeting in vivo Delivery of antigen to CD40 induces protective immune responses against tumors Since tumor cells are poor antigen-presenting cells, cross-presentation of tumor antigens by dendritic cells (DCs) is essential for the generation of tumor-specific cytotoxic T-lymphocyte responses. keywords: antigen; cells; chitosan; class; dcs; delivery; dendritic; dna; effi; gene; mhc; pei; presentation; targeting; transfection; tumor; vivo cache: cord-022142-d4yxgv83.txt plain text: cord-022142-d4yxgv83.txt item: #44 of 106 id: cord-022395-rk31pwoa author: Schuller-Levis, Georgia title: Central Nervous System: Viral Infection and Immune-Mediated Inflammation date: 2012-12-02 words: 8853 flesch: 31 summary: Vi ruses may be able to down regulate appropriate recognition molecules on the surface of immune cells. MHC antigens are expressed only at low levels or not at all on the majority of CNS cells (Hart and Fabre, 1981 ). keywords: antigens; brain; cells; class; cns; disease; eae; endothelial; et al; expression; factor; il-1; immune; infection; inflammation; inflammatory; response; system; virus; viruses cache: cord-022395-rk31pwoa.txt plain text: cord-022395-rk31pwoa.txt item: #45 of 106 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 cache: cord-022888-dnsdg04n.txt plain text: cord-022888-dnsdg04n.txt item: #46 of 106 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 cache: cord-023055-ntbvmssh.txt plain text: cord-023055-ntbvmssh.txt item: #47 of 106 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 cache: cord-023143-fcno330z.txt plain text: cord-023143-fcno330z.txt item: #48 of 106 id: cord-023724-5at0rhqk author: Cann, Alan J. title: Infection date: 2015-07-24 words: 14985 flesch: 44 summary: The former strategy relies on two approaches: public and personal hygiene, which perhaps plays the major role in preventing virus infection (e.g., provision of clean drinking water and disposal of sewage; good medical practice such as the sterilization of surgical instruments) and vaccination, which makes use of the immune system to combat virus infections. A common misconception is that virus infection inevitably results in disease. keywords: cell; dna; expression; gene; host; ifn; ifns; infection; mechanisms; plant; proteins; replication; resistance; response; result; rna; system; vaccines; virus; virus infection; virus replication; viruses cache: cord-023724-5at0rhqk.txt plain text: cord-023724-5at0rhqk.txt item: #49 of 106 id: cord-025523-6ttps1nx author: Barlas, Georgios title: Cross-Domain Authorship Attribution Using Pre-trained Language Models date: 2020-05-06 words: 3612 flesch: 51 summary: In this paper, we modify a successful authorship verification approach based on a multi-headed neural network language model and combine it with pre-trained language models. Recently, the use of pre-trained language models (e.g., BERT, ELMo, ULM-FiT, has been demonstrated to obtain significant gains in several text classification tasks including sentiment analysis, emotion classification, and topic classification [2, 7, 13, 14] . keywords: authorship; cross; genre; language; topic cache: cord-025523-6ttps1nx.txt plain text: cord-025523-6ttps1nx.txt item: #50 of 106 id: cord-028945-p3hhd5ed author: Şahar, Esra Atalay title: Development of a hexavalent recombinant protein vaccine adjuvanted with Montanide ISA 50 V and determination of its protective efficacy against acute toxoplasmosis date: 2020-07-10 words: 7386 flesch: 48 summary: Apart from these, multiplexing recombinant proteins induced strong and balanced Th1 and Th2 immune responses and improved protection against toxoplasmosis and thus showing the the importance of using multivalant recombinant protein vaccines in future vaccine development studies against ruminants, cats or humans. Recombinant protein vaccines are safe and efficient, and have a great potential for prevention or eradication of diseases. keywords: cell; epitopes; glycosylation; gondii; hexavalent; isa; mhc; mice; mixture; montanide; protein; re6; toxoplasmosis; vaccine cache: cord-028945-p3hhd5ed.txt plain text: cord-028945-p3hhd5ed.txt item: #51 of 106 id: cord-259669-fod4xkd7 author: Summerfield, Artur title: The porcine dendritic cell family date: 2008-06-06 words: 9388 flesch: 42 summary: Localization of distinct Peyer's patch dendritic cell subsets and their recruitment by chemokines macrophage inflammatory protein (MIP)-3alpha, MIP-3beta, and secondary lymphoid organ chemokine Myeloid C-type lectins in innate immunity Cooperation of Toll-like receptor signals in innate immune defence Signaling pathways downstream of patternrecognition receptors and their cross talk Dendritic cells interact directly with naive B lymphocytes to transfer antigen and initiate class switching in a primary T-dependent response Critical role of ITIM-bearing FcgammaR on DCs in the capture and presentation of native antigen to B cells Cell surface recycling of internalized antigen permits dendritic cell priming of B cells Immunobiology of dendritic cells Dendritic cells, BAFF, and APRIL: innate players in adaptive antibody responses Pathogen-induced private conversations between natural killer and dendritic cells Close encounters of different kinds: dendritic cells and NK cells take centre stage Two way communication between neutrophils and dendritic cells IPC: professional type 1 interferon-producing cells and plasmacytoid dendritic cell precursors Human natural interferon-alpha producing cells In vitro induction of mucosa-type dendritic cells by all-trans retinoic acid CCR9 is a homing receptor for plasmacytoid dendritic cells to the small intestine Dendritic cells enriched from swine thymus coexpress CD1, CD2 and major histocompatibility complex class II and actively stimulate alloreactive T lymphocytes Culture of dendritic cells from a nonlymphoid organ, the thyroid gland: evidence for TNFalphadependent phenotypic changes of thyroid-derived dendritic cells Circulating fibrocytes define a new leukocyte subpopulation that mediates tissue repair The peripheral blood fibrocyte is a potent antigen-presenting cell capable of priming naive T cells in situ Peripheral blood fibrocytes: differentiation pathway and migration to wound sites Responsiveness of fibrocytes to Toll-like receptor danger signals Regulated production of type I collagen and inflammatory cytokines by peripheral blood fibrocytes Interaction of Borrelia burgdorferi with peripheral blood fibrocytes, antigen-presenting cells with the potential for connective tissue targeting Dendritic cells in immunity and tolerance-do they display opposite functions? keywords: antigen; blood; cd172a; cdc; cells; dendritic; expression; ifn; immune; modc; pdc; porcine; responses; virus cache: cord-259669-fod4xkd7.txt plain text: cord-259669-fod4xkd7.txt item: #52 of 106 id: cord-260485-o5wpcxdp author: Schmidt-Küntzel, Anne title: Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation date: 2018-01-12 words: 7962 flesch: 34 summary: BMc Bioinf Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation The use of reference strand-mediated conformational analysis for the study of cheetah (Acinonyx jubatus) These analyses support the premise that cheetah populations expanded uniformly following a founder event 100,000 years ago. keywords: cat; chapter; cheetah; conservation; diversity; et al; mhc; mtdna; population; species; subspecies; variation cache: cord-260485-o5wpcxdp.txt plain text: cord-260485-o5wpcxdp.txt item: #53 of 106 id: cord-264401-9ogs55xr author: Giotis, Efstathios S. title: Inferring the Urban Transmission Potential of Bat Influenza Viruses date: 2020-06-03 words: 3444 flesch: 30 summary: A viruses A longitudinal study of the prevalence of Nipah virus in Pteropus lylei bats in Thailand: evidence for seasonal preference in disease transmission Herpesvirus interference with major histocompatibility complex class II-restricted T-cell activation Epithelial MHC class II expression and its role in antigen presentation in the gastrointestinal and respiratory tracts Mutations in the NA-like protein of bat influenza H18N11 virus enhance virus replication in mammalian cells, mice, and ferrets Characterization of uncultivable bat influenza virus using a replicative synthetic virus Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza The neuraminidase of bat influenza viruses is not a neuraminidase Entry of the bat influenza H17N10 virus into mammalian cells is enabled by the MHC class II HLA-DR receptor Ecology of zoonotic infectious diseases in bats: current knowledge and future directions The hemagglutinin of bat-associated influenza viruses is activated by TMPRSS2 for pH-dependent entry into bat but not human cells Antigenic determinants of human influenza viruses among the influenza viruses isolated from animals Global patterns of terrestrial vertebrate diversity and conservation MHC class II proteins and disease: a structural perspective An infectious bat-derived chimeric influenza virus harbouring the entry machinery of an influenza A virus MHC class II proteins mediate cross-species entry of bat influenza viruses Haemagglutination inhibition antibodies against influenza virus in bats Structural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza keywords: bat; bativs; bats; cell; et al; influenza; viruses cache: cord-264401-9ogs55xr.txt plain text: cord-264401-9ogs55xr.txt item: #54 of 106 id: cord-267266-0lybzcz7 author: Stockwin, Luke H title: Dendritic cells: Immunological sentinels with a central role in health and disease date: 2000-04-01 words: 8395 flesch: 32 summary: 6Ckine and macrophage inflammatory protein-3 beta are potent chemoattractants for in vitro and in vivo derived dendritic cells Adhesion of epidermal Langerhans cells to keratinocytes mediated by E-cadherin Langerhans cells require signals from both tumour necrosis factor alpha and interleukin 1 beta for migration Developmental regulation of MHC class II transport in mouse dendritic cells Efficient presentation of soluble antigen by cultured dendritic cells is maintained by granulocyte/macrophage colony-stimulating factor plus interleukin 4 and down regulated by tumour necrosis factor alpha A comparison of murine epidermal Langerhans cells with spleen dendritic cells A dendritic-cellderived C-C chemokine that preferentially attracts naive T cells Activated murine B lymphocytes and dendritic cells produce a novel CC chemokine which acts selectively on activated T cells Reciprocal control of T helper cell and dendritic cell differentiation Ligation of CD40 on dendritic cells triggers production of high levels of interleukin-12 and enhances T cell stimulatory capacity: T-T help via APC activation Dendritic cell secretion of IL-15 is induced by recombinant huCD40LT and augments the stimulation of antigen-specific cytolytic T cells Dendritic cells and resting B cells form clusters in vitro and in vivo: T cell independence, partial LFA-1 dependence, and regulation by cross-linking surface molecules Human interdigitating dendritic cells directly stimulate CD40-activated naive B cells Dendritic cells enhance the differentiation of naive B cells into plasma cells in vitro Towards a role of dendritic cells in the germinal center reaction: Triggering of B cell proliferation and isotype switching Critical role of IL-12 in dendritic cell-induced differentiation of naive B lymphocytes Human dendritic cells skew isotype switching of CD40-activated naive B cells towards IgA1 and IgA2 Maturation stages of mouse dendritic cells in growth factor-dependent long term cultures Cytolysis of human dendritic cells by autologous lymphokine-activated killer cells: Participation of both T cells and NK cells in the killing Dendritic cells efficiently induce protective antiviral immunity Antigen-pulsed epidermal Langerhans cells protect susceptible mice from infection with the intracellular parasite Leishmania major The role of skin dendritic cells in the initiation of human immunodeficiency virus infection Human aminopeptidase N is a receptor for human coronavirus 229E CD13 (human aminopeptidase N) mediates human cytomegalovirus infection Induction of maturation of human blood dendritic cell precursor by measles virus is associated with immunosuppression Dendritic cells route human immunodeficiency virus to lymph nodes after vaginal or intravenous administration to mice Virus replication begins in dendritic cells during the transmission of HIV-1 from mature dendritic cells to T cells Immature dendritic cells selectively replicate macrophage tropic (M-tropic) human immunodeficiency virus type 1, while mature cells efficiently transmit both M-and T-tropic virus to T cells Human immunodeficiency virus type 1 derived from cocultures of immature dendritic cells with autologous T cells carries T-cell-specific molecules on its surface and is highly infectious Measles suppresses cell-mediated immunity by interfering with the survival and functions of dendritic and T-cells Measles virus infects human dendritic cells and blocks their allostimulatory properties for CD4+ T-cells Viruses use stealth technology to escape from host immune system Viral interleukin 10 (IL-10), the human herpes virus 4 cellular IL-10 homologue, induces local anergy to allogenic and syngeneic tumours Low stimulatory capacity of lymphoid dendritic cells expressing hepatitis C virus genes CD40 ligand is not essential for induction of type 1 cytokine responses or protective immunity after primary or secondary infection with histoplasma capsulatum Interleukin-12 is capable of generating an antigen-specific Th1-type response in the presence of an ongoing infectiondriven Th2-type response Acquired resistance but not innate resistance to mycobacterium bovis bacillus Calmette-Guerin is compromised by interleukin-12 ablation Human dendritic cell (DC)-based anti-infective therapy: Dendritic cells and the control of immunity Response of naive antigenspecific CD4+ T cells in vitro: Characteristics and antigen presenting requirements B lymphocytes in vivo fail to prime naive T cells but can stimulate antigen-experienced T lymphocytes Dendritic cells are critical accessory cells for thymus dependent antibody responses in mouse and man The natural killer T (NKT) cell ligand alpha-galactosylceramide demonstrates its immunopotentiating effect by inducing interleukin (IL)-12 production by dendritic cells and IL-12 receptor expression on NKT cells MHC class II expression on dendritic cells is necessary and sufficient for survival of CD4+ T cells Targeted expression of MHC class II molecules demonstrates that dendritic cells can induce negative but no positive selection of thymocytes in vivo Human peripheral blood dendritic cell subsets. keywords: activation; antigen; cells; dendritic; disease; expression; factor; function; human; immunity; lymphocytes; maturation; mhc; molecules; presentation; tissue cache: cord-267266-0lybzcz7.txt plain text: cord-267266-0lybzcz7.txt item: #55 of 106 id: cord-269917-j0t8rjkc author: Odales, Josué title: Immunogenic properties of immunoglobulin superfamily members within complex biological networks date: 2020-10-11 words: 3445 flesch: 26 summary: Furthermore, experiments in which T cells interact with naïve or resting anti-idiotypic T cells demonstrated the induction of anergy or apoptosis in the idiotypic T cell [58] . The previous hypotheses agree with the need to generate T cell responses to help to achieve and regulate memory responses; furthermore, they propose mechanisms for affinity maturation based on idiotype-anti-idiotype interactions. keywords: antibody; cancer; cells; idiotype; idiotypic; immune; mhc; molecules cache: cord-269917-j0t8rjkc.txt plain text: cord-269917-j0t8rjkc.txt item: #56 of 106 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 cache: cord-273906-s7l0yxc0.txt plain text: cord-273906-s7l0yxc0.txt item: #57 of 106 id: cord-275433-58unu79x author: Levine, Beth title: Unveiling the roles of autophagy in innate and adaptive immunity date: 2007 words: 8413 flesch: 27 summary: Although there is perhaps less direct in vitro evidence for viruses, compared with bacteria, that autophagy functions in pathogen elimination, studies with viruses have provided the first in vivo evidence for a role of autophagy in immunity. The broad spectrum of autophagy functions is intricately linked to a wide range of health and disease states 3, 4 . keywords: antigens; autophagy; bacteria; cell; class; disease; immunity; membrane; mhc; pathogens; pathway; presentation; protein; role; viruses cache: cord-275433-58unu79x.txt plain text: cord-275433-58unu79x.txt item: #58 of 106 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 cache: cord-275608-joyan7ij.txt plain text: cord-275608-joyan7ij.txt item: #59 of 106 id: cord-277054-eq4obbte author: Kaur, Manpreet title: Rabies DNA vaccine: No impact of MHC Class I and Class II targeting sequences on immune response and protection against lethal challenge date: 2009-03-26 words: 6916 flesch: 40 summary: key: cord-277054-eq4obbte authors: Kaur, Manpreet; Rai, Anant; Bhatnagar, Rakesh title: Rabies DNA vaccine: No impact of MHC Class I and Class II targeting sequences on immune response and protection against lethal challenge date: 2009-03-26 journal: Vaccine DOI: 10.1016/j.vaccine.2009.01.128 sha: doc_id: 277054 cord_uid: eq4obbte Rabies is progressive fatal encephalitis. Rabies DNA vaccine has also been found to be highly efficient in large size mammals [21] . keywords: antibodies; antibody; antigen; cells; class; constructs; dna; glycoprotein; mhc; mice; pbs; rabies; response; vaccination; vaccine; virus cache: cord-277054-eq4obbte.txt plain text: cord-277054-eq4obbte.txt item: #60 of 106 id: cord-279498-ez3yq7xi author: Suzumura, Akio title: Immune Response in the Brain: Glial Response and Cytokine Production date: 2008-12-31 words: 5324 flesch: 42 summary: I. Induction of Ia antigen expression on astrocytes by T cells via immune interferon and its effect on antigen presentation MHC antigen expression on bulk isolated macrophage-microglia from newborn mouse brain: Induction of Ia antigen expression by gamma-interferon Immunohistochemical analysis of the rat central nervous system during experimental allergic encephalomyelitis, with special reference to Ia positive cells with dendritic morphology An immunoelectron microscopical study of class II major hsitocompatibility complex during chronic relapsing experimental allergic encephalomyelitis in Biozzi AB/H mice Microglial involvement in autoimmune inflammation of the central and peripheral nervous system Expression of Ia antigen on perivascular and microglial cells after sublethal and lethal motoneuron injury Induction of MHC class II antigen expression on murine microglia by interleukin-3 Rat microglial interleukin-3 In situ hybridization histochemistry localization of interleukin-3 mRNA in mouse brain Production of granulocyte/macrophage colony stimulating factor by cultured astrocytes Effects of colony stimulating factors on isolated microglia Morphological transformation of microglia in vitro Transforming growth factor beta suppresses activation and proliferation of microglia in vitro IL-4 induces proliferation and activation of microglia but suppressed their induction of class II major histocompatibility complex antigen expression Production of interleukin-10 by mouse glial cells in culture Macrophage-, and astrocyte-derived transforming growth factor beta as a mediator of central nervous system dysfunction in acquired immunodeficiency syndrome Differential expression of transforming growth factor beta1,2, and 3 by glioblastoma cells, astrocytes, and microglia Expression of cytokine receptors in cultured neuronal and glial cells Corona virus infection induces H-2 antigen expression on oligodendrocytes and astrocytes Viral particles induce Ia antigen expression on astrocytes Interleukin-1 of the central nervous system is produced by ameboid microglia On the cellular source and function of interleukin-6 produced in the central nervous system in viral diseases Production of tumor necrosis factor alpha by microglia and astrocytes in culture TNFa induces IL-6 production by astrocytes but not by microglia Production of interleukin-5 by mouse astrocytes and microglia in culture Production of interleukin-12 and the expression of its receptors by murine microglia IFNs are critical regulators of IL-1 receptor antagonist and IL-1 expression in human microglia Murine microglial cells produce and respond to interleukin-18 Production of interferon-g by microglia Production of IL-27 and IL-12 family cytokines by microglia and their subpopulations Cytokine network in the central nervous system and its roles in growth and differentiation of glial and neuronal cells Induction of functional IL-2 receptor in mouse microglia Proliferation of astroglia and oligodendroglia in response to human T cell-derived factors Cytokines, chemokines, and cytokine receptors in human microglia IL-12 production by central nervous system microglia is inhibited by astrocytes African trypanosomes activate human fetal brain cells to proliferation and IFN-g production IFN-a production by antigen presenting cells: Mechanisms emerge Astrocytes present myelin basic protein to encephalitogenic T-cell lines Expression of Ia molecules by astrocytes during acute experimental allergic encephalomyelitis in the Lewis rat Perivascular microglial cells of the CNS are bone marrow-derived and present antigen in vivo Antigen presentation and tumor cytotoxicity by interferon-gamma-treated microglial cells Immune regulation by brain cells in the central nervous system; microglia but not astrocytes present myelin basic protein to encephalitogenic T-cells under in vivo-mimicking conditions Normal adult ramified microglia separated from other central nervous system macrophages by flow cytometric sorting The costimulatory molecule B7 is expressed in human microglia in culture and multiple sclerosis acute lesions T-cell costimulatory molecules B71 (CD80) and B7-2 (CD86) are expressed in human microglia but not in astrocytes in culture Analysis of B7-1 and B7-2 costimulatory ligands in cultured mouse microglia: Upregulation by interferon-gamma and lipopolysaccharide and downregulation by interleukin-10, prostaglandin E2 and cyclic AMP-elevating agents Antigen-specific damage to brain vascular endothelial cells mediated by encephalitogenic and nonencephalitogenic CD4 T cell lines in vitro Antigen presentation by brain microvessel smooth muscle and endothelium Soluble tumor necrosis factor receptor inhibits interleukin 12 production by stimulated human adult microglial cells in vitro Cultures of astrocytes and microglia express interleukin 18 Caspase-1 expression in multiple sclerosis plaques and cultured glial cells CCR5(+) and CXCR3(+) Glial cells have also been shown to produce various cytokines and chemokines. keywords: antigen; astrocytes; cells; class; cytokines; expression; mhc; microglia; production; tnf cache: cord-279498-ez3yq7xi.txt plain text: cord-279498-ez3yq7xi.txt item: #61 of 106 id: cord-279924-09uwhxs9 author: Plaisted, Warren C. title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells date: 2014-01-01 words: 5588 flesch: 34 summary: Together, these findings suggest that T cells play a critical role in controlling replication of a neurotropic virus in NPCs, a finding which has important implications when considering immune modulation for NPC-based therapies for treatment of human neurologic diseases. Collectively, our findings argue that T cells are important for controlling viral replication within NPCs through both cytolytic activity and IFN-γ secretion. keywords: cells; expression; ifn; infection; jhmv; mhc; npcs; replication; virus cache: cord-279924-09uwhxs9.txt plain text: cord-279924-09uwhxs9.txt item: #62 of 106 id: cord-281691-3tl7f6tt author: Liu, Guangliang title: Construction and functional test of a chicken MHC-I (BF2*15)/peptide tetramer date: 2008-03-15 words: 4018 flesch: 48 summary: This method is notoriously subject to variability, which probably reflected the frequency of specific cells, their expansion potential in vitro, and the ability to lyse appropriate targets (Rehermann et al., 1996a,b) . The monomeric complex was tetramerized by binding to fluorescently labeled streptavidin to generate BF2*15/ peptide tetramer. keywords: antigen; bf2; bsp; cells; chb2; chicken; class; mhc; peptide; tetramer cache: cord-281691-3tl7f6tt.txt plain text: cord-281691-3tl7f6tt.txt item: #63 of 106 id: cord-283035-tpqf458q author: Thanthrige-Don, Niroshan title: Analyses of the spleen proteome of chickens infected with Marek's disease virus date: 2009-08-01 words: 7910 flesch: 38 summary: Arrows with accompanying spot numbers show successfully identified protein spots that were uniquely expressed (qualitative differences) in each group at corresponding time point. Comparison of total numbers of significantly differentially expressed protein spots in MDV-infected spleens at various sampling time points. keywords: cell; changes; chickens; disease; dpi; et al; expression; host; infection; marek; mdv; proteins; spleen; spots; study; time; virus cache: cord-283035-tpqf458q.txt plain text: cord-283035-tpqf458q.txt item: #64 of 106 id: cord-285091-2i2v5ecg author: Kopitar-Jerala, Nataša title: The Role of Cysteine Proteinases and their Inhibitors in the Host-Pathogen Cross Talk date: 2012-12-17 words: 6220 flesch: 39 summary: The translocation of pseudovirions bearing 20 kDa GP into cytoplasm was strongly inhibited by cathepsin B inhibitors, while the entry of pseudovirions bearing 19 kDa GP1 was not [123, 124] . Cysteine cathepsins were long known to be involved in protein degradation in lysosomes [22] . keywords: activation; activity; cathepsin; cells; class; cystatin; cysteine; host; human; inhibitors; macrophages; proteases; protein; receptor; virus cache: cord-285091-2i2v5ecg.txt plain text: cord-285091-2i2v5ecg.txt item: #65 of 106 id: cord-289606-hypqpqs0 author: Sigal, Luis J. title: Activation of CD8 T Lymphocytes during Viral Infections date: 2016-05-09 words: 3522 flesch: 39 summary: While the basic principles of antigen recognition by CD4 and CD8 T cells are similar, there are also major differences. This article focuses on the activation of CD8 T cells. keywords: antigen; cd8; cells; lymphocytes; mhc cache: cord-289606-hypqpqs0.txt plain text: cord-289606-hypqpqs0.txt item: #66 of 106 id: cord-291070-y0wf456f author: Zhang, Guang Lan title: PRED(BALB/c): a system for the prediction of peptide binding to H2(d) molecules, a haplotype of the BALB/c mouse date: 2005-07-01 words: 2674 flesch: 48 summary: Although the majority of H2 d class II binding peptides are 12-20 amino acids long, their binding cores are 9 amino acids long (22, 23) . In our previous work, an artificial neural network method and hidden Markov models were applied to the prediction of human leukocyte antigens (HLAs) binding peptides (24, 25) , where more training data were available. keywords: binding; class; molecules; peptides; prediction cache: cord-291070-y0wf456f.txt plain text: cord-291070-y0wf456f.txt item: #67 of 106 id: cord-292596-ulu5y140 author: Lee, Su Hae title: Characterization of changes in global gene expression in the hearts and kidneys of transgenic mice overexpressing human angiotensin-converting enzyme 2 date: 2020-07-29 words: 5980 flesch: 44 summary: Especially, it has been reported that ACE2 gene expression is upregulated in humans with heart failure [13] . A first step in understanding SARS pathogenesis Distribution of angiotensin-(1-7) and ACE2 in human placentas of normal and pathological pregnancies Age-and gender-related difference of ACE2 expression in rat lung Myocardial infarction increases ACE2 expression in rat and humans ACE2 gene expression is upregulated in the human failing heart Organ-specific distribution of ACE2 mRNA and correlating peptidase activity in rodents Characterization of renal angiotensin-converting enzyme 2 in diabetic nephropathy Glomerular localization and expression of angiotensin-converting enzyme 2 and angiotensinconverting enzyme: implications for albuminuria in diabetes Angiotensin metabolism in renal proximal tubules, urine, and serum of sheep: evidence for ACE2-dependent processing of angiotensin II ACE and ACE2: their role to balance the expression of angiotensin II and angiotensin Temporal-spatial expression of ANG-(1-7) and angiotensin-converting enzyme 2 in the kidney of normal and hypertensive pregnant rats keywords: angiotensin; dox; dtg; expression; genes; hace2; heart; kidney; mhc; mice; non; protein; rtta cache: cord-292596-ulu5y140.txt plain text: cord-292596-ulu5y140.txt item: #68 of 106 id: cord-296347-fanlvxqs author: Loureiro, Joana title: Antigen Presentation and the Ubiquitin‐Proteasome System in Host–Pathogen Interactions date: 2006-12-02 words: 29009 flesch: 29 summary: The knowledge that the TMD of US11 is essential for its function (Lilley et al., 2003) , led to the discovery of Derlins (Lilley and Ploegh, 2004) and of multiprotein complexes at the ER membrane that function in US11-mediated dislocation of HCs and US11-independent dislocation of a subset of ERAD substrates (Lilley and Ploegh, 2005a; Oda et al., 2006; Ye et al., 2005) . The US2 TMD, although dispensable for interaction with SPP, is also required for HC dislocation (Loureiro et al., 2006) . keywords: activation; activity; antigen; binding; cd4; cell; class; class ii; complex; complexes; control; cytomegalovirus; degradation; dislocation; domain; endoplasmic; et al; function; hcmv; host; human; ii mhc; immune; ligase; membrane; mhc; mhc class; molecules; nef; pathogen; pathway; peptide; presentation; proteasome; protein; receptor; recognition; response; reticulum; role; signal; signaling; spp; substrate; surface; system; t cells; type; ubiquitin; ubiquitination; us11; us2; virus cache: cord-296347-fanlvxqs.txt plain text: cord-296347-fanlvxqs.txt item: #69 of 106 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 cache: cord-298169-2133gahl.txt plain text: cord-298169-2133gahl.txt item: #70 of 106 id: cord-299786-wuve0tjz author: Anderson, Robert title: Manipulation of cell surface macromolecules by flaviviruses date: 2004-02-27 words: 13601 flesch: 19 summary: Interestingly, lymphocytes do not appear to undergo antibody-enhanced dengue virus infection (Brandt et al., 1979; Kurane et al., 1990) , even though B cells do have Fc receptors (Dijstelbloem et al., 2001 ; see Section IV,C). It has long been recognized that dengue virus passaged in various host cell types can give rise to virus variants with altered cell specificity (Brandt et al., 1979; Halstead et al., 1984a Halstead et keywords: adhesion; antibody; binding; blood; cells; dengue; dengue virus; disease; encephalitis; endothelial; et al; expression; fever; flaviviruses; halstead; human; immune; infection; mast; molecules; monocytes; platelets; protein; receptor; role; sulfate; surface; virus; virus infection cache: cord-299786-wuve0tjz.txt plain text: cord-299786-wuve0tjz.txt item: #71 of 106 id: cord-301293-jqy7lcbk author: Gupta, Vandana title: SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens date: 2006-03-30 words: 7679 flesch: 30 summary: The pronounced Th-2 and humoral response to N protein plus adjuvant are in contrast to the balanced IFN-γ and IL-4 responses and strong memory CTL responses to the LAMP-N chimera. N protein was purified from lysates of infected High5 cells using Ni-NTA agarose beads (Invitrogen), and the protein preparation was verified by Western blot analysis with mouse monoclonal Penta-His-antibody (Qiagen, GmBH) and anti-N (Imgenex) antibodies. keywords: antigen; cell; class; dna; et al; gst; ifn; lamp; mhc; mice; peptides; processing; protein; responses cache: cord-301293-jqy7lcbk.txt plain text: cord-301293-jqy7lcbk.txt item: #72 of 106 id: cord-303069-ss6g3jkg author: Jakhar, Renu title: An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2 date: 2020-05-26 words: 3387 flesch: 44 summary: The Allergenicity of predicted epitopes was analyzed by AllerTOP tool and the coverage was determined throughout the worlds. The Allergenicity of predicted epitopes was analyzed by AllerTOP Tool keywords: binding; cell; envelope; epitopes; mhc; prediction; protein; vaccine cache: cord-303069-ss6g3jkg.txt plain text: cord-303069-ss6g3jkg.txt item: #73 of 106 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 cache: cord-304635-z5vmhopa.txt plain text: cord-304635-z5vmhopa.txt item: #74 of 106 id: cord-306096-2yl07bdq author: OLDSTONE, M. B. A. title: Viruses and Autoimmune Diseases date: 2003-11-03 words: 3511 flesch: 36 summary: Furthermore, molecular mimicry occurred between human transaldolase expressed selectively in oligodendrocytes, and human T cell lymphotropic virus, human immunodeficiency virus type 1, gag proteins Overview: Infectious agents as etiologic triggers of autoimmune disease Molecular mimicry as a mechanism for the cause and as a probe uncovering etiologic agent(s) of autoimmune disease Virus induced autoimmunity Using transgenic mouse models to dissect the pathogenesis of virusinduced autoimmune disorders of the islets of Langerhans and the central nervous system Virus-induced autoimmune disease Virus infection triggers insulin-dependent diabetes mellitus in a transgenic model: role of anti-self (virus) immune response Ablation of tolerance and induction of diabetes by virus infection in viral antigen transgenic mice Infection breaks T-cell tolerance Sensitization to self antigens by in situ expression of interferon-g Co-expression of B7.1 and viral (self) transgenes in pancreatic bcells can break peripheral ignorance and lead to spontaneous autoimmune diabetes Induction of diabetes is influenced by the infectious virus and local expression of MHC class I and TNF-a Interferon-g is essential for destruction of b cells and development of insulin-dependent diabetes mellitus Coxsackie viruses and diabetes mellitus High frequency of diabetes mellitus in young adults with congenital rubella Molecular mimicry Virus-induced diabetes mellitus SV40 large T shares an antigenic determinant with a cellular protein of molecular weight 68,000 Molecular mimicry in virus infection: Cross-reaction of measles virus phosphoprotein or of herpes simplex virus protein with human intermediate filaments Infection with vaccinia favors the selection of hybridomas synthesizing auto-antibodies against intermediate filaments, among them one cross-reacting with the virus hemagglutinin Molecular mimicry: Frequency of reactivity of monoclonal antiviral antibodies with normal tissues Molecular mimicry and autoimmune disease Molecular mimicry in T-cell mediated autoimmunity: viral peptides activate human T-cell clones specific for myelin basic protein Myelin basic protein and human coronavirus 229E: Cross-reactive T cells in multiple sclerosis Oligodendrocyte-specific expression and autoantigenicity in transaldolase in multiple sclerosis Comparative analysis of antibody and cell-mediated autoimmunity to transaldolase and myelin basic protein in patients with multiple sclerosis T cell cross-reactivity between coxsackievirus and glutamate decarboxylase is associated with a murine diabetes susceptibility allele Cellular immunity to a determinant common to glutamate decarboxylase and coxsackie virus in insulin-dependent diabetes Structure of the human class I histocompatibility antigen, HLA-A2 The alphabeta T cell receptor structure at 2.5 Å and its orientation in the TCR-MHC complex Binding of viral antigens to major histocompatibility complex class I H-2D b molecules is controlled by dominant negative elements at peptide non-anchor residues: Implications for peptide selection and presentation Antigen analogs/MHC complexes as specific T cell receptor antagonists Essential flexibility in the T-cell recognition of antigen A single T cell receptor recognizes structurally distinct MHC/peptide complexes with high specificity Superantigens: mechanism of T-cell stimulation and role in immune responses Specific T cell recognition of minimally homologous peptides: evidence for multiple endogenous ligands Amino acid homology between the encephalitogenic site of myelin basic protein and virus: mechanism for autoimmunity Cardiac myosin induces myocarditis in genetically predisposed mice Autoantibodies to cardiac myosin in mouse cytomegalovirus myocarditis How virus induces a rapid or slow onset insulin-dependent diabetes mellitus in a transgenic model Expression of IL-4 in b cells of the islets of Langerhans aborts insulin dependent diabetes mellitus in a transgenic model Viral infection of transgenic mice expressing a viral protein in oligodendrocytes leads to chronic central nervous system autoimmune disease Thymic selection and adaptability of cytotoxic T lymphocyte responses in transgenic mice expressing a viral protein in the thymus Development of insulitis without diabetes in transgenic mice lacking perforin-dependent cytotoxicity Molecules involved in b cell destruction Induction of diabetes is influenced by the infectious virus and local expression of MHC class I and tumor necrosis factor-alpha Oral insulin treatment suppresses virus-induced antigen-specific destruction of b cells and prevents autoimmune diabetes in transgenic mice A specific MHC class I restricted 'blocking peptide' prevent activation of virus-induced CTL and the development of virusinduced autoimmune diabetes Expression of adenoviral E3 transgenes in b-cells prevents autoimmune diabetes A single amino acid change in the B-chain of insulin completely abrogates the efficacy of this compound to induce 'oral tolerance' and prevent autoimmune diabetes A single amino acid change in the B-chain of insulin completely abrogates the efficacy of this compound to induce 'oral tolerance' and prevent autoimmune diabetes Design of high-affinity major histocompatibility complex-specific antagonist peptides that inhibit cytotoxic T-lymphocyte activity: keywords: autoimmune; cells; diabetes; disease; iddm; mhc; molecular; virus cache: cord-306096-2yl07bdq.txt plain text: cord-306096-2yl07bdq.txt item: #75 of 106 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 cache: cord-306308-zjq6cscm.txt plain text: cord-306308-zjq6cscm.txt item: #76 of 106 id: cord-307445-r2os3kn9 author: Lu, Dan title: Peptide presentation by bat MHC class I provides new insight into the antiviral immunity of bats date: 2019-09-09 words: 8170 flesch: 55 summary: Sequences analyses, based on bat MHC I genes identified thus far, show that many of these bat MHC I molecules have a 3-or 5-amino acid (aa) insertion in the α1 domain compared with other mammals [20, 29] . However, the molecular basis for the peptide binding and presentation by bat MHC I remains unclear. keywords: asp; bat; bat mhc; bats; binding; fig; insertion; mhc; peptides; ptal; residues cache: cord-307445-r2os3kn9.txt plain text: cord-307445-r2os3kn9.txt item: #77 of 106 id: cord-308043-h0knm8y4 author: Hussey, Séamus title: Autophagy as an emerging dimension to adaptive and innate immunity date: 2009-08-31 words: 6956 flesch: 31 summary: A morphometric approach to the kinetics of intracellular degradation by autophagy Quantitative characterization of dense body, autophagic vacuole, and acid phosphatase-bearing particle populations during the early phases of glucagon-induced autophagy in rat liver 3-Methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes A unified nomenclature for yeast autophagy-related genes Cis1/Atg31 is required for autophagosome formation in Saccharomyces cerevisiae Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae ATG genes involved in nonselective autophagy are conserved from yeast to man, but the selective Cvt and pexophagy pathways also require organism-specific genes Toward unraveling membrane biogenesis in mammalian autophagy Ultrastructural characterization of the delimiting membranes of isolated autophagosomes and amphisomes by freeze-fracture electron microscopy Studies on the mechanisms of autophagy: formation of the autophagic vacuole Autophagy: a forty-year search for a missing membrane source Studies on induced cellular autophagy. Other essential groups of autophagy proteins participate in isolation membrane formation. keywords: activation; autophagosome; autophagy; cells; class; complex; degradation; formation; immune; kinase; lc3; membrane; mhc; mtor; protein; role cache: cord-308043-h0knm8y4.txt plain text: cord-308043-h0knm8y4.txt item: #78 of 106 id: cord-310194-f5jtufja author: Benedictus, Lindert title: Bovine Neonatal Pancytopenia is a heritable trait of the dam rather than the calf and correlates with the magnitude of vaccine induced maternal alloantibodies not the MHC haplotype date: 2014-12-17 words: 8625 flesch: 52 summary: The difference in protein sequence between the extracellular parts of the MDBK and dam MHC class I alleles was 13.6% (0.35%) for vaccinated non-BNP dams and 12.9% (0.40%) for BNP dams, with a P-value of 0.266 this was not significantly different between both groups (Additional file 4). Alloantibodies were detected in both vaccinated BNP and non-BNP dams and we found no differences in alloantibody characteristics between these groups, but alloantibody levels were significantly higher in BNP dams. keywords: alloantibody; bnp; bnp dams; calf; calves; class; mdbk; mhc; mhc class; non; pregsure ©; vaccinated; © bvd cache: cord-310194-f5jtufja.txt plain text: cord-310194-f5jtufja.txt item: #79 of 106 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 cache: cord-310252-0cdqhrcw.txt plain text: cord-310252-0cdqhrcw.txt item: #80 of 106 id: cord-310395-ae2x2wpg author: Vieira, G. F. title: Immunodominant viral peptides as determinants of cross-reactivity in the immune system – Can we develop wide spectrum viral vaccines? date: 2005-12-31 words: 4469 flesch: 37 summary: As previously mentioned, the number of MHC-pep complexes that could be generated exceeds that of T cells in the repertoire of an individual. Human T cell clones were generated against two autoantigens which are frequent targets of autoantibodies and T cells in the same lupus patient. keywords: amino; cells; cross; peptides; reactivity; tcr; virus cache: cord-310395-ae2x2wpg.txt plain text: cord-310395-ae2x2wpg.txt item: #81 of 106 id: cord-310563-71940dh7 author: Kumar, Ashutosh title: A multiepitopic theoretical fusion construct based on in-silico epitope screening of known vaccine candidates for protection against wide range of enterobacterial pathogens date: 2019-02-12 words: 3571 flesch: 44 summary: Mr. Ashutosh Kumar was granted financial support in the form of Senior Research Fellowship from Indian Council of Medical Computer-aided biotechnology: from immuno-informatics to reverse vaccinology Epitope-based immunoinformatics and molecular docking studies of nucleocapsid protein and ovarian tumor domain of Crimean-Congo hemorrhagic fever virus Sequence-based in silico analysis of well studied hepatitis C virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds Structural analysis and epitope prediction of HCV E1 protein isolated in Pakistan: an in-silico approach Epitope-based vaccine target screening against highly pathogenic MERS-CoV: an in silico approach applied to emerging infectious diseases Enhancing in silico protein-based vaccine discovery for eukaryotic pathogens using predicted peptide-MHC binding and peptide conservation scores Identification of a universal Group B streptococcus vaccine by multiple genome screen In silico analysis of Acinetobacter baumannii outer membrane protein BamA as a potential immunogen In-silico analysis of Burkholderia pseudomallei proteome to predict potential vaccine candidate proteins A multiepitope subunit vaccine conveys protection against extraintestinal pathogenic Escherichia coli in mice The pesticin receptor of Yersinia enterocolitica: a novel virulence factor with dual function Reduced synthesis of the Ybt siderophore or production of aberrant Ybt-like molecules activates transcription of yersiniabactin genes in Yersinia pestis Immunization with the yersiniabactin receptor, FyuA, protects against pyelonephritis in a murine model of urinary tract infection The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5 Flagellin, a novel mediator of Salmonella-induced epithelial activation and systemic inflammation: IκBα degradation, induction of nitric oxide synthase, induction of proinflammatory mediators, and cardiovascular dysfunction Role of flagellin in the pathogenesis of shock and acute respiratory distress syndrome: therapeutic opportunities Humoral immune response to flagellin requires T cells and activation of innate immunity Stenotrophomonas maltophilia flagellin induces a compartmentalized innate immune response in mouse lung Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide The protein data bank CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site Protein secondary structure prediction based on position-specific scoring matrices Comparative protein modelling by satisfaction of spatial restraints MolProbity: all-atom structure validation for macromolecular crystallography Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking None to declare. Protein sequences of Yersiniabactin receptor of Escherichia coli UMN026 and Flagellin of Stenotrophomonas maltophilia were analyzed for the presence of linear epitopes using Bepipred portal of IEDB server. keywords: binding; class; epitopes; flagellin; mhc; peptides; protein; region cache: cord-310563-71940dh7.txt plain text: cord-310563-71940dh7.txt item: #82 of 106 id: cord-313138-y485ev30 author: Magor, Katharine E. title: Defense genes missing from the flight division date: 2013-04-24 words: 10647 flesch: 40 summary: In comparison with mammals, birds have partial repertoires of pattern recognition receptors including TLR receptors (Boyd et al., 2007; Brownlie and Allan, 2011; Cormican et al., 2009 ) and RIG-like receptors (Barber et al., 2010; Karpala et al., 2012) . We demonstrated that ducks have a functional RIG-I (Barber et al., 2010) . keywords: avian; birds; cells; chicken; class; ducks; et al; family; genes; human; igd; igy; influenza; interferon; mhc; receptor; response; rig; rna; tapasin; tlr8; viral; virus cache: cord-313138-y485ev30.txt plain text: cord-313138-y485ev30.txt item: #83 of 106 id: cord-319761-bu5pzbnv author: Miller, Craig S. title: Pleiotropic mechanisms of virus survival and persistence date: 2005-07-16 words: 5660 flesch: 29 summary: The origins of virology Further studies on the proliferation in vitro of single isolated tissue cells The infection of cells in tissue culture with Rous sarcoma virus The structure of DNA A plaque assay for foot-and-mouth disease virus and kinetics of virus reproduction Exotic emerging viral diseases: progress and challenges Persistent toll-like receptor signals are required for reversal of regulatory T cellemediated CD8 tolerance The many mechanisms of viral membrane fusion proteins Proteinaseactivated receptors: novel mechanisms of signaling by serine proteases Inflammatory caspases: linking an intracellular innate immune system to autoinflammatory diseases Interleukin-18 Newly identified pair of proteasomal subunits regulated reciprocally by interferon gamma Apoptosis: an innate immune response to virus infection Viruses and apoptosis Life, death, and the pursuit of apoptosis Regulation of p53-dependent apoptosis, transcriptional repression, and cell transformation by phosphorylation of the 55-kilodalton E1B protein of human adenovirus type 5 Adenovirus-mediated gene expression in vivo is enhanced by the antiapoptotic Bcl-2 gene Inhibition of DNA-dependent transcription by the leader RNA of vesicular stomatitis virus: role of specific nucleotide sequences and cell protein binding The IAP proteins: caspase inhibitors and beyond Prevention of vertebrate neuronal death by the crmA gene Neutralization of Smac/Diablo by inhibitors of apoptosis (IAPs). As a result, greater knowledge of virus replication, viral and cellular receptors, and immunologic interactions was achieved. keywords: apoptosis; cell; gene; host; human; ifn; infection; interferon; mhc; proteins; replication; response; virus; viruses cache: cord-319761-bu5pzbnv.txt plain text: cord-319761-bu5pzbnv.txt item: #84 of 106 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 cache: cord-319993-er3sm4u8.txt plain text: cord-319993-er3sm4u8.txt item: #85 of 106 id: cord-322575-3goj00ej author: Karl, Julie A. title: Major Histocompatibility Complex Class I Haplotype Diversity in Chinese Rhesus Macaques date: 2013-07-01 words: 4455 flesch: 37 summary: I A region in rhesus macaques: extensive haplotype diversity at the population level as revealed by microsatellites Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque Screening and confirmatory testing of MHC class I alleles in pigtailed macaques Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques An optimized SIV DNA vaccine can serve as a boost for Ad5 and provide partial protection from a high-dose SIVmac251 challenge Identification of MHC class I sequences in Chinese-origin rhesus macaques Mitochondrial DNA of the Mauritian macaques (Macaca fascicularis): an example of the founder effect Preliminary observations of MHC class I A region polymorphism in three populations of Chinese-origin rhesus macaques Characterization of peripheral blood T lymphocyte subsets in Chinese rhesus macaques with repeated or long-term infection with Plasmodium cynomolgi Effect of combination antiretroviral therapy on Chinese rhesus macaques of SIV infection Epithelial cells lining salivary gland ducts are early target cells of severe acute respiratory syndrome coronavirus infection in the upper respiratory tracts of rhesus macaques Mamu-B genes and their allelic repertoires in different populations of Chinese-origin rhesus macaques Identification of 17 novel major histocompatibility complex-A alleles in a population of Chinese-origin rhesus macaques Characterization of the peptide-binding specificity of Mamu-BÃ17 and identification of Mamu-BÃ17-restricted epitopes derived from simian immunodeficiency virus proteins Efficient mucosal transmissibility but limited pathogenicity of R5 SHIVSF162P3N in Chinese origin rhesus macaques Diversity of MHC class I genes in Burmese-origin rhesus macaques MHC class This unexpected conservation of Indian rhesus macaque MHC class I haplotypes in the Chinese rhesus macaque population suggests that immunologic insights originally gleaned from studies using Indian rhesus macaques may be more applicable to Chinese rhesus macaques than previously appreciated and may provide an opportunity for studies of CD8(+) T-cell responses between populations. keywords: chinese; class; haplotypes; indian; macaques; mamu; mhc; rhesus cache: cord-322575-3goj00ej.txt plain text: cord-322575-3goj00ej.txt item: #86 of 106 id: cord-329036-4bf8eiix author: None title: Coronavirus induction of class I major histocompatibility complex expression in murine astrocytes is virus strain specific date: 1994-09-01 words: 6958 flesch: 37 summary: These data also suggest that class I expression was induced directly by virus infection, and not by the secretion of a soluble substance into the medium by infected astrocytes. Since class I molecules play a key role in the interaction between infected target cells and CD8 + cytotoxic T cells (CTL; 35, 36) , any change in their expression after virus infection has potential implications for the outcome of the infection. keywords: a59; activity; astrocytes; cells; class; expression; hepatitis; inducing; infection; jhmv; mhv; mouse; strains; virus cache: cord-329036-4bf8eiix.txt plain text: cord-329036-4bf8eiix.txt item: #87 of 106 id: cord-331555-yqhzyqs3 author: Umemoto, Eric Y. title: Rapid changes in shape and number of MHC class II expressing cells in rat airways after Mycoplasma pulmonis infection date: 2003-03-04 words: 4342 flesch: 40 summary: We conclude that M. pulmonis infection creates a potent immunologic stimulus that augments and transforms the OX6-immunoreactive cell population in the airways by changing the functional state of airway dendritic cells, initiating an influx of MHC class II expressing cells, and activating expression of MHC class II molecules by airway epithelial cells. Such stimuli can also evoke transient expression of MHC class II molecules by airway epithelial cells [8] [9] [10] . keywords: cells; class; infection; mhc; mucosa; ox6; pulmonis; rats cache: cord-331555-yqhzyqs3.txt plain text: cord-331555-yqhzyqs3.txt item: #88 of 106 id: cord-333309-21czobqy author: Byun, Hyewon title: ERAD and how viruses exploit it date: 2014-07-03 words: 11777 flesch: 33 summary: The cytosolic domain of MHC-I is required for US11mediated ERAD targeting (Story et al., 1999; Barel et al., 2003) , and deletion of the C-terminal valine of MHC-I reduced interaction with Derlin-1 (Cho et al., 2013a) . Cho et al. speculated that US11 recognizes MHC-I through its cytosolic domain and transfers it to Derlin-1, which then interacts with the p97 ATPase for membrane dislocation (Cho et al., 2013a ; Figure 2B ). keywords: atpase; cd4; cell; complex; components; cytosolic; degradation; endoplasmic; erad; et al; figure; ligase; membrane; mhc; p97; protein; rem; replication; reticulum; retrotranslocation; substrates; transmembrane; ubiquitin; virus; yeast cache: cord-333309-21czobqy.txt plain text: cord-333309-21czobqy.txt item: #89 of 106 id: cord-334592-54dofkxh author: Levine, Beth title: Autophagy in immunity and inflammation date: 2011-01-20 words: 10295 flesch: 21 summary: Autophagy proteins function in adaptive immunity, including in the development and homeostasis of the immune system and in antigen presentation (Table 1 and Fig. 3) . Autophagy proteins function in both the activation and inactivation of innate immune signalling 4 . keywords: atg16l1; autophagosome; autophagy; cells; disease; function; immune; immunity; infection; inflammation; inflammatory; intracellular; membrane; pathway; presentation; proteins; role; signalling; viral; virus cache: cord-334592-54dofkxh.txt plain text: cord-334592-54dofkxh.txt item: #90 of 106 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 cache: cord-334603-yt2pmxi3.txt plain text: cord-334603-yt2pmxi3.txt item: #91 of 106 id: cord-335342-u0ys2xcm author: Zhang, Qian‐Jin title: TAP expression reduces IL‐10 expressing tumor infiltrating lymphocytes and restores immunosurveillance against melanoma date: 2007-02-02 words: 5353 flesch: 46 summary: The expression of IL-10, a Th2 cytokine capable of inhibiting cytotoxic T-cell responses, was measured in T lymphocytes infiltrating B16F10 cells tumors treated with VV-rTAP1, VV-PJS-5 or PBS. [1] [2] [3] However, cases of spontaneous remission and reoccurrence of the disease many years after remission or resection, and correlation of remission with immune cell infiltrates all suggest that there is an immune surveillance process that could be leveraged to develop treatments for late stage disease. keywords: antigen; b16; b16f10; cells; class; expression; melanoma; mhc; mouse; rtap1; surface; tumor cache: cord-335342-u0ys2xcm.txt plain text: cord-335342-u0ys2xcm.txt item: #92 of 106 id: cord-336343-qbcb9qi3 author: Agarwal, Ajay title: in-silica Analysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA date: 2020-06-16 words: 2333 flesch: 53 summary: AllerTOP v2 (https://www.ddg-pharmfac.net/AllerTOP/) was used for determining the allergenicity of selected epitopes. For MHC Class-I T-cell epitope prediction for ORF1ab leader proteins, NetMHCpan EL 4.0 method was used. keywords: analysis; cell; class; epitopes; mhc; proteins cache: cord-336343-qbcb9qi3.txt plain text: cord-336343-qbcb9qi3.txt item: #93 of 106 id: cord-339091-3xk2w0d2 author: Flower, Darren R title: Computer aided selection of candidate vaccine antigens date: 2010-11-03 words: 10671 flesch: 37 summary: However, rather than look at nucleic acid sequences, or at protein sequences directly, a new approach, based upon alignment-free techniques, has been developed which shows significant potential; we examine this next. In attempting to overcome the limitations imposed by alignment-dependent sequence similarity methods, we have implemented a novel alignment-independent method for antigen identification based on auto cross covariance (ACC) transformation of protein sequences into uniform equal-length vectors. keywords: antigens; approach; binding; cell; database; epitopes; host; identification; immunogenicity; location; methods; mhc; peptides; prediction; properties; protein; sequence; similarity; system; vaccines cache: cord-339091-3xk2w0d2.txt plain text: cord-339091-3xk2w0d2.txt item: #94 of 106 id: cord-340781-z348xbn0 author: Namvar, Ali title: In silico/In vivo analysis of high-risk papillomavirus L1 and L2 conserved sequences for development of cross-subtype prophylactic vaccine date: 2019-10-23 words: 6672 flesch: 48 summary: The red blood cell-depleted pooled splenocytes (2 × 10 6 cells/ml) were cultured in 48-well plates for 72 h in the presence of 5 μg/mL of L1 + L2 peptides, RPMI 5% as negative control and 5 μg/mL of concanavalin A (ConA) as positive control in complete RPMI culture medium. The level of Granzyme B in group receiving L1 DNA construct was similar to that in group receiving L2 DNA construct (p > 0.05). keywords: analysis; cell; constructs; dna; epitope; hpv; mhc; peptide; prediction; protein; type; vaccine cache: cord-340781-z348xbn0.txt plain text: cord-340781-z348xbn0.txt item: #95 of 106 id: cord-344105-9bw9rm6e author: Teraguchi, Shunsuke title: Methods for sequence and structural analysis of B and T cell receptor repertoires date: 2020-07-17 words: 6933 flesch: 41 summary: In this review, after briefly reviewing recent technologies for repertoire sequencing, we explore tools for interpreting BCR and TCR sequences in terms of their structures and targeted antigens. The ability to predict epitope(s) from TCR sequence and MHC allele would be highly valuable in elucidating disease etiology, monitoring the immune system, developing diagnostic assays and designing vaccines. keywords: analysis; antibody; antigen; bcr; cell; docking; epitope; methods; modeling; prediction; protein; receptor; repertoire; sequence; sequencing; tcr; tcrs cache: cord-344105-9bw9rm6e.txt plain text: cord-344105-9bw9rm6e.txt item: #96 of 106 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 cache: cord-346032-188gnf8j.txt plain text: cord-346032-188gnf8j.txt item: #97 of 106 id: cord-347039-eap592i7 author: Lee, Seung-Hwan title: Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date: 2003-08-31 words: 6191 flesch: 32 summary: To date more than 30 mouse loci (Table 1 ) and many fewer human genes ( Table 2 ) have been associated with the outcome of virus infection [1, 2] . In this review we illustrate the contribution of mouse genetics to our understanding of mechanisms of host resistance to virus infection. keywords: cells; class; gene; host; human; infection; mhc; mice; mouse; receptor; resistance; strains; susceptibility; virus cache: cord-347039-eap592i7.txt plain text: cord-347039-eap592i7.txt item: #98 of 106 id: cord-347298-7kqrl3rv author: Hedger, M.P. title: Immunology of the Testis and Male Reproductive Tract date: 2010-07-12 words: 21190 flesch: 40 summary: Tung et al. 1981) . In many seasonally breeding species, annual regression of the bloodtestis barrier occurs without inducing overt inflammation or autoimmunity (Pelletier 1986; Tung et al. 1981) . keywords: activation; activin; activity; cells; cytokines; epithelium; et al; expression; function; germ; ifn; il1; immune; immunity; inflammation; leydig; macrophages; male; molecules; production; proteins; rat; receptor; responses; role; sertoli; sertoli cells; studies; system; t cells; testicular; testis; tnf; tract; type cache: cord-347298-7kqrl3rv.txt plain text: cord-347298-7kqrl3rv.txt item: #99 of 106 id: cord-349225-504kr50e author: Alcami, Antonio title: Viral mechanisms of immune evasion date: 2000-09-01 words: 3615 flesch: 35 summary: The basic concepts of virus immune evasion will be discussed, with some examples to illustrate particular points; however, space constraints have not allowed a comprehensive review of all immune-evasion strategies. key: cord-349225-504kr50e authors: Alcami, Antonio; Koszinowski, Ulrich H. title: Viral mechanisms of immune evasion date: 2000-09-01 journal: Mol Med Today DOI: 10.1016/s1357-4310(00)01775-5 sha: doc_id: 349225 cord_uid: 504kr50e During the millions of years they have coexisted with their hosts, viruses have learned how to manipulate host immune control mechanisms. keywords: cell; class; functions; genes; host; mhc; proteins; receptors; virus; viruses cache: cord-349225-504kr50e.txt plain text: cord-349225-504kr50e.txt item: #100 of 106 id: cord-350083-kldu8q8x author: Oany, Arafat Rahman title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 words: 5025 flesch: 41 summary: Though at present, most of the vaccines are based on B cell immunity; vaccines based on T cell epitope have been encouraged recently. Thus, vaccination based on T cell epitope is a unique approach to obtain strong immune response against infectious agents, such as, viruses (Klein et al. 2005) . keywords: analysis; cell; ebola; epitope; et al; mhc; prediction; protein; rna; sequence; vaccine; virus cache: cord-350083-kldu8q8x.txt plain text: cord-350083-kldu8q8x.txt item: #101 of 106 id: cord-350583-0t1kly3i author: Salmier, Arielle title: Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species date: 2016-10-26 words: 8926 flesch: 43 summary: The key hypothesis of this study was that composition and distribution of MHC DRB alleles were specific to the environments (forests vs. disturbed areas), rather than randomly distributed in space. Observation of trans-species polymorphism within bat families (e.g., Phyllostomidae) strengthens the scenario of independent modes of evolution of MHC DRB alleles, allowing balancing selection to retain substantial allelic lineages before speciation events [95, 96] . keywords: alleles; bats; class; diversity; drb; file; gene; mhc; molossus; pathogen; perspicillata; rotundus; selection; sequences; sites; species; table cache: cord-350583-0t1kly3i.txt plain text: cord-350583-0t1kly3i.txt item: #102 of 106 id: cord-350772-fp5d9if0 author: Malone, Karen E. title: Induction of class I antigen processing components in oligodendroglia and microglia during viral encephalomyelitis date: 2008-01-18 words: 6043 flesch: 42 summary: By contrast, microglia only moderately upregulated mRNAs encoding antigen presentation machinery, yet expressed MHC Class To assess basal transcript levels of genes required for MHC Class I peptide presentation, oligodendroglia and microglia were FACS purified from spinal cords of na€ ıve mice. keywords: antigen; cells; class; et al; expression; ifng; levels; mhc; mice; microglia; oligodendroglia; presentation cache: cord-350772-fp5d9if0.txt plain text: cord-350772-fp5d9if0.txt item: #103 of 106 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 cache: cord-352150-ey9kc7zj.txt plain text: cord-352150-ey9kc7zj.txt item: #104 of 106 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 cache: cord-353877-wzndpcq3.txt plain text: cord-353877-wzndpcq3.txt item: #105 of 106 id: cord-354030-8tfg881h author: Dong, Rong title: Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date: 2020-07-28 words: 7986 flesch: 46 summary: The pdb file of vaccine protein and receptor complex (TLR3, MHC-I, and MHC-II) were used to start the molecular dynamic (MD) simulations. The sequence homology of final vaccine protein to human protein sequence shown that there were no significant alignments ( Figure S4 ). keywords: amino; binding; cell; cell epitopes; complex; cov-2; epitopes; figure; immunoinformatics; mhc; model; prediction; protein; sars; sequence; server; structure; table; vaccine; virus cache: cord-354030-8tfg881h.txt plain text: cord-354030-8tfg881h.txt item: #106 of 106 id: cord-355075-ieb35upi author: Papenfuss, Anthony T title: The immune gene repertoire of an important viral reservoir, the Australian black flying fox date: 2012-06-20 words: 8959 flesch: 48 summary: The GO classification demonstrates that a diverse range of genes were identified in each of our two datasets providing a broad survey of bat genes. We have also begun to identify some of the genes involved in immune responses in this species and carry out functional studies in bat cells keywords: alecto; antiviral; bat; bats; cells; class; contigs; datasets; genes; immune; mammals; mhc; protein; receptors; sequences; species; thymus; transcriptome; transcripts; viruses cache: cord-355075-ieb35upi.txt plain text: cord-355075-ieb35upi.txt