Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 106 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 14669 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 47 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 105 MHC 25 HLA 23 cell 14 IFN 12 protein 10 CD8 9 dna 8 TCR 7 epitope 7 CD4 6 virus 6 SARS 6 RNA 6 Fig 6 CNS 5 vaccine 5 mouse 4 response 4 infection 4 antigen 4 TNF 4 CTL 3 patient 3 gene 3 class 3 autophagy 3 University 3 HIV 3 Ebola 3 DRB 3 Class 2 viral 2 transplantation 2 sequence 2 result 2 prediction 2 immune 2 expression 2 TLR4 2 SPP 2 JHMV 2 IL-6 2 IL-2 2 IEDB 2 HCV 2 EBOV 2 EAE 2 DRB1 2 CMV 2 BCR Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 16927 cell 5034 protein 4190 t 4018 virus 3909 antigen 3828 response 3774 peptide 3413 class 3240 mouse 3107 epitope 2972 % 2930 expression 2520 infection 2455 gene 2156 vaccine 2079 patient 2076 study 2043 molecule 1955 receptor 1812 disease 1757 antibody 1750 sequence 1695 level 1640 result 1600 b 1561 role 1520 analysis 1360 type 1328 function 1310 system 1303 activation 1240 effect 1176 method 1160 cytokine 1155 group 1125 lymphocyte 1114 model 1104 factor 1070 number 1070 complex 1068 mechanism 1042 allele 1018 datum 1011 activity 1003 population 958 control 956 surface 950 pathway 934 production 908 presentation Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 4679 MHC 4074 al 3490 T 3410 et 2948 . 2152 HLA 1596 II 1319 CD4 1290 IFN 1227 CD8 996 TCR 748 CTL 710 DC 630 Fig 569 I 562 B 531 RNA 528 C 502 TNF 473 CNS 446 ER 428 HIV 401 SARS 391 A 344 N 302 NK 299 DNA 293 g 291 t 291 Table 271 DR 266 PCR 259 Class 256 HIV-1 252 University 246 IL-4 232 M. 225 M 223 K 222 y 217 BALB 216 m 215 • 209 CMV 205 - 199 IL-2 199 IL-10 197 mRNA 197 MS 195 Treg Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 3704 we 2928 i 1803 it 807 they 234 them 95 us 65 itself 57 themselves 35 one 30 he 20 you 8 she 4 me 3 ourselves 3 mrnas 3 i- 2 u 2 s 2 oneself 2 interleukin-15 2 imm+ 2 igmcic 2 ifit5 2 esat-6 2 e3s 2 e2f2-/-mice 2 crx-527 2 clustalx 2 beta-2-m 2 anti-(self 1 ≥10× 1 z"ikv 1 yourself 1 yos9p 1 y8tcr.s 1 tritc 1 theirs 1 silico/ 1 rab4a 1 rab3b 1 pi3kg 1 pep005 1 pdcs 1 p62 1 n.m.we 1 myself 1 mtecs 1 mhv)-a59 1 mg 1 m157 Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 33583 be 5682 have 3517 use 2273 show 2168 induce 1952 bind 1595 express 1309 associate 1227 increase 1173 base 1137 suggest 1132 mediate 1093 include 1090 identify 1029 find 1024 do 997 compare 953 follow 868 present 865 activate 864 involve 821 predict 812 demonstrate 810 determine 803 derive 789 indicate 776 produce 763 infect 725 contain 706 observe 687 require 678 generate 666 provide 666 lead 660 recognize 660 develop 651 result 622 know 618 detect 617 regulate 613 stimulate 590 reduce 567 perform 557 occur 554 describe 530 encode 513 analyze 506 reveal 499 select 498 treat Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 3231 not 3033 - 2647 immune 2309 specific 2247 also 2102 human 1880 high 1592 viral 1470 other 1344 different 1293 such 1232 more 1148 well 1125 only 1117 however 1032 anti 1015 low 897 major 856 non 854 most 785 as 760 important 733 cellular 723 inflammatory 716 thus 703 further 683 first 666 significantly 657 dendritic 649 molecular 642 several 632 significant 631 dependent 621 early 598 similar 572 many 560 long 550 multiple 548 single 532 new 532 functional 526 cytotoxic 524 present 523 positive 523 highly 519 large 518 genetic 506 clinical 496 normal 487 acute Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 245 most 182 least 165 high 104 good 89 Most 54 low 33 large 25 great 17 strong 14 early 8 close 8 bad 7 late 6 simple 5 long 4 weak 4 small 4 poor 4 near 3 steep 3 new 3 fast 3 clear 3 big 2 topmost 2 sick 2 fit 2 deadly 2 common 2 B27 1 αGal 1 young 1 theb 1 sincere 1 short 1 severe 1 rich 1 outermost 1 innermost 1 degradati 1 clean 1 cellqu 1 broad 1 VEGFR-1 1 PRA>10 1 P=0.0002).Our 1 Least 1 CFP10 1 B7.2 1 -which Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 609 most 117 least 42 well 3 highest 2 lowest 2 early 1 ko→wt 1 furthest 1 fast 1 clustalw 1 -psmb10 Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 19 tools.iedb.org 11 www.cbs.dtu.dk 6 doi.org 4 www 4 creativecommons.org 4 crdd.osdd.net 3 www.syfpeithi.de 3 www.ncbi.nlm.nih.gov 3 www.iedb.org 3 www.ebi.ac.uk 3 www.ddg-pharmfac.net 3 www.cbs 3 blast.ncbi.nlm.nih.gov 2 www.uniprot.org 2 www.mdpi.com 2 swissmodel.expasy.org 2 galaxy.seoklab.org 2 biocomp.chem.uw.edu.pl 1 www3.niaid.nih.gov 1 www.tvfac.lanl.gov 1 www.tcells.org 1 www.sbg.bio 1 www.sbg 1 www.rcsb.org 1 www.pymol.org 1 www.proteinatlas.org 1 www.paproc.de 1 www.ncbi.nlm.nih.gov.in 1 www.ncbi 1 www.mpiibberlin.mpg.de 1 www.mgc.ac.cn 1 www.merops 1 www.medicine.virginia 1 www.lynnon.com 1 www.jenner.ac.uk 1 www.jcat.de 1 www.jalview.org 1 www.iucnredlist.org 1 www.imtech.res.in 1 www.immunome-research.com 1 www.immuneepitope.org 1 www.graphpad.com 1 www.genome.ad.jp 1 www.gem.re.kr 1 www.g3journal.org 1 www.frontiersin.org 1 www.fenyolab.org 1 www.dovepress.com 1 www.ddgpharmfac.net 1 www.data Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 5 http://tools.iedb.org/mhcii/ 4 http://www 3 http://www.cbs 3 http://tools.iedb.org/immunogenicity/ 3 http://creativecommons.org/licenses/by/4.0/ 2 http://www.uniprot.org/ 2 http://www.syfpeithi.de 2 http://www.ncbi.nlm.nih.gov/ 2 http://www.cbs.dtu.dk/services/TMHMM/ 2 http://www.cbs.dtu.dk/services/NetMHCpan/ 2 http://www.cbs.dtu.dk/services/ 2 http://tools.iedb.org/population/ 2 http://tools.iedb.org/bcell/ 2 http://tools.iedb.org/ 2 http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins 1 http://www3.niaid.nih.gov/topics/ 1 http://www.tvfac.lanl.gov/ 1 http://www.tcells.org 1 http://www.syfpeithi.de/0-Home 1 http://www.sbg.bio 1 http://www.sbg 1 http://www.rcsb.org/ 1 http://www.pymol.org/ 1 http://www.proteinatlas.org/humanproteome/ 1 http://www.paproc.de 1 http://www.ncbi.nlm.nih.gov/protein 1 http://www.ncbi.nlm.nih.gov.in 1 http://www.ncbi 1 http://www.mpiibberlin.mpg.de/MAPPP/ 1 http://www.mgc.ac.cn/VFs/ 1 http://www.merops 1 http://www.medicine.virginia 1 http://www.mdpi.com/2076-393X/8/3/408/ 1 http://www.mdpi.com/2076-0817/9/9/705/s1 1 http://www.lynnon.com/ 1 http://www.jenner.ac.uk 1 http://www.jcat.de/ 1 http://www.jalview.org/ 1 http://www.iucnredlist.org 1 http://www.imtech.res.in/raghava/algpred/ 1 http://www.immunome-research.com/supplements/6/S2 1 http://www.immuneepitope.org/MHCalleleId/142 1 http://www.iedb.org/database_export_v3.php 1 http://www.iedb.org/ 1 http://www.iedb.org 1 http://www.graphpad.com 1 http://www.genome.ad.jp 1 http://www.gem.re.kr/paidb 1 http://www.g3journal.org/lookup/ 1 http://www.frontiersin.org/articles/10.3389/fimmu Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 sewellak@cardiff.ac.uk 1 natasa.kopitar@ijs.si 1 lunde@cbs.dtu.dk 1 journals.permissions@oupjournals.org 1 hans.ellegren@bmc.uu.se Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 69 antigen presenting cells 16 cells are not 15 cells were then 14 antibody mediated rejection 13 cells did not 13 levels were significantly 12 cells are able 12 cells do not 12 cells was significantly 11 peptide binding affinity 10 mice did not 9 virus infected cells 8 expression is not 8 peptide binding prediction 7 cell mediated immunity 7 cells is not 7 cells were significantly 6 antigen presenting cell 6 cell mediated rejection 6 cells are capable 6 cells are important 6 cells was not 6 cells were further 6 cells were not 6 infection induces h-2 6 mhc binding affinity 6 protein expressing cells 6 vaccines are not 5 antibody producing cells 5 cells are also 5 cells does not 5 cells was also 5 cells were adoptively 5 cells were co 5 cells were positive 5 epitopes were also 5 expression was not 5 mice were not 5 peptide binding predictions 5 vaccines are available 5 vaccines do not 4 % were male 4 cells are more 4 cells are present 4 cells are specific 4 cells express mhc 4 cells has also 4 cells using flow 4 cells were also 4 cells were present Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 b had no effect 2 vaccines are not currently 2 vaccines are not yet 1 % had no detectable 1 % had no proteinuria 1 % was not statistically 1 antibodies are not rheumatoid 1 antibodies have not yet 1 antibody did not readily 1 antigen are not all 1 antigen has not previously 1 antigen is not always 1 antigen was not due 1 antigens are not epitopes 1 antigens has not yet 1 cell are not well 1 cell were not indentical 1 cells are not able 1 cells are not actively 1 cells are not directly 1 cells are not indicators 1 cells are not necessary 1 cells are not only 1 cells are not preponderant 1 cells are not similarly 1 cells are not usually 1 cells do no longer 1 cells do not necessarily 1 cells do not usually 1 cells had no effect 1 cells is not available 1 cells is not due 1 cells is not sufficient 1 cells is not yet 1 cells was not due 1 cells was not relative 1 cells was not significantly 1 cells was not statistically 1 cells were not anergic 1 cells were not completely 1 cells were not different 1 cells were not tumor 1 disease is not completely 1 disease is not well 1 epitope is not correct 1 epitope is not sufficient 1 epitopes are not antigens 1 epitopes are not simply 1 epitopes are not sufficient 1 epitopes is not common A rudimentary bibliography -------------------------- id = cord-005400-50lmj4op author = Ada, Gordon title = Overview of vaccines and vaccination date = 2005 keywords = MHC; cell; dna; vaccine summary = doi = 10.1385/mb:29:3:255 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 keywords = Class; MHC summary = doi = 10.1101/2020.06.16.154559 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 keywords = HLA; MHC; Spike summary = doi = 10.1101/2020.05.20.106351 id = cord-349225-504kr50e author = Alcami, Antonio title = Viral mechanisms of immune evasion date = 2000-09-01 keywords = MHC; immune; virus summary = doi = 10.1016/s1357-4310(00)01775-5 id = cord-299786-wuve0tjz author = Anderson, Robert title = Manipulation of cell surface macromolecules by flaviviruses date = 2004-02-27 keywords = Halstead; MHC; cell; dengue; infection; virus summary = Dengue virus infection of immature myeloid dendritic cells has been shown to induce their maturation accompanied by the expression of major histocompatibility complex (MHC) class I and II antigens; the costimulatory molecules CD40, CD80, and CD86; and the dendritic cell marker CD83 (Libraty et al., 2001) . Flaviviruses, including dengue and West Nile (Shen et al., 1997) viruses, activate endothelial cell adhesion molecule expression by either direct (virus-mediated) or indirect (cytokine-mediated) mechanisms (see Section V,C). A major candidate event in such a route is the activation of endothelial cell adhesion molecules by a factor(s) (particularly TNF-) produced by dengue virus-infected blood monocytes . Thus the roles of prior immunity, antibody-enhanced virus infection, and immune-mediated pathologic effects on the vascular system are key points in understanding the pathogenesis of dengue hemorrhagic disease. Activation of endothelial cells via antibody-enhanced dengue virus infection of peripheral blood monocytes doi = 10.1016/s0065-3527(03)59007-8 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 keywords = LASV; MHC summary = doi = 10.1038/s41598-020-63640-1 id = cord-025523-6ttps1nx author = Barlas, Georgios title = Cross-Domain Authorship Attribution Using Pre-trained Language Models date = 2020-05-06 keywords = MHC summary = title: Cross-Domain Authorship Attribution Using Pre-trained Language Models An especially challenging but very realistic scenario is cross-domain attribution where texts of known authorship (training set) differ from texts of disputed authorship (test set) in topic or genre. 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] . This method is based on a character-level recurrent (RNN) neural network language model and a multiheaded classifier (MHC) [1] . We examine the use of pre-trained language models (e.g., BERT, ELMo, ULMFiT, GPT-2) in AA and the potentials of MHC. Based on Bagnall''s model [1] , originally proposed for authorship verification, we compare the performance when we use either the original characterlevel RNN trained from scratch in the small-size AA corpus or pre-trained tokenbased language models obtained from general-domain corpora. doi = 10.1007/978-3-030-49161-1_22 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 keywords = BNP; BVD; MHC; Pregsure summary = doi = 10.1186/s13567-014-0129-0 id = cord-005330-4k7hc1ww author = Bien, Christian G. title = T-cells in human encephalitis date = 2005 keywords = CD8; MHC; cell summary = In this review, we attempt to summarize the existing knowledge on T-cell effects and-if availablepotential ways of its therapeutic modification in Rasmussen encephalitis (RE), paraneoplastic encephalomyelitis (PEM), and virus encephalitides. This assumption is based on the neuropathological findings of elements of a cytotoxic T-cell attack within the brains of affected people (Bernal et al., 2002) but also on some other observations regarding anti-Yo, anti-Hu, and anti-Ma syndromes and their respective antigens, cerebellar degenerationrelated protein 2 (cdr2), HuD, and PNMA1. The most prominent evidence for a pathogenetically relevant contribution of T-cells to PEM comes from studies on patients with anti-Yo positive paraneoplastic cerebellar degeneration. study on TCR Vβ families of T-lymphocytes within the brains of anti-Hu positive patients (autopsy specimens) providing evidence for an oligoclonal expansion of CD8 + T-cells are concordant with this concept (Voltz et al., 1998) . Selective expression of Purkinje-cell antigens in tumor tissue from patients with paraneoplastic cerebellar degeneration Modelling paraneoplastic CNS disease: T-cells specific for the onconeuronal antigen PNMA1 mediate autoimmune encephalomyelitis in the rat doi = 10.1385/nmm:7:3:243 id = cord-333309-21czobqy author = Byun, Hyewon title = ERAD and how viruses exploit it date = 2014-07-03 keywords = CD4; ERAD; MHC; Rem; protein summary = Interaction of lectin-type and other chaperones with ERAD substrates allows association with members of the protein disulfide isomerase (PDI) family, which generally are characterized by one or more thioredoxin-like motifs (CXXC; Brodsky and Skach, 2011) . In contrast to the rhomboid proteases, the Derlins lack proteolytic activity, suggesting that these proteins bind to ERAD substrates and target them to E3 ligases for ubiquitination and to p97 for membrane extraction (Brodsky, 2012) . These ubiquitin ligases are members of the cytosolic SCF (S-phase kinase-associated protein 1 (Skp1)-Cullin 1 (Cul1)-F-box) family, where the F-box components of the SCF complex recognize the N-glycans of the retrotranslocated substrate, e.g., Fbs1 and Fbs2 (Yoshida, 2007) . A proteasomal ATPase contributes to dislocation of endoplasmic reticulum-associated degradation (ERAD) substrates The viral E3 ubiquitin ligase mK3 uses the Derlin/p97 endoplasmic reticulum-associated degradation pathway to mediate down-regulation of major histocompatibility complex class I proteins doi = 10.3389/fmicb.2014.00330 id = cord-004518-jd1wxobz author = Běláková, Jana title = DNA vaccines: are they still just a powerful tool for the future? date = 2007-12-03 keywords = MHC; cell; dna; response; vaccine summary = doi = 10.1007/s00005-007-0044-4 id = cord-023724-5at0rhqk author = Cann, Alan J. title = Infection date = 2015-07-24 keywords = IFN; MHC; RNA; cell; dna; infection; virus summary = The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. doi = 10.1016/b978-0-12-801946-7.00006-7 id = cord-013093-aa4cf44u author = Cassotta, Antonino title = Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin date = 2020-07-09 keywords = CD4; H1-HA; HLA; MHC summary = The detailed and unbiased characterization of HA-reactive memory and naive CD4 + T cell repertoires, paralleled by a deep analysis of the naturally presented repertoire of MHC-II-binding HA peptides by mass spectrometry (MS)-based immunopeptidomics, allowed us to shed new light on the factors governing CD4 + T cell clonal selection and immunodominance to influenza HA in humans. We then selected a large number of H1-HA-specific T cell clones derived from naive or memory T cells of donor HD1 and determined their functional avidity by measuring the proliferative response to autologous monocytes pulsed with different concentrations of the H1-HA peptides or H1-HA protein, which need processing for presentation on MHC-II molecules. doi = 10.1084/jem.20200206 id = cord-346032-188gnf8j author = Cheung, Ying-Kit title = Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope date = 2007-08-10 keywords = HLA; MHC; SARS summary = doi = 10.1016/j.vaccine.2007.05.025 id = cord-017819-85x0juiw author = Christe, Philippe title = Biological conservation and parasitism date = 2006 keywords = MHC; host; parasite summary = It is, therefore, not surprising that corticosteroid level is measured in many studies in ecology and conservation biology that have evaluated the effect of different environmental and human perturbations on the stress level of wild animals (Creel et al. 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. Interestingly, Allee effects and parasitism have several features in common that are of interest when studying population dynamics in conservation biology (Deredec 2005) . Invasive host species have another advantage if they have invested in strong immune defences in their natural range, which may then subsequently confer a better capacity to control parasites that they may acquire in the introduced habitat. doi = 10.1007/978-4-431-36025-4_27 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 keywords = MHC summary = 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) Beta-2 microglobulin (B2M) plays a pivotal role in the biology of mammals, including its association with major histocompatibility complex (MHC) Class I gene products. Here we report the results of a longitudinal study of the reproductive performance of a genetically modified B2m deficient mouse strain with low MHC Class I expression. In the course of experiments designed to generate mouse embryos for gene transcription studies and immuno-detection of MHC products [50] [51] , we consistently observed an impaired reproductive capacity in the B2m deficient mice. Therefore, a possible mechanism operating in the B2m-deficient mice is the absence of secreted MHC class I products, and thus the absence of mating signals resulting in impaired breeding. doi = 10.1095/biolreprod.106.057125 id = cord-002463-qhtj1pef author = Dash, Raju title = In silico-based vaccine design against Ebola virus glycoprotein date = 2017-03-21 keywords = EBOV; Ebola; HLA; MHC; epitope summary = doi = 10.2147/aabc.s115859 id = cord-022142-d4yxgv83 author = David, Ayelet title = Polymer-Based DNA Delivery Systems for Cancer Immunotherapy date = 2016-05-28 keywords = MHC; PEI; PLGA; dna summary = A number of polymer-based nanomedicines have been developed to deliver genes into DCs, primarily by incorporating tumor-specific, antigen-encoding plasmid DNA with polycationic molecules to facilitate DNA loading and intracellular trafficking. Direct in vivo targeting of plasmid DNA to DC surface receptors can induce high transfection efficiency and long-term gene expression, essential for antigen loading onto major histocompatibility complex molecules and stimulation of T-cell responses. This chapter highlights the repertoire of non-viral, nanosized polymeric DNA delivery systems (polyplexes) available to achieve effi cient gene transfer into DCs for immunotherapeutic applications in cancer therapy. With respect to clinical translation, effi cacious non-viral gene delivery into DCs will depend on the combination of intelligent material design, the appropriate tumor specifi c antigen-encoding DNA and immuno-stimulatory molecules to promote DC maturation and activation. doi = 10.1007/978-1-4939-3634-2_10 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 keywords = Class; HIV; HLA; MHC; epitope summary = doi = 10.1007/978-0-387-79208-8_3 id = cord-352150-ey9kc7zj author = Degauque, Nicolas title = Cross-Reactivity of TCR Repertoire: Current Concepts, Challenges, and Implication for Allotransplantation date = 2016-03-24 keywords = CD8; HLA; MHC; TCR summary = doi = 10.3389/fimmu.2016.00089 id = cord-017296-jdp8kgg5 author = Deschler, Barbara title = Particular Treatment Procedures date = 2008 keywords = Chap; MHC; PBSC; cell; stem; transplantation summary = doi = 10.1007/978-3-540-73277-8_5 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 keywords = MHC; TCR; Vγ9Vδ2; cell summary = doi = 10.1038/s41423-020-0503-y id = cord-354030-8tfg881h author = Dong, Rong title = Contriving Multi-Epitope Subunit of Vaccine for COVID-19: Immunoinformatics Approaches date = 2020-07-28 keywords = MHC; SARS; epitope; figure; protein; vaccine summary = doi = 10.3389/fimmu.2020.01784 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 keywords = DRB; MHC; dna summary = The Swedish moose was analysed for genetic variability at major histocompatibility complex (MHC) class I and class II DQA, DQB and DRB loci using restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP) techniques. Since the SSCP analysis concerned an expressed DRB gene it can be concluded that the level of functional MHC class II polymorphism, at least at the DRB locus, is low in Swedish moose. 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@) . There is a clear difference between the moose and cattle as regards their degrees of MHC polymorphism in relation to their genome-wide genetic variability measured by DNA fingerprinting. doi = 10.1111/j.1365-294x.1996.tb00286.x id = cord-339091-3xk2w0d2 author = Flower, Darren R title = Computer aided selection of candidate vaccine antigens date = 2010-11-03 keywords = MHC; antigen; epitope; prediction; protein; vaccine summary = The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. Initially, the pathogenic genome is scanned for "open reading frames" or ORFs. Once all ORFs have been identified, proteins are selected on the basis that they will be accessible to immune system surveillance, usually using some form of informatic-based prediction methodology or, more likely, set of methdologies. We shall below examine three key approaches: subcellular location prediction, sequence similarity, and empirical statistical approaches, typified by VaxiJen. For a protein to be accessible to surveillance by the immune system, it is often assumed to be physically external to the microbial organism or at least present on its surface rather than being sequestered away far from the roving eye of the immune system. doi = 10.1186/1745-7580-6-s2-s1 id = cord-016594-lj0us1dq author = Flower, Darren R. title = Identification of Candidate Vaccine Antigens In Silico date = 2012-09-28 keywords = MHC; antigen; prediction; protein; sequence; vaccine summary = doi = 10.1007/978-1-4614-5070-2_3 id = cord-264401-9ogs55xr author = Giotis, Efstathios S. title = Inferring the Urban Transmission Potential of Bat Influenza Viruses date = 2020-06-03 keywords = MHC summary = doi = 10.3389/fcimb.2020.00264 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 keywords = MHC; TCR summary = Both clinical and experimental evidence supports the hypothesis that immune mechanisms are involved in the pathogenesis of inflammatory demyelination in multiple sclerosis (MS) and that autoreactive T lymphocytes initiate the process of central nervous system (CNS) myelin damage. This disease model has provided insight into the pathogenic "steps" that may be relevant to MS, including (1) genetic susceptibility, (2) priming and activation of myelin-specific T cells, (3) interaction of autoreactive T cells with endothelium and migration into the CNS, and (4) recognition of myelin antigens and initiation of inflammatory or demyelinating damage (Fig 1) . 44, 45 Molecular mimicry motifs that would satisfy both MHC binding and recognition by specific TCR were used by Wucherpfennig and Strominger 46 to identify microbial peptides that were effective in activating three MBPspecific T-cell clones (TCCs) derived from MS patients (Table 1) . Molecular mimicry in T cell-mediated autoimmunity: viral peptides activate human T cell clones specific for myelin basic protein doi = 10.1002/1531-8249(199905)45:5<559::aid-ana3>3.0.co;2-q 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 keywords = MHC; dna summary = doi = 10.1016/j.virol.2005.11.042 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 keywords = CD8; Fig; HLA; MHC summary = doi = 10.1038/s41598-020-62244-z id = cord-347298-7kqrl3rv author = Hedger, M.P. title = Immunology of the Testis and Male Reproductive Tract date = 2010-07-12 keywords = Hedger; IFN; IL1; Leydig; MHC; Sertoli; TNF; cell; testis summary = doi = 10.1016/b978-0-08-046884-6.01112-x 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 keywords = B19; MHC summary = For the first time, this study used homology modelling techniques to construct three-dimensional structures of the peptide-binding domains of chicken MHC class Ι molecules for four commonly encountered unique haplotypes, i.e., B4, B12, B15, and B19. The NP protein sequence of H5N1 isolate A/Goose/Gongdong/1/96 (H5N1) was downloaded from the UniProt database (UniProtID: NCAP_I96A0) and automatically parsed as octapep-tides or nonapeptides using a computer program, which was developed in our laboratory, based on the peptide-binding motifs of chicken MHC class I molecules belonging to the B4, B12, B15, and B19 haplotypes [22] . Using a motif combined with a structure-based method, 25 potential T cell epitope peptides were predicted in the H5N1 AIV NP in chickens of B4, B12, B15, and B19 haplotypes. 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. doi = 10.1371/journal.pone.0039344 id = cord-308043-h0knm8y4 author = Hussey, Séamus title = Autophagy as an emerging dimension to adaptive and innate immunity date = 2009-08-31 keywords = Beclin-1; MHC; autophagy; cell; protein summary = These lines of evidence suggest a more elaborate TLR control of autophagy whereby TLR-adapter molecules interact with proteins from the autophagic pathway rather than by simply activating the classic hierarchical signaling cascades described heretofore. The authors demonstrated that the Atg5-Atg12 conjugate negatively regulates the antiviral immune response by interacting with the RIG-I-like receptor (s protein retinoic acid-inducible gene I (RIG-I) and IFN-␤ promoter stimulator 1 (IPS-1) thus, implying autophagy contributes to viral replication. In another study, the same group demonstrated that the fusion of influenza matrix protein 1 (MP1) with Atg8/LC3 drives this molecule to autophagosomes in different cell types and enhances recognition by antigen specific CD4+ T cells [117] . Accordingly, Atg6 silencing dampened this process, while rapamycin treatment enhanced priming of 85B-specific CD4 + T cells, strongly suggesting a role for autophagy in MHC class II presentation of antigens of bacterial origin. doi = 10.1016/j.smim.2009.05.004 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 keywords = MHC; SARS summary = A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. The aim of this study is to analyze envelope protein strains using in silico approaches looking for the conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine [22, 23, 24] . Envelope protein from the SARS-CoV-2 was analyzed using the IEDB MHC-1 binding prediction tool to predict the T cell epitope suggested interacting with different types of MHC Class I alleles. Analysis of the genome sequence and prediction of B-cell epitopes of the envelope protein of Middle East respiratory syndrome-coronavirus doi = 10.1101/2020.05.26.115790 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 keywords = HLA; MHC summary = title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner However, based on the structures of a series of MHC I molecules, such as human HLA-B*2705 (Madden et al., 1991) , rhesus macaque Mamu-A*02 , and mouse H-2K d (Mitaksov and Fremont, 2006; Zhou et al., 2004) , there is a salt bridge positioned over the peptides formed by opposite charged residues from the α1 and α2 helices of MHC I, respectively. Herein, by determining the crystal structures of human MHC I HLA-B*4001 complexed with a severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid (N)-derived T-cell epitope (Oh et al., 2011) and mouse MHC I H-2K d bound to an immunodominant T-cell epitope from human hepatitis B virus (HBV) core antigen (HBc) (Li et al., 2005) , we clearly demonstrated the molecular features of MHC I molecules with two different salt bridges formed by the residues pairs Arg62-Glu163 and Arg66-Glu163, respectively. doi = 10.1016/j.molimm.2019.06.005 id = cord-322575-3goj00ej author = Karl, Julie A. title = Major Histocompatibility Complex Class I Haplotype Diversity in Chinese Rhesus Macaques date = 2013-07-01 keywords = MHC; Mamu; chinese; indian summary = doi = 10.1534/g3.113.006254 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 keywords = Class; MHC; PBS; dna summary = doi = 10.1016/j.vaccine.2009.01.128 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 keywords = Fig; MHC; epitope summary = doi = 10.1371/journal.pcbi.1002884 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 keywords = Ebola; MHC; cathepsin summary = showed that inhibitors of cysteine proteinases cystatin C and p41 form of major histocompatibility complex invariant chain did not inhibit cathepsin L and the authors suggested that cystatin F might be the inhibitor that selectively regulated cathepsin L activity in macrophages [69] . Gene targeting studies showed a critical role for the lysosomal cysteine protease cathepsin S in the late stages of Ii degradation in B cells, DCs and macrophages [89] [90] [91] and cathepsin L (V in humans) in thymic cortical epithelium [92] . An additional level of control is achieved by the proteolysis full length TLR7 and TLR9 by endosomal cysteine cathepsins and AEP.TLR9 can bind its ligand CpG DNA, but it cannot trigger activation signals without first being processed by endolysosomal proteases, which remove N-terminal region [98] [99] [100] [101] . The study shows that the functions of proteinases in the virus entry into the cell as well as in host immune response are relevant for the possible therapy with inhibitors. doi = 10.2174/138920312804871102 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 keywords = Fig; IEDB; MHC summary = doi = 10.1016/j.humimm.2019.02.008 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 keywords = HSV; MHC; RPEC summary = doi = 10.1007/bf01880670 id = cord-347039-eap592i7 author = Lee, Seung-Hwan title = Maneuvering for advantage: the genetics of mouse susceptibility to virus infection date = 2003-08-31 keywords = MHC; cell; infection; mouse; virus summary = Receptors are recognized as important determinants of virus host range and tissue tropism; and some host resistance/susceptibility loci encode molecules that are expressed on the cell surface. Another example of natural host resistance is the restriction of ecotropic Murine LEUKEMIA VIRUS (MuLV) infection by the mouse Fv4 gene. The effort to understand the genetic basis of susceptibility to viral disease is driven by three considerations: (1) the increased public awareness of the toll imposed by viruses on the host; (2) the increase in susceptible human populations because of longer life expectancy, frequently accompanied by chronic illness, and the consequences of advances in medical technology, including immunosuppressive therapies for organ transplantation or treatment of malignancy; and (3) the need to develop new therapies for infections caused by multidrug-resistant Human killer-cell immunoglobulin-type receptor (KIR) is considered to be a functional homolog of mouse Ly49. Mouse genetics has also demonstrated that recognition and destruction of virus-infected cells by NK cells is mediated by specific interactions between activating NKcell receptors and viral target molecules. doi = 10.1016/s0168-9525(03)00172-0 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 keywords = ACE2; Dox; MHC; mouse summary = doi = 10.1186/s42826-020-00056-y id = cord-275433-58unu79x author = Levine, Beth title = Unveiling the roles of autophagy in innate and adaptive immunity date = 2007 keywords = MHC; autophagy; cell summary = The process of autophagy may degrade intracellular pathogens, deliver endogenous antigens to MHC-class-II-loading compartments, direct viral nucleic acids to Toll-like receptors and regulate T-cell homeostasis. The class III PI3K vPS34 (also known as PIK3C3) generates phosphatidylinositol-3-phosphate (PtdIns3P) by phosphorylating The cellular events during digestion of self constituents or intracellular pathogens follow three distinct stages: initiation (formation of the phagophore), elongation (growth and closure) and maturation of a double membrane autophagosome into an autolysosome. In principle, autophagy may function in the direct elimination of viruses (as shown in vitro), in the breakdown of host factors required for viral replication or the inhibition of innate immune signalling, and in the promotion of cell survival either by maintaining bioenergetics in virally infected cells or by removing toxic self or viral components. In addition, numerous viruses inhibit the PKR (IFN-inducible doublestranded-RNA-dependent protein kinase) antiviral signalling pathway that is required for the induction of autophagy in virally infected cells or activate the autophagy-inhibitory class I PI3K-AKT-mTOR signalling pathway 63 . doi = 10.1038/nri2161 id = cord-334592-54dofkxh author = Levine, Beth title = Autophagy in immunity and inflammation date = 2011-01-20 keywords = Crohn; MHC; autophagy; cell; function; protein summary = Moreover, p62 is required for starvation and IFN-γ-induced targeting of Fau (and perhaps other ubiquitylated protein complexes) to mycobacteria-containing phagosomes, resulting in the generation of antimycobacterial Fau-derived peptides 42 .The role of p62 in innate immunity is probably evolutionarily ancient, as the Drosophila p62 orthologue REF(2)P was originally identified in a screen for modifiers of sigma virus replication 43 . The mechanisms by which autophagy genes mediate in vivo resistance to infection are not fully understood, but are likely to involve a combination of xenophagy, other autophagy-protein-dependent effects on microbial replication or survival, activation of innate and adaptive immune responses, and/or alterations in pathogen-induced cell death (Fig. 3 ). doi = 10.1038/nature09782 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 keywords = MHC summary = Data from animal studies in the EAE model established that CD4 + Thl cells specific to myelin antigens can play a central role in the induction and progression of autoimmune demyelinating disease [2, 3] . In examining the immune response to MBP, we found that complementary mutations in an antigenic peptide allow for cross-reactivity of autoreacfive T cell clones that may be related to shifts of the TCR structure itself [11] . The new knowledge obtained from this study was 1) that of highly degenerative recognition of peptides by autoreactive CD4 § T cells, including identification of stimulatory ligands not sharing a single amino acid in corresponding positions with the antigen used to establish the T cell clone and 2) the identification of more potent agonistic peptides than cognate self-peptide. Molecular mimicry in T cell-mediated autoimmunity: Viral peptides activate human T cell clones specific for myelin basic protein Cross-reactive human autoreactive T-ceU receptor responses to altered peptide ligands presented by different MHC class II molecules doi = 10.1016/b978-044451271-0.50004-1 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 keywords = BF2; Chb2; MHC summary = doi = 10.1016/j.vetimm.2007.10.019 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 keywords = IFN; MHC; WNV summary = doi = 10.1016/0165-5728(89)90171-9 id = cord-296347-fanlvxqs author = Loureiro, Joana title = Antigen Presentation and the Ubiquitin‐Proteasome System in Host–Pathogen Interactions date = 2006-12-02 keywords = CD4; HCMV; MHC; Nef; SPP; US11; US2; protein summary = doi = 10.1016/s0065-2776(06)92006-9 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 keywords = Fig; MHC; Ptal summary = doi = 10.1371/journal.pbio.3000436 id = cord-007301-5m269nzi author = Lundegaard, Claus title = Modeling the adaptive immune system: predictions and simulations date = 2007-12-15 keywords = HLA; MHC summary = doi = 10.1093/bioinformatics/btm471 id = cord-313138-y485ev30 author = Magor, Katharine E. title = Defense genes missing from the flight division date = 2013-04-24 keywords = MHC; RNA; TLR8; gene; rig summary = doi = 10.1016/j.dci.2013.04.010 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 keywords = CD8; MHC; class summary = doi = 10.1002/glia.20625 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 keywords = DRB1; HLA; MHC summary = doi = 10.1371/journal.pbio.3000131 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 keywords = DRB; DRB1; MHC summary = title: Non-neutral evolution of the major histocompatibility complex class II gene DRB1 in the sac-winged bat Saccopteryx bilineata Thus, the data are consistent with the hypothesis that recombination gives rise to new alleles at the DRB locus of the sac-winged bat, and these are maintained in the population through balancing selection. We analysed the antigen-binding region of the MHC class II gene DRB of the sac-winged bat Saccopteryx bilineata by sequencing cloned PCR products. In this study, we describe the genetic diversity within exon 2 of the MHC class II gene DRB, and discuss the role of recombination and selection in generating and maintaining high levels of genetic diversity in colonies of the sac-winged bat. Variation at the DRB1 locus; evidence of recombination/ gene conversion Ten alleles were detected within the main sample of 79 individuals from the La Selva population. doi = 10.1038/sj.hdy.6800989 id = cord-319761-bu5pzbnv author = Miller, Craig S. title = Pleiotropic mechanisms of virus survival and persistence date = 2005-07-16 keywords = IFN; MHC; cell; viral; virus summary = Accordingly, this review focuses on specific viral cell interactions that allow the virus to survive the cellular attack and evade the immune system, establish persistent infections, and cause chronic disease. 13, 14 Viruses regulate apoptosis by several mechanisms including the targeting of the tumor suppressor gene product p53, the Fas death receptor, and by producing caspase inhibitors and viral Bcl-2 homologs. 24, 25 The alpha herpesvirus HSV-1 encodes several antiapoptotic gene products (ie, ICP4, ICP27, c34.5, U s 3, gJ) [26] [27] [28] [29] [30] that modulate apoptosis at several levels, including antagonism of double-stranded RNA-activated protein kinase (PKR), a downstream induction molecule of the interferon signaling pathway 31, 32 Of note, all c-herpesviruses express viral homologues of cellular antiapoptotic genes, including 1 or 2 Bcl-2 homologues. In the majority of infections, viruses encode products that antagonize either the IFN signal transduction pathway or cellular proteins induced by IFN that are responsible for inhibiting virus replication (Fig 2) . doi = 10.1016/j.tripleo.2005.03.017 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 keywords = MHC; Nipah summary = doi = 10.1155/2020/2567957 id = cord-011173-c1i0a92f author = Moore, Tamson V. title = Improved MHC II epitope prediction — a step towards personalized medicine date = 2019-12-13 keywords = MHC summary = Whereas the presence and expression of neoantigen proteins can be identified through sequencing of the tumour exome, the neoepitopes presented by MHC II molecules must be either discovered empirically using expensive and time-consuming mass spectrometry (MS) techniques 4 or predicted using software-based estimations of peptide-MHC II binding affinity. The deconvoluted peptidomic datasets were then used to train a prediction algorithm, MixMHC2pred, which returns an MHC II binding score for a given peptide sequence and HLA-D allele. The efficacy of such neoantigen-based immunotherapies will be dependent on the identification of a sufficient number of MHC II-binding peptides to stimulate CD4 + T cell responses. Both MARIA and MixMHC2pred have the potential to make personalized neoantigen-based therapies more accessible to patients, including patients with tumours harbouring fewer mutations, by identifying more MHC II-binding epitopes to which CD4 + T cells can respond within each patient''s pool of putative neoantigens. doi = 10.1038/s41571-019-0315-0 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 keywords = DNA; MHC summary = Moreover, in vivo studies indicated that the combination of L1 and L2 DNA constructs without any adjuvant or delivery system induced effective immune responses, and protected mice against C3 tumor cells (the percentage of tumor-free mice: ~66.67%). The framework begins with conservancy analysis of all 13 high-risk HPV strains following with (1) B-cell epitope mapping, (2) T-cell epitope mapping (CD4 + and CD8 + ), (3) allergenicity assessment, (4) tap transport and proteasomal cleavage, (5) population coverage, (6) global and template-based docking and (7) data collection, analysis, and design of the L1 and L2 DNA constructs. In this study, for the first time, comprehensively integrated methods (using sequence-based tools in combination with flexible peptide-protein docking) were used to design highly immunogenic and protective vaccine candidates which were able to boost both humoral and cellular Table 12 . doi = 10.1038/s41598-019-51679-8 id = cord-306096-2yl07bdq author = OLDSTONE, M. B. A. title = Viruses and Autoimmune Diseases date = 2003-11-03 keywords = IDDM; MHC summary = In the absence of viral infection, IDDM can be induced when such anergic CTL clones (of high or low affinity) in the periphery are activated as they pass into an islet environment where interferon-g or B7.1 are expressed [9, 10] . To examine whether molecular mimicry between a virus and a protein expressed in oligodendrocytes could lead to a central nervous system (CNS) autoimmune disease much like the demyelinating disease, multiple sclerosis, transgenic mice were generated whose oligodendrocytes expressed either the nucleoprotein or glycoprotein of a virus [41] . Virus infection triggers insulin-dependent diabetes mellitus in a transgenic model: role of anti-self (virus) immune response Molecular mimicry in T-cell mediated autoimmunity: viral peptides activate human T-cell clones specific for myelin basic protein Oral insulin treatment suppresses virus-induced antigen-specific destruction of b cells and prevents autoimmune diabetes in transgenic mice doi = 10.1046/j.1365-3083.1997.d01-145.x 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 keywords = HLA; MHC; Shigella summary = doi = 10.1155/2017/6412353 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 keywords = EBOV; Ebola; MHC; RNA summary = title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. To date, information regarding the processing, structure and functions of Ebola virus (EBOV) protein L (EBOL) demonstrates that it is an RNA-dependent RNA polymerase, with the assistance of VP35. In the present study, we have followed immunoinformatics approaches for designing potential conserved epitope candidate for the utility of vaccine development against the deadly Ebola virus, with an expectation of further wet lab validation. Protein variability server predicted the variability of the conserved region of the RNA-dependent RNA polymerase-L ( Fig. 10) to ensure that the proposed epitope is within the invariable region. Design of an epitope-based peptide vaccine against spike protein of human corona virus: an in silico approach doi = 10.1186/s40203-015-0011-4 id = cord-269917-j0t8rjkc author = Odales, Josué title = Immunogenic properties of immunoglobulin superfamily members within complex biological networks date = 2020-10-11 keywords = MHC summary = doi = 10.1016/j.cellimm.2020.104235 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 keywords = MHC; SPP; tap summary = doi = 10.3389/fimmu.2015.00298 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 keywords = MHC; Mafa summary = doi = 10.1007/s00251-009-0412-9 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 keywords = HLA; IEDB; MHC summary = In the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and in the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens'' analyses were carried out successively by different tools. For the first step, MHC-I and II binding, MHC-I processing, MHC-I population coverage and MHC-I immunogenicity prediction analyses, and for the second step, MHC-I and II protein-peptide docking, epitope conservation, and cross-reactivity with host antigens analyses were considered. In this study, the binding ability of the first step selected peptides to human and mouse MHC molecules, was analyzed by CABS-dock (http://biocomp.chem.uw.edu.pl/CABSdock/) server. In cancer immunotherapy, the CTL-mediated responses play the central role in eradication of malignant cells, and the binding of epitopes to MHC-I molecules is an essential step for antigen presentation to CTLs. Thus, in this study, predicted epitopes were primarily selected by their MHC-I binding and processing scores. doi = 10.1371/journal.pone.0205933 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 keywords = MHC; RNA; bat; gene; sequence summary = alecto transcriptome provides information on a variety of immune genes not previously identified in any bat species and represents an important starting point for examining the antiviral activity of these molecules. To enrich for sequences corresponding to cytokines and innate immune genes, the second dataset was derived from pooled total RNA obtained from mitogen-stimulated spleen, white blood cells and lymph node and unstimulated thymus and bone marrow obtained from one pregnant female and one adult male flying fox. A full length transcript, encoding a 667 amino acid protein was identified in our bat transcriptome datasets and found to be orthologous to Mx1 based on comparison with known mammalian Mx1 and Mx2 family members (Figure 4a and data not shown). Genes involved in the adaptive immune system, including MHC class I and II genes and T and B cell receptors and co-receptors were highly represented in both the thymus and pooled datasets providing evidence that bats have all of the components necessary to mount an adaptive immune response. doi = 10.1186/1471-2164-13-261 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 keywords = A*11:01; HLA; MHC; SLA-1; molecule summary = doi = 10.1007/s00251-011-0555-3 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 keywords = CD8; CNS; CTL; MHC summary = doi = 10.1016/s0065-3527(01)56029-7 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 keywords = Fig; IFN; JHMV; MHC summary = doi = 10.1016/j.virol.2013.11.025 id = cord-005393-rhji4io9 author = Popko, Brian title = The effects of interferon-γ on the central nervous system date = 1997 keywords = CNS; EAE; IFN; IFN-7; MHC summary = doi = 10.1007/bf02740619 id = cord-000224-2lz03oqb author = Porter, Kristen A. title = Class II Transactivator (CIITA) Enhances Cytoplasmic Processing of HIV-1 Pr55Gag date = 2010-06-24 keywords = CIITA; Gag; HLA; MHC summary = METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that both stable and transient expression of CIITA in HIV producer cells does not induce HLA-DR-associated intracellular retention of Gag, but does increase the infectivity of virions. We hypothesized that recapitulating endogenous expression of the entire class II antigen presentation pathway in producer cells via expression of CIITA would restore infectious virus release and provide a more physiologically relevant model for HIV-1 assembly studies. Virus release, both infectious and particle titers) were reduced when cells were transfected with either HLA-DR or other components of the MHC class II antigen presentation pathway ( Figure S2 ), confirming a correlation between Gag retention and reduced virus titers in the presence of HLA-DR, as previously demonstrated [8] . Together, these data suggest CIITA has two effects on the HIV replicative cycle in producer cells, both of which are independent of the MHC II antigen processing pathway; i) it does not induce HLA-DR, mediated intracellular retention of Gag and ii) it increases the infectivity of HIV virions. doi = 10.1371/journal.pone.0011304 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 keywords = CNS; GFAP; MHC summary = doi = 10.1016/0165-5728(94)90163-5 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 keywords = HLA; MHC; SARS; Table summary = doi = 10.3390/vaccines8030408 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 keywords = DRB; MHC summary = doi = 10.1186/s12862-016-0802-1 id = cord-260485-o5wpcxdp author = Schmidt-Küntzel, Anne title = Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation date = 2018-01-12 keywords = Mhc; cheetah; diversity; genetic summary = doi = 10.1016/b978-0-12-804088-1.00006-x id = cord-022395-rk31pwoa author = Schuller-Levis, Georgia title = Central Nervous System: Viral Infection and Immune-Mediated Inflammation date = 2012-12-02 keywords = CNS; EAE; IL-1; MHC; cell summary = Acute and chronic relapsing EAE can be induced in laboratory animals by an injection of CNS tissue, CNS myelin, myelin basic protein, or more recently, T-cell lines specific for nervous system antigens. Infection with mouse hepatitis virus (MHV), has been shown to block expression of MHC molecules on murine cerebral endothelial cells (see later discussion) (Joseph et al., 1991) . Until recently, the HLA Class I molecules were thought to be the primary, if not the only, HLA recognition structure for CTLs. Studies of measles and Epstein-Barr virus (EBV) infection suggest that HLA Class II molecules can also serve as recognition sites, further expanding the potential action of CTLs. Viral antigens recognized by CTLs have also been expanded beyond the traditional cell surface molecules (Braciale and Braciale, 1986) . The subsequent activation of specific cellular transcription factors in response to extracellular stimuli can induce the expression of virus and lead to CNS disease. Immune response gene products (la antigens) on glial and endothelial cells in virus-induced demyelination doi = 10.1016/b978-0-12-628930-5.50019-9 id = cord-310252-0cdqhrcw author = Seliger, Barbara title = Chapter 7 IFN Inducibility of Major Histocompatibility Antigens in Tumors date = 2008-12-03 keywords = APM; HLA; IFN; MHC; stat1 summary = doi = 10.1016/s0065-230x(08)00407-7 id = cord-275608-joyan7ij author = Sewell, Andrew K. title = Why must T cells be cross-reactive? date = 2012-08-24 keywords = HLA; MHC; TCR; cell summary = doi = 10.1038/nri3279 id = cord-289606-hypqpqs0 author = Sigal, Luis J. title = Activation of CD8 T Lymphocytes during Viral Infections date = 2016-05-09 keywords = CD8; MHC summary = doi = 10.1016/b978-0-12-374279-7.14009-3 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 keywords = Langerhans; MHC; cell; dendritic summary = These ''danger'' or activation signals induce profound changes in dendritic cell physiology, facilitating the efficient stimulation of both adaptive and innate immunity. The DC are sensitive to a wide range of these stimuli that serve not only to activate innate immunity via the release of chemokines and proinflammatory mediators, but also trigger DC migration towards local lymphoid tissue in order to generate antigen-specific (adaptive) immunity. 37, 38 For the Langerhans cell, activation is also accompanied by the loss of specific markers, such as cutaneous lymphocyte antigen (CLA) and Birbeck granules, along with altered surface expression of cell adhesion molecules that facilitate movement into the afferent lymph. 138 Flt-3 is able to induce protective antitumour immunity in some animal models, 139, 140 which is thought to be a consequence of increased presentation of tumour antigens combined with increased NK cell activity. FcγR-mediated induction of dendritic cell maturation and MHC class I-restricted antigen presentation after immune complex internalisation doi = 10.1046/j.1440-1711.2000.00888.x id = cord-000479-u87eaaj8 author = Stolf, Beatriz S. title = Protein Disulfide Isomerase and Host-Pathogen Interaction date = 2011-10-11 keywords = Leishmania; MHC; PDI; protein summary = doi = 10.1100/2011/289182 id = cord-259669-fod4xkd7 author = Summerfield, Artur title = The porcine dendritic cell family date = 2008-06-06 keywords = IFN; MHC; cell summary = Being strategically located at sites of pathogen entry, such as mucosal surfaces and Considering the pivotal roles played by dendritic cells (DCs) in both innate and adaptive immune responses, advances in the field of porcine immunology DC biology have recently progressed rapidly. The function of porcine monocyte-derived DC has not only been characterized in terms of antigen presentation and lymphocyte activation, but also their response to various ligands of pattern recognition receptors. The function of porcine monocyte-derived DC has not only been characterized in terms of antigen presentation and lymphocyte activation, but also their response to various ligands of pattern recognition receptors. Altogether, the co-expression of CD172a and CD1 along with relatively high levels of both CD80/86 and MHC class II represent phenotypic characteristics of porcine MoDC but no marker clearly differentiating them from monocyte-derived macrophages has been identified. doi = 10.1016/j.dci.2008.05.005 id = cord-279498-ez3yq7xi author = Suzumura, Akio title = Immune Response in the Brain: Glial Response and Cytokine Production date = 2008-12-31 keywords = MHC; TNF summary = doi = 10.1016/s1567-7443(07)10014-4 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 keywords = HLA; MHC; disorder summary = Despite evidence of prominent immune implication in a significant subset of major psychiatric disorder patients such as schizophrenia, bipolar disorder or depression (Khandaker, Dantzer, Jones, 2017) or autism spectrum disorder (Meltzer & Van de Water, 2017) , deciphering the mechanistic link between the HLA system and these disorders was difficult, primarily because of the complex genetic architecture of the HLA system. This section reviews investigations of HLA gene candidate association in schizophrenia, bipolar disorders and Autism Spectrum Disorders, focusing on the risk/protection that HLA alleles/haplotypes may confer on specific sub-groups. Influenza and other infections prenatally can also increase risk of schizophrenia and autism spectrum disorders in the offspring, suggesting that HLA/MHC genetic variations may interact with prenatal infection in the etiology of major psychiatric disorders, although complicated by the immune-suppression that occurs in pregnancy (Shah et al, 2010) . doi = 10.1016/j.bbi.2020.09.033 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 keywords = BCR; CDR3; MHC; TCR; repertoire summary = After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. The Immcantation framework [18, 19] and TRUST (TCR repertoire utilities for solid tissue) [20] can be also used for the same purpose among many other available tools not covered here Though single chain information alone is usually not enough to explain the binding of the receptor to the target epitope, there are several methods applicable to bulk sequencing data. Based on the observation that there are specific positions in TCR CDR3 regions that contact antigen peptides and that the presence of particular sequence motifs can define TCR clusters, Glanville et al., developed the GLIPH (grouping of lymphocyte interactions by paratope hotspots) algorithm [63, 64] . doi = 10.1016/j.csbj.2020.07.008 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 keywords = HLA; MHC; NTD; cell; epitope summary = doi = 10.1586/14760584.2015.955478 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 keywords = MDV; MHC; Marek; protein; spot summary = doi = 10.1016/j.virol.2009.05.020 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 keywords = MAP; MHC; Mycobacterium; epitope; protein summary = The prompt identification and isolation of the infected animals in the subclinical stage would prevent the spread of the infection.In the present study, an immunoinformatic approach has been used to investigate the immunogenic properties of 10 MAP proteins. For each previously-described immunoreactive protein, we predicted the epitopes capable of eliciting an immune response by binding both B-cells and/or class I MHC antigens. The class I MHC epitopes as of Figure 3 are further aligned against both the mycobacteria and cow databases to assess the specificity of the predicted epitope sequences for MAP. To prove selected epitopes as suitable candidates for the unbiased diagnosis of MAP infection, we aligned the peptides sequences against a database comprising the closest taxonomically-related bacteria. Selected peptide sequences of the immunoreactive proteins were searched against the NCBInr database restricted to Mycobacterium avium subsp. Gene expression profiles during subclinical Mycobacterium avium subspecies paratuberculosis infection in sheep can predict disease outcome doi = 10.3390/pathogens9090705 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 keywords = MHC summary = title: Rapid changes in shape and number of MHC class II expressing cells in rat airways after Mycoplasma pulmonis infection We sought to determine the effect of this infection on the shape and number of dendritic cells and other major histocompatibility complex (MHC) class II expressing cells in the airway mucosa of Wistar rats. pulmonis infection as a model of chronic inflammation to determine the time course of changes in shape, number, and distribution of MHC class II expressing cells in the airway mucosa, with a focus on the region beneath the airway epithelium where M. In pathogen-free rats, a network of MHC class II expressing cells, identified by their OX6 immunoreactivity, occupied a thin layer just beneath the epithelium of the tracheal mucosa (Fig. 1A) . pulmonis infection resulted in conspicuous changes in the shape, number, and distribution of MHC class II expressing cells in the tracheal mucosa. doi = 10.1016/s0008-8749(03)00026-1 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 keywords = IFN; MHC; RNA; TNF summary = Previous data from this laboratory had shown that the cytokine tumor necrosis factor-α (TNF-α) enhances IFN-γ-mediated class II antigen expression on astrocytes. To determine the steady-state level of mRNA for class II, Northern blot analysis was performed using a eDNA probe for murine class Ii genes (E-a), with total RNA isolated from cultured astrocytes. The duration of protein synthesis required to allow expression of the class II MHC gene in astrocytes was examined in cells that were pretreated with IFN-y or IFN-7/TNF-a for different lengths of time prior to the addition of CHX. In this study we have shown that primary neonatal rat astrocytes, upon stimulation with IFN-~,, express mRNA transcripts for class II MHC genes, and that TNF-a enhances the expression of IFN-~,-induced class II mRNA. The expression of class II mRNA was completely inhibited when CHX was included with IFN-~, and IFN-''t/TNF-~ treatment, indicating that newly synthesized protein is required for astrocyte class II MHC gene expression. doi = 10.1016/0165-5728(90)90103-t 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 keywords = MHC; TCR summary = doi = 10.1016/j.mehy.2005.05.041 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 keywords = MHC summary = doi = 10.1016/0165-5728(90)90074-w id = cord-021079-m6nbs2c0 author = Yong, Voon Wee title = Major histocompatibility complex molecules on glial cells date = 2004-11-23 keywords = MHC summary = doi = 10.1016/1044-5765(92)90006-n 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 keywords = BALB; MHC summary = PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. To our knowledge, this is the first online server for the prediction of peptides binding to a complete set of major histocompatibility complex molecules in a model organism (H2(d) haplotype). PRED BALB/c is a computational system for the prediction of peptides binding to all five MHC molecules in BALB/c mice (H2 d ) class I (H2-K d , H2-L d and H2-D d ) and class II (I-A d and I-E d ) that allows analysis of proteins for the presence of binding motifs to all five H2 d molecules in parallel. We derived the initial quantitative matrices for PRED BALB/c using logarithmic equations based on the frequency of amino acids at specific positions within the training set of 9mer peptides as described previously (16) . To our knowledge, PRED BALB/c is the first online server for the prediction of peptides binding to a complete set of MHC molecules in a model organism (H2 d haplotype). doi = 10.1093/nar/gki479 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 keywords = B16; MHC; TAP1; b16f10 summary = 11 The nature of the immune suppression may include secretion of immunosuppressive cytokines, 12 the expression of ligands (FAS-L) that initiate apoptosis in cytotoxic T-cells 13 and tumor variants that are deficient in antigen processing and presentation. As a consequence, specific cytotoxic T-cells generated by the vaccine protocol are unable to recognize and kill these tumor variants due to defective presentation of tumor associated antigen-derived peptides recognized by the CTLs. The MHC Class I restricted antigen presentation pathway consists of a number of genes encoded in the MHC Class I locus of human chromosome 6. [16] [17] [18] Conversely TAP1 expression has been associated with tumor infiltrating lymphocytes (TILs), a characteristic of good clinical outcome 8, 16, 19 and spontaneous regression of MAAs. 4 In our study, we examine the effect of the restoration of TAP1 expression on MHC Class I antigen surface expression in the murine MAA cell line, B16F10. doi = 10.1002/ijc.22371 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 keywords = HLA; MHC; SARS summary = Aiming at better understanding the biology of the infection and the immune response against the virus in the Brazilian population, we analysed SARS-CoV-2 protein S peptides in order to identify epitopes able to elicit an immune response mediated by the most frequent MHC-I alleles using in silico methods. METHODS: Our analyses consisted in searching for the most frequent Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-C alleles in the Brazilian population, excluding the genetic isolates; then, we performed: molecular modelling for unsolved structures, MHC-I binding affinity and antigenicity prediction, peptide docking and molecular dynamics of the best fitted MHC-I/protein S complexes. CONCLUSIONS: Being aware of the intrinsic limitations of in silico analysis (mainly the differences between the real and the Protein Data Bank (PDB) structure; and accuracy of the methods for simulate proteasome cleavage), we identified 24 epitopes able to interact with 17 MHC-I more frequent alleles in the Brazilian population that could be useful for the development of strategic methods for vaccines against SARS-CoV-2. doi = 10.1136/jclinpath-2020-206946 id = cord-334603-yt2pmxi3 author = de Sousa, Eric title = Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants date = 2020-07-18 keywords = HLA; MHC; SARS summary = title: Mortality in COVID-19 disease patients: Correlating Association of Major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants Abstract As the 2019 (COVID-19) pandemic caused by the novel coronavirus, SARS-CoV-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. HLA-DQB1*06:02 has been selected for increased resistance to Yersinia pestis in immigrants from Africa to Europe, engagement of CD4+ T-cells to HLA-DQB1*06:02 leads to increased, pro-inflammatory IL-17 production, independent of the MHC class II presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . DRB3*02:02 is linked to Grave''s disease (44) , serum IgG antibodies to Chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) In conclusion, there appears to be no selective pressure from MHC class I alleles for SARS-CoV-2 variants tested. doi = 10.1016/j.ijid.2020.07.016 id = cord-005953-5z89yeb6 author = nan title = Abstracts des 114. Internistenkongresses 2008 date = 2008 keywords = Gruppe; HBV; HZV; IFN; MHC; Patienten; Studie; Therapie; Zellen; der; die; eine; expression; ldl; mit; patient; und; von summary = Die anderen beiden Gruppen zeigten zwar in Hinblick auf die Wandstärken einen positiven Effekt, hinsichtlich der Herzfunktion konnten sie jedoch bei bereits deutlich erniedrigten Funktionswerten zum Baseline-Zeitpunkt lediglich stabilisiert werden (Reduktion der Wandstärke nach 3 Jahren ERT: Gruppe wenig Fibrose= 10 mm; Gruppe viel Fibrose= 12 mm) Schlussfolgerung: Die Enzymersatztherapie ist eine effektive Langzeitbehandlung bei Patienten mit Fabry Kardiomyopathie. Der Einfluss der sauren Sphingomyelinase auf die Expression von Matrix-Metalloproteinase-1 in intestinalen Epithelzellen und Fibroblasten Background: The calcineurin (Cn)/NF-AT signaling cascade takes a crucial role during T-cell activation and the development of myocardial hypertrophy. Effective and safe reduction of blood pressue by the combination of amlodipine 5/valsartan 160 mg in patients with hypertension and metabolic risk factors not controlled by amlodipine 5 mg or felodipine 5 mga subanalysis of the express-m trial Introduction: Atrial fibrillation (AF) is the most common cardiac arrhythmia and frequently occurs in patients with coronary heart disease. doi = 10.1007/s00063-008-1026-y id = cord-009567-osstpum6 author = nan title = Abstracts Oral date = 2008-04-23 keywords = AMR; BALB; CD25; CD4; CD8; CMV; CNI; DSA; GFR; Group; HCV; HLA; IFN; IL-6; IRI; MELD; MHC; MMF; OLT; SRL; TAC; TLR4; Treg; University; cell; foxp3; graft; kidney; patient; recipient; result; transplant; transplantation summary = Introduction: Previously, it has been demonstrated that FOXP3, a gene required for the development and function of regulatory T cells, was highly expressed in the graft during cardiac rejection, suggesting infiltration of regulatory T cells in the transplanted organ during an allogeneic response. Efficacy and safety parameters assessed at follow-up included: acute rejection; patient and graft survival; renal function, vital signs, basic lab results and immunosuppressive regimen for the patients 10 years after completion of the original study. We analyzed, for the first time, the expression of TLR4 in PBMC from kidney recipients with contrasted situations: operational tolerance and chronic immune-mediated rejection (Banff 2005), compared to patients with normal histology and stable graft function, non transplant patients with renal failure and healthy volunteers. doi = 10.1111/j.1600-6143.2008.02254.x id = cord-018034-gx5c9mk8 author = nan title = Cell and Tissue Reactions date = 2006 keywords = BBB; CNS; CSF; Fig; ICP; MHC; brain; cell; injury; tissue summary = doi = 10.1007/3-540-28995-x_4 id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 keywords = APC; BCR; CD14; CD4; CD8; CMV; CTL; EBV; ELISA; Germany; HCV; HIV; HLA; IBD; IFN; IL-10; IL-2; IL-4; IL-6; Immunology; Institute; LPS; MHC; NKT; PCR; RNA; SLE; TCR; TGF; TLR; TLR4; TNF; University; antigen; cell; dna; expression; immune; mouse; patient; protein; response; result; study; th1; th2 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. doi = 10.1002/eji.200990224 id = cord-023055-ntbvmssh author = nan title = Immunogenicity date = 2004-02-19 keywords = APC; CD2; CD3; CD4; CD8; CTL; HLA; IL-2; MHC; TCR; University; antigen; cell; class; clone; dna; gene; mouse; response; specific summary = Antigen is internalized into acidic vesicles, proteolyzed, and peptides containing T ceU antigenic determinants are transported to the APC surface where they are recognized by the antigen-specific T cell in conjunction with Ia. Most Ia-"pressing cells are competent APC, however, only B cells have antigen-specilic receptors on their surface aUowing bound antigen to be processed and presented at 1/lW the antigen concentration required by nonspecific APC Little is known about B cell antigen processing function during differentiation, or if Ig-mediated APC function is altered at different maturational stages, thus allowing regulation of B cell-helper T cell interactions. These results indicate that the poor response of murine CTL to human class I antigens is not determined by selection in the thymus, but by species-specific constraints on the interaction of MHC antigens with T-cell recognition structures. doi = 10.1002/jcb.240410506 id = cord-023143-fcno330z author = nan title = Molecular aspects of viral immunity date = 2004-02-19 keywords = CD4; CD8; CNS; CTL; HIV; HIV-1; HLA; IFN; LCMV; MHC; cell; infection; mouse; protein; response; viral; virus summary = doi = 10.1002/jcb.240591009 id = cord-329036-4bf8eiix author = nan title = Coronavirus induction of class I major histocompatibility complex expression in murine astrocytes is virus strain specific date = 1994-09-01 keywords = A59; JHMV; MHC; MHV; class summary = doi = nan 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 keywords = IFN; ISA; MHC; Montanide summary = doi = 10.1186/s12879-020-05220-2