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?' ---------------------------------------------------------- 117 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 33815 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 5 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 117 HLA 33 cell 28 SARS 25 MHC 24 patient 19 CD8 11 CD4 10 HIV 10 CMV 9 PCR 8 result 8 donor 8 dna 8 HSCT 8 HCV 8 GVHD 8 Fig 8 CD34 8 AML 7 figure 7 RIC 7 Hospital 7 HBV 6 transplantation 6 study 6 response 6 protein 6 platelet 6 method 6 disease 6 day 6 University 6 NRM 6 NAT 6 IFN 6 CTL 6 ABO 5 test 5 group 5 epitope 5 blood 5 antibody 5 TCR 5 RNA 5 RHD 5 RBC 5 HCT 5 DAT 5 ATG 5 ASCT Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 28406 % 28307 cell 25918 patient 13535 blood 10855 donor 7260 day 7172 study 6867 result 6586 group 6442 disease 6095 t 5614 response 5509 transfusion 5202 method 5127 year 4779 antibody 4606 treatment 4583 infection 4450 transplantation 4365 peptide 4356 time 4249 antigen 4166 p 4131 analysis 4052 protein 4050 risk 4048 level 4042 platelet 3953 case 3837 epitope 3728 transplant 3468 month 3410 sample 3348 datum 3186 expression 3168 number 3100 system 3033 virus 3020 mouse 2970 stem 2862 age 2860 graft 2853 factor 2769 conclusion 2759 therapy 2759 effect 2636 unit 2630 gene 2629 survival 2617 vaccine Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 7023 HLA 5213 T 3870 HSCT 2257 GVHD 2236 MHC 1954 CD8 1862 al 1793 CD4 1729 II 1561 SARS 1503 et 1492 C 1485 . 1481 CMV 1474 mg 1460 RBC 1427 SCT 1184 B 1171 HIV 1149 OS 1138 CD34 1084 AML 1033 A 991 IFN 982 - 973 HCV 972 NK 953 GvHD 946 TCR 943 PCR 918 G 914 Blood 907 CTL 881 CoV-2 863 University 853 Fig 820 CI 814 ATG 807 S 806 Background 760 D 758 ABO 745 ASCT 740 HBV 717 M 676 I 671 Hospital 661 IV 660 Table 655 Hb Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 9398 we 4240 it 2291 i 1488 they 1013 them 411 he 293 she 259 us 141 one 71 itself 62 you 48 themselves 15 himself 14 him 10 ourselves 10 her 10 haec 8 me 6 p210bcr 5 netmhcpan4.0 5 itma 3 s 3 mg 3 igg4 3 ifitm3 2 yourself 2 u 2 ours 2 interleukin-15 2 imm+ 2 igmcic 2 esat-6 2 e2f2-/-mice 2 crx-527 2 beta-2-m 2 anti-(self 1 ≥65 1 ≥10× 1 αat 1 ya 1 y8tcr.s 1 theirs 1 tdcs 1 srbcs 1 sepsis-(or 1 s382 1 rab4a 1 rab3b 1 pt#3 1 prets Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 100024 be 16467 have 9376 use 5210 show 3911 include 3881 receive 3555 compare 3482 associate 3431 increase 3374 perform 3149 follow 2884 do 2784 base 2772 find 2574 identify 2489 develop 2397 induce 2389 observe 2380 reduce 2275 report 2229 treat 1962 evaluate 1960 relate 1957 bind 1918 suggest 1892 determine 1856 test 1820 detect 1792 present 1771 provide 1710 express 1700 analyze 1650 occur 1649 require 1583 undergo 1570 give 1517 demonstrate 1467 remain 1450 obtain 1450 indicate 1413 result 1411 improve 1372 predict 1343 lead 1343 collect 1276 match 1242 aim 1240 consider 1221 cause 1219 assess Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 10246 - 7731 not 6900 high 4091 also 4043 anti 3423 specific 3414 low 3408 more 3407 other 3331 immune 3330 clinical 3252 only 3216 well 3159 median 3109 positive 2961 acute 2856 human 2662 significant 2662 non 2630 respectively 2616 different 2566 however 2562 first 2343 most 2342 severe 2197 significantly 2060 such 1984 negative 1931 viral 1861 as 1735 further 1642 chronic 1639 early 1553 new 1522 single 1520 overall 1515 red 1473 long 1419 autologous 1391 important 1375 peripheral 1327 post 1283 normal 1270 major 1252 large 1240 pre 1208 hematopoietic 1205 similar 1200 unrelated 1196 primary Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 639 most 443 least 346 high 345 good 292 Most 123 low 76 large 55 great 33 bad 32 strong 24 late 24 early 22 common 21 safe 19 young 14 old 13 long 11 big 9 small 7 poor 6 near 6 close 6 B27 5 short 5 p=0.016 5 new 5 fresh 5 easy 5 clear 4 weak 4 steep 4 few 4 broad 4 -t 4 -E 3 postsurgery 3 fast 3 E(13.4 3 226/303 3 -H 3 -Diagast 2 wide 2 simple 2 sick 2 fit 1 ≤180 1 −118 1 αGal 1 v\'hich 1 theb Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 1704 most 371 least 53 well 10 highest 4 lowest 2 -hla 1 s2&3 1 ko→wt 1 hard 1 furthest 1 freshest 1 fast 1 cm² 1 -psmb10 1 -chest Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 34 doi.org 14 tools.iedb.org 6 www.cbs.dtu.dk 5 www.syfpeithi.de 5 www.ncbi.nlm.nih.gov 5 bit.ly 4 www.iedb.org 4 www.hiv.lanl.gov 4 www.ebi.ac.uk 4 orcid.org 4 crdd.osdd.net 3 www.uniprot.org 3 www.nrlqa.net 3 www.mederrors.com. 3 www.hsph.harvard.edu 3 www.allelefrequencies.net 3 scratch.proteomics.ics.uci.edu 2 www.worldometers.info 2 www.who.int 2 www.rcsb.org 2 www.mdpi.com 2 www.graphpad.com 2 www.frontiersin.org 2 www.custommune.com 2 www-bimas.cit.nih.gov 2 npsa-prabi.ibcp.fr 2 clinicaltrials.gov 1 zha 1 www3.niaid.nih.gov 1 www.wwpdb.org 1 www.wwarn.org 1 www.who-umc 1 www.tcells.org 1 www.syfpeithi 1 www.siopen-r-net.org 1 www.python.org 1 www.pymol.org 1 www.proteinatlas.org 1 www.paproc.de 1 www.nrz-hygiene.de 1 www.nature.com 1 www.mpiibberlin.mpg.de 1 www.medicine.virginia 1 www.jenner.ac.uk 1 www.jalview.org 1 www.isbtweb.org 1 www.internationalinnovation.com 1 www.immuneepitope.org 1 www.imgt.org 1 www.genscript.com Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 20 http://doi.org/10.1101/2020.10.02.20206086 5 http://tools.iedb.org/mhcii/ 4 http://doi.org/10.1101/2020.04 3 http://www.uniprot.org/ 3 http://www.syfpeithi.de/ 3 http://www.nrlqa.net 3 http://www.ncbi.nlm.nih.gov/ 3 http://www.mederrors.com. 3 http://www.hsph.harvard.edu/cearegistry 3 http://tools.iedb.org/immunogenicity/ 3 http://scratch.proteomics.ics.uci.edu/ 3 http://doi.org/10.1101/2020.06.17.20133637 2 http://www.worldometers.info/coronavirus/ 2 http://www.hiv.lanl.gov/content/immunology 2 http://www.frontiersin.org/articles/10.3389/fimmu 2 http://www.custommune.com 2 http://www.cbs.dtu.dk/services/NetMHC/ 2 http://www-bimas.cit.nih.gov/molbio/hla 2 http://tools.iedb.org/population/ 1 http://zha 1 http://www3.niaid.nih.gov/topics/ 1 http://www.wwpdb.org/ 1 http://www.wwarn.org/ 1 http://www.who.int/who-documents-detail/draft-landscape-of-covid-19-candidate-vaccines 1 http://www.who.int/emergencies/diseases/ 1 http://www.who-umc 1 http://www.tcells.org 1 http://www.syfpeithi.de/0-Home 1 http://www.syfpeithi.de 1 http://www.syfpeithi 1 http://www.siopen-r-net.org 1 http://www.rcsb.org/structure/3nvq 1 http://www.rcsb.org/ 1 http://www.python.org 1 http://www.pymol.org/ 1 http://www.proteinatlas.org/humanproteome/ 1 http://www.paproc.de 1 http://www.nrz-hygiene.de/surveillance/onko.htm] 1 http://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ 1 http://www.ncbi.nlm.nih.gov/blast/ 1 http://www.nature.com/leu 1 http://www.mpiibberlin.mpg.de/MAPPP/ 1 http://www.medicine.virginia 1 http://www.mdpi.com/2076-393X/8/3/408/ 1 http://www.mdpi.com/2076-393X/8/3/355/s1 1 http://www.jenner.ac.uk 1 http://www.jalview.org/ 1 http://www.isbtweb.org/working-parties/red-cell-immunogenetics-and-bloodgroup-terminology/ 1 http://www.internationalinnovation.com/build/wp-content/uploads/2016/05/David_Lanar_Intl_Innovation_ 1 http://www.immuneepitope.org/MHCalleleId/142 Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 siegel_robert@lilly.com 1 sewellak@cardiff.ac.uk 1 reviewer17106@ebi.ac.uk 1 maris@email.chop.edu 1 maris@chop.edu 1 mail@wmda.info 1 lunde@cbs.dtu.dk 1 cerf@necker.fr 1 arocha@ufc.br 1 florent_ginhoux@immunol.astar.edu.sg Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 74 antigen presenting cells 71 patients are alive 41 patients did not 28 cells did not 28 treatment related mortality 26 patients were alive 25 cells were then 24 levels were significantly 23 % were male 22 cells was significantly 21 cells do not 20 patients received myeloablative 19 patient did not 19 patients were male 18 patients were positive 16 patients developed acute 16 patients were not 15 cells are not 15 patients had grade 14 donors were more 14 patients were also 13 cells was not 13 cells were also 13 patient was not 13 patients developed grade 13 patients had significantly 12 groups did not 12 patients are often 12 patients received bone 12 patients received hsct 12 patients were randomly 12 transfusion related acute 11 cells are able 11 cells were not 11 cells were significantly 11 donor was unrelated 11 donors were hla 11 patients had more 11 patients were evaluable 11 results were not 10 % were female 10 % were hla 10 cells were co 10 cells were further 10 groups were similar 10 patients developed chronic 10 patients had acute 10 patients is not 10 peptide binding affinity 10 platelets were not Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 4 cells are not available 4 donor is not available 4 patient had no history 4 patients is not clear 3 antibodies are not clinically 3 antibodies had no apparent 3 antibodies had no effect 3 antibodies were not anymore 3 blood was not less 3 cell was not present 3 cells do not consistently 3 cells was not significantly 3 donors are not available 3 donors had no major 3 donors have no intention 3 groups did not significantly 3 groups has not statistical 3 levels are not relevant 3 methods are not sufficiently 3 patient had no transfusion 3 patient was not essentially 3 platelets were not available 3 results show no evidence 3 results showed no discrepancies 3 transfusion are not well 3 transfusions are not consistent 3 treatment did not significantly 3 treatment is not available 2 % had no confidence 2 cells had no effect 2 cells were not different 2 donor has not yet 2 donors were not able 2 groups were not statistically 2 patient has not yet 2 patient was not statistically 2 patients were not evaluable 2 patients were not subsequently 2 results were not available 2 transfusion had no effect 2 transplantation were not significantly 2 treatment had no effect 2 treatment had no impact 2 years was not different 1 % had no change 1 % had no clinical 1 % had no detectable 1 % had no proteinuria 1 % has no negative 1 % is not much A rudimentary bibliography -------------------------- id = cord-347714-vxxhglx7 author = Abitogun, Folagbade title = COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding date = 2020-10-14 keywords = HLA; SARS; epitope; protein summary = (10, 11) The structure of the spike glycoprotein of the virus is also an extended similarity with SARS-CoV, (4) which together with COVID19: Exploring uncommon epitopes for a stable immune response through MHC1 binding other proteins of the virus are candidates for vaccine development and are being explored in different settings due to the active roles of the proteins in the infectivity of the virus. (18) However studies have shown that full length spike protein vaccines for SARS-CoV may lead to antibody mediated disease enhancement causing inflammatory and liver damage in animal models (19, 20) which is why in this manuscript, we applied immuno-informatics "in silico" approaches to identify potential CD8+ cytotoxic T Cell epitopes from proteins of SARS-CoV-2, SARS-CoV and MERS-CoV. Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach doi = 10.1101/2020.10.14.339689 id = cord-353877-wzndpcq3 author = Albagi, Sahar Obi Abd title = A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach date = 2020-05-20 keywords = HLA; MHC; Spike summary = Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. Consistent with global efforts, this study aims to predict potential COVID-19 Peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. The molecular docking results showed that the Spike peptide FTISVTTEI has the lowest docking energy score with the MHC I HLA-B1503 allele, hence it is predicted to have the highest binding affinity. Regarding the interaction with the MHC II molecule, the Spike peptide EVFNATRFASVYAWN showed the lowest docking energy score with the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1*06:02, and HLA-DRB1, hence it is predicted to have the highest binding affinity to the three alleles. doi = 10.1101/2020.05.20.106351 id = cord-009836-7o6htufh author = Borrow, Persephone title = Cytotoxic T‐lymphocyte escape viral variants: how important are they in viral evasion of immune clearance in vivo? date = 2006-04-28 keywords = CTL; HLA; response; virus summary = Epitope mapping performed using the Gpl 60 sequence of the patient''s autologous early HIV-1 population indicated that this response was in fact extremely focused on a single epitope encompassing Gpl60 amino acids 30-38(9), recognized in association with HLA-B44, The frequency of epitope-specific CTL was extremely high: at the earhest timepoint available for study, which may have been shghtly after the peak of the primary immune response, 1 in 1 7 peripheral blood mononuclear cells (EBMCs) were found to score as virus-specific CTL precursors by limiting dilution analysis, a technique which has recently been shown to greatly underestimate the total numher of epitope-specific T cells (55, 56) , As shown in Fig, 1 , viral variants bearing mutations in the epitopic sequence which conferred escape from recognition by epitope-specific CTL rapidly appeared in this patienc, and then increased in frequency until 164/1998 they had cotnpieteiy repiaced the transmitted virai strain. doi = 10.1111/j.1600-065x.1998.tb01206.x id = cord-333391-6l0cpvgr author = Bortolotti, Daria title = SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway date = 2020-08-26 keywords = HLA; SARS; figure summary = title: SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway When we stained the cells with anticlassical HLA class I molecules (HLA-A, HLA-B, HLA-C) antibody, we recognized a significant decrease in their membrane expression when lung epithelial cells were transfected with SP1 protein (p < 0.001; Student t test) ( Figure 3D ,E). To be sure that the increase in HLA-E expression in lung epithelial cells transfected with SP1 protein is controlled by GATA3 transcription factor, we treated the cells with pyrrothiogatain. When NK cells were co-cultured with SP1-transfected Beas-2B cells, we observed an increase in the protein (p < 0.001; Student t test) ( Figure 6A ,B) and mRNA (p < 0.01; Student t test) ( Figure 6C ) expression of the inhibitory receptor NKG2A/CD94. On the contrary, lung cells, which express HLA-E molecules in the presence of SARS-CoV spike 1 protein, are able to inhibit IFN-gamma secretion and NK cell activation. doi = 10.3390/cells9091975 id = cord-004395-erqmbi2b author = Bugembe, Daniel Lule title = Computational MHC-I epitope predictor identifies 95% of experimentally mapped HIV-1 clade A and D epitopes in a Ugandan cohort date = 2020-02-22 keywords = HIV-1; HLA summary = doi = 10.1186/s12879-020-4876-4 id = cord-013093-aa4cf44u author = Cassotta, Antonino title = Deciphering and predicting CD4(+) T cell immunodominance of influenza virus hemagglutinin date = 2020-07-09 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 = title: Induction of T-cell response by a DNA vaccine encoding a novel HLA-A*0201 severe acute respiratory syndrome coronavirus epitope The severe acute respiratory syndrome coronavirus nucleocapsid protein (SARS-CoV N) is one of the major targets for SARS vaccine due to its high potency in triggering immune responses. The results of the T-cell stimulation assay demonstrated that the novel N-protein peptide revealed in the present study is able to trigger specific cytotoxic T-cell response in human PBMCs. The four most immunogenic peptides (N220, N223, N227 and N317) selected in the T2-cell binding assay and the human T-cell stimulation assay were further tested for their potency in triggering immune response against the SARS N-protein expressing cells in an animal model. A peptide sequence useful for inducing the cytotoxic T-cell response should be presented as endogenous peptide epitope through proteasome digestion and have a high binding affinity towards the human MHC class I molecules. doi = 10.1016/j.vaccine.2007.05.025 id = cord-355374-e8k72955 author = Clemens, E. Bridie title = Harnessing the Power of T Cells: The Promising Hope for a Universal Influenza Vaccine date = 2018-03-26 keywords = CD4; CD8; HLA; Trm; cell; influenza summary = Influenza virus-specific CD8 + Trm in human lung tissue also maintain diverse TCR profiles-a feature important for effective T cell function and protection against the generation of viral-escape mutants [128] . HLA-I allele expression is an important predictor of cross-reactive influenza-specific CD8 + T cell immunity, with a recent study identifying five alleles (A*02:01, A*03:01, B*57:01, B*18:01, and B*08:01) capable of eliciting robust CD8 + T cell responses against immunogenic NP and M1 peptides that are conserved across all human influenza A virus, including the novel avian-derived H7N9 virus [18] . Thus, upon infection with H7N9, individuals with these HLA alleles will need time to activate and amplify new primary CD8 + T cell responses to distinct H7N9 peptide variants rather than recalling T cell responses generated against seasonal influenza viruses, potentially resulting in longer time to recovery and greater risk of severe disease compared to individuals with pre-existing cross-protective CD8 + T cell memory. doi = 10.3390/vaccines6020018 id = cord-018714-i291z2ju author = Criado, Paulo Ricardo title = Adverse Drug Reactions date = 2016-12-31 keywords = DIHS; Fig; HHV-6; HLA; SJS; case; cutaneous; dress; drug; eruption; patient; reaction; syndrome summary = doi = 10.1007/978-3-319-33919-1_26 id = cord-265277-ymvrserl author = Crooke, Stephen N. title = Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome date = 2020-05-14 keywords = HLA; SARS summary = A final round of selection on the basis of HLA 197 promiscuity (i.e., predicted binding to > 3 HLA molecules) and predicted antigenicity scoring using the 198 VaxiJen 2.0 server produced a subset of five candidate peptides (four ORF1ab, one S protein) as potential 199 targets for vaccine development (Table 1) with the hypothesis that increased HLA binding promiscuity 200 meant broader population base coverage by those peptides. As selective pressures are known to introduce viral mutations that promote fitness and can lead 266 to evasion of immune responses (59, 60), we first sought to investigate the genetic similarity of all 267 reported SARS-CoV-2 clinical isolates and identify a consensus sequence for use in our epitope 268 prediction studies. An increasing number of studies have employed predictive algorithms to identify potential HLA 285 class I epitopes for SARS-CoV-2, although relatively few have comprehensively analyzed the entire viral 286 proteome. doi = 10.1101/2020.05.14.093757 id = cord-002463-qhtj1pef author = Dash, Raju title = In silico-based vaccine design against Ebola virus glycoprotein date = 2017-03-21 keywords = EBOV; Ebola; HLA; MHC; epitope summary = Top scored eiptope subjected to 100 ns MD simulation **RMSF **RMSD **Hydrogen bond occupency analysis Secquence, having highest vaxijen score Prediction of B cell epitope, using-**T cell epitope prediction by proteasomal C terminal cleavage, TAP transport efficiency and MHC class 1 binding **Epitopes with IC50 value less than 50 for their binding to MHC class 1 molecule from IEDB analysis along with binding to highest number of alleles in both analyses were chosen **Epitope conservancy analysis **Population coverage analysis **Kolaskar and Tongaonkar antigenicity scale 48 **Emini surface accessibility prediction 47 **Karplus and Schulz flexibility prediction 49 **Bepipred linear epitope prediction 50 **Chou and Fasman beta turn prediction 52 Vaxijen analysis with a threshold score of >0. We also validated each epitope by molecular docking simulation and MM-GBSA/MM-PBSA studies with HLA-A*32:15 protein, as it was found common in the results from MHC-I binding interaction analysis. doi = 10.2147/aabc.s115859 id = cord-017629-fuv157f1 author = De Groot, Anne S. title = Epitope-Based Immunome-Derived Vaccines: A Strategy for Improved Design and Safety date = 2008-07-31 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 = Keywords: TCR repertoire, transplantation, cross-reactivity, alloreactivity, TCR, MHC, T cell UNDeRSTANDiNG THe CROSS-ReACTiviTY Shaping the T Lymphocyte Receptor Repertoire Through evolution, numerous processes have been selected to generate a diverse repertoire of TCRαβ able to protect mammalian from pathogenic insults (Figure 1) . Despite the high diversity of the TCR repertoire, a high degree of cross-reactivity has been reported that could be explained by the "natural" ability of TCR to interact with MHC molecules (MHC focus model) as well as the interaction of TCR to a limited number of amino acids of the peptide bound to the MHC peptide groove. Cross-reactivity can be defined by the ability of a given TCR to interact with more than one pMHC complex with different presented peptides or MHC molecules. Before presenting the experimental approach aiming to quantify the number of peptides recognized by a single TCR, we would like to present clear evidences of the cross-reactivity involving memory T cells without previous antigen encounter. doi = 10.3389/fimmu.2016.00089 id = cord-007626-n51v4ior author = Dhib-Jalbut, Suhayl title = Adult human glial cells can present target antigens to HLA-restricted cytotoxic T-cells date = 2002-11-11 keywords = HLA; cell summary = doi = 10.1016/0165-5728(90)90163-h id = cord-018595-x3tleomb author = Dodiuk-Gad, Roni P. title = Adverse Medication Reactions date = 2017-04-25 keywords = HLA; Johnson; SJS; Stevens; cutaneous; dress; drug; patient; reaction; skin; type summary = 2. Delayed-type drug hypersensitivity: Delayed-type drug hypersensitivity reactions usually take several days to weeks following drug exposure, with variable clinical presentations that may include Maculopapular Eruption (MPE), Fixed Drug Eruption (FDE), Acute Generalized Exanthematous Pustulosis (AGEP), Stevens-Johnson Syndrome (SJS), Toxic Epidermal Necrolysis (TEN) and Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS). Examples of strong associations of HLA alleles with specific drug-induced hypersensitivity reactions include abacavir, nevirapine, carbamazepine, and allopurinol (Table 25. [61] , who reported the weak associations of HLA-A29, B12, and MPE maculopapular drug eruption, DRESS drug reaction with eosinophilia and systemic symptoms, SJS/TEN Stevens-Johnson syndrome/toxic epidermal necrolysis DR7 in sulfonamide-related TEN, and HLA-A2, B12 in oxicam-related TEN in Europeans [61] . Drug specific cytotoxic T-cells in the skin lesions of a patient with toxic epidermal necrolysis doi = 10.1007/978-3-319-29785-9_25 id = cord-347647-m9vk9m7h author = Eapen, Mary title = Hematopoietic cell transplantation with cryopreserved grafts for severe aplastic anemia date = 2020-05-08 keywords = HLA summary = We recorded higher 1-year rates of graft failure (HR 2.26, 95% CI 1.17 – 4.35, p=0.01) and of 1-year overall mortality (HR 3.13, 95% CI 1.60 – 6.11, p=0.0008) after transplantation of cryopreserved compared to non-cryopreserved grafts with adjustment for sex, performance score, comorbidity, cytomegalovirus serostatus, and ABO blood group match). To study the effect of cryopreserved compared to non-cryopreserved grafts, (matched-pairs) marginal Cox regression models were built and adjusted for sex, cytomegalovirus serostatus, performance score, comorbidity score, and donor-recipient ABO blood group match. The current analysis was undertaken to examine whether there are differences in survival or other transplant outcomes after transplantation of cryopreserved bone marrow or peripheral blood for severe aplastic anemia. 21 An analysis of non-cryopreserved bone marrow cellular subsets for unrelated donor transplantations failed to show an effect of graft composition on hematopoietic recovery or survival although that report included only 7 patients with aplastic anemia. doi = 10.1016/j.bbmt.2020.04.027 id = cord-016413-lvb79oxo author = Efthimiou, Petros title = Adult-Onset Still’s Disease date = 2018-07-14 keywords = AOSD; HLA; adult; disease; patient summary = Adult-onset Still''s disease (AOSD) is a rare systemic, autoinflammatory disorder that often presents in adolescence and early adulthood with fever, rash, and polyarthritis. Mutation of perforin and the MUNC13-4 genes have been seen in patients with macrophage activation syndrome (MAS), a known severe, life-threatening complication of AOSD [3] . Patients who have the chronic articular disease pattern can present with joint erosions making the differential diagnosis from RA problematic, especially in the absence of systemic signs and symptoms. Interleukin-1 receptor antagonist (anakinra) treatment in patients with systemic-onset juvenile idiopathic arthritis or adult onset Still disease: preliminary experience in France Effectiveness of first-line treatment with recombinant interleukin-1 receptor antagonist in steroid-naive patients with new-onset systemic juvenile idiopathic arthritis: results of a prospective cohort study Clinical manifestations of adult-onset Still''s disease presenting with erosive arthritis: association with low levels of ferritin and Interleukin-18 doi = 10.1007/978-3-319-96929-9_19 id = cord-002704-cpa2sl50 author = El Bissati, Kamal title = Protein nanovaccine confers robust immunity against Toxoplasma date = 2017-09-05 keywords = CD8; GLA; HLA; SAPN summary = doi = 10.1038/s41541-017-0024-6 id = cord-280641-zqdrzyzl author = Fernández Fabrellas, Estrella title = Epidemiología de la sarcoidosis date = 2007-02-28 keywords = HLA; los; que; sarcoidosis summary = Además de investigar la posible etiología de la enfermedad, este estudio examina el situación psicosocial 15 y el curso clínico de 736 pacientes incluidos en los 6 primeros meses desde el diagnóstico histológico de sarcoidosis, y los compara con otros tantos controles pareados por edad, sexo y raza, con un seguimiento de los primeros 215 casos durante los 2 años siguientes a la inclusión 16 . Tanto la piel como los pulmones -órganos más comúnmente afectados-están siempre en contacto con estos antígenos; los estudios sobre la inmunopatogenia de la sarcoidosis apoyan que la enfermedad es el resultado de una superrespuesta inmunitaria y que hay un gran número de potenciales antígenos ambientales que pueden inducir la sensibilización y la consiguiente respuesta mediada por células responsable del desarrollo de granulomas 43 . doi = 10.1157/13098420 id = cord-326983-h6gdck2u author = Ferretti, Andrew P. title = Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein date = 2020-10-20 keywords = CD8; HLA; SARS summary = We focused on memory cells to identify epitopes that are functionally recognized during the course of SARS-CoV-2 infection and included patients with a J o u r n a l P r e -p r o o f range of symptoms to determine if any obvious associations are observed between CD8 + T cell response and disease severity. To determine the global landscape of CD8 + T cell recognition in an unbiased fashion, we built upon a genome-wide screening technology, termed T-Scan (Kula et al., 2019) , that enabled us to simultaneously screen all the memory CD8 + T cells in a patient, one HLA allele at a time, against every possible viral epitope in SARS-CoV-2, as well as the four seasonal coronaviruses that cause the common cold ( Figure 1A ). doi = 10.1016/j.immuni.2020.10.006 id = cord-344933-k23kzqxl author = Flahou, Charlotte title = Innovations dans la culture de plaquettes à partir de cellules souches pluripotentes induites* date = 2020-09-28 keywords = HLA; des; plaquettes summary = Dans cette revue, nous souhaitons apporter une vue d''ensemble de la production in vitro de plaquettes à partir de cellules iPS, et de son possible potentiel transformatif, d''importance capitale dans le domaine de la transfusion des produits sanguins. De plus, contrairement aux réponses allo-immunitaires (par exemple la maladie du greffon contre l''hôte), qui sont évitables par la déplétion des leucocytes ou l''irradiation des produits dérivés du sang, être les cas réfractaires aux transfusions de plaquettes nonconcordantes pour les Antigènes des Leucocytes Humains (HLA) et des Antigènes Plaquettaires Humains (HPA) n''ont pour l''instant pas de solution [6] . La production de plaquettes ex-vivo à partir de cellules souches pluripotentes induites (iPSC) est une solution pour résoudre les problèmes liés à la transfusion allogénique. D''une part, il est possible de produire des plaquettes dérivées d''iPSC produite à partir des cellules du patient, qui dans ce cas n''éliciteront pas de réponse immunitaire. Ex vivo megakaryocyte expansion and platelet production from human cord blood stem cells doi = 10.1016/j.banm.2020.09.040 id = cord-017702-v46ye328 author = Ganguly, Nirmal Kumar title = Pharmacogenomics and Personalized Medicine for Infectious Diseases date = 2013-06-11 keywords = HLA; Leishmania; NAT2; disease; drug; treatment summary = Deciphering the pathogen virulence factors, host susceptibility genes, and the molecular programs involved in the pathogenesis of disease has paved the way for discovery of new molecular targets for drugs, diagnostic markers, and vaccines. The pathogen genome on one hand gives us the information about the important genes conferring disease pathogenesis as well as drug resistance, while the genome of the host on the other hand will reveal the susceptibility genes, and the further knowledge of polymorphisms in genes of the host metabolic and immune system will lead to the new vaccine strategies, drugs targets, and also their treatment outcomes. Several fi eld studies have further suggested that there is a need for calibration of isoniazid dosage as per the individual tuberculosis patient''s age, acetylator status, and disease process for an effective antimicrobial outcome of drug treatment (Jeena et al. doi = 10.1007/978-81-322-1184-6_27 id = cord-280979-0vaarrji author = Gauttier, V. title = Tissue-resident memory CD8 T-cell responses elicited by a single injection of a multi-target COVID-19 vaccine date = 2020-08-14 keywords = CD8; HLA; SARS summary = doi = 10.1101/2020.08.14.240093 id = cord-329825-e9mepqvn author = Giamarellos-Bourboulis, Evangelos J. title = Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure date = 2020-04-21 keywords = HLA; SARS summary = doi = 10.1016/j.chom.2020.04.009 id = cord-288916-i8ukefp8 author = Gómez-Herranz, Maria title = The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis date = 2019-04-02 keywords = Fig; HLA; IFITM1/3; Supplementary; cell; ifitm1 summary = A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The HPV16+ and IFITM1/3 positive cervical cancer cell line SiHa [38] [39] exhibit IFNγ inducible STAT1, IRF1, and IFITM1/3 proteins (Fig. 1G ). Also of note is attenuation of HLA-A, HLA-B, HLA-C, and ISG15 protein synthesis 24 h post-IFNγ treatment in the IFITM1/IFITM3 double null cells compared to parental SiHa (Fig. 5F vs 5B). By contrast, basal HLA-B protein expression was attenuated in the IFITM1/IFITM3 double null cells after IFNγ treatment (Fig. 6F vs 6E) . doi = 10.1016/j.cellsig.2019.03.024 id = cord-007851-v6h1yro7 author = Han, Ki-Cheol title = Streamlined selection of cancer antigens for vaccine development through integrative multi-omics and high-content cell imaging date = 2020-04-03 keywords = CD8; Fig; HLA; MHC summary = We used a combined application of this method involving immune-specific signature analysis and HLA-associated peptidomics using samples from six patients with triple-negative breast cancer (TNBC) in order to select immunogenic HLA epitopes for in vitro testing. Integrated WTS data revealed a higher priority to select promising HLA-peptides via high-resolution bioinformatics analysis, showing immune-cell-specific signatures and TCR-repertoire diversity in tumors. We then found a positive correlation between TCR diversity, reflecting clonal composition, and the expression of MHC-class І molecules, suggesting that active tumor-antigen presentation promotes the generation of antigen-specific TILs. Additionally, immune-specific signature analysis can discriminate specific immune-cell types in each patient and thus enhance the efficiency of selective HLA-peptidomic approaches. In this study, the HLA-peptidomics approach combined with comprehensive analysis of immune-specific signatures and TCR repertories showed high selectivity to determine the immunogenic T-cell epitopes. Identification of potential vaccine epitopes coupled with immune-specific signature analysis, HLA-peptidomics, and single-cell-based immunogenicity testing offers a discriminative and powerful tool for cancer-vaccine development. doi = 10.1038/s41598-020-62244-z id = cord-104099-xhi0oxtr author = Hensen, L. title = CD8+ T-cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph date = 2020-10-05 keywords = A24; CD8; Fig; HLA; indigenous summary = We defined CD8+ T-cell immune landscapes against influenza A (IAV) and B (IBV) viruses in HLA-A*24:02-expressing Indigenous and non-Indigenous individuals, human tissues, influenza-infected patients and HLA-A*24:02-transgenic mice. Our data present the first evidence of influenza-specific CD8+ T-cell responses in Indigenous Australians, and advocate for T-cell-mediated vaccines that target and boost the breadth of IAV/IBV-specific CD8+ T-cells to protect high-risk HLA-A*24:02-expressing Indigenous and non-Indigenous populations from severe influenza disease. 10 .02.20206086 doi: medRxiv preprint immunogenicity of novel peptides in HLA-A24-expressing mice, peripheral blood of Indigenous and non-Indigenous HLA-A24 + healthy and influenza-infected individuals, and human tissues. To determine the immunogenicity of novel IAV-and IBV-derived peptides during primary and secondary influenza virus infection in vivo, we utilized HLA-A24-expressing transgenic (HHD-A24) mice 45 Table 2 ). . https://doi.org/10.1101/2020.10.02.20206086 doi: medRxiv preprint across virus strains circulating in South-East Asia and Australia suggests that the prominent HLA-A24-restricted CD8 + T-cell responses are likely to confer broad cross-reactive immunity to IAV. doi = 10.1101/2020.10.02.20206086 id = cord-320490-3jmo35jc author = Ismail, Saba title = Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine date = 2020-04-12 keywords = HLA; MEPVC; SARS; TLR3; energy; mol summary = In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. The study presented, herein, is an attempt to get insights about antigenic determinants of SARS-CoV-2 spike glycoprotein and highlight all antigenic epitopes [31] of the spike that can be used specifically for the design of a multi-epitope peptide vaccine construct (MEPVC) [32] to counter COVID-19 infections. The epitopes predicted by immunoinformatics techniques were fused together as well as to β-defensin adjuvant [33, 34] to boost the antibody production and longThe MEPVC affinity for an appropriate immune receptor as an agonist was checked in the step of molecular docking [60] . doi = 10.1101/2020.04.05.026005 id = cord-330615-h8sktgo6 author = Jabri, ‡ § Bana title = Selective expansion of intraepithelial lymphocytes expressing the HLA-E–specific natural killer receptor CD94 in celiac disease date = 2000-05-31 keywords = CD94; HLA; TCR summary = Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. Methods: Flow-cytometric analysis of isolated IELs and/or immunohistochemical staining of frozen sections were performed in 51 celiac patients and 50 controls with a panel of monoclonal antibodies against T-cell and natural killer (NK) receptors. In preliminary immunohistochemical studies of intestinal frozen tissue sections, the pattern of staining of IELs with anti-CD56, -Pen5, -p46, -p58, and -CD94 antibodies was compared in 4 adult patients with active celiac disease and in 4 normal controls. Cytolytic T lymphocytes displaying natural killer (NK)-like activity: expression of NK-related functional receptors for HLA class I molecules (p58 and CD94) and inhibitory effect on the TCR-mediated target cell lysis or lymphokine production doi = 10.1016/s0016-5085(00)70173-9 id = cord-304635-z5vmhopa author = Ji, Wei title = Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner date = 2019-06-18 keywords = HLA; MHC summary = doi = 10.1016/j.molimm.2019.06.005 id = cord-326554-iphe3rni author = Joshi, Amit title = In-Silico Proteomic Exploratory Quest: Crafting T-Cell Epitope Vaccine Against Whipple’s Disease date = 2020-05-18 keywords = HLA; Whipple summary = This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. Nowadays epitope based vaccines provide better options in search of good treatment strategy for such type of harmful and rare malady, even if the individuals are genetically predisposed as in case of classical Whipple''s disease (Trotta et al. Immune Epitope Database (IEDB) analysis Resource tool of population coverage was used to predict population coverage of the putative epitopes that are exhibiting interaction to HLA alleles and based on MHC-II restriction data (Bui et al. PatchDock tool was deployed for interaction between selected structures of epitopes and HLA DRB1 proteins. Still no one has used vaccine based treatments for Whipple''s disease, as it is thought to be rare and possess reduced genome but considered one of the harmful pathogen of human ( Raoult et al. doi = 10.1007/s10989-020-10077-9 id = cord-103837-iuvigqdx author = Knierman, Michael D. title = The Human Leukocyte Antigen Class II Immunopeptidome of SARS-CoV-2 Spike Glycoprotein date = 2020-11-13 keywords = HLA; SARS; cluster; peptide summary = doi = 10.1016/j.celrep.2020.108454 id = cord-288146-xqxznv1r author = Kohyama, Shunsuke title = Efficient induction of cytotoxic T lymphocytes specific for severe acute respiratory syndrome (SARS)-associated coronavirus by immunization with surface-linked liposomal peptides derived from a non-structural polyprotein 1a date = 2009-09-11 keywords = CD8; CTL; HLA; SARS summary = doi = 10.1016/j.antiviral.2009.09.004 id = cord-126015-zc7u3g34 author = Krieger, Elizabeth title = Immunological determinants of clinical outcomes in COVID-19: A quantitative perspective date = 2020-05-13 keywords = HLA; KIR; SARS; response summary = doi = nan id = cord-255069-9xueqdri author = Leary, Shay title = Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence date = 2020-04-11 keywords = HLA; SARS summary = The findings suggest that homologous recombination may have occurred since its introduction into humans and be a mechanism for increased viral fitness and adaptation of SARS-CoV-2 to human populations. Evidence of viral adaptation to selective pressures as it spreads among diverse human populations has implications for the ongoing potential for changes in viral fitness over time, which in turn may impact transmissibility, disease pathogenesis and immunogenicity. Here we describe a new emerging strain of SARS-CoV-2 within the LGG clade that appears to be the result of a homologous recombination event that introduced three adjacent nucleotide changes spanning two residues of the nucleocapsid protein. Evidence for such adaptations with closely linked compensatory mutations are known to occur under host immune pressure as is well established for other adaptable RNA viruses such as HIV 1,2 and Hepatitis C virus (HCV) 3 . doi = 10.1101/2020.04.10.029454 id = cord-009323-sfxpchma author = Link, Hartmut title = Die Transplantation hämatopoetischer Stammzellen: Teil I: Definitionen, prinzipielle Anwendungsmöglichkeiten, Komplikationen date = 1997 keywords = HLA; Patienten; Stammzelltransplantation; Zellen; die; graft; marrow; transplantation summary = doi = 10.1007/bf03044917 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-346957-bmajkabp author = Lv, Yanbo title = Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV date = 2009-12-03 keywords = CTL; HLA; SARS summary = RESULTS: First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. To investigate the capacity of candidate peptides to mobilize a human CTL repertoire, HLA-A2 + PBLs from ten HLA-A2 + donors were stimulated in vitro by DCs loaded with Alignment of the putative amino acid sequences of S proteins from eighteen SARS-CoV strains A dot among the individual sequences denoted nucleotides that are the same as the consensus. Furthermore, SARS-CoV/S-derived peptides Sp6, Sp7 and Sp8 could not only induce the increased S protein specific IFN-γ secreting T cell frequency but also the enhanced cytolytic capacity of these CTLs. To further address whether the immunogenic candidate peptide is naturally processed and presented, HLA-A2.1/ K b transgenic mice were immunized with S/pVAX1 plasmid containing a full-length cDNA encoding the SARS-CoV/S protein. doi = 10.1186/1471-2172-10-61 id = cord-281141-ouno4jpl author = Mahajan, Swapnil title = Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals date = 2020-11-05 keywords = CD8; HLA; SARS summary = A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. We performed T-cell activation assay using the selected 11 epitopes from the SARS-CoV-2 spike antigen in unexposed donors. As shown in Figure Multiple studies have reported pre-existing T-cell immunity in unexposed donors using spike peptide pools and attributed the response to T-cells recognizing epitopes from common coldcausing coronaviruses to which a large section of the global population is exposed (7, 8, 10) . A recent large-scale study mapped a few immunogenic regions in the SARS-CoV-2 proteome responsible for expanding many unique TCRs in a large number of convalescent COVID-19 patients and unexposed healthy donors (21) . doi = 10.1101/2020.11.03.367375 id = cord-003472-ml4pbewf author = Manczinger, Máté title = Pathogen diversity drives the evolution of generalist MHC-II alleles in human populations date = 2019-01-31 keywords = DRB1; HLA; MHC summary = doi = 10.1371/journal.pbio.3000131 id = cord-261392-dw56h8vj author = Matijevic, Mark title = Immunization with a poly (lactide co-glycolide) encapsulated plasmid DNA expressing antigenic regions of HPV 16 and 18 results in an increase in the precursor frequency of T cells that respond to epitopes from HPV 16, 18, 6 and 11 date = 2011-12-31 keywords = HLA; HPV; cell summary = doi = 10.1016/j.cellimm.2011.04.005 id = cord-007664-c5snhymz author = Mauerhoff, Thekla title = Differential expression and regulation of major histocompatibility complex (MHC) products in neural and glial cells of the human fetal brain date = 2002-11-13 keywords = HLA; IFN; class summary = To gain an insight into the regulation of HLA in the different cell types in the CNS and to compare it to that observed in the endocrine organs, we have studied the effect of the lympho/monokines interferon (IFN)-α and -γ, tumour necrosis factor (TNF)-α, and interleukin (IL)-2 and other agents on this aspect of the biology of human fetal brain cells in culture. It has previously been reported that primary cultures of human fetal brain tissue can be a useful substrate for studying the expression of cell type-specific antigens, e.g. gangliosides, tetanus toxin receptors (Dickson et al., 1982 (Dickson et al., , 1985 , and the present data confirm that they can also be successfully employed to investigate the expression and modulation of HLA molecules. doi = 10.1016/0165-5728(88)90049-5 id = cord-286858-zbhtl2yn author = Mishra, B. title = tamasomā jyotirgamaya: Seeking the Self Amidst Covids’ Cytokine Cyclones date = 2020-10-22 keywords = HLA; cell; game; signal; system summary = doi = 10.1007/s41745-020-00186-1 id = cord-296007-1gsgd22t author = Mohseni, Amir Hossein title = Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines date = 2020-09-12 keywords = HLA; SARS summary = doi = 10.1101/2020.09.12.294413 id = cord-333670-qv1orlv5 author = Mutti, Luciano title = Coronavirus Disease (Covid-19): What Are We Learning in a Country With High Mortality Rate? date = 2020-05-28 keywords = COVID-19; HLA; SARS summary = In Italy, the possibility of performing autopsies or post-mortem diagnostic studies on suspect, probable, or confirmed COVID-19 cases has been intensively debated (5, 6) ; however, postmortem pathological analysis of COVID-19 patients in China has shown findings consistent with Acute Respiratory Distress Syndrome (ARDS) (7-9) (Figure 1 ). Consistently, recent results indicate that a systemic immune dysregulation that triggers auto-sustaining inflammatory lung damage, causing fatal respiratory-failure and consequent multiorgan-failure, is the main virus-related-death cause in patients who develop SARS-CoV-2 (10). Overall, understanding the role of pro-inflammatory cytokines certainly unravels a new battleground against the lethal clinical effect of CODIV-19 infection; this, along with the identification of a high-risk autoimmune profile, including the genotyping of Class I and II HLA, which have a key role in shaping the anti-viral immune response and Th1/Th2 lymphocyte subset response (Figure 1) , and immune-profiling, could also help to prevent these dangerous evolutions of the disease (29) . doi = 10.3389/fimmu.2020.01208 id = cord-287709-y247lan1 author = Navarrete, Cristina title = Cord Blood Banking: Operational and Regulatory Aspects date = 2014-12-12 keywords = CBB; CD34; HLA; UCB; unit summary = doi = 10.1016/b978-0-12-407785-0.00015-3 id = cord-348283-7xorq5ce author = Naz, Anam title = Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach date = 2020-07-10 keywords = HADDOCK; HLA; SARS; vaccine summary = The spike protein aids in receptor binding and viral entry within the host and therefore represents a potential target for vaccine and therapeutic development. In the current study, the spike protein of SARS-CoV-2 was explored for potential immunogenic epitopes to design multi-epitope vaccine constructs. We adapted a comprehensive predictive framework to provide novel insights into immunogenic epitopes of spike proteins, which can further be evaluated as potential vaccine candidates against COVID-19. Designed vaccines were then tested with different epitopes, including Truncated Ov-ASP-1 Protein (residues 10-153) and Beta defensin (45 residues long), and constructs having higher antigenicity and that are predicted to produce high antibody titers were added with the multi epitope vaccine construct to the enhance immune response (30) . For the interaction analysis of vaccine 3 and BCR (CD79), the HADDOCK server clustered 140 probable structures into 13 different clusters, which represented a total of 70% of the water-refined models. doi = 10.3389/fimmu.2020.01663 id = cord-286968-ud1uerc8 author = Nienhold, R. title = Two distinct immunopathological profiles in lungs of lethal COVID-19 date = 2020-06-19 keywords = HLA; ISG; figure summary = doi = 10.1101/2020.06.17.20133637 id = cord-002686-zzongyfa author = Oany, Arafat Rahman title = Vaccinomics Approach for Designing Potential Peptide Vaccine by Targeting Shigella spp. Serine Protease Autotransporter Subfamily Protein SigA date = 2017-09-07 keywords = HLA; MHC; Shigella summary = In the present study, we have tried to impose the vaccinomics approach for designing a common peptide vaccine candidate against the immunogenic SigA of Shigella spp. Initially, these peptides were assessed for the affinity with MHC class I and class II alleles, and four potential core epitopes VTARAGLGY, FHTVTVNTL, HTTWTLTGY, and IELAGTLTL were selected. The generalized modules of membrane antigen-(GMMA-) based outer membrane proteins including SigA were also shown to be highly immunogenic [12] , which prompted us to target SigA as one of the best vaccine candidates and to design potential peptide vaccine covering all the Shigella spp. The SigA protein sequences of different strains of Shigella species were retrieved from the NCBI GenBank [22] database and analysed in the VaxiJen v2.0 [23] server for the determination of the most potent antigenic protein. IEDB analysis resource predicted both MHC class I-and MHC class II-based coverage of the selected epitopes for the world population to assess the feasibility of being a potential vaccine candidate. doi = 10.1155/2017/6412353 id = cord-010222-5oxie0zc author = Oldstone, Michael B.A. title = Virus-induced autoimmunity: Molecular mimicry as a route to autoimmune disease date = 2004-04-11 keywords = B27; HLA; virus summary = doi = 10.1016/0896-8411(89)90130-3 id = cord-023675-sidvbzqy author = Oldstone, Michael B.A. title = Virus-induced Autoimmunity: Molecular Mimicry as a Route to Autoimmune Disease date = 2013-11-17 keywords = B27; HLA summary = doi = 10.1016/b978-0-12-252682-4.50023-8 id = cord-004435-l66ost6q author = Oli, Angus Nnamdi title = Immunoinformatics and Vaccine Development: An Overview date = 2020-02-26 keywords = HLA; antigenic; immune; protein; vaccine summary = Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/re-emerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines'' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. 13 An approach that must accommodate many factors affecting vaccine development like pathogen antigenic variability, the emergence of infectious disease, human genetic variation is the goal of immunoinformatics [ Figure 1 ]. 110 The surface glycoprotein can be regarded as antigen and hence can serve as a target for the immune system which if sequenced, using the new immunoinformatics approach and a common site for the varying proteins identified, a potent vaccine can be developed which can accommodate the antigenic drift/shifts of the virus. doi = 10.2147/itt.s241064 id = cord-003270-vu9b5a14 author = Panahi, Heidar Ali title = A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins date = 2018-10-24 keywords = HLA; IEDB; MHC summary = doi = 10.1371/journal.pone.0205933 id = cord-000488-x5ardo5j author = Pedersen, Lasse Eggers title = Porcine major histocompatibility complex (MHC) class I molecules and analysis of their peptide-binding specificities date = 2011-07-08 keywords = A*11:01; HLA; MHC; SLA-1; molecule summary = We have recently developed efficient methods to generate recombinant human MHC-I (also known as human leukocyte antigen class I, HLA-I) molecules, accompanying peptide-binding assays and predictors, and HLA tetramers for specific CTL staining and manipulation. Recombinant constructs encoding chimeric and SLA-1*0401 molecules A synthetic gene encoding a transmembrane-truncated fragment encompassing residues 1 to 275 of human HLA-A*11:01 alpha chain followed by a FXa-BSP-HAT tag (FXa = factor Xa cleavage site comprised of the amino acid sequence IEGR, BSP = biotinylation signal peptide, HAT = histidine affinity tag for purification purposes; see Online Resource 1) had previously been generated and inserted into the pET28 expression plasmid (Novagen) (Ferre et al. doi = 10.1007/s00251-011-0555-3 id = cord-002724-gtv9syzi author = Pfortmueller, Carmen Andrea title = Assessment of immune organ dysfunction in critical illness: utility of innate immune response markers date = 2017-10-23 keywords = HLA; expression; patient summary = doi = 10.1186/s40635-017-0163-0 id = cord-266204-ipa017wz author = Poland, G. A. title = Personalized vaccinology: A review date = 2018-08-28 keywords = HLA; immune; influenza; response; vaccine summary = This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing "downstream" adaptive humoral and cellular responses to infectious pathogens and vaccines. A decade ago, we described the idea of vaccinomics and adversomics, based on the immune response network theory [5, 6] , which utilizes immunogenetics/imunogenomics and systems biology approaches to understand the basis for inter-individual variations in vaccineinduced immune responses in humans, as well as the basis for adverse side effects from vaccines [7] . Published data reveal that innate and adaptive immunity is decreased with age, but the systems-level mechanisms for these findings are unclear [66, 68] , particularly in regard to influenza and other viral vaccine responses where the morbidity, mortality, and associated healthcare costs are greater in older individuals [11] . doi = 10.1016/j.vaccine.2017.07.062 id = cord-000224-2lz03oqb author = Porter, Kristen A. title = Class II Transactivator (CIITA) Enhances Cytoplasmic Processing of HIV-1 Pr55Gag date = 2010-06-24 keywords = CIITA; Gag; HLA; MHC summary = doi = 10.1371/journal.pone.0011304 id = cord-329669-z3t7plvh author = Poulton, Kay title = A role for human leucocyte antigens in the susceptibility to SARS‐Cov‐2 infection observed in transplant patients date = 2020-07-05 keywords = Group; HLA summary = HLA frequencies observed were compared against two control populations: first, against published frequencies in a UK deceased donor population (n = 10,000) representing the target population of the virus, and second, using a cohort of individuals from the combined transplant waiting lists of both centres (n = 308), representing a comparator group of unaffected individuals of the same demographic. This study investigated HLA profiles of patients admitted with PCR-confirmed SARS-CoV-2 infection to identify any potential HLA bias which might indicate an impaired capacity to mount an effective immune response to the infection. All patients included in the study had previously been HLA typed to support transplantation and required hospital treatment for COVID-19 disease, indicating that their symptoms were severe, requiring clinical support or intervention. Statistical analysis was performed using MedCalc v19.3 (MedCalc Software) to compare frequencies of allele group carriage between the patient and control populations using Fisher''s exact test. doi = 10.1111/iji.12505 id = cord-275677-hbv49e01 author = Ramana, Lakshmi Narashimhan title = Targeting strategies for delivery of anti-HIV drugs date = 2014-10-28 keywords = CD4; HIV; HIV-1; HLA; LFA-1; cell; target summary = Immunoliposomes loaded with the protease inhibitor indinavir and surface modified with anti-HLA-DR were found to effectively bind to HIV infected cells and deliver the antiretroviral drug leading to a significant reduction in the viral load [44] . In a recent work, lipid nanoparticles conjugated with two peptide sequences that were derived from the binding domains of CD4 designated as CD4-BP2 and CD4-BP4 were used for targeted delivery of the protease inhibitor indinavir to HIV infected CD4 + cells with high specificity [54] . The lectin actinohivin isolated from the actinomycete Longisporum albida has also been identified as an important targeting moiety that binds to the mannose residues present in the gp120 at lower concentrations with an affinity greater than anti-gp120 antibodies thereby preventing the interaction of the viral glycoprotein with CXCR4 and CCR5 chemokine receptors [13] . doi = 10.1016/j.jconrel.2014.08.003 id = cord-316330-55nd3pwe author = Ramos-Lopez, Omar title = Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19 date = 2020-10-19 keywords = HLA; SARS; genetic summary = doi = 10.1155/2020/6901217 id = cord-273906-s7l0yxc0 author = Ranga, Vipin title = Immunogenic SARS-CoV-2 Epitopes: In Silico Study Towards Better Understanding of COVID-19 Disease—Paving the Way for Vaccine Development date = 2020-07-23 keywords = HLA; MHC; SARS; Table summary = doi = 10.3390/vaccines8030408 id = cord-028275-szb45jm2 author = Reza Khorramizadeh, M. title = Animal models for human disease date = 2020-06-26 keywords = CIA; HLA; animal; arthritis; cell; disease summary = doi = 10.1016/b978-0-12-811710-1.00008-2 id = cord-349451-vak2p7ac author = Rocha, Francisco Airton Castro title = Microbes, Helminths and Rheumatic Diseases date = 2020-05-07 keywords = B27; Chlamydia; HLA; arthritis; disease; immune summary = Studies suggest the billions of germs that compose the gut microbiota influence one''s innate and adaptive immune responses at the intestinal level, but these microorganisms may also impact rheumatic diseases. Evidence indicates that changes in the gut microbiome alter the pathogenesis of immune-mediated diseases such as rheumatoid arthritis and ankylosing spondylitis but also of other disorders like atherosclerosis and osteoarthritis. The pathogenesis of Chlamydia-related arthritis can be considered distinct from that associated with enteric bacteria since it involves metabolically active organisms residing long-term within monocytic cells in synovial tissues, after resolution of the primary genital infection and migration of the cells to the joint, a process that is known as persistence [56, [61] [62] [63] . Studies indicate inflammatory bowel disease, or, at least, intestinal inflammation, is more prevalent in SpA patients (AS or others) and some genes associated with AS are also associated with IBD [83, 85] , including genes related to gut physiology and immunology. doi = 10.1016/j.berh.2020.101528 id = cord-016235-2lhrkmrv author = Roden, Anja C. title = Lung date = 2010-05-17 keywords = BOS; HLA; acute; lung; patient; rejection; transplantation summary = Unlike the situation with heart transplant recipients, chronic vascular rejection in lung transplants has not resulted in graft loss; however, some patients develop pulmonary hypertension particularly those with BOS [92, 111] . However, based on the link between acute rejection and development of BOS, surveillance transbronchial biopsies in asymptomatic lung transplant recipients has become common practice in many large lung transplantation centers because evidence suggests that patients who have multiple episodes of low grade (A1) lesions within the first 12 months posttransplantation develop early onset BOS. A study [49] in which surveillance transbronchial biopsies were performed at 3, 6, 9, and 12 weeks posttransplantation, at the time of symptoms, and for follow-up of acute rejection or CMV pneumonia showed that patients who develop acute small airways rejection within the first year after transplantation are at risk of development of BOS at 1.76, 3.3, and 5.5 years after detection of B3/ B4 lesion (by 1996 ISHLT criteria, see Table 7 .2), B2 lesion or B0/B1 lesion, respectively. doi = 10.1007/978-3-540-79343-4_7 id = cord-017856-4fccnygg author = Roden, Anja C. title = Pathology of Lung Rejection: Cellular and Humoral Mediated date = 2018-04-24 keywords = AMR; HLA; acute; lung; rejection summary = doi = 10.1007/978-3-319-91184-7_13 id = cord-299279-v0vznri2 author = Røder, Gustav title = Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501 date = 2008-05-17 keywords = B*1501; HLA summary = The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making it available for interactions with a potential T-cell receptor. The overall structure of the present HLA-B*1501 peptide-binding groove is similar to the previously two determined HLA-B*1501 structures (Røder et al., 2006) and to other MHC-I molecules (see Fig. 1 ). The pGln2 peptide residue is located in the B pocket in the same orientation as the pGlu2 in the previously described HLA-B*1501-LEKARGSTY structure (Røder et al., 2006) . The pGlu4 peptide residue points away from the peptide-binding groove and the side chain does not interact with any HLA-B*1501 residues. The conformation observed does not interact with any HLA-B*1501 residues, but makes a hydrogen bond to two water molecules (HOH67 and HOH348) present between the peptide and the floor of the peptide-binding groove, thereby forming water-mediated contacts with the HLA-B*1501 protein. doi = 10.1107/s1744309108012396 id = cord-280172-6o1gqe8v author = Sanami, Samira title = Design of a Multi-epitope Vaccine against SARS-CoV-2 using Immunoinformatics approach date = 2020-07-15 keywords = HLA; SARS; vaccine summary = doi = 10.1016/j.ijbiomac.2020.07.117 id = cord-271032-imc6woht author = Schulte-Schrepping, Jonas title = Severe COVID-19 is marked by a dysregulated myeloid cell compartment date = 2020-08-05 keywords = Fig; HLA; PBMC; Table; cell; cluster; covid-19 summary = Given the dramatic changes in various immune cell populations (Fig. 1C+D) , we next 171 assessed their composition and activation state by droplet-based scRNA-seq in 27 samples 172 from 18 COVID-19 patients (8 mild & 10 severe, cohort 1, Table S1 ) collected between day 173 3 and day 20 after symptom onset. All LDNs also expressed high levels of alarmins S100A8 and S100A9 (Fig. 5D) , whereas 343 other S100 genes (e.g. S100A4, S100A12) were strongly induced in selected neutrophil 344 Alterations of the neutrophil compartment were further interrogated by mass cytometry of 362 whole blood samples of COVID-19 patients (n=8 mild + 9 severe, cohort 1), FLI patients 363 (n=8), and age-and gender-matched controls (n=9) (Table S1), using a panel designed to 364 detect myeloid cell maturation and activation states as well as markers of 365 immunosuppression or dysfunction (Table S2) . doi = 10.1016/j.cell.2020.08.001 id = cord-310252-0cdqhrcw author = Seliger, Barbara title = Chapter 7 IFN Inducibility of Major Histocompatibility Antigens in Tumors date = 2008-12-03 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 = However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide–MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide-MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. Box 1 | Extensive T cell cross-reactivity and apparent specificity are not incongruous From the 20 proteinogenic amino acids, it is possible to generate vast numbers of peptides of a length that can be presented by MHC molecules (see the table). First, a cross-reactive T cell repertoire generates a near perfect solution to the huge challenge of providing effective immune cover by allowing a limited number of T cells to provide immunity against virtually all foreign peptides that can bind to self MHC molecules. doi = 10.1038/nri3279 id = cord-284944-hcgfe9wv author = Silvin, Aymeric title = Elevated calprotectin and abnormal myeloid cell subsets discriminate severe from mild COVID-19 date = 2020-08-05 keywords = CD10; CD16; HLA; Low; covid-19; figure; patient summary = doi = 10.1016/j.cell.2020.08.002 id = cord-344691-vmc0rrrk author = Srinivasan, K.N. title = Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens date = 2004-08-04 keywords = ANN; HLA summary = Results: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. A number of predictive methods for MHC classes I and II binding peptides are available, including those based on binding motifs (Rammensee et al., 1995) , quantitative matrices (Parker et al., 1994) , artificial neural networks (ANNs) , hidden Markov models (HMMs) (Mamitsuka, 1998) , multivariate statistical approaches (Guan et al., 2003) , support vector machines (Zhao et al., 2003) and decision trees (Savoie et al., 1999) . In our prediction of promiscuous class I T-cell epitopes, we made predictions of T-cell epitope hot spots in nucleocapsid protein of the severe acute respiratory syndrome coronavirus (SARS-CoV). MULTIPRED, a computational system developed for human leukocyte antigen (HLA) classes I-A2 and I-A3 binding, predicts individual 9-mer T-cell epitopes and also promiscuous class I regions as immunological hot spots, based on HMM and ANN models (Zhang et al., 2003) . doi = 10.1093/bioinformatics/bth943 id = cord-343262-zopxdw1d author = Srinivasan, Raghuraman C. title = Effects of Cryogenic Storage on Human Amnion Epithelial Cells date = 2020-07-15 keywords = HLA; cell; epithelial; figure summary = In this study, hAEC were isolated from full-term human placenta from 14 different donors, cryopreserved using a protocol and reagents commonly adopted for epithelial cell preservation. In anticipation that the transplant product used in any future clinical trial will be previously cryopreserved cells, the current study was undertaken to determine if there are any significant differences between the populations initially isolated from the amnion membranes, and the cells recovered following the cryopreservation procedure. The presence of CD45, a receptor linked to protein tyrosine phosphatase present in cells of the hematopoietic lineage, was detected in 9/12 of hAEC preparations immediately after isolation at an average level of 1.2% ± 1.4% cells, but greatly reduced after cryopreservation and washing steps, where only four preparations still contained an extremely low number of CD45 positive cells (0.3% ± 0.4%; p = 0.0146) ( Figure 2D ). The presence of HLA-G on hAEC after isolation was confirmed using a specific antibody, and HLA-G Amnion epithelial cells have been reported to express characteristic immunomodulatory molecules, such as HLA class Ib [21, 22] . doi = 10.3390/cells9071696 id = cord-034402-64xz1j9i author = Srivastava, Shivani title = Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach date = 2020-10-29 keywords = HLA; Listeria; epitope summary = This present study aims at the prediction of B cell epitopes for subunit vaccine designing against Listeria monocytogenes using a reverse vaccinology approach. For computational identification and characterization of epitopes for the preparation of subunit vaccine designing, complete proteome analysis of Listeria monocytogenes F2365 strain (GenBank accession number AE017262.2) was performed using the UniProtKB database. The first requirement in the reverse vaccinology approach of vaccine designing is to eliminate all non-allergic proteins from a complete proteome set of bacteria, Listeria monocytogenes. In this exploration and investigation, the prediction of B cell epitopes has been performed by the authors for the designing of the vaccine against listeriosis by using a reverse vaccinology approach. Tertiary structure modeling of alleles was generated with the help of HLA alleles were performed Based on low binding energy, 4 peptides were selected viz., CEETFGIRL, MKFLFPLKL, FLKIDPPIL, and VRH-HGGGHK. doi = 10.1007/s10989-020-10128-1 id = cord-342942-1s32o9m8 author = Stamatakis, George title = Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases date = 2020-06-22 keywords = HLA; SARS; erap1 summary = Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. In this study, we utilized a novel approach to analyze antigen trimming by intracellular aminopeptidases ERAP1, ERAP2 and IRAP, focusing on the largest antigen of SARS-CoV-2, namely S1 spike glycoprotein. To investigate the trimming of antigenic epitope precursors by intracellular aminopeptidases that generate antigenic peptides, we used a mixture of 315 synthetic peptides derived from the sequence of the SARS-CoV-2 S1 spike glycoprotein. Our analysis of the largest antigen of SARS-CoV-2, S1 spike glycoprotein, suggests that aminopeptidase trimming can be a significant filter that helps shape which peptides will be presented by HLA. doi = 10.1101/2020.06.22.164681 id = cord-288496-7rrh2gg6 author = Stryhn, Anette title = A Systematic, Unbiased Mapping of CD8(+) and CD4(+) T Cell Epitopes in Yellow Fever Vaccinees date = 2020-08-31 keywords = CD4; CD8; HLA; cell summary = Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4 + and/or CD8 + T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. doi = 10.3389/fimmu.2020.01836 id = cord-001247-pxzbirqd author = Sun, Lu title = A new unconventional HLA-A2-restricted epitope from HBV core protein elicits antiviral cytotoxic T lymphocytes date = 2014-03-22 keywords = Fig; HBV; HLA summary = Our data therefore provide insights into the structure characteristics of this unconventional epitope binding to MHC-I molecules, as well as epitope specific CTL activity that orchestrate T cell response and immune evasion in HBV infected patients. To identify immune-dominant HBV-specific CTL epitopes, especially epitopes from HBc protein, is therefore necessary for monitoring T cell responses during disease progression, as well as for developing epitope-based therapeutic vaccines against CHB (Inchauspe and Michel, 2007; Gordon et al., 2013; Liu et al., 2013a, b) . To further determine the epitope-specific CTLs, fresh PBMCs from HLA-A2 + AHB patients were stimulated with HBc141-149 peptide and detected by ex vivo IFN-γ ELISPOT assays. In this study, we identified a new HLA-A2-restricted CD8 + T cell epitope HBc141-149 by screening an overlapping 9-mer peptide pool covering HBV core protein. doi = 10.1007/s13238-014-0041-4 id = cord-312865-nno2yjae author = Sylvester‐Hvid, C. title = SARS CTL vaccine candidates; HLA supertype‐, genome‐wide scanning and biochemical validation date = 2004-04-23 keywords = HLA summary = One would therefore expect that an effective vaccine should induce mucosal immunity such as that effected by secretory immunoglobulin A (IgA), which specifically prevents an infectious agent from penetrating the mucosal epithelium, and by cytotoxic T lymphocytes (CTLs), which specifically eradicate infected cells (5) . Human CTLs are specific for peptides presented in the context of human leukocyte antigen (HLA) molecules [generically known as ''''major histocompatibility complex (MHC) molecules'''']. Thus, 13 of the 15 peptides predicted to be good binders to A*0301 were found to bind to another member of the A3 supertype, HLA-A*1101. Similarly, nine of the 15 peptides predicted to be good binders to A*1101 were found to bind to HLA-A*0301 (Table 1) Once all nine supertypes have been tested, we would project to have found well over 100 different vaccine candidates. Immunogenicity of a human immunodeficiency virus (HIV) polytope vaccine containing multiple HLA A2 HIV CD8(þ) cytotoxic T-cell epitopes doi = 10.1111/j.0001-2815.2004.00221.x id = cord-333966-st6gyozv author = Taherkhani, Reza title = Design and production of a multiepitope construct derived from hepatitis E virus capsid protein date = 2015-03-17 keywords = HEV; HLA; ORF2; protein summary = The aim of this study was to design a high density multiepitope protein, which can be a promising multiepitope vaccine candidate against Hepatitis E virus (HEV). Therefore, the present study was undertaken to design a high density multiepitope protein compromising four HTL epitopes with high-affinity binding to the HLA molecules using the in silico analysis, and to evaluate the immunological properties of this protein in vitro. In brief, approximately 1 Â 10 5 cells/well of PBMCs of each sample in RPMI 1640 and 10% FCS were added to four wells of round-bottom 96-well plates in total volume of 180 ml/well, stimulated with 20 ml/well of truncated ORF2 protein (10 mg/ml), high density multiepitope (10 mg/ml) and Phytohemagglutinin (PHA) (5 mg/ml) (Sigma-Aldrich) separately, and incubated at 37˚C for 4 days. IFN-g ELISPOT responses to high density multiepitope protein and truncated ORF2 protein were found significantly higher in HEV-recovered individuals than control group (P < 0.001). doi = 10.1002/jmv.24171 id = cord-298169-2133gahl author = Tamouza, Ryad title = Understanding the genetic contribution of the Human Leukocyte Antigen system to common major psychiatric disorders in a world pandemic context date = 2020-10-05 keywords = HLA; MHC; disorder summary = doi = 10.1016/j.bbi.2020.09.033 id = cord-103662-a4ok5wqc author = Tarek, M. title = Custommune: a web tool to design personalized and population-targeted vaccine epitopes date = 2020-04-29 keywords = ACE2; Custommune; HIV-1; HLA; SARS summary = When applied to HIV-1, Custommune predicted personalized epitopes using patient specific Human Leukocyte Antigen (HLA) alleles and viral sequences, as well as the expected HLA-peptide binding strength and potential immune escape mutations. The results allowed the identification of peptides tailored for each population and predicted to elicit both CD8+ T-cell immunity and neutralizing antibodies against structurally conserved epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this aim, by intersecting input data from patient-specific viral sequences and HLA alleles, Custommune provides an output of epitopes of desired length filtered for their predicted specificity, immunogenicity and mutation potential. Class I and Class II HLA alleles which were predicted by Custommune to bind RBDp and RBDg epitopes of SARS-CoV-2 were used to estimate potential vaccine coverage in the populations of interest. doi = 10.1101/2020.04.25.20079426 id = cord-022474-xxy83c6u author = Tenorio, Grace C. title = Transfusion Medicine and Immunohematology date = 2007 keywords = ABO; HLA; antigen; blood; cell; donor; transfusion summary = doi = 10.1007/978-1-59745-149-9_22 id = cord-319993-er3sm4u8 author = Terry, Frances E title = Time for T? Immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases date = 2015-01-02 keywords = HLA; MHC; NTD; cell; epitope summary = doi = 10.1586/14760584.2015.955478 id = cord-346445-hgqohdct author = Toyoshima, Yujiro title = SARS-CoV-2 genomic variations associated with mortality rate of COVID-19 date = 2020-07-22 keywords = HLA; SARS summary = Our findings suggest that SARS-CoV-2 mutations as well as BCG-vaccination status and a host genetic factor, HLA genotypes might affect the susceptibility to SARS-CoV-2 infection or severity of COVID-19. In this study, we comprehensively analyzed 12,343 SARS-CoV-2 genome sequences isolated from patients/ individuals in six geographic areas, including Asia, North America, South America, Europe, Oceania, and Africa, and investigated their correlations to the fatality rates in 28 different countries. In this study, we investigated the SARS-CoV-2 virus mutations and found that the frequencies of S protein 614G variant and its highly linked variant, ORF1ab 4715L, were significantly correlated with fatality rates in the 28 countries and 17 states of the United States. In summary, we comprehensively investigated SARS-CoV-2 genome mutations, BCG-vaccination status, and HLA genotypes in the 28 different countries and identified significant associations of some virus genome variants with the fatality rates. doi = 10.1038/s10038-020-0808-9 id = cord-254190-bxfne94u author = Tu, Wenwei title = Application of Humanized Mice in Immunological Research date = 2015-07-07 keywords = HIV; HLA; humanized; mouse summary = On the contrary, humanized mice established by peripheral blood cells provide a ready platform for studying the functions of mature immune cells but the length of window appropriate for research is still limited by chronic GVHD and ongoing reduced engraftment. Distinct from their T cell companion, reconstitution of functional B lymphocytes is generally poor in humanized mice and needed to improve in the future although their primary repertoire were principally unaltered by the differences between mouse and human stromal environments [ 53 ] and their ability to produce antigen-specifi c antibody was partly developed [ 54 ] . In above three studies, investigators planted solid grafts into immunodefi cient mice before reconstitution of human immune system and induced rejection by infusion of mature human cells. Humanized immune system (HIS) mice as a tool to study human NK cell development Humanized mice as a model to study human hematopoietic stem cell transplantation doi = 10.1007/978-1-4939-3139-2_10 id = cord-031937-qhlatg84 author = Verma, Anukriti title = Elucidating potential molecular signatures through host-microbe interactions for reactive arthritis and inflammatory bowel disease using combinatorial approach date = 2020-09-15 keywords = HLA; IBD; KYNU; host; microbe; protein summary = In-silico analysis involving text mining, metabolic network reconstruction, simulation, filtering, host-microbe interaction, docking and molecular mimicry studies results in robust drug target/s and biomarker/s for co-evolved IBD and ReA. The contributions of the microorganisms in the co-evolved IBD and ReA as part of the disease network was created through the interactive maps of the essential host interaction proteins (verified using literature survey) and the information processed through gene expression data analysis 64 . The pathways of the above host interacting proteins were found out using KEGG database that provides ontologies for proteins related to biological processes 67 www.nature.com/scientificreports/ Subsequently, the role of drugs or inhibitors used to suppress the effect of IBD and ReA such as indomethacin, prednisone, ciprofloxacin, sulfasalazine, azathioprine, methotrexate and hydroxychloroquine was scored in the disease network through their docking studies against the potential targets (both host as well microbial targets) as per published methodologies 68, 69 . doi = 10.1038/s41598-020-71674-8 id = cord-294212-nlekz39f author = Wang, Dongliang title = Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design date = 2020-07-03 keywords = CoV-2; HLA; SARS summary = doi = 10.3390/vaccines8030355 id = cord-007719-3ypv9k9p author = Wang, Mingjun title = Classification of Human Leukocyte Antigen (HLA) Supertypes date = 2014-05-06 keywords = HLA summary = Identification of new antigenic peptides, derived from infectious agents or cancer cells, which bind to human leukocyte antigen (HLA) class I and II molecules, is of importance for the development of new effective vaccines capable of activating the cellular arm of the immune response. Thus, identifi cation of new antigenic peptides, derived from infectious agents or tumor antigens, which may bind to HLA-I or HLA-II molecules in exchange with self-peptides normally occupying the HLA-binding site ( see below), is important for developing new effective vaccines capable of activating the cellular arm of the immune responses. To reduce this complexity, one option is to group thousands of different HLA molecules into clusters of several so-called HLA supertypes: a classifi cation that refers to a group of HLA alleles with largely overlapping peptide binding specifi cities. doi = 10.1007/978-1-4939-1115-8_17 id = cord-013894-1bgvj62a author = Wang, Qihui title = Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex date = 2019-07-04 keywords = D3D4; HLA; LILRB1 summary = Through cis or trans interactions with human leukocyte antigen (HLA)-G, the two most abundantly expressed inhibitory LILRs, LILRB1, and LILRB2 (LILRB1/2, also known as CD85j/d and ILT2/4), are involved in immunotolerance in pregnancy and transplantation, autoimmune diseases, and immune evasion by tumors. Structural comparisons of LILRB1/2 binding to different HLA alleles Similar to previous reports, 14,17 D1 interacts with the HLA-G1 α3 domain. As assessed by the SPR assay, dimeric HLA-G1 presenting variable peptides displayed similar binding strengths for LILRB1 and LILRB2 (with four Ig-like domains or D1D2), indicating that the peptides seem to have no effect on the interactions. Structural data in this study indicate that through trans interaction, one HLA-G1 monomer binds to one LILRB1/2 molecule. The complex structure reported here provides the first direct evidence that D1D2 is responsible for all of the interactions with HLA-Is, while D3D4 is not the reason to explain why HLA-Is that carry a single residue substitution in their α1α2 domains or in the presented peptides display variable binding affinities to LILRB2. doi = 10.1038/s41423-019-0258-5 id = cord-344364-vu389d88 author = Wang, Wei title = Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease‐2019 (COVID‐19) date = 2020-06-02 keywords = HLA; SARS summary = Here, 82 individuals with COVID-19 were genotyped for HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 loci using next-generation sequencing (NGS). Frequencies of the HLA-C*07:29, C*08:01G, B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 alleles were higher, while the frequencies of the DRB1*12:02 and DPB1*04:01 alleles were lower in COVID-19 patients than in the control population, with uncorrected statistical significance. The allele distributions of HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1 loci were compared between COVID-19 patients and control individuals. HLA-C*07:29, C*08:01G (including C*08:01 and C*08:22), B*15:27, B*40:06, DRB1*04:06, and DPB1*36:01 frequencies were higher in COVID-19 patients than in the control population, with uncorrected statistical significance (P < .05). 8 In the present study, HLA-C*07:29 was found in one COVID-19 patient, but in no individuals in the control group. 15, 16 In the present study, these SARS-susceptibility alleles were not found to occur at a significantly different frequency in COVID-19 patients after P-value correction. doi = 10.1111/tan.13941 id = cord-266902-wuty839o author = Wang, Yan title = Weak binder for MHC molecule is a potent Mycobacterium tuberculosis-specific CTL epitope in the context of HLA-A24 allele date = 2012-10-31 keywords = A24; HLA summary = doi = 10.1016/j.micpath.2012.07.002 id = cord-006273-xcw0kxjg author = Willemze, R title = KIR-ligand incompatibility in the graft-versus-host direction improves outcomes after umbilical cord blood transplantation for acute leukemia date = 2009-01-08 keywords = HLA; KIR; ligand summary = doi = 10.1038/leu.2008.365 id = cord-289711-4ab3d00h author = Yarmarkovich, Mark title = Identification of SARS-CoV-2 Vaccine Epitopes Predicted to Induce Long-term Population-Scale Immunity date = 2020-06-08 keywords = HLA; SARS summary = Summary Here we propose a SARS-CoV-2 vaccine design concept based on identification of highly conserved regions of the viral genome and newly acquired adaptations, both predicted to generate epitopes presented on MHC class I and II across the vast majority of the population. Here we describe an approach for prioritizing viral epitopes derived 105 from a prioritized list of 33mer peptides predicted to safely target the vulnerabilities of 106 SARS-CoV-2, generate highly immunogenic epitopes on both MHC class I and II in the 107 vast majority of the population, and maximize the likelihood that these peptides will drive 108 an adaptive memory response. Here we present a comprehensive immunogenicity map of the SARS-CoV-2 248 virus (Table S1) , and propose sixty-five 33mer peptide sequences predicted to generate 249 B and T cell epitopes from a diverse sampling of viral domains across all 10 SARS-250 doi = 10.1016/j.xcrm.2020.100036 id = cord-003143-n6b0r92e author = Zhao, Min title = Heterosubtypic Protections against Human-Infecting Avian Influenza Viruses Correlate to Biased Cross-T-Cell Responses date = 2018-08-07 keywords = Fig; H5N1; H7N9; HLA summary = doi = 10.1128/mbio.01408-18 id = cord-306308-zjq6cscm author = de Moura, Ronald Rodrigues title = Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population date = 2020-08-05 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-005453-4057qib7 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Poster Session date = 2019-07-03 keywords = AML; ASCT; ATG; BMT; CD19; CD34; CD4; CD8; CMV; CSF; DFS; DLI; EBMT; EBV; ECP; GVHD; HCT; HLA; HSCT; Hodgkin; Hospital; III; January; MDS; MRD; MSD; NHL; NRM; PBSC; PCR; PFS; PNH; RIC; TBI; TMA; TRM; University; VOD; background; car; cell; conclusion; day; disease; donor; figure; graft; group; high; median; method; mud; patient; result; transplantation summary = To compare the safety and efficacy of prophylactic DLI for prevention of relapse after allogeneic peripheral blood stem cell transplantation from haploidentical donors (HID-SCT) and matched-sibling donors (MSD-SCT) in patients with very high-risk acute myeloid leukemia (AML), we performed a retrospective, observational cohort study enrolled in 21 HID-SCT and 13 MSD-SCT recipients. The aim of this study is to identify the prognostic impact of pre-transplant TIM3 levels on early and late transplant related complications as well as post-transplant relapse and survival Methods: A total of 177 hematopoietic stem cell transplantation (HSCT) recipients with an initial diagnosis of acute leukemia [median age: 36(16-66) years; male/ female: 111/66] were included in the study. doi = 10.1038/s41409-019-0559-4 id = cord-005460-ezrn8cva author = nan title = Physicians – Poster Session date = 2017-07-28 keywords = AML; ASCT; ATG; BEAM; CD34; CD4; CD8; CMV; CSF; DFS; DLI; Department; EBV; ECP; GVHD; HCT; HLA; HSCT; Hematology; Hodgkin; Hospital; III; January; MDS; MRD; MSC; NHL; NRM; PBSC; PCR; PFS; RIC; SOS; TBI; TRM; Table; University; VOD; cell; day; figure; patient; transplantation summary = Still the optimal combination of immunosuppressive agents with PTCy should be elucidated for different types of SCTs. We report the 2-year update of the prospective NCT02294552 single-center trial that evaluated risk-adapted graft-versushost disease (GVHD) prophylaxis with PTCy in related, unrelated and haploidentical SCTs. 200 adult patients (median age 32 y.o., range: 18-62) with hematologic malignancies, including AML (47.5%), ALL (26.5%), CML (10.5%), MDS (4%), and lymphomas (11.5%), were enrolled in the study. Long-term follow-up from the prospective randomized phase III multicenter trial comparing a standard GvHD prophylaxis with cyclosporine A and methotrexate with or without additional pretransplant ATLG (Grafalon, previously ATG-FRESENIUS S) (given 20 mg/kg/day, days − 3 to − 1) in unrelated donor hematopoietic cell transplantation after myeloablative conditioning resulted in a significant reduction of acute and chronic GvHD without compromising relapse rate and survival [1, 2, 3] . doi = 10.1038/bmt.2017.134 id = cord-005478-5iu38pr6 author = nan title = The 45th Annual Meeting of the European Society for Blood and Marrow Transplantation: Physicians – Oral Session date = 2019-07-03 keywords = AML; ATG; CMV; EBMT; GVHD; HCT; HLA; HSCT; MRD; NRM; RIC; VOD; background; car; cell; day; figure; patient summary = There were some differences among groups: patients in group-1 were younger (median age 46 years, p< 0.02) were transplanted in more recent year (2015, p< 0.001), received more frequently a regimen based on TBF (thiotepa, fludarabine and busulfan) (83%, p< 0.001) and bone marrow (BM) as source of stem cells (77%, p< 0.001), with no ATG (100%, p< 0.001). Clinical Trial Registry: NCT01217723 Disclosure: None of the Authors have any conflicts of interest to declare O105 Immune reconstitution -based score at diagnosis of CGVHD predicts GVHD severity and overall-survival: A novel prognostication tool for GVHD treatment tailoring Background: Allogeneic stem cell transplantation (HSCT) survivors are at a relevant risk of developing chronic GvHD (cGvHD), which importantly affects quality of life and increases morbidity and mortality. doi = 10.1038/s41409-019-0562-9 id = cord-005480-yg7salqt author = nan title = Oral Sessions and Working Party date = 2008-03-26 keywords = AML; ASCT; CD8; CMV; EBMT; GVHD; HCT; HLA; HSCT; MSC; NRM; RIC; TBI; TRM; cell; patient summary = Standard NIH or Eurolupus cyclophosphamide (CY) protocols and mycophenolate Mofetil (MMF) as induction therapy in severe BILAG A SLE is still associated with 20 % failure, 50% relapse and 10% to 15 % death at 10 years In the absence of a single standard treatment worldwide for refractory SLE, phase I-II studies analysed the use of: a) rituximab (anti CD20 mAb) in more than 1 000 patients showing complete to partial early response around 100% with relapse in 50 to 60% of the cases; b) autologous Hematopoietic Stem Cell Transplantation (HSCT) since 1997 under the auspices of the joined EBMT-EULAR working party, reporting durable remission with reduced or no immunosuppressive drug requirement in 66%, one-third of whom later relapsed to some degree with a 74 ± 7% (n= 62/79) overall survival at 5 years for SLE among the 863 HSCT procedures registered: in 2007 in the EBMT data base. doi = 10.1038/bmt.2008.30 id = cord-005487-vac061r8 author = nan title = Physicians Abstracts: EBMT 2010 date = 2010-04-07 keywords = AML; ASCT; CD34; CD8; CMV; CR1; EBMT; GVHD; HLA; HSCT; NRM; RIC; TBI; cell; patient summary = We retrospectively analyzed 1257 patients (pts), 755 children (age≤18) and 502 adults, receiving fi rst single (n = 1080) or double UCBT (n = 177) in EBMT centers, between 1995 and 2009 , for malignant and non-malignant diseases, who survived at least 100 days from transplantation with neutrophils recovery and without relapse or autologous reconstitution. Prochymal® improves response rates in patients with steroid-refractory acute graft-versus-host disease involving the liver and gut: results of a randomized, placebo-controlled, multicentre phase III trial in GvHD P.J. Martin (1) , J.P. Uberti (2) Background and methods: Steroid-refractory acute GVHD (SR-GVHD) remains a signifi cant and life-threatening complication of allogeneic hematopoietic cell transplantation (HCT). A. Nagler (1) Background: Allogeneic transplantation of hematopoietic stem cells (allo-SCT) from an HLA-matched related (MRD) or unrelated donor (URD) is a curative option for patients (pts) with high-risk hematological disease (HRHD). doi = 10.1038/bmt.2010.40 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-009571-mygj2nd4 author = nan title = Proceedings of the 42nd annual meeting of the american rheumatism association a section of the arthritis foundation june 1 & 2, 1978 new york city abstracts of papers presented date = 2005-11-23 keywords = HLA; SLE; antibody; cell; disease; dna; normal; nzb; patient; study summary = doi = 10.1002/art.1780210508 id = cord-010088-s9tfvtao author = nan title = Oral Abstracts date = 2013-11-01 keywords = HBV; HCV; HLA; HNA; HPA; ISBT; Japan; NAT; PRT; TRALI; antibody; blood; cell; donor; patient; platelet; transfusion summary = doi = 10.1111/vox.12100_1 id = cord-010092-uftc8inx author = nan title = Abstract of 29th Regional Congress of the ISBT date = 2019-06-07 keywords = ABO; AIHA; Alinity; Background; Blood; CD34; Conclusions; DAT; December; HBV; HCV; HDFN; HEV; HIV; HLA; Health; Hospital; January; NAT; National; PBM; PCR; PLT; RBC; RHD; RNA; Red; SCD; Service; Summary; Transfusion; aim; anti; cell; dna; donation; donor; group; method; patient; platelet; result; sample; study; test summary = Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. doi = 10.1111/vox.12792 id = cord-010119-t1x9gknd author = nan title = Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date = 2017-09-04 keywords = ABO; Anti; Background; Blood; CD36; Case; Center; DAT; DTT; Design; FDA; FFP; HBV; HCV; HIV; HLA; Hospital; IPC; MTP; Medical; Medicine; NAT; PCR; PLT; RBC; RHD; Red; Studies; Study; System; TPE; University; WBC; ZIKV; Zika; cd341; cell; conclusion; day; dna; donor; finding; method; patient; platelet; result; sample; table; test; transfusion; type summary = Conclusion: The wide distribution in the concentration of bioactive lipids among 405 stored RBC units suggests that lipid degradation is highly donor-Background/Case Studies: To ensure availability of biological products to hospitals, blood banks have developed and validated multiple storage conditions for each of their products to maximize shelf life and quality. 1 The Department of Blood Transfusion, The PLA General Hospital, 2 The Department of Blood Transfusion, Air Force General Hospital, PLA Background/Case Studies: Recently, multi researches have reported that longer term-stored red blood cells(RBCs) units were associated with increased risks of clinically adverse events, especially in critically ill patients. Weak D types 1, 2 and 3 express all the major RhD epitopes and these patients can be managed as RhD-positive, which may lead to a reduction in unnecessary Rh immunoglobulin (RhIG) administration and conservation of RhD-negative RBCs. Study Design/Method: RHD genotyping was performed on all patient samples with weaker than expected or discrepant RhD typing results, utilizing a commercially available genotyping kit manufactured by Immucor (RHD BeadChip). doi = 10.1111/trf.14286 id = cord-014976-546zaoxn author = nan title = Publication only date = 2006-03-08 keywords = AML; ASCT; ATG; CD34; CSF; GVHD; HLA; HSCT; PBSC; PCR; RIC; SCT; cell; day; patient; stem; transplantation summary = In order to evaluate if malignant and non malignant hematological diseases quantitatively and qualitatively affect BM derived MSCs, bone marrow from children with acute lymphoblastic leukemia (ALL diagnosis n=9, different phases of treatment n=29, end of therapy n=10), idiopathic thrombocytopenic purpura (n=16), autoimmune neutropenia (n=12) and control patients (solid tumors without BM involvement, n=30) was harvested and the mononuclear cell (MNC) fraction isolated. Case: In our hospital a total of 3 patients with relapsed Hodgkin''s disease underwent reduced-intensity conditioning (RIC) allogeneic stem cell transplantation (allo-SCT) from an HLA-identical sibling. We report a case of a young male patient of 19 years old with aggressive MS who was treated with a high-dose immunosuppressive regimen (HDIS) using myeloablation followed by autologous blood stem cell transplantation (ASCT) that has induced a dramatic and long-lasting remission of the disease. doi = 10.1038/sj.bmt.1705327 id = cord-015389-vwgai4k9 author = nan title = Publication only date = 2009-03-25 keywords = AML; CD34; CMV; CSF; GVHD; HLA; HSCT; cell; day; median; patient summary = This study evaluates the safety of this approach, in terms of infusion-related toxicity and hematopoietic reconstitution, in 385 consecutive autologous transplantations performed from 4/97 to 9/08 in 348 patients (median age 46; underlying disease: lymphoma in 178, myeloma in 131, acute leukaemia in 17, breast cancer in 22). Patients and methods: Eight pts after allogeneic hematopoetic stem cell transplantation (HSCT) underwent MSCs infusions (median age of pts was 11 years, male/female: 6/2) between 2006 and 2009. Akiyama Tokyo Metropolitan Komagome Hospital (Tokyo, JP) Acute graft-versus-host disease (GVHD) is one of the major factors that have infl uence on the outcomes of allogeneic hematopoietic stem cell transplantation (HSCT). Material and methods: during a 8 years period we have performed 144 stem cells transplantation in 134 patients with different hematological malignancies(AML: 74; ALL: 6; CML: 7; CLL: 1, NHL: 13; Hodgkin Diseases: 16; Multiple myelomas: 24; Aplastic anaemia: 1;Myelofi brosis:1 Ewing Sarcoma: 1; Male:78 Female 66. doi = 10.1038/bmt.2009.50 id = cord-016998-6n662amh author = nan title = Nierentransplantation date = 2007 keywords = Abstoßung; CMV; Ciclosporin; HLA; Jahren; Patienten; Transplantation; der; die; und; von summary = doi = 10.1007/978-3-540-48556-8_13 id = cord-017184-1ewi3dka author = nan title = Primary Immunodeficiencies date = 2008 keywords = BMT; CD4; CD8; Fig; HLA; IFN; SCID; Table; cell; child; deficiency; infection; patient summary = doi = 10.1007/978-3-540-33395-1_22 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-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 keywords = ABO; DAT; FFP; HBV; HCV; HIV; HLA; Hospital; NAT; PCR; RBC; RHD; RNA; TRALI; Transfusion; anti; antibody; blood; cell; dna; donor; group; method; patient; platelet; result; study; system; test summary = • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. doi = 10.1111/j.1423-0410.2005.00652.x id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 keywords = ABO; DAT; FFP; HBV; HCV; HIV; HLA; Hospital; NAT; PCR; RBC; RHD; RNA; TRALI; Transfusion; anti; antibody; blood; cell; dna; donor; group; method; patient; platelet; result; study; system; test summary = • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. doi = 10.1111/j.1423-0410.2005.00654.x id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 keywords = ABO; DAT; FFP; HBV; HCV; HIV; HLA; Hospital; NAT; PCR; RBC; RHD; RNA; TRALI; Transfusion; anti; antibody; blood; cell; dna; donor; group; method; patient; platelet; result; study; system; test summary = • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. doi = 10.1111/j.1423-0410.2005.00651.x id = cord-313474-1gux1gsi author = nan title = Physicians Abstracts date = 2015-03-20 keywords = AML; ATG; CD34; CMV; GVHD; HCT; HLA; HSCT; Interest; NRM; RIC; cell; patient summary = Materials (or patients) and methods: We performed a multicenter, multinational, open-label, randomized study comparing anti-lymphocyte globulin (ATG-Fresenius s ) 10 mg/kg on day -3, -2 and -1 with no ATG in patients with AML (n ¼ 110) or ALL (n ¼ 45) in 1 st complete remission (CR; n ¼ 139) or 2 nd CR (n ¼ 16) who received peripheral blood stem cells from their HLA-identical sibling after standard TBI (12 Gy)/Ccclophosphamide (120 mg/kg) or busulfan (16 mg/ kg)/Cy (120 mg/kg) based myeloablative conditioning regimen. After allo-HSCT, detection of positive WT1 was followed by immunomodulatory therapeutic interventions according to the time from transplant, the presence of active graft-versus-host disease (GvHD) and the general clinical conditions: tapering and/or discontinuation of immunosuppressive drugs (IS), donor lymphocytes infusions (DLI), administration of hypomethylating agents. Introduction: Haploidentical hematopoietic stem cell transplantation(Haplo-HSCT)is feasible option for patients with acute leukemia(AL)at high risk of relapse who do not have HLA-matched related or unrelated donors. doi = 10.1038/bmt.2015.27