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PMC:7402624 / 75601-79396 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T562 47-52 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T563 1551-1554 Body_part denotes MBP http://purl.org/sig/ont/fma/fma242151
T564 1883-1889 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T565 1903-1911 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T566 2227-2230 Body_part denotes MBP http://purl.org/sig/ont/fma/fma242151
T567 2944-2952 Body_part denotes Pancreas http://purl.org/sig/ont/fma/fma7198
T568 3054-3058 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T569 3140-3145 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T570 3222-3227 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T42 47-52 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T43 2944-2952 Body_part denotes Pancreas http://purl.obolibrary.org/obo/UBERON_0001264

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T442 154-156 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T443 161-163 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T444 481-489 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T445 671-673 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T447 917-923 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T448 1035-1041 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T449 1075-1081 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T450 1204-1206 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T452 1249-1251 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T454 1293-1295 Disease denotes NM http://purl.obolibrary.org/obo/MONDO_0008091|http://purl.obolibrary.org/obo/MONDO_0011603
T456 1371-1379 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T457 1459-1461 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T458 1466-1468 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T459 1537-1539 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T461 1607-1609 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T463 1773-1775 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T465 1825-1828 Disease denotes EMA http://purl.obolibrary.org/obo/MONDO_0009282
T466 1866-1874 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T467 2178-2180 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T469 2286-2288 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T471 2817-2827 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T472 2832-2838 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T473 2944-2952 Disease denotes Pancreas http://purl.obolibrary.org/obo/MONDO_0021040

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1067 47-52 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T1068 47-52 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T1069 161-163 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T1070 915-916 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1071 1418-1420 http://purl.obolibrary.org/obo/CLO_0008246 denotes OK
T1072 1466-1468 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T1073 1564-1566 http://purl.obolibrary.org/obo/CLO_0001547 denotes AP
T1074 1568-1570 http://purl.obolibrary.org/obo/CLO_0052676 denotes FC
T1075 1786-1788 http://purl.obolibrary.org/obo/CLO_0052676 denotes FC
T1076 1839-1842 http://purl.obolibrary.org/obo/CLO_0002599 denotes CPA
T1077 1883-1889 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T1078 2254-2256 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T1079 2400-2403 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T1080 2540-2541 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1081 2602-2605 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T1082 2606-2607 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1083 2702-2703 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1084 2938-2943 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T1085 2944-2952 http://purl.obolibrary.org/obo/UBERON_0001264 denotes Pancreas
T1086 3052-3058 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T1087 3128-3145 http://purl.obolibrary.org/obo/CL_0000895 denotes Naive CD4 T cells
T1088 3216-3219 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T1089 3220-3227 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T1090 3316-3317 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1091 3518-3519 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1092 3709-3710 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T64579 154-156 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T34479 161-163 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T69904 671-673 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T712 747-750 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T40913 981-983 Chemical denotes AH http://purl.obolibrary.org/obo/CHEBI_73771
T41500 1204-1206 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T84118 1249-1251 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T12270 1293-1295 Chemical denotes NM http://purl.obolibrary.org/obo/CHEBI_141423
T86921 1459-1461 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T35838 1466-1468 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T5332 1478-1480 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T68846 1537-1539 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T19371 1556-1558 Chemical denotes NH http://purl.obolibrary.org/obo/CHEBI_29339|http://purl.obolibrary.org/obo/CHEBI_73424
T73697 1564-1566 Chemical denotes AP http://purl.obolibrary.org/obo/CHEBI_28971|http://purl.obolibrary.org/obo/CHEBI_73393|http://purl.obolibrary.org/obo/CHEBI_81686
T136 1607-1609 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T21111 1773-1775 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T138 1820-1823 Chemical denotes ECG http://purl.obolibrary.org/obo/CHEBI_70255
T5355 1835-1837 Chemical denotes SG http://purl.obolibrary.org/obo/CHEBI_74814
T140 2058-2061 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T81966 2063-2065 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817
T10321 2116-2119 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T24442 2125-2127 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817
T96953 2178-2180 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T63835 2200-2203 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T952 2232-2234 Chemical denotes SA http://purl.obolibrary.org/obo/CHEBI_35962|http://purl.obolibrary.org/obo/CHEBI_38358|http://purl.obolibrary.org/obo/CHEBI_45373|http://purl.obolibrary.org/obo/CHEBI_74801
T38534 2286-2288 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T22801 2642-2644 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T154 2794-2796 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T41990 3366-3368 Chemical denotes CC http://purl.obolibrary.org/obo/CHEBI_28940

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T137 3436-3448 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T19 917-923 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T20 1035-1041 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T21 1075-1081 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T22 2520-2528 Phenotype denotes Oncology http://purl.obolibrary.org/obo/HP_0002664
T23 2561-2569 Phenotype denotes Oncology http://purl.obolibrary.org/obo/HP_0002664
T24 2832-2838 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T467 0-15 Sentence denotes Acknowledgments
T468 16-114 Sentence denotes The authors thank patients and blood donors, their families and surrogates, and medical personnel.
T469 115-126 Sentence denotes We thank L.
T470 127-164 Sentence denotes Bershaw for recruitment of HD and RD.
T471 165-176 Sentence denotes We thank S.
T472 177-226 Sentence denotes Ngiow for essential infrastructure support and C.
T473 227-303 Sentence denotes Ash for donation of computational equipment and design of schematic figures.
T474 304-382 Sentence denotes We thank the Wherry lab for discussions and critically reading the manuscript.
T475 383-391 Sentence denotes Funding:
T476 392-623 Sentence denotes This work was supported by the University of Pennsylvania Institute for Immunology Glick COVID-19 research award (MRB), NIH AI105343, AI082630, and the Allen Institute for Immunology (EJW) and NIH grants HL137006 and H137915 (NJM).
T477 624-670 Sentence denotes ACH was funded by grant CA230157 from the NIH.
T478 671-709 Sentence denotes DM and JG were funded by T32 CA009140.
T479 710-746 Sentence denotes ZC was funded by NIH grant CA234842.
T480 747-777 Sentence denotes DAO was funded by NHLBI StARR:
T481 778-791 Sentence denotes 1R38HL143613.
T482 792-907 Sentence denotes NJM reports funding to her institution from Athersys, Inc., Biomarck, Inc., and the Marcus Foundation for Research.
T483 908-966 Sentence denotes JRG is a Cancer Research Institute-Mark Foundation Fellow.
T484 967-1135 Sentence denotes JRG, JEW, CA, AH, and EJW are supported by the Parker Institute for Cancer Immunotherapy which supports the Cancer Immunology program at the University of Pennsylvania.
T485 1136-1181 Sentence denotes The authors declare no conflicts of interest.
T486 1182-1292 Sentence denotes Author contributions: DM, NJM, MJB, and EJW conceived the project; DM, JRG, AEB, and EJW designed experiments.
T487 1293-1469 Sentence denotes NM conceived the clinical cohort, obtained clinical samples and metadata from COVID-19 patients and provided clinical input; OK and JD provided clinical samples from HD and RD.
T488 1470-1536 Sentence denotes AEB and KD coordinated clinical sample procurement and processing.
T489 1537-1606 Sentence denotes DM, ARG, LKC, MBP, NH, JK, AP, FC, and SFL processed patient samples.
T490 1607-1734 Sentence denotes DM, ZC, and YJH stained and JEW acquired flow cytometry samples; JRG, AEB, and KN performed downstream flow cytometry analysis.
T491 1735-1772 Sentence denotes HR and SCC performed qRT-PCR of PBMC.
T492 1773-1819 Sentence denotes DM, SFL, and FC performed Luminex experiments.
T493 1820-1917 Sentence denotes ECG, EMA, MEW, SG, CPA, MJB, and SEH analyzed COVID-19 patient plasma and provided antibody data.
T494 1918-2052 Sentence denotes ACH and LAV provided additional clinical data; CA compiled and JRG, DO, and CA analyzed clinical metadata with input from ACH and LAV.
T495 2053-2177 Sentence denotes JRG, DAO, SM, and EJW designed data analysis and JRG, ARG, CA, DAO, and SM performed computational and statistical analyses.
T496 2178-2221 Sentence denotes DM, JRG, ARG, CA, and DAO compiled figures.
T497 2222-2285 Sentence denotes LKC, MBP, SA, ACH, LAV, NJM and MB provided intellectual input.
T498 2286-2371 Sentence denotes DM, AEB, ARG, JEW, and EJW wrote the manuscript; all authors reviewed the manuscript.
T499 2372-2529 Sentence denotes Competing interests: E.J.W. has consulting agreements with and/or is on the scientific advisory board for Merck, Roche, Pieris, Elstar, and Surface Oncology.
T500 2530-2594 Sentence denotes E.J.W. is a founder of Surface Oncology and Arsenal Biosciences.
T501 2595-2676 Sentence denotes E.J.W. has a patent licensing agreement on the PD-1 pathway with Roche/Genentech.
T502 2677-2839 Sentence denotes E.J.W. is an inventor on a patent (US Patent number 10,370,446) submitted by Emory University that covers the use of PD-1 blockade to treat infections and cancer.
T503 2840-2872 Sentence denotes Data and materials availability:
T504 2873-3051 Sentence denotes Flow Cytometry data collected in this study was deposited to the Human Pancreas Analysis Program (HPAP-RRID:SCR_016202) Database and Cytobank (61) (https://hpap.pmacs.upenn.edu).
T505 3052-3123 Sentence denotes B cell data (https://premium.cytobank.org/cytobank/experiments/308353).
T506 3124-3205 Sentence denotes Non Naive CD4 T cells (https://premium.cytobank.org/cytobank/experiments/308354).
T507 3206-3287 Sentence denotes Non Naive CD8 T cells (https://premium.cytobank.org/cytobank/experiments/308357).
T508 3288-3509 Sentence denotes This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
T509 3510-3593 Sentence denotes To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.
T510 3594-3795 Sentence denotes This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.