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PMC:7402624 / 75617-79396 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T562 31-36 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T563 1535-1538 Body_part denotes MBP http://purl.org/sig/ont/fma/fma242151
T564 1867-1873 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T565 1887-1895 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T566 2211-2214 Body_part denotes MBP http://purl.org/sig/ont/fma/fma242151
T567 2928-2936 Body_part denotes Pancreas http://purl.org/sig/ont/fma/fma7198
T568 3038-3042 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T569 3124-3129 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T570 3206-3211 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T42 31-36 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T43 2928-2936 Body_part denotes Pancreas http://purl.obolibrary.org/obo/UBERON_0001264

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T442 138-140 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T443 145-147 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T444 465-473 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T445 655-657 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T447 901-907 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T448 1019-1025 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T449 1059-1065 Disease denotes Cancer http://purl.obolibrary.org/obo/MONDO_0004992
T450 1188-1190 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T452 1233-1235 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T454 1277-1279 Disease denotes NM http://purl.obolibrary.org/obo/MONDO_0008091|http://purl.obolibrary.org/obo/MONDO_0011603
T456 1355-1363 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T457 1443-1445 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T458 1450-1452 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T459 1521-1523 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T461 1591-1593 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T463 1757-1759 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T465 1809-1812 Disease denotes EMA http://purl.obolibrary.org/obo/MONDO_0009282
T466 1850-1858 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T467 2162-2164 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T469 2270-2272 Disease denotes DM http://purl.obolibrary.org/obo/MONDO_0005015|http://purl.obolibrary.org/obo/MONDO_0016367
T471 2801-2811 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T472 2816-2822 Disease denotes cancer http://purl.obolibrary.org/obo/MONDO_0004992
T473 2928-2936 Disease denotes Pancreas http://purl.obolibrary.org/obo/MONDO_0021040

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1067 31-36 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T1068 31-36 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T1069 145-147 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T1070 899-900 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1071 1402-1404 http://purl.obolibrary.org/obo/CLO_0008246 denotes OK
T1072 1450-1452 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T1073 1548-1550 http://purl.obolibrary.org/obo/CLO_0001547 denotes AP
T1074 1552-1554 http://purl.obolibrary.org/obo/CLO_0052676 denotes FC
T1075 1770-1772 http://purl.obolibrary.org/obo/CLO_0052676 denotes FC
T1076 1823-1826 http://purl.obolibrary.org/obo/CLO_0002599 denotes CPA
T1077 1867-1873 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T1078 2238-2240 http://purl.obolibrary.org/obo/PR_000010213 denotes MB
T1079 2384-2387 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T1080 2524-2525 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1081 2586-2589 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T1082 2590-2591 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1083 2686-2687 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1084 2922-2927 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T1085 2928-2936 http://purl.obolibrary.org/obo/UBERON_0001264 denotes Pancreas
T1086 3036-3042 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T1087 3112-3129 http://purl.obolibrary.org/obo/CL_0000895 denotes Naive CD4 T cells
T1088 3200-3203 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T1089 3204-3211 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T1090 3300-3301 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1091 3502-3503 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T1092 3693-3694 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T64579 138-140 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T34479 145-147 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T69904 655-657 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T712 731-734 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T40913 965-967 Chemical denotes AH http://purl.obolibrary.org/obo/CHEBI_73771
T41500 1188-1190 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T84118 1233-1235 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T12270 1277-1279 Chemical denotes NM http://purl.obolibrary.org/obo/CHEBI_141423
T86921 1443-1445 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T35838 1450-1452 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T5332 1462-1464 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T68846 1521-1523 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T19371 1540-1542 Chemical denotes NH http://purl.obolibrary.org/obo/CHEBI_29339|http://purl.obolibrary.org/obo/CHEBI_73424
T73697 1548-1550 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 1591-1593 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T21111 1757-1759 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T138 1804-1807 Chemical denotes ECG http://purl.obolibrary.org/obo/CHEBI_70255
T5355 1819-1821 Chemical denotes SG http://purl.obolibrary.org/obo/CHEBI_74814
T140 2042-2045 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T81966 2047-2049 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817
T10321 2100-2103 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T24442 2109-2111 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817
T96953 2162-2164 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T63835 2184-2187 Chemical denotes DAO http://purl.obolibrary.org/obo/CHEBI_30805
T952 2216-2218 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 2270-2272 Chemical denotes DM http://purl.obolibrary.org/obo/CHEBI_141426
T22801 2626-2628 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T154 2778-2780 Chemical denotes PD http://purl.obolibrary.org/obo/CHEBI_74756
T41990 3350-3352 Chemical denotes CC http://purl.obolibrary.org/obo/CHEBI_28940

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T137 3420-3432 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T19 901-907 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T20 1019-1025 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T21 1059-1065 Phenotype denotes Cancer http://purl.obolibrary.org/obo/HP_0002664
T22 2504-2512 Phenotype denotes Oncology http://purl.obolibrary.org/obo/HP_0002664
T23 2545-2553 Phenotype denotes Oncology http://purl.obolibrary.org/obo/HP_0002664
T24 2816-2822 Phenotype denotes cancer http://purl.obolibrary.org/obo/HP_0002664

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T468 0-98 Sentence denotes The authors thank patients and blood donors, their families and surrogates, and medical personnel.
T469 99-110 Sentence denotes We thank L.
T470 111-148 Sentence denotes Bershaw for recruitment of HD and RD.
T471 149-160 Sentence denotes We thank S.
T472 161-210 Sentence denotes Ngiow for essential infrastructure support and C.
T473 211-287 Sentence denotes Ash for donation of computational equipment and design of schematic figures.
T474 288-366 Sentence denotes We thank the Wherry lab for discussions and critically reading the manuscript.
T475 367-375 Sentence denotes Funding:
T476 376-607 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 608-654 Sentence denotes ACH was funded by grant CA230157 from the NIH.
T478 655-693 Sentence denotes DM and JG were funded by T32 CA009140.
T479 694-730 Sentence denotes ZC was funded by NIH grant CA234842.
T480 731-761 Sentence denotes DAO was funded by NHLBI StARR:
T481 762-775 Sentence denotes 1R38HL143613.
T482 776-891 Sentence denotes NJM reports funding to her institution from Athersys, Inc., Biomarck, Inc., and the Marcus Foundation for Research.
T483 892-950 Sentence denotes JRG is a Cancer Research Institute-Mark Foundation Fellow.
T484 951-1119 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 1120-1165 Sentence denotes The authors declare no conflicts of interest.
T486 1166-1276 Sentence denotes Author contributions: DM, NJM, MJB, and EJW conceived the project; DM, JRG, AEB, and EJW designed experiments.
T487 1277-1453 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 1454-1520 Sentence denotes AEB and KD coordinated clinical sample procurement and processing.
T489 1521-1590 Sentence denotes DM, ARG, LKC, MBP, NH, JK, AP, FC, and SFL processed patient samples.
T490 1591-1718 Sentence denotes DM, ZC, and YJH stained and JEW acquired flow cytometry samples; JRG, AEB, and KN performed downstream flow cytometry analysis.
T491 1719-1756 Sentence denotes HR and SCC performed qRT-PCR of PBMC.
T492 1757-1803 Sentence denotes DM, SFL, and FC performed Luminex experiments.
T493 1804-1901 Sentence denotes ECG, EMA, MEW, SG, CPA, MJB, and SEH analyzed COVID-19 patient plasma and provided antibody data.
T494 1902-2036 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 2037-2161 Sentence denotes JRG, DAO, SM, and EJW designed data analysis and JRG, ARG, CA, DAO, and SM performed computational and statistical analyses.
T496 2162-2205 Sentence denotes DM, JRG, ARG, CA, and DAO compiled figures.
T497 2206-2269 Sentence denotes LKC, MBP, SA, ACH, LAV, NJM and MB provided intellectual input.
T498 2270-2355 Sentence denotes DM, AEB, ARG, JEW, and EJW wrote the manuscript; all authors reviewed the manuscript.
T499 2356-2513 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 2514-2578 Sentence denotes E.J.W. is a founder of Surface Oncology and Arsenal Biosciences.
T501 2579-2660 Sentence denotes E.J.W. has a patent licensing agreement on the PD-1 pathway with Roche/Genentech.
T502 2661-2823 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 2824-2856 Sentence denotes Data and materials availability:
T504 2857-3035 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 3036-3107 Sentence denotes B cell data (https://premium.cytobank.org/cytobank/experiments/308353).
T506 3108-3189 Sentence denotes Non Naive CD4 T cells (https://premium.cytobank.org/cytobank/experiments/308354).
T507 3190-3271 Sentence denotes Non Naive CD8 T cells (https://premium.cytobank.org/cytobank/experiments/308357).
T508 3272-3493 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 3494-3577 Sentence denotes To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/.
T510 3578-3779 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.