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PMC:7402624 / 36943-39187 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T343 455-459 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T344 588-591 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T345 617-622 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T346 669-674 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T347 753-758 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T348 852-856 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T349 1010-1015 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T350 1140-1144 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T351 1217-1220 Body_part denotes HLA http://purl.org/sig/ont/fma/fma84795
T352 1444-1448 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T353 1557-1562 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T354 1755-1758 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T355 1819-1821 Body_part denotes PB http://purl.org/sig/ont/fma/fma84371
T356 1859-1864 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T357 1942-1946 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T358 1952-1956 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T359 2191-2195 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1352 595-599 Gene denotes CD38 Gene:952
1353 611-614 Gene denotes CD4 Gene:920
1354 747-750 Gene denotes CD8 Gene:925
1355 846-849 Gene denotes CD8 Gene:925
1356 1004-1007 Gene denotes CD8 Gene:925
1357 1134-1137 Gene denotes CD8 Gene:925
1358 1224-1228 Gene denotes CD38 Gene:952
1359 1240-1243 Gene denotes CD8 Gene:925
1360 1430-1433 Gene denotes CD8 Gene:925
1361 1438-1441 Gene denotes CD4 Gene:920
1362 1543-1546 Gene denotes CD8 Gene:925
1363 1551-1554 Gene denotes CD4 Gene:920
1364 110-118 Species denotes patients Tax:9606
1365 204-211 Species denotes patient Tax:9606
1366 423-431 Species denotes patients Tax:9606
1367 560-568 Species denotes patients Tax:9606
1368 653-661 Species denotes patients Tax:9606
1369 931-939 Species denotes patients Tax:9606
1370 1275-1283 Species denotes patients Tax:9606
1371 1604-1612 Species denotes smallpox Tax:10255
1372 1635-1649 Species denotes vaccinia virus Tax:10245
1373 1796-1804 Species denotes patients Tax:9606
1374 1902-1910 Species denotes patients Tax:9606
1375 2023-2031 Species denotes patients Tax:9606
1376 2078-2086 Species denotes patients Tax:9606
1377 1819-1821 Chemical denotes PB
1378 414-422 Disease denotes COVID-19 MESH:C000657245
1379 1073-1075 Disease denotes HD MESH:D006816
1380 1171-1180 Disease denotes infection MESH:D007239
1381 1485-1500 Disease denotes viral infection MESH:D001102
1382 1576-1592 Disease denotes viral infections MESH:D001102
1383 1679-1684 Disease denotes fever MESH:D005334
1384 1723-1738 Disease denotes virus infection MESH:D001102
1385 1749-1768 Disease denotes acute HIV infection MESH:D015658

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T290 414-422 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T291 1073-1075 Disease denotes HD http://purl.obolibrary.org/obo/MONDO_0007739
T292 1080-1082 Disease denotes RD http://purl.obolibrary.org/obo/MONDO_0009973
T293 1171-1180 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T294 1485-1500 Disease denotes viral infection http://purl.obolibrary.org/obo/MONDO_0005108
T295 1491-1500 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T296 1576-1592 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T297 1604-1612 Disease denotes smallpox http://purl.obolibrary.org/obo/MONDO_0004651
T298 1635-1643 Disease denotes vaccinia http://purl.obolibrary.org/obo/MONDO_0002595
T299 1672-1684 Disease denotes yellow fever http://purl.obolibrary.org/obo/MONDO_0020502
T300 1713-1722 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T301 1723-1738 Disease denotes virus infection http://purl.obolibrary.org/obo/MONDO_0005108
T302 1729-1738 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T303 1755-1768 Disease denotes HIV infection http://purl.obolibrary.org/obo/MONDO_0005109
T304 1759-1768 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T305 1819-1821 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T622 229-230 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T623 455-459 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T624 595-599 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T625 605-622 http://purl.obolibrary.org/obo/CL_0000895 denotes naïve CD4 T cells
T626 669-674 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T627 747-750 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T628 751-758 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T629 846-849 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T630 850-856 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T631 1004-1007 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T632 1008-1015 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T633 1080-1082 http://purl.obolibrary.org/obo/CLO_0008770 denotes RD
T634 1122-1123 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T635 1134-1137 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T636 1138-1144 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T637 1182-1183 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T638 1224-1228 http://purl.obolibrary.org/obo/PR_000001408 denotes CD38
T639 1240-1243 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T640 1288-1289 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T641 1403-1412 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T642 1430-1433 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T643 1438-1441 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T644 1442-1448 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T645 1543-1546 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T646 1551-1554 http://purl.obolibrary.org/obo/PR_000001004 denotes CD4
T647 1555-1562 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T648 1644-1649 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T649 1697-1700 http://purl.obolibrary.org/obo/CLO_0001134 denotes 17D
T650 1702-1704 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48
T651 1723-1728 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T652 1770-1772 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T653 1857-1864 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T654 1940-1946 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T655 1950-1956 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T656 1957-1967 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T657 2117-2127 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T658 2189-2195 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T659 2196-2206 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T266 592-594 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T267 1073-1075 Chemical denotes HD http://purl.obolibrary.org/obo/CHEBI_73925
T268 1080-1082 Chemical denotes RD http://purl.obolibrary.org/obo/CHEBI_73812
T269 1221-1223 Chemical denotes DR http://purl.obolibrary.org/obo/CHEBI_73445
T270 1819-1821 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T79 1485-1500 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infection
T80 1576-1592 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T81 1950-1967 http://purl.obolibrary.org/obo/GO_0042113 denotes B cell activation
T82 1952-1967 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T83 2189-2206 http://purl.obolibrary.org/obo/GO_0042113 denotes B cell activation
T84 2191-2206 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T10 1679-1684 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T213 0-179 Sentence denotes However, in all cases, these temporal patterns were complex, with frequencies of subpopulations in individual patients appearing to increase, decrease, or stay the same over time.
T214 180-350 Sentence denotes To quantify these inter-patient changes, we used a previously described data set (46) to define the stability of populations of interest in healthy individuals over time.
T215 351-530 Sentence denotes We then used the range of this variation over time to identify COVID-19 patients with changes in immune cell subpopulations beyond that expected in healthy subjects (see methods).
T216 531-726 Sentence denotes Using this approach, ~50% of patients had an increase in HLA-DR+CD38+ non-naïve CD4 T cells over time, whereas in ~30% of patients, these cells were stable and, in ~20%, they decreased (Fig. 5E).
T217 727-817 Sentence denotes For KI67+ non-naïve CD8 T cells, there were no individuals in whom the response decreased.
T218 818-917 Sentence denotes Instead, this proliferative CD8 T cell response stayed stable (~70%) or increased (~30%; fig. S6A).
T219 918-1098 Sentence denotes Notably, for patients in the stable category, the median frequency of KI67+ non-naïve CD8 T cells was ~10%, almost 5-fold higher than the ~1% detected for HD and RD subjects (Figs.
T220 1099-1181 Sentence denotes 5C and 2E), suggesting a sustained CD8 T cell proliferative response to infection.
T221 1182-1373 Sentence denotes A similar pattern was observed for HLA-DR+CD38+ non-naïve CD8 (fig. S6B), where only ~10% of patients had a decrease in this population, whereas ~65% were stable and ~25% increased over time.
T222 1374-1774 Sentence denotes The high and even increasing activated or proliferating CD8 and CD4 T cell responses over ~1 week during acute viral infection contrasted with the sharp peak of KI67 in CD8 and CD4 T cells during acute viral infections, including smallpox vaccination with live vaccinia virus (47), live attenuated yellow fever vaccine YFV-17D (48), acute influenza virus infection (49), and acute HIV infection (35).
T223 1775-1890 Sentence denotes Approximately 42% of patients had sustained PB responses, at high levels (>10% of B cells) in many cases (Fig. 5F).
T224 1891-2052 Sentence denotes Thus, some patients displayed dynamic changes in T cell or B cell activation over 1 week in the hospital, but there were also other patients who remained stable.
T225 2053-2244 Sentence denotes In the latter case, some patients remained stable without clear activation of key immune populations whereas others had stable T and or B cell activation or numerical perturbation (fig. S6C).

2_test

Id Subject Object Predicate Lexical cue
32669297-28397821-135105212 262-264 28397821 denotes 46
32669297-18468462-135105213 1651-1653 18468462 denotes 47
32669297-29236685-135105214 1702-1704 29236685 denotes 48
32669297-22286307-135105215 1740-1742 22286307 denotes 49
32669297-26362266-135105216 1770-1772 26362266 denotes 35