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PMC:7417788 / 33765-36837 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T778 13-20 CHEBI:59132;CHEBI:59132 denotes antigen
T779 42-56 GO:0019814 denotes immunoglobulin
T780 183-188 GO:0007568 denotes aging
T781 329-335 UBERON:0002405;CL:0000738 denotes immune
T782 336-340 CL:0000738 denotes cell
T783 815-820 GO:0007568 denotes aging
T784 836-846 CL:0000542 denotes lymphocyte
T785 882-890 GO:0051866 denotes adaptive
T786 891-899 GO:0051866;UBERON:0002405 denotes immunity
T787 1156-1162 GO:0007613 denotes memory
T788 1262-1267 GO:0007568 denotes aging
T789 1359-1369 GO:0010467 denotes expression
T790 1373-1381 CHEBI:35224;CHEBI:35224 denotes effector
T791 1386-1392 GO:0007613 denotes memory
T792 1418-1422 PR:000003499 denotes GZMB
T793 1424-1428 PR:000003472 denotes GZMK
T794 1430-1435 PR:000001208 denotes CXCR4
T795 1437-1441 PR:000002123 denotes CCL3
T796 1458-1463 SO:0000704 denotes genes
T797 1536-1541 GO:0007568 denotes aging
T798 1582-1592 GO:0010467 denotes expression
T799 1609-1614 SO:0000704 denotes genes
T800 1655-1660 SO:0000704 denotes genes
T801 1669-1673 PR:000008963 denotes IGHM
T802 1678-1683 PR:000016193 denotes TCL1A
T803 1809-1814 GO:0007568 denotes aging
T804 2124-2130 CL:0000084 denotes T cell
T805 2205-2211 CL:0000236 denotes B cell
T806 2295-2309 CL:0000084 denotes clonal T cells
T807 2507-2514 CL:0000236 denotes B cells

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T295 42-56 Body_part denotes immunoglobulin http://purl.org/sig/ont/fma/fma62871
T296 275-279 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T297 336-340 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T298 836-846 Body_part denotes lymphocyte http://purl.org/sig/ont/fma/fma62863
T299 1305-1310 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T300 2126-2130 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T301 2207-2211 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T302 2304-2309 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T303 2509-2514 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T50 1669-1673 Disease denotes IGHM http://purl.obolibrary.org/obo/MONDO_0015977

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T641 75-78 http://purl.obolibrary.org/obo/CLO_0050938 denotes TCs
T642 75-78 http://purl.obolibrary.org/obo/CL_0000084 denotes TCs
T643 90-93 http://purl.obolibrary.org/obo/CL_0000236 denotes BCs
T644 236-239 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T645 275-279 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T646 336-340 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T647 372-374 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T648 427-429 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T649 456-457 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T650 762-764 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T651 959-961 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T652 1139-1142 http://purl.obolibrary.org/obo/CLO_0053438 denotes CD8
T653 1163-1166 http://purl.obolibrary.org/obo/CL_0000236 denotes BCs
T654 1174-1176 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T655 1237-1240 http://purl.obolibrary.org/obo/CLO_0050938 denotes TCs
T656 1237-1240 http://purl.obolibrary.org/obo/CL_0000084 denotes TCs
T657 1305-1310 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T658 1326-1328 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T659 1458-1463 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T660 1525-1528 http://purl.obolibrary.org/obo/CL_0000236 denotes BCs
T661 1609-1614 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T662 1655-1660 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T663 1696-1699 http://purl.obolibrary.org/obo/CL_0000236 denotes BCs
T664 1817-1818 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T665 1874-1876 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T666 1886-1887 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T667 1943-1945 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T668 2010-2012 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T669 2081-2083 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T670 2124-2130 http://purl.obolibrary.org/obo/CL_0000084 denotes T cell
T671 2162-2164 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T672 2205-2211 http://purl.obolibrary.org/obo/CL_0000236 denotes B cell
T673 2243-2245 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T674 2302-2309 http://purl.obolibrary.org/obo/CL_0000084 denotes T cells
T675 2329-2331 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T676 2371-2372 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T677 2400-2404 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T678 2507-2514 http://purl.obolibrary.org/obo/CL_0000236 denotes B cells
T679 2534-2536 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T680 2576-2577 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T681 2605-2609 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T682 2676-2681 http://purl.obolibrary.org/obo/CLO_0050421 denotes Chord
T683 2757-2759 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T684 2767-2772 http://purl.obolibrary.org/obo/CLO_0050421 denotes Chord
T685 2823-2824 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T686 2877-2882 http://purl.obolibrary.org/obo/CLO_0050421 denotes Chord
T687 2958-2960 http://purl.obolibrary.org/obo/CLO_0001627 denotes AA
T688 2968-2973 http://purl.obolibrary.org/obo/CLO_0050421 denotes Chord
T689 3024-3025 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T246 13-20 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T247 365-367 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T248 372-374 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T250 413-415 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T251 416-421 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T252 427-429 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T254 430-435 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T255 535-537 Chemical denotes 5B http://purl.obolibrary.org/obo/CHEBI_27560
T256 762-764 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T258 765-770 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T259 783-785 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T260 786-791 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T261 959-961 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T263 962-967 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T264 984-986 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T265 987-992 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T266 1174-1176 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T268 1177-1182 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T269 1319-1321 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T270 1326-1328 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T272 1373-1381 Chemical denotes effector http://purl.obolibrary.org/obo/CHEBI_35224
T273 1476-1481 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T274 1867-1869 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T275 1874-1876 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T277 1936-1938 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T278 1943-1945 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T280 1995-1997 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T281 2010-2012 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T283 2066-2068 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T284 2081-2083 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T286 2147-2149 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T287 2162-2164 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T289 2228-2230 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T290 2243-2245 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T292 2322-2324 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T293 2329-2331 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T295 2527-2529 Chemical denotes YA http://purl.obolibrary.org/obo/CHEBI_74879
T296 2534-2536 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T298 2757-2759 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T300 2760-2765 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T301 2958-2960 Chemical denotes AA http://purl.obolibrary.org/obo/CHEBI_15843|http://purl.obolibrary.org/obo/CHEBI_72816
T303 2961-2966 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T187 183-188 http://purl.obolibrary.org/obo/GO_0007568 denotes aging
T188 815-820 http://purl.obolibrary.org/obo/GO_0007568 denotes aging
T189 1156-1162 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T190 1262-1267 http://purl.obolibrary.org/obo/GO_0007568 denotes aging
T191 1386-1392 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T192 1430-1435 http://purl.obolibrary.org/obo/GO_0038147 denotes CXCR4
T193 1536-1541 http://purl.obolibrary.org/obo/GO_0007568 denotes aging
T194 1809-1814 http://purl.obolibrary.org/obo/GO_0007568 denotes aging

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T176 0-286 Sentence denotes Although the antigen repertoire sensed by immunoglobulin receptors on both TCs (TCRs) and BCs (BCRs) is known to continuously evolve with age (Yuseff et al., 2013), the phenomenon of aging-associated TCR and BCR repertoire constriction has not yet been studied at the single-cell level.
T177 287-382 Sentence denotes Here, we employed scTCR/BCR-seq to assess immune cell clonal expansion in the YA and AA groups.
T178 383-602 Sentence denotes We found that relative to the YA group, the AA group was associated with a substantial decrease in unique clonotypes both in TCRs and BCRs (Fig. 5A and 5B), suggesting that both TCR and BCR clonality increased with age.
T179 603-802 Sentence denotes Moreover, quantification of the most highly expanded (maximum) clone for each research subject showed that the ratios of the maximum clones were higher in the AA group than in the YA group (Fig. 5C).
T180 803-1003 Sentence denotes Although an aging-related clonal lymphocyte population may reflect an existing adaptive immunity of the elderly, the overall diversity was decreased in the AA group compared to the YA group (Fig. 5D).
T181 1004-1200 Sentence denotes Analysis of TCR and BCR distributions across different TC and BC subtypes revealed that loss of repertoire diversity was pronounced in CD8+, T-mito and memory BCs of the AA group (Fig. 5E and 5F).
T182 1201-1504 Sentence denotes To understand how clonally expanded TCs could be affected by aging, we performed DEG analysis of clonal cells between YA and AA groups and revealed increased expression of effector and memory TC signatures, including GZMB, GZMK, CXCR4, CCL3 and various TCR genes in the aged group (Fig. 5G; Table S12A).
T183 1505-1760 Sentence denotes In addition, clonal BCs showed aging-associated changes, including increased expression of S100A family genes and decreased levels of naive signature genes such as IGHM and TCL1A in the aged BCs compared to their young counterparts (Fig. 5H; Table S 12B).
T184 1761-2339 Sentence denotes Figure 5 Abnormal TCR and BCR repertoire during aging. (A) Pie plots showing TCR clone differences across YA and AA groups. (B) Pie plots showing BCR clone differences across YA and AA groups. (C) Percentage of maximum clones between YA (n = 8) and AA groups (n = 8). (D) Diversity of TCR and BCR between YA (n = 8) and AA groups (n = 8). (E) Diversity of TCR in T cell subsets between YA (n = 8) and AA groups (n = 8). (F) Diversity of BCR in B cell subsets between YA (n = 8) and AA groups (n = 8). (G) Volcano plot showing DEGs of clonal T cells between the YA and AA groups.
T185 2340-2544 Sentence denotes P values were calculated using a paired, two-sided Wilcoxon test and FDR was corrected using the Benjamini-Hochberg procedure. (H) Volcano plot showing DEGs of clonal B cells between the YA and AA groups.
T186 2545-2766 Sentence denotes P values were calculated using a paired, two-sided Wilcoxon test and FDR was corrected using the Benjamini-Hochberg procedure. (I) Chord diagram showing pairing of V and J segments within the TRB subset from the AA group.
T187 2767-2967 Sentence denotes Chord widths represent the proportion of sequences with a given V (colored) and J (gray) segment pairing. (J) Chord diagram showing pairing of V and J segments within the IGH subset from the AA group.
T188 2968-3072 Sentence denotes Chord widths represent the proportion of sequences with a given V (colored) and J (gray) segment pairing

2_test

Id Subject Object Predicate Lexical cue
32780218-29891535-132718702 158-162 29891535 denotes 2013

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
746 1779-1782 Gene denotes TCR Gene:6962
747 1787-1790 Gene denotes BCR Gene:613
748 2737-2740 Gene denotes TRB Gene:6957
749 2938-2941 Gene denotes IGH Gene:3492
750 2054-2057 Gene denotes BCR Gene:613
751 2198-2201 Gene denotes BCR Gene:613
752 1907-1910 Gene denotes BCR Gene:613
753 2117-2120 Gene denotes TCR Gene:6962
754 2046-2049 Gene denotes TCR Gene:6962
755 1838-1841 Gene denotes TCR Gene:6962
771 208-211 Gene denotes BCR Gene:613
772 311-314 Gene denotes BCR Gene:613
773 561-564 Gene denotes TCR Gene:6962
774 569-572 Gene denotes BCR Gene:613
775 1024-1027 Gene denotes BCR Gene:613
776 1139-1142 Gene denotes CD8 Gene:925
777 1418-1422 Gene denotes GZMB Gene:3002
778 1424-1428 Gene denotes GZMK Gene:3003
779 1430-1435 Gene denotes CXCR4 Gene:7852
780 1437-1441 Gene denotes CCL3 Gene:6348
781 1454-1457 Gene denotes TCR Gene:6962
782 1669-1673 Gene denotes IGHM Gene:3507
783 1678-1683 Gene denotes TCL1A Gene:8115
784 1016-1019 Gene denotes TCR Gene:6962
785 200-203 Gene denotes TCR Gene:6962