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PMC:7463108 / 73539-76918 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T713 0-3 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T714 41-44 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T715 85-88 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T716 297-300 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T717 333-337 Body_part denotes HAND http://purl.org/sig/ont/fma/fma9712
T718 444-448 Body_part denotes HAND http://purl.org/sig/ont/fma/fma9712
T719 626-629 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T720 639-650 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T721 1015-1019 Body_part denotes HAND http://purl.org/sig/ont/fma/fma9712
T722 1240-1247 Body_part denotes neurons http://purl.org/sig/ont/fma/fma54527
T723 1370-1378 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T724 1438-1446 Body_part denotes monocyte http://purl.org/sig/ont/fma/fma62864
T725 1478-1483 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T726 1673-1675 Body_part denotes A2 http://purl.org/sig/ont/fma/fma66595
T727 1688-1698 Body_part denotes astrocytes http://purl.org/sig/ont/fma/fma54537
T728 1989-1992 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T729 2198-2201 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T730 2300-2303 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T731 2321-2324 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T732 2410-2414 Body_part denotes HAND http://purl.org/sig/ont/fma/fma9712
T733 2442-2445 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T734 2470-2473 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T735 2508-2511 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T736 2837-2840 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T737 2884-2888 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T738 2949-2952 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T739 3118-3121 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T740 3168-3172 Body_part denotes HAND http://purl.org/sig/ont/fma/fma9712
T741 3235-3238 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T167 1478-1483 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T172 685-716 Disease denotes severe combined immunodeficient http://purl.obolibrary.org/obo/MONDO_0015974
T173 723-727 Disease denotes SCID http://purl.obolibrary.org/obo/MONDO_0015974
T174 2615-2617 Disease denotes R5 http://purl.obolibrary.org/obo/MONDO_0016654
T175 2827-2829 Disease denotes R5 http://purl.obolibrary.org/obo/MONDO_0016654
T176 2866-2874 Disease denotes hepatoma http://purl.obolibrary.org/obo/MONDO_0007256
T177 3097-3099 Disease denotes R5 http://purl.obolibrary.org/obo/MONDO_0016654
T178 3104-3106 Disease denotes R4 http://purl.obolibrary.org/obo/MONDO_0015439

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T784 61-62 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T785 488-489 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T786 517-518 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T787 613-614 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T788 753-754 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T789 985-986 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T790 1062-1065 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T791 1191-1192 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T792 1275-1277 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T793 1275-1277 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T794 1438-1446 http://purl.obolibrary.org/obo/CL_0000576 denotes monocyte
T795 1478-1483 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T796 1478-1483 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T797 1650-1652 http://purl.obolibrary.org/obo/CLO_0002860 denotes E2
T798 1673-1675 http://purl.obolibrary.org/obo/CLO_0001562 denotes A2
T799 1688-1698 http://purl.obolibrary.org/obo/CL_0000127 denotes astrocytes
T800 1740-1741 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T801 1870-1871 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T802 2147-2148 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T803 2196-2197 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T804 2310-2317 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T805 2752-2756 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T806 2858-2859 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T807 2860-2865 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T808 2884-2893 http://purl.obolibrary.org/obo/CLO_0000031 denotes cell line

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T58410 924-926 Chemical denotes CC http://purl.obolibrary.org/obo/CHEBI_28940
T18687 1275-1277 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T241 1397-1399 Chemical denotes IL http://purl.obolibrary.org/obo/CHEBI_63895|http://purl.obolibrary.org/obo/CHEBI_74072
T26700 1636-1652 Chemical denotes prostaglandin E2 http://purl.obolibrary.org/obo/CHEBI_15551|http://purl.obolibrary.org/obo/CHEBI_606564
T67686 1636-1649 Chemical denotes prostaglandin http://purl.obolibrary.org/obo/CHEBI_26333
T87939 1661-1675 Chemical denotes thromboxane A2 http://purl.obolibrary.org/obo/CHEBI_15627|http://purl.obolibrary.org/obo/CHEBI_57445
T85438 1661-1672 Chemical denotes thromboxane http://purl.obolibrary.org/obo/CHEBI_26995
T77864 2553-2561 Chemical denotes Morphine http://purl.obolibrary.org/obo/CHEBI_17303
T86034 2800-2808 Chemical denotes morphine http://purl.obolibrary.org/obo/CHEBI_17303|http://purl.obolibrary.org/obo/CHEBI_58097
T48999 2988-2996 Chemical denotes morphine http://purl.obolibrary.org/obo/CHEBI_17303|http://purl.obolibrary.org/obo/CHEBI_58097
T254 3373-3378 Chemical denotes drugs http://purl.obolibrary.org/obo/CHEBI_23888

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2515 0-5 Species denotes HIV-1 Tax:11676
2540 1193-1196 Gene denotes Tat Gene:6898
2541 1270-1273 Gene denotes Tat Gene:6898
2542 1397-1401 Gene denotes IL-6 Gene:3569
2543 1406-1411 Gene denotes TNF-α Gene:7124
2544 1755-1760 Gene denotes gp120 Gene:3700
2545 1826-1831 Gene denotes gp120 Gene:3700
2546 1504-1507 Gene denotes Rao Gene:237940
2547 1120-1123 Gene denotes Rao Gene:237940
2548 1041-1044 Gene denotes Rao Gene:237940
2549 854-857 Gene denotes Rao Gene:237940
2551 41-46 Species denotes HIV-1 Tax:11676
2552 717-721 Species denotes mice Tax:10090
2553 729-733 Species denotes mice Tax:10090
2554 85-88 Species denotes HIV Tax:12721
2555 297-300 Species denotes HIV Tax:12721
2556 1673-1675 Gene denotes A2 Gene:170589
2557 902-905 Gene denotes Tat Gene:6898
2558 1636-1652 Chemical denotes prostaglandin E2 MESH:D015232
2559 624-638 Disease denotes C HIV-infected MESH:D015658
2560 701-716 Disease denotes immunodeficient MESH:D007153
2561 723-727 Disease denotes SCID MESH:D053632
2562 784-799 Disease denotes memory deficits MESH:D008569
2563 820-852 Disease denotes astrogliosis and neuronal damage MESH:D009410
2571 2083-2086 Gene denotes Tat Gene:6898
2572 1989-1992 Species denotes HIV Tax:12721
2573 2198-2201 Species denotes HIV Tax:12721
2574 2300-2303 Species denotes HIV Tax:12721
2575 2442-2445 Species denotes HIV Tax:12721
2576 2048-2056 Disease denotes toxicity MESH:D064420
2577 2321-2335 Disease denotes HIV-1 infected MESH:D015658
2591 2625-2630 Gene denotes gp120 Gene:3700
2592 3001-3005 Gene denotes Hage Gene:55510
2593 2677-2681 Gene denotes Hage Gene:55510
2594 2837-2842 Species denotes HIV-1 Tax:11676
2595 2860-2865 Species denotes human Tax:9606
2596 2949-2954 Species denotes HIV-1 Tax:11676
2597 2470-2473 Species denotes HIV Tax:12721
2598 2553-2561 Chemical denotes Morphine MESH:D009020
2599 2800-2808 Chemical denotes morphine MESH:D009020
2600 2988-2996 Chemical denotes morphine MESH:D009020
2601 2508-2519 Disease denotes HIV tropism MESH:D015658
2602 2866-2874 Disease denotes hepatoma MESH:D006528
2603 2875-2883 CellLine denotes Huh7.5.1 CVCL:E049
2607 3235-3240 Species denotes HIV-1 Tax:11676
2608 3118-3121 Species denotes HIV Tax:12721
2609 3337-3347 Disease denotes neurotoxic MESH:D020258

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T146 784-790 http://purl.obolibrary.org/obo/GO_0007613 denotes memory
T147 1370-1389 http://purl.obolibrary.org/obo/GO_0001816 denotes cytokine production
T148 2415-2427 http://purl.obolibrary.org/obo/GO_0009405 denotes pathogenesis
T149 2512-2519 http://purl.obolibrary.org/obo/GO_0009606 denotes tropism

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1003 0-14 Sentence denotes HIV-1 Genetics
T1004 15-204 Sentence denotes Genetic differences among HIV-1 variants have a significant impact on HIV transmission, disease progression, as well as the response to ARV therapy (see reviews, Geretti 2006; Taylor et al.
T1005 205-222 Sentence denotes 2008; Tyor et al.
T1006 223-245 Sentence denotes 2013; Tables 1 and 2).
T1007 246-351 Sentence denotes Pre-cART studies provide substantial evidence that HIV clade differences can influence HAND (Gupta et al.
T1008 352-372 Sentence denotes 2007; Sacktor et al.
T1009 373-392 Sentence denotes 2009; Boivin et al.
T1010 393-414 Sentence denotes 2010; McArthur et al.
T1011 415-431 Sentence denotes 2010; Rao et al.
T1012 432-538 Sentence denotes 2013), with HAND severity being highest for clade D and B strains, followed by C and A clades (Tyor et al.
T1013 539-545 Sentence denotes 2013).
T1014 546-734 Sentence denotes These findings are supported by preclinical studies in which clade B or clade C HIV-infected macrophages were intracranially injected into severe combined immunodeficient mice (SCID) mice.
T1015 735-864 Sentence denotes Exposure to clade B isolates induced more severe memory deficits, as well as greater astrogliosis and neuronal damage (Rao et al.
T1016 865-877 Sentence denotes 2008, 2013).
T1017 878-1034 Sentence denotes In another example, the Tat dicysteine motif (CC) at positions 30 and 31, which is commonly found in clade B isolates, appears to worsen HAND (Mishra et al.
T1018 1035-1051 Sentence denotes 2008; Rao et al.
T1019 1052-1113 Sentence denotes 2013) and has been studied extensively in vitro (Ranga et al.
T1020 1114-1130 Sentence denotes 2004; Rao et al.
T1021 1131-1147 Sentence denotes 2008; Zou et al.
T1022 1148-1184 Sentence denotes 2011; Krishnan and Chatterjee 2015).
T1023 1185-1284 Sentence denotes Clade B Tat is more intrinsically cytotoxic to primary neurons in vitro than clade C Tat (Li et al.
T1024 1285-1306 Sentence denotes 2008; Campbell et al.
T1025 1307-1323 Sentence denotes 2011; Zou et al.
T1026 1324-1427 Sentence denotes 2011), resulting in increased proinflammatory cytokine production (e.g., IL-6 and TNF-α) (Gandhi et al.
T1027 1428-1497 Sentence denotes 2009) and monocyte recruitment/migration into the brain (Ranga et al.
T1028 1498-1514 Sentence denotes 2004; Rao et al.
T1029 1515-1572 Sentence denotes 2008), and increased disruption of the BBB (Gandhi et al.
T1030 1573-1579 Sentence denotes 2010).
T1031 1580-1779 Sentence denotes Similarly, the production of the inflammatory mediators prostaglandin E2 and the thromboxane A2 receptor by astrocytes is more significantly increased by clade B than clade C gp120 (Samikkannu et al.
T1032 1780-1786 Sentence denotes 2011).
T1033 1787-1896 Sentence denotes Sequence and structural alterations in gp120 have been demonstrated between clades B and C (Gnanakaran et al.
T1034 1897-1960 Sentence denotes 2007) and potentially contribute to these observed differences.
T1035 1961-2173 Sentence denotes When considering effects of HIV clade variants in the presence of opioids, the overall toxicity in MSNs seen with clade C Tat (30% neuronal losses) was considerably less than with clade B (70% losses) (Zou et al.
T1036 2174-2180 Sentence denotes 2011).
T1037 2181-2461 Sentence denotes Although clade B HIV predominates in Western countries, future clinical longitudinal studies are necessary that employ HIV clade testing in HIV-1 infected opioid users to confirm the hypothesis that opioid interactive effects on HAND pathogenesis depend on the HIV clade assessed.
T1038 2462-2552 Sentence denotes Besides HIV genetic diversity, differences in HIV tropism add another level of complexity.
T1039 2553-2688 Sentence denotes Morphine interactions can differ significantly between X4 and R5-tropic gp120 variants depending on the outcome measure (El-Hage et al.
T1040 2689-2712 Sentence denotes 2011b; Podhaizer et al.
T1041 2713-2734 Sentence denotes 2012; Balinang et al.
T1042 2735-2751 Sentence denotes 2017; Kim et al.
T1043 2752-2758 Sentence denotes 2018).
T1044 2759-3012 Sentence denotes Increased infectivity in the presence of morphine was noted for the R5-tropic HIV-1SF162 strain in a human hepatoma Huh7.5.1 cell line model, whereas the infectivity rate with the X4-tropic HIV-1LAI/IIIB strain was unaffected by morphine (El-Hage et al.
T1045 3013-3020 Sentence denotes 2011b).
T1046 3021-3173 Sentence denotes To date, no clinical studies have assessed whether opioid interactions with R5- or R4-preferring HIV strains differentially impact the severity of HAND.
T1047 3174-3379 Sentence denotes However, the findings from preclinical studies indicate that HIV-1 strain-specific differences are critical determinants in shaping both the timing and pattern of neurotoxic interactions with opioid drugs.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T57 685-716 Phenotype denotes severe combined immunodeficient http://purl.obolibrary.org/obo/HP_0004430
T58 2092-2107 Phenotype denotes neuronal losses http://purl.obolibrary.org/obo/HP_0002529

2_test

Id Subject Object Predicate Lexical cue
32876803-16374210-62958230 185-189 16374210 denotes 2006
32876803-18403767-62958231 205-209 18403767 denotes 2008
32876803-20517932-62958232 415-419 20517932 denotes 2010
32876803-23758766-62958233 432-436 23758766 denotes 2013
32876803-18829958-62958234 865-869 18829958 denotes 2008
32876803-23758766-62958235 871-875 23758766 denotes 2013
32876803-18074388-62958236 1035-1039 18074388 denotes 2008
32876803-23758766-62958237 1052-1056 23758766 denotes 2013
32876803-14963162-62958238 1114-1118 14963162 denotes 2004
32876803-18829958-62958239 1131-1135 18829958 denotes 2008
32876803-14963162-62958240 1498-1502 14963162 denotes 2004
32876803-18829958-62958241 1515-1519 18829958 denotes 2008
32876803-17166900-62958242 1897-1901 17166900 denotes 2007
32876803-22101471-62958244 2713-2717 22101471 denotes 2012
32876803-28099189-62958245 2735-2739 28099189 denotes 2017