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PMC:7346000 / 16379-19686 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T48 1784-1789 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T49 2063-2086 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T50 2965-2970 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T16 1784-1789 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 2063-2086 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T18 2069-2086 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T19 2965-2970 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id tao:has_standard_notation
518 999-1007 Species denotes patients Tax:9606
519 1095-1103 Species denotes patients Tax:9606
520 1230-1238 Species denotes children Tax:9606
521 1619-1626 Species denotes patient Tax:9606
522 1701-1713 Species denotes A. fumigatus Tax:746128
523 2180-2188 Species denotes patients Tax:9606
524 2221-2233 Species denotes A. fumigatus Tax:746128
525 2427-2439 Species denotes A. fumigatus Tax:746128
526 2647-2659 Species denotes A. fumigatus Tax:746128
527 3072-3079 Species denotes patient Tax:9606
528 3139-3151 Species denotes A. fumigatus Tax:746128
529 3286-3295 Species denotes A. flavus Tax:5059
530 1206-1215 Species denotes influenza Tax:11309
531 2019-2030 Species denotes Aspergillus Tax:746128
532 3186-3197 Species denotes Aspergillus Tax:746128
533 1790-1803 Chemical denotes galactomannan MESH:C012990
534 2099-2104 Chemical denotes azole MESH:D001393
535 2203-2208 Chemical denotes azole MESH:D001393
536 2388-2393 Chemical denotes azole MESH:D001393
537 2411-2416 Chemical denotes Azole MESH:D001393
538 2527-2532 Chemical denotes azole MESH:D001393
539 2631-2636 Chemical denotes azole MESH:D001393
540 2669-2681 Chemical denotes itraconazole MESH:D017964
541 2683-2695 Chemical denotes voriconazole MESH:D065819
542 2701-2713 Chemical denotes posaconazole MESH:C101425
543 2952-2964 Chemical denotes voriconazole MESH:D065819
544 3045-3057 Chemical denotes voriconazole MESH:D065819
545 3061-3066 Chemical denotes l-AmB
546 146-154 Disease denotes COVID-19 MESH:C000657245
547 166-170 Disease denotes ARDS MESH:D012128
548 644-653 Disease denotes mortality MESH:D003643
549 747-756 Disease denotes mortality MESH:D003643
550 1086-1094 Disease denotes COVID-19 MESH:C000657245
551 1119-1123 Disease denotes ARDS MESH:D012128
552 1178-1182 Disease denotes ARDS MESH:D012128
553 1192-1200 Disease denotes infected MESH:D007239
554 1424-1433 Disease denotes mortality MESH:D003643
555 2148-2157 Disease denotes mortality MESH:D003643
556 2189-2197 Disease denotes infected MESH:D007239
557 2797-2801 Mutation denotes L98H p.L98H

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T174 135-139 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T175 146-154 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T176 166-170 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T177 236-240 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T178 360-364 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T179 557-561 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T180 1086-1094 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T181 1119-1123 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T182 1178-1182 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T183 1206-1215 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T184 1315-1319 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T185 1831-1835 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T186 2602-2606 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T130 188-190 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T131 264-265 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 554-556 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T133 597-598 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T134 668-670 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T135 671-673 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T136 694-700 http://purl.obolibrary.org/obo/UBERON_0003100 denotes female
T137 702-705 http://purl.obolibrary.org/obo/CLO_0001382 denotes 4/8
T138 724-728 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T139 724-728 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T140 730-732 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T141 733-735 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T142 1469-1470 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T143 1644-1645 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T144 1701-1702 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T145 1804-1808 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T146 1888-1889 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 2139-2140 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T148 2221-2222 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T149 2307-2314 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T150 2427-2428 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T151 2600-2601 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T152 2647-2648 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T153 2724-2729 http://purl.obolibrary.org/obo/CLO_0001002 denotes 16, 2
T154 2769-2770 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T155 3061-3066 http://purl.obolibrary.org/obo/NCBITaxon_9940 denotes l-AmB
T156 3139-3140 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T157 3286-3287 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T99 724-728 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T100 1790-1803 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T101 1947-1957 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T102 2099-2104 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T103 2203-2208 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T104 2281-2291 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T105 2334-2344 Chemical denotes antifungal http://purl.obolibrary.org/obo/CHEBI_35718
T106 2388-2393 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T107 2527-2532 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T108 2631-2636 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T109 2669-2681 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T110 2683-2695 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T111 2701-2713 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T112 2879-2882 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T113 2952-2964 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T114 3045-3057 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T3 1790-1803 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T86 0-216 Sentence denotes More recently, several studies and case-series from Europe (France, Germany, Belgium, and the Netherlands) have reported high rates of CAPA among COVID-19 cases with ARDS, ranging from 20–35% (Table 1) [47,50,51,52].
T87 217-334 Sentence denotes The development of CAPA was fairly rapid, with a median of 6 days and range of 3–28 days after ICU admission [47,52].
T88 335-547 Sentence denotes Moreover, two additional CAPA cases have been reported from Germany [61] and single cases have also been reported from the Netherlands [62], Austria [60], Italy [59], Australia [63], and France [57,58] (Table 1).
T89 548-631 Sentence denotes Among 35 CAPA cases reported to date, there were a total of 5 proven cases [52,59].
T90 632-742 Sentence denotes The overall mortality rate was 63% (22/35), among whom 4 were female (4/8; 50%) and 14 were male (18/27; 67%).
T91 743-867 Sentence denotes The mortality in case series reported from France, Germany, Belgium and Netherlands ranged between 44.5–66.7% [47,50,51,52].
T92 868-1057 Sentence denotes Of particular importance was the 100% fatality rate of those with underlying diseases reported from the Netherlands, while the two patients without underlying conditions both survived [47].
T93 1058-1283 Sentence denotes Noteworthy is the fact that COVID-19 patients presented with ARDS typically fall into the elderly category [6], whereas ARDS in those infected with influenza involves both children <5 years old and elderly >65 years old [76].
T94 1284-1440 Sentence denotes The difficulties in diagnosing CAPA, which are outlined in more detail in the next section of this review, may also contribute to increased mortality rates.
T95 1441-1640 Sentence denotes The most notable example is a study from France [57], where both culture and serology assays were negative for the initial respiratory samples and became only positive after the patient expired [57].
T96 1641-1830 Sentence denotes In a case from Italy, initial BALF culture was positive for A. fumigatus but the treatment was delayed for two days and only started after the serum galactomannan test became positive [59].
T97 1831-1884 Sentence denotes CAPA was later confirmed by autopsy examination [59].
T98 1885-2092 Sentence denotes As a result, authors encouraged prompt initiation of systemic antifungal therapy immediately after obtaining positive results even if Aspergillus is detected in samples from the upper respiratory tract [59].
T99 2093-2410 Sentence denotes Since azole resistance can be associated with a higher mortality rate when compared to patients infected with azole susceptible A. fumigatus isolates, it is of paramount importance to use antifungal susceptibility testing to inform targeted antifungal treatment, especially in regions with high azole resistance [77].
T100 2411-2626 Sentence denotes Azole-resistant A. fumigatus isolates were also persistently recovered from tracheal aspirates during the course of azole treatment in the most recent study from the Netherlands implicated a CAPA case for whom [62].
T101 2627-2865 Sentence denotes The azole-resistant A. fumigatus isolate (itraconazole, voriconazole, and posaconazole MICs were 16, 2, and 0.5 µg/mL, respectively) harbored a well-known mutation, TR34/L98H [62], presumed to have been acquired from the environment [77].
T102 2866-3129 Sentence denotes The in vitro MIC value of the isolate obtained at day 19 (2 mg/L) was higher than the voriconazole serum trough concentration measured on day 17 (1.43 mg/L) and despite switching voriconazole to l-AmB, the patient died due to deteriorating health conditions [62].
T103 3130-3307 Sentence denotes Overall, A. fumigatus appeared to be the most prevalent Aspergillus spp. isolated among respiratory samples with positive culture (26/29; 90%), followed by A. flavus (2/29; 7%).

2_test

Id Subject Object Predicate Lexical cue
32599813-32339350-60095124 206-208 32339350 denotes 50
32599813-32488446-60095125 212-214 32488446 denotes 52
32599813-32488446-60095126 330-332 32488446 denotes 52
32599813-32517166-60095127 471-473 32517166 denotes 62
32599813-32470620-60095128 497-499 32470620 denotes 59
32599813-32488446-60095129 624-626 32488446 denotes 52
32599813-32470620-60095130 627-629 32470620 denotes 59
32599813-32339350-60095131 857-859 32339350 denotes 50
32599813-32488446-60095132 863-865 32488446 denotes 52
32599813-31324202-60095133 1279-1281 31324202 denotes 76
32599813-32470620-60095134 1826-1828 32470620 denotes 59
32599813-32470620-60095135 1880-1882 32470620 denotes 59
32599813-32470620-60095136 2088-2090 32470620 denotes 59
32599813-30580035-60095137 2406-2408 30580035 denotes 77
32599813-32517166-60095138 2622-2624 32517166 denotes 62
32599813-32517166-60095139 2803-2805 32517166 denotes 62
32599813-30580035-60095140 2861-2863 30580035 denotes 77
32599813-32517166-60095141 3125-3127 32517166 denotes 62