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PMC:7267243 / 8827-12112 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
266 25-30 Species denotes woman Tax:9606
267 306-313 Species denotes patient Tax:9606
268 361-368 Species denotes patient Tax:9606
269 449-459 Species denotes SARS‐CoV‐2 Tax:2697049
270 464-485 Species denotes human metapneumovirus Tax:162145
271 487-491 Species denotes hMPV Tax:162145
272 519-526 Species denotes patient Tax:9606
273 688-709 Species denotes Aspergillus fumigatus Tax:746128
274 653-668 Chemical denotes tranexamic acid MESH:D014148
275 728-741 Chemical denotes galactomannan MESH:C012990
276 759-771 Chemical denotes voriconazole MESH:D065819
277 95-99 Disease denotes ARDS MESH:D012128
278 180-189 Disease denotes emphysema MESH:D004646
279 559-567 Disease denotes bleeding MESH:D006470
289 826-834 Species denotes patients Tax:9606
290 897-904 Species denotes Patient Tax:9606
291 1011-1018 Species denotes Patient Tax:9606
292 1097-1104 Species denotes Patient Tax:9606
293 1223-1230 Species denotes Patient Tax:9606
294 1350-1357 Species denotes Patient Tax:9606
295 840-848 Disease denotes COVID‐19 MESH:C000657245
296 860-892 Disease denotes Invasive Pulmonary Aspergillosis MESH:D055744
297 1243-1252 Disease denotes emphysema MESH:D004646
307 1627-1631 Species denotes hMPV Tax:162145
308 1633-1643 Species denotes SARS‐CoV‐2 Tax:2697049
309 1648-1669 Species denotes Aspergillus fumigatus Tax:746128
310 1875-1882 Species denotes patient Tax:9606
311 1694-1707 Chemical denotes galactomannan MESH:C012990
312 1758-1771 Chemical denotes galactomannan MESH:C012990
313 2017-2030 Chemical denotes isavuconazole MESH:C508735
314 1551-1555 Disease denotes ARDS MESH:D012128
315 1905-1924 Disease denotes acute renal failure MESH:D058186
322 2140-2150 Species denotes SARS‐CoV‐2 Tax:2697049
323 2168-2189 Species denotes Aspergillus fumigatus Tax:746128
324 2377-2384 Species denotes patient Tax:9606
325 2224-2237 Chemical denotes galactomannan MESH:C012990
326 2412-2424 Chemical denotes voriconazole MESH:D065819
327 2087-2091 Disease denotes ARDS MESH:D012128
335 2542-2552 Species denotes SARS‐CoV‐2 Tax:2697049
336 2558-2579 Species denotes Aspergillus fumigatus Tax:746128
337 2730-2737 Species denotes patient Tax:9606
338 2519-2521 Chemical denotes TA
339 2766-2778 Chemical denotes voriconazole MESH:D065819
340 2502-2506 Disease denotes ARDS MESH:D012128
341 2637-2646 Disease denotes emphysema MESH:D004646
350 2804-2809 Species denotes woman Tax:9606
351 3141-3148 Species denotes patient Tax:9606
352 3240-3247 Species denotes patient Tax:9606
353 2884-2894 Species denotes SARS‐CoV‐2 Tax:2697049
354 2861-2863 Chemical denotes TA
355 2902-2915 Chemical denotes galactomannan MESH:C012990
356 3177-3188 Chemical denotes caspofungin MESH:D000077336
357 2844-2848 Disease denotes ARDS MESH:D012128

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T13 577-596 Body_part denotes right main bronchus http://purl.org/sig/ont/fma/fma7395
T14 807-812 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T15 1181-1189 Body_part denotes cavities http://purl.org/sig/ont/fma/fma76576
T16 1688-1693 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T17 1773-1778 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T18 1990-1995 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T19 2239-2244 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T20 2328-2336 Body_part denotes cavities http://purl.org/sig/ont/fma/fma76576
T21 2607-2612 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T22 2896-2901 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T23 2953-2958 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T24 2968-2973 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 577-596 Body_part denotes right main bronchus http://purl.obolibrary.org/obo/UBERON_0002177
T8 583-596 Body_part denotes main bronchus http://purl.obolibrary.org/obo/UBERON_0002182
T9 588-596 Body_part denotes bronchus http://purl.obolibrary.org/obo/UBERON_0002185
T10 807-812 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T11 1688-1693 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T12 1773-1778 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T13 1990-1995 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T14 2239-2244 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T15 2607-2612 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T16 2896-2901 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 2953-2958 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T18 2968-2973 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T101 95-99 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T102 180-189 Disease denotes emphysema http://purl.obolibrary.org/obo/MONDO_0004849
T103 449-453 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T104 840-848 Disease denotes COVID‐19 http://purl.obolibrary.org/obo/MONDO_0100096
T105 879-892 Disease denotes Aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T106 1243-1252 Disease denotes emphysema http://purl.obolibrary.org/obo/MONDO_0004849
T107 1551-1555 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T108 1633-1637 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T109 1905-1924 Disease denotes acute renal failure http://purl.obolibrary.org/obo/MONDO_0002492
T110 1911-1924 Disease denotes renal failure http://purl.obolibrary.org/obo/MONDO_0001106
T111 2087-2091 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T112 2128-2130 Disease denotes TA http://purl.obolibrary.org/obo/MONDO_0017991
T113 2140-2144 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T114 2502-2506 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T115 2519-2521 Disease denotes TA http://purl.obolibrary.org/obo/MONDO_0017991
T116 2542-2546 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T117 2637-2646 Disease denotes emphysema http://purl.obolibrary.org/obo/MONDO_0004849
T118 2844-2848 Disease denotes ARDS http://purl.obolibrary.org/obo/MONDO_0006502
T119 2861-2863 Disease denotes TA http://purl.obolibrary.org/obo/MONDO_0017991
T120 2884-2888 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T61 11-12 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T62 105-106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 163-164 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 302-304 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T65 412-420 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T66 464-469 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T67 588-596 http://purl.obolibrary.org/obo/UBERON_0002185 denotes bronchus
T68 807-812 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T69 894-895 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T70 1008-1009 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T71 1181-1189 http://purl.obolibrary.org/obo/UBERON_0002553 denotes cavities
T72 1498-1499 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T73 1561-1562 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 1607-1613 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T75 1738-1744 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T76 1773-1778 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T77 1871-1873 http://purl.obolibrary.org/obo/CLO_0008922 denotes S2
T78 1871-1873 http://purl.obolibrary.org/obo/CLO_0050052 denotes S2
T79 1990-1995 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T80 1990-1995 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T81 2054-2058 http://purl.obolibrary.org/obo/CLO_0001599 denotes A 54
T82 2097-2098 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T83 2239-2244 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T84 2328-2336 http://purl.obolibrary.org/obo/UBERON_0002553 denotes cavities
T85 2450-2451 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T86 2522-2528 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T87 2607-2612 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T88 2790-2794 http://purl.obolibrary.org/obo/CLO_0001599 denotes A 54
T89 2864-2870 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T90 2968-2973 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T91 3137-3139 http://purl.obolibrary.org/obo/CLO_0008933 denotes S5

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T77 131-133 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T79 653-668 Chemical denotes tranexamic acid http://purl.obolibrary.org/obo/CHEBI_48669
T80 664-668 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T81 728-741 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T82 759-771 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T83 1587-1589 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T85 1694-1707 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T86 1758-1771 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T87 1871-1873 Chemical denotes S2 http://purl.obolibrary.org/obo/CHEBI_29387
T88 2017-2030 Chemical denotes isavuconazole http://purl.obolibrary.org/obo/CHEBI_85979
T89 2124-2126 Chemical denotes Hg http://purl.obolibrary.org/obo/CHEBI_16170|http://purl.obolibrary.org/obo/CHEBI_25195
T91 2128-2130 Chemical denotes TA http://purl.obolibrary.org/obo/CHEBI_74824
T92 2224-2237 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T93 2373-2375 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T94 2412-2424 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T95 2519-2521 Chemical denotes TA http://purl.obolibrary.org/obo/CHEBI_74824
T96 2726-2728 Chemical denotes S4 http://purl.obolibrary.org/obo/CHEBI_29401
T97 2766-2778 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T98 2861-2863 Chemical denotes TA http://purl.obolibrary.org/obo/CHEBI_74824
T99 2902-2915 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T100 3137-3139 Chemical denotes S5 http://purl.obolibrary.org/obo/CHEBI_29386
T101 3177-3188 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T3 728-741 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 1694-1707 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 1758-1771 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T6 2224-2237 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T7 2902-2915 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T105 0-10 Sentence denotes 3 RESULTS
T106 11-55 Sentence denotes A 62‐year‐old woman was admitted to our ICU.
T107 56-134 Sentence denotes She was intubated and developed severe ARDS with a Horowitz‐Index of 53 mm Hg.
T108 135-329 Sentence denotes At the contrast‐enhanced CT a combination of emphysema, bilateral ground‐glass opacities with crazy paving and some peripheral nodular consolidations were seen (Video S1, patient #1, Figure 1A).
T109 330-440 Sentence denotes Despite prone positioning, the patient required rescue veno‐venous extracorporeal membrane oxygenation (ECMO).
T110 441-514 Sentence denotes PCR for SARS‐CoV‐2 and human metapneumovirus (hMPV) was positive in BALF.
T111 515-669 Sentence denotes The patient developed severe intrapulmonary bleeding from the right main bronchus, which was stanched by cold lavages and instillation of tranexamic acid.
T112 670-796 Sentence denotes BALF culture grew Aspergillus fumigatus, was positive for galactomannan, and intravenous voriconazole treatment was commenced.
T113 797-893 Sentence denotes FIGURE 1 Chest CT images of patients with COVID‐19 Associated Invasive Pulmonary Aspergillosis.
T114 894-908 Sentence denotes A, Patient #1:
T115 909-1007 Sentence denotes Combined bilateral ground‐glass opacities with crazy paving and peripheral nodular consolidations.
T116 1008-1022 Sentence denotes B, Patient #2:
T117 1023-1093 Sentence denotes Ground‐glass opacities with small nodular infiltrations of up to 1 cm.
T118 1094-1108 Sentence denotes C, Patient #3:
T119 1109-1219 Sentence denotes Bilateral ground‐glass opacities diffuse nodular infiltrates and cystic cavities and partly air crescent sign.
T120 1220-1234 Sentence denotes D, Patient #4:
T121 1235-1346 Sentence denotes Bullous emphysema and ground‐glass opacities, interstitial changes and consolidations with nodular infiltrates.
T122 1347-1361 Sentence denotes E, Patient #5:
T123 1362-1590 Sentence denotes Ground‐glass opacities, smaller areas with crazy paving pattern, central and peripheral consolidations, and smaller nodular infiltrates A 70‐year‐old man was admitted to the ICU because of ARDS with a Horowitz‐Index of 93 mm Hg.
T124 1591-1670 Sentence denotes PCR on BALF was tested positive for hMPV, SARS‐CoV‐2 and Aspergillus fumigatus.
T125 1671-1728 Sentence denotes Two days before, serum galactomannan had turned positive.
T126 1729-1772 Sentence denotes BALF was tested positive for galactomannan.
T127 1773-1897 Sentence denotes Chest CT showed ground‐glass opacities with some small nodular infiltrations of up to 1 cm (Video S2, patient #2 Figure 1B).
T128 1898-2053 Sentence denotes Due to acute renal failure requiring slow low‐efficient daily dialysis (SLEDD) and elevated liver enzymes, intravenous isavuconazole treatment was started.
T129 2054-2127 Sentence denotes A 54‐year‐old man presented with ARDS with a Horowitz‐Index of 128 mm Hg.
T130 2128-2201 Sentence denotes TA revealed SARS‐CoV‐2 PCR positive and Aspergillus fumigatus in culture.
T131 2202-2238 Sentence denotes BALF was positive for galactomannan.
T132 2239-2399 Sentence denotes Chest CT showed bilateral ground‐glass opacities, diffuse nodular infiltrates and cystic cavities and partly air crescent sign (Video S3, patient #3 Figure 1C).
T133 2400-2449 Sentence denotes Intravenous voriconazole treatment was initiated.
T134 2450-2606 Sentence denotes A 73‐year‐old man was transferred to the ICU due to ARDS with PCR on TA tested positive for SARS‐CoV‐2, and Aspergillus fumigatus that also grew in culture.
T135 2607-2753 Sentence denotes Chest CT showed known bullous emphysema with ground‐glass opacities and consolidations with nodular infiltrates (Video S4, patient #4, Figure 1D).
T136 2754-2789 Sentence denotes Intravenous voriconazole was begun.
T137 2790-2895 Sentence denotes A 54‐year‐old woman was transferred to the ICU due to ARDS with PCR on TA tested positive for SARS‐CoV‐2.
T138 2896-2967 Sentence denotes Serum galactomannan returned positive in two consecutive serum samples.
T139 2968-3164 Sentence denotes Chest CT showed bilateral ground‐glass opacities, smaller areas with crazy paving pattern, central and peripheral consolidations, and smaller nodular infiltrates (Video S5, patient #5, Figure 1E).
T140 3165-3201 Sentence denotes Intravenous caspofungin was started.
T141 3202-3230 Sentence denotes No autopsies were performed.
T142 3231-3285 Sentence denotes Detailed patient characteristics are given in Table 1.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T39 180-189 Phenotype denotes emphysema http://purl.obolibrary.org/obo/HP_0002097
T40 860-892 Phenotype denotes Invasive Pulmonary Aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T41 1201-1218 Phenotype denotes air crescent sign http://purl.obolibrary.org/obo/HP_0032172
T42 1243-1252 Phenotype denotes emphysema http://purl.obolibrary.org/obo/HP_0002097
T43 1905-1924 Phenotype denotes acute renal failure http://purl.obolibrary.org/obo/HP_0001919
T44 1981-2003 Phenotype denotes elevated liver enzymes http://purl.obolibrary.org/obo/HP_0002910
T45 2348-2365 Phenotype denotes air crescent sign http://purl.obolibrary.org/obo/HP_0032172
T46 2637-2646 Phenotype denotes emphysema http://purl.obolibrary.org/obo/HP_0002097