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PMC:7344504 / 821-14430 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1579-1582 Body_part denotes hip http://purl.org/sig/ont/fma/fma24964
T2 2647-2654 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 2732-2742 Body_part denotes leucocytes http://purl.org/sig/ont/fma/fma62852
T4 2763-2774 Body_part denotes neutrophils http://purl.org/sig/ont/fma/fma62860
T5 2800-2805 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T6 2905-2915 Body_part denotes calcitonin http://purl.org/sig/ont/fma/fma83348
T7 3034-3041 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T8 3092-3098 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T9 3128-3133 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T10 3664-3668 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T11 3676-3681 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T12 3718-3729 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T13 4773-4779 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T14 4944-4949 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T15 5122-5127 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T16 5397-5410 Body_part denotes noradrenaline http://purl.org/sig/ont/fma/fma61799
T17 5945-5950 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T18 6029-6034 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T19 7157-7162 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T20 8022-8026 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T21 8501-8505 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T22 11263-11268 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T23 11477-11482 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T24 11583-11588 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T25 11840-11845 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1579-1582 Body_part denotes hip http://purl.obolibrary.org/obo/UBERON_0001464
T2 2595-2600 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 2800-2805 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T4 3092-3098 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T5 3128-3133 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T6 3288-3305 Body_part denotes pleural effusions http://purl.obolibrary.org/obo/UBERON_0000175
T7 3676-3681 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T8 3718-3729 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T9 4773-4779 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T10 4944-4949 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T11 5122-5127 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T12 5945-5950 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T13 6029-6034 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T14 7157-7162 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T15 11263-11268 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T16 11477-11482 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 11583-11588 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T18 11840-11845 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
50 308-316 Species denotes patients Tax:9606
51 404-412 Species denotes patients Tax:9606
52 440-448 Species denotes patients Tax:9606
53 470-478 Species denotes patients Tax:9606
54 720-728 Species denotes patients Tax:9606
55 1129-1150 Species denotes Aspergillus fumigatus Tax:746128
56 1156-1166 Species denotes SARS-CoV-2 Tax:2697049
57 1192-1199 Species denotes patient Tax:9606
58 1005-1010 Chemical denotes azole MESH:D001393
59 1113-1118 Chemical denotes azole MESH:D001393
60 49-73 Disease denotes coronavirus disease 2019 MESH:C000657245
61 75-83 Disease denotes COVID-19 MESH:C000657245
62 151-183 Disease denotes invasive pulmonary aspergillosis MESH:D055744
63 193-202 Disease denotes infection MESH:D007239
64 208-216 Disease denotes COVID-19 MESH:C000657245
65 228-251 Disease denotes pulmonary aspergillosis MESH:D055732
66 359-382 Disease denotes pulmonary abnormalities MESH:D008171
67 783-815 Disease denotes invasive pulmonary aspergillosis MESH:D055744
68 860-869 Disease denotes mortality MESH:D003643
69 961-983 Disease denotes invasive aspergillosis MESH:D055744
70 988-996 Disease denotes infected MESH:D007239
71 1057-1066 Disease denotes mortality MESH:D003643
85 1263-1270 Species denotes patient Tax:9606
86 1789-1796 Species denotes Patient Tax:9606
87 2047-2054 Species denotes patient Tax:9606
88 1679-1690 Chemical denotes pantoprazol MESH:D000077402
89 1695-1705 Chemical denotes etoricoxib MESH:D000077613
90 1295-1320 Disease denotes respiratory insufficiency MESH:D012131
91 1330-1338 Disease denotes COVID-19 MESH:C000657245
92 1407-1412 Disease denotes fever MESH:D005334
93 1429-1438 Disease denotes dry cough MESH:D003371
94 1486-1494 Disease denotes diarrhea MESH:D003967
95 1550-1554 Disease denotes pain MESH:D010146
96 1562-1582 Disease denotes arthrosis of the hip MESH:D010003
97 1894-1902 Disease denotes COVID-19 MESH:C000657245
108 2636-2654 Gene denotes C-reactive protein Gene:1401
109 2656-2659 Gene denotes CRP Gene:1401
110 3062-3072 Species denotes SARS-CoV-2 Tax:2697049
111 2399-2401 Chemical denotes O2 MESH:D010100
112 3034-3041 Chemical denotes glucose MESH:D005947
113 2202-2210 Disease denotes dyspneic
114 2315-2333 Disease denotes pulmonary wheezing MESH:D012135
115 2590-2594 Disease denotes Coma MESH:D003128
116 2956-2975 Disease denotes bacterial infection MESH:D001424
117 3288-3305 Disease denotes pleural effusions MESH:D010996
122 3598-3608 Species denotes SARS-CoV-2 Tax:2697049
123 3773-3780 Species denotes patient Tax:9606
124 3469-3480 Chemical denotes chloroquine MESH:D002738
125 3447-3467 Disease denotes SARS-CoV-2 infection MESH:C000657245
131 3914-3917 Gene denotes CRP Gene:1401
132 4022-4029 Species denotes patient Tax:9606
133 4316-4323 Species denotes patient Tax:9606
134 4166-4177 Chemical denotes ceftriaxone MESH:D002443
135 4242-4244 Chemical denotes O2 MESH:D010100
149 5234-5243 Gene denotes factor Xa Gene:2159
150 4668-4675 Species denotes patient Tax:9606
151 5335-5342 Species denotes patient Tax:9606
152 4432-4438 Chemical denotes oxygen MESH:D010100
153 4525-4536 Chemical denotes ceftriaxone MESH:D002443
154 4615-4629 Chemical denotes amphotericin B MESH:D000666
155 4644-4654 Chemical denotes tobramycin MESH:D014031
156 4677-4688 Chemical denotes ceftriaxone MESH:D002443
157 5217-5228 Chemical denotes enoxaparine MESH:D017984
158 5397-5410 Chemical denotes noradrenaline MESH:D009638
159 5445-5459 Chemical denotes hydrocortisone MESH:D006854
160 5183-5199 Disease denotes pulmonary emboli MESH:D011655
161 5548-5571 Disease denotes tricuspid insufficiency MESH:D014262
179 5596-5617 Species denotes Aspergillus fumigatus Tax:746128
180 6374-6386 Species denotes A. fumigatus Tax:746128
181 5744-5755 Species denotes Aspergillus Tax:746128
182 5860-5870 Chemical denotes β-d-glucan
183 6035-6048 Chemical denotes galactomannan MESH:C012990
184 6103-6115 Chemical denotes Voriconazole MESH:D065819
185 6161-6172 Chemical denotes caspofungin MESH:D000077336
186 6271-6276 Chemical denotes azole MESH:D001393
187 6412-6426 Chemical denotes amphotericin B MESH:D000666
188 6437-6447 Chemical denotes micafungin MESH:D000077551
189 6452-6465 Chemical denotes anidulafungin MESH:D000077612
190 6479-6491 Chemical denotes itraconazole MESH:D017964
191 6500-6512 Chemical denotes voriconazole MESH:D065819
192 6528-6540 Chemical denotes posaconazole MESH:C101425
193 6553-6565 Chemical denotes Voriconazole MESH:D065819
194 6641-6652 Chemical denotes caspofungin MESH:D000077336
195 5708-5733 Disease denotes Aspergillus galactomannan MESH:D001228
202 6883-6895 Species denotes A. fumigatus Tax:746128
203 6960-6972 Chemical denotes voriconazole MESH:D065819
204 6987-6997 Chemical denotes β-d-glucan
205 7108-7120 Chemical denotes voriconazole MESH:D065819
206 7144-7156 Chemical denotes Voriconazole MESH:D065819
207 6862-6881 Disease denotes acute renal failure MESH:D058186
224 7553-7560 Species denotes patient Tax:9606
225 7618-7630 Species denotes A. fumigatus Tax:746128
226 7754-7766 Species denotes A. fumigatus Tax:746128
227 8173-8180 Species denotes patient Tax:9606
228 7643-7655 Chemical denotes itraconazole MESH:D017964
229 7660-7672 Chemical denotes voriconazole MESH:D065819
230 7792-7806 Chemical denotes amphotericin B MESH:D000666
231 7817-7830 Chemical denotes anidulafungin MESH:D000077612
232 7835-7845 Chemical denotes micafungin MESH:D000077551
233 7859-7871 Chemical denotes itraconazole MESH:D017964
234 7881-7893 Chemical denotes voriconazole MESH:D065819
235 7905-7917 Chemical denotes posaconazole MESH:C101425
236 7928-7940 Chemical denotes Voriconazole MESH:D065819
237 7976-7990 Chemical denotes amphotericin B MESH:D000666
238 8109-8114 Chemical denotes azole MESH:D001393
239 8056-8060 Mutation denotes L98H p.L98H
250 8481-8493 Species denotes A. fumigatus Tax:746128
251 8539-8546 Species denotes patient Tax:9606
252 8686-8694 Species denotes patients Tax:9606
253 8919-8927 Species denotes patients Tax:9606
254 8349-8354 Chemical denotes azole MESH:D001393
255 8462-8467 Chemical denotes azole MESH:D001393
256 8745-8750 Chemical denotes azole MESH:D001393
257 8959-8967 Chemical denotes triazole MESH:D014230
258 8700-8726 Disease denotes azole-resistant infections MESH:D007239
259 8511-8515 Mutation denotes L98H p.L98H
272 9101-9113 Species denotes A. fumigatus Tax:746128
273 9273-9285 Species denotes A. fumigatus Tax:746128
274 9340-9353 Species denotes mixed culture Tax:1306155
275 9434-9446 Species denotes A. fumigatus Tax:746128
276 9526-9539 Species denotes mixed culture Tax:1306155
277 9184-9189 Chemical denotes azole MESH:D001393
278 9206-9211 Chemical denotes azole MESH:D001393
279 9416-9421 Chemical denotes azole MESH:D001393
280 9644-9656 Chemical denotes itraconazole MESH:D017964
281 9680-9692 Chemical denotes voriconazole MESH:D065819
282 9241-9250 Disease denotes infection MESH:D007239
283 9613-9617 Mutation denotes L98H p.L98H
297 9927-9934 Species denotes patient Tax:9606
298 10026-10033 Species denotes patient Tax:9606
299 10209-10217 Species denotes patients Tax:9606
300 10446-10454 Species denotes patients Tax:9606
301 10488-10496 Species denotes patients Tax:9606
302 10556-10564 Species denotes patients Tax:9606
303 10724-10731 Species denotes patient Tax:9606
304 10755-10767 Species denotes A. fumigatus Tax:746128
305 11042-11054 Species denotes A. fumigatus Tax:746128
306 10929-10934 Chemical denotes azole MESH:D001393
307 11062-11074 Chemical denotes voriconazole MESH:D065819
308 9976-9999 Disease denotes invasive fungal disease MESH:D000072742
309 10437-10445 Disease denotes COVID-19 MESH:C000657245
328 11368-11376 Species denotes patients Tax:9606
329 11443-11451 Species denotes patients Tax:9606
330 11900-11907 Species denotes patient Tax:9606
331 12307-12315 Species denotes patients Tax:9606
332 11718-11729 Species denotes Aspergillus Tax:746128
333 11269-11282 Chemical denotes galactomannan MESH:C012990
334 11483-11496 Chemical denotes galactomannan MESH:C012990
335 11589-11602 Chemical denotes galactomannan MESH:C012990
336 11699-11709 Chemical denotes β-d-glucan
337 11846-11856 Chemical denotes β-d-glucan
338 11982-11992 Chemical denotes β-d-glucan
339 12338-12348 Chemical denotes β-d-glucan
340 11399-11421 Disease denotes invasive aspergillosis MESH:D055744
341 11806-11814 Disease denotes COVID-19 MESH:C000657245
342 11955-11970 Disease denotes invasive fungal MESH:D000072742
343 12158-12181 Disease denotes invasive fungal disease MESH:D000072742
344 12266-12288 Disease denotes invasive aspergillosis MESH:D055744
345 12292-12306 Disease denotes critically ill MESH:D016638
354 12733-12741 Species denotes patients Tax:9606
355 13044-13051 Species denotes patient Tax:9606
356 13315-13323 Species denotes patients Tax:9606
357 12649-12662 Chemical denotes galactomannan MESH:C012990
358 12672-12682 Chemical denotes β-d-glucan
359 12847-12860 Chemical denotes galactomannan MESH:C012990
360 13137-13150 Chemical denotes galactomannan MESH:C012990
361 13300-13314 Disease denotes critically ill MESH:D016638
366 13404-13411 Species denotes patient Tax:9606
367 13459-13471 Species denotes A. fumigatus Tax:746128
368 13417-13422 Chemical denotes azole MESH:D001393
369 13486-13494 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T7 49-73 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T8 75-83 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 170-183 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T10 193-202 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T11 208-216 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 238-251 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T13 253-257 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T14 523-527 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T15 604-608 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T16 686-695 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T17 703-712 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 802-815 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T19 961-983 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T20 970-983 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T21 1156-1164 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1330-1338 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 1486-1494 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T24 1562-1571 Disease denotes arthrosis http://purl.obolibrary.org/obo/MONDO_0006816
T25 1894-1902 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 2956-2975 Disease denotes bacterial infection http://purl.obolibrary.org/obo/MONDO_0005113
T27 2966-2975 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 3062-3070 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 3447-3455 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 3458-3467 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 3598-3606 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 5548-5571 Disease denotes tricuspid insufficiency http://purl.obolibrary.org/obo/MONDO_0002870
T33 6014-6018 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T34 6223-6225 Disease denotes BV http://purl.obolibrary.org/obo/MONDO_0005316
T35 6862-6881 Disease denotes acute renal failure http://purl.obolibrary.org/obo/MONDO_0002492
T36 6868-6881 Disease denotes renal failure http://purl.obolibrary.org/obo/MONDO_0001106
T37 8365-8369 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T38 8716-8726 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T39 8909-8918 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T40 9241-9250 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T41 9914-9918 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T42 10204-10208 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T43 10437-10445 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 11399-11421 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T45 11408-11421 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T46 11806-11814 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 12266-12288 Disease denotes invasive aspergillosis http://purl.obolibrary.org/obo/MONDO_0000240
T48 12275-12288 Disease denotes aspergillosis http://purl.obolibrary.org/obo/MONDO_0005657
T49 13433-13437 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T50 13486-13494 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 13586-13590 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T7 262-263 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 437-439 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T9 665-668 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T10 729-732 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T11 1154-1155 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 1249-1250 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T13 1427-1428 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 1579-1582 http://www.ebi.ac.uk/efo/EFO_0001929 denotes hip
T15 1613-1614 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 1641-1642 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 2386-2388 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T18 2406-2407 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 2732-2742 http://purl.obolibrary.org/obo/CL_0000738 denotes leucocytes
T20 2800-2805 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T21 2800-2805 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T22 2815-2835 http://purl.obolibrary.org/obo/PR_000023540 denotes alkaline phosphatase
T23 2836-2839 http://purl.obolibrary.org/obo/CLO_0001409 denotes 528
T24 3117-3118 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 3128-3133 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T26 3288-3305 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusions
T27 3407-3409 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T28 3616-3617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 3664-3668 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T30 3676-3681 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T31 3676-3681 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T32 3989-3990 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 4065-4066 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 4112-4113 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 4570-4571 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 4628-4629 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T37 4900-4901 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 4944-4949 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T39 4944-4949 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T40 5073-5074 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 5098-5099 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T42 5122-5127 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T43 5540-5541 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 5836-5837 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 5955-5959 http://purl.obolibrary.org/obo/CLO_0053133 denotes 1590
T46 5960-5962 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T47 5990-5991 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 6374-6375 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T49 6425-6426 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T50 6883-6884 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 7042-7044 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T52 7049-7053 http://purl.obolibrary.org/obo/CLO_0001757 denotes at 1
T53 7564-7565 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 7618-7619 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55 7754-7755 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T56 7805-7806 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T57 7989-7990 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T58 8022-8026 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T59 8049-8050 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 8134-8136 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T61 8440-8441 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 8481-8482 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T63 8501-8505 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T64 8547-8550 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T65 8887-8890 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T66 9101-9102 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T67 9132-9138 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T68 9273-9274 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T69 9338-9339 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 9434-9435 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T71 9492-9493 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 9524-9525 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 9622-9623 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T74 9786-9788 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T75 10071-10077 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T76 10373-10376 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T77 10384-10385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 10755-10756 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T79 10786-10794 http://purl.obolibrary.org/obo/OBI_0100026 denotes organism
T80 10786-10794 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organism
T81 10854-10860 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T82 11042-11043 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T83 11283-11290 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T84 11291-11294 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T85 11312-11313 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T86 11523-11526 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T87 11542-11544 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T88 11752-11758 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T89 11927-11928 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 11993-12000 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T91 12004-12005 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T92 12027-12030 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T93 12138-12150 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colonization
T94 12226-12227 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T95 12474-12476 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T96 12563-12566 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T97 12580-12581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 12664-12666 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T99 12797-12798 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 12861-12868 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T101 12906-12907 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 12942-12945 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T103 13014-13020 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T104 13459-13460 http://purl.obolibrary.org/obo/CLO_0001020 denotes A

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T8 185-188 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T10 880-883 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T12 1005-1010 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T13 1113-1118 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T14 1615-1621 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T15 1627-1636 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T16 1643-1678 Chemical denotes nonsteroidal anti-inflammatory drug http://purl.obolibrary.org/obo/CHEBI_35475
T17 1656-1678 Chemical denotes anti-inflammatory drug http://purl.obolibrary.org/obo/CHEBI_35472
T18 1674-1678 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T19 1679-1690 Chemical denotes pantoprazol http://purl.obolibrary.org/obo/CHEBI_7915
T20 1695-1705 Chemical denotes etoricoxib http://purl.obolibrary.org/obo/CHEBI_6339
T21 2399-2401 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T22 2616-2619 Chemical denotes ECG http://purl.obolibrary.org/obo/CHEBI_70255
T23 2647-2654 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24 2858-2861 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T25 2870-2872 Chemical denotes LD http://purl.obolibrary.org/obo/CHEBI_74332
T26 2905-2915 Chemical denotes calcitonin http://purl.obolibrary.org/obo/CHEBI_3306
T27 3034-3041 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T29 3347-3349 Chemical denotes CO http://purl.obolibrary.org/obo/CHEBI_17245
T30 3469-3480 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T31 4166-4177 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T32 4242-4244 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T33 4432-4438 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T34 4525-4536 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T35 4615-4629 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T36 4631-4639 Chemical denotes colistin http://purl.obolibrary.org/obo/CHEBI_37943
T37 4644-4654 Chemical denotes tobramycin http://purl.obolibrary.org/obo/CHEBI_28864|http://purl.obolibrary.org/obo/CHEBI_73678
T39 4677-4688 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T40 5397-5410 Chemical denotes noradrenaline http://purl.obolibrary.org/obo/CHEBI_33569
T41 5445-5459 Chemical denotes hydrocortisone http://purl.obolibrary.org/obo/CHEBI_17650
T42 5720-5733 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T43 5773-5775 Chemical denotes La http://purl.obolibrary.org/obo/CHEBI_33336
T44 5864-5870 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T45 5933-5935 Chemical denotes MA http://purl.obolibrary.org/obo/CHEBI_474859|http://purl.obolibrary.org/obo/CHEBI_73610|http://purl.obolibrary.org/obo/CHEBI_90325
T48 6035-6048 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T49 6161-6172 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T50 6271-6276 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T51 6412-6426 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T52 6437-6447 Chemical denotes micafungin http://purl.obolibrary.org/obo/CHEBI_600520
T53 6452-6465 Chemical denotes anidulafungin http://purl.obolibrary.org/obo/CHEBI_55346
T54 6479-6491 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T55 6500-6512 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T56 6528-6540 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T57 6641-6652 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T58 6960-6972 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T59 6991-6997 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T60 7108-7120 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T61 7175-7179 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T62 7643-7655 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T63 7660-7672 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T64 7792-7806 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T65 7817-7830 Chemical denotes anidulafungin http://purl.obolibrary.org/obo/CHEBI_55346
T66 7835-7845 Chemical denotes micafungin http://purl.obolibrary.org/obo/CHEBI_600520
T67 7859-7871 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T68 7881-7893 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T69 7905-7917 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T70 7976-7990 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T71 8109-8114 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T72 8349-8354 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T73 8462-8467 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T74 8700-8705 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T75 8745-8750 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T76 8959-8967 Chemical denotes triazole http://purl.obolibrary.org/obo/CHEBI_38597
T77 9184-9189 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T78 9206-9211 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T79 9416-9421 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T80 9644-9656 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T81 9657-9660 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T82 9680-9692 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T83 9693-9696 Chemical denotes MIC http://purl.obolibrary.org/obo/CHEBI_59059
T84 9791-9794 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T86 10132-10135 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T87 10513-10516 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T88 10611-10614 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T89 10929-10934 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T90 11062-11074 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T91 11245-11248 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T93 11269-11282 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T94 11483-11496 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T95 11589-11602 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T96 11703-11709 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T97 11760-11763 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T98 11799-11802 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T100 11850-11856 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T101 11986-11992 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T102 12334-12337 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T103 12342-12348 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T104 12483-12486 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T105 12626-12629 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T106 12649-12662 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T107 12676-12682 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T108 12691-12694 Chemical denotes IPA http://purl.obolibrary.org/obo/CHEBI_17824|http://purl.obolibrary.org/obo/CHEBI_30802
T110 12772-12775 Chemical denotes LFD http://purl.obolibrary.org/obo/CHEBI_73571
T111 12847-12860 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T112 12872-12875 Chemical denotes BAL http://purl.obolibrary.org/obo/CHEBI_64198
T113 13137-13150 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T114 13417-13422 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2824-2835 http://purl.obolibrary.org/obo/GO_0016791 denotes phosphatase

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 5720-5733 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 6035-6048 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T3 11269-11282 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T4 11483-11496 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T5 11589-11602 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T6 12649-12662 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T7 12847-12860 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T8 13137-13150 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T9 0-2 Sentence denotes 1.
T10 3-15 Sentence denotes Introduction
T11 16-207 Sentence denotes There have been suggestions that coronavirus disease 2019 (COVID-19) might increase the risk of superinfections [1] and, particularly, invasive pulmonary aspergillosis (IPA) co-infection [2].
T12 208-383 Sentence denotes COVID-19-associated pulmonary aspergillosis (CAPA) is a recently described disease entity affecting patients in intensive care unit (ICUs) with severe pulmonary abnormalities.
T13 384-570 Sentence denotes Small cohorts of 31 patients in the Netherlands [3], 27 patients in France [4] and 19 patients in Germany [5] have been published, showing CAPA rates of 19.4%, 33% and 26%, respectively.
T14 571-638 Sentence denotes An additional two fatal cases of CAPA were recently reported [6,7].
T15 639-894 Sentence denotes The numbers resemble what has been observed in influenza, where influenza in ICU patients has been identified as an independent risk factor for invasive pulmonary aspergillosis and which is associated with an even higher mortality rate than IPA alone [8].
T16 895-1083 Sentence denotes In addition, in the Netherlands, an estimated 11.3% of cases with invasive aspergillosis are infected with an azole-resistant isolate [9], potentially increasing mortality to 50–100% [10].
T17 1084-1220 Sentence denotes We present the first case of azole-resistant Aspergillus fumigatus in a SARS-CoV-2-positive immunocompetent patient admitted to the ICU.
T18 1222-1224 Sentence denotes 2.
T19 1225-1248 Sentence denotes Case Report and Results
T20 1249-1346 Sentence denotes A 74-year-old patient was admitted because of respiratory insufficiency amid the COVID-19 crisis.
T21 1347-1439 Sentence denotes Eleven days prior to admission, she had been suffering from fever (38.5 °C) and a dry cough.
T22 1440-1495 Sentence denotes Three days after symptom onset, she developed diarrhea.
T23 1496-1720 Sentence denotes Her medical history included complaints of reflux and pain due to arthrosis of the hip and knees, for which she uses a proton-pump inhibitor and a nonsteroidal anti-inflammatory drug pantoprazol and etoricoxib, respectively.
T24 1721-1788 Sentence denotes She stopped smoking 20 years ago and was healthy and fit otherwise.
T25 1789-1837 Sentence denotes Patient characteristics can be found in Table 1.
T26 1838-2121 Sentence denotes This study, “Clinical course and prognostic factors for COVID-19” with project identification code CWZ-nr 027-2020, was approved in March 20202 by the Canisius Wilhelmina Hospital medical ethics committee and patient informed consent was acquired antemortem with opt out possibility.
T27 2122-2224 Sentence denotes At presentation to the emergency department, she had been feeling progressively dyspneic for two days.
T28 2225-2361 Sentence denotes On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration.
T29 2362-2457 Sentence denotes Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech.
T30 2458-2511 Sentence denotes Her BMI was 27.7 (80 kg) and her temperature 37.8 °C.
T31 2512-2577 Sentence denotes No other aberrant observations on physical examination were made.
T32 2578-2631 Sentence denotes Her Glasgow Coma Scale was 15 and her ECG was normal.
T33 2632-3061 Sentence denotes Her C-reactive protein (CRP) was 214 mg/L, and other laboratory findings included slightly elevated leucocytes (12.6 × 109 /L) and neutrophils (8.4 × 109 /L), elevated liver enzymes (alkaline phosphatase 528 U/L; GGT 376 U/L; AST 76 U/L; LD 745 U/L), slightly elevated pro-calcitonin (0.25 µg/L; <0.5 µg/L not suggestive of bacterial infection), increased ferritin (1442 µg/L), and normal electrolyte, glucose and renal function.
T34 3062-3116 Sentence denotes SARS-CoV-2 nasopharyngeal and throat swabs were taken.
T35 3117-3342 Sentence denotes A low-dose chest CT demonstrated extensive centralized and peripheral bilateral ground glass opacities with left-sided consolidations and bilateral fibrotic bands without pleural effusions and vascular enlargement (Figure 1).
T36 3343-3411 Sentence denotes The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11].
T37 3412-3593 Sentence denotes Because of the high probability of SARS-CoV-2 infection, chloroquine treatment was started (600 mg and 300 mg on day 1, 300 mg q12h days 2–5), which was national policy at the time.
T38 3594-3675 Sentence denotes The SARS-CoV-2 PCR of a nasopharyngeal swab was positive (Ct 30.59; E gene [12]).
T39 3676-3768 Sentence denotes Blood cultures remained negative, as were nasopharynx bacterial cultures taken at admission.
T40 3769-3849 Sentence denotes The patient was subsequently admitted to our general inpatient respiratory ward.
T41 3850-3909 Sentence denotes An overview of her hospital course is depicted in Figure 2.
T42 3910-4008 Sentence denotes The CRP remained highly stable over the following days at around 200 mg/L with a range of 192–214.
T43 4009-4088 Sentence denotes However, the patient needed increasing oxygenation with a non-rebreathing mask.
T44 4089-4182 Sentence denotes Empirical treatment of a suspected bacterial superinfection was started with ceftriaxone i.v.
T45 4183-4196 Sentence denotes 2000 mg q24h.
T46 4197-4397 Sentence denotes Five days after admission, the maximum (15 L O2) oxygenation with the non-rebreathing mask became insufficient and the patient was admitted to the ICU for respiratory support and intensive monitoring.
T47 4398-4541 Sentence denotes In the ICU, HFNO (high-flow nasal oxygen therapy) and selective digestive decontamination (SDD) were initiated, which includes ceftriaxone i.v.
T48 4542-4659 Sentence denotes 2000 mg q24h for 4 days and a combined oral non-absorbable suspension of amphotericin B, colistin and tobramycin q6h.
T49 4660-4731 Sentence denotes In this patient, ceftriaxone was continued de facto for another 4 days.
T50 4732-4892 Sentence denotes Routine bacterial and fungal (peri-anal, throat and tracheal aspirate) surveillance cultures were done twice weekly in adherence with our local SDD policy [13].
T51 4893-5023 Sentence denotes Within a few hours after admission to the ICU, her blood oxygenation became insufficient with HFNO at FiO2 100% and 60 L/min flow.
T52 5024-5097 Sentence denotes Therefore, she was sedated, intubated and put on a mechanical ventilator.
T53 5098-5200 Sentence denotes A CT angiography of the chest was performed which demonstrated significant bilateral pulmonary emboli.
T54 5201-5283 Sentence denotes Anticoagulants (enoxaparine anti-factor Xa) were initiated in therapeutic dosages.
T55 5284-5361 Sentence denotes Pressure control ventilation was required with the patient in prone position.
T56 5362-5513 Sentence denotes Because of the need for increasing noradrenaline dosages during circulatory shock, hydrocortisone 100 mg q8h was initiated and continued for five days.
T57 5514-5595 Sentence denotes Cardiac ultrasound showed a minor tricuspid insufficiency but no major pathology.
T58 5596-5707 Sentence denotes Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission.
T59 5708-6028 Sentence denotes Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was >3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made.
T60 6029-6102 Sentence denotes Serum galactomannan remained negative (<0.5) in three subsequent samples.
T61 6103-6120 Sentence denotes Voriconazole i.v.
T62 6121-6177 Sentence denotes 6 mg/kg q12h was started in addition to caspofungin i.v.
T63 6178-6302 Sentence denotes 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative.
T64 6303-6552 Sentence denotes MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin <0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L.
T65 6553-6653 Sentence denotes Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin.
T66 6654-6734 Sentence denotes During SDD, bacterial cultures remained negative throughout her stay in the ICU.
T67 6735-6882 Sentence denotes On day 6 after admission (day 2 at the ICU), continuous venovenous hemofiltration was initiated because of rapidly progressive acute renal failure.
T68 6883-7143 Sentence denotes A. fumigatus was persistently cultured from tracheal aspirate samples during voriconazole treatment and β-d-glucan levels remained positive with 1149 and 1458 pg/µl, at 1 and 6 days (day 8 and 13 after hospital admission) of voriconazole therapy, respectively.
T69 7144-7331 Sentence denotes Voriconazole serum therapeutic drug monitoring was performed as recommended [15], with therapeutic concentrations of 4.72 mg/L, 2.78 mg/L and 1.43 mg/L at day 13, 15 and 17, respectively.
T70 7332-7436 Sentence denotes The respiratory situation improved marginally in the subsequent 7 days but declined steadily thereafter.
T71 7437-7603 Sentence denotes Pressure support and pressure control ventilation were alternated between days 12 and 19 and attempts to return the patient to a supine position failed several times.
T72 7604-7740 Sentence denotes After 7 days, A. fumigatus grew on the itraconazole and voriconazole wells of the second VIPcheck on day 19 (tracheal aspirate culture).
T73 7741-7927 Sentence denotes MICs of this A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, anidulafungin and micafungin <0.016 mg/L, itraconazole 16 mg/L, voriconazole 2 mg/L and posaconazole 0.5 mg/L.
T74 7928-8003 Sentence denotes Voriconazole treatment was changed to liposomal amphotericin B 200 mg q24h.
T75 8004-8126 Sentence denotes Subsequent cyp51A gene sequencing identified a TR34/L98H mutation, probably responsible for the observed azole resistance.
T76 8127-8275 Sentence denotes On day 22, ventilation and oxygenation of the patient deteriorated further without further treatment options and therapy was discontinued on day 23.
T77 8276-8305 Sentence denotes An autopsy was not performed.
T78 8307-8309 Sentence denotes 3.
T79 8310-8320 Sentence denotes Discussion
T80 8321-8476 Sentence denotes We report the first case of azole-resistant CAPA, which occurred in an immunocompetent host during ICU support without a previous history of azole therapy.
T81 8477-8769 Sentence denotes The A. fumigatus cyp51A gene TR34/L98H mutation found in this patient has been well described as an environmentally acquired mutation [16], which is in line with data from clinical studies where two-thirds of patients with azole-resistant infections had no history of azole pretreatment [10].
T82 8770-8987 Sentence denotes This case underscores the importance of early diagnosis and the need for resistance surveillance, comparable to what has been described in influenza patients [9,17], given the emergence of triazole resistance [18,19].
T83 8988-9256 Sentence denotes The sensitivity for detection of resistance in primary cultures with the VIPcheck plate depends on the number of A. fumigatus colonies that are tested, as clinical cultures may contain both mixed azole-susceptible and azole-resistant isolates during an infection [20].
T84 9257-9454 Sentence denotes We suspect that A. fumigatus isolated in the first tracheal aspirate was already a mixed culture but was missed in initial fungal cultures due to abundance of azole-susceptible A. fumigatus spores.
T85 9455-9603 Sentence denotes Molecular detection could have given a suggestion to the presence of a mixed culture [21] but PCR could not be performed due to absence of material.
T86 9604-9790 Sentence denotes The TR34/L98H had a phenotype with high itraconazole MIC (>16 mg/L) and low voriconazole MIC (2 mg/L), similar to strains which have been described only recently in the Netherlands [22].
T87 9791-9871 Sentence denotes IPA is known to be problematic to diagnose in the non-neutropenic ICU host [23].
T88 9872-10148 Sentence denotes Regardless of the compelling evidence for CAPA in this patient, the EORTC/MSGERC [24] host criteria for invasive fungal disease were not met, nor did the patient meet the AspICU algorithm because we tested tracheal aspirates instead of bronchoalveolar lavage (BAL) fluid [25].
T89 10149-10279 Sentence denotes This is in line with findings from other groups, where CAPA patients did not meet the EORTC/MSGERC host criteria either [3,4,5,6].
T90 10280-10512 Sentence denotes In addition, the American Association for Bronchology and Interventional Pulmonology (AABIP) has issued a statement advising against routine bronchoscopy in COVID-19 patients, as it poses substantial risk to patients and staff [26].
T91 10513-10662 Sentence denotes BAL should only be considered in intubated patients if upper respiratory samples are negative and BAL would significantly change clinical management.
T92 10663-10803 Sentence denotes Tracheal aspirate cultures, as performed twice weekly in our patient, repeatedly identified A. fumigatus as the only micro-organism present.
T93 10804-10951 Sentence denotes In the first positive culture, five colonies were tested for resistance with the VIPcheck plate as is recommended to exclude azole resistance [15].
T94 10952-11222 Sentence denotes When surveillance cultures of tracheal aspirates were persistently cultured positive with A. fumigatus during voriconazole therapy, we suspected the selection of resistant isolates which were probably already present in the first samples, albeit in undetectable numbers.
T95 11223-11262 Sentence denotes An autopsy to confirm IPA was not done.
T96 11263-11430 Sentence denotes Serum galactomannan testing has been shown to be a fairly sensitive diagnostic tool (70%) in neutropenic patients with pathology-proven invasive aspergillosis [27,28].
T97 11431-11686 Sentence denotes However, in patients who are non-neutropenic, serum galactomannan sensitivity of around 25% has been reported [27], which may explain the low number of serum galactomannan positive findings in recently published case reports [6,7] and case series [3,4,5].
T98 11687-11839 Sentence denotes The role of β-d-glucan and the Aspergillus-specific lateral flow device (LFD) as an adjunct to the diagnosis of IPA in COVID-19 is not yet clear [2,23].
T99 11840-11934 Sentence denotes Serum β-d-glucan was persistently strongly positive in this patient over the course of a week.
T100 11935-12182 Sentence denotes The specificity for invasive fungal disease of β-d-glucan testing in a mixed ICU population has been shown to be high (86%), with two consecutive positive results [29] compared to those with only fungal colonization and no invasive fungal disease.
T101 12183-12333 Sentence denotes In addition, multiple other studies report a good sensitivity for the diagnosis of invasive aspergillosis in critically ill patients [30,31,32,33,34].
T102 12334-12478 Sentence denotes BAL β-d-glucan in the ICU setting is, however, not recommended, due to its poor specificity and confounders causing false positive results [35].
T103 12479-12559 Sentence denotes The LFD is particularly interesting in the ICU due to its short turnaround time.
T104 12560-12742 Sentence denotes It has demonstrated a higher sensitivity but lower specificity in BAL fluids compared to galactomannan [36] and β-d-glucan [37] in IPA-probable and proven immunocompromised patients.
T105 12743-12891 Sentence denotes In the ICU setting, however, LFD is suggested to have a lower sensitivity but comparable specificity to galactomannan testing in BAL fluids [35,38].
T106 12892-12984 Sentence denotes Noteworthily, a negative predictive value of >96% has been reported in the ICU setting [39].
T107 12985-13158 Sentence denotes We used the OLM lateral flow device (AspLFD) on sequential patient tracheal aspirates, yielding positive results on all samples confirming the positive galactomannan result.
T108 13159-13337 Sentence denotes Although suitable for its negative predictive value or as an additional diagnostic measure, further evaluation of lateral flow technology in critically ill patients is warranted.
T109 13338-13438 Sentence denotes Altogether, we describe the clinical course of the first reported patient with azole-resistant CAPA.
T110 13439-13609 Sentence denotes The contribution of A. fumigatus to this fatal COVID-19 course is highly likely, although autopsy was not performed, as in all previously reported CAPA cases [3,4,5,6,7].

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 151-183 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T2 185-188 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T3 783-815 Phenotype denotes invasive pulmonary aspergillosis http://purl.obolibrary.org/obo/HP_0020103
T4 880-883 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T5 1295-1320 Phenotype denotes respiratory insufficiency http://purl.obolibrary.org/obo/HP_0002093
T6 1407-1412 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T7 1429-1438 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T8 1486-1494 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T9 1550-1554 Phenotype denotes pain http://purl.obolibrary.org/obo/HP_0012531
T10 2325-2333 Phenotype denotes wheezing http://purl.obolibrary.org/obo/HP_0030828
T11 2590-2594 Phenotype denotes Coma http://purl.obolibrary.org/obo/HP_0001259
T12 2791-2813 Phenotype denotes elevated liver enzymes http://purl.obolibrary.org/obo/HP_0002910
T13 2978-2996 Phenotype denotes increased ferritin http://purl.obolibrary.org/obo/HP_0003281
T14 3288-3305 Phenotype denotes pleural effusions http://purl.obolibrary.org/obo/HP_0002202
T15 5438-5443 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T16 5548-5571 Phenotype denotes tricuspid insufficiency http://purl.obolibrary.org/obo/HP_0005180
T17 6862-6881 Phenotype denotes acute renal failure http://purl.obolibrary.org/obo/HP_0001919
T18 9791-9794 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T19 11245-11248 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T20 11799-11802 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103
T21 12691-12694 Phenotype denotes IPA http://purl.obolibrary.org/obo/HP_0020103

2_test

Id Subject Object Predicate Lexical cue
32517166-32361747-60114378 129-130 32361747 denotes 1
32517166-32396381-60114379 433-434 32396381 denotes 3
32517166-32339350-60114380 491-492 32339350 denotes 5
32517166-30076119-60114381 891-892 30076119 denotes 8
32517166-32297377-60114382 1030-1031 32297377 denotes 9
32517166-32339082-60114383 3407-3409 32339082 denotes 11
32517166-31992387-60114384 3670-3672 31992387 denotes 12
32517166-31811917-60114385 5677-5679 31811917 denotes 14
32517166-29544767-60114386 7221-7223 29544767 denotes 15
32517166-24204249-60114387 8612-8614 24204249 denotes 16
32517166-32297377-60114388 8929-8930 32297377 denotes 9
32517166-29570855-60114389 8931-8933 29570855 denotes 17
32517166-28911045-60114390 8980-8982 28911045 denotes 18
32517166-30580035-60114391 8983-8985 30580035 denotes 19
32517166-25326091-60114392 9252-9254 25326091 denotes 20
32517166-31361683-60114393 9867-9869 31361683 denotes 23
32517166-31802125-60114394 9954-9956 31802125 denotes 24
32517166-22517788-60114395 10144-10146 22517788 denotes 25
32517166-32396381-60114396 10270-10271 32396381 denotes 3
32517166-32339350-60114397 10274-10275 32339350 denotes 5
32517166-32195687-60114398 10508-10510 32195687 denotes 26
32517166-29544767-60114399 10947-10949 29544767 denotes 15
32517166-17885264-60114400 11423-11425 17885264 denotes 27
32517166-11015433-60114401 11426-11428 11015433 denotes 28
32517166-17885264-60114402 11542-11544 17885264 denotes 27
32517166-32396381-60114403 11679-11680 32396381 denotes 3
32517166-32339350-60114404 11683-11684 32339350 denotes 5
32517166-31361683-60114405 11835-11837 31361683 denotes 23
32517166-28384600-60114406 12099-12101 28384600 denotes 29
32517166-20825441-60114407 12317-12319 20825441 denotes 30
32517166-21811868-60114408 12320-12322 21811868 denotes 31
32517166-30015290-60114409 12323-12325 30015290 denotes 32
32517166-21880959-60114410 12326-12328 21880959 denotes 33
32517166-27475024-60114411 12329-12331 27475024 denotes 34
32517166-25903568-60114412 12664-12666 25903568 denotes 36
32517166-24671798-60114413 12684-12686 24671798 denotes 37
32517166-30565352-60114414 12887-12889 30565352 denotes 38
32517166-25927915-60114415 12980-12982 25927915 denotes 39
32517166-32396381-60114416 13598-13599 32396381 denotes 3
32517166-32339350-60114417 13602-13603 32339350 denotes 5