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PMC:7344504 / 2043-9126 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 357-360 Body_part denotes hip http://purl.org/sig/ont/fma/fma24964
T2 1425-1432 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T3 1510-1520 Body_part denotes leucocytes http://purl.org/sig/ont/fma/fma62852
T4 1541-1552 Body_part denotes neutrophils http://purl.org/sig/ont/fma/fma62860
T5 1578-1583 Body_part denotes liver http://purl.org/sig/ont/fma/fma7197
T6 1683-1693 Body_part denotes calcitonin http://purl.org/sig/ont/fma/fma83348
T7 1812-1819 Body_part denotes glucose http://purl.org/sig/ont/fma/fma82743
T8 1870-1876 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T9 1906-1911 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T10 2442-2446 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T11 2454-2459 Body_part denotes Blood http://purl.org/sig/ont/fma/fma9670
T12 2496-2507 Body_part denotes nasopharynx http://purl.org/sig/ont/fma/fma54878
T13 3551-3557 Body_part denotes throat http://purl.org/sig/ont/fma/fma228738
T14 3722-3727 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T15 3900-3905 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T16 4175-4188 Body_part denotes noradrenaline http://purl.org/sig/ont/fma/fma61799
T17 4723-4728 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T18 4807-4812 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T19 5935-5940 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T20 6800-6804 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 357-360 Body_part denotes hip http://purl.obolibrary.org/obo/UBERON_0001464
T2 1373-1378 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T3 1578-1583 Body_part denotes liver http://purl.obolibrary.org/obo/UBERON_0002107
T4 1870-1876 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T5 1906-1911 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T6 2066-2083 Body_part denotes pleural effusions http://purl.obolibrary.org/obo/UBERON_0000175
T7 2454-2459 Body_part denotes Blood http://purl.obolibrary.org/obo/UBERON_0000178
T8 2496-2507 Body_part denotes nasopharynx http://purl.obolibrary.org/obo/UBERON_0001728
T9 3551-3557 Body_part denotes throat http://purl.obolibrary.org/obo/UBERON_0000341
T10 3722-3727 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T11 3900-3905 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T12 4723-4728 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T13 4807-4812 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T14 5935-5940 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
85 41-48 Species denotes patient Tax:9606
86 567-574 Species denotes Patient Tax:9606
87 825-832 Species denotes patient Tax:9606
88 457-468 Chemical denotes pantoprazol MESH:D000077402
89 473-483 Chemical denotes etoricoxib MESH:D000077613
90 73-98 Disease denotes respiratory insufficiency MESH:D012131
91 108-116 Disease denotes COVID-19 MESH:C000657245
92 185-190 Disease denotes fever MESH:D005334
93 207-216 Disease denotes dry cough MESH:D003371
94 264-272 Disease denotes diarrhea MESH:D003967
95 328-332 Disease denotes pain MESH:D010146
96 340-360 Disease denotes arthrosis of the hip MESH:D010003
97 672-680 Disease denotes COVID-19 MESH:C000657245
108 1414-1432 Gene denotes C-reactive protein Gene:1401
109 1434-1437 Gene denotes CRP Gene:1401
110 1840-1850 Species denotes SARS-CoV-2 Tax:2697049
111 1177-1179 Chemical denotes O2 MESH:D010100
112 1812-1819 Chemical denotes glucose MESH:D005947
113 980-988 Disease denotes dyspneic
114 1093-1111 Disease denotes pulmonary wheezing MESH:D012135
115 1368-1372 Disease denotes Coma MESH:D003128
116 1734-1753 Disease denotes bacterial infection MESH:D001424
117 2066-2083 Disease denotes pleural effusions MESH:D010996
122 2376-2386 Species denotes SARS-CoV-2 Tax:2697049
123 2551-2558 Species denotes patient Tax:9606
124 2247-2258 Chemical denotes chloroquine MESH:D002738
125 2225-2245 Disease denotes SARS-CoV-2 infection MESH:C000657245
131 2692-2695 Gene denotes CRP Gene:1401
132 2800-2807 Species denotes patient Tax:9606
133 3094-3101 Species denotes patient Tax:9606
134 2944-2955 Chemical denotes ceftriaxone MESH:D002443
135 3020-3022 Chemical denotes O2 MESH:D010100
149 4012-4021 Gene denotes factor Xa Gene:2159
150 3446-3453 Species denotes patient Tax:9606
151 4113-4120 Species denotes patient Tax:9606
152 3210-3216 Chemical denotes oxygen MESH:D010100
153 3303-3314 Chemical denotes ceftriaxone MESH:D002443
154 3393-3407 Chemical denotes amphotericin B MESH:D000666
155 3422-3432 Chemical denotes tobramycin MESH:D014031
156 3455-3466 Chemical denotes ceftriaxone MESH:D002443
157 3995-4006 Chemical denotes enoxaparine MESH:D017984
158 4175-4188 Chemical denotes noradrenaline MESH:D009638
159 4223-4237 Chemical denotes hydrocortisone MESH:D006854
160 3961-3977 Disease denotes pulmonary emboli MESH:D011655
161 4326-4349 Disease denotes tricuspid insufficiency MESH:D014262
179 4374-4395 Species denotes Aspergillus fumigatus Tax:746128
180 5152-5164 Species denotes A. fumigatus Tax:746128
181 4522-4533 Species denotes Aspergillus Tax:746128
182 4638-4648 Chemical denotes β-d-glucan
183 4813-4826 Chemical denotes galactomannan MESH:C012990
184 4881-4893 Chemical denotes Voriconazole MESH:D065819
185 4939-4950 Chemical denotes caspofungin MESH:D000077336
186 5049-5054 Chemical denotes azole MESH:D001393
187 5190-5204 Chemical denotes amphotericin B MESH:D000666
188 5215-5225 Chemical denotes micafungin MESH:D000077551
189 5230-5243 Chemical denotes anidulafungin MESH:D000077612
190 5257-5269 Chemical denotes itraconazole MESH:D017964
191 5278-5290 Chemical denotes voriconazole MESH:D065819
192 5306-5318 Chemical denotes posaconazole MESH:C101425
193 5331-5343 Chemical denotes Voriconazole MESH:D065819
194 5419-5430 Chemical denotes caspofungin MESH:D000077336
195 4486-4511 Disease denotes Aspergillus galactomannan MESH:D001228
202 5661-5673 Species denotes A. fumigatus Tax:746128
203 5738-5750 Chemical denotes voriconazole MESH:D065819
204 5765-5775 Chemical denotes β-d-glucan
205 5886-5898 Chemical denotes voriconazole MESH:D065819
206 5922-5934 Chemical denotes Voriconazole MESH:D065819
207 5640-5659 Disease denotes acute renal failure MESH:D058186
224 6331-6338 Species denotes patient Tax:9606
225 6396-6408 Species denotes A. fumigatus Tax:746128
226 6532-6544 Species denotes A. fumigatus Tax:746128
227 6951-6958 Species denotes patient Tax:9606
228 6421-6433 Chemical denotes itraconazole MESH:D017964
229 6438-6450 Chemical denotes voriconazole MESH:D065819
230 6570-6584 Chemical denotes amphotericin B MESH:D000666
231 6595-6608 Chemical denotes anidulafungin MESH:D000077612
232 6613-6623 Chemical denotes micafungin MESH:D000077551
233 6637-6649 Chemical denotes itraconazole MESH:D017964
234 6659-6671 Chemical denotes voriconazole MESH:D065819
235 6683-6695 Chemical denotes posaconazole MESH:C101425
236 6706-6718 Chemical denotes Voriconazole MESH:D065819
237 6754-6768 Chemical denotes amphotericin B MESH:D000666
238 6887-6892 Chemical denotes azole MESH:D001393
239 6834-6838 Mutation denotes L98H p.L98H

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T22 108-116 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 264-272 Disease denotes diarrhea http://purl.obolibrary.org/obo/MONDO_0001673
T24 340-349 Disease denotes arthrosis http://purl.obolibrary.org/obo/MONDO_0006816
T25 672-680 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 1734-1753 Disease denotes bacterial infection http://purl.obolibrary.org/obo/MONDO_0005113
T27 1744-1753 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T28 1840-1848 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 2225-2233 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 2236-2245 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 2376-2384 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 4326-4349 Disease denotes tricuspid insufficiency http://purl.obolibrary.org/obo/MONDO_0002870
T33 4792-4796 Disease denotes CAPA http://purl.obolibrary.org/obo/MONDO_0007163
T34 5001-5003 Disease denotes BV http://purl.obolibrary.org/obo/MONDO_0005316
T35 5640-5659 Disease denotes acute renal failure http://purl.obolibrary.org/obo/MONDO_0002492
T36 5646-5659 Disease denotes renal failure http://purl.obolibrary.org/obo/MONDO_0001106

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T12 27-28 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T13 205-206 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 357-360 http://www.ebi.ac.uk/efo/EFO_0001929 denotes hip
T15 391-392 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 419-420 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T17 1164-1166 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T18 1184-1185 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 1510-1520 http://purl.obolibrary.org/obo/CL_0000738 denotes leucocytes
T20 1578-1583 http://purl.obolibrary.org/obo/UBERON_0002107 denotes liver
T21 1578-1583 http://www.ebi.ac.uk/efo/EFO_0000887 denotes liver
T22 1593-1613 http://purl.obolibrary.org/obo/PR_000023540 denotes alkaline phosphatase
T23 1614-1617 http://purl.obolibrary.org/obo/CLO_0001409 denotes 528
T24 1895-1896 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T25 1906-1911 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T26 2066-2083 http://purl.obolibrary.org/obo/UBERON_0000175 denotes pleural effusions
T27 2185-2187 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T28 2394-2395 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 2442-2446 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T30 2454-2459 http://purl.obolibrary.org/obo/UBERON_0000178 denotes Blood
T31 2454-2459 http://www.ebi.ac.uk/efo/EFO_0000296 denotes Blood
T32 2767-2768 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 2843-2844 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 2890-2891 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 3348-3349 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 3406-3407 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T37 3678-3679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 3722-3727 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T39 3722-3727 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T40 3851-3852 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 3876-3877 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T42 3900-3905 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T43 4318-4319 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 4614-4615 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 4733-4737 http://purl.obolibrary.org/obo/CLO_0053133 denotes 1590
T46 4738-4740 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T47 4768-4769 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 5152-5153 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T49 5203-5204 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T50 5661-5662 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 5820-5822 http://purl.obolibrary.org/obo/CLO_0008426 denotes pg
T52 5827-5831 http://purl.obolibrary.org/obo/CLO_0001757 denotes at 1
T53 6342-6343 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 6396-6397 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55 6532-6533 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T56 6583-6584 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T57 6767-6768 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T58 6800-6804 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T59 6827-6828 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 6912-6914 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T14 393-399 Chemical denotes proton http://purl.obolibrary.org/obo/CHEBI_24636
T15 405-414 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T16 421-456 Chemical denotes nonsteroidal anti-inflammatory drug http://purl.obolibrary.org/obo/CHEBI_35475
T17 434-456 Chemical denotes anti-inflammatory drug http://purl.obolibrary.org/obo/CHEBI_35472
T18 452-456 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T19 457-468 Chemical denotes pantoprazol http://purl.obolibrary.org/obo/CHEBI_7915
T20 473-483 Chemical denotes etoricoxib http://purl.obolibrary.org/obo/CHEBI_6339
T21 1177-1179 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T22 1394-1397 Chemical denotes ECG http://purl.obolibrary.org/obo/CHEBI_70255
T23 1425-1432 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24 1636-1639 Chemical denotes AST http://purl.obolibrary.org/obo/CHEBI_76649
T25 1648-1650 Chemical denotes LD http://purl.obolibrary.org/obo/CHEBI_74332
T26 1683-1693 Chemical denotes calcitonin http://purl.obolibrary.org/obo/CHEBI_3306
T27 1812-1819 Chemical denotes glucose http://purl.obolibrary.org/obo/CHEBI_17234|http://purl.obolibrary.org/obo/CHEBI_4167
T29 2125-2127 Chemical denotes CO http://purl.obolibrary.org/obo/CHEBI_17245
T30 2247-2258 Chemical denotes chloroquine http://purl.obolibrary.org/obo/CHEBI_3638
T31 2944-2955 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T32 3020-3022 Chemical denotes O2 http://purl.obolibrary.org/obo/CHEBI_15379
T33 3210-3216 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T34 3303-3314 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T35 3393-3407 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T36 3409-3417 Chemical denotes colistin http://purl.obolibrary.org/obo/CHEBI_37943
T37 3422-3432 Chemical denotes tobramycin http://purl.obolibrary.org/obo/CHEBI_28864|http://purl.obolibrary.org/obo/CHEBI_73678
T39 3455-3466 Chemical denotes ceftriaxone http://purl.obolibrary.org/obo/CHEBI_29007
T40 4175-4188 Chemical denotes noradrenaline http://purl.obolibrary.org/obo/CHEBI_33569
T41 4223-4237 Chemical denotes hydrocortisone http://purl.obolibrary.org/obo/CHEBI_17650
T42 4498-4511 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T43 4551-4553 Chemical denotes La http://purl.obolibrary.org/obo/CHEBI_33336
T44 4642-4648 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T45 4711-4713 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 4813-4826 Chemical denotes galactomannan http://purl.obolibrary.org/obo/CHEBI_27680
T49 4939-4950 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T50 5049-5054 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452
T51 5190-5204 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T52 5215-5225 Chemical denotes micafungin http://purl.obolibrary.org/obo/CHEBI_600520
T53 5230-5243 Chemical denotes anidulafungin http://purl.obolibrary.org/obo/CHEBI_55346
T54 5257-5269 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T55 5278-5290 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T56 5306-5318 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T57 5419-5430 Chemical denotes caspofungin http://purl.obolibrary.org/obo/CHEBI_474180
T58 5738-5750 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T59 5769-5775 Chemical denotes glucan http://purl.obolibrary.org/obo/CHEBI_37163
T60 5886-5898 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T61 5953-5957 Chemical denotes drug http://purl.obolibrary.org/obo/CHEBI_23888
T62 6421-6433 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T63 6438-6450 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T64 6570-6584 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T65 6595-6608 Chemical denotes anidulafungin http://purl.obolibrary.org/obo/CHEBI_55346
T66 6613-6623 Chemical denotes micafungin http://purl.obolibrary.org/obo/CHEBI_600520
T67 6637-6649 Chemical denotes itraconazole http://purl.obolibrary.org/obo/CHEBI_6076
T68 6659-6671 Chemical denotes voriconazole http://purl.obolibrary.org/obo/CHEBI_10023
T69 6683-6695 Chemical denotes posaconazole http://purl.obolibrary.org/obo/CHEBI_64355
T70 6754-6768 Chemical denotes amphotericin B http://purl.obolibrary.org/obo/CHEBI_2682
T71 6887-6892 Chemical denotes azole http://purl.obolibrary.org/obo/CHEBI_68452

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 1602-1613 http://purl.obolibrary.org/obo/GO_0016791 denotes phosphatase

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 4498-4511 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510
T2 4813-4826 GlycoEpitope denotes galactomannan http://www.glycoepitope.jp/epitopes/EP0510

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T18 0-2 Sentence denotes 2.
T19 3-26 Sentence denotes Case Report and Results
T20 27-124 Sentence denotes A 74-year-old patient was admitted because of respiratory insufficiency amid the COVID-19 crisis.
T21 125-217 Sentence denotes Eleven days prior to admission, she had been suffering from fever (38.5 °C) and a dry cough.
T22 218-273 Sentence denotes Three days after symptom onset, she developed diarrhea.
T23 274-498 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 499-566 Sentence denotes She stopped smoking 20 years ago and was healthy and fit otherwise.
T25 567-615 Sentence denotes Patient characteristics can be found in Table 1.
T26 616-899 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 900-1002 Sentence denotes At presentation to the emergency department, she had been feeling progressively dyspneic for two days.
T28 1003-1139 Sentence denotes On physical examination, her oxygenation was 82%, with 28 breaths per minute in room air, pulmonary wheezing and an extended expiration.
T29 1140-1235 Sentence denotes Oxygenation improved to 94% with 5 L O2 via a nasal cannula, but she desaturated during speech.
T30 1236-1289 Sentence denotes Her BMI was 27.7 (80 kg) and her temperature 37.8 °C.
T31 1290-1355 Sentence denotes No other aberrant observations on physical examination were made.
T32 1356-1409 Sentence denotes Her Glasgow Coma Scale was 15 and her ECG was normal.
T33 1410-1839 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 1840-1894 Sentence denotes SARS-CoV-2 nasopharyngeal and throat swabs were taken.
T35 1895-2120 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 2121-2189 Sentence denotes The CO-RADS score was 5 and CT-severity score was 24 out of 25 [11].
T37 2190-2371 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 2372-2453 Sentence denotes The SARS-CoV-2 PCR of a nasopharyngeal swab was positive (Ct 30.59; E gene [12]).
T39 2454-2546 Sentence denotes Blood cultures remained negative, as were nasopharynx bacterial cultures taken at admission.
T40 2547-2627 Sentence denotes The patient was subsequently admitted to our general inpatient respiratory ward.
T41 2628-2687 Sentence denotes An overview of her hospital course is depicted in Figure 2.
T42 2688-2786 Sentence denotes The CRP remained highly stable over the following days at around 200 mg/L with a range of 192–214.
T43 2787-2866 Sentence denotes However, the patient needed increasing oxygenation with a non-rebreathing mask.
T44 2867-2960 Sentence denotes Empirical treatment of a suspected bacterial superinfection was started with ceftriaxone i.v.
T45 2961-2974 Sentence denotes 2000 mg q24h.
T46 2975-3175 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 3176-3319 Sentence denotes In the ICU, HFNO (high-flow nasal oxygen therapy) and selective digestive decontamination (SDD) were initiated, which includes ceftriaxone i.v.
T48 3320-3437 Sentence denotes 2000 mg q24h for 4 days and a combined oral non-absorbable suspension of amphotericin B, colistin and tobramycin q6h.
T49 3438-3509 Sentence denotes In this patient, ceftriaxone was continued de facto for another 4 days.
T50 3510-3670 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 3671-3801 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 3802-3875 Sentence denotes Therefore, she was sedated, intubated and put on a mechanical ventilator.
T53 3876-3978 Sentence denotes A CT angiography of the chest was performed which demonstrated significant bilateral pulmonary emboli.
T54 3979-4061 Sentence denotes Anticoagulants (enoxaparine anti-factor Xa) were initiated in therapeutic dosages.
T55 4062-4139 Sentence denotes Pressure control ventilation was required with the patient in prone position.
T56 4140-4291 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 4292-4373 Sentence denotes Cardiac ultrasound showed a minor tricuspid insufficiency but no major pathology.
T58 4374-4485 Sentence denotes Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission.
T59 4486-4806 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 4807-4880 Sentence denotes Serum galactomannan remained negative (<0.5) in three subsequent samples.
T61 4881-4898 Sentence denotes Voriconazole i.v.
T62 4899-4955 Sentence denotes 6 mg/kg q12h was started in addition to caspofungin i.v.
T63 4956-5080 Sentence denotes 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative.
T64 5081-5330 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 5331-5431 Sentence denotes Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin.
T66 5432-5512 Sentence denotes During SDD, bacterial cultures remained negative throughout her stay in the ICU.
T67 5513-5660 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 5661-5921 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 5922-6109 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 6110-6214 Sentence denotes The respiratory situation improved marginally in the subsequent 7 days but declined steadily thereafter.
T71 6215-6381 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 6382-6518 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 6519-6705 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 6706-6781 Sentence denotes Voriconazole treatment was changed to liposomal amphotericin B 200 mg q24h.
T75 6782-6904 Sentence denotes Subsequent cyp51A gene sequencing identified a TR34/L98H mutation, probably responsible for the observed azole resistance.
T76 6905-7053 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 7054-7083 Sentence denotes An autopsy was not performed.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T5 73-98 Phenotype denotes respiratory insufficiency http://purl.obolibrary.org/obo/HP_0002093
T6 185-190 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T7 207-216 Phenotype denotes dry cough http://purl.obolibrary.org/obo/HP_0031246
T8 264-272 Phenotype denotes diarrhea http://purl.obolibrary.org/obo/HP_0002014
T9 328-332 Phenotype denotes pain http://purl.obolibrary.org/obo/HP_0012531
T10 1103-1111 Phenotype denotes wheezing http://purl.obolibrary.org/obo/HP_0030828
T11 1368-1372 Phenotype denotes Coma http://purl.obolibrary.org/obo/HP_0001259
T12 1569-1591 Phenotype denotes elevated liver enzymes http://purl.obolibrary.org/obo/HP_0002910
T13 1756-1774 Phenotype denotes increased ferritin http://purl.obolibrary.org/obo/HP_0003281
T14 2066-2083 Phenotype denotes pleural effusions http://purl.obolibrary.org/obo/HP_0002202
T15 4216-4221 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T16 4326-4349 Phenotype denotes tricuspid insufficiency http://purl.obolibrary.org/obo/HP_0005180
T17 5640-5659 Phenotype denotes acute renal failure http://purl.obolibrary.org/obo/HP_0001919

2_test

Id Subject Object Predicate Lexical cue
32517166-32339082-60114383 2185-2187 32339082 denotes 11
32517166-31992387-60114384 2448-2450 31992387 denotes 12
32517166-31811917-60114385 4455-4457 31811917 denotes 14
32517166-29544767-60114386 5999-6001 29544767 denotes 15