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PMC:7253233 / 4888-8341 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
203 887-894 Species denotes patient Tax:9606
204 922-932 Chemical denotes vancomycin MESH:D014640
205 937-960 Chemical denotes piperacillin–tazobactam MESH:D000077725
206 51-73 Disease denotes asthma on benralizumab MESH:D001249
207 75-87 Disease denotes hypertension MESH:D006973
208 89-111 Disease denotes chronic kidney disease MESH:D051436
209 113-127 Disease denotes hyperlipidemia MESH:D006949
210 129-153 Disease denotes left bundle branch block MESH:D002037
211 155-176 Disease denotes diastolic dysfunction MESH:D007022
212 293-297 Disease denotes pain MESH:D010146
213 299-304 Disease denotes fever MESH:D005334
214 337-351 Disease denotes encephalopathy MESH:D001927
215 401-432 Disease denotes acute lumbosacral radiculopathy MESH:D011843
216 488-513 Disease denotes neutrophilic leukocytosis MESH:D007964
217 551-555 Disease denotes coma MESH:D003128
218 660-687 Disease denotes focal neurological deficits MESH:D009461
219 1047-1059 Disease denotes leukocytosis MESH:D007964
220 1093-1099 Disease denotes fevers MESH:D005334
221 1120-1139 Disease denotes respiratory failure MESH:D012131
223 3373-3380 Species denotes red box Tax:1226038
244 2879-2897 Gene denotes C-reactive protein Gene:1401
245 2738-2748 Gene denotes fibrinogen Gene:2244
246 1519-1526 Species denotes patient Tax:9606
247 3116-3123 Species denotes patient Tax:9606
248 1890-1903 Chemical denotes Levetiracetam MESH:D000077287
249 2018-2028 Chemical denotes Vancomycin MESH:D014640
250 2030-2039 Chemical denotes Meropenem MESH:D000077731
251 2045-2054 Chemical denotes Acyclovir MESH:D000212
252 1607-1621 Disease denotes encephalopathy MESH:D001927
253 1687-1697 Disease denotes drowsiness MESH:D006970
254 1794-1802 Disease denotes seizures MESH:D012640
255 1955-1962 Disease denotes seizure MESH:D012640
256 2167-2196 Disease denotes white matter hyperintensities MESH:D056784
257 2259-2282 Disease denotes venous sinus thrombosis MESH:D012851
258 2288-2306 Disease denotes C5–C6 myelomalacia MESH:C537005
259 2383-2392 Disease denotes infection MESH:D007239
260 2437-2443 Disease denotes fevers MESH:D005334
261 2604-2612 Disease denotes COVID-19 MESH:C000657245
262 2666-2674 Disease denotes COVID-19 MESH:C000657245
263 3146-3158 Disease denotes tracheostomy

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T19 97-103 Body_part denotes kidney http://purl.org/sig/ont/fma/fma7203
T20 129-147 Body_part denotes left bundle branch http://purl.org/sig/ont/fma/fma9487
T21 271-292 Body_part denotes right lower extremity http://purl.org/sig/ont/fma/fma7187
T22 488-500 Body_part denotes neutrophilic http://purl.org/sig/ont/fma/fma62860
T23 522-527 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T24 627-633 Body_part denotes tendon http://purl.org/sig/ont/fma/fma9721
T25 732-737 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T26 796-801 Body_part denotes spine http://purl.org/sig/ont/fma/fma13478
T27 1308-1313 Body_part denotes chest http://purl.org/sig/ont/fma/fma9576
T28 1409-1414 Body_part denotes Chest http://purl.org/sig/ont/fma/fma9576
T29 1439-1443 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T30 1556-1576 Body_part denotes left upper extremity http://purl.org/sig/ont/fma/fma7186
T31 2059-2062 Body_part denotes CSF http://purl.org/sig/ont/fma/fma20935
T32 2084-2089 Body_part denotes brain http://purl.org/sig/ont/fma/fma50801
T33 2094-2108 Body_part denotes cervical spine http://purl.org/sig/ont/fma/fma24138
T34 2167-2179 Body_part denotes white matter http://purl.org/sig/ont/fma/fma83929
T35 2234-2243 Body_part denotes meningeal http://purl.org/sig/ont/fma/fma231572
T36 2890-2897 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T37 3009-3025 Body_part denotes White blood cell http://purl.org/sig/ont/fma/fma62852
T38 3021-3025 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T39 3080-3088 Body_part denotes platelet http://purl.org/sig/ont/fma/fma62851
T40 3358-3364 Body_part denotes vertex http://purl.org/sig/ont/fma/fma46484
T41 3423-3431 Body_part denotes left arm http://purl.org/sig/ont/fma/fma24896

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T20 97-103 Body_part denotes kidney http://purl.obolibrary.org/obo/UBERON_0002113
T21 556-561 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T22 627-633 Body_part denotes tendon http://purl.obolibrary.org/obo/UBERON_0000043
T23 732-737 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955
T24 1308-1313 Body_part denotes chest http://purl.obolibrary.org/obo/UBERON_0001443
T25 1409-1414 Body_part denotes Chest http://purl.obolibrary.org/obo/UBERON_0001443
T26 1439-1443 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T27 2084-2089 Body_part denotes brain http://purl.obolibrary.org/obo/UBERON_0000955
T28 2167-2179 Body_part denotes white matter http://purl.obolibrary.org/obo/UBERON_0002316
T29 2259-2271 Body_part denotes venous sinus http://purl.obolibrary.org/obo/UBERON_0006615
T30 3015-3020 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T31 3428-3431 Body_part denotes arm http://purl.obolibrary.org/obo/UBERON_0001460

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T49 51-57 Disease denotes asthma http://purl.obolibrary.org/obo/MONDO_0004979
T50 75-87 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T51 89-111 Disease denotes chronic kidney disease http://purl.obolibrary.org/obo/MONDO_0005300
T52 97-111 Disease denotes kidney disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T54 113-127 Disease denotes hyperlipidemia http://purl.obolibrary.org/obo/MONDO_0021187
T55 129-153 Disease denotes left bundle branch block http://purl.obolibrary.org/obo/MONDO_0000991
T56 134-153 Disease denotes bundle branch block http://purl.obolibrary.org/obo/MONDO_0007240
T57 337-351 Disease denotes encephalopathy http://purl.obolibrary.org/obo/MONDO_0005560
T58 419-432 Disease denotes radiculopathy http://purl.obolibrary.org/obo/MONDO_0002959
T59 814-830 Disease denotes epidural abscess http://purl.obolibrary.org/obo/MONDO_0005752
T60 823-830 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T61 962-967 Disease denotes Wound http://purl.obolibrary.org/obo/MONDO_0021178
T62 1061-1063 Disease denotes he http://purl.obolibrary.org/obo/MONDO_0017319
T63 1120-1139 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T64 1607-1621 Disease denotes encephalopathy http://purl.obolibrary.org/obo/MONDO_0005560
T65 2272-2282 Disease denotes thrombosis http://purl.obolibrary.org/obo/MONDO_0000831
T66 2383-2392 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T67 2604-2612 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T68 2666-2674 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T48 8-9 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T49 22-26 http://purl.obolibrary.org/obo/UBERON_0003101 denotes male
T50 22-26 http://www.ebi.ac.uk/efo/EFO_0000970 denotes male
T51 97-103 http://purl.obolibrary.org/obo/UBERON_0002113 denotes kidney
T52 97-103 http://www.ebi.ac.uk/efo/EFO_0000927 denotes kidney
T53 97-103 http://www.ebi.ac.uk/efo/EFO_0000929 denotes kidney
T54 283-292 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremity
T55 382-384 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T56 522-527 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T57 541-542 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 627-633 http://www.ebi.ac.uk/cellline#tendon denotes tendon
T59 627-633 http://www.ebi.ac.uk/efo/EFO_0000952 denotes tendon
T60 689-690 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T61 732-737 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T62 732-737 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T63 842-844 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T64 1308-1313 http://www.ebi.ac.uk/efo/EFO_0000965 denotes chest
T65 1409-1414 http://www.ebi.ac.uk/efo/EFO_0000965 denotes Chest
T66 1439-1443 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T67 1439-1443 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T68 1457-1458 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 1486-1487 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T70 1567-1576 http://www.ebi.ac.uk/efo/EFO_0000876 denotes extremity
T71 1584-1592 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T72 1963-1971 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T73 2084-2089 http://purl.obolibrary.org/obo/UBERON_0000955 denotes brain
T74 2084-2089 http://www.ebi.ac.uk/efo/EFO_0000302 denotes brain
T75 2288-2290 http://purl.obolibrary.org/obo/CLO_0002131 denotes C5
T76 2291-2293 http://purl.obolibrary.org/obo/CLO_0002140 denotes C6
T77 2291-2293 http://purl.obolibrary.org/obo/CLO_0051387 denotes C6
T78 2291-2293 http://purl.obolibrary.org/obo/CLO_0051684 denotes C6
T79 2291-2293 http://purl.obolibrary.org/obo/CLO_0051685 denotes C6
T80 2291-2293 http://purl.obolibrary.org/obo/CLO_0051686 denotes C6
T81 2527-2528 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 2592-2599 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T83 2675-2686 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing was
T84 3015-3020 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T85 3021-3025 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T86 3144-3145 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T87 3207-3208 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 3428-3431 http://www.ebi.ac.uk/efo/EFO_0001410 denotes arm

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T5 22-26 Chemical denotes male http://purl.obolibrary.org/obo/CHEBI_30780
T6 922-932 Chemical denotes vancomycin http://purl.obolibrary.org/obo/CHEBI_28001|http://purl.obolibrary.org/obo/CHEBI_76842
T8 937-949 Chemical denotes piperacillin http://purl.obolibrary.org/obo/CHEBI_8232
T9 950-960 Chemical denotes tazobactam http://purl.obolibrary.org/obo/CHEBI_9421
T10 1014-1024 Chemical denotes antibiotic http://purl.obolibrary.org/obo/CHEBI_33281
T11 1767-1770 Chemical denotes EEG http://purl.obolibrary.org/obo/CHEBI_73494
T12 1890-1903 Chemical denotes Levetiracetam http://purl.obolibrary.org/obo/CHEBI_6437
T13 2018-2028 Chemical denotes Vancomycin http://purl.obolibrary.org/obo/CHEBI_28001
T14 2030-2039 Chemical denotes Meropenem http://purl.obolibrary.org/obo/CHEBI_43968
T15 2890-2897 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T16 2986-2999 Chemical denotes antimicrobial http://purl.obolibrary.org/obo/CHEBI_33281

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T4 1248-1256 http://purl.obolibrary.org/obo/GO_0035810 denotes diuresis

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T30 51-57 Phenotype denotes asthma http://purl.obolibrary.org/obo/HP_0002099
T31 75-87 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T32 89-111 Phenotype denotes chronic kidney disease http://purl.obolibrary.org/obo/HP_0012622
T33 113-127 Phenotype denotes hyperlipidemia http://purl.obolibrary.org/obo/HP_0003077
T34 129-153 Phenotype denotes left bundle branch block http://purl.obolibrary.org/obo/HP_0011713
T35 293-297 Phenotype denotes pain http://purl.obolibrary.org/obo/HP_0012531
T36 299-304 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T37 337-351 Phenotype denotes encephalopathy http://purl.obolibrary.org/obo/HP_0001298
T38 501-513 Phenotype denotes leukocytosis http://purl.obolibrary.org/obo/HP_0001974
T39 551-555 Phenotype denotes coma http://purl.obolibrary.org/obo/HP_0001259
T40 823-830 Phenotype denotes abscess http://purl.obolibrary.org/obo/HP_0025615
T41 1047-1059 Phenotype denotes leukocytosis http://purl.obolibrary.org/obo/HP_0001974
T42 1120-1139 Phenotype denotes respiratory failure http://purl.obolibrary.org/obo/HP_0002878
T43 1439-1455 Phenotype denotes lung infiltrates http://purl.obolibrary.org/obo/HP_0002113
T44 1607-1621 Phenotype denotes encephalopathy http://purl.obolibrary.org/obo/HP_0001298
T45 1687-1697 Phenotype denotes drowsiness http://purl.obolibrary.org/obo/HP_0002329
T46 1788-1802 Phenotype denotes focal seizures http://purl.obolibrary.org/obo/HP_0007359
T47 1955-1962 Phenotype denotes seizure http://purl.obolibrary.org/obo/HP_0001250
T48 2167-2196 Phenotype denotes white matter hyperintensities http://purl.obolibrary.org/obo/HP_0030890

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T40 0-7 Sentence denotes Case #1
T41 8-352 Sentence denotes A 76-year-old male with history of chronic asthma on benralizumab, hypertension, chronic kidney disease, hyperlipidemia, left bundle branch block, diastolic dysfunction, and cervical fusion presented to the emergency department with the chief complaint of severe right lower extremity pain, fever (102.5 °F on presentation), and encephalopathy.
T42 353-462 Sentence denotes He was status post recent L3-S1 laminectomy for acute lumbosacral radiculopathy 5 days prior to presentation.
T43 463-533 Sentence denotes Laboratory workup showed neutrophilic leukocytosis (17,200 cells/mm3).
T44 534-688 Sentence denotes He had a Glasgow coma scale of 14, was oriented to name only, and exhibited exaggerated deep tendon reflexes but had no other focal neurological deficits.
T45 689-755 Sentence denotes A computerized tomography (CT) scan of the brain was unremarkable.
T46 756-845 Sentence denotes Magnetic resonance imaging (MRI) of the spine revealed an epidural abscess between L4-S1.
T47 846-961 Sentence denotes Surgical drainage was performed, and the patient was started empirically on vancomycin and piperacillin–tazobactam.
T48 962-1005 Sentence denotes Wound cultures grew Pseudomonas aeruginosa.
T49 1006-1202 Sentence denotes Despite antibiotic therapy, and improved leukocytosis, he continued to have high-grade fevers and acute hypoxemic respiratory failure requiring intensive care unit transfer on postoperative day 1.
T50 1203-1401 Sentence denotes He was initially managed conservatively with diuresis, preload, and afterload optimization; however, his chest X-ray rapidly progressed to bilateral interstitial and airspace opacification (Fig. 1).
T51 1402-1488 Sentence denotes Fig. 1 Chest X-ray showing bilateral lung infiltrates (a) compared to his baseline (b)
T52 1489-1731 Sentence denotes On postoperative day two, the patient suffered several episodes of left upper extremity clonic activity and worsening encephalopathy with decline in level of consciousness as evidenced by increased drowsiness and inability to follow commands.
T53 1732-1889 Sentence denotes Continuous electroencephalography (EEG) confirmed three focal seizures lasting approximately 30 s each arising from the right centroparietal region (Fig. 2).
T54 1890-1981 Sentence denotes Levetiracetam was initiated and both clinical and electrographic seizure activity subsided.
T55 1982-2072 Sentence denotes Antibiotic regimen was broadened to Vancomycin, Meropenem, and Acyclovir for CSF coverage.
T56 2073-2321 Sentence denotes MRI of the brain and cervical spine with and without contrast was remarkable only for chronic white matter hyperintensities, without acute intracranial lesions, meningeal enhancement or venous sinus thrombosis, and C5–C6 myelomalacia, respectively.
T57 2322-2408 Sentence denotes Lumbar puncture was not performed due to the risk of seeding infection into neuroaxis.
T58 2409-2733 Sentence denotes Given persistent high-grade fevers, worsening respiratory status requiring intubation, and recent possible exposures, a respiratory viral panel was sent in addition to separate rapid testing for COVID-19 polymerase chain reaction on postoperative day 4 and COVID-19 testing was confirmed as positive twenty-four hours later.
T59 2734-2878 Sentence denotes His fibrinogen level was elevated at 631 mg/dL (normal range 200–400 mg/dL) and continued to increase to over 860 mg/dL over the following days.
T60 2879-3008 Sentence denotes C-reactive protein increased from 1.7 mg/dL on prior admission to 27.3 mg/dL and remained elevated despite antimicrobial therapy.
T61 3009-3111 Sentence denotes White blood cell count steadily improved over his hospitalization, and platelet count remained stable.
T62 3112-3273 Sentence denotes Our patient ultimately received a tracheostomy and after 30 days of ICU stay was discharged to a long-term acute care hospital for further ventilator management.
T63 3274-3304 Sentence denotes Fig. 2 Electroencephalography.
T64 3305-3453 Sentence denotes Rhythmic discharges noted in the right frontocentral/vertex region (red box) corresponding to clonic movements of the left arm (Color figure online)