LitCovid-sentences  

PMC:7267243 / 1778-8825 JSONTXT 11 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T20 0-23 Sentence denotes 2 PATIENTS AND METHODS
T21 24-259 Sentence denotes We performed a retrospective chart review of patients with COVID‐19 and ARDS admitted to the medical and surgical ICU at the University Hospital of Cologne, a 1540‐bed teaching hospital between 7 March 2020 and 22 April 2020 (Table 1).
T22 260-362 Sentence denotes TABLE 1 Patient characteristics of patients with COVID‐19 associated invasive pulmonary aspergillosis
T23 363-438 Sentence denotes Characteristics Patient #1 Patient #2 Patient #3 Patient #4 Patient #5
T24 439-479 Sentence denotes Gender Female Male Male Male Female
T25 480-507 Sentence denotes Age (y) 62 70 54 73 54
T26 508-563 Sentence denotes Medical history Lap. cholecystectomy for cholecystitis
T27 564-585 Sentence denotes Arterial hypertension
T28 586-621 Sentence denotes Obesity with sleep apnea (BMI 31.5)
T29 622-642 Sentence denotes Hypercholesterolemia
T30 643-676 Sentence denotes Ex‐smoker (30 PY; 5 y previously)
T31 677-761 Sentence denotes Moderate COPD (GOLD 2) Vertebral disc prolapse left L4/5, flavectomy and nucleotomy
T32 762-816 Sentence denotes Ex‐smoker (4 months previously) Arterial hypertension
T33 817-834 Sentence denotes Diabetes mellitus
T34 835-895 Sentence denotes Aneurysm coiling right A. vertebralis Arterial hypertension
T35 896-913 Sentence denotes Bullous Emphysema
T36 914-920 Sentence denotes Smoker
T37 921-941 Sentence denotes Severe COPD (GOLD 3)
T38 942-966 Sentence denotes Previous Hepatitis B No
T39 967-1148 Sentence denotes Underlying immuno‐compromising condition (inhalational steroids for COPD) No (intravenous corticosteroid therapy 0.4 mg/kg/d, total of 13 d) (inhalational steroids for COPD) No
T40 1149-1187 Sentence denotes ICU Ward MICU MICU SICU SICU MICU
T41 1188-1192 Sentence denotes ARDS
T42 1193-1322 Sentence denotes Horowitz‐Index, admission 12 Severe (53 mm Hg) Severe (93 mm Hg) Moderate (128 mm Hg) Severe (83 mm Hg) Moderate (167 mm Hg)
T43 1323-1365 Sentence denotes Prone positioning Yes Yes Yes Yes Yes
T44 1366-1393 Sentence denotes vvECMO Yes No No No No
T45 1394-1438 Sentence denotes Acute renal failure Yes Yes Yes Yes Yes
T46 1439-1476 Sentence denotes Dialysis No SLEDD SLEDD SLEDD No
T47 1477-1489 Sentence denotes Microbiology
T48 1490-1578 Sentence denotes Serum GM (>0.5) Negative Positive (0.7) Negative Negative 2× positive (2.7 and 1.3)
T49 1579-1600 Sentence denotes Fungal culture BALF:
T50 1601-1643 Sentence denotes Aspergillus fumigatus BALF: negative TA:
T51 1644-1670 Sentence denotes Aspergillus fumigatus TA:
T52 1671-1706 Sentence denotes Aspergillus fumigatus TA: negative
T53 1707-1785 Sentence denotes Susceptibility testing Azole susceptible a Not applicable Azole susceptible
T54 1786-1815 Sentence denotes Itraconazole MIC 0.380 (mg/L)
T55 1816-1864 Sentence denotes Voriconazole MIC 0.094 (mg/L) Azole susceptible
T56 1865-1894 Sentence denotes Itraconazole MIC 0.380 (mg/L)
T57 1895-1940 Sentence denotes Voriconazole MIC 0.094 (mg/L) Not applicable
T58 1941-1958 Sentence denotes Fungal PCR BALF:
T59 1959-1987 Sentence denotes Aspergillus fumigatus BALF:
T60 1988-2016 Sentence denotes Aspergillus fumigatus BALF:
T61 2017-2043 Sentence denotes Aspergillus fumigatus TA:
T62 2044-2079 Sentence denotes Aspergillus fumigatus TA: negative
T63 2080-2104 Sentence denotes TA/BALF GM (>0.5) BALF:
T64 2105-2127 Sentence denotes Positive (>2.5) BALF:
T65 2128-2150 Sentence denotes Positive (>2.5) BALF:
T66 2151-2196 Sentence denotes Positive (>2.5) Not available Not available
T67 2197-2214 Sentence denotes Definition of IPA
T68 2215-2425 Sentence denotes EORTC/MSG Criteria 8 Not classifiable (no host criterion) Not classifiable (no host criterion) Not classifiable (no host criterion) Not classifiable (no host criterion) Not classifiable (no host criterion)
T69 2426-2566 Sentence denotes (modified) AspICU algorithm 3 , 7 Putative Modified putative 3 (GM positivity) Putative Putative Modified putative 3 (GM positivity)
T70 2567-2575 Sentence denotes Virology
T71 2576-2626 Sentence denotes PCR TA: positive for hMPV and SARS‐CoV‐2 (E‐gene:
T72 2627-2645 Sentence denotes C t 13.29; S‐gene:
T73 2646-2702 Sentence denotes C t 12.61) TA: positive for hMPV and SARS‐CoV‐2(E‐gene:
T74 2703-2723 Sentence denotes C t 34.29; ORF1 a/b:
T75 2724-2771 Sentence denotes C t 31.47) TA positive for SARS‐CoV‐2 (E‐gene:
T76 2772-2792 Sentence denotes C t 29.74; ORF1 a/b:
T77 2793-2840 Sentence denotes C t 27.86) TA positive for SARS‐CoV‐2 (E‐gene:
T78 2841-2861 Sentence denotes C t 21.47; ORF1 a/b:
T79 2862-2927 Sentence denotes C t 20.12) TA positive for SARS‐CoV‐2 (C t values not available)
T80 2928-3504 Sentence denotes CT imaging studies Combined bilateral ground‐glass opacities with crazy paving and peripheral nodular consolidations (Video S1, Figure 1A) Ground‐glass opacities with occasional nodules (Video S2, Figure 1B) Bilateral ground‐glass opacities, nodular infiltrates with cavities and air crescent sign (Video S3, Figure 1C) Ground‐glass opacities with occasional nodules, known bullous emphysema (Video S4, Figure 1D) Ground‐glass opacities, smaller areas with crazy paving pattern, central and peripheral consolidations, and smaller nodular infiltrates (Video S5, Figure 1E)
T81 3505-3512 Sentence denotes Therapy
T82 3513-3877 Sentence denotes Antifungal treatment Voriconazole iv (6/4 mg/kg BW twice daily) Isavuconazole iv (200 mg thrice daily for 2 d; 200 mg once daily from 3 d) Caspofungin (70/50 mg once daily) followed by voriconazole iv (6/4 mg/kg BW twice daily) Voriconazole iv (6/4 mg/kg BW twice daily) Caspofungin (70/50 mg once daily) followed by voriconazole iv (6/4 mg/kg BW twice daily)
T83 3878-4140 Sentence denotes Antiviral therapy Supportive only Supportive only Hydroxychloroquine, darunavir and cobicistat at external hospital, in house changed to supportive only Supportive only Ribavirin, lopinavir/ritonavir at external hospital, in house changed to supportive only
T84 4141-4180 Sentence denotes Outcome Died Died Alive Died Alive
T85 4181-4935 Sentence denotes Abbreviations: ARDS, acute respiratory distress syndrome; BALF, bronchoalveolar lavage fluid; BW, body weight; COPD, chronic obstructive pulmonary disease; C t, threshold cycle; EORTC/MSG, European Organization for Research and Treatment of Cancer/Mycoses Study Group; GOLD, global initiative for chronic obstructive lung disease; hMPV, human metapneumovirus; IPA, invasive pulmonary aspergillosis; kg, kilogram; lap, laparoscopic; LVB, lumbar vertebral body; mg, milligram; MIC, minimal inhibitory concentration; MICU, medical ICU; ORF, open reading frame; PCR, polymerase chain reaction; PY, pack‐year history; SICU, surgical ICU; SLEDD, slow low‐efficient daily dialysis; TA, tracheal aspirate; vvECMO, veno‐venous extracorporeal membrane oxygenation.
T86 4936-4986 Sentence denotes a Antifungal susceptibility testing by VIPcheck™.
T87 4987-4988 Sentence denotes 6
T88 4989-5136 Sentence denotes John Wiley & Sons, Ltd This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response.
T89 5137-5319 Sentence denotes It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.
T90 5320-5450 Sentence denotes For patient #1 SARS‐CoV‐2 RT‐PCR Kit (altona Diagnostics) and for patients #2, #3 and #4 cobas® SARS‐CoV‐2 Test (Roche) were used.
T91 5451-5500 Sentence denotes For patient #5, kit manufacturer remains unknown.
T92 5501-5633 Sentence denotes Respective C t values are given in Table 1 where available. hMPV‐PCR was performed with NxTAG® Respiratory Pathogen Panel (Luminex).
T93 5634-5726 Sentence denotes Aspergillus 28S rDNA‐Realtime PCR was performed as in‐house PCR test for screening purposes.
T94 5727-5791 Sentence denotes Species identification was performed by artus® Aspergillus diff.
T95 5792-5812 Sentence denotes RG PCR kit (Qiagen).
T96 5813-5980 Sentence denotes For galactomannan testing from serum, bronchoalveolar lavage fluid (BALF) or tracheal aspirate (TA) Platelia Aspergillus antigen ELISA (Bio‐Rad Laboratories) was used.
T97 5981-6085 Sentence denotes Antifungal susceptibility testing was performed using concentration gradient strips on RPMI agar plates.
T98 6086-6248 Sentence denotes In brief, spore suspensions of the fungal isolates were adjusted to 106 CFU/mL and inoculated with MIC test strips for itraconazole and voriconazole (bioMérieux).
T99 6249-6316 Sentence denotes MICs were determined visually after 48 hours of incubation at 35°C.
T100 6317-6414 Sentence denotes VIPcheck™ (Mediaproducts BV) was performed in patient #1 for early detection of azole resistance.
T101 6415-6416 Sentence denotes 6
T102 6417-6678 Sentence denotes COVID‐19 associated IPA was classified according to the (modified) 3 AspICU algorithm 7 with the addition that positive galactomannan (≥1) from BALF or TA, or two consecutively but separately drawn positive serum samples (≥1) were accepted as entry criterion.
T103 6679-6788 Sentence denotes 8 Severe SARS‐CoV2 infection with ARDS was accepted as host criterion (acquired immunodeficiency) (Table 1).
T104 6789-7047 Sentence denotes This study was carried out in accordance with the ethical principles reflected in the Declaration of Helsinki 9 and was approved by the ethic committee of the University Hospital of Cologne (Identifier of the University of Cologne Ethics Committee 20‐1157).