PMC:7267243 / 2038-7097 JSON TXT

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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":1230,"end":1235},"obj":"Body_part"},{"id":"T2","span":{"begin":2361,"end":2365},"obj":"Body_part"},{"id":"T3","span":{"begin":2380,"end":2384},"obj":"Body_part"},{"id":"T4","span":{"begin":2437,"end":2441},"obj":"Body_part"},{"id":"T5","span":{"begin":2506,"end":2510},"obj":"Body_part"},{"id":"T6","span":{"begin":2575,"end":2579},"obj":"Body_part"},{"id":"T7","span":{"begin":2938,"end":2946},"obj":"Body_part"},{"id":"T8","span":{"begin":4019,"end":4023},"obj":"Body_part"},{"id":"T9","span":{"begin":4238,"end":4242},"obj":"Body_part"},{"id":"T10","span":{"begin":4358,"end":4379},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma76576"},{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma256135"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma16075"}],"text":"TABLE 1 Patient characteristics of patients with COVID‐19 associated invasive pulmonary aspergillosis\nCharacteristics Patient #1 Patient #2 Patient #3 Patient #4 Patient #5\nGender Female Male Male Male Female\nAge (y) 62 70 54 73 54\nMedical history Lap. cholecystectomy for cholecystitis\nArterial hypertension\nObesity with sleep apnea (BMI 31.5)\nHypercholesterolemia\nEx‐smoker (30 PY; 5 y previously)\nModerate COPD (GOLD 2) Vertebral disc prolapse left L4/5, flavectomy and nucleotomy\nEx‐smoker (4 months previously) Arterial hypertension\nDiabetes mellitus\nAneurysm coiling right A. vertebralis Arterial hypertension\nBullous Emphysema\nSmoker\nSevere COPD (GOLD 3)\nPrevious Hepatitis B No\nUnderlying 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\nICU Ward MICU MICU SICU SICU MICU\nARDS\nHorowitz‐Index, admission 12 Severe (53 mm Hg) Severe (93 mm Hg) Moderate (128 mm Hg) Severe (83 mm Hg) Moderate (167 mm Hg)\nProne positioning Yes Yes Yes Yes Yes\nvvECMO Yes No No No No\nAcute renal failure Yes Yes Yes Yes Yes\nDialysis No SLEDD SLEDD SLEDD No\nMicrobiology\nSerum GM (\u003e0.5) Negative Positive (0.7) Negative Negative 2× positive (2.7 and 1.3)\nFungal culture BALF: Aspergillus fumigatus BALF: negative TA: Aspergillus fumigatus TA: Aspergillus fumigatus TA: negative\nSusceptibility testing Azole susceptible a Not applicable Azole susceptible\nItraconazole MIC 0.380 (mg/L)\nVoriconazole MIC 0.094 (mg/L) Azole susceptible\nItraconazole MIC 0.380 (mg/L)\nVoriconazole MIC 0.094 (mg/L) Not applicable\nFungal PCR BALF: Aspergillus fumigatus BALF: Aspergillus fumigatus BALF: Aspergillus fumigatus TA: Aspergillus fumigatus TA: negative\nTA/BALF GM (\u003e0.5) BALF: Positive (\u003e2.5) BALF: Positive (\u003e2.5) BALF: Positive (\u003e2.5) Not available Not available\nDefinition of IPA\nEORTC/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)\n(modified) AspICU algorithm 3 , 7 Putative Modified putative 3 (GM positivity) Putative Putative Modified putative 3 (GM positivity)\nVirology\nPCR TA: positive for hMPV and SARS‐CoV‐2 (E‐gene: C t 13.29; S‐gene: C t 12.61) TA: positive for hMPV and SARS‐CoV‐2(E‐gene: C t 34.29; ORF1 a/b: C t 31.47) TA positive for SARS‐CoV‐2 (E‐gene: C t 29.74; ORF1 a/b: C t 27.86) TA positive for SARS‐CoV‐2 (E‐gene: C t 21.47; ORF1 a/b: C t 20.12) TA positive for SARS‐CoV‐2 (C t values not available)\nCT 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)\nTherapy\nAntifungal 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)\nAntiviral 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\nOutcome Died Died Alive Died Alive\nAbbreviations: 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.\na Antifungal susceptibility testing by VIPcheck™. 6\nJohn Wiley \u0026 Sons, Ltd This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. 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."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":441,"end":450},"obj":"Body_part"},{"id":"T2","span":{"begin":1230,"end":1235},"obj":"Body_part"},{"id":"T3","span":{"begin":4238,"end":4242},"obj":"Body_part"},{"id":"T4","span":{"begin":4365,"end":4374},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_3010224"},{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_3010224"}],"text":"TABLE 1 Patient characteristics of patients with COVID‐19 associated invasive pulmonary aspergillosis\nCharacteristics Patient #1 Patient #2 Patient #3 Patient #4 Patient #5\nGender Female Male Male Male Female\nAge (y) 62 70 54 73 54\nMedical history Lap. cholecystectomy for cholecystitis\nArterial hypertension\nObesity with sleep apnea (BMI 31.5)\nHypercholesterolemia\nEx‐smoker (30 PY; 5 y previously)\nModerate COPD (GOLD 2) Vertebral disc prolapse left L4/5, flavectomy and nucleotomy\nEx‐smoker (4 months previously) Arterial hypertension\nDiabetes mellitus\nAneurysm coiling right A. vertebralis Arterial hypertension\nBullous Emphysema\nSmoker\nSevere COPD (GOLD 3)\nPrevious Hepatitis B No\nUnderlying 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\nICU Ward MICU MICU SICU SICU MICU\nARDS\nHorowitz‐Index, admission 12 Severe (53 mm Hg) Severe (93 mm Hg) Moderate (128 mm Hg) Severe (83 mm Hg) Moderate (167 mm Hg)\nProne positioning Yes Yes Yes Yes Yes\nvvECMO Yes No No No No\nAcute renal failure Yes Yes Yes Yes Yes\nDialysis No SLEDD SLEDD SLEDD No\nMicrobiology\nSerum GM (\u003e0.5) Negative Positive (0.7) Negative Negative 2× positive (2.7 and 1.3)\nFungal culture BALF: Aspergillus fumigatus BALF: negative TA: Aspergillus fumigatus TA: Aspergillus fumigatus TA: negative\nSusceptibility testing Azole susceptible a Not applicable Azole susceptible\nItraconazole MIC 0.380 (mg/L)\nVoriconazole MIC 0.094 (mg/L) Azole susceptible\nItraconazole MIC 0.380 (mg/L)\nVoriconazole MIC 0.094 (mg/L) Not applicable\nFungal PCR BALF: Aspergillus fumigatus BALF: Aspergillus fumigatus BALF: Aspergillus fumigatus TA: Aspergillus fumigatus TA: negative\nTA/BALF GM (\u003e0.5) BALF: Positive (\u003e2.5) BALF: Positive (\u003e2.5) BALF: Positive (\u003e2.5) Not available Not available\nDefinition of IPA\nEORTC/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)\n(modified) AspICU algorithm 3 , 7 Putative Modified putative 3 (GM positivity) Putative Putative Modified putative 3 (GM positivity)\nVirology\nPCR TA: positive for hMPV and SARS‐CoV‐2 (E‐gene: C t 13.29; S‐gene: C t 12.61) TA: positive for hMPV and SARS‐CoV‐2(E‐gene: C t 34.29; ORF1 a/b: C t 31.47) TA positive for SARS‐CoV‐2 (E‐gene: C t 29.74; ORF1 a/b: C t 27.86) TA positive for SARS‐CoV‐2 (E‐gene: C t 21.47; ORF1 a/b: C t 20.12) TA positive for SARS‐CoV‐2 (C t values not available)\nCT 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)\nTherapy\nAntifungal 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)\nAntiviral 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\nOutcome Died Died Alive Died Alive\nAbbreviations: 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.\na Antifungal susceptibility testing by VIPcheck™. 6\nJohn Wiley \u0026 Sons, Ltd This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. 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."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T4","span":{"begin":339,"end":344},"obj":"http://purl.obolibrary.org/obo/GO_0030431"}],"text":"TABLE 1 Patient characteristics of patients with COVID‐19 associated invasive pulmonary aspergillosis\nCharacteristics Patient #1 Patient #2 Patient #3 Patient #4 Patient #5\nGender Female Male Male Male Female\nAge (y) 62 70 54 73 54\nMedical history Lap. cholecystectomy for cholecystitis\nArterial hypertension\nObesity with sleep apnea (BMI 31.5)\nHypercholesterolemia\nEx‐smoker (30 PY; 5 y previously)\nModerate COPD (GOLD 2) Vertebral disc prolapse left L4/5, flavectomy and nucleotomy\nEx‐smoker (4 months previously) Arterial hypertension\nDiabetes mellitus\nAneurysm coiling right A. vertebralis Arterial hypertension\nBullous Emphysema\nSmoker\nSevere COPD (GOLD 3)\nPrevious Hepatitis B No\nUnderlying 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\nICU Ward MICU MICU SICU SICU MICU\nARDS\nHorowitz‐Index, admission 12 Severe (53 mm Hg) Severe (93 mm Hg) Moderate (128 mm Hg) Severe (83 mm Hg) Moderate (167 mm Hg)\nProne positioning Yes Yes Yes Yes Yes\nvvECMO Yes No No No No\nAcute renal failure Yes Yes Yes Yes Yes\nDialysis No SLEDD SLEDD SLEDD No\nMicrobiology\nSerum GM (\u003e0.5) Negative Positive (0.7) Negative Negative 2× positive (2.7 and 1.3)\nFungal culture BALF: Aspergillus fumigatus BALF: negative TA: Aspergillus fumigatus TA: Aspergillus fumigatus TA: negative\nSusceptibility testing Azole susceptible a Not applicable Azole susceptible\nItraconazole MIC 0.380 (mg/L)\nVoriconazole MIC 0.094 (mg/L) Azole susceptible\nItraconazole MIC 0.380 (mg/L)\nVoriconazole MIC 0.094 (mg/L) Not applicable\nFungal PCR BALF: Aspergillus fumigatus BALF: Aspergillus fumigatus BALF: Aspergillus fumigatus TA: Aspergillus fumigatus TA: negative\nTA/BALF GM (\u003e0.5) BALF: Positive (\u003e2.5) BALF: Positive (\u003e2.5) BALF: Positive (\u003e2.5) Not available Not available\nDefinition of IPA\nEORTC/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)\n(modified) AspICU algorithm 3 , 7 Putative Modified putative 3 (GM positivity) Putative Putative Modified putative 3 (GM positivity)\nVirology\nPCR TA: positive for hMPV and SARS‐CoV‐2 (E‐gene: C t 13.29; S‐gene: C t 12.61) TA: positive for hMPV and SARS‐CoV‐2(E‐gene: C t 34.29; ORF1 a/b: C t 31.47) TA positive for SARS‐CoV‐2 (E‐gene: C t 29.74; ORF1 a/b: C t 27.86) TA positive for SARS‐CoV‐2 (E‐gene: C t 21.47; ORF1 a/b: C t 20.12) TA positive for SARS‐CoV‐2 (C t values not available)\nCT 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)\nTherapy\nAntifungal 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)\nAntiviral 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\nOutcome Died Died Alive Died Alive\nAbbreviations: 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.\na Antifungal susceptibility testing by VIPcheck™. 6\nJohn Wiley \u0026 Sons, Ltd This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. 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."}

LitCovid-sentences

LitCovid-PD-HP

PMC:7267243 / 2038-7097 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7267243 / 2038-7097 JSON TXT