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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T4","span":{"begin":1663,"end":1669},"obj":"http://purl.obolibrary.org/obo/GO_0040007"},{"id":"T5","span":{"begin":2619,"end":2629},"obj":"http://purl.obolibrary.org/obo/GO_0036074"},{"id":"T6","span":{"begin":3358,"end":3368},"obj":"http://purl.obolibrary.org/obo/GO_0000917"},{"id":"T7","span":{"begin":3560,"end":3570},"obj":"http://purl.obolibrary.org/obo/GO_0036074"}],"text":"CASE REPORT\nA 71-year-old male patient with prior history of hypertension, type II diabetes mellitus, and chronic kidney disease was admitted to the Hospital e Pronto-Socorro Delphina Rinaldi Abdel Aziz, a referral unit for the treatment of patients with COVID-19 in Manaus. The patient was transferred from another hospital, where he had already been diagnosed with COVID-19 by RT-qPCR. Upon admission into the ICU, he was placed under orotracheal intubation, received high-dose vasoactive drugs, was hemodynamically unstable, and presented cyanosis and cold extremities. He was administered high-flow norepinephrine (1.41 µg/kg/min) and placed on invasive mechanical ventilation under aspiration of an orotracheal tube with high parameters (positive end-expiratory pressure [PEEP] 8/FiO2 60%/respiratory rate 26; volume 360). The PaO2/FiO2 ratio was 86.6. The patient received oseltamivir (75 mg twice daily) and chloroquine (450 mg twice on the first day) via a nasoenteral tube, IV azithromycin (500 mg/day), IV ceftriaxone (2g/day), IV furosemide (20mg TID), and prophylactic subcutaneous enoxaparin (40 mg/day). No corticosteroid drugs were used.\nLaboratory parameters showed increased urea (360.7 mg/dL), creatinine (8.46 mg/dL), and C-reactive protein (12 mg/L). Normal values were seen for potassium and sodium (5.24 mmol/L; and 136.8 mmol/L, respectively). Leukocytes 6,530/µL, platelets 285x109/µL, hemoglobin 11.2 g/dL, hematocrit 34.5%, neutrophilia (84%), and lymphopenia (12,8%) were also observed. Chest x-rays showed infiltrate and nodular consolidation in the right lower lobe. No CT scan was performed. Blood culture was negative for bacterial growth.\nOn day three, following admission, the patient progressed with hemodynamic worsening and refractory shock, with irreversible hypotension and bradycardia. He died the following day. The autopsy was authorized by legal representatives (an informed consent form was signed), as the patient was enrolled prior to death in the CloroCovid-19 Study (ClinicalTrials.gov Identifier: NCT04323527, approved by the Brazilian National Ethics Review Board CAAE 30152620.1.0000.0005). An autopsy was performed in the same hospital by trained technicians and under strict biosafety rules.\nMacroscopically, the lung showed focal areas of consolidation in the right lower lobe. Microscopic visualization of the lung showed the presence of clearly defined Aspergillus structures, including hyphae and fungal spores, and a well-defined Aspergillus head with phialides, conidia, and spores, as well as bronchopneumonia, fibrin thrombi occluding an artery, and squamous metaplasia (Figure 1). The stored peripheral blood tested positive for the GM antigen (index 4.290). Since the diagnosis was made postmortem, and aspergillosis was not considered antemortem, no sputum was collected for fungus culture and no antifungal drugs were used.\nFIGURE 1: Histopathology of the lung. A. Numerous hyphae and fungal spores shown by H\u0026E staining. Microscopic cavitation surrounded by numerous hypahes and fungal spores (40x). B. Well-defined Aspergillus head, allowing the visualization of phialides and conidia, with numerous fungal spores (PAS, 400x). C. Well-defined aspergillary structure showing conidiophore, aspergillary vesicle, phialides, and conidia, as well as several hyphae of regular diameter, some with septations and dichotomous branches (Gomori-Grocott, 400x). D. Bronchopneumonia with alveoli filled by neutrophils (H\u0026E, 400x). E. Fibrin thrombi occluding a medium-sized artery (H\u0026E, 400x) F. Squamous metaplasia in alveolar epithelial cells (H\u0026E, 400x).\nThe histopathological finding of Aspergillus spp was confirmed by nucleotide sequencing. The internal transcribed spacer 1 (ITS1) and ITS2 regions and the 5.8S ribosomal DNA (rDNA) were amplified by polymerase chain reaction using the universal primers ITS1 and ITS4, as described. 10 Sequencing was performed using the BigDye® Terminator v3.1 Cycle Sequencing (Applied Biosystems) and the above primers on an individual basis. Only the best sequences were used to perform contig assembly and conduct comparative analysis with the GenBank database using the Basic Local Alignment Search Tool. The best hit returns were Aspergillus penicillioides. The sequence was submitted to GenBank and received the accession number MT582426."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T5","span":{"begin":2694,"end":2696},"obj":"GlycoEpitope"}],"attributes":[{"id":"A5","pred":"glyco_epitope_db_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"CASE REPORT\nA 71-year-old male patient with prior history of hypertension, type II diabetes mellitus, and chronic kidney disease was admitted to the Hospital e Pronto-Socorro Delphina Rinaldi Abdel Aziz, a referral unit for the treatment of patients with COVID-19 in Manaus. The patient was transferred from another hospital, where he had already been diagnosed with COVID-19 by RT-qPCR. Upon admission into the ICU, he was placed under orotracheal intubation, received high-dose vasoactive drugs, was hemodynamically unstable, and presented cyanosis and cold extremities. He was administered high-flow norepinephrine (1.41 µg/kg/min) and placed on invasive mechanical ventilation under aspiration of an orotracheal tube with high parameters (positive end-expiratory pressure [PEEP] 8/FiO2 60%/respiratory rate 26; volume 360). The PaO2/FiO2 ratio was 86.6. The patient received oseltamivir (75 mg twice daily) and chloroquine (450 mg twice on the first day) via a nasoenteral tube, IV azithromycin (500 mg/day), IV ceftriaxone (2g/day), IV furosemide (20mg TID), and prophylactic subcutaneous enoxaparin (40 mg/day). No corticosteroid drugs were used.\nLaboratory parameters showed increased urea (360.7 mg/dL), creatinine (8.46 mg/dL), and C-reactive protein (12 mg/L). Normal values were seen for potassium and sodium (5.24 mmol/L; and 136.8 mmol/L, respectively). Leukocytes 6,530/µL, platelets 285x109/µL, hemoglobin 11.2 g/dL, hematocrit 34.5%, neutrophilia (84%), and lymphopenia (12,8%) were also observed. Chest x-rays showed infiltrate and nodular consolidation in the right lower lobe. No CT scan was performed. Blood culture was negative for bacterial growth.\nOn day three, following admission, the patient progressed with hemodynamic worsening and refractory shock, with irreversible hypotension and bradycardia. He died the following day. The autopsy was authorized by legal representatives (an informed consent form was signed), as the patient was enrolled prior to death in the CloroCovid-19 Study (ClinicalTrials.gov Identifier: NCT04323527, approved by the Brazilian National Ethics Review Board CAAE 30152620.1.0000.0005). An autopsy was performed in the same hospital by trained technicians and under strict biosafety rules.\nMacroscopically, the lung showed focal areas of consolidation in the right lower lobe. Microscopic visualization of the lung showed the presence of clearly defined Aspergillus structures, including hyphae and fungal spores, and a well-defined Aspergillus head with phialides, conidia, and spores, as well as bronchopneumonia, fibrin thrombi occluding an artery, and squamous metaplasia (Figure 1). The stored peripheral blood tested positive for the GM antigen (index 4.290). Since the diagnosis was made postmortem, and aspergillosis was not considered antemortem, no sputum was collected for fungus culture and no antifungal drugs were used.\nFIGURE 1: Histopathology of the lung. A. Numerous hyphae and fungal spores shown by H\u0026E staining. Microscopic cavitation surrounded by numerous hypahes and fungal spores (40x). B. Well-defined Aspergillus head, allowing the visualization of phialides and conidia, with numerous fungal spores (PAS, 400x). C. Well-defined aspergillary structure showing conidiophore, aspergillary vesicle, phialides, and conidia, as well as several hyphae of regular diameter, some with septations and dichotomous branches (Gomori-Grocott, 400x). D. Bronchopneumonia with alveoli filled by neutrophils (H\u0026E, 400x). E. Fibrin thrombi occluding a medium-sized artery (H\u0026E, 400x) F. Squamous metaplasia in alveolar epithelial cells (H\u0026E, 400x).\nThe histopathological finding of Aspergillus spp was confirmed by nucleotide sequencing. The internal transcribed spacer 1 (ITS1) and ITS2 regions and the 5.8S ribosomal DNA (rDNA) were amplified by polymerase chain reaction using the universal primers ITS1 and ITS4, as described. 10 Sequencing was performed using the BigDye® Terminator v3.1 Cycle Sequencing (Applied Biosystems) and the above primers on an individual basis. Only the best sequences were used to perform contig assembly and conduct comparative analysis with the GenBank database using the Basic Local Alignment Search Tool. The best hit returns were Aspergillus penicillioides. The sequence was submitted to GenBank and received the accession number MT582426."}

LitCovid-sentences

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T15","span":{"begin":61,"end":73},"obj":"Phenotype"},{"id":"T16","span":{"begin":75,"end":100},"obj":"Phenotype"},{"id":"T17","span":{"begin":106,"end":128},"obj":"Phenotype"},{"id":"T18","span":{"begin":542,"end":550},"obj":"Phenotype"},{"id":"T19","span":{"begin":687,"end":697},"obj":"Phenotype"},{"id":"T20","span":{"begin":1450,"end":1462},"obj":"Phenotype"},{"id":"T21","span":{"begin":1474,"end":1485},"obj":"Phenotype"},{"id":"T22","span":{"begin":1771,"end":1776},"obj":"Phenotype"},{"id":"T23","span":{"begin":1796,"end":1807},"obj":"Phenotype"},{"id":"T24","span":{"begin":1812,"end":1823},"obj":"Phenotype"}],"attributes":[{"id":"A15","pred":"hp_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A16","pred":"hp_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/HP_0005978"},{"id":"A17","pred":"hp_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/HP_0012622"},{"id":"A18","pred":"hp_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/HP_0000961"},{"id":"A19","pred":"hp_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/HP_0002835"},{"id":"A20","pred":"hp_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/HP_0011897"},{"id":"A21","pred":"hp_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/HP_0001888"},{"id":"A22","pred":"hp_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/HP_0031273"},{"id":"A23","pred":"hp_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/HP_0002615"},{"id":"A24","pred":"hp_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/HP_0001662"}],"text":"CASE REPORT\nA 71-year-old male patient with prior history of hypertension, type II diabetes mellitus, and chronic kidney disease was admitted to the Hospital e Pronto-Socorro Delphina Rinaldi Abdel Aziz, a referral unit for the treatment of patients with COVID-19 in Manaus. The patient was transferred from another hospital, where he had already been diagnosed with COVID-19 by RT-qPCR. Upon admission into the ICU, he was placed under orotracheal intubation, received high-dose vasoactive drugs, was hemodynamically unstable, and presented cyanosis and cold extremities. He was administered high-flow norepinephrine (1.41 µg/kg/min) and placed on invasive mechanical ventilation under aspiration of an orotracheal tube with high parameters (positive end-expiratory pressure [PEEP] 8/FiO2 60%/respiratory rate 26; volume 360). The PaO2/FiO2 ratio was 86.6. The patient received oseltamivir (75 mg twice daily) and chloroquine (450 mg twice on the first day) via a nasoenteral tube, IV azithromycin (500 mg/day), IV ceftriaxone (2g/day), IV furosemide (20mg TID), and prophylactic subcutaneous enoxaparin (40 mg/day). No corticosteroid drugs were used.\nLaboratory parameters showed increased urea (360.7 mg/dL), creatinine (8.46 mg/dL), and C-reactive protein (12 mg/L). Normal values were seen for potassium and sodium (5.24 mmol/L; and 136.8 mmol/L, respectively). Leukocytes 6,530/µL, platelets 285x109/µL, hemoglobin 11.2 g/dL, hematocrit 34.5%, neutrophilia (84%), and lymphopenia (12,8%) were also observed. Chest x-rays showed infiltrate and nodular consolidation in the right lower lobe. No CT scan was performed. Blood culture was negative for bacterial growth.\nOn day three, following admission, the patient progressed with hemodynamic worsening and refractory shock, with irreversible hypotension and bradycardia. He died the following day. The autopsy was authorized by legal representatives (an informed consent form was signed), as the patient was enrolled prior to death in the CloroCovid-19 Study (ClinicalTrials.gov Identifier: NCT04323527, approved by the Brazilian National Ethics Review Board CAAE 30152620.1.0000.0005). An autopsy was performed in the same hospital by trained technicians and under strict biosafety rules.\nMacroscopically, the lung showed focal areas of consolidation in the right lower lobe. Microscopic visualization of the lung showed the presence of clearly defined Aspergillus structures, including hyphae and fungal spores, and a well-defined Aspergillus head with phialides, conidia, and spores, as well as bronchopneumonia, fibrin thrombi occluding an artery, and squamous metaplasia (Figure 1). The stored peripheral blood tested positive for the GM antigen (index 4.290). Since the diagnosis was made postmortem, and aspergillosis was not considered antemortem, no sputum was collected for fungus culture and no antifungal drugs were used.\nFIGURE 1: Histopathology of the lung. A. Numerous hyphae and fungal spores shown by H\u0026E staining. Microscopic cavitation surrounded by numerous hypahes and fungal spores (40x). B. Well-defined Aspergillus head, allowing the visualization of phialides and conidia, with numerous fungal spores (PAS, 400x). C. Well-defined aspergillary structure showing conidiophore, aspergillary vesicle, phialides, and conidia, as well as several hyphae of regular diameter, some with septations and dichotomous branches (Gomori-Grocott, 400x). D. Bronchopneumonia with alveoli filled by neutrophils (H\u0026E, 400x). E. Fibrin thrombi occluding a medium-sized artery (H\u0026E, 400x) F. Squamous metaplasia in alveolar epithelial cells (H\u0026E, 400x).\nThe histopathological finding of Aspergillus spp was confirmed by nucleotide sequencing. The internal transcribed spacer 1 (ITS1) and ITS2 regions and the 5.8S ribosomal DNA (rDNA) were amplified by polymerase chain reaction using the universal primers ITS1 and ITS4, as described. 10 Sequencing was performed using the BigDye® Terminator v3.1 Cycle Sequencing (Applied Biosystems) and the above primers on an individual basis. Only the best sequences were used to perform contig assembly and conduct comparative analysis with the GenBank database using the Basic Local Alignment Search Tool. The best hit returns were Aspergillus penicillioides. The sequence was submitted to GenBank and received the accession number MT582426."}

2_test

{"project":"2_test","denotations":[{"id":"32638890-20392915-134289067","span":{"begin":3895,"end":3897},"obj":"20392915"}],"text":"CASE REPORT\nA 71-year-old male patient with prior history of hypertension, type II diabetes mellitus, and chronic kidney disease was admitted to the Hospital e Pronto-Socorro Delphina Rinaldi Abdel Aziz, a referral unit for the treatment of patients with COVID-19 in Manaus. The patient was transferred from another hospital, where he had already been diagnosed with COVID-19 by RT-qPCR. Upon admission into the ICU, he was placed under orotracheal intubation, received high-dose vasoactive drugs, was hemodynamically unstable, and presented cyanosis and cold extremities. He was administered high-flow norepinephrine (1.41 µg/kg/min) and placed on invasive mechanical ventilation under aspiration of an orotracheal tube with high parameters (positive end-expiratory pressure [PEEP] 8/FiO2 60%/respiratory rate 26; volume 360). The PaO2/FiO2 ratio was 86.6. The patient received oseltamivir (75 mg twice daily) and chloroquine (450 mg twice on the first day) via a nasoenteral tube, IV azithromycin (500 mg/day), IV ceftriaxone (2g/day), IV furosemide (20mg TID), and prophylactic subcutaneous enoxaparin (40 mg/day). No corticosteroid drugs were used.\nLaboratory parameters showed increased urea (360.7 mg/dL), creatinine (8.46 mg/dL), and C-reactive protein (12 mg/L). Normal values were seen for potassium and sodium (5.24 mmol/L; and 136.8 mmol/L, respectively). Leukocytes 6,530/µL, platelets 285x109/µL, hemoglobin 11.2 g/dL, hematocrit 34.5%, neutrophilia (84%), and lymphopenia (12,8%) were also observed. Chest x-rays showed infiltrate and nodular consolidation in the right lower lobe. No CT scan was performed. Blood culture was negative for bacterial growth.\nOn day three, following admission, the patient progressed with hemodynamic worsening and refractory shock, with irreversible hypotension and bradycardia. He died the following day. The autopsy was authorized by legal representatives (an informed consent form was signed), as the patient was enrolled prior to death in the CloroCovid-19 Study (ClinicalTrials.gov Identifier: NCT04323527, approved by the Brazilian National Ethics Review Board CAAE 30152620.1.0000.0005). An autopsy was performed in the same hospital by trained technicians and under strict biosafety rules.\nMacroscopically, the lung showed focal areas of consolidation in the right lower lobe. Microscopic visualization of the lung showed the presence of clearly defined Aspergillus structures, including hyphae and fungal spores, and a well-defined Aspergillus head with phialides, conidia, and spores, as well as bronchopneumonia, fibrin thrombi occluding an artery, and squamous metaplasia (Figure 1). The stored peripheral blood tested positive for the GM antigen (index 4.290). Since the diagnosis was made postmortem, and aspergillosis was not considered antemortem, no sputum was collected for fungus culture and no antifungal drugs were used.\nFIGURE 1: Histopathology of the lung. A. Numerous hyphae and fungal spores shown by H\u0026E staining. Microscopic cavitation surrounded by numerous hypahes and fungal spores (40x). B. Well-defined Aspergillus head, allowing the visualization of phialides and conidia, with numerous fungal spores (PAS, 400x). C. Well-defined aspergillary structure showing conidiophore, aspergillary vesicle, phialides, and conidia, as well as several hyphae of regular diameter, some with septations and dichotomous branches (Gomori-Grocott, 400x). D. Bronchopneumonia with alveoli filled by neutrophils (H\u0026E, 400x). E. Fibrin thrombi occluding a medium-sized artery (H\u0026E, 400x) F. Squamous metaplasia in alveolar epithelial cells (H\u0026E, 400x).\nThe histopathological finding of Aspergillus spp was confirmed by nucleotide sequencing. The internal transcribed spacer 1 (ITS1) and ITS2 regions and the 5.8S ribosomal DNA (rDNA) were amplified by polymerase chain reaction using the universal primers ITS1 and ITS4, as described. 10 Sequencing was performed using the BigDye® Terminator v3.1 Cycle Sequencing (Applied Biosystems) and the above primers on an individual basis. Only the best sequences were used to perform contig assembly and conduct comparative analysis with the GenBank database using the Basic Local Alignment Search Tool. The best hit returns were Aspergillus penicillioides. The sequence was submitted to GenBank and received the accession number MT582426."}

LitCovid-PMC-OGER-BB

PMC:7341831 / 3059-7401 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7341831 / 3059-7401 JSON TXT