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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T9","span":{"begin":2410,"end":2413},"obj":"Body_part"},{"id":"T10","span":{"begin":2617,"end":2623},"obj":"Body_part"},{"id":"T11","span":{"begin":2637,"end":2640},"obj":"Body_part"},{"id":"T12","span":{"begin":2651,"end":2654},"obj":"Body_part"},{"id":"T13","span":{"begin":2753,"end":2757},"obj":"Body_part"}],"attributes":[{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma67095"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma74402"}],"text":"Methods\n\nStudy setting\nThis study was conducted in Wuhan No. 7 Hospital, which was originally a comprehensive Grade 2A hospital and then became one of the first batch designated hospitals for COVID-19 in Hubei Province. The hospital started to treat patients with COVID-19 on January 22, 2020. It comprises general isolation wards, intensive care unit (ICU), fever clinic, clinical laboratory, office areas, and restrooms (Fig 1 ). All regions of the hospital were divided into 2 categories: (1) moderate- and high-risk regions, including the medical areas such as patient room, nurses’ station, buffer room for taking off personal protective equipment (PPE), and fever clinic, and (2) low-risk regions, including the living quarters such as the restrooms, office areas, and buffer room for taking on PPE.\nFig 1 Room layout of the general isolation ward 1 and the living quarters showing environmental and air sampling sites. Numbered labels correspond to environmental sampling sites. ① beepers; ② bed rails; ③ desktops;④ bedside tables;⑤ oxygen cylinder valve;⑥ medical equipment such as ventilator, monitors, and X-ray devices, etc;⑦ door handles;⑧ elevator buttons;⑨ keyboards;⑩ computer mouses;⑪ telephones; ⑫ water machine buttons; A refers to air samples. The medical area with moderate and high risk contains patient's room, nurses station, buffer room for taking off PPE, and elevator; the living quarters with low risk contains the rest rooms, office area, and buffer room for taking on PPE.\n\nSample collection\nFlocked swabs, premoistened with viral transport medium, were collected from environmental surfaces that were frequently touched by patients or healthcare workers. The surfaces included beeper, keyboard, computer mouse, telephone, door handle, desktop, medical equipment, bedrail, bedside table, oxygen cylinder valve, elevator button, and others such as refrigerator, IV port, and sample transfer box. Air samples from medical areas were collected through natural precipitation according to the Hygienic Standard for Disinfection in Hospitals.9 All samples were collected under emergency conditions around 8:00 AM before routine cleaning and disinfection and were delivered to the clinical laboratory immediately after collection.\n\nReverse transcription PCR and sequencing\nThe suspension was used for real-time reverse transcription polymerase chain reaction (RT-PCR) assay of SARS-CoV-2 RNA. The real-time RT-PCR assay was performed using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai ZJ Bio-Tech Co., Ltd.). Two different targets on the SARS-CoV-2 genome, namely, the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes, were employed, and a third target, the envelope (E) gene, was used for real-time quantitative PCR.10 A sample was considered positive when the qPCR Ct value was ≤43.\n\nStatistical analysis\nStatistical analyses were performed using SPSS version 20.0 software (SPSS Inc.). The differences in the positive rates between the medical areas and the living quarters and the general isolation ward and ICU were compared by the χ2 test; the Fisher exact test was used when data were limited. A 2-sided α of less than 0.05 was considered to indicate statistical significance."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T5","span":{"begin":1056,"end":1061},"obj":"Body_part"},{"id":"T6","span":{"begin":1833,"end":1838},"obj":"Body_part"}],"attributes":[{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0003978"},{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0003978"}],"text":"Methods\n\nStudy setting\nThis study was conducted in Wuhan No. 7 Hospital, which was originally a comprehensive Grade 2A hospital and then became one of the first batch designated hospitals for COVID-19 in Hubei Province. The hospital started to treat patients with COVID-19 on January 22, 2020. It comprises general isolation wards, intensive care unit (ICU), fever clinic, clinical laboratory, office areas, and restrooms (Fig 1 ). All regions of the hospital were divided into 2 categories: (1) moderate- and high-risk regions, including the medical areas such as patient room, nurses’ station, buffer room for taking off personal protective equipment (PPE), and fever clinic, and (2) low-risk regions, including the living quarters such as the restrooms, office areas, and buffer room for taking on PPE.\nFig 1 Room layout of the general isolation ward 1 and the living quarters showing environmental and air sampling sites. Numbered labels correspond to environmental sampling sites. ① beepers; ② bed rails; ③ desktops;④ bedside tables;⑤ oxygen cylinder valve;⑥ medical equipment such as ventilator, monitors, and X-ray devices, etc;⑦ door handles;⑧ elevator buttons;⑨ keyboards;⑩ computer mouses;⑪ telephones; ⑫ water machine buttons; A refers to air samples. The medical area with moderate and high risk contains patient's room, nurses station, buffer room for taking off PPE, and elevator; the living quarters with low risk contains the rest rooms, office area, and buffer room for taking on PPE.\n\nSample collection\nFlocked swabs, premoistened with viral transport medium, were collected from environmental surfaces that were frequently touched by patients or healthcare workers. The surfaces included beeper, keyboard, computer mouse, telephone, door handle, desktop, medical equipment, bedrail, bedside table, oxygen cylinder valve, elevator button, and others such as refrigerator, IV port, and sample transfer box. Air samples from medical areas were collected through natural precipitation according to the Hygienic Standard for Disinfection in Hospitals.9 All samples were collected under emergency conditions around 8:00 AM before routine cleaning and disinfection and were delivered to the clinical laboratory immediately after collection.\n\nReverse transcription PCR and sequencing\nThe suspension was used for real-time reverse transcription polymerase chain reaction (RT-PCR) assay of SARS-CoV-2 RNA. The real-time RT-PCR assay was performed using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai ZJ Bio-Tech Co., Ltd.). Two different targets on the SARS-CoV-2 genome, namely, the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes, were employed, and a third target, the envelope (E) gene, was used for real-time quantitative PCR.10 A sample was considered positive when the qPCR Ct value was ≤43.\n\nStatistical analysis\nStatistical analyses were performed using SPSS version 20.0 software (SPSS Inc.). The differences in the positive rates between the medical areas and the living quarters and the general isolation ward and ICU were compared by the χ2 test; the Fisher exact test was used when data were limited. A 2-sided α of less than 0.05 was considered to indicate statistical significance."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T31","span":{"begin":192,"end":200},"obj":"Disease"},{"id":"T32","span":{"begin":264,"end":272},"obj":"Disease"},{"id":"T33","span":{"begin":2133,"end":2135},"obj":"Disease"},{"id":"T34","span":{"begin":2399,"end":2407},"obj":"Disease"},{"id":"T35","span":{"begin":2464,"end":2472},"obj":"Disease"},{"id":"T36","span":{"begin":2606,"end":2614},"obj":"Disease"}],"attributes":[{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0020320"},{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A35","pred":"mondo_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Methods\n\nStudy setting\nThis study was conducted in Wuhan No. 7 Hospital, which was originally a comprehensive Grade 2A hospital and then became one of the first batch designated hospitals for COVID-19 in Hubei Province. The hospital started to treat patients with COVID-19 on January 22, 2020. It comprises general isolation wards, intensive care unit (ICU), fever clinic, clinical laboratory, office areas, and restrooms (Fig 1 ). All regions of the hospital were divided into 2 categories: (1) moderate- and high-risk regions, including the medical areas such as patient room, nurses’ station, buffer room for taking off personal protective equipment (PPE), and fever clinic, and (2) low-risk regions, including the living quarters such as the restrooms, office areas, and buffer room for taking on PPE.\nFig 1 Room layout of the general isolation ward 1 and the living quarters showing environmental and air sampling sites. Numbered labels correspond to environmental sampling sites. ① beepers; ② bed rails; ③ desktops;④ bedside tables;⑤ oxygen cylinder valve;⑥ medical equipment such as ventilator, monitors, and X-ray devices, etc;⑦ door handles;⑧ elevator buttons;⑨ keyboards;⑩ computer mouses;⑪ telephones; ⑫ water machine buttons; A refers to air samples. The medical area with moderate and high risk contains patient's room, nurses station, buffer room for taking off PPE, and elevator; the living quarters with low risk contains the rest rooms, office area, and buffer room for taking on PPE.\n\nSample collection\nFlocked swabs, premoistened with viral transport medium, were collected from environmental surfaces that were frequently touched by patients or healthcare workers. The surfaces included beeper, keyboard, computer mouse, telephone, door handle, desktop, medical equipment, bedrail, bedside table, oxygen cylinder valve, elevator button, and others such as refrigerator, IV port, and sample transfer box. Air samples from medical areas were collected through natural precipitation according to the Hygienic Standard for Disinfection in Hospitals.9 All samples were collected under emergency conditions around 8:00 AM before routine cleaning and disinfection and were delivered to the clinical laboratory immediately after collection.\n\nReverse transcription PCR and sequencing\nThe suspension was used for real-time reverse transcription polymerase chain reaction (RT-PCR) assay of SARS-CoV-2 RNA. The real-time RT-PCR assay was performed using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai ZJ Bio-Tech Co., Ltd.). Two different targets on the SARS-CoV-2 genome, namely, the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes, were employed, and a third target, the envelope (E) gene, was used for real-time quantitative PCR.10 A sample was considered positive when the qPCR Ct value was ≤43.\n\nStatistical analysis\nStatistical analyses were performed using SPSS version 20.0 software (SPSS Inc.). The differences in the positive rates between the medical areas and the living quarters and the general isolation ward and ICU were compared by the χ2 test; the Fisher exact test was used when data were limited. A 2-sided α of less than 0.05 was considered to indicate statistical significance."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":1554,"end":1569},"obj":"http://purl.obolibrary.org/obo/GO_0046794"},{"id":"T4","span":{"begin":1560,"end":1569},"obj":"http://purl.obolibrary.org/obo/GO_0006810"},{"id":"T5","span":{"begin":2254,"end":2275},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T6","span":{"begin":2262,"end":2275},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T7","span":{"begin":2333,"end":2354},"obj":"http://purl.obolibrary.org/obo/GO_0001171"},{"id":"T8","span":{"begin":2341,"end":2354},"obj":"http://purl.obolibrary.org/obo/GO_0006351"}],"text":"Methods\n\nStudy setting\nThis study was conducted in Wuhan No. 7 Hospital, which was originally a comprehensive Grade 2A hospital and then became one of the first batch designated hospitals for COVID-19 in Hubei Province. The hospital started to treat patients with COVID-19 on January 22, 2020. It comprises general isolation wards, intensive care unit (ICU), fever clinic, clinical laboratory, office areas, and restrooms (Fig 1 ). All regions of the hospital were divided into 2 categories: (1) moderate- and high-risk regions, including the medical areas such as patient room, nurses’ station, buffer room for taking off personal protective equipment (PPE), and fever clinic, and (2) low-risk regions, including the living quarters such as the restrooms, office areas, and buffer room for taking on PPE.\nFig 1 Room layout of the general isolation ward 1 and the living quarters showing environmental and air sampling sites. Numbered labels correspond to environmental sampling sites. ① beepers; ② bed rails; ③ desktops;④ bedside tables;⑤ oxygen cylinder valve;⑥ medical equipment such as ventilator, monitors, and X-ray devices, etc;⑦ door handles;⑧ elevator buttons;⑨ keyboards;⑩ computer mouses;⑪ telephones; ⑫ water machine buttons; A refers to air samples. The medical area with moderate and high risk contains patient's room, nurses station, buffer room for taking off PPE, and elevator; the living quarters with low risk contains the rest rooms, office area, and buffer room for taking on PPE.\n\nSample collection\nFlocked swabs, premoistened with viral transport medium, were collected from environmental surfaces that were frequently touched by patients or healthcare workers. The surfaces included beeper, keyboard, computer mouse, telephone, door handle, desktop, medical equipment, bedrail, bedside table, oxygen cylinder valve, elevator button, and others such as refrigerator, IV port, and sample transfer box. Air samples from medical areas were collected through natural precipitation according to the Hygienic Standard for Disinfection in Hospitals.9 All samples were collected under emergency conditions around 8:00 AM before routine cleaning and disinfection and were delivered to the clinical laboratory immediately after collection.\n\nReverse transcription PCR and sequencing\nThe suspension was used for real-time reverse transcription polymerase chain reaction (RT-PCR) assay of SARS-CoV-2 RNA. The real-time RT-PCR assay was performed using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai ZJ Bio-Tech Co., Ltd.). Two different targets on the SARS-CoV-2 genome, namely, the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes, were employed, and a third target, the envelope (E) gene, was used for real-time quantitative PCR.10 A sample was considered positive when the qPCR Ct value was ≤43.\n\nStatistical analysis\nStatistical analyses were performed using SPSS version 20.0 software (SPSS Inc.). The differences in the positive rates between the medical areas and the living quarters and the general isolation ward and ICU were compared by the χ2 test; the Fisher exact test was used when data were limited. A 2-sided α of less than 0.05 was considered to indicate statistical significance."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T31","span":{"begin":0,"end":7},"obj":"Sentence"},{"id":"T32","span":{"begin":9,"end":22},"obj":"Sentence"},{"id":"T33","span":{"begin":23,"end":60},"obj":"Sentence"},{"id":"T34","span":{"begin":61,"end":219},"obj":"Sentence"},{"id":"T35","span":{"begin":220,"end":293},"obj":"Sentence"},{"id":"T36","span":{"begin":294,"end":431},"obj":"Sentence"},{"id":"T37","span":{"begin":432,"end":805},"obj":"Sentence"},{"id":"T38","span":{"begin":806,"end":925},"obj":"Sentence"},{"id":"T39","span":{"begin":926,"end":1262},"obj":"Sentence"},{"id":"T40","span":{"begin":1263,"end":1501},"obj":"Sentence"},{"id":"T41","span":{"begin":1503,"end":1520},"obj":"Sentence"},{"id":"T42","span":{"begin":1521,"end":1684},"obj":"Sentence"},{"id":"T43","span":{"begin":1685,"end":1923},"obj":"Sentence"},{"id":"T44","span":{"begin":1924,"end":2252},"obj":"Sentence"},{"id":"T45","span":{"begin":2254,"end":2294},"obj":"Sentence"},{"id":"T46","span":{"begin":2295,"end":2414},"obj":"Sentence"},{"id":"T47","span":{"begin":2415,"end":2576},"obj":"Sentence"},{"id":"T48","span":{"begin":2577,"end":2866},"obj":"Sentence"},{"id":"T49","span":{"begin":2868,"end":2888},"obj":"Sentence"},{"id":"T50","span":{"begin":2889,"end":2970},"obj":"Sentence"},{"id":"T51","span":{"begin":2971,"end":3182},"obj":"Sentence"},{"id":"T52","span":{"begin":3183,"end":3265},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Methods\n\nStudy setting\nThis study was conducted in Wuhan No. 7 Hospital, which was originally a comprehensive Grade 2A hospital and then became one of the first batch designated hospitals for COVID-19 in Hubei Province. The hospital started to treat patients with COVID-19 on January 22, 2020. It comprises general isolation wards, intensive care unit (ICU), fever clinic, clinical laboratory, office areas, and restrooms (Fig 1 ). All regions of the hospital were divided into 2 categories: (1) moderate- and high-risk regions, including the medical areas such as patient room, nurses’ station, buffer room for taking off personal protective equipment (PPE), and fever clinic, and (2) low-risk regions, including the living quarters such as the restrooms, office areas, and buffer room for taking on PPE.\nFig 1 Room layout of the general isolation ward 1 and the living quarters showing environmental and air sampling sites. Numbered labels correspond to environmental sampling sites. ① beepers; ② bed rails; ③ desktops;④ bedside tables;⑤ oxygen cylinder valve;⑥ medical equipment such as ventilator, monitors, and X-ray devices, etc;⑦ door handles;⑧ elevator buttons;⑨ keyboards;⑩ computer mouses;⑪ telephones; ⑫ water machine buttons; A refers to air samples. The medical area with moderate and high risk contains patient's room, nurses station, buffer room for taking off PPE, and elevator; the living quarters with low risk contains the rest rooms, office area, and buffer room for taking on PPE.\n\nSample collection\nFlocked swabs, premoistened with viral transport medium, were collected from environmental surfaces that were frequently touched by patients or healthcare workers. The surfaces included beeper, keyboard, computer mouse, telephone, door handle, desktop, medical equipment, bedrail, bedside table, oxygen cylinder valve, elevator button, and others such as refrigerator, IV port, and sample transfer box. Air samples from medical areas were collected through natural precipitation according to the Hygienic Standard for Disinfection in Hospitals.9 All samples were collected under emergency conditions around 8:00 AM before routine cleaning and disinfection and were delivered to the clinical laboratory immediately after collection.\n\nReverse transcription PCR and sequencing\nThe suspension was used for real-time reverse transcription polymerase chain reaction (RT-PCR) assay of SARS-CoV-2 RNA. The real-time RT-PCR assay was performed using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai ZJ Bio-Tech Co., Ltd.). Two different targets on the SARS-CoV-2 genome, namely, the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes, were employed, and a third target, the envelope (E) gene, was used for real-time quantitative PCR.10 A sample was considered positive when the qPCR Ct value was ≤43.\n\nStatistical analysis\nStatistical analyses were performed using SPSS version 20.0 software (SPSS Inc.). The differences in the positive rates between the medical areas and the living quarters and the general isolation ward and ICU were compared by the χ2 test; the Fisher exact test was used when data were limited. A 2-sided α of less than 0.05 was considered to indicate statistical significance."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":359,"end":364},"obj":"Phenotype"},{"id":"T2","span":{"begin":664,"end":669},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0001945"}],"text":"Methods\n\nStudy setting\nThis study was conducted in Wuhan No. 7 Hospital, which was originally a comprehensive Grade 2A hospital and then became one of the first batch designated hospitals for COVID-19 in Hubei Province. The hospital started to treat patients with COVID-19 on January 22, 2020. It comprises general isolation wards, intensive care unit (ICU), fever clinic, clinical laboratory, office areas, and restrooms (Fig 1 ). All regions of the hospital were divided into 2 categories: (1) moderate- and high-risk regions, including the medical areas such as patient room, nurses’ station, buffer room for taking off personal protective equipment (PPE), and fever clinic, and (2) low-risk regions, including the living quarters such as the restrooms, office areas, and buffer room for taking on PPE.\nFig 1 Room layout of the general isolation ward 1 and the living quarters showing environmental and air sampling sites. Numbered labels correspond to environmental sampling sites. ① beepers; ② bed rails; ③ desktops;④ bedside tables;⑤ oxygen cylinder valve;⑥ medical equipment such as ventilator, monitors, and X-ray devices, etc;⑦ door handles;⑧ elevator buttons;⑨ keyboards;⑩ computer mouses;⑪ telephones; ⑫ water machine buttons; A refers to air samples. The medical area with moderate and high risk contains patient's room, nurses station, buffer room for taking off PPE, and elevator; the living quarters with low risk contains the rest rooms, office area, and buffer room for taking on PPE.\n\nSample collection\nFlocked swabs, premoistened with viral transport medium, were collected from environmental surfaces that were frequently touched by patients or healthcare workers. The surfaces included beeper, keyboard, computer mouse, telephone, door handle, desktop, medical equipment, bedrail, bedside table, oxygen cylinder valve, elevator button, and others such as refrigerator, IV port, and sample transfer box. Air samples from medical areas were collected through natural precipitation according to the Hygienic Standard for Disinfection in Hospitals.9 All samples were collected under emergency conditions around 8:00 AM before routine cleaning and disinfection and were delivered to the clinical laboratory immediately after collection.\n\nReverse transcription PCR and sequencing\nThe suspension was used for real-time reverse transcription polymerase chain reaction (RT-PCR) assay of SARS-CoV-2 RNA. The real-time RT-PCR assay was performed using a SARS-CoV-2 nucleic acid detection kit according to the manufacturer's protocol (Shanghai ZJ Bio-Tech Co., Ltd.). Two different targets on the SARS-CoV-2 genome, namely, the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes, were employed, and a third target, the envelope (E) gene, was used for real-time quantitative PCR.10 A sample was considered positive when the qPCR Ct value was ≤43.\n\nStatistical analysis\nStatistical analyses were performed using SPSS version 20.0 software (SPSS Inc.). The differences in the positive rates between the medical areas and the living quarters and the general isolation ward and ICU were compared by the χ2 test; the Fisher exact test was used when data were limited. A 2-sided α of less than 0.05 was considered to indicate statistical significance."}

PMC:7214329 / 4047-7312 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7214329 / 4047-7312 JSON TXT