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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T3","span":{"begin":506,"end":508},"obj":"Chemical"},{"id":"T4","span":{"begin":1102,"end":1106},"obj":"Chemical"},{"id":"T5","span":{"begin":4168,"end":4174},"obj":"Chemical"},{"id":"T6","span":{"begin":5271,"end":5276},"obj":"Chemical"},{"id":"T7","span":{"begin":5302,"end":5307},"obj":"Chemical"}],"attributes":[{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_27638"},{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"},{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_25805"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_24433"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_24433"}],"text":"Methods\n\nCase selection\nWe performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan. 18, 2020 and Feb. 7, 2020 in Zhuhai, China. A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1]. The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co. This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare. Patient selection for this study was consecutive, and no exclusion criteria were applied.\n\nCT image acquisition\nAll scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging). The scanning range was from the apex to lung base. All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B). Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.\n\nImage interpretation\nImage analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720). All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.). Imaging was reviewed independently and final decisions reached by consensus. For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision. No negative control cases were examined.\nFor each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted. Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].\n\nCT visual quantitative evaluation\nTwo radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information. Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”. Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4. The TSS was reached by summing the five lobe scores (range from 0 to 20) [9]. The final score of each case was decided by a third experienced thoracic radiologist (K.L.).\n\nClinical classifications\nAll cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.\n\nStatistical analysis\nStatistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.). Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed. Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values \u003c 0.4, 0.4~0.75, and \u003e 0.75 represent poor, moderate, and good repeatability, respectively. The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests. Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution. ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":297,"end":310},"obj":"http://purl.obolibrary.org/obo/GO_0003968"},{"id":"T3","span":{"begin":297,"end":310},"obj":"http://purl.obolibrary.org/obo/GO_0003899"}],"text":"Methods\n\nCase selection\nWe performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan. 18, 2020 and Feb. 7, 2020 in Zhuhai, China. A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1]. The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co. This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare. Patient selection for this study was consecutive, and no exclusion criteria were applied.\n\nCT image acquisition\nAll scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging). The scanning range was from the apex to lung base. All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B). Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.\n\nImage interpretation\nImage analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720). All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.). Imaging was reviewed independently and final decisions reached by consensus. For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision. No negative control cases were examined.\nFor each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted. Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].\n\nCT visual quantitative evaluation\nTwo radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information. Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”. Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4. The TSS was reached by summing the five lobe scores (range from 0 to 20) [9]. The final score of each case was decided by a third experienced thoracic radiologist (K.L.).\n\nClinical classifications\nAll cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.\n\nStatistical analysis\nStatistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.). Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed. Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values \u003c 0.4, 0.4~0.75, and \u003e 0.75 represent poor, moderate, and good repeatability, respectively. The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests. Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution. ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group."}

LitCovid-PD-HP

LitCovid-sentences

0_colil

{"project":"0_colil","denotations":[{"id":"32215691-18195376-53397","span":{"begin":2916,"end":2918},"obj":"18195376"}],"text":"Methods\n\nCase selection\nWe performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan. 18, 2020 and Feb. 7, 2020 in Zhuhai, China. A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1]. The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co. This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare. Patient selection for this study was consecutive, and no exclusion criteria were applied.\n\nCT image acquisition\nAll scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging). The scanning range was from the apex to lung base. All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B). Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.\n\nImage interpretation\nImage analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720). All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.). Imaging was reviewed independently and final decisions reached by consensus. For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision. No negative control cases were examined.\nFor each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted. Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].\n\nCT visual quantitative evaluation\nTwo radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information. Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”. Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4. The TSS was reached by summing the five lobe scores (range from 0 to 20) [9]. The final score of each case was decided by a third experienced thoracic radiologist (K.L.).\n\nClinical classifications\nAll cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.\n\nStatistical analysis\nStatistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.). Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed. Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values \u003c 0.4, 0.4~0.75, and \u003e 0.75 represent poor, moderate, and good repeatability, respectively. The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests. Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution. ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group."}

TEST0

{"project":"TEST0","denotations":[{"id":"32215691-230-236-53397","span":{"begin":2916,"end":2918},"obj":"[\"18195376\"]"}],"text":"Methods\n\nCase selection\nWe performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan. 18, 2020 and Feb. 7, 2020 in Zhuhai, China. A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1]. The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co. This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare. Patient selection for this study was consecutive, and no exclusion criteria were applied.\n\nCT image acquisition\nAll scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging). The scanning range was from the apex to lung base. All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B). Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.\n\nImage interpretation\nImage analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720). All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.). Imaging was reviewed independently and final decisions reached by consensus. For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision. No negative control cases were examined.\nFor each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted. Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].\n\nCT visual quantitative evaluation\nTwo radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information. Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”. Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4. The TSS was reached by summing the five lobe scores (range from 0 to 20) [9]. The final score of each case was decided by a third experienced thoracic radiologist (K.L.).\n\nClinical classifications\nAll cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.\n\nStatistical analysis\nStatistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.). Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed. Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values \u003c 0.4, 0.4~0.75, and \u003e 0.75 represent poor, moderate, and good repeatability, respectively. The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests. Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution. ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group."}

2_test

{"project":"2_test","denotations":[{"id":"32215691-18195376-29361452","span":{"begin":2916,"end":2918},"obj":"18195376"}],"text":"Methods\n\nCase selection\nWe performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan. 18, 2020 and Feb. 7, 2020 in Zhuhai, China. A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1]. The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co. This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare. Patient selection for this study was consecutive, and no exclusion criteria were applied.\n\nCT image acquisition\nAll scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging). The scanning range was from the apex to lung base. All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B). Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.\n\nImage interpretation\nImage analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720). All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.). Imaging was reviewed independently and final decisions reached by consensus. For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision. No negative control cases were examined.\nFor each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted. Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].\n\nCT visual quantitative evaluation\nTwo radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information. Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”. Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4. The TSS was reached by summing the five lobe scores (range from 0 to 20) [9]. The final score of each case was decided by a third experienced thoracic radiologist (K.L.).\n\nClinical classifications\nAll cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.\n\nStatistical analysis\nStatistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.). Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed. Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values \u003c 0.4, 0.4~0.75, and \u003e 0.75 represent poor, moderate, and good repeatability, respectively. The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests. Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution. ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group."}

MyTest

{"project":"MyTest","denotations":[{"id":"32215691-18195376-29361452","span":{"begin":2916,"end":2918},"obj":"18195376"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Methods\n\nCase selection\nWe performed a retrospective, single-center study of the SARS-CoV-2 laboratory-confirmed cases with which included 78 cases between Jan. 18, 2020 and Feb. 7, 2020 in Zhuhai, China. A confirmed case was defined as positive by high-throughput sequencing or real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) assay of nasal and pharyngeal swab specimens [1]. The rRT-PCR test kits used on the patients in this study was manufactured by Shanghai Zhijiang Biotechnology Co. This study was approved by the ethics committee of the Fifth Affiliated Hospital of Sun Yat-sen University and the requirement for informed consent was waived since the study had no risk and would not adversely affect the subjects’ rights or welfare. Patient selection for this study was consecutive, and no exclusion criteria were applied.\n\nCT image acquisition\nAll scans were performed with the patient in the supine position during end-inspiration without intravenous contrast on two CT scanners, uCT 760 and uMI 780 scanners (United Imaging). The scanning range was from the apex to lung base. All images were obtained with a standard dose scanning protocol, reconstructed at 1.0 mm slice thickness, with 1 mm increment, 512 mm × 512 mm, and a sharp reconstruction kernel (B_VSHARP_B). Lung window setting was with a window level of − 600 Hounsfield units (HU) and window width of 1500 HU.\n\nImage interpretation\nImage analysis was performed using the institutional digital database system (Neusoft V5.5.4.50720). All CT images were reviewed by two radiologists with 5 and 3 years of experience in imaging (Y.F. and W.L.). Imaging was reviewed independently and final decisions reached by consensus. For disagreement between the two primary radiologist interpretations, a third experienced thoracic radiologist with 17 years of experience (K.L.) adjudicated a final decision. No negative control cases were examined.\nFor each of the 78 patients, the CT scan was evaluated for the following characteristics: (1) distribution: presence of peripheral or peribronchovascular; (2) density: presence of ground-glass opacities, mixed ground-glass opacities, or consolidation; (3) internal structures: presence of air bronchogram, interlobular septal thickening, cavitation; (4) number of lobes affected by ground-glass or consolidative opacities; (5) presence of fibrotic lesions; (6) presence of centrilobular nodules; (7) presence of a pleural effusion; (8) presence of thoracic lymphadenopathy (defined as lymph node size of ≥ 10 mm in short-axis dimension); and (9) presence of underlying lung disease such as tuberculosis, emphysema, or interstitial lung disease were noted. Ground-glass opacification was defined as hazy increased lung attenuation with preservation of bronchial and vascular margins and consolidation was defined as opacification with obscuration of margins of vessels and airway walls [14].\n\nCT visual quantitative evaluation\nTwo radiologists (Y.F. and W.L.) reviewed all images independently blinded to the clinical information. Percentage of involvement in each lobe was recorded as well as the overall lung “total severity score (TSS)”. Each of the five lung lobes was assessed for percentage of the lobar involvement and classified as none (0%), minimal (1–25%), mild (26–50%), moderate (51–75%), or severe (76–100%), with corresponded score as 0, 1, 2, 3, or 4. The TSS was reached by summing the five lobe scores (range from 0 to 20) [9]. The final score of each case was decided by a third experienced thoracic radiologist (K.L.).\n\nClinical classifications\nAll cases were divided into four groups: minimal, common, severe, and critical according to whether there were clinical symptoms, severity of pneumonia, respiratory failure, shock, other organ failure, etc., based on the Diagnosis and Treatment Plan of COVID-19 issued by National Health Commission (7th ed.) (in Chinese) [15]. (1) Mild type: mild clinical symptoms without pneumonia in imaging; (2) common type: fever, respiratory tract and other symptoms with pneumonia in imaging; (3) severe type: respiratory distress, respiratory rate ≥ 30 times/min; in resting state, oxygen saturation ≤ 93%; PaO2/FiO2 ≤ 300MMHG; (4) critical type: respiratory failure requiring mechanical ventilation, shock and other organ failure requiring ICU monitoring and treatment.\n\nStatistical analysis\nStatistical analysis was performed using IBM SPSS Statistics for Windows, Version 25.0 (IBM Corp.). Continuous data conforming to normal distribution expressed by mean ± standard deviation; for those not conformed (median, P25, p75) were listed. Intragroup correlation coefficient (ICC) was used to test the consistency of TSS scores of two observers, ICC values \u003c 0.4, 0.4~0.75, and \u003e 0.75 represent poor, moderate, and good repeatability, respectively. The distribution balance of involved lobes and the number of involved lobes in different clinical types were compared by chi-squared test or Fisher exact test when sample sizes were small and by analysis of variance tests. Wilcoxon-rank test was used for comparison of TSS among different clinical types, since TSS did not conform to the normal distribution. ROC was used to test the differential diagnosis ability of TSS in common-type group and severe-critical-type group."}

LitCovid-PubTator

PMC:7095246 / 4278-9586 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7095246 / 4278-9586 JSON TXT