PMC:7796041 / 6528-10186 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"173","span":{"begin":29,"end":36},"obj":"Species"},{"id":"183","span":{"begin":1563,"end":1570},"obj":"Species"},{"id":"184","span":{"begin":1776,"end":1784},"obj":"Species"},{"id":"185","span":{"begin":664,"end":682},"obj":"Chemical"},{"id":"186","span":{"begin":710,"end":728},"obj":"Chemical"},{"id":"187","span":{"begin":733,"end":745},"obj":"Chemical"},{"id":"188","span":{"begin":590,"end":600},"obj":"Disease"},{"id":"189","span":{"begin":626,"end":638},"obj":"Disease"},{"id":"190","span":{"begin":640,"end":662},"obj":"Disease"},{"id":"191","span":{"begin":1831,"end":1841},"obj":"Disease"},{"id":"194","span":{"begin":1925,"end":1933},"obj":"Species"},{"id":"195","span":{"begin":2002,"end":2020},"obj":"Disease"},{"id":"197","span":{"begin":2269,"end":2279},"obj":"Disease"},{"id":"202","span":{"begin":2769,"end":2777},"obj":"Species"},{"id":"203","span":{"begin":2583,"end":2593},"obj":"Disease"},{"id":"204","span":{"begin":2856,"end":2878},"obj":"Disease"},{"id":"205","span":{"begin":2947,"end":2955},"obj":"Disease"},{"id":"215","span":{"begin":3105,"end":3113},"obj":"Species"},{"id":"216","span":{"begin":3134,"end":3142},"obj":"Species"},{"id":"217","span":{"begin":3278,"end":3286},"obj":"Species"},{"id":"218","span":{"begin":3036,"end":3055},"obj":"Disease"},{"id":"219","span":{"begin":3057,"end":3059},"obj":"Disease"},{"id":"220","span":{"begin":3128,"end":3130},"obj":"Disease"},{"id":"221","span":{"begin":3172,"end":3174},"obj":"Disease"},{"id":"222","span":{"begin":3189,"end":3191},"obj":"Disease"},{"id":"223","span":{"begin":3301,"end":3303},"obj":"Disease"}],"attributes":[{"id":"A173","pred":"tao:has_database_id","subj":"173","obj":"Tax:9606"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"Tax:9606"},{"id":"A184","pred":"tao:has_database_id","subj":"184","obj":"Tax:9606"},{"id":"A185","pred":"tao:has_database_id","subj":"185","obj":"MESH:D006886"},{"id":"A186","pred":"tao:has_database_id","subj":"186","obj":"MESH:D006886"},{"id":"A187","pred":"tao:has_database_id","subj":"187","obj":"MESH:D017963"},{"id":"A188","pred":"tao:has_database_id","subj":"188","obj":"MESH:D001145"},{"id":"A189","pred":"tao:has_database_id","subj":"189","obj":"MESH:D006973"},{"id":"A190","pred":"tao:has_database_id","subj":"190","obj":"MESH:D002318"},{"id":"A191","pred":"tao:has_database_id","subj":"191","obj":"MESH:D001145"},{"id":"A194","pred":"tao:has_database_id","subj":"194","obj":"Tax:9606"},{"id":"A195","pred":"tao:has_database_id","subj":"195","obj":"MESH:D001145"},{"id":"A197","pred":"tao:has_database_id","subj":"197","obj":"MESH:D001145"},{"id":"A202","pred":"tao:has_database_id","subj":"202","obj":"Tax:9606"},{"id":"A203","pred":"tao:has_database_id","subj":"203","obj":"MESH:D001145"},{"id":"A204","pred":"tao:has_database_id","subj":"204","obj":"MESH:D002318"},{"id":"A205","pred":"tao:has_database_id","subj":"205","obj":"MESH:C000657245"},{"id":"A215","pred":"tao:has_database_id","subj":"215","obj":"Tax:9606"},{"id":"A216","pred":"tao:has_database_id","subj":"216","obj":"Tax:9606"},{"id":"A217","pred":"tao:has_database_id","subj":"217","obj":"Tax:9606"},{"id":"A218","pred":"tao:has_database_id","subj":"218","obj":"MESH:D001281"},{"id":"A219","pred":"tao:has_database_id","subj":"219","obj":"MESH:D001281"},{"id":"A220","pred":"tao:has_database_id","subj":"220","obj":"MESH:D001281"},{"id":"A221","pred":"tao:has_database_id","subj":"221","obj":"MESH:D001281"},{"id":"A222","pred":"tao:has_database_id","subj":"222","obj":"MESH:D001281"},{"id":"A223","pred":"tao:has_database_id","subj":"223","obj":"MESH:D001281"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.3. Statistical Methods\nThe patient cohort was described using summary measures of the empirical distribution. Continuous variables are reported as median (with inter-quartile range, 25th percentile = P25; 75th percentile = P75) or mean ± standard deviation (SD). The t-test or Mann-Whitney-Wilcoxon-test were applied for between-group comparisons. Dichotomous variables are presented as absolute and relative frequencies and were compared applying the Fisher Boschloo-test from the R package “Exact” [11].\nFor the purpose of selecting variables with predictive impact on the incidence of arrhythmia, the variables sex, age, hypertension, cardiovascular disease, hydroxychloroquine, and combined therapy with hydroxychloroquine and azithromycin were initially considered in terms of variable selection. First, regularized logistic regression using the elastic net penalty implemented in the package “glmnet” was computed [12,13]. The hyperparameters α (elastic net mixing parameter) and β (shrinkage parameter) were tuned conducting 5-fold cross-validation (CV) and a grid search. Subsequently, multiple logistic regression modeling was conducted only incorporating the selected variables, to estimate the odds ratios (ORs) and their 95% confidence intervals (CI). The area under the curve (AUC) value was computed applying the receiver operating characteristics (ROC) curve to evaluate the model using the package “pROC” [14]. To prevent overestimation of the model’s performance measure, the AUC-value was calculated applying 5-fold CV. During 5-fold CV, each patient is part of the training set for four times and is assigned exactly once to the testing set. Hence, in each step a model is fitted based on 80% of the data whereas a probability of the remaining 20% of the patients is estimated with respect to the incidence of arrhythmia.\nInformation on left ventricular ejection fraction (LVEF) was only available in 44 patients. To account for a potential influence of LVEF on the development of cardiac arrhythmia, we performed attempts to impute the missing data (Supplementary Materials). Due to a high number of missing values, LVEF was omitted from further analyses to ensure reliability of the data.\nTo evaluate the impact of biomarkers on the incidence of arrhythmia, univariate logistic regression modeling was performed. The AUC-values und the Youden index for identifying the optimal cut-off value were computed for each biomarker, respectively [15]. Confidence intervals of the AUC-values were calculated according to DeLong [16].\nTo assess the prognostic impact of arrhythmia on clinical outcomes univariate and multiple regression modeling was performed. To preserve the validity of multiple regression modeling in the light of the limited number of patients, the models were adjusted for a maximum of two additional covariates. Age and cardiovascular disease were chosen due to their clinical significance regarding outcome in COVID-19 shown by previous studies [2,17].\nDue to the high proportion of newly diagnosed atrial fibrillation (AF), we conducted a subgroup analysis comparing patients with incident AF to patients who neither had a history of AF nor displayed AF in the course of the hospitalization. Due to the small sample size in the subgroup of patients with incident AF, only descriptive analyses were performed.\nDue to the exploratory character of this analysis, the p-values are interpreted only in a descriptive sense and no adjustment for multiple testing was applied [18]. p-values \u003c 0.05 were denoted as statistically significant. The statistical analysis was performed using R version 4.0.2. [19] and SPSS version 25."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T35","span":{"begin":590,"end":600},"obj":"Phenotype"},{"id":"T36","span":{"begin":626,"end":638},"obj":"Phenotype"},{"id":"T37","span":{"begin":640,"end":662},"obj":"Phenotype"},{"id":"T38","span":{"begin":1831,"end":1841},"obj":"Phenotype"},{"id":"T39","span":{"begin":2002,"end":2020},"obj":"Phenotype"},{"id":"T40","span":{"begin":2269,"end":2279},"obj":"Phenotype"},{"id":"T41","span":{"begin":2583,"end":2593},"obj":"Phenotype"},{"id":"T42","span":{"begin":2856,"end":2878},"obj":"Phenotype"},{"id":"T43","span":{"begin":3036,"end":3055},"obj":"Phenotype"},{"id":"T44","span":{"begin":3057,"end":3059},"obj":"Phenotype"},{"id":"T45","span":{"begin":3128,"end":3130},"obj":"Phenotype"},{"id":"T46","span":{"begin":3172,"end":3174},"obj":"Phenotype"},{"id":"T47","span":{"begin":3189,"end":3191},"obj":"Phenotype"},{"id":"T48","span":{"begin":3301,"end":3303},"obj":"Phenotype"}],"attributes":[{"id":"A35","pred":"hp_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/HP_0011675"},{"id":"A36","pred":"hp_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A37","pred":"hp_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/HP_0001626"},{"id":"A38","pred":"hp_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/HP_0011675"},{"id":"A39","pred":"hp_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/HP_0011675"},{"id":"A40","pred":"hp_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/HP_0011675"},{"id":"A41","pred":"hp_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/HP_0011675"},{"id":"A42","pred":"hp_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/HP_0001626"},{"id":"A43","pred":"hp_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/HP_0005110"},{"id":"A44","pred":"hp_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/HP_0005110"},{"id":"A45","pred":"hp_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/HP_0005110"},{"id":"A46","pred":"hp_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/HP_0005110"},{"id":"A47","pred":"hp_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/HP_0005110"},{"id":"A48","pred":"hp_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/HP_0005110"}],"text":"2.3. Statistical Methods\nThe patient cohort was described using summary measures of the empirical distribution. Continuous variables are reported as median (with inter-quartile range, 25th percentile = P25; 75th percentile = P75) or mean ± standard deviation (SD). The t-test or Mann-Whitney-Wilcoxon-test were applied for between-group comparisons. Dichotomous variables are presented as absolute and relative frequencies and were compared applying the Fisher Boschloo-test from the R package “Exact” [11].\nFor the purpose of selecting variables with predictive impact on the incidence of arrhythmia, the variables sex, age, hypertension, cardiovascular disease, hydroxychloroquine, and combined therapy with hydroxychloroquine and azithromycin were initially considered in terms of variable selection. First, regularized logistic regression using the elastic net penalty implemented in the package “glmnet” was computed [12,13]. The hyperparameters α (elastic net mixing parameter) and β (shrinkage parameter) were tuned conducting 5-fold cross-validation (CV) and a grid search. Subsequently, multiple logistic regression modeling was conducted only incorporating the selected variables, to estimate the odds ratios (ORs) and their 95% confidence intervals (CI). The area under the curve (AUC) value was computed applying the receiver operating characteristics (ROC) curve to evaluate the model using the package “pROC” [14]. To prevent overestimation of the model’s performance measure, the AUC-value was calculated applying 5-fold CV. During 5-fold CV, each patient is part of the training set for four times and is assigned exactly once to the testing set. Hence, in each step a model is fitted based on 80% of the data whereas a probability of the remaining 20% of the patients is estimated with respect to the incidence of arrhythmia.\nInformation on left ventricular ejection fraction (LVEF) was only available in 44 patients. To account for a potential influence of LVEF on the development of cardiac arrhythmia, we performed attempts to impute the missing data (Supplementary Materials). Due to a high number of missing values, LVEF was omitted from further analyses to ensure reliability of the data.\nTo evaluate the impact of biomarkers on the incidence of arrhythmia, univariate logistic regression modeling was performed. The AUC-values und the Youden index for identifying the optimal cut-off value were computed for each biomarker, respectively [15]. Confidence intervals of the AUC-values were calculated according to DeLong [16].\nTo assess the prognostic impact of arrhythmia on clinical outcomes univariate and multiple regression modeling was performed. To preserve the validity of multiple regression modeling in the light of the limited number of patients, the models were adjusted for a maximum of two additional covariates. Age and cardiovascular disease were chosen due to their clinical significance regarding outcome in COVID-19 shown by previous studies [2,17].\nDue to the high proportion of newly diagnosed atrial fibrillation (AF), we conducted a subgroup analysis comparing patients with incident AF to patients who neither had a history of AF nor displayed AF in the course of the hospitalization. Due to the small sample size in the subgroup of patients with incident AF, only descriptive analyses were performed.\nDue to the exploratory character of this analysis, the p-values are interpreted only in a descriptive sense and no adjustment for multiple testing was applied [18]. p-values \u003c 0.05 were denoted as statistically significant. The statistical analysis was performed using R version 4.0.2. [19] and SPSS version 25."}

{"project":"LitCovid-sentences","denotations":[{"id":"T60","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T61","span":{"begin":5,"end":24},"obj":"Sentence"},{"id":"T62","span":{"begin":25,"end":111},"obj":"Sentence"},{"id":"T63","span":{"begin":112,"end":264},"obj":"Sentence"},{"id":"T64","span":{"begin":265,"end":349},"obj":"Sentence"},{"id":"T65","span":{"begin":350,"end":507},"obj":"Sentence"},{"id":"T66","span":{"begin":508,"end":803},"obj":"Sentence"},{"id":"T67","span":{"begin":804,"end":930},"obj":"Sentence"},{"id":"T68","span":{"begin":931,"end":1081},"obj":"Sentence"},{"id":"T69","span":{"begin":1082,"end":1265},"obj":"Sentence"},{"id":"T70","span":{"begin":1266,"end":1428},"obj":"Sentence"},{"id":"T71","span":{"begin":1429,"end":1539},"obj":"Sentence"},{"id":"T72","span":{"begin":1540,"end":1662},"obj":"Sentence"},{"id":"T73","span":{"begin":1663,"end":1842},"obj":"Sentence"},{"id":"T74","span":{"begin":1843,"end":1934},"obj":"Sentence"},{"id":"T75","span":{"begin":1935,"end":2097},"obj":"Sentence"},{"id":"T76","span":{"begin":2098,"end":2211},"obj":"Sentence"},{"id":"T77","span":{"begin":2212,"end":2335},"obj":"Sentence"},{"id":"T78","span":{"begin":2336,"end":2466},"obj":"Sentence"},{"id":"T79","span":{"begin":2467,"end":2547},"obj":"Sentence"},{"id":"T80","span":{"begin":2548,"end":2673},"obj":"Sentence"},{"id":"T81","span":{"begin":2674,"end":2847},"obj":"Sentence"},{"id":"T82","span":{"begin":2848,"end":2989},"obj":"Sentence"},{"id":"T83","span":{"begin":2990,"end":3229},"obj":"Sentence"},{"id":"T84","span":{"begin":3230,"end":3346},"obj":"Sentence"},{"id":"T85","span":{"begin":3347,"end":3570},"obj":"Sentence"},{"id":"T86","span":{"begin":3571,"end":3658},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.3. Statistical Methods\nThe patient cohort was described using summary measures of the empirical distribution. Continuous variables are reported as median (with inter-quartile range, 25th percentile = P25; 75th percentile = P75) or mean ± standard deviation (SD). The t-test or Mann-Whitney-Wilcoxon-test were applied for between-group comparisons. Dichotomous variables are presented as absolute and relative frequencies and were compared applying the Fisher Boschloo-test from the R package “Exact” [11].\nFor the purpose of selecting variables with predictive impact on the incidence of arrhythmia, the variables sex, age, hypertension, cardiovascular disease, hydroxychloroquine, and combined therapy with hydroxychloroquine and azithromycin were initially considered in terms of variable selection. First, regularized logistic regression using the elastic net penalty implemented in the package “glmnet” was computed [12,13]. The hyperparameters α (elastic net mixing parameter) and β (shrinkage parameter) were tuned conducting 5-fold cross-validation (CV) and a grid search. Subsequently, multiple logistic regression modeling was conducted only incorporating the selected variables, to estimate the odds ratios (ORs) and their 95% confidence intervals (CI). The area under the curve (AUC) value was computed applying the receiver operating characteristics (ROC) curve to evaluate the model using the package “pROC” [14]. To prevent overestimation of the model’s performance measure, the AUC-value was calculated applying 5-fold CV. During 5-fold CV, each patient is part of the training set for four times and is assigned exactly once to the testing set. Hence, in each step a model is fitted based on 80% of the data whereas a probability of the remaining 20% of the patients is estimated with respect to the incidence of arrhythmia.\nInformation on left ventricular ejection fraction (LVEF) was only available in 44 patients. To account for a potential influence of LVEF on the development of cardiac arrhythmia, we performed attempts to impute the missing data (Supplementary Materials). Due to a high number of missing values, LVEF was omitted from further analyses to ensure reliability of the data.\nTo evaluate the impact of biomarkers on the incidence of arrhythmia, univariate logistic regression modeling was performed. The AUC-values und the Youden index for identifying the optimal cut-off value were computed for each biomarker, respectively [15]. Confidence intervals of the AUC-values were calculated according to DeLong [16].\nTo assess the prognostic impact of arrhythmia on clinical outcomes univariate and multiple regression modeling was performed. To preserve the validity of multiple regression modeling in the light of the limited number of patients, the models were adjusted for a maximum of two additional covariates. Age and cardiovascular disease were chosen due to their clinical significance regarding outcome in COVID-19 shown by previous studies [2,17].\nDue to the high proportion of newly diagnosed atrial fibrillation (AF), we conducted a subgroup analysis comparing patients with incident AF to patients who neither had a history of AF nor displayed AF in the course of the hospitalization. Due to the small sample size in the subgroup of patients with incident AF, only descriptive analyses were performed.\nDue to the exploratory character of this analysis, the p-values are interpreted only in a descriptive sense and no adjustment for multiple testing was applied [18]. p-values \u003c 0.05 were denoted as statistically significant. The statistical analysis was performed using R version 4.0.2. [19] and SPSS version 25."}