Additional file 1: of Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Table S1. Correlations between bacteria and laboratory measurements in OC-COPD. Table displays the Spearman correlations between all bacteria-laboratory measurement pairs. P values were adjusted (AdjustedP) using the Bonferroni correction. The last column (NwithGenus) is a count of the number of samples that contained the genus in that correlation-pair. (XLSX 173 kb

Additional file 3: of Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Table S2. Correlations between bacteria or fungi and cytokines in LHMP. Table displays the Spearman correlations between all bacteria/fungi-cytokine pairs. P values were adjusted (AdjustedP) using the Bonferroni correction. The last column (NwithGenus) is a count of the number of samples that contained the genus in that correlation-pair. (XLSX 161 kb

Additional file 2: of Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Figure S1. Additional OC-COPD associations between laboratory measurements and bacteria identified by LassoGLMM. Strong associations between bacteria and (a) percent neutrophils (O1), (b) partial pressure of oxygen PO2(O4) (c) SAT (O5), (d) alkaline phosphatase (O6), and (e) glucose (O10). Each horizontal grey line represents an individual. When a colored circle is located on the grey line, it is the relative abundance of that microbe for that subject. Perfect positive association between clinical variable and bacteria would form a line from the bottom-left to the top-right of the graph and would have a highly positive β coefficient in the LassoGLMM. Perfect negative association would form a line from the top-left to the bottom-right of the graph and would have a highly negative β coefficient. (PDF 287 kb

ROC curves for the selection of the optimal cut point for the Weston score that corresponds to the established cut point of 100 (panel A) and 400 (panel B) for the Agatston score.

<p>ROC curves for the selection of the optimal cut point for the Weston score that corresponds to the established cut point of 100 (panel A) and 400 (panel B) for the Agatston score.</p

Assessment of coronary artery calcium by chest CT compared with EKG-gated cardiac CT in the multicenter AIDS cohort study

<div><p>Rationale</p><p>Individuals with HIV are at increased risk for coronary artery disease (CAD). Early detection of subclinical CAD by assessment of coronary artery calcium (CAC) may help risk stratify and prevent CAD events in these individuals. However, the current standard to quantify CAC i.e. Agatston scoring requires EKG-gated cardiac CT imaging.</p><p>Objective</p><p>To determine if the assessment of CAC using non-EKG-gated chest CT and the Weston scoring system is a useful surrogate for Agatston scores in HIV-infected and HIV-uninfected individuals.</p><p>Methods and measurements</p><p>CAC was assessed by both the Weston and Agatston score in 108 men enrolled in the Multicenter AIDS Cohort Study.</p><p>Results</p><p>Participants were 55.2 (IQR 50.4; 59.9) years old and 62 (57.4%) were seropositive for HIV. Inter-observer agreement (<i>r</i>_<i>s</i> = 0.94, κ = 90.0%, <i>p</i><0.001, <i>n</i> = 21) and intra-observer agreement (<i>r</i>_<i>s</i> = 0.95, κ = 95.2%, <i>p</i><0.001, <i>n</i> = 97) for category of Weston score were excellent. Weston scores were associated with similar CAD risk factors as Agatston scores (age, race, HDL cholesterol level, all <i>p</i><0.05) in our cohort. There was excellent correlation (<i>r</i>_<i>s</i> = 0.92, <i>p</i><0.001) and agreement (κ_w = 0.77, <i>p</i><0.001) between Weston and Agatston scores.</p><p>Conclusions</p><p>This study is the first to examine calcium scoring using chest CT in HIV-infected individuals and to independently validate the Weston score as a surrogate for the Agatston score. In clinical or research settings where EKG-gated cardiac CT is not feasible for the assessment of coronary calcium, Weston scoring by using chest CT should be considered.</p></div

Correlation between Weston and Agatston scores performed on 108 individuals.

<p>Correlation between Weston and Agatston scores performed on 108 individuals.</p

Inter observer agreement for Weston coronary artery calcium score, n = 21 scans.

<p>Inter observer agreement for Weston coronary artery calcium score, n = 21 scans.</p

Additional file 1: of Genome-wide association study of lung function and clinical implication in heavy smokers

Table S1. Association Results of the Top SNPs (P < 10− 4) with Post-bronchodilator FEV1/FVC. Table S2. Association Results of the Top SNPs (P < 10− 4) with Post-bronchodilator % Predicted FEV1.Table S3. Genotype Frequency of rs28929474 in SERPINA1 Stratified by GOLD Stages. Table S4. Prediction Models for Post-bronchodilator Lung Function Using Top 10 SNPs for Post-bronchodilator % Predicted FEV1.Figure S1. Joint analysis of the top10 SNPs for post-bronchodilator % predicted FEV1 in 1075 SPIROMICS non-Hispanic White smokers with COPD. (DOCX 141 kb