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546 protocols using stata software version 14

1

Conditional Analysis of SIDT2 Variants

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To evaluate if the the two selected variants in the SIDT2 gene were independent, we performed a conditional analysis in the replication stage data employing a logistic regression model. Age, sex, family group and identified SNPs genotypes were included as covariables in the model using STATA software, version 14.0 (StataCorp LP, College Station, TX, USA). Haplotype-based association analysis of SIDT2 SNPs rs17120425 and rs1784042 was carried out using a logistic regression model adjusting for age, sex and family group in the replication phase data using Haploview [35 (link)] and STATA software, version 14.0 (StataCorp LP, College Station, TX, USA).
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2

Assessing Neurodevelopmental Outcomes in Malawi

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Data were entered using Open Data Kit and then exported into Stata Software Version 14.0 (StataCorp; College Station, TX, USA) for analysis. We entered the neurodevelopment score from the MDAT assessment into the already existing dataset in Stata Software Version 14.0 (Stata Corp; College Station, TX, USA) to make a complete dataset of exposures and the outcome.
Categorical variables such as neurodevelpmental status, sex, maternal educational status, wealth quintile, cord lactate level and others were summarized into frequencies with percentages and continuous variables such as age into means or medians with corresponding standard deviations and IQR, respectively. Poor neurodevelopment was defined as a score of less than −2 development for age Z scores on the full model from the original Malawi population that was used to validate the tool (https://kieran-bromley.shinyapps.io/mdat_scoring_shiny/ (accessed on 15 August 2022)). We conducted bivariable and multivariable analysis using a generalized linear model for the Poisson family with a log link to assess the strength of association, using risk ratios between exposures and the incidence of neurodevelopmental delay.
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3

Cognitive Reappraisal and Emotional Suppression Analysis

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The Stata software, version 14.0, was used for data processing and treatment. Prevalence, prevalence ratios (PR) and their respective confidence intervals (95% CI) were estimated, as well as absolute and relative frequencies for the categorical variables and minimum and maximum values, mean and standard deviation (SD) for the quantitative variables with normal distribution. To assess the association between the independent variables and each of the outcomes (Cognitive Reappraisal and Emotional Suppression), Pearson’s Chi-square test was employed in the bivariate analysis, selecting for inclusion those that presented p-values ≤ 0.20 in the multivariate stage. In multivariate modeling, Poisson regression with robust variation was conducted, using the backward procedure, to define the useful subset of terms. All the variables that 5% presented statistical significance remained in the final model. To determine the best final model, the one with the lowest Akaike Information Criterion (AIC) value was selected. The statistical significance level of the tests was 5% (p-value ≤ 0.05).
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4

Cluster RCT for Intervention Evaluation

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Data from the trial will be analyzed using STATA software version 14.0 (Stata Corp, College Station, Texas, USA). All data will be checked for accuracy and a missing data analysis will be undertaken. The trial will adhere to the ‘CONSORT statement: extension to cluster randomized trials’ [34 (link)]. The data will be analyzed on an intention-to-treat basis, based on patient assignment.
A mixed linear regression model will be adopted to compare the significant differences between groups over a 12-month period. The mixed linear regression model will be adjusted by baseline value and potential confounding variables, for example, the sites and staff education levels [35 (link)]. Two-sided tests will be performed for all analyses and the level of significance will be set at P < 0.05. Where appropriate, 95% confidence interval will also be reported along with the P values.
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5

Statistical Analysis Methodology for Missing Data

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All analyses were performed using Stata software version 14.0 (StataCorp LP). Two-tailed test with P < 0.05 was considered statistically significant. Predictors with more than 20% of the values missing were excluded from the primary analysis. To address the missing data, however, all other missing values were imputed with a multiple imputation technique33 (link),34 (link). For the predictors with less than 10% of missing values, the complete case was accepted and considered in the primary analysis35 (link). Nevertheless, the multiple imputation analysis was examined as a sensitivity analysis.
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6

Physiological Response Comparison in Blind and Sighted

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Data analysis was performed using the STATA software, version 14.0 (StataCorp LLC, Texas, USA). HR values during the resting, walking, and jogging periods (excluding the extreme values) were averaged and the PCI was calculated. 14 The skewed variables were logarithmically (Ln) transformed. The mean of the kinematic and physiological variables was adjusted with respect to important predictors (i.e., the weight of a participant and the test duration). The mean of the differences between the blind and sighted students was determined using the independent sample t test. Data were presented as mean±SD and P<0.05 was considered statistically significant.
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7

Sleep's Impact on Mental Health

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All variables were examined for outliers and physiologically implausible values. Continuous variables were reported as mean and standard deviation, and categorical variables were reported as percentages. Linear regression analyses, with mental health variable as outcome and sleep variable as predictor, were adjusted for age, sex, and year in school. Unstandardized regression coefficients (B) and 95% CIs were calculated. To determine whether these relationships are accounted for by stress, PSS score was entered as an additional covariate in all models for which stress was not the outcome assessed. All analyses were performed using STATA software version 14.0 (STATA Corp).
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8

PD-L1 Scoring Reproducibility in Cancer

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The inter-observer reproducibility of PD-L1 scoring was evaluated by kappa statistics. Simple and weighted kappa (κ) values were calculated, and agreement was described according to Landis et al [18 (link)] as moderate, substantial, and almost perfect for κ values of 0.41–0.60, 0.61–0.80, and 0.81–1, respectively.
The endpoint OS was defined as time from operation to death of any cause or last follow-up. RFS was defined as time from operation to death of any cause or recurrence of CC. Patients later diagnosed with another cancer were censored at the date of diagnosis (N = 102). The median age was used as cut-off to dichotomize the parameter age. Survival curves were generated according to the Kaplan-Meier method and the log-rank test was used to test for differences between groups. The multivariable Cox-regression model was used to test for independent prognostic value with hazard ratio (HR) of 1.0 as reference and a 95% confidence interval (CI). A cut-off significance level of 0.10 was pre-specified for a variable to be included in the multivariable Cox regression model.
Chi2-statistics were used to test associations between clinicopathological variables. A p-value < 0.05 was considered significant. The statistical analyses were performed using STATA software version 14.0 (StataCorp, Texas, USA), and all statistical tests were two-sided.
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9

LCAT Activity in Endothelial Cells and Diabetes

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The values of mean ± standard deviation (SD), median, and interquartile range (IQR) were calculated. The normality test was done using the Shapiro–Wilk test. One‐way analysis of variance and post‐hoc test as well as analysis of covariance were used to compare groups based on age, BMI, SBP, DBP, TC, TG, HDL‐C, LDL‐C, ox‐LDL, and LCAT activity level. Student's t‐test was used to compare EC with or without type 2 diabetes and the diabetic group based on fasting blood sugar (FBS) and HbA1c. Due to the nonnormal distribution of type 2 diabetes duration, the nonparametric Mann–Whitney U‐test was utilized to compare the durations of type 2 diabetes between groups. χ2‐test was performed to compare the menopausal status among the groups. The association between LCAT level and other variables in each group was also studied using a Pearson correlation coefficient. Linear regression analyses were performed to assess the effects of diabetes, EC, and concurrent status on LCAT activity in STATA. Due to the number of patients, we tried to have no missing values in all studied variables.  Two‐sided tests with p < 0.05 were considered statistically significant. Data were analyzed using IBM SPSS software version 24.0 (SPSS Inc., Chicago, Illinois, USA) and Stata software version 14.0 (StataCorp LLC).
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10

Implementation Levels and Enrollment in TX CORD

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The 1957 referred patients from 11 primary care clinics were categorized as enrolled or not enrolled in the TX CORD secondary prevention study. The implementation index scores for the primary care clinics were converted into categorical variables with quartile splits collapsed into three categories: (a) relatively high level of implementation (upper quartile of the index), (b) medium level of implementation (middle two quartiles), and (c) relatively low level of implementation (lower quartile of the index). We then conducted a mixed effects logistic regression test with a random intercept term for primary care clinics to examine the association between implementation index levels and enrollment of children with overweight and obesity into the TX CORD secondary prevention study, separately for each year. Similar regression models were also used to examine the associations of underlying constructs, including acceptability, adoption, appropriateness, and feasibility with the enrollment of children into the TX CORD secondary prevention study. Significance was set at P value< 0.05. STATA software version 14.0 (College Station, TX) was used for data analysis.
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