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Background: A platform trial approach allows adding arms to on-going trials to speed up intervention discovery programs. A control arm remains open for recruitment in a platform trial while intervention arms may be added after the onset of the study and could be terminated early for efficacy and/or futility when early stopping is allowed. The topic of utilising non-concurrent control data in the analysis of platform trials has been explored and discussed extensively. A less familiar issue is the presence of heterogeneity, which may exist for example due to modification of enrolment criteria and recruitment strategy. Method: We conduct a simulation study to explore the impact of heterogeneity on the analysis of a two-stage platform trial design. We consider heterogeneity in treatment effects and heteroscedasticity in outcome data across stages for a normally distributed endpoint. We examine the performance of some hypothesis testing procedures and modelling strategies. The use of non-concurrent control data is also considered accordingly. Alongside standard regression analysis, we examine the performance of a novel method that was known as the pairwise trials analysis. It is similar to a network meta-analysis approach but adjusts for treatment comparisons instead of individual studies using fixed effects. Results: Several testing strategies with concurrent control data seem to control the type I error rate at the required level when there is heteroscedasticity in outcome data across stages and/or a random cohort effect. The main parameter of treatment effects in some analysis models correspond to overall treatment effects weighted by stage wise sample sizes; while others correspond to the effect observed within a single stage. The characteristics of the estimates are not affected significantly by the presence of a random cohort effect and/ or heteroscedasticity. Conclusion: In view of heterogeneity in treatment effect across stages, the specification of null hypotheses in platform trials may need to be more subtle. We suggest employing testing procedure of adaptive design as opposed to testing the statistics from regression models; comparing the estimates from the pairwise trials analysis method and the regression model with interaction terms may indicate if heterogeneity is negligible. [ABSTRACT FROM AUTHOR]

Purpose: The 2016 EQ-5D-3L value set for Trinidad and Tobago (T&T) allows for the calculation of EQ-5D-5L values via the crosswalk algorithm. The 2016 value set was based on methods predating the EQ-VT protocol, now considered the gold standard for developing EQ-5D value sets. Furthermore, direct elicitation of EQ-5D-5L is preferred over crosswalked values. This study aimed to produce an EQ-5D-5L value set for T&T. Methods: A representative sample (age, sex, geography) of adults each completed 10 composite Time Trade-Off (cTTO) tasks and 12 Discrete Choice Experiment (DCE) tasks in face-to-face interviews. The cTTO data were analyzed using a Tobit model that corrects for heteroskedasticity. DCE data were analyzed using a mixed logit model. The cTTO and DCE data were combined in hybrid models. Results: One thousand and seventy-nine adults completed the valuation interviews. Among the modelling approaches that were explored, the hybrid heteroskedastic Tobit model produced all internally consistent, statistically significant coefficients, and performed best in terms of out-of-sample predictivity for single states. Compared to the existing EQ-5D-5L crosswalk set, the new value set had a higher number of negative values (236 or 7.6% versus 21 or 0.7%). The mean absolute difference was 0.157 and the correlation coefficient between the two sets was 0.879. Conclusion: This study provides a value set for the EQ-5D-5L for T&T using the EQ-VT protocol. We recommend this value set for QALY computations relating to T&T. [ABSTRACT FROM AUTHOR]

Background: The non-inferiority test is a reasonable approach to assessing a new treatment in a three-arm trial. The three-arm trial consists of a placebo, reference, and an experimental treatment. The non-inferiority is often measured by the mean differences between the experimental and the placebo groups relative to the mean differences between the reference and the placebo groups. Methods: To cope with possible estimation distortion due to the allowance of heteroskedasticity, we adjust the measurement of non-inferiority by the incorporation of coefficient of variation (CV) of the experimental, the reference and the placebo groups. In this research, we propose a generalized p -value based method (GPV-based method) to facilitate non-inferiority tests for the means with unknown coefficient of variation in a three-arm trial. Results: The simulation results show that the GPV-based method can not only adequately control type I error rate at nominal level better but also provide power higher than those from Delta method and the empirical bootstrap method, which verifies the feasibility of our adjustment. Conclusions: We revise the measurement of non-inferiority by deducting the CV of each kind of treatment from the average effect of trials. CVs are included in the non-inferiority explicitly to help prevent possible estimating distortion if heteroskedasticity is allowed. Through the simulation study, the performance of GPV-based method for facilitating non-inferiority tests for the means with unknown CV in a three-arm trial is better than those from empirical bootstrap method and Delta method for small, medium and large sample sizes. Hence, the GPV-based method is recommended to be used to conduct the non-inferiority test for the means with unknown CV in a three-arm trial. The GPV-based method still performs well in non-normality cases. [ABSTRACT FROM AUTHOR]

Background: Respondents in a health valuation study may have different sources of error (i.e., heteroskedasticity), tastes (differences in the relative effects of each attribute level), and scales (differences in the absolute effects of all attributes). Although prior studies have compared values by preference-elicitation tasks (e.g., paired comparison [PC] and best-worst scaling case 2 [BWS]), no study has yet controlled for heteroskedasticity and heterogeneity (taste and scale) simultaneously in health valuation.Methods: Preferences on EQ-5D-5L profiles were elicited from a random sample of 380 adults from the general population of the Netherlands, using 24 PC and 25 BWS case 2 tasks. To control for heteroskedasticity and heterogeneity (taste and scale) simultaneously, we estimated Dutch EQ-5D-5L values using conditional, heteroskedastic, and scale-adjusted latent class (SALC) logit models by maximum likelihood.Results: After controlling for heteroskedasticity, the PC and BWS values were highly correlated (Pearson's correlation: 0.9167, CI: 0.9109-0.9222) and largely agreed (Lin's concordance: 0.7658, CI: 0.7542-0.7769) on a pits scale. In terms of preference heterogeneity, some respondents (mostly young men) failed to account for any of the EQ-5D-5L attributes (i.e., garbage class), and others had a lower scale (59%; p-value: 0.123). Overall, the SALC model produced a consistent Dutch EQ-5D-5L value set on a pits scale, like the original study (Pearson's correlation:0.7295; Lin's concordance: 0.6904).Conclusions: This paper shows the merits of simultaneously controlling for heteroskedasticity and heterogeneity in health valuation. In this case, the SALC model dispensed with a garbage class automatically and adjusted the scale for those who failed the PC dominant task. Future analysis may include more behavioral variables to better control heteroskedasticity and heterogeneity in health valuation.Highlights: The Dutch EQ-5D-5L values based on paired comparison [PC] and best-worst scaling [BWS] responses were highly correlated and largely agreed after controlling for heteroskedasticity. Controlling for taste and scale heterogeneity simultaneously enhanced the Dutch EQ-5D-5Lvalues by automatically dispensing with a garbage class and adjusting the scale for those who failed the dominant task. After controlling for heteroskedasticity and heterogeneity, this study produced Dutch EQ-5D-5L values on a pits scale moderately concordant with the original values. [ABSTRACT FROM AUTHOR]

Background: Randomized pre-post designs, with outcomes measured at baseline and after treatment, have been commonly used to compare the clinical effectiveness of two competing treatments. There are vast, but often conflicting, amount of information in current literature about the best analytic methods for pre-post designs. It is challenging for applied researchers to make an informed choice.Methods: We discuss six methods commonly used in literature: one way analysis of variance ("ANOVA"), analysis of covariance main effect and interaction models on the post-treatment score ("ANCOVAI" and "ANCOVAII"), ANOVA on the change score between the baseline and post-treatment scores ("ANOVA-Change"), repeated measures ("RM") and constrained repeated measures ("cRM") models on the baseline and post-treatment scores as joint outcomes. We review a number of study endpoints in randomized pre-post designs and identify the mean difference in the post-treatment score as the common treatment effect that all six methods target. We delineate the underlying differences and connections between these competing methods in homogeneous and heterogeneous study populations.Results: ANCOVA and cRM outperform other alternative methods because their treatment effect estimators have the smallest variances. cRM has comparable performance to ANCOVAI in the homogeneous scenario and to ANCOVAII in the heterogeneous scenario. In spite of that, ANCOVA has several advantages over cRM: i) the baseline score is adjusted as covariate because it is not an outcome by definition; ii) it is very convenient to incorporate other baseline variables and easy to handle complex heteroscedasticity patterns in a linear regression framework.Conclusions: ANCOVA is a simple and the most efficient approach for analyzing pre-post randomized designs. [ABSTRACT FROM AUTHOR]

Background: Survival analysis is the most appropriate method of analysis for time-to-event data. The classical accelerated failure-time model is a more powerful and interpretable model than the Cox proportional hazards model, provided that model imposed distribution and homoscedasticity assumptions satisfied. However, most of the real data are heteroscedastic which violates the fundamental assumption and consequently, the statistical inference could be erroneous in accelerated failure-time modeling. The weighted least-squares estimation for the accelerated failure-time model is an efficient semi-parametric approach for time-to-event data without the homoscedasticity assumption, which is developed recently and not often utilized for real data analysis. Thus, this study was conducted to ascertain the better performance of the weighted least-squares estimation method over the classical methods.Methods: We analyzed a REAL dataset on Antiretroviral Therapy patients we recently collected. We compared the results from classical methods of estimation for the accelerated failure-time model with the results revealed from the weighted least-squares estimation.Results: We found that the data are heteroscedastic and indicated that the weighted least-square method should be used to analyze this data. The weighted least-squares estimation revealed more accurate, and efficient estimates of covariates effect since its confidence intervals were shorter and it identified more significant covariates. Accordingly, the survival of HIV positives was found to be significantly linked with age, weight, functional status, CD4 (Cluster of Differentiation agent 4 glycoproteins), and clinical stages.Conclusions: The weighted least-squares estimation performed the best in providing more significant effects and precise estimates than the classical accelerated failure-time methods of estimation if data are heteroscedastic. Thus, we recommend future researchers should utilize weighted least-squares estimation rather than the classical methods when the homoscedasticity assumption is violated. [ABSTRACT FROM AUTHOR]

Background: Proxies are mathematical calculations based on fasting glucose and/or insulin concentrations developed to allow prediction of insulin sensitivity (IS) and β-cell response. These proxies have not been evaluated in horses with insulin dysregulation. The first objective of this study was to evaluate how fasting insulin (FI) and proxies for IS (1/Insulin, reciprocal of the square root of insulin (RISQI) and the quantitative insulin sensitivity check index (QUICKI)) and β-cell response (the modified insulin-to-glucose ratio (MIRG) and the homeostatic model assessment of β-cell function (HOMA-β)) were correlated to measures of IS (M index) using the euglycemic hyperinsulinemic clamp (EHC) in horses with insulin resistance (IR) and normal IS. A second objective was to evaluate the repeatability of FI and proxies in horses based on sampling on consecutive days. The last objective was to investigate the most appropriate cut-off value for the proxies and FI. Results: Thirty-four horses were categorized as IR and 26 as IS based on the M index. The proxies and FI had coefficients of variation (CVs) ≤ 25.3 % and very good reliability (intraclass correlation coefficients ≥ 0.89). All proxies and FI were good predictors of the M index (r = 0.76–0.85; P < 0.001). The proxies for IS had a positive linear relationship with the M index whereas proxies for β-cell response and FI had an inverse relationship with the M index. Cut-off values to distinguish horses with IR from horses with normal IS based on the M index were established for all proxies and FI using receiver operating characteristic curves, with sensitivity between 79 % and 91 % and specificity between 85 % and 96 %. The cut-off values to predict IR were < 0.32 (RISQI), < 0.33 (QUICKI) and > 9.5 µIU/mL for FI. Conclusions: All proxies and FI provided repeatable estimates of horses' IS. However, there is no advantage of using proxies instead of FI to estimate IR in the horse. Due to the heteroscedasticity of the data, proxies and FI in general are more suitable for epidemiological studies and larger clinical studies than as a diagnostic tool for measurement of IR in individual horses. [ABSTRACT FROM AUTHOR]

Background: The CHRNA5/A3/B4 gene locus is associated with nicotine dependence and other smoking related disorders. While the non-synonymous CHRNA5 variant rs16969968 appears to be the main risk factor, linkage disequilibrium (LD) bins in the gene cluster carry frequent variants that regulate expression. Pairwise LD and haplotype analyses had identified at least three haplotype tagging SNPs including rs16969968 as main genetic risk factors. Searching for variants with evidence of regulatory functions, we have reported interactions between CHRNA5 and CHRNA3 enhancer variants (tagged by rs880395 and rs1948, respectively) and rs16969968, forming 3-SNP haplotypes and diplotypes that may more accurately reflect the cluster's combined effects on nicotine dependence (Barrie et al., Hum Mutat 38:112–9, 2017). Here we address further contributions by variants affecting CHRNB4, a possibly limiting component of nicotinic receptors. Results: We identify an LD bin (tagged by rs4887074) associated with expression of CHRNB4. Additive logistic regression models indicate that rs4887074 is associated with nicotine dependence and modulates the effect of rs16969968 in GWAS datasets (COGEND, UW-TTURC, SAGE). 4-SNP haplotype and diplotype analyses (rs880395-rs16969968-rs1948 -rs4887074) yield nicotine dependence risk values that further differentiate those obtained with the 3-SNP model. Moreover, both the main G allele of rs16969968 and the minor G allele of rs4887074 (associated with reduced expression of CHRNB4), residing predominantly on common haplotypes that are protective, represent significant allele-specific variance QTLs, indicating that they interact with each other. Conclusions: These results indicate rs4887074 is associated with CHRNB4 expression, and along with two regulatory variants of CHRNA3 and CHRNA5, modulates the effect of rs16969968 on nicotine dependence risk. Assignable to individuals because of strong LD structures, 4-SNP haplotypes and diplotypes serve to assess the combined genetic influence of this multi-gene cluster on complex traits, accounting for complex LD relationships and tissue-specific genetic effects (CHRNA5/3) relevant to the traits analyzed. The 4-SNP haplotypes account at least in part for previous tagging SNPs, including the highly GWAS-significant rs6495308, located in a distinct pair-wise LD bin but included in protective 4-SNP haplotypes. Our approach refines and integrates the cluster's overall genetic influence, an important variable when integrating the genetics of multiple genomic loci. [ABSTRACT FROM AUTHOR]

Background: Using next-generation sequencing technology to measure gene expression, an empirically intriguing question concerns the identification of differentially expressed genes across treatment groups. Existing methods aim to identify genes whose mean expressions differ among treatment groups by assuming equal dispersion across all groups. For syndromes, however, various combinations of gene expression alterations can result in the same disease, leading to greater heteroscedasticity in the biological replicates in the disease group compared to the normal group. Traditional methods that only consider changes in the mean will fail to fully analyze gene expression in such a scenario. In addition, sequencing technology is relatively expensive; most labs can only afford a few replicates per treatment group, which poses further challenges to reliably estimating the mean and dispersion under each treatment condition. Results: We designed an empirical Bayes method and a pooled permutation test to simultaneously consider the change in mean and dispersion across treatment groups. We further computed confidence intervals based on Bayes estimates to identify differentially expressed genes that are unique to each disease sample as well as those that are common across all disease samples. We illustrated our method by applying it to gene expression data from a large offspring syndrome experiment, which motivated this study. We compared our method to competing approaches through simulation studies that mimicked the real datasets to demonstrate the effectiveness of our proposed method. Conclusions: We will show that, compared to popular methods that only aim to find the difference in the mean, our method can capture greater variation in the disease group to effectively identify differentially expressed genes for syndromes. [ABSTRACT FROM AUTHOR]

Key message : The effects on large-area volume estimates of uncertainty in individual tree volume model predictions were negligible when using simple random sampling estimators for large-area estimation, but non-negligible when using stratified estimators which reduced the effects of sampling variability. Context : Forest inventory estimates of tree volume for large areas are typically calculated by adding model predictions of volumes for individual trees at the plot level and calculating the per unit area mean over plots. The uncertainty in the model predictions is generally ignored with the result that the precision of the large-area volume estimate is optimistic. Aims : The primary objective was to estimate the effects on large-area volume estimates of volume model prediction uncertainty due to diameter and height measurement error, parameter uncertainty, and model residual variance. Methods : Monte Carlo simulation approaches were used because of the complexities associated with multiple sources of uncertainty, the non-linear nature of the models, and heteroskedasticity. Results : The effects of model prediction uncertainty on large-area volume estimates of growing stock volume were negligible when using simple random sampling estimators. However, with stratified estimators that reduce the effects of sampling variability, the effects of model prediction uncertainty were not necessarily negligible. The adverse effects of parameter uncertainty and residual variance were greater than the effects of diameter and height measurement errors. Conclusion : The uncertainty of large-area volume estimates that do not account for model prediction uncertainty should be regarded with caution. [ABSTRACT FROM AUTHOR]

Background: The 2 × 2 factorial design is widely used for assessing the existence of interaction and the extent of generalizability of two factors where each factor had only two levels. Accordingly, research problems associated with the main effects and interaction effects can be analyzed with the selected linear contrasts.Methods: To correct for the potential heterogeneity of variance structure, the Welch-Satterthwaite test is commonly used as an alternative to the t test for detecting the substantive significance of a linear combination of mean effects. This study concerns the optimal allocation of group sizes for the Welch-Satterthwaite test in order to minimize the total cost while maintaining adequate power. The existing method suggests that the optimal ratio of sample sizes is proportional to the ratio of the population standard deviations divided by the square root of the ratio of the unit sampling costs. Instead, a systematic approach using optimization technique and screening search is presented to find the optimal solution.Results: Numerical assessments revealed that the current allocation scheme generally does not give the optimal solution. Alternatively, the suggested approaches to power and sample size calculations give accurate and superior results under various treatment and cost configurations.Conclusions: The proposed approach improves upon the current method in both its methodological soundness and overall performance. Supplementary algorithms are also developed to aid the usefulness and implementation of the recommended technique in planning 2 × 2 factorial designs. [ABSTRACT FROM AUTHOR]

Background: Classical genetic canalization models, which accommodate the mean and variance of a trait separately, provide a flexible approach to take heteroscedasticity for continuous traits into account. However, this model is not appropriate for discrete traits. The aim of this work was to propose heteroscedastic threshold models suitable for the genetic analysis of ordinal data. Methods: In order to first fit the mean and variance of ordinal traits separately, we extended the classical threshold model (TM) for discrete data by introducing non-genetic and genetic factors of heterogeneity on the variance of its underlying variable, which leads to a homothetic threshold model HTM and its alternative parameterization HTM' in which the thresholds of different individuals are linked by a homothetic-translation. Relaxing the constraint between the thresholds led us to propose an independent threshold model ITM that was more flexible than HTM' but required the estimation of more parameters. TM, HTM and ITM models were applied to study 19,671 records on litter size in Romane sheep. Results: Both HTM and ITM were able to disentangle the link between the mean and variance that holds in the classical homoscedastic threshold model. The results obtained for the litter size of Romane ewes showed that the data was best fitted with HTM compared to ITM and TM. The correlations between the observed and predicted variances were equal to 0.6 and 0.2 for HTM and TM, respectively. These analyses showed the existence of a genetic component for the heterogeneity of litter size in sheep that was taken into account in HTM. Conclusions: HTM is the most suitable model to study the variability of litter size in sheep. It accommodates both the mean and variance separately while requiring the estimation of only a few parameters. [ABSTRACT FROM AUTHOR]

Background Stroke patients have impaired postural balance that increases the risk of falls and impairs their mobility. Assessment of postural balance is commonly carried out by recording centre of pressure (CoP) displacements, but the lack of data concerning reliability of these measures compromises their interpretation. The purpose of this study was to investigate the betweenday reliability of six CoP-based variables, in order to provide i) reliability data for monitoring postural sway and weight-bearing asymmetry of stroke patients in clinical practice and ii) consistent assessment method of measurement error for applications in physical medicine and rehabilitation. Methods Postural balance of 20 stroke patients was assessed in quiet standing on a force platform, in two sessions, 7 days apart. Six CoP-based variables were collected in eyes open and eyes closed conditions: postural sway was assessed with mean and standart deviation of CoPvelocity, CoP-velocity along the mediolateral and anteroposterior axes, and confidence ellipse area (CEAREA); weight-bearing asymmetry was assessed with mean CoP position along the mediolateral axis (CoPML). The intraclass correlation coefficient (ICC) was used to determine the level of agreement between test-retest. Small real difference (SRD), corresponding to the smallest change that indicates a real improvement for a single individual, was used to determine the extent of measurement error. Results ICCs were satisfactory (>0.9) for all CoP-based variables, except for CEAREA in eyes open condition and CoPML (<0.8). The SRDs (eyes open/closed conditions) were: 6.1/9.5 mm.s-1 for mean velocity; 12.3/12.2 mm.s-1 for standard deviation of CoP-velocity; 3.6/5.5 mm.s-1 and 4.9/7.3 mm.s-1 for CoP-velocity in mediolateral and anteroposterior axes, respectively; 17.4/21.4 mm for CoPML. Because CEAREA showed heteroscedasticity of measurement error distribution, SRD (eyes open/closed conditions) was expressed as a percentage (121/75%) and a ratio (3.68/2.16) obtained after log-antilog procedure. Conclusions In clinical practice, the CoP-based velocity variables should be prefer to CEAREA to assess and monitor postural sway over time in hemiplegic stroke patients. The poor reliability of CoPML compromises its use to assess weight-bearing asymmetry. The procedure we used could be applied in reliability studies concerning other CoP-based variables or other biological variables in the field of physical medicine and rehabilitation. [ABSTRACT FROM AUTHOR]

Background: The synthesis of information across microarray studies has been performed by combining statistical results of individual studies (as in a mosaic), or by combining data from multiple studies into a large pool to be analyzed as a single data set (as in a melting pot of data). Specific issues relating to data heterogeneity across microarray studies, such as differences within and between labs or differences among experimental conditions, could lead to equivocal results in a melting pot approach. Results: We applied statistical theory to determine the specific effect of different means and heteroskedasticity across 19 groups of microarray data on the sign and magnitude of gene-to-gene Pearson correlation coefficients obtained from the pool of 19 groups. We quantified the biases of the pooled coefficients and compared them to the biases of correlations estimated by an effect-size model. Mean differences across the 19 groups were the main factor determining the magnitude and sign of the pooled coefficients, which showed largest values of bias as they approached ±1. Only heteroskedasticity across the pool of 19 groups resulted in less efficient estimations of correlations than did a classical meta-analysis approach of combining correlation coefficients. These results were corroborated by simulation studies involving either mean differences or heteroskedasticity across a pool of N > 2 groups. Conclusions: The combination of statistical results is best suited for synthesizing the correlation between expression profiles of a gene pair across several microarray studies. [ABSTRACT FROM AUTHOR]

Background: Statistical analysis of genome-wide microarrays can result in many thousands of identical statistical tests being performed as each probe is tested for an association with a phenotype of interest. If there were no association between any of the probes and the phenotype, the distribution of P values obtained from statistical tests would resemble a Uniform distribution. If a selection of probes were significantly associated with the phenotype we would expect to observe P values for these probes of less than the designated significance level, alpha, resulting in more P values of less than alpha than expected by chance. Results: In data from a whole genome methylation promoter array we unexpectedly observed P value distributions where there were fewer P values less than alpha than would be expected by chance. Our data suggest that a possible reason for this is a violation of the statistical assumptions required for these tests arising from heteroskedasticity. A simple but statistically sound remedy (a heteroskedasticity-consistent covariance matrix estimator to calculate standard errors of regression coefficients that are robust to heteroskedasticity) rectified this violation and resulted in meaningful P value distributions. Conclusions: The statistical analysis of 'omics data requires careful handling, especially in the choice of statistical test. To obtain meaningful results it is essential that the assumptions behind these tests are carefully examined and any violations rectified where possible, or a more appropriate statistical test chosen. [ABSTRACT FROM AUTHOR]

The article reports on the use of the flexible shrinkage error estimators considering both between-gene and within-gene heteroscedasticity in construction of F-like test statistics for testing interactions. It reports on the comparison of the proposed test statistics with other existing shrinkage-type test statistics through extensive simulation studies. The results show that choice of permutation procedures influence the detection power more than the choice of F or F-like test statistics.

Background: High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes. The microarray-based Infinium methylation assay by Illumina is one platform for low-cost high-throughput methylation profiling. Both Beta-value and M-value statistics have been used as metrics to measure methylation levels. However, there are no detailed studies of their relations and their strengths and limitations. Results: We demonstrate that the relationship between the Beta-value and M-value methods is a Logit transformation, and show that the Beta-value method has severe heteroscedasticity for highly methylated or unmethylated CpG sites. In order to evaluate the performance of the Beta-value and M-value methods for identifying differentially methylated CpG sites, we designed a methylation titration experiment. The evaluation results show that the M-value method provides much better performance in terms of Detection Rate (DR) and True Positive Rate (TPR) for both highly methylated and unmethylated CpG sites. Imposing a minimum threshold of difference can improve the performance of the M-value method but not the Beta-value method. We also provide guidance for how to select the threshold of methylation differences. Conclusions: The Beta-value has a more intuitive biological interpretation, but the M-value is more statistically valid for the differential analysis of methylation levels. Therefore, we recommend using the M-value method for conducting differential methylation analysis and including the Beta-value statistics when reporting the results to investigators. [ABSTRACT FROM AUTHOR]

Although little evidence supports cannabis-induced amotivational syndrome, sources continue to assert that the drug saps motivation [1], which may guide current prohibitions. Few studies report low motivation in chronic users; another reveals that they have higher subjective wellbeing. To assess differences in motivation and subjective wellbeing, we used a large sample (N = 487) and strict definitions of cannabis use (7 days/week) and abstinence (never). Standard statistical techniques showed no differences. Robust statistical methods controlling for heteroscedasticity, non-normality and extreme values found no differences in motivation but a small difference in subjective wellbeing. Medical users of cannabis reporting health problems tended to account for a significant portion of subjective wellbeing differences, suggesting that illness decreased wellbeing. All p-values were above p = .05. Thus, daily use of cannabis does not impair motivation. Its impact on subjective wellbeing is small and may actually reflect lower wellbeing due to medical symptoms rather than actual consumption of the plant. [ABSTRACT FROM AUTHOR]

Background: Frequent use of self-reports for investigating recent and past behavior in medical research requires statistical techniques capable of analyzing complex sources of bias associated with this methodology. In particular, although decreasing accuracy of recalling more distant past events is commonplace, the bias due to differential in memory errors resulting from it has rarely been modeled statistically. Methods: Covariance structure analysis was used to estimate the recall error of self-reported number of sexual partners for past periods of varying duration and its implication for the bias. Results: Results indicated increasing levels of inaccuracy for reports about more distant past. Considerable positive bias was found for a small fraction of respondents who reported ten or more partners in the last year, last two years and last five years. This is consistent with the effect of heteroscedastic random error where the majority of partners had been acquired in the more distant past and therefore were recalled less accurately than the partners acquired more recently to the time of interviewing. Conclusions: Memory errors of this type depend on the salience of the events recalled and are likely to be present in many areas of health research based on self-reported behavior. [ABSTRACT FROM AUTHOR]

Background: Appraisal delay is the time a patient takes to consider a symptom as not only noticeable, but a sign of illness. The study's objective was to determine the association between appraisal delay in seeking tuberculosis (TB) treatment and geographic distance measured by network travel (driving and pedestrian) time (in minutes) and distance (Euclidean and self-reported) (in kilometers) and to identify other risk factors from selected covariates and how they modify the core association between delay and distance.Methods: This was part of a longitudinal cohort study known as the Kawempe Community Health Study based in Kampala, Uganda. The study enrolled households from April 2002 to July 2012. Multivariable interval regression with multiplicative heteroscedasticity was used to assess the impact of time and distance on delay. The delay interval outcome was defined using a comprehensive set of 28 possible self-reported symptoms. The main independent variables were network travel time (in minutes) and Euclidean distance (in kilometers). Other covariates were organized according to the Andersen utilization conceptual framework.Results: A total of 838 patients with both distance and delay data were included in the network analysis. Bivariate analyses did not reveal a significant association of any distance metric with the delay outcome. However, adjusting for patient characteristics and cavitary disease status, the multivariable model indicated that each minute of driving time to the clinic significantly (p = 0.02) and positively predicted 0.25 days' delay. At the median distance value of 47 min, this represented an additional delay of about 12 (95% CI: [3, 21]) days to the mean of 40 days (95% CI: [25, 56]). Increasing Euclidean distance significantly predicted (p = 0.02) reduced variance in the delay outcome, thereby increasing precision of the mean delay estimate. At the median Euclidean distance of 2.8 km, the variance in the delay was reduced by more than 25%.Conclusion: Of the four geographic distance measures, network travel driving time was a better and more robust predictor of mean delay in this setting. Including network travel driving time with other risk factors may be important in identifying populations especially vulnerable to delay. [ABSTRACT FROM AUTHOR]

Background: Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip’s law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i.e., varying exponent values) in a log-log plot. If transcript abundance is truly power-law distributed, the varying exponent signifies changing mathematical moments (e.g., mean, variance) and creates heteroskedasticity which compromises statistical rigor in analysis. The impact of this deviation from the asymptotic power-law on sequencing count data has never truly been examined and quantified. Results: The anecdotal description of transcript abundance being almost Zipf’s law-like distributed can be conceptualized as the imperfect mathematical rendition of the Pareto power-law distribution when subjected to the finite-size effects in the real world; This is regardless of the advancement in sequencing technology since sampling is finite in practice. Our conceptualization agrees well with our empirical analysis of two modern day NGS (Next-generation sequencing) datasets: an in-house generated dilution miRNA study of two gastric cancer cell lines (NUGC3 and AGS) and a publicly available spike-in miRNA data; Firstly, the finite-size effects causes the deviations of sequencing count data from Zipf’s law and issues of reproducibility in sequencing experiments. Secondly, it manifests as heteroskedasticity among experimental replicates to bring about statistical woes. Surprisingly, a straightforward power-law correction that restores the distribution distortion to a single exponent value can dramatically reduce data heteroskedasticity to invoke an instant increase in signal-to-noise ratio by 50% and the statistical/detection sensitivity by as high as 30% regardless of the downstream mapping and normalization methods. Most importantly, the power-law correction improves concordance in significant calls among different normalization methods of a data series averagely by 22%. When presented with a higher sequence depth (4 times difference), the improvement in concordance is asymmetrical (32% for the higher sequencing depth instance versus 13% for the lower instance) and demonstrates that the simple power-law correction can increase significant detection with higher sequencing depths. Finally, the correction dramatically enhances the statistical conclusions and eludes the metastasis potential of the NUGC3 cell line against AGS of our dilution analysis. Conclusions: The finite-size effects due to undersampling generally plagues transcript count data with reproducibility issues but can be minimized through a simple power-law correction of the count distribution. This distribution correction has direct implication on the biological interpretation of the study and the rigor of the scientific findings. Reviewers: This article was reviewed by Oliviero Carugo, Thomas Dandekar and Sandor Pongor. [ABSTRACT FROM AUTHOR]