Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum.

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits

A review of R-packages for random-intercept probit regression in small clusters

Generalized Linear Mixed Models (GLMMs) are widely used to model clustered categorical outcomes. To tackle the intractable integration over the random effects distributions, several approximation approaches have been developed for likelihood-based inference. As these seldom yield satisfactory results when analyzing binary outcomes from small clusters, estimation within the Structural Equation Modeling (SEM) framework is proposed as an alternative. We compare the performance of R-packages for random-intercept probit regression relying on: the Laplace approximation, adaptive Gaussian quadrature (AGQ), Penalized Quasi-Likelihood (PQL), an MCMC-implementation, and integrated nested Laplace approximation within the GLMM-framework, and a robust diagonally weighted least squares estimation within the SEM-framework. In terms of bias for the fixed and random effect estimators, SEM usually performs best for cluster size two, while AGQ prevails in terms of precision (mainly because of SEM's robust standard errors). As the cluster size increases, however, AGQ becomes the best choice for both bias and precision

Narrative Health Communication and Behavior Change: The Influence of Exemplars in the News on Intention to Quit Smoking.

This study investigated psychological mechanisms underlying the effect of narrative health communication on behavioral intention. Specifically, the study examined how exemplification in news about successful smoking cessation affects recipients\u27 narrative engagement, thereby changing their intention to quit smoking. Nationally representative samples of U.S. adult smokers participated in 2 experiments. The results from the 2 experiments consistently showed that smokers reading a news article with an exemplar experienced greater narrative engagement compared to those reading an article without an exemplar. Those who reported more engagement were in turn more likely to report greater smoking cessation intentions

The effect of skewness and kurtosis on the Kenward-Roger approximation when group distributions differ

This study examined the independent effect of skewness and kurtosis on the robustness of the linear mixed model (LMM), with the Kenward-Roger (KR) procedure, when group distributions are different, sample sizes are small, and sphericity cannot be assumed. Methods: A Monte Carlo simulation study considering a split-plot design involving three groups and four repeated measures was performed. Results: The results showed that when group distributions are different, the effect of skewness on KR robustness is greater than that of kurtosis for the corresponding values. Furthermore, the pairings of skewness and kurtosis with group size were found to be relevant variables when applying this procedure. Conclusions: With sample sizes of 45 and 60, KR is a suitable option for analyzing data when the distributions are: (a) mesokurtic and not highly or extremely skewed, and (b) symmetric with different degrees of kurtosis. With total sample sizes of 30, it is adequate when group sizes are equal and the distributions are: (a) mesokurtic and slightly or moderately skewed, and sphericity is assumed; and (b) symmetric with a moderate or high/extreme violation of kurtosis. Alternative analyses should be considered when the distributions are highly or extremely skewed and samples sizes are small

Detecting single-trial EEG evoked potential using a wavelet domain linear mixed model: application to error potentials classification

Objective. The main goal of this work is to develop a model for multi-sensor signals such as MEG or EEG signals, that accounts for the inter-trial variability, suitable for corresponding binary classification problems. An important constraint is that the model be simple enough to handle small size and unbalanced datasets, as often encountered in BCI type experiments. Approach. The method involves linear mixed effects statistical model, wavelet transform and spatial filtering, and aims at the characterization of localized discriminant features in multi-sensor signals. After discrete wavelet transform and spatial filtering, a projection onto the relevant wavelet and spatial channels subspaces is used for dimension reduction. The projected signals are then decomposed as the sum of a signal of interest (i.e. discriminant) and background noise, using a very simple Gaussian linear mixed model. Main results. Thanks to the simplicity of the model, the corresponding parameter estimation problem is simplified. Robust estimates of class-covariance matrices are obtained from small sample sizes and an effective Bayes plug-in classifier is derived. The approach is applied to the detection of error potentials in multichannel EEG data, in a very unbalanced situation (detection of rare events). Classification results prove the relevance of the proposed approach in such a context. Significance. The combination of linear mixed model, wavelet transform and spatial filtering for EEG classification is, to the best of our knowledge, an original approach, which is proven to be effective. This paper improves on earlier results on similar problems, and the three main ingredients all play an important role

Proper Data Analysis Techniques to Reduce Experimental Error in Longitudinal Data

This study presents findings of research conducted to improve analysis techniques of experimental data from coconut research. It highlights the ways of handling unaccountable variability due to the inconsistent temporal behavior of the experimental units in perennial crop research to obtain a precise research output. Properly designed field experiments are essential to identify the influence of independent variable/s on the dependent/s at the various stages. This document highlights the ways how the improved methodologies can be successfully used to reduce the experimental error in most commonly used experimental designs and types of analysis. The first example, the study on long term coconut fertilizer experiment designed as a randomized complete block design in Badalgama, Sri Lanka, compares different types of analyses via evaluating the model residuals and calculating the coefficient of variability (CV) to reduce the error and thereby improve the output. The statistical methods used in the first case study includes Repeated Measure Analysis of Variance (RMANOVA) as the classical method and Repeated Measure ANOVA (With single palm per plots), Linear Mix Model, and MANOVA with two Principal Components that represent approximately 80% variation of the data as dependent variables as improved methods. The model adequacy of each approach was accepted after testing normality, homogeneity of variance and independence of residuals. CV resulted from classical RMANOVA was 39.95%, while it was 39.2% from Repeated Measure ANOVA (With single palm per plots) and 16.51% from the Linear Mixed model. The lowermost CV (10.04%) resulted from MANOVA with two principal components indicating that it can be more powerfully used to analyze long term experiments of coconuts. The second example, the study on long term coconut fertilizer experiment from Bandirippuwa, Sri Lanka that failed to have normality assumption of parametric methods, illustrates appropriate types of the Non-Parametric analysis(F2-LD-F1) for the longitudinal data. The regularity of the results should be studied further with few more comparable data sets

Sphericity estimation bias for repeated measures designs in simulation studies

In this study, we explored the accuracy of sphericity estimation and analyzed how the sphericity of covariance matrices may be affected when the latter are derived from simulated data. We analyzed the consequences that normal and nonnormal data generated from an unstructured population covariance matrix with low (ε = .57) and high (ε = .75) sphericity can have on the sphericity of the matrix that is fitted to these data. To this end, data were generated for four types of distributions (normal, slightly skewed, moderately skewed, and severely skewed or log-normal), four sample sizes (very small, small, medium, and large), and four values of the within-subjects factor (K = 4, 6, 8, and 10). Normal data were generated using the Cholesky decomposition of the correlation matrix, whereas the Vale-Maurelli method was used to generate nonnormal data. The results indicate the extent to which sphericity is altered by recalculating the covariance matrix on the basis of simulated data. We concluded that bias is greater with spherical covariance matrices, nonnormal distributions, and small sample sizes, and that it increases in line with the value of K. An interaction was also observed between sample size and K: With very small samples, the observed bias was greater as the value of K increased