Updating Knowledge in The Estimation of The Genetics Parameters Multi-trait and Multi-Environment Bayesian Analysis in Rice (Oryza Sativa L.)

Among the multi-trait models used to jointly study several traits and environments, the Bayesian framework has been a preferable tool for using a more complex and biologically realistic model. In most cases, the non-informative prior distributions are adopted in studies using the Bayesian approach. Still, the Bayesian approach tends to present more accurate estimates when it uses informative prior distributions. The present study was developed to evaluate the efficiency and applicability of multi-trait multi-environment (MTME) models under a Bayesian framework utilizing a strategy for eliciting informative prior distribution using previous data from rice. The study involved data pertained to rice genotypes in three environments and five agricultural years (2010/2011 until 2014/2015) for the following traits: grain yield (GY), flowering in days (FLOR) and plant height (PH). Variance components and genetic and non-genetic parameters were estimated by the Bayesian method. In general, the informative prior distribution in Bayesian MTME models provided higher estimates of heritability and variance components, as well as minor lengths for the highest probability density interval (HPD), compared to their respective non-informative prior distribution analyses. The use of more informative prior distributions makes it possible to detect genetic correlations between traits, which cannot be achieved with the use of non-informative prior distributions. Therefore, this mechanism presented for updating knowledge to the elicitation of an informative prior distribution can be efficiently applied in rice genetic selection.

Restricted maximum-likelihood method for learning latent variance components in gene expression data with known and unknown confounders

Random effects models are popular statistical models for detecting and correcting spurious sample correlations due to hidden confounders in genome-wide gene expression data. In applications where some confounding factors are known, estimating simultaneously the contribution of known and latent variance components in random effects models is a challenge that has so far relied on numerical gradient-based optimizers to maximize the likelihood function. This is unsatisfactory because the resulting solution is poorly characterized and the efficiency of the method may be suboptimal. Here we prove analytically that maximum-likelihood latent variables can always be chosen orthogonal to the known confounding factors, in other words, that maximum-likelihood latent variables explain sample covariances not already explained by known factors. Based on this result we propose a restricted maximum-likelihood method which estimates the latent variables by maximizing the likelihood on the restricted subspace orthogonal to the known confounding factors, and show that this reduces to probabilistic PCA on that subspace. The method then estimates the variance-covariance parameters by maximizing the remaining terms in the likelihood function given the latent variables, using a newly derived analytic solution for this problem. Compared to gradient-based optimizers, our method attains greater or equal likelihood values, can be computed using standard matrix operations, results in latent factors that don’t overlap with any known factors, and has a runtime reduced by several orders of magnitude. Hence the restricted maximum-likelihood method facilitates the application of random effects modelling strategies for learning latent variance components to much larger gene expression datasets than possible with current methods.

Measuring motivational relationship processes in experience sampling: A reliability model for moments, days, and persons nested in couples

The investigation of within-person process models, often done in experience sampling designs, requires a reliable assessment of within-person change. In this paper, we focus on dyadic intensive longitudinal designs where both partners of a couple are assessed multiple times each day across several days. We introduce a statistical model for variance decomposition based on generalizability theory (extending P. E. Shrout & S. P. Lane, 2012), which can estimate the relative proportion of variability on four hierarchical levels: moments within a day, days, persons, and couples. Based on these variance estimates, four reliability coefficients are derived: between-couples, between-persons, within-persons/between-days, and within-persons/between-moments. We apply the model to two dyadic intensive experience sampling studies (n1 = 130 persons, 5 surveys each day for 14 days, ≥ 7508 unique surveys; n2 = 508 persons, 5 surveys each day for 28 days, ≥ 47764 unique surveys). Five different scales in the domain of motivational processes and relationship quality were assessed with 2 to 5 items: State relationship satisfaction, communal motivation, and agentic motivation; the latter consists of two subscales, namely power and independence motivation. Largest variance components were on the level of persons, moments, couples, and days, where within-day variance was generally larger than between-day variance. Reliabilities ranged from .32 to .76 (couple level), .93 to .98 (person level), .61 to .88 (day level), and .28 to .72 (moment level). Scale intercorrelations reveal differential structures between and within persons, which has consequences for theory building and statistical modeling.

The Influence of Nursing Home, Ward, and Eldercare Workers on the Number of Resident Handlings Performed Per Shift in Eldercare

The purpose of our study was to investigate which organizational levels and factors determine the number of resident handlings in eldercare. We conducted a multi-level study, stratified on day and evening shifts, including information on four levels: nursing homes (n = 20), wards within nursing homes (day, n = 120; evening, n = 107), eldercare workers within wards (day, n = 619; evening, n = 382), and within eldercare workers (i.e., days within eldercare workers; day, n = 5572; evening, n = 2373). We evaluated the influence of each level on the number of resident handlings using variance components analysis and multivariate generalized linear mixed models. All four levels contributed to the total variance in resident handlings during day and evening shifts, with 13%/20% at “nursing homes”, 21%/33% at “wards within nursing homes”, 25%/31% at “elder-care workers within wards”, and 41%/16% “within eldercare workers”, respectively. The percentage of residents with a higher need for physical assistance, number of residents per shift, occupational position (only within day shifts), and working hours per week (only within day shifts) were significantly associated with the number of resident handlings performed per shift. Interventions aiming to modify number of resident handlings in eldercare ought to target all levels of the eldercare organization.

Heritability and genetic correlations of plasma metabolites of pigs with production, resilience and carcass traits under natural polymicrobial disease challenge

Metabolites in plasma of healthy nursery pigs were quantified using nuclear magnetic resonance. Heritabilities of metabolite concentration were estimated along with their phenotypic and genetic correlations with performance, resilience, and carcass traits in growing pigs exposed to a natural polymicrobial disease challenge. Variance components were estimated by GBLUP. Heritability estimates were low to moderate (0.11 ± 0.08 to 0.19 ± 0.08) for 14 metabolites, moderate to high (0.22 ± 0.09 to 0.39 ± 0.08) for 17 metabolites, and highest for l-glutamic acid (0.41 ± 0.09) and hypoxanthine (0.42 ± 0.08). Phenotypic correlation estimates of plasma metabolites with performance and carcass traits were generally very low. Significant genetic correlation estimates with performance and carcass traits were found for several measures of growth and feed intake. Interestingly the plasma concentration of oxoglutarate was genetically negatively correlated with treatments received across the challenge nursery and finisher (− 0.49 ± 0.28; P < 0.05) and creatinine was positively correlated with mortality in the challenge nursery (0.85 ± 0.76; P < 0.05). These results suggest that some plasma metabolite phenotypes collected from healthy nursery pigs are moderately heritable and genetic correlations with measures of performance and resilience after disease challenge suggest they may be potential genetic indicators of disease resilience.