Ratio Of Variance Components Research Articles

Elucidation of gene action and estimation of combining ability effects for fruit yield attributes and biochemical traits in brinjal (Solanum melongena L.)

Abstract The present investigation was undertaken in brinjal (Solanum melongena L.) to estimate combining ability and gene action following a half diallel mating design using ten parents. The ratio of genetic variance components, σ2gca/σ2sca and σ2D/σ2A, showed dominant gene action, indicating the presence of non-additive genetic variance for days to 50% flowering, fruit yield per plant, total phenol, antioxidant activity and total soluble sugar. The traits fruits per plant, fruit girth, and fruit weight showed additive genetic variance. Among the parental genotypes, AB 15-08, ABSR 2 and AB 20-13 were found to be good general combiners for fruit yield, fruits per plant, and total soluble solids. The three highest-ranking hybrids were AB 15-08 × AB 20-13, AB 15-08 × AB 20-03 and AB 20-07 × GP BRJ 224. The above hybrids would be rewarding for harnessing heterosis. Keywords: Diallel cross, brinjal, combining ability, fruit yield, antioxidant activity

Effects of radial growth rate on juvenile wood properties of Pinus sylvestris planted in Mongolia

The establishment of forest plantations in boreal zones in Mongolia is important for wood production as well as carbon dioxide fixation. The present study aims to elucidate the juvenile wood properties (basic density, modulus of elasticity [MOE], modulus of rupture [MOR], and compressive strength parallel to grain) of plantation-grown Pinus sylvestris to promote the establishment of plantations. In addition, the effect of the radial growth rate on wood properties was also evaluated using a linear mixed-effects model. In the juvenile wood phase, wood properties were increased from the pith to bark side based on the results of model selections. Up to the 20th annual ring from the pith, the estimated mean values of basic density, MOE, MOR, and compressive strength were 0.40 g/cm3, 5.35 GPa, 65.1 MPa, and 28.4 MPa, respectively. Variance component ratios of growth categories were low in wood properties, with the exception of basic density, suggesting that the radial growth rate did not affect wood properties in the juvenile wood phase in this species growing in Mongolia. Based on the results obtained in the present study, we have concluded that although basic density in the faster growth category yielded relatively lower values, appropriate radial growth promotion during the initial stage of growth in P. sylvestris trees planted in Mongolia exerted no negative impact on juvenile wood properties. Keywords: annual ring width, basic density, compressive strength, modulus of elasticity, modulus of rupture

Examining the normality assumption of a design-comparable effect size in single-case designs.

What Works Clearinghouse (WWC, 2022) recommends a design-comparable effect size (D-CES; i.e., gAB) to gauge an intervention in single-case experimental design (SCED) studies, or to synthesize findings in meta-analysis. So far, no research has examined gAB's performance under non-normal distributions. This study expanded Pustejovsky et al.(2014) to investigate the impact of data distributions, number of cases (m), number of measurements (N), within-case reliability or intra-class correlation (ρ), ratio of variance components (λ), and autocorrelation (ϕ) on gAB in multiple-baseline (MB) design. The performance of gAB was assessed by relative bias (RB), relative bias of variance (RBV), MSE, and coverage rate of 95% CIs (CR). Findings revealed that gAB was unbiased even under non-normal distributions. gAB's variance was generally overestimated, and its 95% CI was over-covered, especially when distributions were normal or nearly normal combined with small m and N. Large imprecision of gAB occurred when m was small and ρ was large. According to the ANOVA results,data distributions contributed to approximately 49% of variance in RB and 25% of variance in both RBV and CR. m and ρ each contributed to 34% of variance in MSE. We recommend gAB for MB studies and meta-analysis with N ≥ 16 and when either (1) data distributions are normal or nearly normal, m = 6, and ρ = 0.6 or 0.8, or (2) data distributions are mildly or moderately non-normal, m ≥ 4, and ρ = 0.2, 0.4, or 0.6. The paper concludes with a discussion of gAB's applicability and design-comparability, and sound reporting practices of ES indices.

Bootstrap inference for unbalanced one-way classification model with skew-normal random effects

In this article, the one-sided hypothesis testing and interval estimation problems for fixed effect and variance component functions are considered in the unbalanced one-way classification model with skew-normal random effects. First, the Bootstrap approach is used to establish test statistics for fixed effects. Second, based on the matrix decomposition technique, Bootstrap approach and generalized approach, the test statistics, and confidence intervals for the single variance component and sum of variance components are constructed. Next, the exact test statistics for the ratio of variance components are obtained. The Monte Carlo simulation results indicate that the Bootstrap approach performs better than the generalized approach in most cases. Finally, the above approaches are illustrated with a real example of carbon fibers’ strength.

A family of unbiased confidence intervals for a ratio of variance components

For linear mixed models having two variance components, one can compute exact confidence intervals for a ratio of the variances. We show that there is a family of unbiased intervals and highlight those unbiased intervals which have short expected length.

Bootstrap inference on variance component functions in the unbalanced two-way random effects model

In this paper, we consider the one-sided hypothesis testing problems for variance component functions in the unbalanced two-way random effects model. Firstly, using the Bootstrap approach and generalized approach, the test statistics and confidence intervals for the sum and ratio of variance components are constructed respectively. Next, the Monte Carlo simulation results indicate that the Bootstrap approach is better than the generalized approach in most cases. Finally, the above approaches are applied to the real data example of the efficiency of assembly lines workers in a manufacturing plant.

Bootstrap Inference on the Variance Component Functions in the Two-Way Random Effects Model with Interaction

In this paper, using the Bootstrap approach and generalized approach, the authors consider the one-sided hypothesis testing problems for variance component functions in the two-way random effects model. Firstly, the test statistics and confidence intervals for the sum of variance components are constructed. Next, the one-sided hypothesis testing problems for the ratio of variance components are also discussed. The Monte Carlo simulation results indicate that the Bootstrap approach is better than the generalized approach in most cases. Finally, the above approaches are applied to the real data examples of mice blood pH and molded plastic part’s dimensions.

Attrition, physical integrity and insecticidal activity of long-lasting insecticidal nets in sub-Saharan Africa and modelling of their impact on vectorial capacity

BackgroundLong-lasting insecticidal nets (LLINs) are the primary malaria prevention and control intervention in many parts of sub-Saharan Africa. While LLINs are expected to last at least 3 years under normal use conditions, they can lose effectiveness because they fall out of use, are discarded, repurposed, physically damaged, or lose insecticidal activity. The contributions of these different interrelated factors to durability of nets and their protection against malaria have been unclear.MethodsStarting in 2009, LLIN durability studies were conducted in seven countries in Africa over 5 years. WHO-recommended measures of attrition, LLIN use, insecticidal activity, and physical integrity were recorded for eight different net brands. These data were combined with analyses of experimental hut data on feeding inhibition and killing effects of LLINs on both susceptible and pyrethroid resistant malaria vectors to estimate the protection against malaria transmission—in terms of vectorial capacity (VC)—provided by each net cohort over time. Impact on VC was then compared in hypothetical scenarios where one durability outcome measure was set at the best possible level while keeping the others at the observed levels.ResultsThere was more variability in decay of protection over time by country than by net brand for three measures of durability (ratios of variance components 4.6, 4.4, and 1.8 times for LLIN survival, use, and integrity, respectively). In some countries, LLIN attrition was slow, but use declined rapidly. Non-use of LLINs generally had more effect on LLIN impact on VC than did attrition, hole formation, or insecticide loss.ConclusionsThere is much more variation in LLIN durability among countries than among net brands. Low levels of use may have a larger impact on effectiveness than does variation in attrition or LLIN degradation. The estimated entomological effects of chemical decay are relatively small, with physical decay probably more important as a driver of attrition and non-use than as a direct cause of loss of effect. Efforts to maximize LLIN impact in operational settings should focus on increasing LLIN usage, including through improvements in LLIN physical integrity. Further research is needed to understand household decisions related to LLIN use, including the influence of net durability and the presence of other nets in the household.

Improvement of Genetic Purity of Breeder Seed by Introducing Line Cultivation Method for Myanmar’s Major Rice Cultivars

Aims: Since the genetic purity of rice seed significantly affects paddy yield and quality, many rice production countries have been attempting to improve seed quality. This study aimed to demonstrate the effectiveness of breeder seed production using line cultivation to ensure traceability of ancestral information by line and individual selection, to improve the genetic purity of breeder seed in Myanmar that has been degraded due to pedigree mixtures.
 Study Design: Observational and analytic study design was used to evaluate the effect of the introduction of line cultivation method in practical activities of breeder seed production in Myanmar under the project for improvement of seed purity of breeder seed.
 Place and Duration of Study: Department of Agricultural Research at Yezin, Ministry of Agriculture, Livestock and Irrigation, Myanmar, from June 2012 to December 2016.
 Methodology: Using nine major rice cultivars in Myanmar, the line cultivation method was evaluated through measurement of the standard deviation and the variance component ratio in heading date, culm length, panicle length, and panicle number from 2012 to 2016. DNA polymorphism analysis by simple sequence repeat (SSR) markers was also conducted using breeder seed of the Sinthukha variety multiplied in 2013, 2014, 2015, and 2016 for the evaluation.
 Results: Standard deviations of heading date, culm length, panicle length and panicle number in 2016 were significantly decreased compared to the first year of the introduction of the line cultivation method. Average heading duration among sister lines of all varieties was reduced from 8.25 days in 2013 to 5.25 days in 2016, and the uniformity of heading time among sister lines was improved. The variance component ratio of each trait in 2016 was the highest since 2013. The analysis of breeder seed by SSR markers revealed that the DNA polymorphism ratio of Sinthukha seed in 2016 was lower than that of 2013. This demonstrated that Sinthukha seed in 2016 had improved genetic purity. Consequently, it is considered that other cultivars multiplied by the line cultivation method have improved their genetic purity as well.
 Conclusion: Line cultivation is an effective method to improve genetic purity and maintain genetic stability of the breeder seed in Myanmar’s rice cultivars. Genetically pure breeder seed would improve quality of downstream seed such as certified seed. Consequently, it is expected that productivity and quality of rice will be improved thus income of farmers will increase.

Maximum Likelihood and Bayesian Estimation of Repeatability Index: Application of Estimating Ratio of Variance Components

An index of repeatability is constructed to evaluate the relative magnitude of measurement error. This index is constructed as a ratio of two variance components. Estimation of the index is derived under the one-way random effects model. We compare the well-known maximum likelihood estimator to the Bayesian estimation procedure using non-informative prior. Large sample variance of the of the maximum likelihood estimator are obtained using the inverse of Fisher’s information matrix and the delta method. Inference procedure using the. We also construct a test statistic on the equality of two repeatability indices using the Monte Carlo integration and sampling Importance re-sampling method. We illustrate the methodologies on the estimation of the index of repeatability of Gamma-glutamyl-transferase, an enzyme found in many organs all over the human body, with the highest concentrations found in the liver. This enzyme’s level is raised in the blood in most diseases that cause damage to the liver or bile ducts and is considered an essential serum marker for alcohol-related liver disease.

Utjecaj uzgoja u srodstvu na porodnu masu jaradi sanske pasmine

The study aimed to examine the effect of inbreeding on the birth weight (BW) of Saanen goat kids under the framework of the genetic animal model for maternal traits. The BW of the kids was analyzed as the inherent phenotypic trait of the kid, and not of their mothers (does) which means that the impact of the direct inbreeding (not maternal) was examined. The estimated ratios of variance components for direct genetic, indirect maternal genetic, maternal permanent environmental, and herd effects were 0.127, 0.026, 0.163, and 0.373, respectively. The average coefficient of inbreeding (F) was 2.5%, and 4.2% among the inbreds. The results of the preliminary conducted glm ANCOVA analysis implicated statistically significant inbreeding depression for BW (βF=-0.0076, P 0.05).

Confidence intervals for variance component ratios in unbalanced linear mixed models

AbstractMethods for constructing confidence intervals for variance component ratios in general unbalanced mixed models are developed. The methods are based on inverting the distribution of the signed root of the log‐likelihood ratio statistic constructed from either the restricted maximum likelihood or the full likelihood. As this distribution is intractable, the inversion is rather based on using a saddlepoint approximation to its distribution. Apart from Wald's exact method, the resulting intervals are unrivalled in terms of achieving accuracy in overall coverage, underage, and overage. Issues related to the proper “reference set” with which to judge the coverage as well as issues connected to variance ratios being nonnegative with lower bound 0 are addressed. Applications include an unbalanced nested design and an unbalanced crossed design.

Variance components and parent–offspring cor- relations of growth traits vary among the initial planting spacings in Zelkova serrata

Abstract Variance components of tree height (HT) and stem diameter at 1.3 m above the ground (DBH) were investigated for the eight open-pollinated families of Zelkova serrata (Thumb.) Makino planted with three different initial planting spacings in a progeny test site, Chiba, Japan. Parent–offspring correlations were also evaluated by using these families and their mother trees. The smallest values of HT and DBH were observed in the narrowest initial planting spacing (1.10 x 1.10 m) compared to those in medium (1.30 x 1.36 m) and wide (2.00 x 1.80 m) spacings, suggesting that adverse effects of competition with neighboring trees occurred on both height and radial growth. Similar to HT and DBH, the initial planting spacings also affected the genetic parameter estimates: the ratio of family variance component to total phenotypic variance showed the highest value in narrow initial planting spacing for both HT and DBH. Thus, family variance component might include competition effects, leading to biased genetic parameter estimates. In contrast, parent–offspring correlation coefficients showed the highest value in wide initial planting spacing where competition effect might be smaller. Therefore, the growth traits of Z. serrata might be inherited from the parent to the offspring when competition effect was small.

Nonorthogonal Optimal Partial Diallel Cross Designs for Consistent Estimation of Heritability

Diallel cross designs in the framework of random effects model are considered for the estimation of ratio of variance components, viz. heritability of crosses of inbred lines. New methods for construction of partial diallel cross (PDC) design sunder unblocked and blocked set up are proposed. The resulting designs of these methods are capable of minimizing variance of the estimator of heritability. Consistency of the estimator is also established. One of the practical advantage of the proposed series of designs is attributed to its ability to reduce number of distinct crosses over those for complete diallel cross (CDC) to an extent of 10 to 20 percent. Another heartening aspect of the proposed methods is that the blocks of these designs are incomplete and have smaller block sizes up to one-third than those of complete block designs. Note that, the variance-minimization criterion for optimality reduces to MS-optimality criterion of PDC designs defined in the context of fixed effects model. Further, the newly constructed designs are proved to be asymptotically universally optimal under fixed effects model. Since construction of these designs under blocked set up is quite involved, therefore a computer program is written in C++ for generating these designs which is provided in the Appendix.

Scaled weighted total least-squares adjustment for partial errors-in-variables model

Abstract Scaled total least-squares (STLS) unify LS, Data LS, and TLS with a different choice of scaled parameter. The function of the scaled parameter is to balance the effect of random error of coefficient matrix and observation vector for the estimate of unknown parameter. Unfortunately, there are no discussions about how to determine the scaled parameter. Consequently, the STLS solution cannot be obtained because the scaled parameter is unknown. In addition, the STLS method cannot be applied to the structured EIV casewhere the coefficient matrix contains the fixed element and the repeated random elements in different locations or both. To circumvent the shortcomings above, the study generalize it to a scaledweighted TLS (SWTLS) problem based on partial errors-in-variable (EIV) model. And the maximum likelihood method is employed to derive the variance component of observations and coefficient matrix. Then the ratio of variance component is proposed to get the scaled parameter. The existing STLS method and WTLS method is just a special example of the SWTLS method. The numerical results show that the proposed method proves to bemore effective in some aspects.

Hierarchical Bayes Small Area Estimation under a Unit Level Model with Applications in Agriculture

To studied Bayesian aspect of small area estimation using Unit level model. In this paper we proposed and evaluated new prior distribution for the ratio of variance components in unit level model rather than uniform prior. To approximate the posterior moments of small area means, Laplace approximation method is applied. This choice of prior avoids the extreme skewness, usually present in the posterior distribution of variance components. This property leads to more accurate Laplace approximation. We apply the proposed model to the analysis of horticultural data and results from the model are compared with frequestist approach and with Bayesian model of uniform prior in terms of average relative bias, average squared relative bias and average absolute bias. The numerical results obtained highlighted the superiority of using the proposed prior over the uniform prior. Thus Bayes estimators (with new prior) of small area means have good frequentist properties such as MSE and ARB as compared to other traditional methods viz., Direct, Synthetic and Composite estimators.

Quantifying intraclass correlations for count and time-to-event data.

The intraclass correlation is commonly used with clustered data. It is often estimated based on fitting a model to hierarchical data and it leads, in turn, to several concepts such as reliability, heritability, inter-rater agreement, etc. For data where linear models can be used, such measures can be defined as ratios of variance components. Matters are more difficult for non-Gaussian outcomes. The focus here is on count and time-to-event outcomes where so-called combined models are used, extending generalized linear mixed models, to describe the data. These models combine normal and gamma random effects to allow for both correlation due to data hierarchies as well as for overdispersion. Furthermore, because the models admit closed-form expressions for the means, variances, higher moments, and even the joint marginal distribution, it is demonstrated that closed forms of intraclass correlations exist. The proposed methodology is illustrated using data from agricultural and livestock studies.

Genetic Variability of Show Jumping Attributes in Young Horses Commencing Competing.

The aim of the study was to select traits that may constitute a prospective criterion for breeding value prediction of young horses. The results of 1,232 starts of 894 four-, five-, six-, and seven-year-old horses, obtained during jumping championships for young horses which had not been evaluated in, alternative to championships, training centres were analyed. Nine traits were chosen of those recorded: ranking in the championship, elimination (y/n), conformation, rating of style on day one, two, and three, and penalty points on day one, two, and three of a championship. (Co)variance components were estimated via the Gibbs sampling procedure and adequate (co)variance component ratios were calculated. Statistical classifications were trait dependent but all fitted random additive genetic and permanent environment effects. It was found that such characteristics as penalty points and jumping style are potential indicators of jumping ability, and the genetic variability of the traits was within the range of 14% to 27%. Given the low genetic correlations between the conformation and other results achieved on the parkour, the relevance of assessment of conformation in four-years-old horses has been questioned.

Improved Large-Sample Confidence Intervals for Ratios of Variance Components in Nonnormal Distributions

The confidence level of the usual interval for a ratio of variance components is contingent on normally distributed random variables. In this article we focus on confidence intervals for ratios of variance components in balanced one-way random effects models based on the large-sample properties of restricted maximum likelihood (REML) estimators. While this procedure does not require that the random variables be normally distributed, one must estimate a parameter that is a function of the kurtosis of the underlying distributions. Simulation results indicate that REML-based confidence interval methods outperform other well-known methods in the majority of the cases considered.

Bayes Factor Consistency for One-way Random Effects Model

In this article, we consider Bayesian hypothesis testing for the balanced one-way random effects model. A special choice of the prior formulation for the ratio of variance components is shown to yield an explicit closed-form Bayes factor without integral representation. Furthermore, we study the consistency issue of the resulting Bayes factor under three asymptotic scenarios: either the number of units goes to infinity, the number of observations per unit goes to infinity, or both go to infinity. Finally, the behavior of the proposed approach is illustrated by simulation studies.