scholarly journals Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population

Genetics ◽  
2020 ◽  
Vol 215 (3) ◽  
pp. 579-595 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Dorcus C. Gemenet ◽  
Marcelo Mollinari ◽  
Bode A. Olukolu ◽  
Joshua C. Wood ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Ipomoea Batatas ◽  
Random Effect ◽  
Random Effect Model ◽  
Phenotypic Data ◽  
Mixed Effect ◽  
Gene Search ◽  
Effect Model ◽  
Multiple Qtl ◽  
Model Approach

In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n=6x=90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population (‘Beauregard’ × ‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

scholarly journals Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population

2019 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Dorcus C. Gemenet ◽  
Marcelo Mollinari ◽  
Bode A. Olukolu ◽  
Joshua C. Wood ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Ipomoea Batatas ◽  
Random Effect ◽  
Random Effect Model ◽  
Phenotypic Data ◽  
Mixed Effect ◽  
Gene Search ◽  
Effect Model ◽  
Multiple Qtl ◽  
Model Approach

ABSTRACTIn developing countries, the sweetpotato,Ipomoea batatas(L.) Lam. (2n= 6x= 90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can only fit a single QTL and are generally hard to interpret. Here we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato bi-parental population (‘Beauregard’בTanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly predicted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every cM position. Multiple interval mapping was performed using our R package QTLPOLY and detected a total of 41 QTL, ranging from one to ten QTL per trait. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits and provided basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions allowed us to characterize additive allele effects as well as to compute QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids.

scholarly journals Effectiveness of Chitosan as a Dietary Supplement in Lowering Cholesterol in Murine Models: A Meta-Analysis

Marine Drugs ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. 26
Author(s):  
Sung-Il Ahn ◽  
Sangbuem Cho ◽  
Nag-Jin Choi
Keyword(s):  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Hdl Cholesterol ◽  
Effect Sizes ◽  
Murine Models ◽  
Mixed Effect ◽  
Related Disease ◽  
Effect Model ◽  
Regression Test

This study presents a meta-analysis of studies that investigate the effectiveness of chitosan administration on lifestyle-related disease in murine models. A total of 34 published studies were used to evaluate the effect of chitosan supplementation. The effect sizes for various items after chitosan administration were evaluated using the standardized mean difference. Using Cochran’s Q test, the heterogeneity of effect sizes was assessed, after which a meta-ANOVA and -regression test was conducted to explain the heterogeneity of effect sizes using the mixed-effect model. Publication bias was performed using Egger’s linear regression test. Among the items evaluated, blood triglyceride and HDL-cholesterol showed the highest heterogeneity, respectively. Other than blood HDL-cholesterol, total cholesterol, and triglyceride in feces, most items evaluated showed a negative effect size with high significance in the fixed- and random-effect model (p < 0.0001). In the meta-ANOVA and -regression test, administering chitosan and resistant starch was revealed to be most effective in lowering body weight. In addition, chitosan supplementation proved to be an effective solution for serum TNF-α inhibition. In conclusion, chitosan has been shown to be somewhat useful in improving symptoms of lifestyle-related disease. Although there are some limitations in the results of this meta-analysis due to the limited number of animal experiments conducted, chitosan administration nevertheless shows promise in reducing the risk of cholesterol related metabolic disorder.

Sparse Canonical Covariance Analysis for High-throughput Data

2011 ◽  
Vol 10 (1) ◽  
Author(s):  
Woojoo Lee ◽  
Donghwan Lee ◽  
Youngjo Lee ◽  
Yudi Pawitan
Keyword(s):  
Random Effect ◽  
Random Effect Model ◽  
Model Identification ◽  
Penalty Functions ◽  
Covariance Analysis ◽  
Simulation Studies ◽  
Linear Combinations ◽  
Cancer Dataset ◽  
Effect Model ◽  
Model Approach

Canonical covariance analysis (CCA) has gained popularity as a method for the analysis of two sets of high-dimensional genomic data. However, it is often difficult to interpret the results because canonical vectors are linear combinations of all variables, and the coefficients are typically nonzero. Several sparse CCA methods have recently been proposed for reducing the number of nonzero coefficients, but these existing methods are not satisfactory because they still give too many nonzero coefficients. In this paper, we propose a new random-effect model approach for sparse CCA; the proposed algorithm can adapt arbitrary penalty functions to CCA without much computational demands. Through simulation studies, we compare various penalty functions in terms of the performance of correct model identification. We also develop an extension of sparse CCA to address more than two sets of variables on the same set of observations. We illustrate the method with an analysis of the NCI cancer dataset.

Analisis Pengaruh Kepemilikan Blockholder, Kepemilikan Manajerial, Kepemilikan Institusional, dan Komite Audit terhadap Nilai Perusahaan

2018 ◽  
Vol 2 (1) ◽  
pp. 96-121
Author(s):  
Iwan Wirawardhana ◽  
Meco Sitardja
Keyword(s):  
Firm Value ◽  
Audit Committee ◽  
Stock Exchange ◽  
Random Effect ◽  
Random Effect Model ◽  
Institutional Ownership ◽  
Managerial Ownership ◽  
Estimation Model ◽  
Effect Model ◽  
Positive Effect

The aim of this study is to analyse the effect of Blockholder Ownership, Managerial Ownership,Institutional Ownership, and Audit Committee towards Firm Value. The background of this research isthe agency theory and ownership theory. The population in this study are 46 property companies listedon the Indonesia Stock Exchange (IDX) for the period 2012-2016. By using purposive samplingtechnique, 35 companies are qualified as data samples. This research uses the random effect model asthe estimation model and multiple regression as the method of analysis. The results of this study showsthat Institutional Ownership has a positive effect on Firm Value. Meanwhile, Blockholder Ownership,Managerial Ownership, and Audit Committee have no effect on Firm Value. Moreover, the F-testimplies that the variables, blockholder ownership, managerial ownership, institutional ownership, andaudit committee, simultaneously influence firm value.

scholarly journals Alteration of Postural Balance in Patients with Fibromyalgia Syndrome—A Systematic Review and Meta-Analysis

Diagnostics ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 127
Author(s):  
David Núñez-Fuentes ◽  
Esteban Obrero-Gaitán ◽  
Noelia Zagalaz-Anula ◽  
Alfonso Javier Ibáñez-Vera ◽  
Alexander Achalandabaso-Ochoa ◽  
...  
Keyword(s):  
Systematic Review ◽  
Postural Balance ◽  
Fibromyalgia Syndrome ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Healthy Controls ◽  
Functional Balance ◽  
Sensory Organization ◽  
Effect Model

Balance problems are one of the most frequent symptoms in patients with Fibromyalgia Syndrome (FMS). However, the extent and nature of this balance disorder are not known. The objective of this work was to determine the best evidence for the alteration of postural balance in patients with FMS and analyze differences with healthy controls. To meet this objective, a systematic review with meta-analysis was performed. A bibliographical search was carried out in PubMed Medline, Scopus, Web of Science, CINAHL and SciELO. Observational studies that assessed postural balance in patients with FMS compared to healthy subjects in baseline conditions, were selected. In a random-effect model, the pooled effect was calculated with the Standardized Mean Difference (SMD) and its 95% confidence interval (CI). Nineteen studies reporting data of 2347 participants (95% female) were included. FMS patients showed poor balance with a large effect on static (SMD = 1.578; 95% CI = 1.164, 1.992), dynamic (SMD = 0.946; 95% CI = 0.598, 1.294), functional balance (SMD = 1.138; 95% CI = 0.689, 1.588) and on balance confidence (SMD = 1.194; 95% CI = 0.914, 1.473). Analysis of the Sensory Organization Test showed large alteration of vestibular (SMD = 1.631; 95% CI = 0.467, 2.795) and visual scores (SMD = 1.317; 95% CI = 0.153, 2.481) compared to healthy controls. Patients with FMS showed worse scores for different measures of postural balance compared to healthy controls. Concretely, FMS patients appear to have poor vestibular and visual scores with a possible somatosensory dependence.

scholarly journals Designing a Bonus-Malus system reflecting the claim size under the dependent frequency–severity model

2021 ◽  
pp. 1-25
Author(s):  
Rosy Oh ◽  
Joseph H.T. Kim ◽  
Jae Youn Ahn
Keyword(s):  
Recent Literature ◽  
Insurance Industry ◽  
Random Effect ◽  
Random Effect Model ◽  
Partial Solution ◽  
Risk Classification ◽  
Transition Rule ◽  
Auto Insurance ◽  
Dependent Frequency ◽  
Effect Model

In the auto insurance industry, a Bonus-Malus System (BMS) is commonly used as a posteriori risk classification mechanism to set the premium for the next contract period based on a policyholder's claim history. Even though the recent literature reports evidence of a significant dependence between frequency and severity, the current BMS practice is to use a frequency-based transition rule while ignoring severity information. Although Oh et al. [(2020). Bonus-Malus premiums under the dependent frequency-severity modeling. Scandinavian Actuarial Journal 2020(3): 172–195] claimed that the frequency-driven BMS transition rule can accommodate the dependence between frequency and severity, their proposal is only a partial solution, as the transition rule still completely ignores the claim severity and is unable to penalize large claims. In this study, we propose to use the BMS with a transition rule based on both frequency and size of claim, based on the bivariate random effect model, which conveniently allows dependence between frequency and severity. We analytically derive the optimal relativities under the proposed BMS framework and show that the proposed BMS outperforms the existing frequency-driven BMS. Later, numerical experiments are also provided using both hypothetical and actual datasets in order to assess the effect of various dependencies on the BMS risk classification and confirm our theoretical findings.

scholarly journals Magnitude and determinants of neural tube defect in Africa: a systematic review and meta-analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Daniel Atlaw ◽  
Yohannes Tekalegn ◽  
Biniyam Sahiledengle ◽  
Kenbon Seyoum ◽  
Damtew Solomon ◽  
...  
Keyword(s):  
Systematic Review ◽  
Neural Tube ◽  
Meta Analysis ◽  
Random Effect ◽  
Random Effect Model ◽  
Folic Acid Supplementation ◽  
Maternal Exposure ◽  
X Ray ◽  
Effect Model ◽  
Pooled Prevalence

Abstract Background Neural tube defects (NTDs) are a group of disorders that arise from the failure of the neural tube close between 21 and 28 days after conception. About 90% of neural tube defects and 95% of death due to these defects occurs in low-income countries. Since these NTDs cause considerable morbidity and mortality, this study aimed to determine the prevalence and associated factors of NTDs in Africa. Methods The protocol of this study was registered in the International Prospective Register of Systematic Reviews (PROSPERO number: CRD42020149356). All major databases such as PubMed/MEDLINE, EMBASE, CINAHL, Web of Science, African Journals Online (AJOL), and Google Scholar search engine were systematically searched. A random-effect model was used to estimate the pooled prevalence of NTDs in Africa, and Cochran’s Q-statistics and I2 tests were used to assess heterogeneity between included studies. Publication bias was assessed using Begg ’s tests, and the association between determinant factors and NTDs was estimated using a random-effect model. Results Of the total 2679 articles, 37 articles fulfilled the inclusion criteria and were included in this systematic review and meta-analysis. The pooled prevalence of NTDs in Africa was 50.71 per 10,000 births (95% CI: 48.03, 53.44). Folic acid supplementation (AOR: 0.40; 95% CI: 0.19–0.85), maternal exposure to pesticide (AOR: 3.29; 95% CI: 1.04–10.39), mothers with a previous history of stillbirth (AOR: 3.35, 95% CI: 1.99–5.65) and maternal exposure to x-ray radiation (AOR 2.34; 95% CI: 1.27–4.31) were found to be determinants of NTDs. Conclusions The pooled prevalence of NTDs in Africa was found to be high. Maternal exposure to pesticides and x-ray radiation were significantly associated with NTDs. Folic acid supplementation before and within the first month of pregnancy was found to be a protective factor for NTDs.

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