A regression model with skew-normal errors provides a useful extension for traditional normal regression models when the data involve asymmetric outcomes.Moreover,data that arise from a heterogeneous population can be...A regression model with skew-normal errors provides a useful extension for traditional normal regression models when the data involve asymmetric outcomes.Moreover,data that arise from a heterogeneous population can be efficiently analysed by a finite mixture of regression models.These observations motivate us to propose a novel finite mixture of median regression model based on a mixture of the skew-normal distributions to explore asymmetrical data from several subpopulations.With the appropriate choice of the tuning parameters,we establish the theoretical properties of the proposed procedure,including consistency for variable selection method and the oracle property in estimation.A productive nonparametric clustering method is applied to select the number of components,and an efficient EM algorithm for numerical computations is developed.Simulation studies and a real data set are used to illustrate the performance of the proposed methodologies.展开更多
Familial colorectal cancer constitutes a heterogeneous group of patients in whom the underlying molecular mechanism is still unknown.Predisposition to a such neoplasms in this setting seems to be due to common low-pen...Familial colorectal cancer constitutes a heterogeneous group of patients in whom the underlying molecular mechanism is still unknown.Predisposition to a such neoplasms in this setting seems to be due to common low-penetrance genetic components,but the role of genetic testing in clinical practice has to be determined.Although screening guidelines in this moderate-risk population are empiric,data obtained in epidemiologic,meta-analyses and cohort studies and,more recently,the increased risk of advanced adenomas in first degree relatives who underwent screening colonoscopy support the need to include these individuals in specific screening programs.However,data to determine what test to use,how often to use and which organizational strategy to implement are needed.At present,screening uptake in this population is less than optimal;offering the opportunity to access to screening and improving screening uptake is a first significant step.展开更多
The main purpose of this paper is to obtain estimates of parameters, reliability and hazard rate functions of a heterogeneous population represented by finite mixture of two general components. The doubly Type II cens...The main purpose of this paper is to obtain estimates of parameters, reliability and hazard rate functions of a heterogeneous population represented by finite mixture of two general components. The doubly Type II censoring of generalized order statistics scheme is used. Maximum likelihood and Bayes methods of estimation are used for this purpose. The two methods of estimation are compared via a Monte Carlo Simulation study.展开更多
This article is concerned with the problem of prediction for the future generalized order statistics from a mixture of two general components based on doubly?type II censored sample. We consider the one sample predict...This article is concerned with the problem of prediction for the future generalized order statistics from a mixture of two general components based on doubly?type II censored sample. We consider the one sample prediction and two sample prediction techniques. Bayesian prediction intervals for the median of future sample of generalized order statistics having odd and even sizes are obtained. Our results are specialized to ordinary order statistics and ordinary upper record values. A mixture of two Gompertz components model is given as an application. Numerical computations are given to illustrate the procedures.展开更多
Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study...Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.展开更多
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics.The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a cons...We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics.The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte Carlo method to simulate time-dependent statistical characteristics of growing cell populations.To benchmark performance,we compare simulation results with steadystate and time-dependent analytical solutions for several scenarios,including steadystate and time-dependent gene expression,and the effects on population heterogeneity of cell growth,division,and DNA replication.This comparison demonstrates that the algorithm provides an efficient and accurate approach to simulate how complex biological features influence gene expression.We also use the algorithm to model gene expression dynamics within"bet-hedging"cell populations during their adaption to environmental stress.These simulations indicate that the algorithm provides a framework suitable for simulating and analyzing realistic models of heterogeneous population dynamics combining molecular-level stochastic reaction kinetics,relevant physiological details and phenotypic variability.展开更多
Since the F_(5)(2005),three winter wheat composite cross populations(CCPs)based on germplasm specifically suitable for low-input conditions were subjected to natural selection under organic and conventional management...Since the F_(5)(2005),three winter wheat composite cross populations(CCPs)based on germplasm specifically suitable for low-input conditions were subjected to natural selection under organic and conventional management.In the F_(6),each CCP was divided into two parallel populations(12 CCPs in total)and maintained continuously until 2018.Commonly used modern cultivars with different disease susceptibilities were grown alongside to assess the agronomic performance of the CCPs.The organically managed CCPs were comparable in yield and foliar disease resistance to two continuously used reference cultivars,Achat and Capo.In contrast,under conventional management the cv.Capo outyielded the CCPs(Achat was not tested),highlighting the importance of parental cultivar choice for specific management systems.The CCPs were found to be moderately resistant to brown rust and even to the newly emerged stripe rust races prevalent in Europe since 2011.Differences between the CCPs were mainly due to parental genetic background and were significant in the first five generations,but were no longer so in the last five generations.In addition,these differences tended to vary depending on the experimental year and the environmental stresses present.In conclusion,the CCPs despite being derived from older cultivars are able to compete with more recently released reference cultivars under organic farming practices and represent a dynamic germplasm resource.展开更多
基金the National Natural Science Foundation of China[grant number 11861041]the Natural Science Research Foundation of Kunming University of Science and Technology[grant number KKSY201907003].
文摘A regression model with skew-normal errors provides a useful extension for traditional normal regression models when the data involve asymmetric outcomes.Moreover,data that arise from a heterogeneous population can be efficiently analysed by a finite mixture of regression models.These observations motivate us to propose a novel finite mixture of median regression model based on a mixture of the skew-normal distributions to explore asymmetrical data from several subpopulations.With the appropriate choice of the tuning parameters,we establish the theoretical properties of the proposed procedure,including consistency for variable selection method and the oracle property in estimation.A productive nonparametric clustering method is applied to select the number of components,and an efficient EM algorithm for numerical computations is developed.Simulation studies and a real data set are used to illustrate the performance of the proposed methodologies.
文摘Familial colorectal cancer constitutes a heterogeneous group of patients in whom the underlying molecular mechanism is still unknown.Predisposition to a such neoplasms in this setting seems to be due to common low-penetrance genetic components,but the role of genetic testing in clinical practice has to be determined.Although screening guidelines in this moderate-risk population are empiric,data obtained in epidemiologic,meta-analyses and cohort studies and,more recently,the increased risk of advanced adenomas in first degree relatives who underwent screening colonoscopy support the need to include these individuals in specific screening programs.However,data to determine what test to use,how often to use and which organizational strategy to implement are needed.At present,screening uptake in this population is less than optimal;offering the opportunity to access to screening and improving screening uptake is a first significant step.
文摘The main purpose of this paper is to obtain estimates of parameters, reliability and hazard rate functions of a heterogeneous population represented by finite mixture of two general components. The doubly Type II censoring of generalized order statistics scheme is used. Maximum likelihood and Bayes methods of estimation are used for this purpose. The two methods of estimation are compared via a Monte Carlo Simulation study.
文摘This article is concerned with the problem of prediction for the future generalized order statistics from a mixture of two general components based on doubly?type II censored sample. We consider the one sample prediction and two sample prediction techniques. Bayesian prediction intervals for the median of future sample of generalized order statistics having odd and even sizes are obtained. Our results are specialized to ordinary order statistics and ordinary upper record values. A mixture of two Gompertz components model is given as an application. Numerical computations are given to illustrate the procedures.
基金supported by National Natural Science Foundation of China(31790413)supported by National Natural Science Foundation of China(31760657)。
文摘Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.
基金the National Science and Engineering Research Council of Canada(NSERC)the Canadian Institutes of Health Research(CIHR)+1 种基金the Academy of Finland(Application Number 129657,Finnish Programme for Centres of Excellence in Research 2006-2011,and 124615)the Tampere Graduate School in Information Science and Engineering(TISE).
文摘We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics.The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte Carlo method to simulate time-dependent statistical characteristics of growing cell populations.To benchmark performance,we compare simulation results with steadystate and time-dependent analytical solutions for several scenarios,including steadystate and time-dependent gene expression,and the effects on population heterogeneity of cell growth,division,and DNA replication.This comparison demonstrates that the algorithm provides an efficient and accurate approach to simulate how complex biological features influence gene expression.We also use the algorithm to model gene expression dynamics within"bet-hedging"cell populations during their adaption to environmental stress.These simulations indicate that the algorithm provides a framework suitable for simulating and analyzing realistic models of heterogeneous population dynamics combining molecular-level stochastic reaction kinetics,relevant physiological details and phenotypic variability.
基金This work was financed partly through the“Zentrale Forschungsförderung”University of Kassel,“Bundesprogramm Okologischer Landbau und andere Formen nachhaltiger Landwirtschaft”Project No.2812OE021 in the framework of CORE Organic II and through the INSUSFAR(INnovative approaches to optimize genetic diversity for SUStainable FARming systems of the future)Project(FKZ 031A350C)financed by the“Bundesministerium für Bildung und Forschung”in the framework of the IPAS(Innovative Pflanzenzüchtung im Anbausystem)Initiative and the EU-project ReMIX(Horizon 2020 Project No.727217).
文摘Since the F_(5)(2005),three winter wheat composite cross populations(CCPs)based on germplasm specifically suitable for low-input conditions were subjected to natural selection under organic and conventional management.In the F_(6),each CCP was divided into two parallel populations(12 CCPs in total)and maintained continuously until 2018.Commonly used modern cultivars with different disease susceptibilities were grown alongside to assess the agronomic performance of the CCPs.The organically managed CCPs were comparable in yield and foliar disease resistance to two continuously used reference cultivars,Achat and Capo.In contrast,under conventional management the cv.Capo outyielded the CCPs(Achat was not tested),highlighting the importance of parental cultivar choice for specific management systems.The CCPs were found to be moderately resistant to brown rust and even to the newly emerged stripe rust races prevalent in Europe since 2011.Differences between the CCPs were mainly due to parental genetic background and were significant in the first five generations,but were no longer so in the last five generations.In addition,these differences tended to vary depending on the experimental year and the environmental stresses present.In conclusion,the CCPs despite being derived from older cultivars are able to compete with more recently released reference cultivars under organic farming practices and represent a dynamic germplasm resource.
