Bayesian hierarchical regression models for detecting QTLs in plant experiments

Quantitative trait loci (QTL) mapping is a growing field in statistical genetics. In plants, QTL detection experiments often feature replicates or clones within a specific genetic line. In this work, a Bayesian hierarchical regression model is applied to simulated QTL data and to a dataset from the Arabidopsis thaliana plants for locating the QTL mapping associated with cotyledon opening. A conditional model search strategy based on Bayesian model averaging is utilized to reduce the computational burden.     

A frequentist assessment of Bayesian inclusion probabilities for screening predictors

Bayesian inclusion probabilities have become a popular tool for variable assessment. From a frequentist perspective, it is often difficult to evaluate these probabilities as typically no Type I error rates are considered, neither are any explorations of power of the methods given. This paper considers how a frequentist may evaluate Bayesian inclusion probabilities for screening predictors. This evaluation looks at both unrestricted and restricted model spaces and develops a framework which a frequentist can utilize inclusion probabilities that preserve Type I error rates. Furthermore, this framework is applied to an analysis of the Arabidopsis thaliana with respect to determining quantitative trait loci associated with cotelydon opening angle.     

“合同履行地”管辖规则在“网上履行”合同案件中的适用

由于“网上履行”合同的履行发生在网上，不存在物理交付，使得在依“合同履行地”特别管辖规则对此类电子合同案件确定管辖权时，因合同履行地难以寻找而遭遇困境。在网上履行的情况下，合同履行地管辖规则适用的重点在于：根据合同交易的内容和方式，确定其交易性质，以确定合同履行地；需兼顾诉讼各方利益，在运用信息传送地、接收地方法的同时，考量网上行为与管辖地的关联度，合理确定管辖权。     

Mapping quantitative trait loci using both extremely discordant and concordant sib pairs: a unified approach for meta-analysis

Extremely discordant (ED) and concordant (EC) sib pairs are recommended by Risch and Zhang ( 1995, 1996 ) and Zhang and Risch ( 1996 ) for the detection of linkage on the basis of power analysis. They did not, however, include both discordant and concordant sib pairs simultaneously in the test statistic. We construct a new test statistic including both types of sib pairs. The size of the sample needed to identify the sib pairs and parents, who will be genotyped, is reduced substantially by including a hybrid of discordant and concordant sib pairs in the analysis. This mixed design also provides a common parameter that simplifies meta-analysis of sib pair linkage studies.     

Identification of quantitative trait loci for canine hip dysplasia by two sequential multipoint linkage analyses

Canine hip dysplasia (CHD) is characterized by hip laxity and subluxation that can lead to hip osteoarthritis. Studies have shown the involvement of multiple genetic regions in the expression of CHD. Although we have associated some variants in the region of fibrillin 2 with CHD in a subset of dogs, no major disease-associated gene has been identified. The focus of this study is to identify quantitative trait loci (QTL) associated with CHD. Two sequential multipoint linkage analyses based on a reversible jump Markov chain Monte Carlo approach were applied on a cross-breed pedigree of 366 dogs. Hip radiographic trait (Norberg Angle, NA) on both hips of each dog was tested for linkage to 21,455 single nucleotide polymorphisms across 39 chromosomes. Putative QTL for the NA was found on 11 chromosomes (1, 2, 3, 4, 7, 14, 19, 21, 32, 36, and 39). Identification of genes in the QTL region(s) can assist in identification of the aberrant genes and biochemical pathways involving hip dysplasia in both dogs and humans.     

Evaluation of incomplete multiple diagnostic tests,with an application in the colon cancer family registry study

Accurate diagnosis of a molecularly defined subtype of cancer is often an important step toward its effective control and treatment. For the diagnosis of some subtypes of a cancer, a gold standard with perfect sensitivity and specificity may be unavailable. In those scenarios, tumor subtype status is commonly measured by multiple imperfect diagnostic markers. Additionally, in many such studies, some subjects are only measured by a subset of diagnostic tests and the missing probabilities may depend on the unknown disease status. In this paper, we present statistical methods based on the EM algorithm to evaluate incomplete multiple imperfect diagnostic tests under a missing at random assumption and one missing not at random scenario. We apply the proposed methods to a real data set from the National Cancer Institute (NCI) colon cancer family registry on diagnosing microsatellite instability for hereditary non-polyposis colorectal cancer to estimate diagnostic accuracy parameters (i.e. sensitivities and specificities), prevalence, and potential differential missing probabilities for 11 biomarker tests. Simulations are also conducted to evaluate the small-sample performance of our methods.     

Standard statistical tools for the breed allocation problem

Modern technologies are frequently used in order to deal with new genomic problems. For instance, the STRUCTURE software is usually employed for breed assignment based on genetic information. However, standard statistical techniques offer a number of valuable tools which can be successfully used for dealing with most problems. In this paper, we investigated the capability of microsatellite markers for individual identification and their potential use for breed assignment of individuals in seventy Lidia breed lines and breeders. Traditional binomial logistic regression is applied to each line and used to assign one individual to a particular line. In addition, the area under receiver operating curve (AUC) criterion is used to measure the capability of the microsatellite-based models to separate the groups. This method allows us to identify which microsatellite loci are related to each line. Overall, only one subject was misclassified or a 99.94% correct allocation. The minimum observed AUC was 0.986 with an average of 0.997. These results suggest that our method is competitive for animal allocation and has some interpretative advantages and a strong relationship with methods based on SNPs and related techniques.     

中国园林化教育环境的场所精神及其文化传统浅析

园林的核心本质与教育环境的场所精神有密切的关系。中国古代园林化教育环境与近代校园规划实例虽然形态各异,但在场所精神的追求上却一脉相承。在以儒学、理学为代表的传统文化影响下,园林化环境中蕴涵的人生理想、美学意识和人文关怀,是中国文化中最富生命力的基因,也是教育环境的场所精神之所在。     

Order-restricted hypothesis testing in a variation of the normal mixture model

This paper examines likelihood-ratio tests concerning the relationships among a fixed number of univariate normal means given a sample of normal observations whose population membership is uncertain. The asymptotic null distributions of likelihood-ratio test statistics are derived for a class of tests including hypotheses which place linear inequality constraints on the normal means. The use of such tests in the interval mapping of quantitative trait loci is addressed.     

Kin-related social organization in a winter population of the voleClethrionomys rufocanus

Kinship amongClethrionomys rufocanus was investigated during the winter of 1992/93 in a 3-ha enclosure using both molecular and catch-mark-release techniques. Forty-six adult voles (22 males and 24 females) having high heterozygosities, which were collected from several natural populations, were released into the enclosure on 29 September 1992. Most fall-born individuals of both sexes stayed in their natal site during the non-breeding period (December–March), although reproductively active females dispersed during the fall breeding season (October–November). These philopatric individuals aggregated and formed an maternal family in the winter. Several females which failed to reproduce were solitary during this season. Some individuals which were derived from several families also aggregated into a mixed lineage group. Survival rate of fall-born voles from earlier litters was higher than that from later ones. Maternal families broke up soon after the onset of spring reproduction. Most females established a territory near the wintering site and made a kincluster, in which close relatives neighbored each other. Maternal families in winter bring about female kin-clusters in spring, which may influence reproductive output in the breeding season.