De novo construction of polyploid linkage maps using discrete graphical models

Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. We propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a nonparanormal skeptic approach. Linkage groups (LGs), typically chromosomes, and the order of markers in each LG are determined by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors and are incomplete. We apply the proposed method to two genotype datasets: barley and potato from diploid and polypoid populations, respectively. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We have implemented the method in the R package netgwas.Comment: 25 pages, 7 figure

Performance of multicell, axial-entry cyclones for industrial gas cleaning

Imperial Users onl

netgwas: An R Package for Network-Based Genome-Wide Association Studies

Graphical models are powerful tools for modeling and making statistical inferences regarding complex associations among variables in multivariate data. In this paper we introduce the R package netgwas, which is designed based on undirected graphical models to accomplish three important and interrelated goals in genetics: constructing linkage map, reconstructing linkage disequilibrium (LD) networks from multi-loci genotype data, and detecting high-dimensional genotype-phenotype networks. The netgwas package deals with species with any chromosome copy number in a unified way, unlike other software. It implements recent improvements in both linkage map construction (Behrouzi and Wit, 2018), and reconstructing conditional independence network for non-Gaussian continuous data, discrete data, and mixed discrete-and-continuous data (Behrouzi and Wit, 2017). Such datasets routinely occur in genetics and genomics such as genotype data, and genotype-phenotype data. We demonstrate the value of our package functionality by applying it to various multivariate example datasets taken from the literature. We show, in particular, that our package allows a more realistic analysis of data, as it adjusts for the effect of all other variables while performing pairwise associations. This feature controls for spurious associations between variables that can arise from classical multiple testing approach. This paper includes a brief overview of the statistical methods which have been implemented in the package. The main body of the paper explains how to use the package. The package uses a parallelization strategy on multi-core processors to speed-up computations for large datasets. In addition, it contains several functions for simulation and visualization. The netgwas package is freely available at https://cran.r-project.org/web/packages/netgwasComment: 32 pages, 9 figures; due to the limitation "The abstract field cannot be longer than 1,920 characters", the abstract appearing here is slightly shorter than that in the PDF fil

The Stone–Čech Compactification of Groupoids

Let G be a discrete groupoid. Consider the Stone–Čech compactification βG of G. We extend the operation on the set of composable elements G (²) of G to the operation * on a subset (βG)(²) of βG×βG such that the triple (βG, (βG)(²), *) is a compact right topological semigroupoid.Нехай G — дискретний групоїд. Розглянемо компактифікацію Стоуна-Чexa βG групоїда G. Розширимо операцію на множині G(²) єлємєнтів G, що компонуються, до операції "*" на підмножині (βG)(²) множини βG×βG такої, що трійка (βG,(βG)(²) є компактним топологічним напівгрупоїдом

The Relationship Between Teachers’ and Learners’ Gender and Their View on Principles of Critical Pedagogy

Although there are a lot of research studies conducted in the area of critical pedagogy (CP), little attention has been paid to the comparative investigation of Iranian EFL teachers and learners’ views toward CP with regard to their gender. This study aimed to investigate the relationship between teachers’ and learners’ gender and their view on principles of critical pedagogy. To this end, 143 students and 37 teachers were randomly selected from language institutes in Shiraz, Iran. Based on the results of a Quick Placement Test (QPT), the students were homogeneously divided into three groups of elementary (scoring from 0 to 29), intermediate (scoring from 30 to 47), and advanced (scoring from 48 to 60) levels. Then, to explore teachers’ views and their views toward CP, the Farsi version of Yilmaz (2009) CP questionnaire was administered. Findings showed that there is not a significant difference between male and female participants with regard to their views toward CP. Findings of this study can not only be used by learners and teachers as well as curriculum developers, but they also can be useful as new windows for further research by experts.  Keywords: critical pedagogy, attitude, critical thinking, gender, EFL learners and teachers

Jewish North African head adornment: Traditions and Transition

The author discusses the craftsmanship of head adornment, particularly jewellery and embroidery, made by diáspora Jews in the Maghreb in the late 19th and the 20th centuries. The religious meaning of the iconographic elements involved was part of an artistic tradition that goes back to the work of the Spanish Jews before 1492; nevertheless, the craftsmen had to deal with the Islamic environment of the societies in which they lived. The 20th century has seen a gradual departure from these traditional patterns and a subsequent preference for those of contemporary western culture.La autora analiza la artesanía del tocado, particularmente en joyería y bordado, hecha por judíos de la diáspora residentes en el Magreb a finales del siglo XIX y a lo largo del XX. El sentido religioso de los diversos elementos iconográficos incorporados al trabajo revela una tradición artística que se remonta a los artesanos judíos de la España anterior a 1492, pero que tenía que recibir influencias del contexto islámico de las sociedades en las que ese trabajo tenía lugar. A lo largo del siglo XX, esta tradición ha ido desapareciendo progresivamente, surgiendo en su lugar elementos procedentes de la cultura occidental contemporánea