Efficiency of genomic selection using Bayesian multi-marker models for traits selected to reflect a wide range of heritabilities and frequencies of detected quantitative traits loci in mice

BACKGROUND: Genomic selection uses dense single nucleotide polymorphisms (SNP) markers to predict breeding values, as compared to conventional evaluations which estimate polygenic effects based on phenotypic records and pedigree information. The objective of this study was to compare polygenic, genomic and combined polygenic-genomic models, including mixture models (labelled according to the percentage of genotyped SNP markers considered to have a substantial effect, ranging from 2.5% to 100%). The data consisted of phenotypes and SNP genotypes (10,946 SNPs) of 2,188 mice. Various growth, behavioural and physiological traits were selected for the analysis to reflect a wide range of heritabilities (0.10 to 0.74) and numbers of detected quantitative traits loci (QTL) (1 to 20) affecting those traits. The analysis included estimation of variance components and cross-validation within and between families. RESULTS: Genomic selection showed a high predictive ability (PA) in comparison to traditional polygenic selection, especially for traits of moderate heritability and when cross-validation was between families. This occurred although the proportion of genomic variance of traits using genomic models was 22 to 33% smaller than using polygenic models. Using a 2.5% mixture genomic model, the proportion of genomic variance was 79% smaller relative to the polygenic model. Although the proportion of variance explained by the markers was reduced further when a smaller number of SNPs was assumed to have a substantial effect on the trait, PA of genomic selection for most traits was little affected. These low mixture percentages resulted in improved estimates of single SNP effects. Genomic models implemented for traits with fewer QTLs showed even lower PA than the polygenic models. CONCLUSIONS: Genomic selection generally performed better than traditional polygenic selection, especially in the context of between family cross-validation. Reducing the number of markers considered to affect the trait did not significantly change PA for most traits, particularly in the case of within family cross-validation, but increased the number of markers found to be associated with QTLs. The underlying number of QTLs affecting the trait has an effect on PA, with a smaller number of QTLs resulting in lower PA using the genomic model compared to the polygenic model

Pilot erfemissie van bloembollenbedrijven in Noord-Holland (Breezand)

In het Noordelijk Zandgebied in Noord-Holland worden voor enkele gewasbeschermingsmiddelen de waterkwaliteitsnormen (MTR) geregeld overschreden. In 2009 zijn telers uit een deel van de Westpolder van Anna Paulowna in de Kop van Noord Holland een samenwerkingsproject gestart om inzicht te krijgen in emissieroutes van gewasbeschermingsmiddelen vanaf het erf om daarmee emissie via deze routes te voorkomen en de waterkwaliteit in de polder te verbeteren. Eind 2010 hebben zich vier gewasbeschermingsmiddelenfabrikanten aangesloten bij de samenwerking: Certis, Bayer, Syngenta en BASF

Структурно-семантичний аналіз еврісемантів української мови (на матеріалі лексико-семантичного поля "річ")

В статье рассматриваются лексико-семантические особенности эврисемантов в украинском языке, осуществляется их семантическая классификация, методом компонентного анализа проводится структурный анализ. Представлен фрагмент иерархично упорядоченной парадигмы широкозначных имен существительных, состоящий из ЛСГ "Предмет" и "Дело".У статті розглядаються лексико-семантичні особливості еврісемантів української мови, здійснюється їх семантична класифікація, за допомогою компонентного аналізу проводиться структурний аналіз. Подається фрагмент ієрархічно впорядкованої парадигми широкозначних іменників, представлений ЛСГ "Предмет" та "Справа".In this article lexica-semantic peculiarities of everysemantical nouns in Ukrainian are considered. It was made semantic distinguishing and structural analysis of those elements. The everysemants of a lexica-semantic field "Thing", represented by two groups "Subject" and "Work", are disposed in specific hierarchy

Dependence of the Ice Water Content and Snowfall Rate on Temperature, Globally: Comparison of In-Situ Observations, Satellite Active Remote Sensing Retrievals and Global Climate Model Simulations

Cloud ice microphysical properties measured or estimated from in-situ aircraft observations are compared to global climate models and satellite active remote sensor retrievals. Two large datasets, with direct measurements of the ice water content (IWC) and encompassing data from polar to tropical regions, are combined to yield a large database of in-situ measurements. The intention of this study is to identify strengths and weaknesses of the various methods used to derive ice cloud microphysical properties. The in-situ data are measured with total water hygrometers, condensed water probes, and particle spectrometers. Data from polar, midlatitude, and tropical locations are included. The satellite data are retrieved from CloudSat/CALIPSO (2C-ICE, 2C-SNOWPROFILE), and Global Precipitation Measurement (GPM) Level2A. Although the 2CICE retrieval is for IWC, we developed a method to use the IWC to get snowfall rates (S). The GPM retrievals are for snowfall rate only. Model results are derived using the Community Atmosphere Model (CAM5) and the UK Met Office Unified Model (GA7). The retrievals and model results are related to the in-situ observations using temperature and partitioned by geographical region. Specific variables compared between the in-situ observations, models, and retrievals are the IWC and S. The retrieved IWCs are reasonably close in value to the in-situ observations, whereas the models' values are relatively low by comparison. Differences between the in-situ IWCs and those from the other methods are compounded when S is considered, leading to model snowfall rates that are considerably lower than derived from the in-situ data. Anomalous trends with temperature are noted in some instances

Modality- and task-specific brain regions involved in Chinese lexical processing

fMRI was used to examine lexical processing in native adult Chinese speakers. A 2 task (semantics and phonology) x 2 modality (visual and auditory) within-subject design was adopted. The semantic task involved a meaning association judgment and the phonological task involved a rhyming judgment to two sequentially presented words. The overall effect across tasks and modalities was used to identify seven ROIs, including the left fusiform gyrus (FG), the left superior temporal gyrus (STG), the left ventral inferior frontal gyrus (VIFG), the left middle temporal gyrus (MTG), the left dorsal inferior frontal gyrus (DIFG), the left inferior parietal lobule (IPL), and the left middle frontal gyrus (MFG). ROI analyses revealed two modality-specific areas, FG for visual and STG for auditory, and three task-specific areas, IPL and DIFG for phonology and VIFG for semantics. Greater DIFG activation was associated with conflicting tonal information between words for the auditory rhyming task, suggesting this region's role in strategic phonological processing, and greater VIFG activation was correlated with lower association between words for both the auditory and the visual meaning task, suggesting this region's role in retrieval and selection of semantic representations. The modality- and task-specific effects in Chinese revealed by this study are similar to those found in alphabetical languages. Unlike English, we found that MFG was both modality- and task-specific, suggesting that MFG may be responsible for the visuospatial analysis of Chinese characters and orthography-to-phonology integration at a syllabic level