Strategies for implementing genomic selection in family-based aquaculture breeding schemes: double haploid sib test populations

<p>Abstract</p> <p>Background</p> <p>Simulation studies have shown that accuracy and genetic gain are increased in genomic selection schemes compared to traditional aquaculture sib-based schemes. In genomic selection, accuracy of selection can be maximized by increasing the precision of the estimation of SNP effects and by maximizing the relationships between test sibs and candidate sibs. Another means of increasing the accuracy of the estimation of SNP effects is to create individuals in the test population with extreme genotypes. The latter approach was studied here with creation of double haploids and use of non-random mating designs.</p> <p>Methods</p> <p>Six alternative breeding schemes were simulated in which the design of the test population was varied: test sibs inherited maternal (<it>Mat</it>), paternal (<it>Pat</it>) or a mixture of maternal and paternal (<it>MatPat</it>) double haploid genomes or test sibs were obtained by maximum coancestry mating (<it>MaxC</it>), minimum coancestry mating (<it>MinC</it>), or random (<it>RAND</it>) mating. Three thousand test sibs and 3000 candidate sibs were genotyped. The test sibs were recorded for a trait that could not be measured on the candidates and were used to estimate SNP effects. Selection was done by truncation on genome-wide estimated breeding values and 100 individuals were selected as parents each generation, equally divided between both sexes.</p> <p>Results</p> <p>Results showed a 7 to 19% increase in selection accuracy and a 6 to 22% increase in genetic gain in the <it>MatPat</it> scheme compared to the <it>RAND</it> scheme. These increases were greater with lower heritabilities. Among all other scenarios, i.e. <it>Mat, Pat, MaxC</it>, and <it>MinC</it>, no substantial differences in selection accuracy and genetic gain were observed.</p> <p>Conclusions</p> <p>In conclusion, a test population designed with a mixture of paternal and maternal double haploids, i.e. the <it>MatPat</it> scheme, increases substantially the accuracy of selection and genetic gain. This will be particularly interesting for traits that cannot be recorded on the selection candidates and require the use of sib tests, such as disease resistance and meat quality.</p

What is the 'problem' that outreach work seeks to address and how might it be tackled? Seeking theory in a primary health prevention programme

&lt;b&gt;Background&lt;/b&gt; Preventive approaches to health are disproportionately accessed by the more affluent and recent health improvement policy advocates the use of targeted preventive primary care to reduce risk factors in poorer individuals and communities. Outreach has become part of the health service response. Outreach has a long history of engaging those who do not otherwise access services. It has, however, been described as eclectic in its purpose, clientele and mode of practice; its effectiveness is unproven. Using a primary prevention programme in the UK as a case, this paper addresses two research questions: what are the perceived problems of non-engagement that outreach aims to address; and, what specific mechanisms of outreach are hypothesised to tackle these.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; Drawing on a wider programme evaluation, the study undertook qualitative interviews with strategically selected health-care professionals. The analysis was thematically guided by the concept of 'candidacy' which theorises the dynamic process through which services and individuals negotiate appropriate service use.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; The study identified seven types of engagement 'problem' and corresponding solutions. These 'problems' lie on a continuum of complexity in terms of the challenges they present to primary care. Reasons for non-engagement are congruent with the concept of 'candidacy' but point to ways in which it can be expanded.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt; The paper draws conclusions about the role of outreach in contributing to the implementation of inequalities focused primary prevention and identifies further research needed in the theoretical development of both outreach as an approach and candidacy as a conceptual framework

Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology

Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large. To address this concern, we proposed a random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) for GWAS. The RMLM simply treats the SNP-effect as random, but it allows a modified Bonferroni correction to be used to calculate the threshold p value for significance tests. The MRMLM is a multi-locus model including markers selected from the RMLM method with a less stringent selection criterion. Due to the multi-locus nature, no multiple test correction is needed. Simulation studies show that the MRMLM is more powerful in QTN detection and more accurate in QTN effect estimation than the RMLM, which in turn is more powerful and accurate than the EMMA. To demonstrate the new methods, we analyzed six flowering time related traits in Arabidopsis thaliana and detected more genes than previous reported using the EMMA. Therefore, the MRMLM provides an alternative for multi-locus GWAS

Search for direct pair production of the top squark in all-hadronic final states in proton-proton collisions at s√=8 TeV with the ATLAS detector

The results of a search for direct pair production of the scalar partner to the top quark using an integrated luminosity of 20.1fb−1 of proton–proton collision data at √s = 8 TeV recorded with the ATLAS detector at the LHC are reported. The top squark is assumed to decay via t˜→tχ˜01 or t˜→ bχ˜±1 →bW(∗)χ˜01 , where χ˜01 (χ˜±1 ) denotes the lightest neutralino (chargino) in supersymmetric models. The search targets a fully-hadronic final state in events with four or more jets and large missing transverse momentum. No significant excess over the Standard Model background prediction is observed, and exclusion limits are reported in terms of the top squark and neutralino masses and as a function of the branching fraction of t˜ → tχ˜01 . For a branching fraction of 100%, top squark masses in the range 270–645 GeV are excluded for χ˜01 masses below 30 GeV. For a branching fraction of 50% to either t˜ → tχ˜01 or t˜ → bχ˜±1 , and assuming the χ˜±1 mass to be twice the χ˜01 mass, top squark masses in the range 250–550 GeV are excluded for χ˜01 masses below 60 GeV

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Are differential consumption patterns in health-related behaviours an explanation for persistent and widening social inequalities in health in England?

During the last two decades, differential consumption patterns in health-related behaviours have increasingly been highlighted as playing an important role in explaining persistent and widening health inequalities. This period has also seen government public health policies in England place a greater emphasis on changing ‘lifestyle’ behaviours, in an attempt to tackle social inequalities in health. The aim of this study was to empirically examine the variation in health-related behaviour in relation to socio-economic position, in the English adult population, to determine the nature of this relationship and whether it has changed over time

Decadal predictions with the HiGEM high resolution global coupled climate model: description and basic evaluation

This paper describes the development and basic evaluation of decadal predictions produced using the HiGEM coupled climate model. HiGEM is a higher resolution version of the HadGEM1 Met Office Unified Model. The horizontal resolution in HiGEM has been increased to 1.25◦ × 0.83◦ in longitude and latitude for the atmosphere, and 1/3◦ × 1/3◦ globally for the ocean. The HiGEM decadal predictions are initialised using an anomaly assimilation scheme that relaxes anomalies of ocean temperature and salinity to observed anomalies. 10 year hindcasts are produced for 10 start dates (1960, 1965,..., 2000, 2005). To determine the relative contributions to prediction skill from initial conditions and external forcing, the HiGEM decadal predictions are compared to uninitialised HiGEM transient experiments. The HiGEM decadal predictions have substantial skill for predictions of annual mean surface air temperature and 100 m upper ocean temperature. For lead times up to 10 years, anomaly correlations (ACC) over large areas of the North Atlantic Ocean, the Western Pacific Ocean and the Indian Ocean exceed values of 0.6. Initialisation of the HiGEM decadal predictions significantly increases skill over regions of the Atlantic Ocean,the Maritime Continent and regions of the subtropical North and South Pacific Ocean. In particular, HiGEM produces skillful predictions of the North Atlantic subpolar gyre for up to 4 years lead time (with ACC > 0.7), which are significantly larger than the uninitialised HiGEM transient experiments

"Liberalizing" the English National Health Service: background and risks to healthcare entitlement

Resumo: A recente reforma do Serviço Nacional de Saúde (NHS) inglês por meio do Health and Social Care Act de 2012 introduziu mudanças importantes na organização, gestão e prestação de serviços públicos de saúde na Inglaterra. O objetivo deste estudo é analisar as reformas do NHS no contexto histórico de predomínio de teorias neoliberais desde 1980 e discutir o processo de "liberalização" do NHS. São identificados e analisados três momentos: (i) gradativa substituição ideológica e teórica (1979-1990) - transição da lógica profissional e sanitária para uma lógica gerencial/comercial; (ii) burocracia e mercado incipiente (1991-2004) - estruturação de burocracia voltada à administração do mercado interno e expansão de medidas pró-mercado; e (iii) abertura ao mercado, fragmentação e descontinuidade de serviços (2005-2012) - fragilização do modelo de saúde territorial e consolidação da saúde como um mercado aberto a prestadores públicos e privados. Esse processo gradual e constante de liberalização vem levando ao fechamento de serviços e à restrição do acesso, comprometendo a integralidade, a equidade e o direito universal à saúde no NHS

Search for R-parity-violating supersymmetry in events with four or more leptons in sqrt(s) =7 TeV pp collisions with the ATLAS detector

A search for new phenomena in final states with four or more leptons (electrons or muons) is presented. The analysis is based on 4.7 fb−1 of $\sqrt{s}=7\;\mathrm{TeV}$ proton-proton collisions delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in two signal regions: one that requires moderate values of missing transverse momentum and another that requires large effective mass. The results are interpreted in a simplified model of R-parity-violating supersymmetry in which a 95% CL exclusion region is set for charged wino masses up to 540 GeV. In an R-parity-violating MSUGRA/CMSSM model, values of m 1/2 up to 820 GeV are excluded for 10 < tan β < 40

Measurement of the cross-section of high transverse momentum vector bosons reconstructed as single jets and studies of jet substructure in pp collisions at √s = 7 TeV with the ATLAS detector

This paper presents a measurement of the cross-section for high transverse momentum W and Z bosons produced in pp collisions and decaying to all-hadronic final states. The data used in the analysis were recorded by the ATLAS detector at the CERN Large Hadron Collider at a centre-of-mass energy of √s = 7 TeV;{\rm Te}{\rm V}$and correspond to an integrated luminosity of$4.6\;{\rm f}{{{\rm b}}^{-1}}$. The measurement is performed by reconstructing the boosted W or Z bosons in single jets. The reconstructed jet mass is used to identify the W and Z bosons, and a jet substructure method based on energy cluster information in the jet centre-of-mass frame is used to suppress the large multi-jet background. The cross-section for events with a hadronically decaying W or Z boson, with transverse momentum${{p}_{{\rm T}}}\gt 320\;{\rm Ge}{\rm V}$and pseudorapidity$|\eta |\lt 1.9$, is measured to be${{\sigma }_{W+Z}}=8.5\pm 1.7$ pb and is compared to next-to-leading-order calculations. The selected events are further used to study jet grooming techniques