Evaluating aggregate effects of rare and common variants in the 1000 Genomes Project exon sequencing data using latent variable structural equation modeling

Methods that can evaluate aggregate effects of rare and common variants are limited. Therefore, we applied a two-stage approach to evaluate aggregate gene effects in the 1000 Genomes Project data, which contain 24,487 single-nucleotide polymorphisms (SNPs) in 697 unrelated individuals from 7 populations. In stage 1, we identified potentially interesting genes (PIGs) as those having at least one SNP meeting Bonferroni correction using univariate, multiple regression models. In stage 2, we evaluate aggregate PIG effects on trait, Q1, by modeling each gene as a latent construct, which is defined by multiple common and rare variants, using the multivariate statistical framework of structural equation modeling (SEM). In stage 1, we found that PIGs varied markedly between a randomly selected replicate (replicate 137) and 100 other replicates, with the exception of FLT1. In stage 1, collapsing rare variants decreased false positives but increased false negatives. In stage 2, we developed a good-fitting SEM model that included all nine genes simulated to affect Q1 (FLT1, KDR, ARNT, ELAV4, FLT4, HIF1A, HIF3A, VEGFA, VEGFC) and found that FLT1 had the largest effect on Q1 (βstd = 0.33 ± 0.05). Using replicate 137 estimates as population values, we found that the mean relative bias in the parameters (loadings, paths, residuals) and their standard errors across 100 replicates was on average, less than 5%. Our latent variable SEM approach provides a viable framework for modeling aggregate effects of rare and common variants in multiple genes, but more elegant methods are needed in stage 1 to minimize type I and type II error

Heralded single-photon generation using imperfect single-photon sources and a two-photon-absorbing medium

We propose a setup for a heralded, i.e. announced generation of a pure single-photon state given two imperfect sources whose outputs are represented by mixtures of the single-photon Fock state $\ket{1}$ with the vacuum $\ket{0}$. Our purification scheme uses beam splitters, photodetection and a two-photon-absorbing medium. The admixture of the vacuum is fully eliminated. We discuss two potential realizations of the scheme.Comment: 22 pages, 8 figures (LaTeX). In version v2 we have slightly modified our setup so as to increase the success probability of single-photon generation by a factor of two. In addition, in an appendix we discuss alternative realizations of single-photon generation without a Mach-Zehnder interferometer. Three new figures have been added. Version v3 is a revised version published in Phys. Rev. A. It contains numerous minor corrections and clarifications. A new figure has been added in order to clarify our convention regarding labelling the field modes. The action of the beam splitters in the Schroedinger picture is introduced. A new reference has been include

Modeling the Pinning of Au and Ni Clusters on Graphite

The pinning of size-selected AuN and NiN clusters on graphite, for N=7–100, is investigated by means of molecular dynamics simulations and the results are compared to experiment and previous work with Ag clusters. Ab initio calculations of the binding of the metal adatom and dimers on a graphite surface are used to parametrize the potentials used in the simulations. The clusters are projected normally towards a graphite surface and the value of the energy at which pinning first occurs, EP, is determined. Pinning is shown to occur when a surface defect, made by the cluster interaction, is first produced. The simulations give a good agreement with the experimentally determined pinning energy thresholds and the heights of the clusters on the surface. The gold clusters are shown to be flatter and more spread out than the nickel clusters which are more compact

Covenant Marriage Turns Five Years Old

Part I of this article discusses public policy rationales behind covenant marriage legislation, describes relevant aspects of Louisiana\u27s legislation, and summarizes the efforts of other states to enact covenant marriage legislation. Part II discusses methods of data collection and analysis and identifies the demographic characteristics of covenant married couples as opposed to standard married couples in Louisiana. Part III addresses the dynamics behind couples\u27 choice to have a covenant versus standard marriage. Part IV is an analysis of couples\u27 satisfaction with their marriage option and the gendered dynamics of different levels of satisfaction with the marital choice

The U.S. Support Program to IAEA Safeguards - How It Works

The U.S. Support Program to International Atomic Energy Agency (IAEA) Safeguards (USSP) was established in 1977 to transfer US technology and expertise to assist the IAEA Department of Safeguards because its limited budget and scope would not allow for R&D activities and the procurement of specialized or customized equipment. Over the years, the USSP and the Department of Safeguards have worked together continuously to develop and improve processes for requesting, selecting, and managing projects that support the Safeguards verification mission. This paper will discuss the main USSP processes for accepting and processing Safeguards requests, and managing and reporting task progress

Covenant Marriage Turns Five Years Old

Part I of this article discusses public policy rationales behind covenant marriage legislation, describes relevant aspects of Louisiana\u27s legislation, and summarizes the efforts of other states to enact covenant marriage legislation. Part II discusses methods of data collection and analysis and identifies the demographic characteristics of covenant married couples as opposed to standard married couples in Louisiana. Part III addresses the dynamics behind couples\u27 choice to have a covenant versus standard marriage. Part IV is an analysis of couples\u27 satisfaction with their marriage option and the gendered dynamics of different levels of satisfaction with the marital choice

Why alternative teenagers self-harm: exploring the link between non-suicidal self-injury, attempted suicide and adolescent identity

Background: The term ‘self-harm’ encompasses both attempted suicide and non-suicidal self-injury (NSSI). Specific adolescent subpopulations such as ethnic or sexual minorities, and more controversially, those who identify as ‘Alternative’ (Goth, Emo) have been proposed as being more likely to self-harm, while other groups such as ‘Jocks’ are linked with protective coping behaviours (for example exercise). NSSI has autonomic (it reduces negative emotions) and social (it communicates distress or facilitates group ‘bonding’) functions. This study explores the links between such aspects of self-harm, primarily NSSI, and youth subculture.<p></p> Methods: An anonymous survey was carried out of 452 15 year old German school students. Measures included: identification with different youth cultures, i.e. Alternative (Goth, Emo, Punk), Nerd (academic) or Jock (athletic); social background, e.g. socioeconomic status; and experience of victimisation. Self-harm (suicide and NSSI) was assessed using Self-harm Behavior Questionnaire and the Functional Assessment of Self-Mutilation (FASM).<p></p> Results: An “Alternative” identity was directly (r ≈ 0.3) and a “Jock” identity inversely (r ≈ -0.1) correlated with self-harm. “Alternative” teenagers self-injured more frequently (NSSI 45.5% vs. 18.8%), repeatedly self-injured, and were 4–8 times more likely to attempt suicide (even after adjusting for social background) than their non-Alternative peers. They were also more likely to self-injure for autonomic, communicative and social reasons than other adolescents.<p></p> Conclusions: About half of ‘Alternative’ adolescents’ self-injure, primarily to regulate emotions and communicate distress. However, a minority self-injure to reinforce their group identity, i.e. ‘To feel more a part of a group’