Quality of Life and Body Dissatisfaction in Cisgender Men Reporting Sexual Attraction Toward Men or Women.

Gay men report poorer body image than straight men, but no research has examined other dimensions of sexual identity (e.g., sexual attraction).

Diamonds and rust: The affective ambivalence of Nostalgia.

Affective ambivalence is the simultaneous experience of oppositely valenced emotions, such as happiness and sadness. Historic writings on the valence of nostalgia have proposed that nostalgia can best be conceptualized as an ambivalent emotion. A growing body of research provides empirical evidence for this proposal.

Nostalgia in organizations.

Scholars have proposed that nostalgia plays various important roles in organizations. At present, there is no comprehensive overview of the role of nostalgia in this context. To help develop such an overview, we review research on personal nostalgia, insofar as it includes outcomes that are organizationally relevant, and research on organizational nostalgia.

An online hazard prediction test demonstrates differences in the ability to identify hazardous situations between different driving groups.

Previous research has found that the traditional approach to measuring hazard perception, as used by the UK Government, does not necessarily transfer well to other countries. The speeded response times of a hazard perception test were susceptible to threshold bias, differentiating drivers according to cultural background more than driving experience. An alternative method - the hazard prediction test - appears to mitigate these problems when used across different countries.

Self-protection predicts lower willingness to apologize.

Although apologies are effective at promoting reconciliation, perpetrators often choose not to apologize because doing so can be threatening to the self. We hypothesized that dispositional self-protection would be negatively associated with willingness to apologize, but only when the transgression pertained to the self rather than another person. Only in that case would self-positivity be threatened, thereby activating the self-protection motive.

Evaluating the effects of multisystemic therapy for adolescents with intellectual disabilities and antisocial or delinquent behaviour and their parents.

Background: An adaptation of multisystemic therapy (MST) was piloted to find out whether it would yield better outcomes than standard MST in families where the adolescent not only shows antisocial or delinquent behaviour, but also has an intellectual disability.

Method: To establish the comparative effectiveness of MST-ID (n = 55) versus standard MST (n = 73), treatment outcomes were compared at the end of treatment and at 6-month follow-up. Pre-treatment differences were controlled for using the propensity score method.

Organizational nostalgia lowers turnover intentions by increasing work meaning: The moderating role of burnout.

We report 3 studies addressing the relevance of organizational nostalgia for the meaning that employees ascribe to their work (work meaning). We hypothesized, and found, that organizational nostalgia enhances work meaning and thereby reduces turnover intentions. In Study 1, an employee survey, spontaneously experienced organizational nostalgia was associated with higher work meaning.

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain.

Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment.

The human leukocyte antigen-presented ligandome of B lymphocytes.

Peptides presented by human leukocyte antigen (HLA) molecules on the cell surface play a crucial role in adaptive immunology, mediating the communication between T cells and antigen presenting cells. Knowledge of these peptides is of pivotal importance in fundamental studies of T cell action and in cellular immunotherapy and transplantation. In this paper we present the in-depth identification and relative quantification of 14,500 peptide ligands constituting the HLA ligandome of B cells.

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins.

ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats.

MADMAX - Management and analysis database for multiple ~omics experiments.

The rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is designed to provide a solution for storage and analysis of complex ~omics datasets. In addition, analysis results (such as lists of genes) will be merged to reveal candidate genes supported by all datasets.

HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands.

T cell epitopes derived from polymorphic proteins or from proteins encoded by alternative reading frames (ARFs) play an important role in (tumor) immunology. Identification of these peptides is successfully performed with mass spectrometry. In a mass spectrometry-based approach, the recorded tandem mass spectra are matched against hypothetical spectra generated from known protein sequence databases.

Evidence for RNA recombination between distinct isolates of Pepino mosaic virus.

Genetic recombination plays an important role in the evolution of virus genomes. In this study we analyzed publicly available genomic sequences of Pepino mosaic virus (PepMV) for recombination events using several bioinformatics tools. The genome-wide analyses not only confirm the presence of previously found recombination events in PepMV but also provide the first evidence for double recombinant origin of the US2 isolate.

Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.

Background: The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates.

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.

Unlabelled: Multi-netclust is a simple tool that allows users to extract connected clusters of data represented by different networks given in the form of matrices. The tool uses user-defined threshold values to combine the matrices, and uses a straightforward, memory-efficient graph algorithm to find clusters that are connected in all or in either of the networks. The tool is written in C/C++ and is available either as a form-based or as a command-line-based program running on Linux platforms.

A pipeline for high throughput detection and mapping of SNPs from EST databases.

Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice.

Constraint-based probabilistic learning of metabolic pathways from tomato volatiles.

Clustering and correlation analysis techniques have become popular tools for the analysis of data produced by metabolomics experiments. The results obtained from these approaches provide an overview of the interactions between objects of interest. Often in these experiments, one is more interested in information about the nature of these relationships, e.

A comparison of database systems for XML-type data.

Background: In the field of bioinformatics interchangeable data formats based on XML are widely used. XML-type data is also at the core of most web services. With the increasing amount of data stored in XML comes the need for storing and accessing the data.

Microarray data mining using Bioconductor packages.

Background: This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-MA8, and MM8-MM24, of the provided microarray data during this workshop, this analysis aimed to investigate the host reactions in chickens occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. The results of GO enrichment analysis using GO terms annotated to chicken genes and GO terms annotated to chicken-human orthologous genes were also compared.

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment.

Background: The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.

OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity.

Background: High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be designed when a reference genome of the species at hand were completely sequenced, when this genome were completely annotated and when the genetic variation of the sampled individuals were completely known. Unfortunately there is not a single species for which such a complete data set is available.

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.

Background: Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results.