Peer and family support as moderators of the relationship between stress and symptoms in low-income urban youth

Research examining the etiology of psychopathology has largely focused on stress as a predictor of psychological distress. Particular attention has been paid to exploring the mechanisms that explain the influence of stress on psychopathology. However, few studies have examined these constructs in the context of the low-income urban environment (Grant et al., 2005). Recent literature suggests that psychopathology may manifest uniquely in the most stressful situations, found in the low income urban environment. The current research examines the differential effects that family support demonstrates on internalizing and externalizing symptoms. Further, the study demonstrates the strengths of using structural equation modeling (SEM) in examining moderating effects in developmental psychopathology research, applying techniques recommended by Holmbeck to Structural Regression (1997). Further, specific situations are detailed that demonstrate how apparent Net Suppressor effects may be best explained through specification error, in some cases. Finally, the current research demonstrates how mixed methods may be integrated into advanced statistical techniques, such as SEM. Methods The current same consists of 392 urban youth, ranging in grade from 6th to 9th (64% female) and of predominantly African American and Latino ethnicity. Symptoms were assessed using multiple reporters with the Youth Self Report (YSR; youth/child report). Child Behavioral Checklist (CBLC; parent report), and the Children\u27s Depression Inventory (CDI; youth report; Achenbach, 1991a; Kovaks, INSERT YEAR). Qualitative interview and coding procedures were used to collected endorsement of family support and youth perceived severity of stress (Grant et al., 2003). Empirically supported survey instruments were also used measure exposure to violence (Richters & Martinez) and Daily Hassles/ Major Life Events (Allison et al.,2003). Results Results indicate demonstrated a well-fitting model of stress, internalizing, and externalizing psychopathology that utilized multiple indicators of each construct. Models using multiple indicators demonstrate in the literature to reduce the effects of measurement error and eliminate the need for product terms (Holmbeck, 1997). Moderator analyses demonstrate significant moderating effects for youth endorsed family support, although in an unexpected manner. Youth that did not endorse family support demonstrated a stronger positive (and significant) association between stress and externalizing symptoms than youth that endorsed family support, consistent with extant literature. In contrast, youth that endorsed that family support demonstrated a significantly stronger (and positive) association between stress and internalizing symptoms, compared to their non-endorsing counter-parts. These findings may support extant literature that suggests that low-income urban youth may be more likely to externalize (Grant et al, 2005), but this effect may be influenced by family interactions, leading to traditional internalizing symptom expression. Implications for interventions are discussed

The evolution of novel fungal genes from non-retroviral RNA viruses

<p>Abstract</p> <p>Background</p> <p>Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles.</p> <p>Results</p> <p>Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated <it>Totivirus</it>-like sequences in three fungi (<it>Candida parapsilosis</it>, <it>Penicillium marneffei </it>and <it>Uromyces appendiculatus</it>). The phylogenetic evidence strongly indicated that the direction of transfer was from <it>Totivirus </it>to fungus. However, there was evidence of transfer of <it>Totivirus</it>-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning.</p> <p>Conclusions</p> <p>Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.</p

The Ethical Review of Health Care Quality Improvement Initiatives: Findings From the Field

Based on surveys, examines the review mechanisms of quality improvement initiatives, including frequency; type, such as use of independent review boards; and consideration for ethical issues such as minimal risk and patient privacy and confidentiality

Genome-Wide Association Study of Feed Efficiency in Beef Cattle

Feed costs comprise the majority of beef production costs and feed intake has long been recognized as an economically relevant trait for beef cattle. Residual feed intake (RFI) is a function of feed intake and performance and reflects whether animals eat more or less than expected for a given level of production. The objectives of this study were to map quantitative trait loci (QTL) associated with feedlot RFI in 4 different beef cattle populations. A total of 13 significant QTL over 10 different chromosomes were detected. The identified QTL had no overlap across 4 beef cattle populations reflecting different genetic makeup of RFI across different beef populations. Further genotyping and statistical analyses are needed to find the casual mutations. Once found, knowledge of such mutations would create new opportunities for the selection of more efficient animals

Evolutionary maintenance of filovirus-like genes in bat genomes

<p>Abstract</p> <p>Background</p> <p>Little is known of the biological significance and evolutionary maintenance of integrated non-retroviral RNA virus genes in eukaryotic host genomes. Here, we isolated novel filovirus-like genes from bat genomes and tested for evolutionary maintenance. We also estimated the age of filovirus VP35-like gene integrations and tested the phylogenetic hypotheses that there is a eutherian mammal clade and a marsupial/ebolavirus/Marburgvirus dichotomy for filoviruses.</p> <p>Results</p> <p>We detected homologous copies of VP35-like and NP-like gene integrations in both Old World and New World species of <it>Myotis </it>(bats). We also detected previously unknown VP35-like genes in rodents that are positionally homologous. Comprehensive phylogenetic estimates for filovirus NP-like and VP35-like loci support two main clades with a marsupial and a rodent grouping within the ebolavirus/Lloviu virus/Marburgvirus clade. The concordance of VP35-like, NP-like and mitochondrial gene trees with the expected species tree supports the notion that the copies we examined are orthologs that predate the global spread and radiation of the genus <it>Myotis</it>. Parametric simulations were consistent with selective maintenance for the open reading frame (ORF) of VP35-like genes in <it>Myotis</it>. The ORF of the filovirus-like VP35 gene has been maintained in bat genomes for an estimated 13. 4 MY. ORFs were disrupted for the NP-like genes in <it>Myotis</it>. Likelihood ratio tests revealed that a model that accommodates positive selection is a significantly better fit to the data than a model that does not allow for positive selection for VP35-like sequences. Moreover, site-by-site analysis of selection using two methods indicated at least 25 sites in the VP35-like alignment are under positive selection in <it>Myotis</it>.</p> <p>Conclusions</p> <p>Our results indicate that filovirus-like elements have significance beyond genomic imprints of prior infection. That is, there appears to be, or have been, functionally maintained copies of such genes in mammals. "Living fossils" of filoviruses appear to be selectively maintained in a diverse mammalian genus (<it>Myotis</it>).</p

Virus-host co-evolution under a modified nuclear genetic code

Among eukaryotes with modified nuclear genetic codes, viruses are unknown. However, here we provide evidence of an RNA virus that infects a fungal host (Scheffersomyces segobiensis) with a derived nuclear genetic code where CUG codes for serine. The genomic architecture and phylogeny are consistent with infection by a double-stranded RNA virus of the genus Totivirus. We provide evidence of past or present infection with totiviruses in five species of yeasts with modified genetic codes. All but one of the CUG codons in the viral genome have been eliminated, suggesting that avoidance of the modified codon was important to viral adaptation. Our mass spectroscopy analysis indicates that a congener of the host species has co-opted and expresses a capsid gene from totiviruses as a cellular protein. Viral avoidance of the host’s modified codon and host co-option of a protein from totiviruses suggest that RNA viruses co-evolved with yeasts that underwent a major evolutionary transition from the standard genetic code

Ranking Edges by their Impact on the Spectral Complexity of Information Diffusion over Networks

Despite the numerous ways now available to quantify which parts or subsystems of a network are most important, there remains a lack of centrality measures that are related to the complexity of information flows and are derived directly from entropy measures. Here, we introduce a ranking of edges based on how each edge's removal would change a system's von Neumann entropy (VNE), which is a spectral-entropy measure that has been adapted from quantum information theory to quantify the complexity of information dynamics over networks. We show that a direct calculation of such rankings is computationally inefficient (or unfeasible) for large networks: e.g.\ the scaling is $\mathcal{O}(N^3)$ per edge for networks with $N$ nodes. To overcome this limitation, we employ spectral perturbation theory to estimate VNE perturbations and derive an approximate edge-ranking algorithm that is accurate and fast to compute, scaling as $\mathcal{O}(N)$ per edge. Focusing on a form of VNE that is associated with a transport operator $e^{-\beta{ L}}$, where ${ L}$ is a graph Laplacian matrix and $\beta>0$ is a diffusion timescale parameter, we apply this approach to diverse applications including a network encoding polarized voting patterns of the 117th U.S. Senate, a multimodal transportation system including roads and metro lines in London, and a multiplex brain network encoding correlated human brain activity. Our experiments highlight situations where the edges that are considered to be most important for information diffusion complexity can dramatically change as one considers short, intermediate and long timescales $\beta$ for diffusion.Comment: 24 pages, 7 figure

Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle

The impact of pedigree information and SNP location determined from either the UMD3.1 genome sequence assembly or the USDA-AIPL map on phasing accuracy were evaluated for 2 chromosomes in 2,778 parent verified Angus sire/offspring pairs. DAGPHASE (Druet and Georges, 2010), using a single generation pedigree was superior to BEAGLE software (Browning and Browning, 2007) for phasing. Results based on USDA-AIPL map are closer to expectation than those based on UMD3.1, but the difference is not significant. Recombination hotspots weredetected near 4 and 82Mb on BTA14, and near 25Mb on BTA15

Identifying Chromosomal Recombinations in Beef Cattle from Genotyped Parent-Offspring Pairs

This study investigated meiotic recombination in two breeds of cattle by comparing phased SNP haplotypes in sire-offspring pairs. The positions and number of recombination events were identified. The number of recombination events varies between individuals and is a heritable trait. A genome-wide association analysis identified quantitative trait loci (QTL) associated with variation in the number of recombination events. Regions that had more recombination events than expected were identified in both breeds, and many of these hotspots were in common. Recombination is important biologically because it is the mechanism for reassembling paternal and maternal alleles. Recombination impacts the accuracy of imputation, a commonly-used approach to infer the genotypes of some individuals based on genotypes of others