A distributed computation of Interpro Pfam, PROSITE and ProDom for protein annotation

Interpro is a widely used tool for protein annotation in genome sequencing projects, demanding a large amount of computation and representing a huge time-consuming step. We present a strategy to execute programs using databases Pfam, PROSITE and ProDom of Interpro in a distributed environment using a Java-based messaging system. We developed a two-layer scheduling architecture of the distributed infrastructure. Then, we made experiments and analyzed the results. Our distributed system gave much better results than Interpro Pfam, PROSITE and ProDom running in a centralized platform. This approach seems to be appropriate and promising for highly demanding computational tools used for biological applications

Amenability of groups and GG-sets

This text surveys classical and recent results in the field of amenability of groups, from a combinatorial standpoint. It has served as the support of courses at the University of G\"ottingen and the \'Ecole Normale Sup\'erieure. The goals of the text are (1) to be as self-contained as possible, so as to serve as a good introduction for newcomers to the field; (2) to stress the use of combinatorial tools, in collaboration with functional analysis, probability etc., with discrete groups in focus; (3) to consider from the beginning the more general notion of amenable actions; (4) to describe recent classes of examples, and in particular groups acting on Cantor sets and topological full groups

Radio Astronomy

Contains reports on nine research projects.National Science Foundation (Grant AST 86-17172)National Aeronautics and Space Administration (Contract NAS7-918)Jet Propulsion Laboratory (Contract 958048)U.S. Navy - Office of Naval Research (Contract N00014-84-C-2082)U.S. Navy - Office of Naval Research (Contract N00014-86-C-2114)SM Systems and Research, Inc.National Aeronautics and Space Administration/Goddard Space Flight Center (Grant NAG5-10)Center for Advanced Television StudiesBrazil, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Grant 300.832-82)National Aeronautics and Space Administration/Goddard Space Flight Center (Grant NAG5-537

Mental Disorders, Comorbidity, and Pre-enlistment Suicidal Behavior Among New Soldiers in the U.S. Army: Results from the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS)

We examined the associations between mental disorders and suicidal behavior (ideation, plans, and attempts) among new soldiers using data from the New Soldier Study (NSS) component of the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS; n=38,507). Most new soldiers with a pre-enlistment history of suicide attempt reported a prior mental disorder (59.0%). Each disorder examined was associated with increased odds of suicidal behavior (ORs=2.6–8.6). Only PTSD and disorders characterized by irritability and impulsive/aggressive behavior (i.e., bipolar disorder, conduct disorder, oppositional defiant disorder, and attention-deficit/hyperactivity disorder) predicted unplanned attempts among ideators. Mental disorders are important predictors of pre-enlistment suicidal behavior among new soldiers and should figure prominently in suicide screening and prevention efforts.Psycholog

Prevalence and correlates of suicidal behavior among new soldiers in the US Army: results from the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS)

Background The prevalence of suicide among U.S. Army soldiers has risen dramatically in recent years. Prior studies suggest that most soldiers with suicidal behaviors (i.e., ideation, plans, and attempts) had first onsets prior to enlistment. However, those data are based on retrospective self-reports of soldiers later in their Army careers. Unbiased examination of this issue requires investigation of suicidality among new soldiers. Method The New Soldier Study (NSS) of the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS) used fully structured self-administered measures to estimate preenlistment histories of suicide ideation, plans, and attempts among new soldiers reporting for Basic Combat Training in 2011–2012. Survival models examined sociodemographic correlates of each suicidal outcome. Results Lifetime prevalence estimates of preenlistment suicide ideation, plans, and attempts were 14.1, 2.3, and 1.9%, respectively. Most reported onsets of suicide plans and attempts (73.3–81.5%) occurred within the first year after onset of ideation. Odds of these lifetime suicidal behaviors among new soldiers were positively, but weakly associated with being female, unmarried, religion other than Protestant or Catholic, and a race/ethnicity other than non-Hispanic White, non-Hispanic Black, or Hispanic. Conclusions Lifetime prevalence estimates of suicidal behaviors among new soldiers are consistent with retrospective reports of preenlistment prevalence obtained from soldiers later in their Army careers. Given that prior suicidal behaviors are among the strongest predictors of later suicides, consideration should be given to developing methods of obtaining valid reports of preenlistment suicidality from new soldiers to facilitate targeting of preventive interventions.Psycholog

A new model of development of the mammalian ovary and follicles

Ovarian follicular granulosa cells surround and nurture oocytes, and produce sex steroid hormones. It is believed that during development the ovarian surface epithelial cells penetrate into the ovary and develop into granulosa cells when associating with oogonia to form follicles. Using bovine fetal ovaries (n = 80) we identified a novel cell type, termed GREL for Gonadal Ridge Epithelial-Like. Using 26 markers for GREL and other cells and extracellular matrix we conducted immunohistochemistry and electron microscopy and chronologically tracked all somatic cell types during development. Before 70 days of gestation the gonadal ridge/ovarian primordium is formed by proliferation of GREL cells at the surface epithelium of the mesonephros. Primordial germ cells (PGCs) migrate into the ovarian primordium. After 70 days, stroma from the underlying mesonephros begins to penetrate the primordium, partitioning the developing ovary into irregularly-shaped ovigerous cords composed of GREL cells and PGCs/oogonia. Importantly we identified that the cords are always separated from the stroma by a basal lamina. Around 130 days of gestation the stroma expands laterally below the outermost layers of GREL cells forming a sub-epithelial basal lamina and establishing an epithelial-stromal interface. It is at this stage that a mature surface epithelium develops from the GREL cells on the surface of the ovary primordium. Expansion of the stroma continues to partition the ovigerous cords into smaller groups of cells eventually forming follicles containing an oogonium/oocyte surrounded by GREL cells, which become granulosa cells, all enclosed by a basal lamina. Thus in contrast to the prevailing theory, the ovarian surface epithelial cells do not penetrate into the ovary to form the granulosa cells of follicles, instead ovarian surface epithelial cells and granulosa cells have a common precursor, the GREL cell.Katja Hummitzsch, Helen F. Irving-Rodgers, Nicholas Hatzirodos, Wendy Bonner, Laetitia Sabatier, Dieter P. Reinhardt, Yoshikazu Sado, Yoshifumi Ninomiya, Dagmar Wilhelm and Raymond J. Rodger

Monte Carlo Simulations of Metasomatic Enrichment in the Lithosphere and Implications for the Source of Alkaline Basalts

One hypothesis for the origin of alkaline lavas erupted on oceanic islands and in intracontinental settings is that they represent the melts of amphibole-rich veins in the lithosphere (or melts of their dehydrated equivalents if metasomatized lithosphere is recycled into the convecting mantle). Amphibole-rich veins are interpreted as cumulates produced by crystallization of low-degree melts of the underlying asthenosphere as they ascend through the lithosphere. We present the results of trace-element modelling of the formation and melting of veins formed in this way with the goal of testing this hypothesis and for predicting how variability in the formation and subsequent melting of such cumulates (and adjacent cryptically and modally metasomatized lithospheric peridotite) would be manifested in magmas generated by such a process. Because the high-pressure phase equilibria of hydrous near-solidus melts of garnet lherzolite are poorly constrained and given the likely high variability of the hypothesized accumulation and remelting processes, we used Monte Carlo techniques to estimate how uncertainties in the model parameters (e.g. the compositions of the asthenospheric sources, their trace-element contents, and their degree of melting; the modal proportions of crystallizing phases, including accessory phases, as the asthenospheric partial melts ascend and crystallize in the lithosphere; the amount of metasomatism of the peridotitic country rock; the degree of melting of the cumulates and the amount of melt derived from the metasomatized country rock) propagate through the process and manifest themselves as variability in the trace-element contents and radiogenic isotopic ratios of model vein compositions and erupted alkaline magma compositions. We then compare the results of the models with amphibole observed in lithospheric veins and with oceanic and continental alkaline magmas. While the trace-element patterns of the near-solidus peridotite melts, the initial anhydrous cumulate assemblage (clinopyroxene ± garnet ± olivine ± orthopyroxene), and the modelled coexisting liquids do not match the patterns observed in alkaline lavas, our calculations show that with further crystallization and the appearance of amphibole (and accessory minerals such as rutile, ilmenite, apatite, etc.) the calculated cumulate assemblages have trace-element patterns that closely match those observed in the veins and lavas. These calculated hydrous cumulate assemblages are highly enriched in incompatible trace elements and share many similarities with the trace-element patterns of alkaline basalts observed in oceanic or continental setting such as positive Nb/La, negative Ce/Pb, and similiar slopes of the rare earth elements. By varying the proportions of trapped liquid and thus simulating the cryptic and modal metasomatism observed in peridotite that surrounds these veins, we can model the variations in Ba/Nb, Ce/Pb, and Nb/U ratios that are observed in alkaline basalts. If the isotopic compositions of the initial low-degree peridotite melts are similar to the range observed in mid-ocean ridge basalt, our model calculations produce cumulates that would have isotopic compositions similar to those observed in most alkaline ocean island basalt (OIB) and continental magmas after ~0·15 Gyr. However, to produce alkaline basalts with HIMU isotopic compositions requires much longer residence times (i.e. 1–2 Gyr), consistent with subduction and recycling of metasomatized lithosphere through the mantle. EM magmas cannot readily be explained without appealing to other factors such as a heterogeneous asthenosphere. These modelling results support the interpretation proposed by various researchers that amphibole-bearing veins represent cumulates formed during the differentiation of a volatile-bearing low-degree peridotite melt and that these cumulates are significant components of the sources of alkaline OIB and continental magmas. The results of the forward models provide the potential for detailed tests of this class of hypotheses for the origin of alkaline magmas worldwide and for interpreting major and minor aspects of the geochemical variability of these magmas

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure