Project Passport: An Integrated Group-Centered Approach Targeting Pregnant Teens and Their Partners

Objective: To describes the development of Project Passport, a perinatal intervention designed to reduce negative outcomes among pregnant teens. Methods: A logic model guided the planning, development and evaluation plan for the intervention. It included the selection of health goals, behaviors to be targeted, determinants of the selected behaviors, and activities to impact each selected determinant. Results: The process resulted in the formulation of an intervention that incorporates CenteringPregnancy, a group model of prenatal care, Positive Youth Development components, and male involvement. The evaluation examines the effectiveness of the intervention in enhancing health, educational and psychosocial outcomes among pregnant adolescents. Conclusions: The present program was designed to address an important gap in evidence-based interventions targeting pregnant adolescents and their partners

GXD\u27s RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest.

The Gene Expression Database (GXD), an extensive community resource of curated expression information for the mouse, has developed an RNA-Seq and Microarray Experiment Search (http://www.informatics.jax.org/gxd/htexp_index). This tool allows users to quickly and reliably find specific experiments in ArrayExpress and the Gene Expression Omnibus (GEO) that study endogenous gene expression in wild-type and mutant mice. Standardized metadata annotations, curated by GXD, allow users to specify the anatomical structure, developmental stage, mutated gene, strain and sex of samples of interest, as well as the study type and key parameters of the experiment. These searches, powered by controlled vocabularies and ontologies, can be combined with free text searching of experiment titles and descriptions. Search result summaries include link-outs to ArrayExpress and GEO, providing easy access to the expression data itself. Links to the PubMed entries for accompanying publications are also included. More information about this tool and GXD can be found at the GXD home page (http://www.informatics.jax.org/expression.shtml). Database URL: http://www.informatics.jax.org/expression.shtml

Genetic diversity of Streptococcus suis isolates as determined by comparative genome hybridization

<p>Abstract</p> <p>Background</p> <p><it>Streptococcus suis </it>is a zoonotic pathogen that causes infections in young piglets. <it>S. suis </it>is a heterogeneous species. Thirty-three different capsular serotypes have been described, that differ in virulence between as well as within serotypes.</p> <p>Results</p> <p>In this study, the correlation between gene content, serotype, phenotype and virulence among 55 <it>S. suis </it>strains was studied using Comparative Genome Hybridization (CGH). Clustering of CGH data divided <it>S. suis </it>isolates into two clusters, A and B. Cluster A isolates could be discriminated from cluster B isolates based on the protein expression of extracellular factor (EF). Cluster A contained serotype 1 and 2 isolates that were correlated with virulence. Cluster B mainly contained serotype 7 and 9 isolates. Genetic similarity was observed between serotype 7 and serotype 2 isolates that do not express muramidase released protein (MRP) and EF (MRP^-EF^-), suggesting these isolates originated from a common founder. Profiles of 25 putative virulence-associated genes of <it>S. suis </it>were determined among the 55 isolates. Presence of all 25 genes was shown for cluster A isolates, whereas cluster B isolates lacked one or more putative virulence genes. Divergence of <it>S. suis </it>isolates was further studied based on the presence of 39 regions of difference. Conservation of genes was evaluated by the definition of a core genome that contained 78% of all ORFs in P1/7.</p> <p>Conclusions</p> <p>In conclusion, we show that CGH is a valuable method to study distribution of genes or gene clusters among isolates in detail, yielding information on genetic similarity, and virulence traits of <it>S. suis </it>isolates.</p

HI Selected Galaxies in the Sloan Digital Sky Survey I: Optical Data

We present the optical data for 195 HI-selected galaxies that fall within both the Sloan Digital Sky Survey (SDSS) and the Parkes Equatorial Survey (ES). The photometric quantities have been independently recomputed for our sample using a new photometric pipeline optimized for large galaxies, thus correcting for SDSS's limited reliability for automatic photometry of angularly large or low surface brightness (LSB) galaxies. We outline the magnitude of the uncertainty in the SDSS catalog-level photometry and derive a quantitative method for correcting the over-sky subtraction in the SDSS photometric pipeline. The main thrust of this paper is to present the ES/SDSS sample and discuss the methods behind the improved photometry, which will be used in future scientific analysis. We present the overall optical properties of the sample and briefly compare to a volume-limited, optically-selected sample. Compared to the optically-selected SDSS sample (in the similar volume), HI-selected galaxies are bluer and more luminous (fewer dwarf ellipticals and more star formation). However, compared to typical SDSS galaxy studies, which have their own selection effects, our sample is bluer, fainter and less massive.Comment: 14 pages, 8 Figures, accepted for publication in AJ. Complete tables will be available in the AJ electronic version and on the Vizier sit

Binary Contamination in the SEGUE sample: Effects on SSPP Determinations of Stellar Atmospheric Parameters

Using numerical modeling and a grid of synthetic spectra, we examine the effects that unresolved binaries have on the determination of various stellar atmospheric parameters for SEGUE targets measured using the SEGUE Stellar Parameter Pipeline (SSPP). To model undetected binaries that may be in the SEGUE sample, we use a variety of mass distributions for the primary and secondary stars in conjunction with empirically determined relationships for orbital parameters to determine the fraction of G-K dwarf stars, as defined by SDSS color cuts, that will be blended with a secondary companion. We focus on the G-K dwarf sample in SEGUE as it records the history of chemical enrichment in our galaxy. To determine the effect of the secondary on the spectroscopic parameters, we synthesize a grid of model spectra from 3275 to 7850 K (~0.1 to 1.0 \msun) and [Fe/H]=-0.5 to -2.5 from MARCS model atmospheres using TurboSpectrum. We analyze both "infinite" signal-to-noise ratio (S/N) models and degraded versions, at median S/N of 50, 25 and 10. By running individual and combined spectra (representing the binaries) through the SSPP, we determine that ~10% of the blended G-K dwarf pairs with S/N>=25 will have their atmospheric parameter determinations, in particular temperature and metallicity, noticeably affected by the presence of an undetected secondary. To account for the additional uncertainty from binary contamination at a S/N~10, uncertainties of ~140 K and ~0.17 dex in [Fe/H] must be added in quadrature to the published uncertainties of the SSPP. (Abridged)Comment: 68 pages, 20 figures, 9 table

SDSS Standard Star Catalog for Stripe 82: the Dawn of Industrial 1% Optical Photometry

We describe a standard star catalog constructed using multiple SDSS photometric observations (at least four per band, with a median of ten) in the $ugriz$ system. The catalog includes 1.01 million non-variable unresolved objects from the equatorial stripe 82 ($|\delta_{J2000}|<$ 1.266$^\circ$) in the RA range 20h 34m to 4h 00m, and with the corresponding $r$ band (approximately Johnson V band) magnitudes in the range 14--22. The distributions of measurements for individual sources demonstrate that the photometric pipeline correctly estimates random photometric errors, which are below 0.01 mag for stars brighter than (19.5, 20.5, 20.5, 20, 18.5) in $ugriz$, respectively (about twice as good as for individual SDSS runs). Several independent tests of the internal consistency suggest that the spatial variation of photometric zeropoints is not larger than $\sim$0.01 mag (rms). In addition to being the largest available dataset with optical photometry internally consistent at the $\sim$1% level, this catalog provides practical definition of the SDSS photometric system. Using this catalog, we show that photometric zeropoints for SDSS observing runs can be calibrated within nominal uncertainty of 2% even for data obtained through 1 mag thick clouds, and demonstrate the existence of He and H white dwarf sequences using photometric data alone. Based on the properties of this catalog, we conclude that upcoming large-scale optical surveys such as the Large Synoptic Survey Telescope will be capable of delivering robust 1% photometry for billions of sources.Comment: 63 pages, 24 figures, submitted to AJ, version with correct figures and catalog available from http://www.astro.washington.edu/ivezic/sdss/catalogs/stripe82.htm

The role of religion in the longer-range future, April 6, 7, and 8, 2006

This repository item contains a single issue of the Pardee Conference Series, a publication series that began publishing in 2006 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future. This conference that took place during April 6, 7, and 8, 2006. Co-organized by David Fromkin, Director, Frederick S. Pardee Center for the Study of the Longer-Range Future, and Ray L. Hart, Dean ad interim Boston University School of TheologyThe conference brought together some 40 experts from various disciplines to ponder upon the “great dilemma” of how science, religion, and the human future interact. In particular, different panels looked at trends in what is happening to religion around the world, questions about how religion is impacting the current political and economic order, and how the social dynamics unleashed by science and by religion can be reconciled.Carnegie Council on Ethics and International Affair

Harmonizing model organism data in the Alliance of Genome Resources.

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides