Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data

UNLABELLED: As the volume of patient-specific genome sequences increases the focus of biomedical research is switching from the detection of disease-mutations to their interpretation. To this end a number of techniques have been developed that use mutation data collected within a population to predict whether individual genes are likely to be disease-causing or not. As both sequence data and associated analysis tools proliferate, it becomes increasingly difficult for the community to make sense of these data and their implications. Moreover, no single analysis tool is likely to capture all relevant genomic features that contribute to the gene's pathogenicity. Here, we introduce Web-based Gene Pathogenicity Analysis (WGPA), a web-based tool to analyze genes impacted by mutations and rank them through the integration of existing prioritization tools, which assess different aspects of gene pathogenicity using population-level sequence data. Additionally, to explore the polygenic contribution of mutations to disease, WGPA implements gene set enrichment analysis to prioritize disease-causing genes and gene interaction networks, therefore providing a comprehensive annotation of personal genomes data in disease. AVAILABILITY AND IMPLEMENTATION: wgpa.systems-genetics.net

On the harmonicity of normal almost contact metric structures

We consider normal almost contact structures on a Riemannian manifold and, through their associated sections of an ad-hoc twistor bundle, study their harmonicity, as sections or as maps. We rewrite these harmonicity equations in terms of the Riemann curvature tensor and find conditions relating the harmonicity of the almost contact and almost complex structures of the total and base spaces of the Morimoto fibration.Comment: 14 page

A case study of Spanish language use in a Texas border colonia

This case study reveals a Spanish language marginalization in a South Texas community of mostly Latinos, who are the fastest growing group in the U.S. (Colombi & Roca, 2003); furthermore, approximately 77% of English language learners (ELLs) have Spanish as their heritage language (Hopstock & Stephenson, 2003). Nevertheless, ELLs do not receive much academic literacy support in their first language in many schools (Zehler et al., 2003). Thus, out-of- school social practices play an important role on maintaining a native language (e.g., Burrows-Goodwill, 2009; Reyes, 2006). However, researchers have not explored this phenomenon in Texas border colonias, or unincorporated areas where city services are non-existent (U.S. Department of Housing and Urban Development, 2005) and where almost half of residents live below the poverty line (U.S. Census Bureau, 2000). This case study examined Spanish language use in the Texas border colonia of El Palmar (pseudonym). I utilized U.S. Census data, linguistic landscape analysis of the neighborhood, participant observations, language use surveys, language logs, and viii interviews to determine the extent that bilingualism and biliteracy have developed in El Palmar and the factors leading to language maintenance or shift in this colonia. I used the framework of New Literacy Studies traditions (Barton, 2007; Barton & Hamilton, 1998; Gee, 2008; Heath, 1983; Street, 2001) to identify literacy practices involving adults and children in El Palmar, as well as the funds of knowledge concept (González, Moll, & Amanti, 2005; Smith, 2002) to understand and acknowledge the cultural and literacy resources recent immigrants use in new language environments. I also incorporated Fishman‟s (2001) ideas of language shift to analyze the Spanish language maintenance or loss in the colonia. Biliteracy of the community was analyzed by applying the linguistic landscape concept developed by Landry and Bourhis (1997). The analysis of multiple data sources revealed that Spanish continues to be the most spoken language, but bilingualism has grown in El Palmar because more residents, particularly youth, have learned English. On the other hand, biliteracy has not developed. Even though El Palmar youth are fluent speakers of English and Spanish, they have not developed literacy in Spanish. The factors that help the maintenance or loss of Spanish in the colonia were also identified. This study also made a language compartmentalization evident in El Palmar, where Spanish is seen as the language to communicate and express feelings, and English as the language of power to succeed. The role of children and adults as language brokers (e.g., Orellana, 2009) in between these two language worlds was also analyzed. This study demonstrates the need for an awareness among El Palmar residents to value Spanish, not only as a sentimental language (Kelman, 1971), but as a language that will help them to succeed in high-power spheres, such as education and business (Fishman, 2001). Another implication is for a better communication among parents, schools, and community members to affirm colonia residents‟ linguistic resources and biliteracy

Informal Referrals, Employment and Wages: Seeking Causal Directions

Employers and job seekers rely extensively on job informational networks to fill vacancies or to find a job. The widespread use of job contacts to find work has been largely associated with labor outcomes, such as finding a job or even affecting wages. Some scholars have claimed that informal referrals play a determinant role in reducing informational mismatches between potential employers and job seekers. Although several studies have shown that the use of friends and relatives is correlated with labor outcomes, little is known about the causal effect. In this article, I aim to identify whether there is a causal effect of using informal referrals on two main outcomes: the probability of being employed and hourly wages. I use a large data set from Colombia, the Living Standard Survey 2003, to contrast the results from three main methodologies: standard OLS estimation, propensity-score matching, and instrumental variables. Results suggest that much of the positive effect of using informal referrals on employment reflects the prevalence of informal-sector jobs to be filled through this method rather than a causal effect. On the contrary, the results for hourly wages suggest a negative causal effect of using job informational networks, which is explained by the low-quality/poor matches theory. Yet, this is only true in formal-sector firms.informal referrals, job search methods, employment rates, hourly wages, selec- tion bias, OLS, Propensity-Score Matching, Instrumental Variables, Roy Model

A search for brown-dwarf like secondaries in cataclysmic variables

We present VTL/ISAAC infrared spectroscopy of a sample of short orbital period cataclysmic variables which are candidates for harboring substellar companions. We have detected the KI and NaI absorption lines of the companion star in VY Aqr. The overall spectral distribution in this system is best fit with a M9.5 type dwarf spectra, implying a distance of $100 \pm 10$ pc. VY Aqr seems to fall far from the theoretical distribution of secondary star temperatures around the orbital period minimum. Fitting of the IR spectral energy distribution (SED) was performed by comparing the observed spectrum with late-type templates. The application of such a spectral fitting procedure suggests that the continuum shape in the 1.1-2.5 $\mu$m spectral region in short orbital period cataclysmic variables may be an useful indicator of the companion spectral type. The SED fitting for RZ Leo and CU Vel suggests M5 type dwarf companions, and distances of 340 $\pm$ 110 and 150 $\pm$ 50 pc, respectively. These systems may be placed in the upper evolution branch for short period cataclysmic variables.Comment: accepted for publication in MNRAS, 6 pages, 7 figure