Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.

The Effect of Diet-Induced Obesity and Subsequent Weight Loss on Body Composition, Glucose Clearance, Metabolite Profile and Liver Amp-Activated Protein Kinase in Mice

Obesity, currently an epidemic, is a difficult disease to combat because it is marked by both a change in body weight and an underlying dysregulation in metabolism, making consistent weight loss challenging. We sought to elucidate this metabolic dysregulation resulting from diet-induced obesity (DIO) that persists through subsequent weight loss. We hypothesized that weight gain imparts a change in “metabolic set point” persisting through subsequent weight loss and that this modification may involve a persistent change in hepatic AMP-activated protein kinase (AMPK), a key energy-sensing enzyme in the body. To test these hypotheses, we tracked metabolic perturbations through this period, measuring changes in hepatic AMPK. To further understand the role of AMPK we used AICAR, an AMPK activator, following DIO. Our findings established a more dynamic metabolic model of DIO and subsequent weight loss. We observed hepatic AMPK elevation following weight loss, but AICAR administration without similar dieting was unsuccessful in improving metabolic dysregulation. Our findings provide an approach to modeling DIO and subsequent dieting that can be built upon in future studies and hopefully contribute to more effective long-term treatments of obesity.

Employment discrimination against transgender people and self-esteem.

The evocation of gender identity in company anti-discrimination policies is still very rare. This observation is also true forscientific studies. Very few researches have focused exclusively on transgender employees. Transgender are neither sick nor lesscompetent, and yet, the feeling of being strongly discriminated is shared by many transgender people. Such discrimination and thetype of causal attribution do not remain without any effect on the well-being of the concerned individuals. According to Crocker &Quinn (1998), the attribution of the discrimination to the existing prejudices may be a way to protect one-self from the negativeimpact on self-esteem. In this theoretical scope, the "rejection-identification" model (Branscombe, Schmitt & Harvey, 1999) has beenhighly mobilized. It emphasizes the importance of ingroup identification in the causal relationship between perceived discriminationsituation and well-being. Previous studies which did test this model show that the identification to a certain group can counteract thenegative effects on well-being. Following this theoretical frame, the presented study examines the impact of different types of causalattributions on self-esteem: internal causes (e.g. lack of skills), external causes (e.g. economic crisis), and gender identity relatedissues. For that purpose, an online survey has been created and fulfilled by 110 transgender people. Different scales were used to testthe model: the Rosenberg self-esteem scale, a causal attribution scale, the perceived discrimination of the transgender population inthe workplace scale and a group identification scale. The results show that transgender people feel still highly stigmatized today andattribute, significantly, the causes of their situation to the prejudices they are victim of. Also, in accordance with the “rejectionidentification”model, three links are observed: (1) a negative link between perceived discrimination and self-esteem; (2) a positivelink between perceived discrimination and ingroup identification; and (3) a positive link between ingroup identification and selfesteem.This situation reflects a lack in diversity considerations. Nevertheless, the attribution made to group stigmatization seems toplay a protective role towards transgender people self-esteem.

The GEOTRACES Intermediate Data Product 2014

The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEls) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in the IDP2014 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including ASCII spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the IDP2014 also contains data quality flags and 1-sigma data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2014 data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes.

La incidencia de los valores culturales en el voluntariado: el caso de Europa

La realidad del voluntariado es sumamente compleja hasta el punto de que resulta complicado definir y caracterizar el trabajo voluntario, dada la gran variedad de interpretaciones, motivaciones, variables sociodemográficas y aspectos culturales que configuran el perfil de los voluntarios. El objetivo de este trabajo es analizar la influencia conjunta de algunas variables sociodemográficas, así como de los valores culturales de índole secular o tradicional, sobre el perfil de los voluntarios en Europa. Además, se investiga qué variables orientan a los voluntarios hacia un determinado tipo de voluntariado u otro. Para ello se ha aplicado principalmente una metodología de regresión logística a partir de la información disponible en la European Value Study. Los resultados obtenidos ayudan a establecer una caracterización del voluntariado en Europa, y confirman la influencia de los valores culturales, en primer lugar, en la realización o no de trabajos de voluntariado, y en segundo lugar, en la elección que hacen estas personas del tipo de actividad con la que están comprometidos. Al analizar dos tipos de voluntariado de motivación supuestamente muy diferente, se concluye que existe un grupo de valores que influyen en ambos, aunque el sentido y la intensidad en la que lo hacen sea diferente; por otra parte, algunos valores tienen influencia o no en la realización de trabajos de voluntariado, dependiendo del tipo específico al que nos refiramos.

Predictors of attitudes toward inclusion of students with special educational needs in future education professionals

One of the main pillars in the development of inclusive schools is the initial teacher training. Before determining if it is necessary to make changes (and of what type) in training programs or curriculum guides related to the attention to diversity and inclusive education, the attitudes of future education professionals in this area should be analyzed. This includes the identification of the relevant predictors of inclusive attitudes. The research reported in this article pursued this objective, doing so with a quantitative survey methodology based on the use of cross-sectional structured data collection and statistical analyses related to the quality of the attitude questionnaire (factor analysis and Cronbach's alpha), descriptive statistics, correlations, hypothesis tests for difference of means, and regression analysis in order to predict attitudes towards inclusion in education. Firstly, the results show that the participants held very positive attitudes toward the inclusion of students with special educational needs. Particularly, older respondents, those with a longer training and, to a lesser extent, women and those who had been in touch with disabled people stood out within this attitude. Secondly, it is evidenced that self-transcendence values ​and, more weakly, contact, function as robust predictors of attitudes of future practitioners towards the inclusion of students with special needs. Some applications for the initial professionalization of educators are suggested in the discussion.

Maternal mental health and non-organic failure to thrive.

This study reports on the first phase of a large-scale, longitudinal, multidisciplinary community study examining the growth, learning and development of young children with a particular focus on failure to thrive without organic cause. However, the group identified in this study may be better described as weight faltering. This paper examines the psychological data collected using the Parenting Stress Index, Rosenberg Self-Esteem and the General Health Questionnaire in relation to child growth. There were no significant differences between the mothers of the weight faltering and control children in terms of parenting stress, maternal depression, maternal perceptions of their parenting competence or maternal self-esteem. Maternal sensitivity to comments about child size, regardless of direction, had a negative impact on mood.

Safety and Pharmacokinetics of Dapivirine Delivery From Matrix and Reservoir Intravaginal Rings to HIV-Negative Women

Vaginal microbicides for the prevention of HIV transmission may be an important option for protecting women from infection. Incorporation of dapivirine, a lead candidate nonnucleoside reverse transcriptase inhibitor, into intravaginal rings (IVRs) for sustained mucosal delivery may increase microbicide product adherence and efficacy compared with conventional vaginal formulations. Twentyfour
healthy HIV-negative women 18–35 years of age were randomly assigned (1:1:1) to dapivirine matrix IVR, dapivirine reservoir IVR, or placebo IVR. Dapivirine concentrations were measured in plasma
and vaginal fluid samples collected at sequential time points over the 33-day study period (28 days of IVR use, 5 days of follow-up). Safety was assessed by pelvic/colposcopic examinations, clinical laboratory tests, and adverse events. Both IVR types were safe and well tolerated with similar adverse events observed in the placebo and dapivirine groups. Dapivirine from both IVR types was successfully distributed throughout the lower genital tract at concentrations over 4 logs greater than the EC50 against wild-type HIV-1 (LAI) in MT4 cells. Maximum concentration (Cmax) and area under the concentration–time curve (AUC) values were significantly higher with the matrix than reservoir IVR. Mean plasma concentrations of dapivirine were ,2 ng/mL. These findings suggest that IVR delivery of microbicides is a viable option meriting further study.

La amistad cívica en Aristóteles: concordia y fraternidad

El artículo muestra la importancia de la amistad en el contexto de la filosofía política aristotélica. Esta importancia se verifica en su peso específico en comparación con la justicia, puesto que Aristóteles mismo sostiene que la amistad cívica es incluso un objetivo superior al de la búsqueda de la justicia. En concreto, el artículo se centra en la función de la concordia, como tipo especial de amistad cívica, en términos de conservación de la unidad y estabilidad de la polis. Para captar su significación, se plantea el papel de la concordia como complemento a la condición política del ser humano. La concordia es necesaria a la luz de la tendencia a la lucha entre las partes de la ciudad, entre el demos y los oligarcas. Puesto que esta lucha pone en peligro la continuidad de la polis, la concordia entre ciudadanos se convierte en un antecedente privilegiado del principio de fraternidad republicana, el cual todavía no ha gozado de una atención suficiente en el campo de la historia de la filosofía política.

Dose-dependent effects of folic acid on blood concentrations of homocysteine: a meta-analysis of the randomized trials

Background: Dietary supplementation with B vitamins that lower blood homocysteine concentrations is expected to reduce cardiovascular disease risk, but there has been uncertainty about the optimum regimen to use for this purpose.

Strategies for multivessel revascularization in patients with diabetes

In some randomized trials comparing revascularization strategies for patients with diabetes, coronary-artery bypass grafting (CABG) has had a better outcome than percutaneous coronary intervention (PCI). We sought to discover whether aggressive medical therapy and the use of drug-eluting stents could alter the revascularization approach for patients with diabetes and multivessel coronary artery disease.

Development of a genotyping microarray for Usher syndrome

Usher syndrome, a combination of retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction, displays a high degree of clinical and genetic heterogeneity. Three clinical subtypes can be distinguished, based on the age of onset and severity of the hearing impairment, and the presence or absence of vestibular abnormalities. Thus far, eight genes have been implicated in the syndrome, together comprising 347 protein-coding exons.