Novel Distances for Dollo Data

We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), which is consistent for data generated under a Dollo model, and show that it has some useful theoretical properties including an intriguing link to the LogDet distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, Nei Li and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process, which may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology (DArT) datasets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyse gene family presence/absence data on bacteria from the COG database and compare the results to previous phylogenies estimated using the conditioned genome reconstruction approach

The Regulation of Aggrecanase ADAMTS-4 Expression in Human Achilles Tendon and tendon-Derived Cells

Several members of the ADAMTS (A Disintegrin And Metalloproteinase with ThromboSpondin motifs) family have been identified as aggrecanases, whose substrates include versican, the principal large proteoglycan in the tendon extracellular matrix. We have characterized the expression of ADAMTS-4 in human Achilles tendon and tendon-derived cells. ADAMTS-4 mRNA levels were higher in ruptured tendon compared with normal tendon or chronic painful tendinopathy. In tissue extracts probed by Western blotting, mature ADAMTS-4 (68 kDa) was detected only in ruptured tendons, while processed ADAMTS-4 (53 kDa) was detected also in chronic painful tendinopathy and in normal tendon. In cultured Achilles tendon cells, transforming growth factor-ß (TGF-ß) stimulated ADAMTS-4 mRNA expression (typically 20-fold after 24 h), while interleukin-1 induced a smaller, shorter-term stimulation which synergised markedly with that induced by TGF-ß. Increased levels of immunoreactive proteins consistent with mature and processed forms of ADAMTS-4 were detected in TGF-ß-stimulated cells. ADAMTS-4 mRNA was expressed at higher levels by tendon cells in collagen gels than in monolayer cultures. In contrast, the expression of ADAMTS-1 and -5 mRNA was lower in collagen gels compared with monolayers, and these mRNA showed smaller or opposite responses to growth factors and cytokines compared with that of ADAMTS-4 mRNA. We conclude that both ADAMTS-4 mRNA and ADAMTS-4 protein processing may be differentially regulated in normal and damaged tendons and that both the matrix environment and growth factors such as TGF-ß are potentially important factors controlling ADAMTS aggrecanase activities in tendon pathology

Medición de las condiciones habitacionales: una propuesta metodológica para analizar desigualdades inter e intraterritorios urbanos

La medición de las condiciones habitacionales de un territorio resulta de especial interés para la implementación de políticas públicas. Los métodos tradicionales se concentran en la medición de los déficits y dejan de lado aquella parte de la población que se encuentra cerca del umbral. Con base en propuestas específicas, estándares de organismos internacionales, legislación nacional y la importante participación de especialistas, en este estudio se genera una metodología cuantitativa, que evita esa pérdida de información al incluir a toda la población de un territorio, asignándole un puntaje a cada persona de acuerdo a las características del hogar que habita. Para validar la propuesta, se presenta una aplicación con datos de Argentina, donde se constata su versatilidad, dado que permite detectar problemáticas particulares en cada dimensión, y también consigue analizar el nivel promedio, la distribución intra e interterritorios y la pérdida de bienestar por desigualdad.The measurement of the housing conditions of a territory is particularly important for the implementation of public policies. Traditional methods focus on the measurement of deficits and leave aside that part of the population which is closer to the threshold. Based on specific proposals, the standards of international organizations, national legislation, and a significant participation of specialists, this study proposes a quantitative methodology, which avoids said loss of information by including the entire population of a territory, assigning a score to each person according to the characteristics of the household they live in. To validate this proposal, we present an application with data from Argentina, where its versatility is verified given that it allows for the detection of issues in each dimension while also getting to analyze the average level, the intra and interterritorial distribution, and the welfare loss due to inequality.Fil: Actis Di Pasquale, Eugenio. Universidad Nacional de Mar del Plata. Facultad de Ciencias Económicas y Sociales; Argentina

The effectiveness of workplace coaching:a meta-analysis of learning and performance outcomes from coaching

This study presents a meta-analysis synthesizing the existing research on the effectiveness of workplace coaching. We exclusively explore workplace coaching provided by internal or external coaches and therefore exclude cases of manager-subordinate and peer coaching. We propose a framework of potential outcomes from coaching in organizations, which we examine meta-analytically (k = 17). Our analyses indicated that coaching had positive effects on organizational outcomes overall (δ = 0.36), and on specific forms of outcome criteria (skill-based δ = 0.28; affective δ = 0.51; individual-level results δ = 1.24). We also examined moderation by a number of coaching practice factors (use of multisource feedback; type of coach; coaching format; longevity of coaching). Our analyses of practice moderators indicated a significant moderation of effect size for type of coach (with effects being stronger for internal coaches compared to external coaches) and use of multisource feedback (with the use of multisource feedback resulting in smaller positive effects). We found no moderation of effect size by coaching format (comparing face-to-face, with blended face-to-face and e-coaching) or duration of coaching (number of sessions or longevity of intervention). The effect sizes give support to the potential utility of coaching in organizations. Implications for coaching research and practice are discussed

IUPHAR-DB: An Expert-Curated, Peer-Reviewed Database of Receptors and Ion Channels

The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 non-sensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of about a third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry. Individual gene pages provide a comprehensive description of the genes and their functions, with information on protein structure, ligands, expression patterns, signaling mechanisms, functional assays and biologically important receptor variants (e.g. single nucleotide polymorphisms and splice variants). The phenotypes resulting from altered gene expression (e.g. in genetically altered animals) and genetic mutations are described. Links are provided to bioinformatics resources such as NCBI RefSeq, OMIM, PubChem, human, rat and mouse genome databases. Recent developments include the addition of ligand-centered pages summarising information about unique ligand molecules in IUPHAR-DB. IUPHAR-DB represents a novel approach to biocuration because most data are provided through manual curation of published literature by a network of over 60 expert subcommittees coordinated by NC-IUPHAR. Data are referenced to the primary literature and linked to PubMed. The data are checked to ensure accuracy and consistency by the curators, added to the production server using custom-built submission tools and peer-reviewed by NC-IUPHAR, before being transferred to the public database. Data are reviewed and updated regularly (at least biennially). Other website features include comprehensive database search tools, online and downloadable gene lists and links to recent publications of interest to the field, such as reports on receptor-ligand pairings. The database is freely available at "http://www.iuphar-db.org":http://www.iuphar-db.org. Curators can be reached at curators [at] iuphar-db.org. We thank British Pharmacological Society, UNESCO (through the ICSU Grants Programme), Incyte, GlaxoSmithKline, Novartis, Servier and Wyeth for their support

User-centered development of a Virtual Research Environment to support collaborative research events

This paper discusses the user-centred development process within the Collaborative Research Events on the Web (CREW) project, funded under the JISC Virtual Research Environments (VRE) programme. After presenting the project, its aims and the functionality of the CREW VRE, we focus on the user engagement approach, grounded in the method of co-realisation. We describe the different research settings and requirements of our three embedded user groups and the respective activities conducted so far. Finally we elaborate on the main challenges of our user engagement approach and end with the project’s next steps

Cognitive Performance May be Impaired by Exercise in a Hot, Humid Environment: A Preliminary Investigation

The purpose of this study was to examine the effects of acute active dehydration by exercise in a hot, humid environment on cognitive performance. Our findings were inconclusive compared to previous studies that reported decreased cognitive performance in manual laborers and military personnel working in extreme environmental conditions

Preparation of Maps Depicting Geothermal Gradient and Precambrian Structure in the Permian Basin

The objectives of this project were to prepare maps depicting (1) the geothermal gradients, and (2) the structure on the top of the Precambrian in the Permian Basin of West Texas and New Mexico. Both were to be created and distributed in a spatially related Geographic Information System (GIS) project. The preparation of these maps involved two different sets of issues. Prior to this study, no publicly available, detailed map of Precambrian structure with referenced control points existed for the Permian Basin. This is in part a function of the sparsity of data (Precambrian well penetrations) and in part a function of the lack of interest in assembling such a map. Additionally, no digital, GIS-based map of Precambrian structure was previously available. To prepare this map over the entire area of interest, it was necessary to develop new creative approaches. By contrast, more than one map depicting geothermal gradient has been previously published. Additionally, relatively extensive data sets of bottom-hole well temperatures are available. The issues in preparing this map revolve around (1) deciding what data to use, (2) developing ways to deal with possible errors in the data, and (3) making proper corrections to the data.Bureau of Economic Geolog