ORegAnno: an open-access community-driven resource for regulatory annotation

ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the ‘publication queue’ allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or ‘check out’ papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org

Preventing abuse in accommodation services: from procedural responses to protective cultures

This article reviews current approaches of disability accommodation services to addressing the abuse and neglect of people with intellectual disability who live in them.We review international literature and provide practice examples from accommodation services for people with intellectual disability in Australia to develop a framework of current research, policy and practice in this area. The results of this review show that dominant policy and practice approaches do not give adequate consideration to the prevention and protection of people from harm, focusing primarily on responding to individual instances of maltreatment. Managerial, compliance-based systems may be deflecting attention from recognizing and responding more effectively to abuse and neglect at individual, systemic and structural levels. The current dominant approach fails to develop a culture of prevention and protection for people with intellectual disability. Further, somesystemic and structural preconditions are setwhich make abuse and neglect less likely to be prevented

Diagnóstico situacional da violência contra crianças e adolescentes com deficiência em três instituições do Rio de Janeiro Situational diagnostic about violence against children and adolescents with disability in three institutions of Rio de Janeiro

Apresentamos um diagnóstico situacional a respeito da violência contra crianças e adolescentes com deficiência, desenvolvido em três instituições de referência no Rio de Janeiro, da esfera federal, municipal e do terceiro setor, a partir de 53 estudos de caso. Partimos de uma revisão teórica sobre violência na área da deficiência e demonstramos como esse tema é embrionário no Brasil e América Latina. A relevância do estudo está na demonstração da diversidade e riqueza de formas atuais de assistência à pessoa com deficiência. É feita uma análise de como as instituições estão sendo desafiadas a enfrentar a violência e a violação de direitos e a desenvolver estratégias de proteção. Não apenas a violência, mas a pobreza também se coloca como problema para essas organizações. Concluímos que quando as deficiências estão associadas a formas de violência e à violação de direitos, as instituições têm desenvolvido estratégias de amparo social e apoio em rede para melhorar a qualidade de vida de seus usuários. O principal desafio está em se buscar reverter desvantagens cumulativas, ampliar capacidades e assegurar cuidado e proteção às crianças, adolescentes e jovens com deficiência e suas famílias.<br>We present a situational diagnostic about violence against children and adolescent with disability, which were done in three referenced institutions in Rio de Janeiro, from federal and municipal level and from the third sector, based in 53 case studies. This article considered a recent theoretical study of violence in the disability field and it demonstrates that this subject is embryonic in Brazil and Latin American. The relevance of this study is in the description we did of the diversity and richness of the recent forms of assistance in the disability field. It was analyzed how these institutions are being challenged to face violence and rights violation and to build protection strategies. Not only violence, but the poverty is another problem which is pointed out to these organizations. We concluded that when disability is associated to forms of violence and rights violation these institutions have developed social benefits and a social network in order to change disability people´s quality of life. The central challenge is to promote change of cumulative disadvantages, to enhance capacities and to offer care and protection to disabled people and their families

A regulatory toolbox of MiniPromoters to drive selective expression in the brain

The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools designed to study and treat the brain by directed gene expression. Genes with brain expression patterns of interest are subjected to bioinformatic analysis to delineate candidate regulatory regions, which are then incorporated into a panel of compact human MiniPromoters to drive expression to brain regions and cell types of interest. Using single-copy, homologous-recombination “knockins” in embryonic stem cells, each MiniPromoter reporter is integrated immediately 5′ of the Hprt locus in the mouse genome. MiniPromoter expression profiles are characterized in differentiation assays of the transgenic cells or in mouse brains following transgenic mouse production. Histological examination of adult brains, eyes, and spinal cords for reporter gene activity is coupled to costaining with cell-type–specific markers to define expression. The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies

The transcription factor encyclopedia.

Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe