University of Alberta

About: University of Alberta is a education organization based out in Edmonton, Alberta, Canada. It is known for research contribution in the topics: Population & Health care. The organization has 65403 authors who have published 154847 publications receiving 5358338 citations. The organization is also known as: Ualberta & UAlberta.

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

Abstract: Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 � 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these wellannotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/. Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com Supplementary information: Supplementary data are available at Bioinformatics online.

Prime role for an insulin epitope in the development of type 1 diabetes in NOD mice.

Abstract: A fundamental question about the pathogenesis of spontaneous autoimmune diabetes is whether there are primary autoantigens. For type 1 diabetes it is clear that multiple islet molecules are the target of autoimmunity in man and animal models. It is not clear whether any of the target molecules are essential for the destruction of islet beta cells. Here we show that the proinsulin/insulin molecules have a sequence that is a primary target of the autoimmunity that causes diabetes of the non-obese diabetic (NOD) mouse. We created insulin 1 and insulin 2 gene knockouts combined with a mutated proinsulin transgene (in which residue 16 on the B chain was changed to alanine) in NOD mice. This mutation abrogated the T-cell stimulation of a series of the major insulin autoreactive NOD T-cell clones. Female mice with only the altered insulin did not develop insulin autoantibodies, insulitis or autoimmune diabetes, in contrast with mice containing at least one copy of the native insulin gene. We suggest that proinsulin is a primary autoantigen of the NOD mouse, and speculate that organ-restricted autoimmune disorders with marked major histocompatibility complex (MHC) restriction of disease are likely to have specific primary autoantigens.

The biotic ligand model : a historical overview

Abstract: During recent years, the biotic ligand model (BLM) has been proposed as a tool to evaluate quantitatively the manner in which water chemistry affects the speciation and biological availability of metals in aquatic systems. This is an important consideration because it is the bioavailability and bioreactivity of metals that control their potential to cause adverse effects. The BLM approach has gained widespread interest amongst the scientific, regulated and regulatory communities because of its potential for use in developing water quality criteria (WQC) and in performing aquatic risk assessments for metals. Specifically, the BLM does this in a way that considers the important influences of site-specific water quality. This journal issue includes papers that describe recent advances with regard to the development of the BLM approach. Here, the current status of the BLM development effort is described in the context of the longer-term history of advances in the understanding of metal interactions in the environment upon which the BLM is based. Early developments in the aquatic chemistry of metals, the physiology of aquatic organisms and aquatic toxicology are reviewed first, and the degree to which each of these disciplines influenced the development of water quality regulations is discussed. The early scientific advances that took place in each of these fields were not well coordinated, making it difficult for regulatory authorities to take full advantage of the potential utility of what had been learned. However, this has now changed, with the BLM serving as a useful interface amongst these scientific disciplines, and within the regulatory arena as well. The more recent events that have led to the present situation are reviewed, and consideration is given to some of the future needs and developments related to the BLM that are envisioned. The research results that are described in the papers found in this journal issue represent a distinct milestone in the ongoing evolution of the BLM approach and, more generally, of approaches to performing ecological assessments for metals in aquatic systems. These papers also establish a benchmark to which future scientific and regulatory developments can be compared. Finally, they demonstrate the importance and usefulness of the concept of bioavailability and of evaluative tools such as the BLM.

Individual determinants of research utilization by nurses: a systematic review update

Abstract: Interventions that have a better than random chance of increasing nurses' use of research are important to the delivery of quality patient care. However, few reports exist of successful research utilization in nursing interventions. Systematic identification and evaluation of individual characteristics associated with and predicting research utilization may inform the development of research utilization interventions. To update the evidence published in a previous systematic review on individual characteristics influencing research utilization by nurses. As part of a larger systematic review on research utilization instruments, 12 online bibliographic databases were searched. Hand searching of specialized journals and an ancestry search was also conducted. Randomized controlled trials, clinical trials, and observational study designs examining the association between individual characteristics and nurses' use of research were eligible for inclusion. Studies were limited to those published in the English, Danish, Swedish, and Norwegian languages. A vote counting approach to data synthesis was taken. A total of 42,770 titles were identified, of which 501 were retrieved. Of these 501 articles, 45 satisfied our inclusion criteria. Articles assessed research utilization in general (n = 39) or kinds of research utilization (n = 6) using self-report survey measures. Individual nurse characteristics were classified according to six categories: beliefs and attitudes, involvement in research activities, information seeking, education, professional characteristics, and socio-demographic/socio-economic characteristics. A seventh category, critical thinking, emerged in studies examining kinds of research utilization. Positive relationships, at statistically significant levels, for general research utilization were found in four categories: beliefs and attitudes, information seeking, education, and professional characteristics. The only characteristic assessed in a sufficient number of studies and with consistent findings for the kinds of research utilization was attitude towards research; this characteristic had a positive association with instrumental and overall research utilization. This review reinforced conclusions in the previous review with respect to positive relationships between general research utilization and: beliefs and attitudes, and current role. Furthermore, attending conferences/in-services, having a graduate degree in nursing, working in a specialty area, and job satisfaction were also identified as individual characteristics important to research utilization. While these findings hold promise as potential targets of future research utilization interventions, there were methodological problems inherent in many of the studies that necessitate their findings be replicated in further research using more robust study designs and multivariate assessment methods.