Comparative effectiveness of asthma interventions within a practice based research network

<p>Abstract</p> <p>Background</p> <p>Asthma is a chronic lung disease that affects more than 23 million people in the United States, including 7 million children. Asthma is a difficult to manage chronic condition associated with disparities in health outcomes, poor medical compliance, and high healthcare costs. The research network coordinating this project includes hospitals, urgent care centers, and outpatient clinics within Carolinas Healthcare System that share a common electronic medical record and billing system allowing for rapid collection of clinical and demographic data. This study investigates the impact of three interventions on clinical outcomes for patients with asthma. Interventions are: an integrated approach to care that incorporates asthma management based on the chronic care model; a shared decision making intervention for asthma patients in underserved or disadvantaged populations; and a school based care approach that examines the efficacy of school-based programs to impact asthma outcomes including effectiveness of linkages between schools and the healthcare providers.</p> <p>Methods/Design</p> <p>This study will include 95 Practices, 171 schools, and over 30,000 asthmatic patients. Five groups (A-E) will be evaluated to determine the effectiveness of three interventions. Group A is the usual care control group without electronic medical record (EMR). Group B practices are a second control group that has an EMR with decision support, asthma action plans, and population reports at baseline. A time delay design during year one converts practices in Group B to group C after receiving the integrated approach to care intervention. Four practices within Group C will receive the shared decision making intervention (and become group D). Group E will receive a school based care intervention through case management within the schools. A centralized database will be created with the goal of facilitating comparative effectiveness research on asthma outcomes specifically for this study. Patient and community level analysis will include results from patient surveys, focus groups, and asthma patient density mapping. Community variables such as income and housing density will be mapped for comparison. Outcomes to be measured are reduced hospitalizations and emergency department visits; improved adherence to medication; improved quality of life; reduced school absenteeism; improved self-efficacy and improved school performance.</p> <p>Discussion</p> <p>Identifying new mechanisms that improve the delivery of asthma care is an important step towards advancing patient outcomes, avoiding preventable Emergency Department visits and hospitalizations, while simultaneously reducing overall healthcare costs.</p

WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences

BACKGROUND: This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available. RESULTS: We present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence surrounding them. We present tests where we applied the algorithm to the identification of conserved annotated sites in homologous promoters, as well as in distal regions like enhancers. CONCLUSION: Results of the tests show how the algorithm can provide fast and reliable predictions of conserved transcription factor binding sites regulating the transcription of a gene, with better performances than other available methods for the same task. We also show examples on how the algorithm can be successfully employed when promoter annotations of the genes investigated are missing, or when regulatory sites and regions are located far away from the genes

Establishment Failure in Biological Invasions: A Case History of Littorina littorea in California, USA

The early stages of biological invasions are rarely observed, but can provide significant insight into the invasion process as well as the influence vectors have on invasion success or failure.We characterized three newly discovered populations of an introduced gastropod, Littorina littorea (Linné, 1758), in California, USA, comparing them to potential source populations in native Europe and the North American East Coast, where the snail is also introduced. Demographic surveys were used to assess spatial distribution and sizes of the snail in San Francisco and Anaheim Bays, California. Mitochondrial DNA was sequenced and compared among these nascent populations, and various populations from the North American East Coast and Europe, to characterize the California populations and ascertain their likely source. Demographic and genetic data were considered together to deduce likely vectors for the California populations. We found that the three large California L. littorea populations contained only adult snails and had unexpectedly high genetic diversity rather than showing an extreme bottleneck as typically expected in recent introductions. Haplotype diversity in Californian populations was significantly reduced compared to European populations, but not compared to East Coast populations. Genetic analyses clearly suggested the East Coast as the source region for the California introductions.The California L. littorea populations were at an early, non-established phase of invasion with no evidence of recruitment. The live seafood trade is the most likely invasion vector for these populations, as it preferentially transports large numbers of adult L. littorea, matching the demographic structure of the introduced California L. littorea populations. Our results highlight continued operation of live seafood trade vectors and the influence of vectors on the demographic and genetic structure of the resulting populations, especially early stages of the invasion process

From little things, big things grow: trends and fads in 110 years of Australian ornithology

Publishing histories can reveal changes in ornithological effort, focus or direction through time. This study presents a bibliometric content analysis of Emu (1901&ndash;2011) which revealed 115 trends (long-term changes in publication over time) and 18 fads (temporary increases in publication activity) from the classification of 9,039 articles using 128 codes organised into eight categories (author gender, author affiliation, article type, subject, main focus, main method, geographical scale and geographical location). Across 110 years, private authorship declined, while publications involving universities and multiple institutions increased; from 1960, female authorship increased. Over time, question-driven studies and incidental observations increased and decreased in frequency, respectively. Single species and &lsquo;taxonomic group&rsquo; subjects increased while studies of birds at specific places decreased. The focus of articles shifted from species distribution and activities of the host organisation to breeding, foraging and other biological/ecological topics. Site- and Australian-continental-scales slightly decreased over time; non-Australian studies increased from the 1970s. A wide variety of fads occurred (e.g. articles on bird distribution, 1942&ndash;1951, and using museum specimens, 1906&ndash;1913) though the occurrence of fads decreased over time. Changes over time are correlated with technological, theoretical, social and institutional changes, and suggest ornithological priorities, like those of other scientific disciplines, are temporally labil

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers

We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions

Integrating teamwork, clinician occupational well-being and patient safety – development of a conceptual framework based on a systematic review

BACKGROUND: There is growing evidence that teamwork in hospitals is related to both patient outcomes and clinician occupational well-being. Furthermore, clinician well-being is associated with patient safety. Despite considerable research activity, few studies include all three concepts, and their interrelations have not yet been investigated systematically. To advance our understanding of these potentially complex interrelations we propose an integrative framework taking into account current evidence and research gaps identified in a systematic review. METHODS: We conducted a literature search in six major databases (Medline, PsycArticles, PsycInfo, Psyndex, ScienceDirect, and Web of Knowledge). Inclusion criteria were: peer reviewed papers published between January 2000 and June 2015 investigating a statistical relationship between at least two of the three concepts; teamwork, patient safety, and clinician occupational well-being in hospital settings, including practicing nurses and physicians. We assessed methodological quality using a standardized rating system and qualitatively appraised and extracted relevant data, such as instruments, analyses and outcomes. RESULTS: The 98 studies included in this review were highly diverse regarding quality, methodology and outcomes. We found support for the existence of independent associations between teamwork, clinician occupational well-being and patient safety. However, we identified several conceptual and methodological limitations. The main barrier to advancing our understanding of the causal relationships between teamwork, clinician well-being and patient safety is the lack of an integrative, theory-based, and methodologically thorough approach investigating the three concepts simultaneously and longitudinally. Based on psychological theory and our findings, we developed an integrative framework that addresses these limitations and proposes mechanisms by which these concepts might be linked. CONCLUSION: Knowledge about the mechanisms underlying the relationships between these concepts helps to identify avenues for future research, aimed at benefiting clinicians and patients by using the synergies between teamwork, clinician occupational well-being and patient safety. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12913-016-1535-y) contains supplementary material, which is available to authorized users