Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Organizational impact of evidence-informed decision making training initiatives : a case study comparison of two approaches

Background The impact of efforts by healthcare organizations to enhance the use of evidence to improve organizational processes through training programs has seldom been assessed. We therefore endeavored to assess whether and how the training of mid- and senior-level healthcare managers could lead to organizational change. Methods We conducted a theory-driven evaluation of the organizational impact of healthcare leaders’ participation in two training programs using a logic model based on Nonaka’s theory of knowledge conversion. We analyzed six case studies nested within the two programs using three embedded units of analysis (individual, group and organization). Interviews were conducted during intensive one-week data collection site visits. A total of 84 people were interviewed. Results We found that the impact of training could primarily be felt in trainees’ immediate work environments. The conversion of attitudes was found to be easier to achieve than the conversion of skills. Our results show that, although socialization and externalization were common in all cases, a lack of combination impeded the conversion of skills. We also identified several individual, organizational and program design factors that facilitated and/or impeded the dissemination of the attitudes and skills gained by trainees to other organizational members. Conclusions Our theory-driven evaluation showed that factors before, during and after training can influence the extent of skills and knowledge transfer. Our evaluation went further than previous research by revealing the influence—both positive and negative—of specific organizational factors on extending the impact of training programs

Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient.

BACKGROUND: Animals living at high altitude must adapt to environments with hypoxia and low temperatures, but relatively little is known about underlying genetic changes. Toad-headed lizards of the genus Phrynocephalus cover a broad altitudinal gradient of over 4000 m and are useful models for studies of such adaptive responses. In one of the first studies to have considered selection on mitochondrial protein-coding regions in an ectothermic group distributed over such a wide range of environments, we analysed nineteen complete mitochondrial genomes from all Chinese Phrynocephalus (including eight genomes sequenced for the first time). Initial analyses used site and branch-site model (program: PAML) approaches to examine nonsynonymous: synonymous substitution rates across the mtDNA tree. RESULTS: Ten positively selected sites were discovered, nine of which corresponded to subunits ND2, ND3, ND4, ND5, and ND6 within the respiratory chain enzyme mitochondrial Complex I (NADH Coenzyme Q oxidoreductase). Four of these sites showed evidence of general long-term selection across the group while the remainder showed evidence of episodic selection across different branches of the tree. Some of these branches corresponded to increases in altitude and/or latitude. Analyses of physicochemical changes in protein structures revealed that residue changes at sites that were under selection corresponded to major functional differences. Analyses of coevolution point to coevolution of selected sites within the ND4 subunit, with key sites associated with proton translocation across the mitochondrial membrane. CONCLUSIONS: Our results identify mitochondrial Complex I as a target for environment-mediated selection in this group of lizards, a complex that frequently appears to be under selection in other organisms. This makes these lizards good candidates for more detailed future studies of molecular evolution

Integrins as therapeutic targets: lessons and opportunities.

The integrins are a large family of cell adhesion molecules that are essential for the regulation of cell growth and function. The identification of key roles for integrins in a diverse range of diseases, including cancer, infection, thrombosis and autoimmune disorders, has revealed their substantial potential as therapeutic targets. However, so far, pharmacological inhibitors for only three integrins have received marketing approval. This article discusses the structure and function of integrins, their roles in disease and the chequered history of the approved integrin antagonists. Recent advances in the understanding of integrin function, ligand interaction and signalling pathways suggest novel strategies for inhibiting integrin function that could help harness their full potential as therapeutic targets

Stratified primary care versus non-stratified care for musculoskeletal pain: findings from the STarT MSK feasibility and pilot cluster randomized controlled trial

Background: Musculoskeletal (MSK) pain from the five most common presentations to primary care (back, neck, shoulder, knee or multi-site pain), where the majority of patients are managed, is a costly global health challenge. At present, first-line decisionmaking is based on clinical reasoning and stratified models of care have only been tested in patients with low back pain. We therefore, examined the feasibility of; a) a future definitive cluster randomised controlled trial (RCT), and b) General Practitioners (GPs) providing stratified care at the point-of-consultation for these five most common MSK pain presentations. Methods: The design was a pragmatic pilot, two parallel-arm (stratified versus nonstratified care), cluster RCT and the setting was 8 UK GP practices (4 intervention, 4 control) with randomisation (stratified by practice size) and blinding of trial statistician and outcome data-collectors. Participants were adult consulters with MSK pain without indicators of serious pathologies, urgent medical needs, or vulnerabilities. Potential participant records were tagged and individuals sent postal invitations using a GP point-of-consultation electronic medical record (EMR) template. The intervention was supported by the EMR template housing the Keele STarT MSK Tool (to stratify into low, medium and high-risk prognostic subgroups of persistent pain and disability) and recommended matched treatment options. Feasibility outcomes included exploration of recruitment and follow-up rates, selection bias, and GP intervention fidelity. To capture recommended outcomes including pain and function, participants completed an initial questionnaire, brief monthly questionnaire (postal or SMS), and 6-month follow-up questionnaire. An anonymised EMR audit described GP decision-making. Results: GPs screened 3063 patients (intervention=1591, control=1472), completed the EMR template with 1237 eligible patients (intervention=513, control=724) and 524 participants (42%) consented to data collection (intervention=231, control=293). Recruitment took 28 weeks (target 12 weeks) with >90% follow-up retention (target >75%). We detected no selection bias of concern and no harms identified. GP stratification tool fidelity failed to achieve a-priori success criteria, whilst fidelity to the matched treatments achieved “complete success”. Conclusions: A future definitive cluster RCT of stratified care for MSK pain is feasible and is underway, following key amendments including a clinician-completed version of the stratification tool and refinements to recommended matched treatments

Computer-Based Stratified Primary Care for Musculoskeletal Consultations Compared With Usual Care: Study Protocol for the STarT MSK Cluster Randomized Controlled Trial.

BACKGROUND: Musculoskeletal (MSK) pain is a major cause of pain and disability. We previously developed a prognostic tool (STarT Back Tool) with demonstrated effectiveness in guiding primary care low back pain management by supporting decision-making using matched treatments. A logical next step is to determine whether prognostic stratified care has benefits for a broader range of common MSK pain presentations. OBJECTIVE: This study seeks to determine, in patients with 1 of the 5 most common MSK presentations (back, neck, knee, shoulder, and multisite pain), whether stratified care involving the use of the Keele STarT MSK Tool to allocate individuals into low-, medium-, and high-risk subgroups, and matching these subgroups to recommended matched clinical management options, is clinical and cost effective compared with usual nonstratified primary care. METHODS: This is a pragmatic, two-arm parallel (stratified vs nonstratified care), cluster randomized controlled trial, with a health economic analysis and mixed methods process evaluation. The setting is UK primary care, involving 24 average-sized general practices randomized (stratified by practice size) in a 1:1 ratio (12 per arm) with blinding of trial statistician and outcome data collectors. Randomization units are general practices, and units of observation are adult MSK consulters without indicators of serious pathologies, urgent medical needs, or vulnerabilities. Potential participant records are tagged and individuals invited using a general practitioner (GP) point-of-consultation electronic medical record (EMR) template. The intervention is supported by an EMR template (computer-based) housing the Keele STarT MSK Tool (to stratify into prognostic subgroups) and the recommended matched treatment options. The primary outcome using intention-to-treat analysis is pain intensity, measured monthly over 6 months. Secondary outcomes include physical function and quality of life, and an anonymized EMR audit to capture clinician decision making. The economic evaluation is focused on the estimation of incremental quality-adjusted life years and MSK pain-related health care costs. The process evaluation is exploring a range of potential factors influencing the intervention and understanding how it is perceived by patients and clinicians, with quantitative analyses focusing on a priori hypothesized intervention targets and qualitative approaches using focus groups and interviews. The target sample size is 1200 patients from 24 general practices, with >5000 MSK consultations available for anonymized medical record data comparisons. RESULTS: Trial recruitment commenced on May 18, 2018, and ended on July 15, 2019, after a 14-month recruitment period in 24 GP practices. Follow-up and interview data collection was completed in February 2020. CONCLUSIONS: This trial is the first attempt, as far as we know, at testing a prognostic stratified care approach for primary care patients with MSK pain. The results of this trial should be available by the summer of 2020. CLINICALTRIAL: International Standard Randomized Controlled Trial Number (ISRCTN): 15366334; http://www.isrctn.com/ISRCTN15366334

Selecting a BRCA risk assessment model for use in a familial cancer clinic

<p>Abstract</p> <p>Background</p> <p>Risk models are used to calculate the likelihood of carrying a <it>BRCA1 </it>or <it>BRCA2 </it>mutation. We evaluated the performances of currently-used risk models among patients from a large familial program using the criteria of high sensitivity, simple data collection and entry and <it>BRCA </it>score reporting.</p> <p>Methods</p> <p>Risk calculations were performed by applying the BRCAPRO, Manchester, Penn II, Myriad II, FHAT, IBIS and BOADICEA models to 200 non-<it>BRCA </it>carriers and 100 <it>BRCA </it>carriers, consecutively tested between August 1995 and March 2006. Areas under the receiver operating characteristic curves (AUCs) were determined and sensitivity and specificity were calculated at the conventional testing thresholds. In addition, subset analyses were performed for low and high risk probands.</p> <p>Results</p> <p>The BRCAPRO, Penn II, Myriad II, FHAT and BOADICEA models all have similar AUCs of approximately 0.75 for <it>BRCA </it>status. The Manchester and IBIS models have lower AUCs (0. and 0.47 respectively). At the conventional testing thresholds, the sensitivities and specificities for a <it>BRCA </it>mutation were, respectively, as follows: BRCAPRO (0.75, 0.62), Manchester (0.58,0.71), Penn II (0.93,0.31), Myriad II (0.71,0.63), FHAT (0.70,0.63), IBIS (0.20,0.74), BOADICEA (0.70, 0.65).</p> <p>Conclusion</p> <p>The Penn II model most closely met the criteria we established and this supports the use of this model for identifying individuals appropriate for genetic testing at our facility. These data are applicable to other familial clinics provided that variations in sample populations are taken into consideration.</p

Chagasic Thymic Atrophy Does Not Affect Negative Selection but Results in the Export of Activated CD4+CD8+ T Cells in Severe Forms of Human Disease

Extrathymic CD4+CD8+ double-positive (DP) T cells are increased in some pathophysiological conditions, including infectious diseases. In the murine model of Chagas disease, it has been shown that the protozoan parasite Trypanosoma cruzi is able to target the thymus and induce alterations of the thymic microenvironment and the lymphoid compartment. In the acute phase, this results in a severe atrophy of the organ and early release of DP cells into the periphery. To date, the effect of the changes promoted by the parasite infection on thymic central tolerance has remained elusive. Herein we show that the intrathymic key elements that are necessary to promote the negative selection of thymocytes undergoing maturation during the thymopoiesis remains functional during the acute chagasic thymic atrophy. Intrathymic expression of the autoimmune regulator factor (Aire) and tissue-restricted antigen (TRA) genes is normal. In addition, the expression of the proapoptotic Bim protein in thymocytes was not changed, revealing that the parasite infection-induced thymus atrophy has no effect on these marker genes necessary to promote clonal deletion of T cells. In a chicken egg ovalbumin (OVA)-specific T-cell receptor (TCR) transgenic system, the administration of OVA peptide into infected mice with thymic atrophy promoted OVA-specific thymocyte apoptosis, further indicating normal negative selection process during the infection. Yet, although the intrathymic checkpoints necessary for thymic negative selection are present in the acute phase of Chagas disease, we found that the DP cells released into the periphery acquire an activated phenotype similar to what is described for activated effector or memory single-positive T cells. Most interestingly, we also demonstrate that increased percentages of peripheral blood subset of DP cells exhibiting an activated HLA-DR+ phenotype are associated with severe cardiac forms of human chronic Chagas disease. These cells may contribute to the immunopathological events seen in the Chagas disease

Determining relative quality for the study of creative design output

Design creativity is often defined using the terms “novel” and “appropriate”. Measuring creativity within design outputs then relies on developing metrics for these terms that can be applied to the assessment of designs. By comparing design appropriateness to design quality, this paper develops a systematic method of assessing one element of design creativity. Three perspectives from literature are used; the areas in which quality is manifest, the categories into which quality assessment criteria fall, and how well criteria are achieved. The output of the method is a relative ranking of quality for a set of designs, with detailed understanding of the particular strengths and weaknesses of each. The process of assessment is demonstrated through a case study of twelve similar designs. Through such analysis insight into the influences on quality can be gained, which in turn may allow greater control and optimization of the qualities that design outputs display