PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens.

The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities

Flows for native fish in the Murray-Darling Basin: lessons and considerations for future management

Article first published online: 22 APR 2014Increased regulation and extraction of water from rivers has contributed to the decline of fishes, and the use of environmental water allocations (EWAs) is now a key rehabilitation measure. Major reform of water policy in the Murray-Darling Basin (MDB), Australia, has recently provided significant EWAs to improve ecological outcomes. Conflict over water buybacks, the value of the water and the need to maximise environmental benefits and minimise risks of unwanted outcomes has increased the expectation for science to underpin and justify such actions. Recent research has focussed attention on the need to understand fish–flow relationships. The Native Fish Strategy for the Murray-Darling Basin 2003–2013 (NFS), while not specifically targeted at water policy reform or water delivery, has provided fish ecology research and flow restoration experimentation and contributed considerable new scientific knowledge to support flow management. It has contributed to a substantial and positive change in environmental watering for fish, with native fish targets now regularly incorporated into watering objectives. This study documents changes to water management in the MDB, summarises current knowledge of flow-related fish ecology in the MDB, highlights the benefits and risks of some water management practises and provides recommendations for future management and research. A major recommendation is the need for a coordinated, cross-jurisdictional approach to flow restoration for native fish, ensuring that the best available science is being used in all watering allocations. We caution on the use of environmental works such as regulators to artificially inundate floodplains and suggest that such approaches should be viewed as large-scale experiments with the significant risks posed to fish needing to be recognised, adequately monitored and adaptively managed.John D. Koehn, Alison J. King, Leah Beesley, Craig Copeland, Brenton P. Zampatti and Martin Mallen-Coope

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

Diverse migration tactics of fishes within the large tropical Mekong River system

Fish often migrate to feed, reproduce and seek refuge from predators and prevailing environmental conditions. As a result, migration tactics often vary among species based on a diversity of life history needs, although variation within species is increasingly being recognised as important to population resilience. In this study, within- and among-species diversity in life history migratory tactics of six Mekong fish genera was examined using otolith microchemistry to explore diadromous and potamodromous traits. Two species were catadromous and one species was an estuarine resident, while the remaining three species were facultative in their migration strategies, with up to four tactics within a single species. Migrant and resident contingents co-existed within the same species. Management, conservation and mitigation strategies that maintain connectivity in large tropical rivers, such as effective fishway design, should consider a diversity of migration tactics at the individual level for improved outcomes

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

A compendium of ecological knowledge for restoration of freshwater fishes in Australia’s Murray–Darling Basin

Many freshwater fishes are imperilled globally, and there is a need for easily accessible, contemporary ecological knowledge to guide management. This compendium contains knowledge collated from over 600 publications and 27 expert workshops to support the restoration of 9 priority native freshwater fish species, representative of the range of life-history strategies and values in south-eastern Australia’s Murray–Darling Basin. To help prioritise future research investment and restoration actions, ecological knowledge and threats were assessed for each species and life stage. There is considerable new knowledge (80% of publications used were from the past 20 years), but this varied among species and life stages, with most known about adults, then egg, juvenile and larval stages (in that order). The biggest knowledge gaps concerned early life stage requirements, survival, recruitment, growth rates, condition and movements. Key threats include reduced longitudinal and lateral connectivity, altered flows, loss of refugia, reductions in both flowing (lotic) and slackwater riverine habitats, degradation of wetland habitats, alien species interactions and loss of aquatic vegetation. Examples and case studies illustrating the application of this knowledge to underpin effective restoration management are provided. This extensive ecological evidence base for multiple species is presented in a tabular format to assist a range of readers

Risk-based stratified primary care for common musculoskeletal pain presentations (STarT MSK): a cluster-randomised, controlled trial

BACKGROUND: Risk-based stratified care shows clinical effectiveness and cost-effectiveness versus usual primary care for non-specific low back pain but is untested for other common musculoskeletal disorders. We aimed to test the clinical effectiveness and cost-effectiveness of point-of-care risk stratification (using Keele's STarT MSK Tool and risk-matched treatments) versus usual care for the five most common musculoskeletal presentations (back, neck, knee, shoulder, and multi-site pain). METHODS: In this cluster-randomised, controlled trial in UK primary care with embedded qualitative and health economic studies we recruited patients from 24 general practices in the West Midlands region of England. Eligible patients were those aged 18 years or older whose general practitioner (GP) confirmed a consultation for a musculoskeletal presentation. General practices that consented to participate via a representative of the cluster were randomly assigned (1:1) to intervention or usual care, using stratified block randomisation. Researchers involved in data collection, outcome data entry, and statistical analysis were masked at both the cluster and individual participant level. Participating patients were told the study was examining GP treatment of common aches and pains and were not aware they were in a randomised trial. GPs in practices allocated to the intervention group were supported to deliver risk-based stratified care using a bespoke computer-based template, including the risk-stratification tool, and risk-matched treatment options for patients at low, medium, or high risk of poor disability or pain outcomes. There were 15 risk-matched treatment options. In the usual care group, patients with musculoskeletal pain consulting their GP received treatment as usual, typically including advice and education, medication, referral for investigations or tests, or referral to other services. The primary outcome was time-averaged pain intensity over 6 months. All analyses were done by intention to treat. The trial is registered with ISRCTN, ISRCTN15366334. RESULTS: Between May 1, 2018, and April 30, 2019, 104 GPs from 24 practices (12 per study group) identified 2494 patients with musculoskeletal pain. 1211 (49%) participants consented to questionnaires (534 in the intervention group and 677 in the usual care group), with 1070 (88%) completing the follow-up questionnaire at 6 months. We found no significant difference in time-averaged pain intensity (mean(SD) mean 4·4 [SD 2·3] in the intervention group vs 4·6 [2·5] in the control group; adjusted mean difference −0·16, 95% CI −0·65 to 0·34) or in standardised function score (mean −0·06 [SD 0·94] in the intervention group vs 0·05 [1·04]; adjusted mean difference −0·07, 95% CI −0·22 to 0·08). No serious adverse events or adverse events were reported. Risk stratification received positive patient and clinician feedback. INTERPRETATION: Risk stratification for patients in primary care with common musculoskeletal presentations did not lead to significant improvements in pain or function, although some aspects of GP decision making were affected, and GP and patients had positive experiences. The costs of risk-based stratified care were similar to usual care, and such a strategy only offers marginal changes in cost-effectiveness outcomes. The clinical implications from this trial are largely inconclusive. FUNDING: National Institute for Health Research

Hip fracture risk in relation to vitamin D supplementation and serum 25-hydroxyvitamin D levels: a systematic review and meta-analysis of randomised controlled trials and observational studies

<p>Abstract</p> <p>Background</p> <p>Vitamin D supplementation for fracture prevention is widespread despite conflicting interpretation of relevant randomised controlled trial (RCT) evidence. This study summarises quantitatively the current evidence from RCTs and observational studies regarding vitamin D, parathyroid hormone (PTH) and hip fracture risk.</p> <p>Methods</p> <p>We undertook separate meta-analyses of RCTs examining vitamin D supplementation and hip fracture, and observational studies of serum vitamin D status (25-hydroxyvitamin D (25(OH)D) level), PTH and hip fracture. Results from RCTs were combined using the reported hazard ratios/relative risks (RR). Results from case-control studies were combined using the ratio of 25(OH)D and PTH measurements of hip fracture cases compared with controls. Original published studies of vitamin D, PTH and hip fracture were identified through PubMed and Web of Science databases, searches of reference lists and forward citations of key papers.</p> <p>Results</p> <p>The seven eligible RCTs identified showed no significant difference in hip fracture risk in those randomised to cholecalciferol or ergocalciferol supplementation versus placebo/control (RR = 1.13[95%CI 0.98-1.29]; 801 cases), with no significant difference between trials of <800 IU/day and ≥800 IU/day. The 17 identified case-control studies found 33% lower serum 25(OH)D levels in cases compared to controls, based on 1903 cases. This difference was significantly greater in studies with population-based compared to hospital-based controls (χ²₁(heterogeneity) = 51.02, p < 0.001) and significant heterogeneity was present overall (χ²₁₆(heterogeneity) = 137.9, p < 0.001). Serum PTH levels in hip fracture cases did not differ significantly from controls, based on ten case-control studies with 905 cases (χ²₉(heterogeneity) = 149.68, p < 0.001).</p> <p>Conclusions</p> <p>Neither higher nor lower dose vitamin D supplementation prevented hip fracture. Randomised and observational data on vitamin D and hip fracture appear to differ. The reason for this is unclear; one possible explanation is uncontrolled confounding in observational studies. Post-fracture PTH levels are unrelated to hip fracture risk.</p

Mortality and pulmonary complications in patients undergoing surgery with perioperative sars-cov-2 infection: An international cohort study

Background The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (740%) had emergency surgery and 280 (248%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (261%) patients. 30-day mortality was 238% (268 of 1128). Pulmonary complications occurred in 577 (512%) of 1128 patients; 30-day mortality in these patients was 380% (219 of 577), accounting for 817% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 175 [95% CI 128-240], p&lt;00001), age 70 years or older versus younger than 70 years (230 [165-322], p&lt;00001), American Society of Anesthesiologists grades 3-5 versus grades 1-2 (235 [157-353], p&lt;00001), malignant versus benign or obstetric diagnosis (155 [101-239], p=0046), emergency versus elective surgery (167 [106-263], p=0026), and major versus minor surgery (152 [101-231], p=0047). Interpretation Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research