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A species’ success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings (Sturnus vulgaris) established populations in Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.

The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (94.6% BUSCO completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, SAAGA) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counter-intuitive behaviour in traditional BUSCO metrics, and present Buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.

Regulators around the world have mandated the use of eXtensible Business Reporting Language (XBRL) in financial reporting with a goal of serving the public interest by improving the usability of financial data. This study examines the different types of decisions regulators make when adopting XBRL. We further analyze the advantages and disadvantages of the choices regulators make and their impact on both the companies who are required to file the information as well as the users of the information. We posit potential factors that may impact the different decisions regulators make. We also offer a set of recommendations for regulators’ consideration. Regulators should consider extending the scope of information available to users (e.g., sustainability information), refining taxonomies that have suffered from too many unique extensions, continuing to improve data reliability to decrease the “expectations gap”, and improving the ability of user to consume data in order to benefit from the public good. This study informs policy setting in general as well as the specific context of XBRL policy setting.

BACKGROUND: A safe and efficacious vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), if deployed with high coverage, could contribute to the control of the COVID-19 pandemic. We evaluated the safety and efficacy of the ChAdOx1 nCoV-19 vaccine in a pooled interim analysis of four trials. \ud \ud \ud METHODS: This analysis includes data from four ongoing blinded, randomised, controlled trials done across the UK, Brazil, and South Africa. Participants aged 18 years and older were randomly assigned (1:1) to ChAdOx1 nCoV-19 vaccine or control (meningococcal group A, C, W, and Y conjugate vaccine or saline). Participants in the ChAdOx1 nCoV-19 group received two doses containing 5 × 1010 viral particles (standard dose; SD/SD cohort); a subset in the UK trial received a half dose as their first dose (low dose) and a standard dose as their second dose (LD/SD cohort). The primary efficacy analysis included symptomatic COVID-19 in seronegative participants with a nucleic acid amplification test-positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to treatment received, with data cutoff on Nov 4, 2020. Vaccine efficacy was calculated as 1 - relative risk derived from a robust Poisson regression model adjusted for age. Studies are registered at ISRCTN89951424 and ClinicalTrials.gov, NCT04324606, NCT04400838, and NCT04444674. \ud \ud \ud FINDINGS: Between April 23 and Nov 4, 2020, 23 848 participants were enrolled and 11 636 participants (7548 in the UK, 4088 in Brazil) were included in the interim primary efficacy analysis. In participants who received two standard doses, vaccine efficacy was 62·1% (95% CI 41·0-75·7; 27 [0·6%] of 4440 in the ChAdOx1 nCoV-19 group vs71 [1·6%] of 4455 in the control group) and in participants who received a low dose followed by a standard dose, efficacy was 90·0% (67·4-97·0; three [0·2%] of 1367 vs 30 [2·2%] of 1374; pinteraction=0·010). Overall vaccine efficacy across both groups was 70·4% (95·8% CI 54·8-80·6; 30 [0·5%] of 5807 vs 101 [1·7%] of 5829). From 21 days after the first dose, there were ten cases hospitalised for COVID-19, all in the control arm; two were classified as severe COVID-19, including one death. There were 74 341 person-months of safety follow-up (median 3·4 months, IQR 1·3-4·8): 175 severe adverse events occurred in 168 participants, 84 events in the ChAdOx1 nCoV-19 group and 91 in the control group. Three events were classified as possibly related to a vaccine: one in the ChAdOx1 nCoV-19 group, one in the control group, and one in a participant who remains masked to group allocation. \ud \ud \ud INTERPRETATION: ChAdOx1 nCoV-19 has an acceptable safety profile and has been found to be efficacious against symptomatic COVID-19 in this interim analysis of ongoing clinical trials. \ud \ud \ud FUNDING: UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, Bill & Melinda Gates Foundation, Lemann Foundation, Rede D'Or, Brava and Telles Foundation, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, and AstraZeneca.

ObjectivesThe objectives of the Rural Site Visit Project (SV Project) were to develop a successful model for engaging all 201 communities in rural British Columbia, Canada, build relationships and gather data about community health care issues to help modify existing rural health care programs and inform government rural health care policy.DesignAn adapted version of Boelen’s health partnership model was used to identify each community’s Health Care Partners: health providers, academics, policy makers, health managers, and community representatives. Qualitative data was gathered using a semi-structured interview guide. Major themes were identified through content analysis, and this information was fed back to the government and interviewees in reports every six months.SettingThe 107 communities visited thus far have health care services that range from hospitals with surgical programs to remote communities with no medical services at all. The majority have access to local primary care.ParticipantsParticipants were recruited from the Health Care Partner groups identified above using purposeful and snowball sampling.Primary and secondary outcome measuresA successful process was developed to engage rural communities in identifying their health care priorities, whilst simultaneously building and strengthening relationships. The qualitative data was analysed from 185 meetings in 80 communities and shared with policy makers at governmental and community levels.Results36 themes have been identified and three overarching themes that interconnect all the interviews, namely Relationships, Autonomy and Change Over Time, are discussed.ConclusionThe SV Project appears to be unique in that it is physician led, prioritizes relationships, engages all of the health care partners singly and jointly in each community, is ongoing, provides feedback to both the policy makers and all interviewees on a 6-monthly basis and, by virtue of its large scope, has the ability to produce interim reports that have helped support system change.Article SummaryThis study process has adapted Boelen’s health partnership model and is unique in that it is physician led, prioritizes relationships, engages all of the health care partners singly and jointly in each community, is ongoing, provides feedback to both the policy makers and all interviewees on a 6-monthly basis.A successful method of engaging with rural communities and building relationships and trust across multiple stakeholder groups is described that contributed to influencing positive health care system changes.As all communities in one province are being visited a picture of rural health care initiatives and challenges is highly comprehensive and therefore able to influence policy.One of the main limitations in this study is that because the interviewers were experienced health care providers, power differentials may have existed which may have introduced bias in the discussions.A potential limitation is the enormous amount of data to handle and analyze in a rigorous way, which was mitigated by having two full time analysts working together to ensure consistency with frequent meeting with the research team to consider and agree emerging themes.How can rural community-engaged health services planning affect sustainable health care system changes? – A process description and qualitative analysis of data from the Rural Coordination Centre of British Columbia’s Rural Site Visits Project

Gut bacterial communities influence, and are influenced by, the behaviour and ecology of their hosts. Those interactions have been studied primarily in humans and model organisms, but we need field research to understand the relationship between an organism’s gut bacteria and its ecological challenges, such as those imposed by rapid range expansion (as in invasive species) and the presence of host-manipulating parasites. Cane toads (Rhinella marina) provide an excellent model system in this respect, because the species’ ongoing colonization of Australia has enforced major changes in phenotypic traits (including behaviour), and lungworm parasites (Rhabdias pseudosphaerocephala) modify host gut function in ways that enhance the viability of lungworm larvae. We collected female toads from across the species’ invasive range and studied their morphology, behaviour, parasite infection status and gut bacterial community. Range-coreversusrange-edge toads differed in morphology, behaviour, gut bacterial composition and predicted gut bacterial function but did not differ in the occurrence of parasite infection nor in the intensity of infection. Toads infected with lungworms differed from uninfected conspecifics in gut bacterial composition and diversity. Our study demonstrates strong associations between gut bacterial community and host ecology and behaviour.

OBJECTIVE: This study compares patterns of evidence-based osteoporosis medication use among females in community and long-term care settings enrolled in Medicare Part D. DESIGN: Pooled cross-sectional study. SETTING: Medicare beneficiaries enrolled in Medicare Parts A and B, and Part D stand-alone prescription drug plans from January 1, 2006, through December 31, 2008, or death. PARTICIPANTS: Female Medicare Part D enrollees 70 years of age and older with osteoporosis or prior hip fracture. INTERVENTIONS: NA. MAIN OUTCOME MEASUREMENTS: Use of bisphosphonates, calcitonin, teriparatide, and raloxifene was tracked by residential status over the three-year period. RESULTS: The study sample comprised 96,408 female Part D enrollees with osteoporosis. Prevalence of evidence-based medication use was 42.3% in 2006 and dropped slightly to 40.4% in 2008. In unadjusted comparisons, long-term care residents were significantly less likely to use any osteoporosis medication compared with community dwellers (40.6% vs. 53.1%). After adjustment for differences in individual characteristics, utilization was still lower among long-term care residents (relative risk [RR] = 0.89, 95% confidence interval [CI] 0.87-0.91). Bisphosphonates were the top choice among medication users, but were prescribed much less often to long-term care residents (RR = 0.79, 95% CI 0.75-0.83) compared with community residents. CONCLUSION: Prevalence of evidence-based osteoporosis medication use is low in older women enrolled in Part D whether community-dwelling or long-term care residents, but long-term nursing facility residents are more likely to be treated with nonbisphosphonates. Many events that may affect osteoporosis medication use occurred after 2008; therefore, future studies using more recent data are warranted to examine osteoporosis medication use after 2008.

The water–gas shift (WGS) reaction is an attractive process for producing hydrogen gas from lignocellulosic biomass conversion applications. The goal of this study was to investigate hydrogen production via the WGS reaction using carbon monoxide (CO), one of the significant non-condensable gases formed during biomass fast pyrolysis, as reactant over the range of the intermediate-temperature shift (ITS). WGS reaction is typically carried out as a low-temperature shift (LTS;150–300 °C) or a high-temperature shift (HTS; 300–500 °C) with each shift using a different catalyst. In this study, the WGS was conducted at an intermediate temperature range (200–400 °C) relevant to lignocellulosic biomass fast pyrolysis hydrodeoxygenation over a copper (Cu) based catalyst in a CO-lean environment (70 vol% steam, 20 vol% He, and 10 vol% CO). The experimental temperatures were tested over three different weight hourly space velocities (WHSV = 1220, 2040, and 6110 cm3 g−1 min−1). CO conversion increased with increasing temperature and catalyst weight, with a maximum CO conversion of 94% achieved for temperatures greater than 300 °C. We evaluated four models including two mechanistic Langmuir–Hinshelwood (LH) models, one redox mechanistic model, and one reduced order model (ROM). The first (LH1) and second (LH2) Langmuir–Hinshelwood models differ by the intermediate formed on the catalyst surface. LH1 forms product complexes while LH2 produces a formate complex intermediate. LH2 best described our experimental kinetic data, based on statistical and regression analysis, and provided apparent activation energies between 60 and 80 kJ mol−1 at different space velocities. Furthermore, the ROM fit the experimental data well and, due to its simplicity, has potential for incorporation into computationally expensive simulations for similar experimental conditions.

Both broad-area and single-mode strained InGaAs-AlGaAs single quantum well (QW) lasers are indispensable components for both terrestrial and space satellite communications systems due to their excellent power and efficiency characteristics. However, their degradation mode (catastrophic and sudden degradation) due to catastrophic optical damage (COD) is a major concern especially for space applications, since COD-prone lasers typically show no obvious precursor signature of failure. Furthermore, as our group first reported in 2009, these lasers predominantly degrade by a new failure mode (bulk failure) due to catastrophic optical bulk damage (COBD) unlike AlGaAs QW lasers that degrade by a well-known failure mode (facet failure) due to catastrophic optical mirror damage (COMD). Unlike COMD, there have been limited reports on root causes of COBD. In addition, none of decades-long studies of reliability and degradation processes in (Al)GaAs or InGaAs QW lasers by many groups have yielded a reliability model based on the physics of failure. As part of our efforts to develop a physics of failure-based reliability model of InGaAs-AlGaAs strained QW lasers, we continued our investigation by performing short-term and long-term lifetests, failure mode analyses, and root causes investigations using various destructive and non-destructive techniques. All of broad-area and single-mode lasers that we tested degraded by COBD. We employed electron beam induced current (EBIC) techniques to study formation of dark line defects (DLDs) of lasers stressed under different test conditions and time-resolved electroluminescence (TR-EL) techniques to study the dependence of DLD propagation on electrical-thermal stresses via recombination enhanced defect reaction. Also, we employed high-resolution TEM and deep level transient spectroscopy (DLTS) techniques to study extended defects and point defects (and electron traps), respectively. Finally, we report on reliability model parameters obtained from our physics of failure investigation and compare them with those extracted using an empirical model.

In view of the future high power nuclear fusion experiments, the early identification of disruptions is a mandatory requirement, and presently the main goal is moving from the disruption mitigation to disruption avoidance and control. In this work, a deep-convolutional neural network (CNN) is proposed to provide early detection of disruptive events at JET. The CNN ability to learn relevant features, avoiding hand-engineered feature extraction, has been exploited to extract the spatiotemporal information from 1D plasma profiles. The model is trained with regularly terminated discharges and automatically selected disruptive phase of disruptions, coming from the recent ITER-like-wall experiments. The prediction performance is evaluated using a set of discharges representative of different operating scenarios, and an in-depth analysis is made to evaluate the performance evolution with respect to the considered experimental conditions. Finally, as real-time triggers and termination schemes are being developed at JET, the proposed model has been tested on a set of recent experiments dedicated to plasma termination for disruption avoidance and mitigation. The CNN model demonstrates very high performance, and the exploitation of 1D plasma profiles as model input allows us to understand the underlying physical phenomena behind the predictor decision.

Low- and middle-income countries (LMICs) carry a high burden of infectious diseases associated with impaired gut integrity, leading to microbial translocation. Pregnancies in this setting are at high risk of fetal growth restriction (FGR). We examined the association among specific risk factors for impaired gut integrity (schistosomiasis, hookworm infection, and alcohol consumption), blood endotoxin levels, and FGR. Endotoxins, lipopolysaccharide-binding proteins (LBPs), and cytokines were measured in blood from women at 32 weeks gestation, the maternal-fetal interface (MFI) at delivery, and cord blood at delivery. Resolution of schistosomiasis had no impact on endotoxin levels; however, maternal hookworm infection and alcohol consumption were associated with modest increases in endotoxin at the MFI. Cytokines responses within the maternal peripheral blood and blood from the MFI were positively associated with endotoxins, but many cord blood cytokines were negatively associated with endotoxins. Newborns with FGR also had higher levels of endotoxins at the MFI. Risk factors for microbial translocation may lead to increased levels of endotoxins at the MFI, which may contribute to poor growth in utero.

The Countryside Survey (CS) of Great Britain (GB) provides a unique and statistically robust series of datasets, consisting of an extensive set of repeated ecological measurements at a national scale, covering a time span of 29 years. CS was first undertaken in 1978 to provide a baseline for ecological and land use change monitoring in the rural environment of GB, following a stratified random design, based on 1 km squares. Originally, eight random 1 km squares were drawn from each of 32 environmental classes, thus comprising 256 sample squares in the 1978 survey. The number of these sites increased to 382 in 1984, 506 in 1990, 569 in 1998 and 591 in 2007. Detailed information regarding vegetation types and land use was mapped in all five surveys, allowing reporting by defined standard habitat classifications. Additionally, point and linear landscape features (such as trees and hedgerows) are available from all surveys after 1978. From these stratified, randomly located sample squares, information can be converted into national estimates, with associated error terms. Other data, relating to soils, freshwater and vegetation, were also sampled on analogous dates. However, the present paper describes only the surveys of landscape features and habitats. The resulting datasets provide a unique, comprehensive, quantitative ecological coverage of extent and change in these features in GB. Basic results are presented and their implications discussed. However, much opportunity for further analyses remains. Data from each of the survey years are available via the following DOIs: Landscape area data 1978: https://doi.org/10.5285/86c017ba-dc62-46f0-ad13-c862bf31740e, 1984: https://doi.org/10.5285/b656bb43-448d-4b2c-aade-7993aa243ea3, 1990: https://doi.org/10.5285/94f664e5-10f2-4655-bfe6-44d745f5dca7, 1998: https://doi.org/10.5285/1e050028-5c55-42f4-a0ea-c895d827b824, and 2007: https://doi.org/10.5285/bf189c57-61eb-4339-a7b3-d2e81fdde28d; Landscape linear feature data 1984: https://doi.org/10.5285/a3f5665c-94b2-4c46-909e-a98be97857e5, 1990: https://doi.org/10.5285/311daad4-bc8c-485a-bc8a-e0d054889219, 1998: https://doi.org/10.5285/8aaf6f8c-c245-46bb-8a2a-f0db012b2643 and 2007: https://doi.org/10.5285/e1d31245-4c0a-4dee-b36c-b23f1a697f88, Landscape point feature data 1984: https://doi.org/10.5285/124b872e-036e-4dd3-8316-476b5f42c16e, 1990: https://doi.org/10.5285/1481bc63-80d7-4d18-bcba-8804aa0a9e1b, 1998: https://doi.org/10.5285/ed10944f-40c8-4913-b3f5-13c8e844e153 and 2007: https://doi.org/10.5285/55dc5fd7-d3f7-4440-b8a7-7187f8b0550b.