Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort-for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality

Improved maximum likelihood estimators in a heteroskedastic errors-in-variables model

This paper develops a bias correction scheme for a multivariate heteroskedastic errors-in-variables model. The applicability of this model is justified in areas such as astrophysics, epidemiology and analytical chemistry, where the variables are subject to measurement errors and the variances vary with the observations. We conduct Monte Carlo simulations to investigate the performance of the corrected estimators. The numerical results show that the bias correction scheme yields nearly unbiased estimates. We also give an application to a real data set.Comment: 12 pages. Statistical Paper

Doses of neighborhood nature: the benefits for mental health of living with nature

This is the author accepted manuscript. The final version is available from OUP via the DOI in this record.Experiences of nature provide many mental health benefits, particularly for people living in urban areas. The natural characteristics of city residents’ neighborhoods are likely to be critical determinants of the daily nature dose that they receive, however which characteristics are important remains unclear. One possibility is that the greatest benefits are provided by characteristics that are most visible during the day and so most likely to be experienced by people. We demonstrate that of five neighborhood nature characteristics tested, vegetation cover and afternoon bird abundances were positively associated with a lower prevalence of depression, anxiety and stress. Further, dose-response modelling shows a threshold response where the population prevalence of mental health issues is significantly lower beyond minimum limits of neighborhood vegetation cover (depression >20% cover, anxiety >30% cover, stress >20% cover). Our findings demonstrate quantifiable associations of mental health with the characteristics of nearby nature that people actually experience

A preliminary audit of medical and aid provision in English Rugby union clubs:compliance with Regulation 9

BackgroundGoverning bodies are largely responsible for the monitoring and management of risks associated with a safe playing environment, yet adherence to regulations is currently unknown. The aim of this study was to investigate and evaluate the current status of medical personnel, facilities, and equipment in Rugby Union clubs at regional level in England.MethodsA nationwide cross-sectional survey of 242 registered clubs was undertaken, where clubs were surveyed online on their current medical personnel, facilities, and equipment provision, according to regulation 9 of the Rugby Football Union (RFU).ResultsOverall, 91 (45. 04%) surveys were returned from the successfully contacted recipients. Of the completed responses, only 23.61% (n = 17) were found to be compliant with regulations. Furthermore, 30.56% (n = 22) of clubs were unsure if their medical personnel had required qualifications; thus, compliance could not be determined. There was a significant correlation (p = −0.029, r = 0.295) between club level and numbers of practitioners. There was no significant correlation indicated between the number of practitioners/number of teams and number of practitioners/number of players. There were significant correlations found between club level and equipment score (p = 0.003, r = −0.410), club level and automated external defibrillator (AED) access (p = 0.002, r = −0.352) and practitioner level and AED access (p = 0.0001, r = 0.404). Follow-up, thematic analysis highlighted widespread club concern around funding/cost, awareness, availability of practitioners and AED training.ConclusionThe proportion of clubs not adhering overall compliance with Regulation 9 of the RFU is concerning for player welfare, and an overhaul, nationally, is required

Criterion-Based Grading, Agile Goal Setting, and Course (Un)Completion Strategies

Peer reviewe

Therapeutic DNA vaccine induces broad T cell responses in the gut and sustained protection from viral rebound and AIDS in SIV-infected rhesus macaques.

Immunotherapies that induce durable immune control of chronic HIV infection may eliminate the need for life-long dependence on drugs. We investigated a DNA vaccine formulated with a novel genetic adjuvant that stimulates immune responses in the blood and gut for the ability to improve therapy in rhesus macaques chronically infected with SIV. Using the SIV-macaque model for AIDS, we show that epidermal co-delivery of plasmids expressing SIV Gag, RT, Nef and Env, and the mucosal adjuvant, heat-labile E. coli enterotoxin (LT), during antiretroviral therapy (ART) induced a substantial 2-4-log fold reduction in mean virus burden in both the gut and blood when compared to unvaccinated controls and provided durable protection from viral rebound and disease progression after the drug was discontinued. This effect was associated with significant increases in IFN-γ T cell responses in both the blood and gut and SIV-specific CD8+ T cells with dual TNF-α and cytolytic effector functions in the blood. Importantly, a broader specificity in the T cell response seen in the gut, but not the blood, significantly correlated with a reduction in virus production in mucosal tissues and a lower virus burden in plasma. We conclude that immunizing with vaccines that induce immune responses in mucosal gut tissue could reduce residual viral reservoirs during drug therapy and improve long-term treatment of HIV infection in humans

Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England

BACKGROUND: Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient's "bed pathway" - the sequence of transfers of individual patients between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy. METHODS: We obtained data from University College Hospital (UCH) and the ISARIC4C COVID-19 Clinical Information Network (CO-CIN) on hospitalised patients with COVID-19 who required care in general ward or critical care (CC) beds to determine possible bed pathways and LoS. We developed a discrete-time model to examine the implications of using either bed pathways or only average LoS by bed type to forecast bed occupancy. We compared model-predicted bed occupancy to publicly available bed occupancy data on COVID-19 in England between March and August 2020. RESULTS: In both the UCH and CO-CIN datasets, 82% of hospitalised patients with COVID-19 only received care in general ward beds. We identified four other bed pathways, present in both datasets: "Ward, CC, Ward", "Ward, CC", "CC" and "CC, Ward". Mean LoS varied by bed type, pathway, and dataset, between 1.78 and 13.53 days. For UCH, we found that using bed pathways improved the accuracy of bed occupancy predictions, while only using an average LoS for each bed type underestimated true bed occupancy. However, using the CO-CIN LoS dataset we were not able to replicate past data on bed occupancy in England, suggesting regional LoS heterogeneities. CONCLUSIONS: We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19. TRIAL REGISTRATION: The ISARIC WHO CCP-UK study ISRCTN66726260 was retrospectively registered on 21/04/2020 and designated an Urgent Public Health Research Study by NIHR

An ALMA study of hub-filament systems – I. On the clump mass concentration within the most massive cores

The physical processes behind the transfer of mass from parsec-scale clumps to massive star-forming cores remain elusive. We investigate the relation between the clump morphology and the mass fraction that ends up in its most massive core (MMC) as a function of infrared brightness, i.e. a clump evolutionary tracer. Using Atacama Large Millimeter/submillimeter Array (ALMA) 12 m and Atacama Compact Array, we surveyed six infrared dark hubs in 2.9 mm continuum at ∼3 arcsec resolution. To put our sample into context, we also re-analysed published ALMA data from a sample of 29 high-mass surface density ATLASGAL sources. We characterize the size, mass, morphology, and infrared brightness of the clumps using Herschel and Spitzer data. Within the six newly observed hubs, we identify 67 cores, and find that the MMCs have masses between 15 and 911 M⊙ within a radius of 0.018–0.156 pc. The MMC of each hub contains 3–24 per cent of the clump mass (fMMC), becoming 5–36 per cent once core masses are normalized to the median core radius. Across the 35 clumps, we find no significant difference in the median fMMC values of hub and non-hub systems, likely the consequence of a sample bias. However, we find that fMMC is ∼7.9 times larger for infrared dark clumps compared to infrared bright ones. This factor increases up to ∼14.5 when comparing our sample of six infrared dark hubs to infrared bright clumps. We speculate that hub-filament systems efficiently concentrate mass within their MMC early on during its evolution. As clumps evolve, they grow in mass, but such growth does not lead to the formation of more massive MMCs