The VISTA Science Archive

We describe the VISTA Science Archive (VSA) and its first public release of data from five of the six VISTA Public Surveys. The VSA exists to support the VISTA Surveys through their lifecycle: the VISTA Public Survey consortia can use it during their quality control assessment of survey data products before submission to the ESO Science Archive Facility (ESO SAF); it supports their exploitation of survey data prior to its publication through the ESO SAF; and, subsequently, it provides the wider community with survey science exploitation tools that complement the data product repository functionality of the ESO SAF. This paper has been written in conjunction with the first public release of public survey data through the VSA and is designed to help its users understand the data products available and how the functionality of the VSA supports their varied science goals. We describe the design of the database and outline the database-driven curation processes that take data from nightly pipeline-processed and calibrated FITS files to create science-ready survey datasets. Much of this design, and the codebase implementing it, derives from our earlier WFCAM Science Archive (WSA), so this paper concentrates on the VISTA-specific aspects and on improvements made to the system in the light of experience gained in operating the WSA.Comment: 22 pages, 16 figures. Minor edits to fonts and typos after sub-editting. Published in A&

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high- quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open- source software pipeline, ‘ResPipe’

The 6dF galaxy survey: Fundamental Plane data

We report the 6dFGS Fundamental Plane (6dFGSv) catalogue that is used to estimate distances and peculiar velocities for nearly 9000 early-type galaxies in the local (z < 0.055) universe. Velocity dispersions are derived by cross-correlation from 6dF V

Household waste prevention activity in Dorset

The research project spanned the period May 2005 to March 2008. Its key purpose was to evaluate methods for monitoring and evaluating waste prevention as detailed in the National Resource and Waste Forum (NRWF) Household Waste Prevention Toolkit, i.e. the use of control and pilot areas supported by specific research techniques - using weight-based monitoring, measuring campaign activities, and using surveys and focus groups. During this time there were significant changes in waste policy that have significantly raised the profile of waste management issues to the general public. Understanding waste prevention and how to measure it, therefore, has become of primary importance in meeting the challenge of sustainable waste management

USU Teaching Documentation: Dossiers from the Mentoring Program

The nation\u27s land grant institutions were founded on the principle of access for the general public to the knowledge gained through research and creative activity fostered in higher education. Central to our access mission is our dedication to teaching and learning that is informed by research and discovery, both of which must result, at least in part, from our engagement with our external constituents. That teaching and learning informs our research and vice versa; our research informs and aids in our teaching mission. This work, compiled by Professors Maria Luisa Spicer-Escalante and Cathy Ferrand Bullock, is focused on how the best, highly informed teaching is accomplished when done in an intentional manner. That intentional process helps the best university educators thoughtfully build their teaching story in an organized manner. Educators think about how they can successfully reach and engage their appropriate student audiences (or mentees), what they hope to accomplish, and how they intend to accomplish their goals. Further, as learning outcomes are identified and established, first-rate methods for course design, content inclusion, and continuous improvement can be outlined. Those of us who follow these intentional principles may then detail our growth and success along the way as teachers in the development of documents that tell our stories. Undoubtedly, the ability to clearly document and articulate that story will help academic personnel add to their tenure and promotion preparation in a very meaningful way. But as or even more important is the opportunity to describe these journeys with all the efforts, large and small, of improving their product in terms of learning outcomes and student growth and success. The nuggets of wisdom compiled by Professors Spicer-Escalante and Bullock, in USU Teaching Documentation: Dossiers from the Mentoring Program, will help teachers across the board from the new lecturer or assistant professor to the experienced professor dive into their teaching programs and find ways to continuously experiment and refine their approaches to our critically important student audiences. Good luck, teach on, and successfully document some of the most important work you all do! Frank Galey Executive Vice President and Provost Utah State University 2019https://digitalcommons.usu.edu/ua_faculty/1000/thumbnail.jp

Conservative versus interventional treatment for spontaneous pneumothorax

BACKGROUND: Whether conservative management is an acceptable alternative to interventional management for uncomplicated, moderate-to-large primary spontaneous pneumothorax is unknown. METHODS: In this open-label, multicenter, noninferiority trial, we recruited patients 14 to 50 years of age with a first-known, unilateral, moderate-to-large primary spontaneous pneumothorax. Patients were randomly assigned to immediate interventional management of the pneumothorax (intervention group) or a conservative observational approach (conservative-management group) and were followed for 12 months. The primary outcome was lung reexpansion within 8 weeks. RESULTS: A total of 316 patients underwent randomization (154 patients to the intervention group and 162 to the conservative-management group). In the conservative-management group, 25 patients (15.4%) underwent interventions to manage the pneumothorax, for reasons prespecified in the protocol, and 137 (84.6%) did not undergo interventions. In a complete-case analysis in which data were not available for 23 patients in the intervention group and 37 in the conservative-management group, reexpansion within 8 weeks occurred in 129 of 131 patients (98.5%) with interventional management and in 118 of 125 (94.4%) with conservative management (risk difference, -4.1 percentage points; 95% confidence interval [CI], -8.6 to 0.5; P = 0.02 for noninferiority); the lower boundary of the 95% confidence interval was within the prespecified noninferiority margin of -9 percentage points. In a sensitivity analysis in which all missing data after 56 days were imputed as treatment failure (with reexpansion in 129 of 138 patients [93.5%] in the intervention group and in 118 of 143 [82.5%] in the conservative-management group), the risk difference of -11.0 percentage points (95% CI, -18.4 to -3.5) was outside the prespecified noninferiority margin. Conservative management resulted in a lower risk of serious adverse events or pneumothorax recurrence than interventional management. CONCLUSIONS: Although the primary outcome was not statistically robust to conservative assumptions about missing data, the trial provides modest evidence that conservative management of primary spontaneous pneumothorax was noninferior to interventional management, with a lower risk of serious adverse events. (Funded by the Emergency Medicine Foundation and others; PSP Australian New Zealand Clinical Trials Registry number, ACTRN12611000184976.)

Optimal Patch-Leaving Behaviour: A Case Study Using The Parasitoid Cotesia rebecula

1. Parasitoids are predicted to spend longer in patches with more hosts, but previous work on Cotesia rubecula (Marshall) has not upheld this prediction. Tests of theoretical predictions may be affected by the definition of patch leaving behaviour, which is often ambiguous. 2. In this study whole plants were considered as patches and assumed that wasps move within patches by means of walking or flying. Within-patch and between-patch flights were distinguished based on flight distance. The quality of this classification was tested statistically by examination of log-survivor curves of flight times. 3. Wasps remained longer in patches with higher host densities, which is consistent with predictions of the marginal value theorem (Charnov 1976). Under the assumption that each flight indicates a patch departure, there is no relationship between host density and leaving tendency. 4. Oviposition influences the patch leaving behaviour of wasps in a count down fashion (Driessen et al. 1995), as predicted by an optimal foraging model (Tenhumberg, Keller & Possingham 2001). 5. Wasps spend significantly longer in the first patch encountered following release, resulting in an increased rate of superparasitism

Establishing effective conservation management strategies for a poorly known endangered species: A case study using Australia’s night parrot (Pezoporus occidentalis)

An evidence-based approach to the conservation management of a species requires knowledge of that species’ status, distribution, ecology, and threats. Coupled with budgets for specific conservation strategies, this knowledge allows prioritisation of funding toward activities that maximise benefit for the species. However, many threatened species are poorly known, and determining which conservation strategies will achieve this is difficult. Such cases require approaches that allow decision-making under uncertainty. Here we used structured expert elicitation to estimate the likely benefit of potential management strategies for the Critically Endangered and, until recently, poorly known Night Parrot (Pezoporus occidentalis). Experts considered cat management the single most effective management strategy for the Night Parrot. However, a combination of protecting and actively managing existing intact Night Parrot habitat through management of grazing, controlling feral cats, and managing fire specifically to maintain Night Parrot habitat was thought to result in the greatest conservation gains. The most cost-effective strategies were thought to be fire management to maintain Night Parrot habitat, and intensive cat management using control methods that exploit local knowledge of cat movements and ecology. Protecting and restoring potentially suitable, but degraded, Night Parrot habitat was considered the least effective and least cost-effective strategy. These expert judgements provide an informed starting point for land managers implementing on-ground programs targeting the Night Parrot, and those developing policy aimed at the species’ longer-term conservation. As a set of hypotheses, they should be implemented, assessed, and improved within an adaptive management framework that also considers the likely co-benefits of these strategies for other species and ecosystems. The broader methodology is applicable to conservation planning for the management and conservation of other poorly known threatened species

Measurement of high-p_T Single Electrons from Heavy-Flavor Decays in p+p Collisions at sqrt(s) = 200 GeV

The momentum distribution of electrons from decays of heavy flavor (charm and beauty) for midrapidity |y| < 0.35 in p+p collisions at sqrt(s) = 200 GeV has been measured by the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC) over the transverse momentum range 0.3 < p_T < 9 GeV/c. Two independent methods have been used to determine the heavy flavor yields, and the results are in good agreement with each other. A fixed-order-plus-next-to-leading-log pQCD calculation agrees with the data within the theoretical and experimental uncertainties, with the data/theory ratio of 1.72 +/- 0.02^stat +/- 0.19^sys for 0.3 < p_T < 9 GeV/c. The total charm production cross section at this energy has also been deduced to be sigma_(c c^bar) = 567 +/- 57^stat +/- 224^sys micro barns.Comment: 375 authors from 57 institutions, 6 pages, 3 figures. Submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Validating epilepsy diagnoses in routinely collected data

Purpose: Anonymised, routinely-collected healthcare data is increasingly being used for epilepsy research. We validated algorithms using general practitioner (GP) primary healthcare records to identify people with epilepsy from anonymised healthcare data within the Secure Anonymised Information Linkage (SAIL) databank in Wales, UK. Method: A reference population of 150 people with definite epilepsy and 150 people without epilepsy was ascertained from hospital records and linked to records contained within SAIL (containing GP records for 2.4 million people). We used three different algorithms, using combinations of GP epilepsy diagnosis and anti-epileptic drug (AED) prescription codes, to identify the reference population. Results: Combining diagnosis and AED prescription codes had a sensitivity of 84% (95% ci 77–90) and specificity of 98% (95–100) in identifying people with epilepsy; diagnosis codes alone had a sensitivity of 86% (80–91) and a specificity of 97% (92–99); and AED prescription codes alone achieved a sensitivity of 92% (70–83) and a specificity of 73% (65–80). Using AED codes only was more accurate in children achieving a sensitivity of 88% (75–95) and specificity of 98% (88–100). Conclusion: GP epilepsy diagnosis and AED prescription codes can be confidently used to identify people with epilepsy using anonymised healthcare records in Wales, U