Grid tool integration within the eMinerals Project

In this article we describe the eMinerals mini grid, which is now running in production mode. Thisis an integration of both compute and data components, the former build upon Condor, PBS and thefunctionality of Globus v2, and the latter being based on the combined use of the Storage ResourceBroker and the CCLRC data portal. We describe how we have integrated the middleware components,and the different facilities provided to the users for submitting jobs within such an environment. We willalso describe additional functionality we found it necessary to provide ourselves

Diagnosis of pancreaticobiliary malignancy by detection of minichromosome maintenance protein 5 in biliary brush cytology

Background: Biliary brush cytology is the standard method of evaluating biliary strictures, but is insensitive at detecting malignancy. In pancreaticobiliary cancer minichromosome maintenance replication proteins (MCM 2–7) are dysregulated in the biliary epithelium and MCM5 levels are elevated in bile samples. This study aimed to validate an immunocolorimetric ELISA assay for MCM5 as a pancreaticobiliary cancer biomarker in biliary brush samples. methods: Biliary brush specimens were collected prospectively at ERCP from patients with a biliary stricture. Collected samples were frozen at −80 °C. The supernatant was washed and lysed cells incubated with HRP-labelled anti-MCM5 mouse monoclonal antibody. Test positivity was determined by optical density absorbance. Patients underwent biliary brush cytology or additional investigations as per clinical routine. results: Ninety-seven patients were included in the study; 50 had malignant strictures. Median age was 65 years (range 21–94) and 51 were male. Compared with final diagnosis the MCM5 assay had a sensitivity for malignancy of 65.4% compared with 25.0% for cytology. In the 72 patients with paired MCM5 assay and biliary brush cytology, MCM5 demonstrated an improved sensitivity (55.6% vs 25.0%; P=0.0002) for the detection of malignancy. conclusions: Minichromosome maintenance replication protein5 is a more sensitive indicator of pancreaticobiliary malignancy than standard biliary brush cytology

Exploring assumptions in crop breeding for climate resilience: opportunities and principles for integrating climate model projections

Crop breeding for resilience to changing climates is a key area of investment in African agricultural development, but proactively breeding for uncertain future climates is challenging. In this paper, we characterise efforts to breed new varieties of crops for climate resilience in southern Africa and evaluate the extent to which climate model projections currently inform crop breeding activity. Based on a survey of seed system actors, we find that the prioritisation of crops and traits is only informed to a limited extent by modelled projections. We use an ensemble of CORDEX models for mid and end of century for southern Africa to test some of the assumptions that underpin current breeding activity, particularly associated with breeding for reduced durations and drought tolerance in maize, and demonstrate some of the ways in which such projections can help to inform breeding priorities and agenda setting (e.g. through the case of assessing cassava toxicity risk). Based on these examples, we propose five potential applications of climate models in informing breeding priorities. Furthermore, after unpacking the sources of uncertainty within the presented model projections, we discuss general principles for the appropriate use of climate model information in crop breeding

Stressor reflections, sleep, and psychological well-being: A pre-registered experimental test of self-distanced versus self-immersed reflections

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: All data and analysis code are publicly available via our OSF project (https://osf.io/ue9jm/). We pre-registered the design and analysis plan for this experiment via the OSF (https://osf.io/jyf69). Deviations from our registered protocol are reported in the manuscript in the section ‘Deviations from Pre-Registered Protocol’.Evidence supports the effectiveness of cuing people to analyse negative autobiographical experiences from self-distanced rather than self-immersed perspectives. However, the evidence on which this expectation resides is limited largely to static snapshots of mean levels of cognitive and emotional factors. Via a pre-registered, randomised controlled trial (N = 257), we examined the differential effectiveness of self-distanced relative to self-immersed reflections on mean levels and within-person variability of sleep duration and quality as well as psychological well-being over a 5-day working week. Except for sleep quality, we found that reflecting from a psychologically distanced perspective, overall, was no more effective for mean levels and within-person variability of sleep duration, well-being, and stress-related factors than when the current self is fully immersed in the experiential reality of the event. We consider several substantive and methodological considerations (e.g., dosage, salience of stressor event) that require interrogation in future research via experimental and longitudinal observational methods

Micrositing variability and mean flow scaling for marine turbulence in Ramsey Sound

We present turbulence results from two acoustic Doppler current profiler measurement campaigns carried out in Ramsey Sound at two locations within 50mof one another. The first measurements were taken in 2009 and the second in 2011; both include a complete spring–neap cycle. In this paper we characterise turbulence through turbulent kinetic energy (TKE) density and integral lengthscales and their relationships with one another and with mean flow parameters. We briefly describe the methods used to calculate these parameters. We find that a flood–ebb asymmetry is present in the data from both measurement campaigns, but although the flood tides are similar at both locations, the ebb tides are much more energetic in the 2011 data than the 2009 data. We suggest that this may be due to differences in seabed features between the two measurement locations. Dimensional analysis is employed to investigate how TKE scales with mean flow velocity; we find that the expected quadratic scaling is not well supported by the data at either measurement location. As a consequence, flows that have more energetic turbulence may instead appear to be less turbulent if judged by turbulence intensity. We investigate the correlation between lengthscales and TKE density and find that it is highly site-specific: it should not be assumed that for a given measurement location highly energetic turbulence is associated with larger flow structures or vice versa

Negative phenotypic and genetic associations between copulation duration and longevity in male seed beetles

Reproduction can be costly and is predicted to trade-off against other characters. However, while these trade-offs are well documented for females, there has been less focus on aspects of male reproduction. Furthermore, those studies that have looked at males typically only investigate phenotypic associations, with the underlying genetics often ignored. Here, we report on phenotypic and genetic trade-offs in male reproductive effort in the seed beetle, Callosobruchus maculatus. We find that the duration of a male's first copulation is negatively associated with subsequent male survival, phenotypically and genetically. Our results are consistent with life-history theory and suggest that like females, males trade-off reproductive effort against longevity

Can sacrificial feeding areas protect aquatic plants from herbivore grazing? Using behavioural ecology to inform wildlife management

Effective wildlife management is needed for conservation, economic and human well-being objectives. However, traditional population control methods are frequently ineffective, unpopular with stakeholders, may affect non-target species, and can be both expensive and impractical to implement. New methods which address these issues and offer effective wildlife management are required. We used an individual-based model to predict the efficacy of a sacrificial feeding area in preventing grazing damage by mute swans (Cygnus olor) to adjacent river vegetation of high conservation and economic value. The accuracy of model predictions was assessed by a comparison with observed field data, whilst prediction robustness was evaluated using a sensitivity analysis. We used repeated simulations to evaluate how the efficacy of the sacrificial feeding area was regulated by (i) food quantity, (ii) food quality, and (iii) the functional response of the forager. Our model gave accurate predictions of aquatic plant biomass, carrying capacity, swan mortality, swan foraging effort, and river use. Our model predicted that increased sacrificial feeding area food quantity and quality would prevent the depletion of aquatic plant biomass by swans. When the functional response for vegetation in the sacrificial feeding area was increased, the food quantity and quality in the sacrificial feeding area required to protect adjacent aquatic plants were reduced. Our study demonstrates how the insights of behavioural ecology can be used to inform wildlife management. The principles that underpin our model predictions are likely to be valid across a range of different resource-consumer interactions, emphasising the generality of our approach to the evaluation of strategies for resolving wildlife management problems

Chemical and physical heterogeneity within native gold: implications for the design of gold particle studies

Studies of populations of gold particles are becoming increasingly common; however, interpretation of compositional data may not be straightforward. Natural gold is rarely homogenous. Alloy heterogeneity is present as microfabrics formed either during primary mineralization or by modification of pre-existing alloys by chemical and physical drivers during subsequent residence in either hypogene or surficial environments. In electron-probe-microanalysis (EPMA)-based studies, the combination of Cu, Hg, and Pd values and mineral inclusion suites may be diagnostic for source style of mineralization, but Ag alone is rarely sufficient. Gold characterization studies by laser-ablation-ICP mass spectrometry linked to both quadrupole and Time-of-Flight (ToF-MS) systems show that only Ag, Cu, and Hg form homogenous alloys with Au sufficiently often to act as generic discriminants. Where present, other elements are commonly distributed highly heterogeneously at the micron or submicron scale, either as mineral inclusions or in highly localized, but low concentrations. Drawing upon our own data derived from individual inspection and analyses of approximately 40,000 gold particles from 526 placer and in situ localities worldwide, we show that adequate characterization of gold from a specific locality normally requires study of a minimum of 150 particles via a two-stage approach comprising spatial characterization of compositional heterogeneity, plus crystallographic orientation mapping, that informs subsequent targeted acquisition of quantitative compositional data by EPMA and/or laser-ablation ICP-MS methods. Such data provide the platform to review current understanding of the genesis of gold particle characteristics, elevating future compositional studies from empirical descriptions to process-focused interpretations

Inappropriate use of the title 'chiropractor' and term 'chiropractic manipulation' in the peer-reviewed biomedical literature

BACKGROUND: The misuse of the title 'chiropractor' and term 'chiropractic manipulation', in relation to injury associated with cervical spine manipulation, have previously been reported in the peer-reviewed literature. The objectives of this study were to - 1) Prospectively monitor the peer-reviewed literature for papers reporting an association between chiropractic, or chiropractic manipulation, and injury; 2) Contact lead authors of papers that report such an association in order to determine the basis upon which the title 'chiropractor' and/or term 'chiropractic manipulation' was used; 3) Document the outcome of submission of letters to the editors of journals wherein the title 'chiropractor', and/or term 'chiropractic manipulation', had been misused and resulted in the over-reporting of chiropractic induced injury. METHODS: One electronic database (PubMed) was monitored prospectively, via monthly PubMed searches, during a 12 month period (June 2003 to May 2004). Once relevant papers were located, they were reviewed. If the qualifications and/or profession of the care provider/s were not apparent, an attempt was made to confirm them via direct e-mail communication with the principal researcher of each respective paper. A letter was then sent to the editor of each involved journal. RESULTS: A total of twenty four different cases, spread across six separate publications, were located via the monthly PubMed searches. All twenty four cases took place in one of two European countries. The six publications consisted of four case reports, each containing one patient, one case series, involving twenty relevant cases, and a secondary report that pertained to one of the four case reports. In each of the six publications the authors suggest the care provider was a chiropractor and that each patient received chiropractic manipulation of the cervical spine prior to developing symptoms suggestive of traumatic injury. In two of the four case reports contact with the principal researcher revealed that the care provider was not a chiropractor, as defined by the World Federation of Chiropractic. The authors of the other two case reports did not respond to my communications. In the case series, which involved twenty relevant cases, the principal researcher conceded that the term chiropractor had been inappropriately used and that his case series did not relate to chiropractors who had undergone appropriate formal training. The author of the secondary report, a British Medical Journal editor, conceded that he had misused the title chiropractor. Letters to editors were accepted and published by all four journals to which they were sent. To date one of the four journals has published a correction. CONCLUSION: The results of this year-long prospective review suggests that the words 'chiropractor' and 'chiropractic manipulation' are often used inappropriately by European biomedical researchers when reporting apparent associations between cervical spine manipulation and symptoms suggestive of traumatic injury. Furthermore, in those cases reported here, the spurious use of terminology seems to have passed through the peer-review process without correction. Additionally, these findings provide further preliminary evidence, beyond that already provided by Terrett, that the inappropriate use of the title 'chiropractor' and term 'chiropractic manipulation' may be a significant source of over-reporting of the link between the care provided by chiropractors and injury. Finally, editors of peer-reviewed journals were amenable to publishing 'letters to editors', and to a lesser extent 'corrections', when authors had inappropriately used the title 'chiropractor' and/or term 'chiropractic manipulation'