Using machine learning to study the kinematics of cold gas in galaxies

Next generation interferometers, such as the Square Kilometre Array, are set to obtain vast quantities of information about the kinematics of cold gas in galaxies. Given the volume of data produced by such facilities astronomers will need fast, reliable, tools to informatively filter and classify incoming data in real time. In this paper, we use machine learning techniques with a hydrodynamical simulation training set to predict the kinematic behaviour of cold gas in galaxies and test these models on both simulated and real interferometric data. Using the power of a convolutional autoencoder we embed kinematic features, unattainable by the human eye or standard tools, into a 3D space and discriminate between disturbed and regularly rotating cold gas structures. Our simple binary classifier predicts the circularity of noiseless, simulated, galaxies with a recall of 85% and performs as expected on observational CO and H i velocity maps, with a heuristic accuracy of 95%. The model output exhibits predictable behaviour when varying the level of noise added to the input data and we are able to explain the roles of all dimensions of our mapped space. Our models also allow fast predictions of input galaxies’ position angles with a 1σ uncertainty range of ±17° to ±23° (for galaxies with inclinations of 82.5° to 32.5°, respectively), which may be useful for initial parametrization in kinematic modelling samplers. Machine learning models, such as the one outlined in this paper, may be adapted for SKA science usage in the near future

User-centered development of a Virtual Research Environment to support collaborative research events

This paper discusses the user-centred development process within the Collaborative Research Events on the Web (CREW) project, funded under the JISC Virtual Research Environments (VRE) programme. After presenting the project, its aims and the functionality of the CREW VRE, we focus on the user engagement approach, grounded in the method of co-realisation. We describe the different research settings and requirements of our three embedded user groups and the respective activities conducted so far. Finally we elaborate on the main challenges of our user engagement approach and end with the project’s next steps

Understanding acceptability in the context of text messages to encourage medication adherence in people with type 2 diabetes

From Springer Nature via Jisc Publications RouterHistory: received 2021-01-29, accepted 2021-05-11, registration 2021-06-22, pub-electronic 2021-06-28, online 2021-06-28, collection 2021-12Publication status: PublishedAbstract: Background: Acceptability is recognised as a key concept in the development of health interventions, but there has been a lack of consensus about how acceptability should be conceptualised. The theoretical framework of acceptability (TFA) provides a potential tool for understanding acceptability. It has been proposed that acceptability measured before use of an intervention (anticipated acceptability) may differ from measures taken during and after use (experienced acceptability), but thus far this distinction has not been tested for a specific intervention. This paper 1) directly compares ratings of anticipated and experienced acceptability of a text message-based intervention, 2) explores the applicability of the TFA in a technology-based intervention, and 3) uses these findings to inform suggestions for measuring acceptability over the lifespan of technology-based health interventions. Methods: Data were obtained from a quantitative online survey assessing anticipated acceptability of the proposed text messages (n = 59) and a 12-week proof-of-concept mixed methods study assessing experienced acceptability while receiving the text messages (n = 48). Both quantitative ratings by return text message, and qualitative data from participant interviews were collected during the proof-of-concept study. Results: The quantitative analysis showed anticipated and experienced acceptability were significantly positively correlated (rs > .4). The qualitative analysis identified four of the seven constructs of the TFA as themes (burden, intervention coherence, affective attitude and perceived effectiveness). An additional two themes were identified as having an important impact on the TFA constructs (perceptions of appropriateness and participants’ role). Three suggestions are given related to the importance of appropriateness, what may affect ratings of acceptability and what to consider when measuring acceptability. Conclusions: The high correlation between anticipated and experienced acceptability was a surprising finding and could indicate that, in some cases, acceptability of an intervention can be gauged adequately from an anticipated acceptability study, prior to an expensive pilot or feasibility study. Directly exploring perceptions of appropriateness and understanding whether the acceptability described by participants is related to the intervention or the research - and is for themselves or others - is important in interpreting the results and using them to further develop interventions and predict future use

Dead-reckoning animal movements in R: a reappraisal using Gundog.Tracks

BackgroundFine-scale data on animal position are increasingly enabling us to understand the details of animal movement ecology and dead-reckoning, a technique integrating motion sensor-derived information on heading and speed, can be used to reconstruct fine-scale movement paths at sub-second resolution, irrespective of the environment. On its own however, the dead-reckoning process is prone to cumulative errors, so that position estimates quickly become uncoupled from true location. Periodic ground-truthing with aligned location data (e.g., from global positioning technology) can correct for this drift between Verified Positions (VPs). We present step-by-step instructions for implementing Verified Position Correction (VPC) dead-reckoning in R using the tilt-compensated compass method, accompanied by the mathematical protocols underlying the code and improvements and extensions of this technique to reduce the trade-off between VPC rate and dead-reckoning accuracy. These protocols are all built into a user-friendly, fully annotated VPC dead-reckoning R function; Gundog.Tracks, with multi-functionality to reconstruct animal movement paths across terrestrial, aquatic, and aerial systems, provided within the Additional file 4 as well as online (GitHub).ResultsThe Gundog.Tracks function is demonstrated on three contrasting model species (the African lion Panthera leo, the Magellanic penguin Spheniscus magellanicus, and the Imperial cormorant Leucocarbo atriceps) moving on land, in water and in air. We show the effect of uncorrected errors in speed estimations, heading inaccuracies and infrequent VPC rate and demonstrate how these issues can be addressed.ConclusionsThe function provided will allow anyone familiar with R to dead-reckon animal tracks readily and accurately, as the key complex issues are dealt with by Gundog.Tracks. This will help the community to consider and implement a valuable, but often overlooked method of reconstructing high-resolution animal movement paths across diverse species and systems without requiring a bespoke application

The provision of NHS health checks in a community setting: an ethnographic account

Background: The UK National Health Service Health Checks programme aims to reduce avoidable cardiovascular deaths, disability and health inequalities in England. However, due to the reported lower uptake of screening in specific black and minority ethnic communities who are recognised as being more at risk of cardiovascular disease, there are concerns that NHS Health Checks may increase inequalities in health. This study aimed to examine the feasibility and acceptability of community outreach NHS Health Checks targeted at the Afro-Caribbean community. Methods: This paper reports findings from an ethnographic study including direct observation of four outreach events in four different community venues in inner-city Bristol, England and follow up semi-structured interviews with attendees (n = 16) and staff (n = 4). Interviews and field notes were transcribed, anonymized and analysed thematically using a process of constant comparison. Results: Analysis revealed the value of community assets (community engagement workers, churches, and community centres) to publicise the event and engage community members. People were motivated to attend for preventative reasons, often prompted by familial experience of cardiovascular disease. Attendees valued outreach NHS Health Checks, reinforcing or prompting some to make healthy lifestyle changes. The NHS Health Check provided an opportunity for attendees to raise other health concerns with health staff and to discuss their test results with peers. For some participants, the communication of test results, risk and lifestyle information was confusing and unwelcome. The findings additionally highlight the need to ensure community venues are fit for purpose in terms of assuring confidentiality. Conclusions: Outreach events provide evidence of how local health partnerships (family practice staff and health trainers) and community assets, including informal networks, can enhance the delivery of outreach NHS Health Checks and in promoting the health of targeted communities. To deliver NHS Health Checks effectively, the location and timing of events needs to be carefully considered and staff need to be provided with the appropriate training to ensure patients are supported and enabled to make lifestyle changes

Bringing Back a Healthy Buzz? Invertebrate Parasites and Reintroductions:A Case Study in Bumblebees

Reintroductions can play a key role in the conservation of endangered species. Parasites may impact reintroductions, both positively and negatively, but few case studies of how to manage parasites during reintroductions exist. Bumblebees are in decline at regional and global scales, and reintroductions can be used to re-establish extinct local populations. Here we report on how the risks associated with parasites are being managed in an ongoing reintroduction of the short-haired bumblebee, Bombus subterraneus, to the UK. Disease risk analysis was conducted and disease risk management plans constructed to design a capture-quarantine-release system that minimised the impacts on both the bumblebees and on their natural parasites. Given that bumblebee parasites are (i) generalists, (ii) geographically ubiquitous, and (iii) show evidence of local adaptation, the disease risk management plan was designed to limit the co-introduction of parasites from the source population in Sweden to the destination site in the UK. Results suggest that this process at best eliminated, or at least severely curtailed the co-introduction of parasites, and ongoing updates of the plan enabled minimization of impacts on natural host-parasite dynamics in the Swedish source population. This study suggests that methods designed for reintroductions of vertebrate species can be successfully applied to invertebrates. Future reintroductions of invertebrates where the parasite fauna is less well known should take advantage of next-generation barcoding and multiple survey years prior to the start of reintroductions, to develop comprehensive disease risk management plans

The Development of Videoconference-Based Support for People Living With Rare Dementias and Their Carers: Protocol for a 3-Phase Support Group Evaluation

BACKGROUND: People living with rarer dementias face considerable difficulty accessing tailored information, advice, and peer and professional support. Web-based meeting platforms offer a critical opportunity to connect with others through shared lived experiences, even if they are geographically dispersed, particularly during the COVID-19 pandemic. OBJECTIVE: We aim to develop facilitated videoconferencing support groups (VSGs) tailored to people living with or caring for someone with familial or sporadic frontotemporal dementia or young-onset Alzheimer disease, primary progressive aphasia, posterior cortical atrophy, or Lewy body dementia. This paper describes the development, coproduction, field testing, and evaluation plan for these groups. METHODS: We describe a 3-phase approach to development. First, information and knowledge were gathered as part of a coproduction process with members of the Rare Dementia Support service. This information, together with literature searches and consultation with experts by experience, clinicians, and academics, shaped the design of the VSGs and session themes. Second, field testing involved 154 Rare Dementia Support members (people living with dementia and carers) participating in 2 rounds of facilitated sessions across 7 themes (health and social care professionals, advance care planning, independence and identity, grief and loss, empowering your identity, couples, and hope and dementia). Third, a detailed evaluation plan for future rounds of VSGs was developed. RESULTS: The development of the small groups program yielded content and structure for 9 themed VSGs (the 7 piloted themes plus a later stages program and creativity club for implementation in rounds 3 and beyond) to be delivered over 4 to 8 sessions. The evaluation plan incorporated a range of quantitative (attendance, demographics, and geography; pre-post well-being ratings and surveys; psycholinguistic analysis of conversation; facial emotion recognition; facilitator ratings; and economic analysis of program delivery) and qualitative (content and thematic analysis) approaches. Pilot data from round 2 groups on the pre-post 3-word surveys indicated an increase in the emotional valence of words selected after the sessions. CONCLUSIONS: The involvement of people with lived experience of a rare dementia was critical to the design, development, and delivery of the small virtual support group program, and evaluation of this program will yield convergent data about the impact of tailored support delivered to geographically dispersed communities. This is the first study to design and plan an evaluation of VSGs specifically for people affected by rare dementias, including both people living with a rare dementia and their carers, and the outcome of the evaluation will be hugely beneficial in shaping specific and targeted support, which is often lacking in this population

Urinary-Cell mRNA Profile and Acute Cellular Rejection in Kidney Allografts

Background—The standard test for the diagnosis of acute rejection in kidney transplants is the renal biopsy. Noninvasive tests would be preferable. Methods—We prospectively collected 4300 urine specimens from 485 kidney-graft recipients from day 3 through month 12 after transplantation. Messenger RNA (mRNA) levels were measured in urinary cells and correlated with allograft-rejection status with the use of logistic regression. Results—A three-gene signature of 18S ribosomal (rRNA)–normalized measures of CD3ε mRNA and interferon-inducible protein 10 (IP-10) mRNA, and 18S rRNA discriminated between biopsy specimens showing acute cellular rejection and those not showing rejection (area under the curve [AUC], 0.85; 95% confidence interval [CI], 0.78 to 0.91; P<0.001 by receiver-operatingcharacteristic curve analysis). The cross-validation estimate of the AUC was 0.83 by bootstrap resampling, and the Hosmer–Lemeshow test indicated good fit (P = 0.77). In an externalvalidation data set, the AUC was 0.74 (95% CI, 0.61 to 0.86; P<0.001) and did not differ significantly from the AUC in our primary data set (P = 0.13). The signature distinguished acute cellular rejection from acute antibody-mediated rejection and borderline rejection (AUC, 0.78; 95% CI, 0.68 to 0.89; P<0.001). It also distinguished patients who received anti–interleukin-2 receptor antibodies from those who received T-cell–depleting antibodies (P<0.001) and was diagnostic of acute cellular rejection in both groups. Urinary tract infection did not affect the signature (P = 0.69). The average trajectory of the signature in repeated urine samples remained below the diagnostic threshold for acute cellular rejection in the group of patients with no rejection, but in the group with rejection, there was a sharp rise during the weeks before the biopsy showing rejection (P<0.001). Conclusions—A molecular signature of CD3ε mRNA, IP-10 mRNA, and 18S rRNA levels in urinary cells appears to be diagnostic and prognostic of acute cellular rejection in kidney allografts

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study.

BACKGROUND: SARS-CoV-2 lineage B.1.1.7 has been associated with an increased rate of transmission and disease severity among subjects testing positive in the community. Its impact on hospitalised patients is less well documented. METHODS: We collected viral sequences and clinical data of patients admitted with SARS-CoV-2 and hospital-onset COVID-19 infections (HOCIs), sampled 16 November 2020 to 10 January 2021, from eight hospitals participating in the COG-UK-HOCI study. Associations between the variant and the outcomes of all-cause mortality and intensive therapy unit (ITU) admission were evaluated using mixed effects Cox models adjusted by age, sex, comorbidities, care home residence, pregnancy and ethnicity. FINDINGS: Sequences were obtained from 2341 inpatients (HOCI cases=786) and analysis of clinical outcomes was carried out in 2147 inpatients with all data available. The HR for mortality of B.1.1.7 compared with other lineages was 1.01 (95% CI 0.79 to 1.28, p=0.94) and for ITU admission was 1.01 (95% CI 0.75 to 1.37, p=0.96). Analysis of sex-specific effects of B.1.1.7 identified increased risk of mortality (HR 1.30, 95% CI 0.95 to 1.78, p=0.096) and ITU admission (HR 1.82, 95% CI 1.15 to 2.90, p=0.011) in females infected with the variant but not males (mortality HR 0.82, 95% CI 0.61 to 1.10, p=0.177; ITU HR 0.74, 95% CI 0.52 to 1.04, p=0.086). INTERPRETATION: In common with smaller studies of patients hospitalised with SARS-CoV-2, we did not find an overall increase in mortality or ITU admission associated with B.1.1.7 compared with other lineages. However, women with B.1.1.7 may be at an increased risk of admission to intensive care and at modestly increased risk of mortality.This report was produced by members of the COG-UK-HOCI Variant substudy consortium. COG-UK-HOCI is part of COG-UK. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute