Out of Distribution Detection via Domain-Informed Gaussian Process State Space Models

In order for robots to safely navigate in unseen scenarios using learning-based methods, it is important to accurately detect out-of-training-distribution (OoD) situations online. Recently, Gaussian process state-space models (GPSSMs) have proven useful to discriminate unexpected observations by comparing them against probabilistic predictions. However, the capability for the model to correctly distinguish between in- and out-of-training distribution observations hinges on the accuracy of these predictions, primarily affected by the class of functions the GPSSM kernel can represent. In this paper, we propose (i) a novel approach to embed existing domain knowledge in the kernel and (ii) an OoD online runtime monitor, based on receding-horizon predictions. Domain knowledge is provided in the form of a dataset, collected either in simulation or by using a nominal model. Numerical results show that the informed kernel yields better regression quality with smaller datasets, as compared to standard kernel choices. We demonstrate the effectiveness of the OoD monitor on a real quadruped navigating an indoor setting, which reliably classifies previously unseen terrains.Comment: 7 pages, 4 figure

d4eBP acts downstream of both dTOR and dFoxo to modulate cardiac functional aging in Drosophila

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75079/1/ACEL_504_sm_FigS1_TableS1-S2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/75079/2/j.1474-9726.2009.00504.x.pd

Evaluation of an Inexpensive Growth Medium for Direct Detection of Escherichia coli in Temperate and Sub-Tropical Waters

The cost and complexity of traditional methods for the detection of faecal indicator bacteria, including E. coli, hinder widespread monitoring of drinking water quality, especially in lowincome countries and outside controlled laboratory settings. In these settings the problem is exacerbated by the lack of inexpensive media for the detection of E. coli in drinking water. We developed a new low-cost growth medium, aquatest (AT), and validated its use for the direct detection of E. coli in temperate and sub-tropical drinking waters using IDEXX QuantiTray1. AT was compared with IDEXX Colilert-181 and either EC-MUG or MLSB for detecting low levels of E. coli from water samples from temperate (n = 140; Bristol, UK) and subtropical regions (n = 50, Pretoria/Tshwane, South Africa). Confirmatory testing (n = 418 and 588, respectively) and the comparison of quantitative results were used to assess performance. Sensitivity of AT was higher than Colilert-181 for water samples in the UK [98.0% vs. 86.9%; p<0.0001] and South Africa [99.5% vs. 93.2%; p = 0.0030]. There was no significant difference in specificity, which was high for both media (>95% in both settings). Quantitative results were comparable and within expected limits. AT is reliable and accurate for the detection of E. coli in temperate and subtropical drinking water. The composition of the new medium is reported herein and can be used freely

Attitudes of publics who are unwilling to donate DNA data for research

With the use of genetic technology, researchers have the potential to inform medical diagnoses and treatment in actionable ways. Accurate variant interpretation is a necessary condition for the utility of genetic technology to unfold. This relies on the ability to access large genomic datasets so that comparisons can be made between variants of interest. This can only be successful if DNA and medical data are donated by large numbers of people to 'research', including clinical, non-profit and for-profit research initiatives, in order to be accessed by scientists and clinicians worldwide. The objective of the 'Your DNA, Your Say' global survey is to explore public attitudes, values and opinions towards willingness to donate and concerns regarding the donation of one's personal data for use by others. Using a representative sample of 8967 English-speaking publics from the UK, the USA, Canada and Australia, we explore the characteristics of people who are unwilling (n = 1426) to donate their DNA and medical information, together with an exploration of their reasons. Understanding this perspective is important for making sense of the interaction between science and society. It also helps to focus engagement initiatives on the issues of concern to some publics.This work was supported by Wellcome grant [206194] paid to AM, LF, KIM, RM via Wellcome Genome Campus Society and Ethics Research Group, Connecting Science. We would like to thank the following people from GA4GH for their encouragement and infrastructure support: Peter Goodhand, Julia Wilson, Bartha Knoppers. This work was also supported by Global Alliance for Genomics and Health, with their funding delivered via Wellcome (GA4GH grant, with thanks to Audrey Duncansen). DV acknowledges the infrastructure funding received from the Victorian State Government through the Operational Infrastructure Support (OIS) Program

The impact of advertising patient and public involvement on trial recruitment: embedded cluster randomised recruitment trial

BACKGROUND Patient and public involvement in research (PPIR) may improve trial recruitment rates, but it is unclear how. Where trials use PPIR to improve design and conduct, many do not communicate that clearly to potential participants. Better communication of PPIR might encourage patient enrolment, as trials may be perceived as more socially valid, relevant, and trustworthy. We aimed to evaluate the impact on recruitment of directly advertising PPIR to potential trial participants. METHODS A cluster trial, embedded within a host trial ('EQUIP') recruiting service users diagnosed with severe mental illness. The intervention was informed by a systematic review, a qualitative study, social comparison theory and a stakeholder workshop including service users and carers. Adopting Participatory Design approaches, we co-designed the recruitment intervention with PPIR partners using a leaflet to advertise the PPIR in EQUIP and sent potential participants invitations with the leaflet (intervention group) or not (control group). Primary outcome was the proportion of patients enrolled in EQUIP. Secondary outcomes included the proportions of patients who positively responded to the trial invitation. RESULTS 34 community mental health teams were randomised and 8182 service users invited. For the primary outcome, 4% of patients in the PPIR group were enrolled versus 5.3% of the control group. The intervention was ineffective for improving recruitment rates (adjusted OR= 0.75, 95% CI= 0.53 to 1.07, p=0.113). For the secondary outcome of positive response, the intervention was not effective, with 7.3% of potential participants in the intervention group responding positively versus 7.9% of the control group (adjusted OR=0.74, 95% CI= 0.53 to 1.04, p=0.082). We did not find a positive impact of directly advertising PPIR on any other outcomes. CONCLUSION To our knowledge, this is the largest ever embedded trial to evaluate a recruitment or PPIR intervention. Advertising PPIR did not improve enrolment rates, or any other outcome. It is possible that rather than advertising PPIR being the means to improve recruitment, PPIR may have an alternative impact on trials by making them more attractive, acceptable and patient-centred. We discuss potential reasons for our findings and implications for recruitment practice and research

Loss of research and operational equipment in Antarctica: Balancing scientific advances with environmental impact

Antarctica has been subject to widespread, long-term and on-going human activity since the establishment of permanent research stations became common in the 1950s. Equipment may become intentionally or inadvertently lost in Antarctic marine and terrestrial environments as a result of scientific research and associated support activities, but this has been poorly quantified to date. Here we report the quantity and nature of equipment lost by the UK's national operator in Antarctica, the British Antarctic Survey (BAS). Over the 15-year study period (2005–2019), 125 incidents of loss were reported, with c. 23 tonnes of equipment lost of which 18% by mass was considered hazardous. The geographical distribution of lost equipment was widespread across the BAS operational footprint. However, impacts are considered low compared to those associated with research station infrastructure establishment and operation. To reduce environmental impact overall, we recommend that, where possible, better use is made of existing research station capacity to facilitate field research, thereby reducing the need for construction of new infrastructure and the generation of associated impacts. Furthermore, to facilitate reporting on the state of the Antarctic environment, we recommend that national Antarctic programmes reinvigorate efforts to comply with Antarctic Treaty System requirements to actively record the locations of past activities and make available details of lost equipment. In a wider context, analogous reporting is also encouraged in other pristine areas subject to new research activities, including in other remote Earth environments and on extra-terrestrial bodies

The effectiveness of early lens extraction with intraocular lens implantation for the treatment of primary angle-closure glaucoma (EAGLE) : study protocol for a randomized controlled trial

Peer reviewedPublisher PD

Testing the credibility, feasibility and acceptability of an optimised behavioural intervention (OBI) for avoidant chronic low back pain patients: protocol for a randomised feasibility study

Background: Chronic back pain continues to be a costly and prevalent condition. The latest NICE guidelines issued in 2009 state that for patients with persistent back pain (of between six weeks and twelve months duration), who are highly distressed and/or disabled and for whom exercise, manual therapy and acupuncture has not been beneficial, the evidence supports a combination of around 100 hours of combined physical and psychological treatment. This is costly, and may prove unacceptable to many patients. A key recommendation of these guidelines was for further randomised controlled trials (RCTs) of psychological treatment and to target treatment to specific sub-groups of patients. Recent trials that have included psychological interventions have shown only moderate improvement at best, and results are not maintained long term. There is therefore a need to test theoretically driven interventions that focus on specific high-risk sub-groups, in which the intervention is delivered at full integrity against a credible control. Methods/design: A feasibility study of a pragmatic randomised controlled trial comparing psychologist-delivered Contextual Cognitive Behavioural Therapy (CCBT) against Treatment As Usual (TAU) physiotherapy delivered by physiotherapists for the treatment of chronic lower back pain in ‘avoidant’ patients. Ninety-two patients referred for physiotherapy will be recruited and randomised on a 1:1 basis to receive CCBT or TAU. Treatment groups will be balanced by centre and pain interference score. Primary outcomes include assessing the credibility and acceptability of the intervention, and to demonstrate proof of principle through a greater change in pain acceptance in the CCBT arm, measured by the Acceptance and Action –II and the Chronic Pain Acceptance questionnaires. In addition, the feasibility of carrying out a full trial will be explored with reference to recruitment and follow-up rates including the assessment of the burden of outcome measure completion. Secondary patient outcomes include disability, pain, fear of movement, mood, quality of life, and global recovery. Outcomes are measured at three and six months post-randomisation. Discussion: This paper details the rationale, design, therapist training system and recruitment methods to be used in a feasibility study which will inform the design and efficient implementation of a future definitive RCT

Trust in genomic data sharing among members of the general public in the UK, USA, Canada and Australia

Abstract: Trust may be important in shaping public attitudes to genetics and intentions to participate in genomics research and big data initiatives. As such, we examined trust in data sharing among the general public. A cross-sectional online survey collected responses from representative publics in the USA, Canada, UK and Australia (n = 8967). Participants were most likely to trust their medical doctor and less likely to trust other entities named. Company researchers were least likely to be trusted. Low, Variable and High Trust classes were defined using latent class analysis. Members of the High Trust class were more likely to be under 50 years, male, with children, hold religious beliefs, have personal experience of genetics and be from the USA. They were most likely to be willing to donate their genomic and health data for clinical and research uses. The Low Trust class were less reassured than other respondents by laws preventing exploitation of donated information. Variation in trust, its relation to areas of concern about the use of genomic data and potential of legislation are considered. These findings have relevance for efforts to expand genomic medicine and data sharing beyond those with personal experience of genetics or research participants

Top research priorities in liver and gallbladder disorders in the UK

OBJECTIVES: There is a mismatch between research questions considered important by patients, carers and healthcare professionals and the research performed in many fields of medicine. The non-alcohol-related liver and gallbladder disorders priority setting partnership was established to identify the top research priorities in the prevention, diagnostic and treatment of gallbladder disorders and liver disorders not covered by the James-Lind Alliance (JLA) alcohol-related liver disease priority setting partnership. DESIGN: The methods broadly followed the principles of the JLA guidebook. The one major deviation from the JLA methodology was the final step of identifying priorities: instead of prioritisation by group discussions at a consensus workshop involving stakeholders, the prioritisation was achieved by a modified Delphi consensus process. RESULTS: A total of 428 unique valid diagnostic or treatment research questions were identified. A literature review established that none of these questions were considered 'answered' that is, high-quality systematic reviews suggest that further research is not required on the topic. The Delphi panel achieved consensus (at least 80% Delphi panel members agreed) that a research question was a top research priority for six questions. Four additional research questions with highest proportion of Delphi panel members ranking the question as highly important were added to constitute the top 10 research priorities. CONCLUSIONS: A priority setting process involving patients, carers and healthcare professionals has been used to identify the top 10priority areas for research related to liver and gallbladder disorders. Basic, translational, clinical and public health research are required to address these uncertainties