An improved machine learning pipeline for urinary volatiles disease detection:Diagnosing diabetes

Motivation The measurement of disease biomarkers in easily–obtained bodily fluids has opened the door to a new type of non–invasive medical diagnostics. New technologies are being developed and fine–tuned in order to make this possibility a reality. One such technology is Field Asymmetric Ion Mobility Spectrometry (FAIMS), which allows the measurement of volatile organic compounds (VOCs) in biological samples such as urine. These VOCs are known to contain a range of information on the relevant person’s metabolism and can in principle be used for disease diagnostic purposes. Key to the effective use of such data are well–developed data processing pipelines, which are necessary to extract the most useful data from the complex underlying biological structure. Results In this study, we present a new data analysis pipeline for FAIMS data, and demonstrate a number of improvements over previously used methods. We evaluate the effect of a series of candidate operational steps during data processing, such as the use of wavelet transforms, principal component analysis (PCA), and classifier ensembles. We also demonstrate the use of FAIMS data in our pipeline to diagnose diabetes on the basis of a simple urine sample using machine learning classifiers. We present results for data generated from a case-control study of 115 urine samples, collected from 72 type II diabetic patients, with 43 healthy volunteers as negative controls. The resulting pipeline combines the steps that resulted in the best classification model performance. These include the use of a two–dimensional discrete wavelet transform, and the Wilcoxon rank–sum test for feature selection. We are able to achieve a best ROC curve AUC of 0.825 (0.747–0.9, 95% CI) for classification of diabetes vs control. We also note that this result is robust to changes in the data pipeline and different analysis runs, with AUC > 0.80 achieved in a range of cases. This is a substantial improvement in performance over previously used data processing methods in this area. Our ability to make strong statements about FAIMS ability to diagnose diabetes is sadly limited, as we found confounding effects from the demographics when including these data in the pipeline. The demographics alone produced a best AUC of 0.87 (0.795–0.94, 95% CI). While the combination of the demographics and FAIMS data resulted in an improvement on the AUC (0.907; 0.848–0.97, 95% CI), it did not prove to be a significant difference. Nevertheless, the pipeline itself shows a significant improvement in performance over more basic methods which have been used with FAIMS data in the past

Cost-effectiveness of financial incentives to promote adherence to depot antipsychotic medication: economic evaluation of a cluster-randomised controlled trial

Background: Offering a modest financial incentive to people with psychosis can promote adherence to depot antipsychotic medication, but the cost-effectiveness of this approach has not been examined. Methods: Economic evaluation within a pragmatic cluster-randomised controlled trial. 141 patients under the care of 73 teams (clusters) were randomised to intervention or control; 138 patients with diagnoses of schizophrenia, schizo-affective disorder or bipolar disorder participated. Intervention participants received £15 per depot injection over 12 months, additional to usual acute, mental and community primary health services. The control group received usual health services. Main outcome measures: incremental cost per 20% increase in adherence to depot antipsychotic medication; incremental cost of ‘good’ adherence (defined as taking at least 95% of the prescribed number of depot medications over the intervention period). Findings: Economic and outcome data for baseline and 12-month follow-up were available for 117 participants. The adjusted difference in adherence between groups was 12.2% (73.4% control vs. 85.6% intervention); the adjusted costs difference was £598 (95% CI -£4 533, £5 730). The extra cost per patient to increase adherence to depot medications by 20% was £982 (95% CI -£8 020, £14 000). The extra cost per patient of achieving 'good' adherence was £2 950 (CI -£19 400, £27 800). Probability of cost-effectiveness exceeded 97.5%at willingness-to-pay values of £14 000 for a 20% increase in adherence and £27 800 for good adherence. Interpretation: Offering a modest financial incentive to people with psychosis is cost-effective in promoting adherence to depot antipsychotic medication. Direct healthcare costs (including costs of the financial incentive) are unlikely to be increased by this intervention. Trial Registration: ISRCTN.com 7776928

Expertise in research integration and implementation for tackling complex problems: when is it needed, where can it be found and how can it be strengthened?

© 2020, The Author(s). Expertise in research integration and implementation is an essential but often overlooked component of tackling complex societal and environmental problems. We focus on expertise relevant to any complex problem, especially contributory expertise, divided into ‘knowing-that’ and ‘knowing-how.’ We also deal with interactional expertise and the fact that much expertise is tacit. We explore three questions. First, in examining ‘when is expertise in research integration and implementation required?,’ we review tasks essential (a) to developing more comprehensive understandings of complex problems, plus possible ways to address them, and (b) for supporting implementation of those understandings into government policy, community practice, business and social innovation, or other initiatives. Second, in considering ‘where can expertise in research integration and implementation currently be found?,’ we describe three realms: (a) specific approaches, including interdisciplinarity, transdisciplinarity, systems thinking and sustainability science; (b) case-based experience that is independent of these specific approaches; and (c) research examining elements of integration and implementation, specifically considering unknowns and fostering innovation. We highlight examples of expertise in each realm and demonstrate how fragmentation currently precludes clear identification of research integration and implementation expertise. Third, in exploring ‘what is required to strengthen expertise in research integration and implementation?,’ we propose building a knowledge bank. We delve into three key challenges: compiling existing expertise, indexing and organising the expertise to make it widely accessible, and understanding and overcoming the core reasons for the existing fragmentation. A growing knowledge bank of expertise in research integration and implementation on the one hand, and accumulating success in addressing complex societal and environmental problems on the other, will form a virtuous cycle so that each strengthens the other. Building a coalition of researchers and institutions will ensure this expertise and its application are valued and sustained

Obstacles to public health that even pandemics cannot overcome : the politics of Covid-19 on the island of Ireland

The relationship between politics and public health is increasingly evident as governments throughout the world vary in their acceptance and implementation of technical guidance in the response to the SARS-CoV-2 pandemic. This paper reports a qualitative study of public health policies for Covid-19 in Northern Ireland (NI) and the Republic of Ireland (RoI) across a timeline emphasising the first wave of the pandemic (February to June 2020). Inter-jurisdictional commitments for health as contained in the Good Friday Agreement provide a framework for cooperation and coordination of population health on the island of Ireland. This study of north-south cooperation in the response to Covid-19 applies ten indicators from the Oxford Covid-19 Government Response Tracker (OxCGRT) codebook to establish if cooperation and policy alignment of key public health measures are evident in the Northern Ireland Assembly and Government of Ireland responses. The study concludes that notwithstanding the historical and constitutional obstacles to an all-island response to Covid-19, there is evidence of significant public health policy alignment brought about through ongoing dialogue and cooperation between the health administrations in each jurisdiction over the course of the first wave of the pandemic