Decoding uncertainty for clinical decision-making

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: This article has no additional data.In this opinion piece, we examine the pivotal role that uncertainty quantification (UQ) plays in informing clinical decision-making processes. We explore challenges associated with healthcare data and the potential barriers to the widespread adoption of UQ methodologies. In doing so, we highlight how these techniques can improve the precision and reliability of medical evaluations. We delve into the crucial role of understanding and managing the uncertainties present in clinical data (such as measurement error), diagnostic tools and treatment outcomes. We discuss how such uncertainties can impact decision-making in healthcare and emphasize the importance of systematically analysing them. Our goal is to demonstrate how effectively addressing and decoding uncertainties can significantly enhance the accuracy and robustness of clinical decisions, ultimately leading to better patient outcomes and more informed healthcare practices.Engineering and Physical Sciences Research Council (EPSRC)National Institute for Health and Care Research (NIHR)Digital Program of the European Commissio

Research on the Effectiveness of the Local Compliance Regime Within Cornwall and the Isles of Scilly

Executive Summary: There has been a perceived downturn in environmental compliance nationally and this downturn is also observed at the local level, in Cornwall and the Isles of Scilly (IoS). This reduction in environmental compliance sits against a backdrop of a growing biodiversity and climate crisis globally. To investigate this perceived local downturn in compliance and propose recommendations to address this issue, the Local Nature Partnership in Cornwall and the IoS commissioned this research project, through Cornwall Council. This report analyses the roles and responsibilities of eight primary local public authorities: • The Marine Management Organisation (MMO) • Cornwall Inshore Fisheries and Conservation Authority (Cornwall IFCA) • Isles of Scilly Inshore and Conservation Authority (IoS IFCA) • Environment Agency (EA) • Natural England (NE) • Office for Environmental Protection (OEP) • Cornwall Council (CC) • Devon and Cornwall Police [...]Cornwall CouncilResearch Englan

A systematic review of the role of quantitative CT in the prognostication and disease monitoring of interstitial lung disease

This is the final version. Available from European Respiratory Society via the DOI in this record. Background: The unpredictable trajectory and heterogeneity of interstitial lung disease (ILDs) make prognostication challenging. Current prognostic indices and outcome measures have several limitations. Quantitative computed tomography (qCT) provides automated numerical assessment of CT imaging and has shown promise when applied to the prognostication and disease monitoring of ILD. This systematic review aims to highlight the current evidence underpinning the prognostic value of qCT in predicting outcomes in ILD. Methods: A comprehensive search of four databases (Medline, EMCare, Embase and CINAHL (Cumulative Index to Nursing and Allied Health Literature)) was conducted for studies published up to and including 22 November 2024. A modified CHARMS (CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies) checklist was used for data extraction. The risk of bias was assessed using a Quality in Prognostic Studies template. Results: The search identified 1134 unique studies, of which 185 studies met inclusion and exclusion criteria. Commonly studied ILD subtypes included idiopathic pulmonary fibrosis (41%, n=75), mixed subtypes (26%, n=48) and systemic sclerosis ILD (16%, n=30). Numerous studies showed significant prognostic signals, even when adjusted for common covariates and/or significant correlation between serial qCT biomarkers and conventional outcome measures. Heterogenous and nonstandardised reporting methods meant that direct comparison or meta-analysis of studies was not possible. Studies were limited by the use of retrospective methodology without prospective validation and significant study attrition. Discussion: qCT has shown efficacy in the prognostication and disease monitoring of a range of ILDs. Hurdles exist to widespread adoption including governance concerns, appropriate algorithm anchoring and standardisation of image acquisition. International collaboration is underway to address these hurdles, paving the way for regulatory approval and ultimately patient benefit.The Wellcome TrustRoyal United Hospitals Bath NHS Foundation TrustEngineering and Physical Sciences Research Council (EPSRC)National Institute for Health and Care Research (NIHR

Robustness of Question Answering Systems in the Biomedical Domain: a study of the BioASQ dataset

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this recordRobustness is a critical consideration when integrating artificial intelligence (AI) systems into decision-making processes. This concern is particularly relevant for generative AI systems, which are designed to consistently produce convincing outputs but can be prone to hallucinations, risking overconfidence in their outputs. This paper investigates the performance of fine-tuning and retrieval augmented generation (RAG) under external data quality perturbations, including typographical errors and factual inaccuracies. Results from experiments using the BioASQ Task 12b question answering dataset and PubMed articles showed nuanced trade-offs, with either RAG or fine-tuning performing better for different scenarios. Furthermore, an analysis of LLMs’ self-reported confidence scores indicated a tendency toward overconfidence, particularly in the presence of inconsistent or erroneous context data. A novel mitigation strategy, leveraging an LLM for data quality error correction was evaluated, but the results demonstrated limited effectiveness, highlighting the need for more advanced correction techniques.British TelecomInvest Northern Irelan

Rethinking Hydrodynamic Assessments for River Infrastructures: Are Simplified Methods Leaving Bridges Exposed? (dataset)

Dataset in support of the manuscript published in Journal of Flood Risk Management. The dataset contains three files: - DataCS469.csv, which contains the hydraulic calculations of the bridges within the paper according to CS469 - DataHydraulics.csv, which contains the hydraulic data for all simulations at all bridges - DataScour_rev.csv, which contains the calculations of scour depth values for CS469 and HEC-RAS simulations The headers reflect the different variables as per the manuscript

Fluorescence Suppression in Raman Spectroscopy using Low Wavenumber Anti-Stokes Scattering

Raman spectroscopy is a highly effective and important technique, able to provide specific molecular information for sample identification in a variety of fields. One of the key limitations of the method, particularly in biological samples, is interference from fluorescence. Fluorescence emission can be in the same wavelength region as the Raman signals and can be much stronger. Therefore, it can drown out the Raman signals in photon shot noise and other fluorescence-induced spectral artefacts or cause issues due to CCD saturation. This can severely limit the effectiveness of Raman spectroscopy. Many methods, from simple fluorescence background fitting to complex techniques such as SERDS, have been developed to suppress fluorescence and improve Raman signal-to-noise ratio (SNR). These methods of fluorescence suppression all vary in their effectiveness and limitations. This thesis explores low wavenumber anti-Stokes Raman scattering (LWARS) as a new method for fluorescence suppression in Raman spectroscopy. Fluorescence emission is generally significantly weaker in the anti-Stokes region than in the Stokes region. While Raman signals are also weaker in the anti-Stokes region this effect is less significant at lower wavenumbers. Anti-Stokes Raman spectroscopy also has the advantage of being able to use longer excitation wavelengths without the Raman peaks of interest exceeding the spectral sensitivity limit of CCDs. Using longer excitation wavelengths typically results in less fluorescence being induced as the lower energy photons are less likely to have the required energy to do so. This means, that in the presence of strong fluorescence, LWARS may provide higher SNR when compared to other methods of fluorescence suppression. LWARS was first compared to Stokes Raman scattering of the same molecular vibration within the same wavelength region, by using different laser excitation wavelengths (830 nn for anti-Stokes and 785 nm for Stokes). This was done at 350 mW laser power and a 3 s acquisition time. In the presence of the fluorescent dye Patent Blue V, LWARS SNR was found to be 0.75 (± 0.07) times that of its Stokes equivalent. This inefficiency was believed to be due to the Patent Blue V absorption peak being at much shorter wavelengths than the near-infrared (NIR) excitation wavelengths. The experiment was repeated with HITCI, a fluorescent dye with high absorption in the NIR region. This was done at 100 mW laser power and a 6 s acquisition time. LWARS was found to have 1.52 (± 0.10) times higher SNR than its Stokes equivalent. The rapid photobleaching of HITCI in water also allowed for a comparison of LWARS and photobleaching. LWARS was found to provide fluorescence suppression equivalent to 12.5 minutes of 100 mW 785 nm laser illumination. This was achieved instantaneously and without the risk of sample degradation. The experiment was again repeated with HITCI dissolved in ethanol using a 75 mW laser power and an acquisition time of 3.75 s. The relative SNR was found to be 1.45 (± a0.13) which was a negligible change, within the experimental error of the HITCI in water relative SNR. Adding a gelatin phantom between the laser and the fluorescent sample and increasing the acquisition time to 10 s resulted in a relative SNR of 1.49 (± 0.18), i.e. functionally unchanged from the non-gelatin version of the experiment. LWARS was also compared to the spatially-offset Raman difference spectroscopy (SERDS) method with 100 mW laser power and a 4 s acquisition time. The two methods were found to give roughly identical SNR despite SERDS being more experimentally and computationally complex. LWARS also has the advantage of reducing the fluorescence intensity in the raw measured spectra mitigating CCD saturation issues. This experiment also explored the fluorescence suppression potential of anti-Stokes SERDS. However, it was found to provide worse SNR than LWARS and Stokes SERDS, while maintaining the increased complexity of Stokes SERDS

Fully personalized modelling of Duchenne Muscular Dystrophy ambulation

This is the final version. Available from The Royal Society via the DOI in this record. Data accessibility: The code is available via [31]. Supplementary material is available online [32].Duchenne Muscular Dystrophy is a progressive neuromuscular disorder characterized by the gradual weakening and deterioration of muscles, leading to loss of ambulation in affected individuals. This decline in mobility can be effectively assessed using the North Star Ambulatory Assessment (NSAA) scores, along with measures such as the 10-m walk time and the time taken to rise from the floor. We propose a dynamic linear model to predict the trajectories of these clinical outcomes, with a primary focus on NSAA scores. Our model aims to assist clinicians in forecasting the progression of the disease, thereby enabling more informed and personalized treatment plans for their patients. We also evaluate the effectiveness of our models in generating synthetic NSAA score datasets. We assess the performance of our modelling approach and compare the results with those of a previous study. We show that the most robust model demonstrates narrower prediction intervals and improved quantile coverage, indicating superior predictive accuracy and reliability. This article is part of the theme issue 'Uncertainty quantification for healthcare and biological systems (Part 2)'.Engineering and Physical Sciences Research Council (EPSRC)National Institute for Health Research (NIHR)Biomedical Research CentreGreat Ormond Street Hospital for Children NHS Foundation TrustUniversity College LondonMuscular Dystrophy U

Mechanising Mediums: Spiritualism and Media Imaginaries in the Nineteenth and Twentieth Centuries

This is the final version. Available from Taylor and Francis via the DOI in this record. This paper engages with studies by media historians and media archaeologists of the significant role of the imagination in the development of communication technologies. It explores the trajectory of devices built by nineteenth and twentieth century spiritualists to facilitate direct communication with professed spirits of the dead, and whose design was attributed to inspiration from technically-minded denizens of the spirit world. Typically, these devices were built to limit or eliminate problems associated with spiritualist mediums, notably their possible fraudulence and the distorting effect of their minds on the quality of spirit communication. My analysis supports three arguments: first, that we need to take seriously both embodied and disembodied minds as the locations given by historical actors for imagined and realised communication technologies; second, the chequered histories of these devices highlight spiritualists’ doubts about the possibility and desirability of entirely replacing mediums by machines, and their faith in mediums’ ‘imaginations’ to act as superior ‘receivers’ of potentially problematic other-worldly intelligence; third, the devices offer new challenges to rigid distinctions between technological and religious experiences still adopted in the humanities

Bismuth‐based metal‐organic frameworks and derivatives for photocatalytic applications in energy and environment: Advances and challenges

This is the final version. Available from Wiley via the DOI in this record. Photocatalysis is an environmentally friendly technology for the utilizations of solar energy and has garnered significant attention in both scientific and industrial sectors. Developing cost-effective semiconductive materials is the core issue in photocatalysis. Bismuth-based metal-organic frameworks (Bi-MOFs) have emerged as attractive candidates in various photocatalytic applications, and Bi-MOFs derivatives further expand and consolidate their promising potential in the realm of photocatalysis. Various modification strategies including in-situ tailoring or external doping, as well as meticulous design and selection of metal nodes and organic linkers allow for fine control over the surface multifunctionality in Bi-MOF-based and derived photocatalytic composites with adjustable energy band structures and enhanced photocatalytic performance. In this review, the recent progress in the synthesis of diverse Bi-MOFs-based materials, Bi-MOFs derivatives, and their Bi-containing semiconductive composites were systemically analyzed and reviewed. The state-of-the-art research progresses in the applications of Bi-MOFs and derivatives, as well as composites in photocatalytic water splitting for hydrogen production, photodegradation of organic pollutants, and photocatalytic carbon dioxide reduction are comprehensively summarized. The relationships between structures, properties, and photocatalytic performance of Bi-based semiconductive composites are discussed in detail. In addition, the perspectives and future challenges on Bi-MOFs-based and derived materials for photocatalytic applications are also offered.Royal Societ

Logged tropical forests have amplified and diverse ecosystem energetics

This is the final version. Available on open access from Nature Research via the DOI in this record. Data availability: The per species energetics data and REM parameters (mammals) are available in Supplementary Data 1 and 2.Code availability: The code for processing and statistically analysing the data is available as Supplementary Methods. The REM analysis code is available from the corresponding author on reasonable request or from supplementary methods of ref. 38.Old-growth tropical forests are widely recognized as being immensely important for their biodiversity and high biomass1. Conversely, logged tropical forests are usually characterized as degraded ecosystems2. However, whether logging results in a degradation in ecosystem functions is less clear: shifts in the strength and resilience of key ecosystem processes in large suites of species have rarely been assessed in an ecologically integrated and quantitative framework. Here we adopt an ecosystem energetics lens to gain new insight into the impacts of tropical forest disturbance on a key integrative aspect of ecological function: food pathways and community structure of birds and mammals. We focus on a gradient spanning old-growth and logged forests and oil palm plantations in Borneo. In logged forest there is a 2.5-fold increase in total resource consumption by both birds and mammals compared to that in old-growth forests, probably driven by greater resource accessibility and vegetation palatability. Most principal energetic pathways maintain high species diversity and redundancy, implying maintained resilience. Conversion of logged forest into oil palm plantation results in the collapse of most energetic pathways. Far from being degraded ecosystems, even heavily logged forests can be vibrant and diverse ecosystems with enhanced levels of ecological function.Natural Environment Research Council (NERC)Sime Darby FoundationBat Conservation Internationa