Artificial intelligence, bias and clinical safety

This is the final version. Available on open access from BMJ Publishing group via the DOI in this recordEngineering and Physical Sciences Research Council (EPSRC

In situ crosslinking bionanocomposite hydrogels with potential for wound healing applications

In situ forming hydrogels are a class of biomaterials that can fulfil a variety of important biomedically relevant functions and hold promise for the emerging field of patient-specific treatments (e.g., cell therapy, drug delivery). Here we report the results of our investigations on the generation of in situ forming hydrogels with potential for wound healing applications (e.g., complex blast injuries). The combination of polysaccharides that were oxidized to display aldehydes, amine displaying chitosan and nanostructured ZnO yields in situ forming bionanocomposite hydrogels. The physicochemical properties of the components, their cytotoxicity towards HaCat cells and the in vitro release of zinc ions on synthetic skin were studied. The in situ gel formation process was complete within minutes, the components were non-toxic towards HaCat cells at functional levels, Zn2+ was released from the gels, and such materials may facilitate wound healing

Variation in Seagrass-Associated Macroinvertebrate Communities Along the Gulf Coast of Peninsular Florida: An Exploration of Patterns and Ecological Consequences

Seagrasses form vast meadows of structurally complex habitat that support faunal communities with greater numbers of species and individuals than nearby unstructured habitats. The Gulf coast of peninsular Florida represents a natural laboratory ideally suited to the study of processes that shape seagrass-associated invertebrate and fish communities within meadows of a single species of seagrass, Thalassia testudinum. This suitability arises from a pronounced structural and chemical gradient that exists over ecologically relevant spatial and temporal scales, as revealed by extensive monitoring of water quality and seagrass. We hypothesized that seagrass-associated invertebrate communities would vary across five estuarine systems spread along a spatial gradient in phosphorus concentration, an important driver of seagrass and phytoplankton growth in this region. The quantitative results based on data acquired at 25 stations (75 samples, 52,086 specimens, and 161 taxa) indicated that each of the five estuarine systems were distinct with regard to species composition and differences among systems were driven by abundant or relatively common species. In addition, we found evidence to indicate food webs in seagrass meadows along this gradient may differ, especially in the relative dominance of algal grazers and predatory invertebrates. These changes in species composition and trophic roles could be driven by phosphorus directly, through increases in rates of primary production with higher concentrations of phosphorus, or indirectly, through nutrient-mediated changes in the physical structure of the seagrass canopy. Our results suggest that differences in the habitat created by T. testudinum under differing phosphorus supplies lead to ecologically significant shifts in macroinvertebrate communities

Meta-analysis of the severe acute respiratory syndrome coronavirus 2 serial intervals and the impact of parameter uncertainty on the coronavirus disease 2019 reproduction number

This is the final version. Available on open access from SAGE Publications via the DOI in this recordThe serial interval of an infectious disease, commonly interpreted as the time between the onset of symptoms in sequentially infected individuals within a chain of transmission, is a key epidemiological quantity involved in estimating the reproduction number. The serial interval is closely related to other key quantities, including the incubation period, the generation interval (the time between sequential infections), and time delays between infection and the observations associated with monitoring an outbreak such as confirmed cases, hospital admissions, and deaths. Estimates of these quantities are often based on small data sets from early contact tracing and are subject to considerable uncertainty, which is especially true for early coronavirus disease 2019 data. In this paper, we estimate these key quantities in the context of coronavirus disease 2019 for the UK, including a meta-analysis of early estimates of the serial interval. We estimate distributions for the serial interval with a mean of 5.9 (95% CI 5.2; 6.7) and SD 4.1 (95% CI 3.8; 4.7) days (empirical distribution), the generation interval with a mean of 4.9 (95% CI 4.2; 5.5) and SD 2.0 (95% CI 0.5; 3.2) days (fitted gamma distribution), and the incubation period with a mean 5.2 (95% CI 4.9; 5.5) and SD 5.5 (95% CI 5.1; 5.9) days (fitted log-normal distribution). We quantify the impact of the uncertainty surrounding the serial interval, generation interval, incubation period, and time delays, on the subsequent estimation of the reproduction number, when pragmatic and more formal approaches are taken. These estimates place empirical bounds on the estimates of most relevant model parameters and are expected to contribute to modeling coronavirus disease 2019 transmission.Engineering and Physical Sciences Research Council (EPSRC)NHS EnglandAlan Turing InstituteMedical Research Council (MRC)National Institute for Health Research (NIHR

Functional analyses of <i>Agaricus bisporus </i>Serine Proteinase 1 (SPR1) reveals a role in utilisation of humic rich substrates and adaptation to the leaf-litter ecological niche

Agaricus bisporus is a secondary decomposer fungus and an excellent model for the adaptation, persistence and growth of fungi in humic‐rich environments such as soils of temperate woodland and pastures. The A. bisporus serine proteinase SPR1 is induced by humic acids and is highly expressed during growth on compost. Three Spr1 gene silencing cassettes were constructed around sense, antisense and non‐translatable‐stop strategies (pGRsensehph, pGRantihph and pGRstophph). Transformation of A. bisporus with these cassettes generated cultures showing a reduction in extracellular proteinase activity as demonstrated by the reduction, or abolition, of a clearing zone on plate‐based bioassays. These lines were then assessed by detailed enzyme assay, RT‐qPCR and fruiting. Serine proteinase activity in liquid cultures was reduced in 83% of transformants. RT‐qPCR showed reduced Spr1 mRNA levels in all transformants analysed, and these correlated with reduced enzyme activity. When fruiting was induced, highly‐silenced transformant AS5 failed to colonize the compost, whilst for those that did colonize the compost, 60% gave a reduction in mushroom yield. Transcriptional, biochemical and developmental observations, demonstrate that SPR1 has an important role in nutrient acquisition in compost and that SPR1 is a key enzyme in the adaptation of Agaricus to the humic‐rich ecological niche formed during biomass degradation

Emergency management in health: key issues and challenges in the UK

Background Emergency planning in the UK has grown considerably in recent years, galvanised by the threat of terrorism. However, deficiencies in NHS emergency planning were identified and the evidence-base that underpins it is questionable. Inconsistencies in terminologies and concepts also exist. Different models of emergency management exist internationally but the optimal system is unknown. This study examines the evidence-base and evidence requirements for emergency planning in the UK health context. Methods The study involved semi-structured interviews with key stakeholders and opinion leaders. Purposive sampling was used to obtain a breadth of views from various agencies involved in emergency planning and response. Interviews were then analysed using a grounded approach using standard framework analysis techniques. Results We conducted 17 key informant interviews. Interviewees identified greater gaps in operational than technical aspects of emergency planning. Social and behavioural knowledge gaps were highlighted with regards to how individuals and organisations deal with risk and behave in emergencies. Evidence-based approaches to public engagement and for developing community resilience to disasters are lacking. Other gaps included how knowledge was developed and used. Conflicting views with regards to the optimal configuration and operation of the emergency management system were voiced. Conclusions Four thematic categories for future research emerged: (i) Knowledge-base for emergency management: Further exploration is needed of how knowledge is acquired, valued, disseminated, adopted and retained. (ii) Social and behavioural issues: Greater understanding of how individuals approach risk and behave in emergencies is required. (iii) Organisational issues in emergencies: Several conflicting organisational issues were identified; value of planning versus plans, flexible versus standardized procedures, top-down versus bottom-up engagement, generic versus specific planning, and reactive versus proactive approaches to emergencies. (iv) Emergency management system: More study is required of system-wide issues relating to system configuration and operation, public engagement, and how emergency planning is assessed

Factors influencing digital review of pathology test results in an inpatient setting: a cross-sectional study

This is the final version. Available from Oxford University Press via the DOI in this record.Availability of data and material: The datasets generated and/or analysed during the current study are not publicly available due to the remote possibility of targeted patient re-identification through a linkage attack. Limited data may be available from the corresponding author on reasonable request, and review by the information governance and ethics teams.BACKGROUND: Delay or failure to view test results in a hospital setting can lead to delayed diagnosis, risk of patient harm, and represents inefficiency. Factors influencing this were investigated to identify how timeliness and completeness of test review could be improved through an evidence based redesign of the use of clinical test review software. METHODS: A cross section of all abnormal haematology and biochemistry results which were published on a digital test review platform over a three year period were investigated. The time it took for clinicians to view these results, and the results that were not viewed within 30 days, were analysed relative to time of the week, the detailed type of test, and an indicator of patient record data quality. RESULTS: The majority of results were viewed within 90 minutes, and 93.9% of these results viewed on the digital platform within 30 days. There was significant variation in results review throughout the week, shown to be due to an interplay between technical and clinical workflow factors. Routine results were less likely to be reviewed, as were those with patient record data quality issues . CONCLUSION: The evidence suggests that test result review would be improved by stream-lining access to the result platform, differentiating between urgent and routine results, improving handover of responsibility for result review, and improving search for temporary patient records. Altering the timing of phlebotomy rounds, and a review of the appropriateness of routine test requests at the weekend may also improve result review rates.Engineering and Physical Sciences Research Council (EPSRC)NHS EnglandAlan Turing Institut

Comparison of CATs, CURB-65 and PMEWS as Triage Tools in Pandemic Influenza Admissions to UK Hospitals: Case Control Analysis Using Retrospective Data

Triage tools have an important role in pandemics to identify those most likely to benefit from higher levels of care. We compared Community Assessment Tools (CATs), the CURB-65 score, and the Pandemic Medical Early Warning Score (PMEWS); to predict higher levels of care (high dependency - Level 2 or intensive care - Level 3) and/or death in patients at or shortly after admission to hospital with A/H1N1 2009 pandemic influenza. This was a case-control analysis using retrospectively collected data from the FLU-CIN cohort (1040 adults, 480 children) with PCR-confirmed A/H1N1 2009 influenza. Area under receiver operator curves (AUROC), sensitivity, specificity, positive predictive values and negative predictive values were calculated. CATs best predicted Level 2/3 admissions in both adults [AUROC (95% CI): CATs 0.77 (0.73, 0.80); CURB-65 0.68 (0.64, 0.72); PMEWS 0.68 (0.64, 0.73), p<0.001] and children [AUROC: CATs 0.74 (0.68, 0.80); CURB-65 0.52 (0.46, 0.59); PMEWS 0.69 (0.62, 0.75), p<0.001]. CURB-65 and CATs were similar in predicting death in adults with both performing better than PMEWS; and CATs best predicted death in children. CATs were the best predictor of Level 2/3 care and/or death for both adults and children. CATs are potentially useful triage tools for predicting need for higher levels of care and/or mortality in patients of all ages

Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures

This is the final version. Available from The Royal Society via the DOI in this record. Data and code supporting this article can be accessed on GitHub at the following link: https://github.com/terminological/uk-covid-datatools/tree/master/vignettes/current-rt.The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reproduction number has become an essential parameter for monitoring disease transmission across settings and guiding interventions. The UK published weekly estimates of the reproduction number in the UK starting in May 2020 which are formed from multiple independent estimates. In this paper, we describe methods used to estimate the time-varying SARS-CoV-2 reproduction number for the UK. We used multiple data sources and estimated a serial interval distribution from published studies. We describe regional variability and how estimates evolved during the early phases of the outbreak, until the relaxing of social distancing measures began to be introduced in early July. Our analysis is able to guide localized control and provides a longitudinal example of applying these methods over long timescales. This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK’.Engineering and Physical Sciences Research Council (EPSRC)Engineering and Physical Sciences Research Council (EPSRC)Engineering and Physical Sciences Research Council (EPSRC)Medical Research Council (MRC)National Institute for Health Research (NIHR

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost andduringmushroomformation.The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation aremore highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics