The challenges of data in future pandemics

This work was supported by Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/R014604/1. M.C. was funded by the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/V054236/1. G.M. is supported by the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS). J.P-G’s work is supported by funding from the UK Health Security Agency and the UK Department of Health and Social Care. L.P. is funded by the Wellcome Trust, UK and the Royal Society, UK (grant no. 202562/Z/16/Z). L.P. is supported by the UK Research and Innovation (UKRI) through the JUNIPER modelling consortium (grant no. MR/V038613/1). L.P. is also supported by The Alan Turing Institute for Data Science and Artificial Intelligence, UK. R.R was supported by the Natural Environment Research Council (NERC) grant no. NE/T004193/1 and NE/T010355/1, the Engineering and Physical Sciences Research Council (EPSRC) grant no. EP/V054236/1 and the Science and Technology Facilities Council (STFC) grant no. ST/V006126/1.The use of data has been essential throughout the unfolding COVID-19 pandemic. We have needed it to populate our models, inform our understanding, and shape our responses to the disease. However, data has not always been easy to find and access, it has varied in quality and coverage, been difficult to reuse or repurpose. This paper reviews these and other challenges and recommends steps to develop a data ecosystem better able to deal with future pandemics by better supporting preparedness, prevention, detection and response.Publisher PDFPeer reviewe

A questionnaire-based study of Paediatric Dentists’ knowledge of teething signs, symptoms and management

Introduction Signs and symptoms attributed to erupting primary teeth are commonly known as “teething”. Its existence is controversial with concern that overusing this term might mask other illnesses and some treatments may be unnecessary or harmful. Parents/carers can access over-the-counter remedies and may seek professional advice. This survey-based investigation explored gaps in knowledge, training, perceptions and experiences of UK Paediatric Dentists (PDs) regarding teething in young children. Method Cross-sectional study with a convenience sample of PDs with different training levels, accessed through the British Society for Paediatric Dentistry membership lists. A 10-item questionnaire explored participants’ knowledge of teething-related issues and management. Responses are presented using descriptive statistics. Results Of 80 responding PDs (response rate 27%), 62–74% suggested drooling, irritability, oral fixation and flushed cheeks were attributed to primary tooth eruption. Fifty-eight (72%) participants were unaware of guidelines, yet 53 (66%) felt guidance was needed. Conclusion Signs and symptoms of teething might mask underlying conditions so it should be a diagnosis of exclusion. PDs attributed similar signs and symptoms to teething, as have been reported in the literature, although some commented that they did not think teething was a condition. There was a lack of awareness over guidelines

Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations.

From Europe PMC via Jisc Publications RouterHistory: epub 2022-08-15, ppub 2022-10-01Publication status: PublishedFunder: UK Research and Innovation; Grant(s): ST/V006126/1, EP/V054236/1, EP/V033670/1We report on an ongoing collaboration between epidemiological modellers and visualization researchers by documenting and reflecting upon knowledge constructs-a series of ideas, approaches and methods taken from existing visualization research and practice-deployed and developed to support modelling of the COVID-19 pandemic. Structured independent commentary on these efforts is synthesized through iterative reflection to develop: evidence of the effectiveness and value of visualization in this context; open problems upon which the research communities may focus; guidance for future activity of this type and recommendations to safeguard the achievements and promote, advance, secure and prepare for future collaborations of this kind. In describing and comparing a series of related projects that were undertaken in unprecedented conditions, our hope is that this unique report, and its rich interactive supplementary materials, will guide the scientific community in embracing visualization in its observation, analysis and modelling of data as well as in disseminating findings. Equally we hope to encourage the visualization community to engage with impactful science in addressing its emerging data challenges. If we are successful, this showcase of activity may stimulate mutually beneficial engagement between communities with complementary expertise to address problems of significance in epidemiology and beyond. See https://ramp-vis.github.io/RAMPVIS-PhilTransA-Supplement/. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'

Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955

Background The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and grows at elevated temperatures. The latter improves the rate of feed conversion, reduces fermentation cooling costs and minimises the risks of contamination. Full exploitation of its potential has been hindered by a dearth of effective gene tools. Results Here we designed and tested a collection of vectors (pMTL60000 series) in G. thermoglucosidasius NCIMB 11955 equivalent to the widely used clostridial pMTL80000 modular plasmid series. By combining a temperature-sensitive replicon and a heterologous pyrE gene from Geobacillus kaustophilus as a counter-selection marker, a highly effective and rapid gene knock-out/knock-in system was established. Its use required the initial creation of uracil auxotroph through deletion of pyrE using allele-coupled exchange (ACE) and selection for resistance to 5-fluoroorotic acid. The turnaround time for the construction of further mutants in this pyrE minus strain was typically 5 days. Following the creation of the desired mutant, the pyrE allele was restored to wild type, within 3 days, using ACE and selection for uracil prototrophy. Concomitant with this process, cargo DNA (pheB) could be readily integrated at the pyrE locus. The system’s utility was demonstrated through the generation in just 30 days of three independently engineered strains equivalent to a previously constructed ethanol production strain, TM242. This involved the creation of two in-frame deletions (ldh and pfl) and the replacement of a promoter region of a third gene (pdh) with an up-regulated variant. In no case did the production of ethanol match that of TM242. Genome sequencing of the parental strain, TM242, and constructed mutant derivatives suggested that NCIMB 11955 is prone to the emergence of random mutations which can dramatically affect phenotype. Conclusions The procedures and principles developed for clostridia, based on the use of pyrE alleles and ACE, may be readily deployed in G. thermoglucosidasius. Marker-less, in-frame deletion mutants can be rapidly generated in 5 days. However, ancillary mutations frequently arise, which can influence phenotype. This observation emphasises the need for improved screening and selection procedures at each step of the engineering processes, based on the generation of multiple, independent strains and whole-genome sequencing

Does Kin Recognition and Sib-Mating Avoidance Limit the Risk of Genetic Incompatibility in a Parasitic Wasp?

Background: When some combinations of maternal and paternal alleles have a detrimental effect on offspring fitness, females should be able to choose mates on the basis of their genetic compatibility. In numerous Hymenoptera, the sex of an individual depends of the allelic combination at a specific locus (single-locus Complementary Sex Determination), and in most of these species individuals that are homozygous at this sexual locus develop into diploid males with zero fitness. Methods and Findings: In this paper, we tested the hypothesis of genetic incompatibility avoidance by investigating sibmating avoidance in the solitary wasp parasitoid, Venturia canescens. In the context of mate choice we show, for the first time in a non-social hymenopteran species, that females can avoid mating with their brothers through kin recognition. In ‘‘no-choice’ ’ tests, the probability a female will mate with an unrelated male is twice as high as the chance of her mating with her brothers. In contrast, in choice tests in small test arenas, no kin discrimination effect was observed. Further experiments with male extracts demonstrate that chemical cues emanating from related males influence the acceptance rate of unrelated males. Conclusions: Our results are compatible with the genetic incompatibility hypothesis. They suggest that the female wasps recognize sibs on the basis of a chemical signature carried or emitted by males possibly using a ‘‘self-referent phenotyp

Genome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease

Thyroid hormones play a critical role in regulation of multiple physiological functions and thyroid dysfunction is associated with substantial morbidity. Here, we use electronic health records to undertake a genome-wide association study of thyroid-stimulating hormone (TSH) levels, with a total sample size of 247,107. We identify 158 novel genetic associations, more than doubling the number of known associations with TSH, and implicate 112 putative causal genes, of which 76 are not previously implicated. A polygenic score for TSH is associated with TSH levels in African, South Asian, East Asian, Middle Eastern and admixed American ancestries, and associated with hypothyroidism and other thyroid disease in South Asians. In Europeans, the TSH polygenic score is associated with thyroid disease, including thyroid cancer and age-of-onset of hypothyroidism and hyperthyroidism. We develop pathway-specific genetic risk scores for TSH levels and use these in phenome-wide association studies to identify potential consequences of pathway perturbation. Together, these findings demonstrate the potential utility of genetic associations to inform future therapeutics and risk prediction for thyroid diseases

Visualization for epidemiological modelling: challenges, solutions, reflections and recommendations

From The Royal Society via Jisc Publications RouterHistory: received 2021-10-14, accepted 2022-03-18, pub-electronic 2022-08-15, pub-print 2022-10-03Article version: VoRPublication status: PublishedFunder: UK Research and Innovation; Id: http://dx.doi.org/10.13039/100014013; Grant(s): EP/V033670/1, EP/V054236/1, ST/V006126/1We report on an ongoing collaboration between epidemiological modellers and visualization researchers by documenting and reflecting upon knowledge constructs—a series of ideas, approaches and methods taken from existing visualization research and practice—deployed and developed to support modelling of the COVID-19 pandemic. Structured independent commentary on these efforts is synthesized through iterative reflection to develop: evidence of the effectiveness and value of visualization in this context; open problems upon which the research communities may focus; guidance for future activity of this type and recommendations to safeguard the achievements and promote, advance, secure and prepare for future collaborations of this kind. In describing and comparing a series of related projects that were undertaken in unprecedented conditions, our hope is that this unique report, and its rich interactive supplementary materials, will guide the scientific community in embracing visualization in its observation, analysis and modelling of data as well as in disseminating findings. Equally we hope to encourage the visualization community to engage with impactful science in addressing its emerging data challenges. If we are successful, this showcase of activity may stimulate mutually beneficial engagement between communities with complementary expertise to address problems of significance in epidemiology and beyond. See https://ramp-vis.github.io/RAMPVIS-PhilTransA-Supplement/. This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Prescribing Data in General Practice Demonstration (PDGPD) project - a cluster randomised controlled trial of a quality improvement intervention to achieve better prescribing for chronic heart failure and hypertension

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1472-6963/12/273 Extent: 11p.Background: Research literature consistently documents that scientifically based therapeutic recommendations are not always followed in the hospital or in the primary care setting. Currently, there is evidence that some general practitioners in Australia are not prescribing appropriately for patients diagnosed with 1) hypertension (HT) and 2) chronic heart failure (CHF). The objectives of this study were to improve general practitioner’s drug treatment management of these patients through feedback on their own prescribing and small group discussions with peers and a trained group facilitator. The impact evaluation includes quantitative assessment of prescribing changes at 6, 9, 12 and 18 months after the intervention. Methods: A pragmatic multi site cluster RCT began recruiting practices in October 2009 to evaluate the effects of a multi-faceted quality improvement (QI) intervention on prescribing practice among Australian general practitioners (GP) in relation to patients with CHF and HT. General practices were recruited nationally through General Practice Networks across Australia. Participating practices were randomly allocated to one of three groups: two groups received the QI intervention (the prescribing indicator feedback reports and small group discussion) with each group undertaking the clinical topics (CHF and HT) in reverse order to the other. The third group was waitlisted to receive the intervention 6 months later and acted as a "control" for the other two groups. De-identified data on practice, doctor and patient characteristics and their treatment for CHF and HT are extracted at six-monthly intervals before and after the intervention. Post-test comparisons will be conducted between the intervention and control arms using intention to treat analysis and models that account for clustering of practices in a Network and clustering of patients within practices and GPs. Discussion: This paper describes the study protocol for a project that will contribute to the development of acceptable and sustainable methods to promote QI activities within routine general practice, enhance prescribing practices and improve patient outcomes in the context of CHF and HT. Trial registration: Australian New Zealand Clinical Trials Registry (ANZCTR), Trial # 320870.Margaret Williamson, Magnolia Cardona-Morrell, Jeffrey D Elliott, James F Reeve, Nigel P Stocks, Jon Emery, Judith M Mackson and Jane M Gun

Effect of remote ischaemic conditioning on clinical outcomes in patients with acute myocardial infarction (CONDI-2/ERIC-PPCI): a single-blind randomised controlled trial.

BACKGROUND: Remote ischaemic conditioning with transient ischaemia and reperfusion applied to the arm has been shown to reduce myocardial infarct size in patients with ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PPCI). We investigated whether remote ischaemic conditioning could reduce the incidence of cardiac death and hospitalisation for heart failure at 12 months. METHODS: We did an international investigator-initiated, prospective, single-blind, randomised controlled trial (CONDI-2/ERIC-PPCI) at 33 centres across the UK, Denmark, Spain, and Serbia. Patients (age >18 years) with suspected STEMI and who were eligible for PPCI were randomly allocated (1:1, stratified by centre with a permuted block method) to receive standard treatment (including a sham simulated remote ischaemic conditioning intervention at UK sites only) or remote ischaemic conditioning treatment (intermittent ischaemia and reperfusion applied to the arm through four cycles of 5-min inflation and 5-min deflation of an automated cuff device) before PPCI. Investigators responsible for data collection and outcome assessment were masked to treatment allocation. The primary combined endpoint was cardiac death or hospitalisation for heart failure at 12 months in the intention-to-treat population. This trial is registered with ClinicalTrials.gov (NCT02342522) and is completed. FINDINGS: Between Nov 6, 2013, and March 31, 2018, 5401 patients were randomly allocated to either the control group (n=2701) or the remote ischaemic conditioning group (n=2700). After exclusion of patients upon hospital arrival or loss to follow-up, 2569 patients in the control group and 2546 in the intervention group were included in the intention-to-treat analysis. At 12 months post-PPCI, the Kaplan-Meier-estimated frequencies of cardiac death or hospitalisation for heart failure (the primary endpoint) were 220 (8·6%) patients in the control group and 239 (9·4%) in the remote ischaemic conditioning group (hazard ratio 1·10 [95% CI 0·91-1·32], p=0·32 for intervention versus control). No important unexpected adverse events or side effects of remote ischaemic conditioning were observed. INTERPRETATION: Remote ischaemic conditioning does not improve clinical outcomes (cardiac death or hospitalisation for heart failure) at 12 months in patients with STEMI undergoing PPCI. FUNDING: British Heart Foundation, University College London Hospitals/University College London Biomedical Research Centre, Danish Innovation Foundation, Novo Nordisk Foundation, TrygFonden