Public health research in the UK to understand and mitigate the impact of COVID-19 and COVID-19 response measures

This paper reflects concerns that funding and attention should be expanded from the important focus on those suffering and dying from COVID-19, and the safety and resources of healthcare professionals, to address wider questions on the (unequal) health and well-being impacts of COVID-19 and associated response measures. While immediate priorities such as those outlined in the WHO research agenda are undoubtedly important, additional urgent questions must be addressed. These include questions focused on (1) the non-virus impacts of preparing health and social care systems to cope with COVID-19 and (2) the health effects mediated by the educational, economic and social injuries sustained during the pandemic. Long-term, sustained and co-ordinated interdisciplinary research funding will be needed to address the long-lasting impacts of COVID-19 and its response measures

Spatial and Temporal Variability in Macroalgal Blooms 1 in a Eutrophied Coastal Estuary

All three macroalgal clades (Chlorophyta, Rhodophyta, and Phaeophyceae) contain bloom-forming species. Macroalgal blooms occur worldwide and have negative consequences for coastal habitats and economies. Narragansett Bay (NB), Rhode Island, USA, is a medium sized estuary that is heavily influenced by anthropogenic activities and has been plagued by macroalgal blooms for over a century. Over the past decade, significant investment has upgraded wastewater treatment from secondary treatment to water-quality based limits (i.e. tertiary treatment) in an effort to control coastal eutrophication in this system. The goal of this study was to improve the understanding of multi-year macroalgal bloom dynamics through intensive aerial and ground surveys conducted monthly to bi-monthly during low tides in May-October 2006-2013 in NB. Aerial surveys provided a rapid characterization of macroalgal densities across a large area, while ground surveys provided high resolution measurements of macroalgal identity, percent cover, and biomass. Macroalgal blooms in NB are dominated by Ulva and Gracilaria spp. regardless of year or month, although all three clades of macroalgae were documented. Chlorophyta cover and nutrient concentrations were highest in the middle and upper bay. Rhodophyta cover was highest in the middle and lower bay, while drifting Phaeophyceae cover was patchy. Macroalgal blooms of \u3e1000g fresh mass (gfm)/m2 (max=3510gfm/m2) in the intertidal zone and \u3e3000gfm/m3 (max=8555gfm/m3) in the subtidal zone were observed within a heavily impacted embayment (Greenwich Bay). Macroalgal percent cover (intertidal), biomass (subtidal), and diversity varied significantly between year, month-group, site, and even within sites, with the highest species diversity at sites outside of Greenwich Bay. Total intertidal macroalgal percent cover, as well as subtidal Ulva biomass, were positively correlated with temperature. Dissolved inorganic nitrogen concentrations were correlated with the total biomass of macroalgae and the subtidal biomass of Gracilaria spp. but not the biomass of Ulva spp. Despite seasonal reductions in the nutrient output of wastewater treatment facilities emptying into upper Narragansett Bay in recent years, macroalgal blooms still persist. Continued long-term monitoring of water quality, macroalgal blooms, and ecological indicators is essential to understand the changes in macroalgal bloom dynamics that occur after nutrient reductions from management efforts

Deep ROC Analysis and AUC as Balanced Average Accuracy to Improve Model Selection, Understanding and Interpretation

Optimal performance is critical for decision-making tasks from medicine to autonomous driving, however common performance measures may be too general or too specific. For binary classifiers, diagnostic tests or prognosis at a timepoint, measures such as the area under the receiver operating characteristic curve, or the area under the precision recall curve, are too general because they include unrealistic decision thresholds. On the other hand, measures such as accuracy, sensitivity or the F1 score are measures at a single threshold that reflect an individual single probability or predicted risk, rather than a range of individuals or risk. We propose a method in between, deep ROC analysis, that examines groups of probabilities or predicted risks for more insightful analysis. We translate esoteric measures into familiar terms: AUC and the normalized concordant partial AUC are balanced average accuracy (a new finding); the normalized partial AUC is average sensitivity; and the normalized horizontal partial AUC is average specificity. Along with post-test measures, we provide a method that can improve model selection in some cases and provide interpretation and assurance for patients in each risk group. We demonstrate deep ROC analysis in two case studies and provide a toolkit in Python.Comment: 14 pages, 6 Figures, submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), currently under revie

Rights-of-way vegetation management

A manual intended for use by those studying for the Oregon rights-of-way vegetation control exam. Includes chapters on basic weed science, vegetation management strategies; herbicides; factors influencing herbicide performance; special precautions when using herbicides; applying herbicides; calibration, mixing, and calculations; and application equipment. Includes a practice test, glossary, and references. Does not make specific herbicide recommendations.Published June 2004. Reviewed August 2007. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalogKeywords: vegetation control, weeds, herbicide

Correction to: Pulpotomy for the Management of Irreversible Pulpitis in Mature Teeth (PIP): a feasibility study

Background Progression of dental caries can result in irreversible pulpal damage. Partial irreversible pulpitis is the initial stage of this damage, confined to the coronal pulp whilst the radicular pulp shows little or no sign of infection. Preserving the pulp with sustained vitality and developing minimally invasive biologically based therapies are key themes within contemporary clinical practice. However, root canal treatment involving complete removal of the pulp is often the only option (other than extraction) given to patients with irreversible pulpitis, with substantial NHS and patient incurred costs. The European Society of Endodontology’s (ESE 2019) recent consensus statement recommends full pulpotomy, where the inflamed coronal pulp is removed with the goal of keeping the radicular pulp vital, as a more minimally invasive technique, potentially avoiding complex root canal treatment. Although this technique may be provided in secondary care, it has not been routinely implemented or evaluated in UK General Dental Practice. Method This feasibility study aims to identify and assess in a primary care setting the training needs of general dental practitioners and clinical fidelity of the full pulpotomy intervention, estimate likely eligible patient pool and develop recruitment materials ahead of the main randomised controlled trial comparing the clinical and cost-effectiveness of full pulpotomy compared to root canal treatment in pre/molar teeth of adults 16 years and older showing signs indicative of irreversible pulpitis. The feasibility study will recruit and train 10 primary care dentists in the full pulpotomy technique. Dentists will recruit and provide full pulpotomy to 40 participants (four per practice) with indications of partial irreversible pulpitis. Discussion The Pulpotomy for the Management of Irreversible Pulpitis in Mature Teeth (PIP) study will address the lack of high-quality evidence in the treatment of irreversible pulpitis, to aid dental practitioners, patients and policymakers in their decision-making. The PIP feasibility study will inform the main study on the practicality of providing both training and provision of the full pulpotomy technique in general dental practice. Trial registration ISRCTN Registry, ISRCTN17973604. Registered on 28 January 2021. Protocol version Protocol version: 1; date: 03.02.202

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe