Credit Where Credit is Due: Authorship of Open Ocean Data Workshop Report

Schmidt Ocean Institute, in partnership with The Ditchley Foundation, hosted Credit where credit is due: Authorship of open ocean data at Ditchley Park, in Chipping Norton, UK, on October 6-7, 2022, to identify actionable and implementable solutions to recognize and reward the dissemination of acquired data and knowledge. This report outlines the findings from that workshop

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Supporting Responsible Research and Innovation within a University-based digital research programme: reflections from the “hoRRIzon” project

Integration of Responsible Research and Innovation (RRI) principles into a research project is key to ensure outputs are ethically acceptable and socially desirable. However, translating RRI principles into practice is challenging as there are no recipes that fit all projects. Drawing on interviews and case studies with researchers, external partners and support staff associated with two linked programmes of research addressing trustworthy autonomous systems and the ethical use of personal data, this reflective paper provides a bottom-up perspective on RRI as it is understood and “done” within the focussed, often relatively short, research projects that largely comprise the research programmes. Existing RRI frameworks and tools were found to provide useful resources for use in supported RRI activities. However, effective use is dependant on facilitation by experienced staff, and time pressure and timing within a project can limit the application of RRI. Research institutions and funding bodies could provide more practical and sustained support for RRI practice – throughout the research lifespan - including incentives for RRI and clearer RRI/RI roles and career pathways, helping to develop an embedded community of RRI practice throughout the digital research community and beyond

Transferability of principles of evidence based medicine to improve educational quality: systematic review and case study of an online course in primary health care

The success of evidence based medicine has led to pressure to make medical education more evidence based. Greenhalgh and colleagues tested the transferability, of these principles when developing a postgraduate course

Impacts of a United States' biofuel policy on New Zealand's agricultural sector

The rise in oil prices has spurred interest in biofuels. Policies in the United States like the renewable fuel standard (RFS) have led to an expansion of ethanol production, while the New Zealand government has mandated a minimum level of biofuel sales. The research used a partial equilibrium model of international trade to quantify the price and farmgate income effects of the US RFS policy. The goal was to examine the competition between food and biofuel production and to quantify the impact of the policy on the agricultural sector in New Zealand. The RFS policy has a significant impact on corn prices, but a small effect on livestock prices and production. There thus appears to be little conflict between food and fuel uses for corn at the level of the RFS mandate. New Zealand's pasture-based livestock sector benefits from the use of corn for ethanol production: it receives better prices for its products, but does not face the same input cost increases as competitors. The results suggest that New Zealand faces an interesting decision: it could support investment in biofuels research, or benefit from the biofuels boom through the indirect impacts on demand and prices for meat and milk.Biofuel International trade Livestock sector

Responsible Research and Innovation (RRI) prompts and practice cards (version 2.1, August 2022)

These printable cards highlight 18 different aspects of Responsible Research and Innovation (RRI) that may be relevant to researchers and innovators. You can use the cards to reflect on a project and plan RRI activities. You can use the cards to facilitate a discussion about priorities for RRI in a research or application area. Or do something completely different

Equipping community pharmacy workers as agents for health behaviour change: developing and testing a theory-based smoking cessation intervention

Objective To develop a complex intervention for community pharmacy staff to promote uptake of smoking cessation services and to increase quit rates. Design Following the Medical Research Council framework, we used a mixed-methods approach to develop, pilot and then refine the intervention. Methods Phase I: We used information from qualitative studies in pharmacies, systematic literature reviews and the Capability, Opportunity, Motivation—Behaviour framework to inform design of the initial version of the intervention. Phase II: We then tested the acceptability of this intervention with smoking cessation advisers and assessed fidelity using actors who visited pharmacies posing as smokers, in a pilot study. Phase III: We reviewed the content and associated theory underpinning our intervention, taking account of the results of the earlier studies and a realist analysis of published literature. We then confirmed a logic model describing the intended operation of the intervention and used this model to refine the intervention and associated materials. Setting Eight community pharmacies in three inner east London boroughs. Participants 12 Stop Smoking Advisers. Intervention Two, 150 min, skills-based training sessions focused on communication and behaviour change skills with between session practice. Results The pilot study confirmed acceptability of the intervention and showed preliminary evidence of benefit; however, organisational barriers tended to limit effective operation. The pilot data and realist review pointed to additional use of Diffusion of Innovations Theory to seat the intervention in the wider organisational context. Conclusions We have developed and refined an intervention to promote smoking cessation services in community pharmacies, which we now plan to evaluate in a randomised controlled trial. Trial registration number UKCRN ID 18446, Pilot