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1. Hybridised multigrid preconditioners for a compatible finite element dynamical core

Author: Betteridge, Jack D., Cotter, Colin J., Gibson, Thomas H., Griffith, Matthew J., Melvin, Thomas, and Müller, Eike H.
Subjects: Physics - Computational Physics, Mathematics - Numerical Analysis, Physics - Fluid Dynamics, 65F08, 65N55, 76M10, 86A10, 65Y05, G.1.3, G.1.8, J.2
Abstract: Compatible finite element discretisations for the atmospheric equations of motion have recently attracted considerable interest. Semi-implicit timestepping methods require the repeated solution of a large saddle-point system of linear equations. Preconditioning this system is challenging since the velocity mass matrix is non-diagonal, leading to a dense Schur complement. Hybridisable discretisations overcome this issue: weakly enforcing continuity of the velocity field with Lagrange multipliers leads to a sparse system of equations, which has a similar structure to the pressure Schur complement in traditional approaches. We describe how the hybridised sparse system can be preconditioned with a non-nested two-level preconditioner. To solve the coarse system, we use the multigrid pressure solver that is employed in the approximate Schur complement method previously proposed by the some of the authors. Our approach significantly reduces the number of solver iterations. The method shows excellent performance and scales to large numbers of cores in the Met Office next-generation climate- and weather prediction model LFRic., Comment: 24 pages, 13 figures, 5 tables; accepted for publication in Quarterly Journal of the Royal Meteorological Society
Published: 2022

2. SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time

Author: Ashford, Fiona, Best, Angus, Dunn, Steven J, Ahmed, Zahra, Siddiqui, Henna, Melville, Jordan, Wilkinson, Samuel, Mirza, Jeremy, Cumley, Nicola, Stockton, Joanne, Ferguson, Jack, Wheatley, Lucy, Ratcliffe, Elizabeth, Casey, Anna, Plant, Tim, Aggarwal, Dinesh, Blane, Beth, Brooks, Ellena, Carabelli, Alessandro M, Churcher, Carol M, Galai, Katerina, Girgis, Sophia T, Gupta, Ravi K, Hadjirin, Nazreen F, Leek, Danielle, Ludden, Catherine, McManus, Georgina M, Palmer, Sophie, Peacock, Sharon J, Smith, Kim S, Allara, Elias, Bibby, David, Bishop, Chloe, Bosworth, Andrew, Bradshaw, Daniel, Chalker, Vicki, Chand, Meera, Dabrera, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Harrison, Ian, Hartman, Hassan, Hopes, Richard, Hubb, Jonathan, Hutchings, Stephanie, Lackenby, Angie, Ledesma, Juan, Lee, David, Manesis, Nikos, Manso, Carmen, Mbisa, Tamyo, Miah, Shahjahan, Muir, Peter, Myers, Richard, Osman, Husam, Patel, Vineet, Pearson, Clare, Platt, Steven, Pymont, Hannah M, Ramsay, Mary, Robinson, Esther, Schaefer, Ulf, Thornton, Alicia, Twohig, Katherine A, Vipond, Ian B, Williams, David, Hamilton, William L, Warne, Ben, Aigrain, Louise, Alderton, Alex, Amato, Roberto, Ariani, Cristina V, Barrett, Jeff, Bassett, Andrew R, Beale, Mathew A, Beaver, Charlotte, Bellis, Katherine L, Betteridge, Emma, Bonfield, James, Bronner, Iraad F, Chapman, Michael HS, Danesh, John, Davies, Robert, Dorman, Matthew J, Drury, Eleanor, Durham, Jillian, Farr, Ben W, Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan M, Jackson, David K, James, Keith, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, and Keatley, Jon-Paul
Subjects: Human Genome, Prevention, Biodefense, Genetics, Lung, Vaccine Related, Emerging Infectious Diseases, Good Health and Well Being, COVID-19, COVID-19 Testing, Humans, Mutation, SARS-CoV-2, COVID-19 Genomics UK (COG-UK) Consortium, PCR, SNPs, genome sequencing, genotyping, real time, variants of concern, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology
Abstract: Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants. Over a 6-week period during the months of April and May 2021, we set out to assess the ThermoFisher TaqMan mutation panel genotyping assay, initially for three mutations of concern and then for an additional two mutations of concern, against SARS-CoV-2-positive clinical samples and the corresponding COVID-19 Genomics UK Consortium (COG-UK) sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, is an excellent complement to genome sequencing, and has real clinical health value potential, allowing laboratories to report and take action on variants of concern much more quickly.
Published: 2022

3. Code generation for productive portable scalable finite element simulation in Firedrake

Author: Betteridge, Jack D., Farrell, Patrick E., and Ham, David A.
Subjects: Computer Science - Mathematical Software
Abstract: Creating scalable, high performance PDE-based simulations requires a suitable combination of discretizations, differential operators, preconditioners and solvers. The required combination changes with the application and with the available hardware, yet software development time is a severely limited resource for most scientists and engineers. Here we demonstrate that generating simulation code from a high-level Python interface provides an effective mechanism for creating high performance simulations from very few lines of user code. We demonstrate that moving from one supercomputer to another can require significant algorithmic changes to achieve scalable performance, but that the code generation approach enables these algorithmic changes to be achieved with minimal development effort.
Published: 2021

4. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: de Silva, Thushan I, Liu, Guihai, Lindsey, Benjamin B, Dong, Danning, Moore, Shona C, Hsu, Nienyun Sharon, Shah, Dhruv, Wellington, Dannielle, Mentzer, Alexander J, Angyal, Adrienn, Brown, Rebecca, Parker, Matthew D, Ying, Zixi, Yao, Xuan, Turtle, Lance, Dunachie, Susanna, Aanensen, David M, Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad SY, Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Annett, Tara, Aplin, Stephen, Ariani, Cristina V, Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W, Auckland, Cressida, Aydin, Alp, Baker, David J, Baker, Paul, Balcazar, Carlos E, Ball, Jonathan, Barrett, Jeffrey C, Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R, Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H, Beckwith, Shaun M, Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L, Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W, Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T, Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F, Brooks, Ellena, Broos, Alice, Brown, Julianne R, Bucca, Giselda, Buchan, Sarah L, Buck, David, Bull, Matthew, Burns, Phillipa J, Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M, Cargill, James S, and Carlile, Matthew
Subjects: Infectious Diseases, Prevention, Vaccine Related, Biodefense, Immunization, Emerging Infectious Diseases, Clinical Research, Good Health and Well Being, COVID-19 Genomics UK (COG-UK) Consortium, ISARIC4C Investigators, Immune response, Immunology, Molecular biology, Phylogenetics, Virology
Abstract: We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.
Published: 2021

5. Teaching Programming for Mathematical Scientists

Author: Betteridge, Jack, Chan, Eunice Y. S., Corless, Robert M., Davenport, James H., and Grant, James
Subjects: Mathematics - History and Overview, 97D40, 97P80
Abstract: Over the past thirty years or so the authors have been teaching various programming for mathematics courses at our respective Universities, as well as incorporating computer algebra and numerical computation into traditional mathematics courses. These activities are, in some important ways, natural precursors to the use of Artificial Intelligence in Mathematics Education. This paper reflects on some of our course designs and experiences and is therefore a mix of theory and practice. Underlying both is a clear recognition of the value of computer programming for mathematics education. We use this theory and practice to suggest good techniques for and to raise questions about the use of AI in Mathematics Education., Comment: 21 pages, 3 figures
Published: 2020
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6. Multigrid preconditioners for the hybridized Discontinuous Galerkin discretisation of the shallow water equations

Author: Betteridge, Jack D., Gibson, Thomas H., Graham, Ivan G., and Müller, Eike H.
Subjects: Physics - Computational Physics, Mathematics - Numerical Analysis, Physics - Fluid Dynamics, 65F08, 65M60, 65N55, 76M10, 86A10, G.1.3, G.1.8, J.2
Abstract: Numerical climate- and weather-prediction requires the fast solution of the equations of fluid dynamics. Discontinuous Galerkin (DG) discretisations have several advantageous properties. They can be used for arbitrary domains and support a structured data layout, which is important on modern chip architectures. For smooth solutions, higher order approximations can be particularly efficient since errors decrease exponentially in the polynomial degree. Due to the wide separation of timescales in atmospheric dynamics, semi-implicit time integrators are highly efficient, since the implicit treatment of fast waves avoids tight constraints on the time step size, and can therefore improve overall efficiency. However, if implicit-explicit (IMEX) integrators are used, a large linear system of equations has to be solved in every time step. A particular problem for DG discretisations of velocity-pressure systems is that the normal Schur-complement reduction to an elliptic system for the pressure is not possible since the numerical fluxes introduce artificial diffusion terms. For the shallow water equations, which form an important model system, hybridised DG methods have been shown to overcome this issue. However, no attention has been paid to the efficient solution of the resulting linear system of equations. In this paper we address this issue and show that the elliptic system for the flux unknowns can be solved efficiently with a non-nested multigrid algorithm. The method is implemented in the Firedrake library and we demonstrate the excellent performance of the algorithm both for an idealised stationary flow problem in a flat domain and for non-stationary setups in spherical geometry from the Williamson et al. testsuite. In the latter case the performance of our bespoke multigrid preconditioner (although itself not highly optimised) is comparable to that of a highly optimised direct solver., Comment: 41 pages, 16 figures, 13 tables
Published: 2020

7. Test–retest reliability of arterial spin labelling for cerebral blood flow in older adults with small vessel disease

Author: Binnie, Lauren R., Pauls, Mathilde M. H., Benjamin, Philip, Dhillon, Mohani-Preet K., Betteridge, Shai, Clarke, Brian, Ghatala, Rita, Hainsworth, Fearghal A. H., Howe, Franklyn A., Khan, Usman, Kruuse, Christina, Madigan, Jeremy B., Moynihan, Barry, Patel, Bhavini, Pereira, Anthony C., Rostrup, Egill, Shtaya, Anan B. Y., Spilling, Catherine A., Trippier, Sarah, Williams, Rebecca, Isaacs, Jeremy D., Barrick, Thomas R., and Hainsworth, Atticus H.
Published: 2022
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8. Walking orientation randomness metric (WORM) score: pilot study of a novel gait parameter to assess walking stability and discriminate fallers from non-fallers using wearable sensors

Author: Mobbs, Ralph Jasper, Natarajan, Pragadesh, Fonseka, R. Dineth, Betteridge, Callum, Ho, Daniel, Mobbs, Redmond, Sy, Luke, and Maharaj, Monish
Published: 2022
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9. Walking orientation randomness metric (WORM) score: pilot study of a novel gait parameter to assess walking stability and discriminate fallers from non-fallers using wearable sensors

Author: Ralph Jasper Mobbs, Pragadesh Natarajan, R. Dineth Fonseka, Callum Betteridge, Daniel Ho, Redmond Mobbs, Luke Sy, and Monish Maharaj
Subjects: Musculoskeletal disease, Gait disorders, Falls, Wearable device, Sensors, Gait analysis, Diseases of the musculoskeletal system, RC925-935
Abstract: Abstract Background Musculoskeletal disorders can contribute to injurious falls and incur significant societal and healthcare burdens. Identification of fallers from non-fallers through wearable-based gait analysis can facilitate timely intervention to assist mobility and prevent falls whilst improving care and attention for high fall-risk patients. In this study, we use wearable sensor-based gait analysis to introduce a novel variable to assess walking stability in fallers and non-fallers – the Walking Orientation Randomness Metric. The WORM score quantifies the stability, or ‘figure-of-eight’ motion of a subject’s trunk during walking as an indicator of a falls-predictive (pathological) gait. Methods WORM is calculated as the ‘figure-of-eight’ oscillation mapped out in the transverse-plane by the upper body’s centre-point during a walking bout. A sample of patients presenting to the Prince of Wales Hospital (Sydney, Australia) with a primary diagnosis of “falls for investigation” and age-matched healthy controls (non-fallers) from the community were recruited. Participants were fitted at the sternal angle with the wearable accelerometer, MetaMotionC (Mbientlab Inc., USA) and walked unobserved (at self-selected pace) for 5-50 m along an obstacle-free, carpeted hospital corridor. Results Participants comprised of 16 fallers (mean age: 70 + 17) and 16 non-fallers (mean age: 70 + 9) based on a recent fall(s) history. The (median) WORM score was 17-fold higher (p 0.51 cm) show high sensitivity (88%) and specificity (94%). Conclusion In this pilot study we have introduced the WORM score, demonstrating its discriminative performance in a preliminary sample size of 16 fallers. WORM is a novel gait metric assessing walking stability as measured by truncal way during ambulation and shows promise for objective and clinical evaluation of fallers.
Published: 2022
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10. Testing the cognitive effects of tadalafil. Neuropsychological secondary outcomes from the PASTIS trial

Author: Mathilde MH Pauls, Jessica Fish, Lauren R Binnie, Philip Benjamin, Shai Betteridge, Brian Clarke, Mohani-Preet K Dhillon, Rita Ghatala, Fearghal AH Hainsworth, Franklyn A Howe, Usman Khan, Christina Kruuse, Jeremy B Madigan, Barry Moynihan, Bhavini Patel, Anthony C Pereira, Egill Rostrup, Anan BY Shtaya, Catherine A Spilling, Sarah Trippier, Rebecca Williams, Robin Young, Thomas R Barrick, Jeremy D Isaacs, and Atticus H Hainsworth
Subjects: Clinical trials, Tadalafil, Pde5, Small vessel disease, Vascular cognitive impairment, Vascular dementia, Specialties of internal medicine, RC581-951, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Cerebral small vessel disease (SVD) is a major cause of cognitive impairment in older people. As secondary endpoints in a phase-2 randomised clinical trial, we tested the effects of single administration of a widely-used PDE5 inhibitor, tadalafil, on cognitive performance in older people with SVD. In a double-blinded, placebo-controlled, cross-over trial, participants received tadalafil (20 mg) and placebo on two visits ≥ 7 days apart (randomised to order of treatment). The Montreal Cognitive Assessment (MOCA) was administered at baseline, alongside a measure to estimate optimal intellectual ability (Test of Premorbid Function). Then, before and after treatment, a battery of neuropsychological tests was administered, assessing aspects of attention, information processing speed, working memory and executive function. Sixty-five participants were recruited and 55 completed the protocol (N = 55, age: 66.8 (8.6) years, range 52–87; 15/40 female/male). Median MOCA score was 26 (IQR: 23, 27], range 15–30). No significant treatment effects were seen in any of the neuropsychological tests. There was a trend towards improved performance on Digit Span Forward (treatment effect 0.37, C.I. 0.01, 0.72; P = 0.0521). We did not identify significant treatment effects of single-administration tadalafil on neuropsychological performance in older people with SVD. The trend observed on Digit Span Forward may help to inform future studies. Clinical trial registration: http://www.clinicaltrials.gov. Unique identifier: NCT00123456, https://eudract.ema.europa.eu. Unique identifier: 2015–001,235–20NCT00123456.
Published: 2023
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11. Non-pharmacological interventions to promote work participation in people with rheumatic and musculoskeletal diseases: a systematic review and meta-analysis from the EULAR taskforce on healthy and sustainable work participation

Author: Casper Webers, Johannes W J Bijlsma, Louise Falzon, Dieter Wiek, Robin Christensen, Suzanne M M Verstappen, Anthony D Woolf, Neil Betteridge, and Maarten H P Butink
Subjects: Medicine
Abstract: Objective To summarise the evidence on effectiveness of non-pharmacological (ie, non-drug, non-surgical) interventions on work participation (sick leave, work status and presenteeism) in people with rheumatic and musculoskeletal diseases (RMDs).Methods A systematic review of randomised controlled trials (RCTs) and longitudinal observational studies (LOS) was performed. Qualitative (RCTs/LOS) and quantitative (RCTs) evidence syntheses were conducted. Mixed-effects restricted maximum likelihood models were used to combine effect estimates, using standardised mean differences (SMDs) as the summary measure for each outcome domain separately, with a negative SMD favouring the intervention over comparator. Subgroup analyses were performed for type of RMD, risk status at baseline regarding adverse work outcomes and intervention characteristics.Results Of 10 153 records, 64 studies (37 RCTs and 27 LOS; corresponding to k=71 treatment comparisons) were included. Interventions were mostly conducted in clinical settings (44 of 71, 62%). Qualitative synthesis suggested clear beneficial effects of 7 of 64 (11%) interventions for sick leave, 1 of 18 (6%) for work status and 1 of 17 (6%) for presenteeism. Quantitative synthesis (37 RCTs; k=43 treatment comparisons) suggested statistically significant but only small clinical effects on each outcome (SMDsick leave (95% CI)=−0.23 (−0.33 to −0.13; k=42); SMDwork status=−0.38 (−0.63 to −0.12; k=9); SMDpresenteeism=−0.25 (−0.39 to −0.12; k=13)).Conclusion In people with RMDs, empirical evidence shows that non-pharmacological interventions have small effects on work participation. Effectiveness depends on contextual factors such as disease, population risk status, intervention characteristics and outcome of interest, highlighting the importance of tailoring interventions.
Published: 2023
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12. Treating axial spondyloarthritis and peripheral spondyloarthritis, especially psoriatic arthritis, to target: 2017 update of recommendations by an international task force

Author: Smolen, Josef S, Schöls, Monika, Braun, Jürgen, Dougados, Maxime, FitzGerald, Oliver, Gladman, Dafna D, Kavanaugh, Arthur, Landewé, Robert, Mease, Philip, Sieper, Joachim, Stamm, Tanja, Wit, Maarten de, Aletaha, Daniel, Baraliakos, Xenofon, Betteridge, Neil, Bosch, Filip van den, Coates, Laura C, Emery, Paul, Gensler, Lianne S, Gossec, Laure, Helliwell, Philip, Jongkees, Merryn, Kvien, Tore K, Inman, Robert D, McInnes, Iain B, Maccarone, Mara, Machado, Pedro M, Molto, Anna, Ogdie, Alexis, Poddubnyy, Denis, Ritchlin, Christopher, Rudwaleit, Martin, Tanew, Adrian, Thio, Bing, Veale, Douglas, Vlam, Kurt de, and van der Heijde, Désirée
Subjects: Biomedical and Clinical Sciences, Clinical Sciences, Arthritis, Autoimmune Disease, Clinical Research, Rare Diseases, Inflammatory and immune system, Advisory Committees, Arthritis, Psoriatic, Axis, Cervical Vertebra, Consensus, Decision Making, Humans, Severity of Illness Index, Spondylitis, Ankylosing, Ankylosing Spondylitis, Outcomes Research, Psoriatic Arthritis, Spondyloarthritis, Treatment, Immunology, Public Health and Health Services, Arthritis & Rheumatology, Clinical sciences
Abstract: Therapeutic targets have been defined for axial and peripheral spondyloarthritis (SpA) in 2012, but the evidence for these recommendations was only of indirect nature. These recommendations were re-evaluated in light of new insights. Based on the results of a systematic literature review and expert opinion, a task force of rheumatologists, dermatologists, patients and a health professional developed an update of the 2012 recommendations. These underwent intensive discussions, on site voting and subsequent anonymous electronic voting on levels of agreement with each item. A set of 5 overarching principles and 11 recommendations were developed and voted on. Some items were present in the previous recommendations, while others were significantly changed or newly formulated. The 2017 task force arrived at a single set of recommendations for axial and peripheral SpA, including psoriatic arthritis (PsA). The most exhaustive discussions related to whether PsA should be assessed using unidimensional composite scores for its different domains or multidimensional scores that comprise multiple domains. This question was not resolved and constitutes an important research agenda. There was broad agreement, now better supported by data than in 2012, that remission/inactive disease and, alternatively, low/minimal disease activity are the principal targets for the treatment of PsA. As instruments to assess the patients on the path to the target, the Ankylosing Spondylitis Disease Activity Score (ASDAS) for axial SpA and the Disease Activity index for PSoriatic Arthritis (DAPSA) and Minimal Disease Activity (MDA) for PsA were recommended, although not supported by all. Shared decision-making between the clinician and the patient was seen as pivotal to the process. The task force defined the treatment target for SpA as remission or low disease activity and developed a large research agenda to further advance the field.
Published: 2018

13. Self-Healing: A Concept for Musculoskeletal Body Pain Management – Scientific Evidence and Mode of Action

Author: McSwan J, Gudin J, Song XJ, Grinberg Plapler P, Betteridge NJ, Kechemir H, Igracki-Turudic I, and Pickering G
Subjects: innate, complementary, intrinsic ability, multi-modal, acute, equilibrium, Medicine (General), R5-920
Abstract: Joyce McSwan,1,* Jeffrey Gudin,2,* Xue-Jun Song,3 Perola Grinberg Plapler,4 Neil John Betteridge,5 Hayet Kechemir,6 Iva Igracki-Turudic,7 Gisele Pickering8 1GCPHN Persistent Pain Program, PainWISE, Gold Coast, QLD, Australia; 2Department of Anesthesiology, University of Miami, Miller School of Medicine, Miami, FL, USA; 3SUSTech Center of Pain Medicine, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, People’s Republic of China; 4Division of Physical Medicine, Institute of Orthopedics and Traumatology, Hospital das Clínicas, Faculty of Medicine, University of São Paulo, São Paulo, Brazil; 5Neil Betteridge Associates Ltd, London, UK; 6Consumer Healthcare Medical Affairs Department, Sanofi CHC, Paris, France; 7Consumer Healthcare Medical Affairs Department, Sanofi CHC, Frankfurt, Germany; 8Clinical Investigation Center CIC Inserm 1405, University Hospital Clermont-Ferrand, Clermont-Ferrand, France*These authors contributed equally to this workCorrespondence: Gisele PickeringClinical Investigation Center CIC Inserm 1405, University Hospital Clermont-Ferrand, rue Montalembert, CHU G Montpied, Clermont-Ferrand, 63000, FranceTel +33 4 73 17 84 16Fax +33 4 73 17 84 12Email gisele.pickering@uca.frAbstract: Traditionally, musculoskeletal pain management has focused on the use of conventional treatments to relieve pain. However, multi-modal integrative medicine including alternative/complementary treatments is becoming more widely used and integrated into treatment guidelines around the world. The uptake of this approach varies according to country, with generally a higher uptake in developed countries and in females aged more than 40 years. Integral to the concept described here, is that the body has an innate ability to self-heal, which can be optimized by the use of integrative medical strategies. Stress triggers for acute or recurring musculoskeletal pain are diverse and can range from physical to psychological. The mechanism by which the body responds to triggers and initiates the self-healing processes is complex, but five body networks or processes are thought to be integral: the nervous system, microcirculation/vasodilation, immune modulation, muscular relaxation/contraction and psychological balance. Multi-modal integrative medicine approaches include nutritional/dietary modification, postural/muscular training exercises, and cognitive behavioral mind/body techniques. This article will review the self-healing concept and provide plausible scientific evidence where available.Keywords: innate, complementary, intrinsic ability, multi-modal, acute, equilibrium
Published: 2021

14. Proposed objective scoring algorithm for walking performance, based on relevant gait metrics: the Simplified Mobility Score (SMoS™)—observational study

Author: Callum Betteridge, Ralph Jasper Mobbs, and Daniel Ho
Subjects: Walking, Gait analysis, Walking speed, Gait speed, Step count, Daily step count, Orthopedic surgery, RD701-811, Diseases of the musculoskeletal system, RC925-935
Abstract: Abstract Background Walking is a fundamental part of living, and its importance is not limited by age or medical status. Reduced walking speed (WS), or gait velocity, is a sign of advancing age, various disease states, cognitive impairment, mental illness and early mortality. Activity levels, as defined in the literature as “daily step count” (DSC), is also a relevant measure of health status. A deterioration in our walking metrics, such as reduced WS and DSC, is associated with poor health outcomes. These objective measures are of such importance, that walking speed has been dubbed “the 6th vital sign”. We report a new objective measure that scores walking using the relevant metrics of walking speed and daily step count, into an easy-to-understand score from 0 (nil mobility) to 100 (excellent mobility), termed the Simplified Mobility Score (SMoS™). We have provided equal weighting to walking speed and daily step count, using a simple algorithm to score each metric out of 50. Methods Gait data was collected from 182 patients presenting to a tertiary hospital spinal unit with complaints of pain and reduced mobility. Walking speed was measured from a timed walk along an unobstructed pathway. Daily step count information was obtained from patients who had enabled step count tracking on their devices. The SMoS of the sample group were compared to expected population values calculated from the literature using 2-tailed Z tests. Results There were significantly reduced SMoS in patients who presented to the spinal unit than those expected at each age group for both genders, except for the 50–59 age bracket where no statistically significant reduction was observed. Even lower scores were present in those that went on to have surgical management. There was a significant correlation of SMoS scores with subjective disability scores such as the Oswestry Disability Index (ODI) and Visual Analogue Scale (VAS) in this cohort. Conclusions The SMoS is a simple and effective scoring tool which is demonstrably altered in spinal patients across age and gender brackets and correlates well with subjective disability scores. The SMoS has the potential to be used as a screening tool in primary and specialised care settings.
Published: 2021
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15. Meta-analysis of genome-wide association studies of HDL cholesterol response to statins

Author: Postmus, Iris, Warren, Helen R, Trompet, Stella, Arsenault, Benoit J, Avery, Christy L, Bis, Joshua C, Chasman, Daniel I, de Keyser, Catherine E, Deshmukh, Harshal A, Evans, Daniel S, Feng, QiPing, Li, Xiaohui, Smit, Roelof AJ, Smith, Albert V, Sun, Fangui, Taylor, Kent D, Arnold, Alice M, Barnes, Michael R, Barratt, Bryan J, Betteridge, John, Boekholdt, S Matthijs, Boerwinkle, Eric, Buckley, Brendan M, Chen, Y-D Ida, de Craen, Anton JM, Cummings, Steven R, Denny, Joshua C, Dubé, Marie Pierre, Durrington, Paul N, Eiriksdottir, Gudny, Ford, Ian, Guo, Xiuqing, Harris, Tamara B, Heckbert, Susan R, Hofman, Albert, Hovingh, G Kees, Kastelein, John JP, Launer, Leonore J, Liu, Ching-Ti, Liu, Yongmei, Lumley, Thomas, McKeigue, Paul M, Munroe, Patricia B, Neil, Andrew, Nickerson, Deborah A, Nyberg, Fredrik, O'Brien, Eoin, O'Donnell, Christopher J, Post, Wendy, Poulter, Neil, Vasan, Ramachandran S, Rice, Kenneth, Rich, Stephen S, Rivadeneira, Fernando, Sattar, Naveed, Sever, Peter, Shaw-Hawkins, Sue, Shields, Denis C, Slagboom, P Eline, Smith, Nicholas L, Smith, Joshua D, Sotoodehnia, Nona, Stanton, Alice, Stott, David J, Stricker, Bruno H, Stürmer, Til, Uitterlinden, André G, Wei, Wei-Qi, Westendorp, Rudi GJ, Whitsel, Eric A, Wiggins, Kerri L, Wilke, Russell A, Ballantyne, Christie M, Colhoun, Helen M, Cupples, L Adrienne, Franco, Oscar H, Gudnason, Vilmundur, Hitman, Graham, Palmer, Colin NA, Psaty, Bruce M, Ridker, Paul M, Stafford, Jeanette M, Stein, Charles M, Tardif, Jean-Claude, Caulfield, Mark J, Jukema, J Wouter, Rotter, Jerome I, and Krauss, Ronald M
Subjects: Atherosclerosis, Genetics, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Stroke, Good Health and Well Being, Cholesterol Ester Transfer Proteins, Cholesterol, HDL, Female, Genome-Wide Association Study, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Male, Pharmacogenomic Variants, Polymorphism, Single Nucleotide, Treatment Outcome, White People, Genome-wide association study, HDL-cholesterol, Statins, pharmacogenetics, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract: BackgroundIn addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation.Methods and resultsWe performed a meta-analysis of genome-wide association studies (GWAS) to identify variants with an effect on statin-induced high density lipoprotein cholesterol (HDL-C) changes. The 123 most promising signals with p
Published: 2016

16. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author: Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, Erich D. Jarvis, and The Vertebrate Genomes Project Consortium
Subjects: Mitochondrial DNA, Vertebrate, Assembly, Long reads, Sequencing, Duplications, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract: Abstract Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
Published: 2021
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17. Nocebo effects and participant information leaflets: evaluating information provided on adverse effects in UK clinical trials

Author: Nigel Kirby, Victoria Shepherd, Jeremey Howick, Sophie Betteridge, and Kerenza Hood
Subjects: Nocebo, Placebo, Patient information leaflets, Adverse effects, Readability, Medicine (General), R5-920
Abstract: Abstract Background Nocebo effects (‘negative placebo’ effects) experienced by clinical trial participants can arise from an underlying condition or through communication about side effects in the participant information leaflets (or elsewhere). Misattributing nocebo effects to the medicinal intervention can lead to participants experiencing harmful nocebo effects and may result in distortion of adverse effect reporting. However, little is known about how information on potential side effects is provided to trial participants. There is increasing concern that the way in which potential side effects in clinical trials are described to patients in participant information leaflets (PIL) can in itself cause harm by either increased anxiety, poor adherence or inducing the side effect itself. In this study, we aimed to explore these concerns and identify the way in which potential side effects from investigational medicinal products used in trials are presented in written information to potential participants. Methods Trials were identified from the International Standard Randomised Controlled Trials Number (ISRCTN) clinical trial registry (a primary registry of the WHO International Clinical Trials Registry Platform (ICTRP)). Eligible studies were placebo-controlled clinical trials of investigational medicinal products (IMP) in adults conducted in the UK. We assessed readability using the Flesch Reading Ease scale, Gunning-Fog Index and Flesch-Kincaid Grade. Data extracted from the PILs were divided into 8 predefined qualitative themes for analysis in NVivo11. Results Most of the patient information leaflets were ranked as ‘fairly difficult to read’ or ‘difficult to read’ according to the Flesch Reading Ease scale. All studies presented information about adverse events, whereas only a third presented information about intervention benefits. Where intervention or study benefits were presented, they were usually after adverse events (21/33, 64%). Discussion Participant information leaflets scored poorly on ease of readability and had more content relating to adverse effects than any potential beneficial effects. The way in which adverse events were presented was heterogeneous in terms of their likelihood and severity and the amount and level of detail provided. By comparison, potential benefits from the intervention and/or study were described less often, by shorter text, and only after information about harms.
Published: 2020
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18. Treatment Mode Preferences in Rheumatoid Arthritis: Moving Toward Shared Decision-Making

Author: Taylor PC, Betteridge N, Brown TM, Woolcott J, Kivitz AJ, Zerbini C, Whalley D, Olayinka-Amao O, Chen C, Dahl P, Ponce de Leon D, Gruben D, and Fallon L
Subjects: drug administration, patient perspective, qualitative research, surveys, Medicine (General), R5-920
Abstract: Peter C Taylor, 1 Neil Betteridge, 2 T Michelle Brown, 3 John Woolcott, 4 Alan J Kivitz, 5 Cristiano Zerbini, 6 Diane Whalley, 7 Oyebimpe Olayinka-Amao, 3 Connie Chen, 8 Palle Dahl, 9 Dario Ponce de Leon, 10 David Gruben, 11 Lara Fallon 12 1Botnar Research Centre, University of Oxford, Oxford, UK; 2Neil Betteridge Associates, London, UK; 3Patient-Centered Outcomes Assessment Group, RTI Health Solutions, Research Triangle Park, NC, USA; 4Patient and Health Impact, Health Economics and Outcomes Research, Pfizer Inc, Collegeville, PA, USA; 5Altoona Center for Clinical Research, Duncansville, PA, USA; 6Department of Rheumatology, Centro Paulista De Investigação Clinica, São Paulo, Brazil; 7Patient-Centered Outcomes Assessment Group, RTI Health Solutions, Manchester, UK; 8Xeljanz, Rheumatology, Inflammation & Immunology Medical Affairs, Pfizer Inc, New York, NY, USA; 9Medical Affairs, International Developed Markets, Inflammation & Immunology, Pfizer Inc, Ballerup, Denmark; 10Medical Affairs Latin-America, Pfizer Inc, New York, NY, USA; 11Statistical Research and Data Science Center, Pfizer Inc, Groton, CT, USA; 12Global Medical Affairs, Pfizer Inc, Montreal, QC, CanadaCorrespondence: Peter C TaylorBotnar Research Centre, University of Oxford, Windmill Road, Headington, Oxford OX3 7LD, UKTel +441865 227323Email peter.taylor@kennedy.ox.ac.ukPurpose: Current knowledge of the reasons for patients’ preference for rheumatoid arthritis (RA) treatment modes is limited. This study was designed to identify preferences for four treatment modes, and to obtain in-depth information on the reasons for these preferences.Patients and Methods: In this multi-national, cross-sectional, qualitative study, in-depth interviews were conducted with adult patients with RA in the United States, France, Germany, Italy, Spain, Switzerland, the United Kingdom, and Brazil. Patients’ strength of preference was evaluated using a 100-point allocation task (0– 100; 100=strongest) across four treatment modes: oral, self-injection, clinic-injection, and infusion. Qualitative descriptive analysis methods were used to identify, characterize, and summarize patterns found in the interview data relating to reasons for these preferences.Results: 100 patients were interviewed (female, 75.0%; mean age, 53.9 years; mean 11.6 years since diagnosis). Among the four treatment modes, oral administration was allocated the highest mean (standard deviation) preference points (47.3 [33.1]) and was ranked first choice by the greatest percentage of patients (57.0%), followed by self-injection (29.7 [27.7]; 29.0%), infusion (15.4 [24.6]; 16.0%), and clinic-injection (7.5 [14.1]; 2.0%). Overall, 56.0% of patients had a “strong” first-choice preference (ie, point allocation ≥ 70); most of these patients chose oral (62.5%) vs self-injection (23.2%), infusion (10.7%), or clinic-injection (3.6%). Speed and/or ease of administration were the most commonly reported reasons for patients choosing oral (52.6%) or self-injection (55.2%). The most common reasons for patients not choosing oral or self-injection were not wanting to take another pill (37.2%) and avoiding pain due to needles (46.5%), respectively.Conclusion: These data report factors important to patients regarding preferences for RA treatment modes. Patients may benefit from discussions with their healthcare professionals and/or patient support groups, regarding RA treatment modes, to facilitate shared decision-making.Keywords: drug administration, patient perspective, qualitative research, surveys
Published: 2020

19. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: Thushan I. de Silva, Guihai Liu, Benjamin B. Lindsey, Danning Dong, Shona C. Moore, Nienyun Sharon Hsu, Dhruv Shah, Dannielle Wellington, Alexander J. Mentzer, Adrienn Angyal, Rebecca Brown, Matthew D. Parker, Zixi Ying, Xuan Yao, Lance Turtle, Susanna Dunachie, Mala K. Maini, Graham Ogg, Julian C. Knight, Yanchun Peng, Sarah L. Rowland-Jones, Tao Dong, David M. Aanensen, Khalil Abudahab, Helen Adams, Alexander Adams, Safiah Afifi, Dinesh Aggarwal, Shazaad S.Y. Ahmad, Louise Aigrain, Adela Alcolea-Medina, Nabil-Fareed Alikhan, Elias Allara, Roberto Amato, Tara Annett, Stephen Aplin, Cristina V. Ariani, Hibo Asad, Amy Ash, Paula Ashfield, Fiona Ashford, Laura Atkinson, Stephen W. Attwood, Cressida Auckland, Alp Aydin, David J. Baker, Paul Baker, Carlos E. Balcazar, Jonathan Ball, Jeffrey C. Barrett, Magdalena Barrow, Edward Barton, Matthew Bashton, Andrew R. Bassett, Rahul Batra, Chris Baxter, Nadua Bayzid, Charlotte Beaver, Angela H. Beckett, Shaun M. Beckwith, Luke Bedford, Robert Beer, Andrew Beggs, Katherine L. Bellis, Louise Berry, Beatrice Bertolusso, Angus Best, Emma Betteridge, David Bibby, Kelly Bicknell, Debbie Binns, Alec Birchley, Paul W. Bird, Chloe Bishop, Rachel Blacow, Victoria Blakey, Beth Blane, Frances Bolt, James Bonfield, Stephen Bonner, David Bonsall, Tim Boswell, Andrew Bosworth, Yann Bourgeois, Olivia Boyd, Declan T. Bradley, Cassie Breen, Catherine Bresner, Judith Breuer, Stephen Bridgett, Iraad F. Bronner, Ellena Brooks, Alice Broos, Julianne R. Brown, Giselda Bucca, Sarah L. Buchan, David Buck, Matthew Bull, Phillipa J. Burns, Shirelle Burton-Fanning, Timothy Byaruhanga, Matthew Byott, Sharon Campbell, Alessandro M. Carabelli, James S. Cargill, Matthew Carlile, Silvia F. Carvalho, Anna Casey, Anibolina Castigador, Jana Catalan, Vicki Chalker, Nicola J. Chaloner, Meera Chand, Joseph G. Chappell, Themoula Charalampous, Wendy Chatterton, Yasmin Chaudhry, Carol M. Churcher, Gemma Clark, Phillip Clarke, Benjamin J. Cogger, Kevin Cole, Jennifer Collins, Rachel Colquhoun, Thomas R. Connor, Kate F. Cook, Jason Coombes, Sally Corden, Claire Cormie, Nicholas Cortes, Marius Cotic, Seb Cotton, Simon Cottrell, Lindsay Coupland, MacGregor Cox, Alison Cox, Noel Craine, Liam Crawford, Aidan Cross, Matthew R. Crown, Dorian Crudgington, Nicola Cumley, Tanya Curran, Martin D. Curran, Ana da Silva Filipe, Gavin Dabrera, Alistair C. Darby, Rose K. Davidson, Alisha Davies, Robert M. Davies, Thomas Davis, Daniela de Angelis, Elen De Lacy, Leonardo de Oliveira Martins, Johnny Debebe, Rebecca Denton-Smith, Samir Dervisevic, Rebecca Dewar, Jayasree Dey, Joana Dias, Donald Dobie, Matthew J. Dorman, Fatima Downing, Megan Driscoll, Louis du Plessis, Nichola Duckworth, Jillian Durham, Kirstine Eastick, Lisa J. Easton, Richard Eccles, Jonathan Edgeworth, Sue Edwards, Kate El Bouzidi, Sahar Eldirdiri, Nicholas Ellaby, Scott Elliott, Gary Eltringham, Leah Ensell, Michelle J. Erkiert, Marina Escalera Zamudio, Sarah Essex, Johnathan M. Evans, Cariad Evans, William Everson, Derek J. Fairley, Karlie Fallon, Arezou Fanaie, Ben W. Farr, Christopher Fearn, Theresa Feltwell, Lynne Ferguson, Laia Fina, Flavia Flaviani, Vicki M. Fleming, Sally Forrest, Ebenezer Foster-Nyarko, Benjamin H. Foulkes, Luke Foulser, Mireille Fragakis, Dan Frampton, Sarah Francois, Christophe Fraser, Timothy M. Freeman, Helen Fryer, Marc Fuchs, William Fuller, Kavitha Gajee, Katerina Galai, Abbie Gallagher, Eileen Gallagher, Michael D. Gallagher, Marta Gallis, Amy Gaskin, Bree Gatica-Wilcox, Lily Geidelberg, Matthew Gemmell, Iliana Georgana, Ryan P. George, Laura Gifford, Lauren Gilbert, Sophia T. Girgis, Sharon Glaysher, Emily J. Goldstein, Tanya Golubchik, Andrea N. Gomes, Sónia Gonçalves, Ian G. Goodfellow, Scott Goodwin, Salman Goudarzi, Marina Gourtovaia, Clive Graham, Lee Graham, Paul R. Grant, Luke R. Green, Angie Green, Jane Greenaway, Richard Gregory, Martyn Guest, Rory N. Gunson, Ravi K. Gupta, Bernardo Gutierrez, Sam T. Haldenby, William L. Hamilton, Samantha E. Hansford, Tanzina Haque, Kathryn A. Harris, Ian Harrison, Ewan M. Harrison, Jennifer Hart, John A. Hartley, William T. Harvey, Matthew Harvey, Mohammed O. Hassan-Ibrahim, Judith Heaney, Thomas Helmer, John H. Henderson, Andrew R. Hesketh, Jessica Hey, David Heyburn, Ellen E. Higginson, Verity Hill, Jack D. Hill, Rachel A. Hilson, Ember Hilvers, Matthew T.G. Holden, Amy Hollis, Christopher W. Holmes, Nadine Holmes, Alison H. Holmes, Richard Hopes, Hailey R. Hornsby, Myra Hosmillo, Catherine Houlihan, Hannah C. Howson-Wells, Jonathan Hubb, Hannah Huckson, Warwick Hughes, Joseph Hughes, Margaret Hughes, Stephanie Hutchings, Giles Idle, Chris J. Illingworth, Robert Impey, Dianne Irish-Tavares, Miren Iturriza-Gomara, Rhys Izuagbe, Chris Jackson, Ben Jackson, Leigh M. Jackson, Kathryn A. Jackson, David K. Jackson, Aminu S. Jahun, Victoria James, Keith James, Christopher Jeanes, Aaron R. Jeffries, Sarah Jeremiah, Andrew Jermy, Michaela John, Rob Johnson, Kate Johnson, Ian Johnston, Owen Jones, Sophie Jones, Hannah Jones, Christopher R. Jones, Neil Jones, Amelia Joseph, Sarah Judges, Gemma L. Kay, Sally Kay, Jon-Paul Keatley, Alexander J. Keeley, Anita Kenyon, Leanne M. Kermack, Manjinder Khakh, Stephen P. Kidd, Maimuna Kimuli, Stuart Kirk, Christine Kitchen, Katie Kitchman, Bridget A. Knight, Cherian Koshy, Moritz U.G. Kraemer, Sara Kumziene-Summerhayes, Dominic Kwiatkowski, Angie Lackenby, Kenneth G. Laing, Temi Lampejo, Cordelia F. Langford, Deborah Lavin, Andrew I. Lawton, Jack Lee, David Lee, Stefanie V. Lensing, Steven Leonard, Lisa J. Levett, Thanh Le-Viet, Jonathan Lewis, Kevin Lewis, Jennifier Liddle, Steven Liggett, Patrick J. Lillie, Michelle M. Lister, Rich Livett, Stephanie Lo, Nicholas J. Loman, Matthew W. Loose, Stavroula F. Louka, Katie F. Loveson, Sarah Lowdon, Hannah Lowe, Helen L. Lowe, Anita O. Lucaci, Catherine Ludden, Jessica Lynch, Ronan A. Lyons, Katrina Lythgoe, Nicholas W. Machin, George MacIntyre-Cockett, Andrew Mack, Ben Macklin, Alasdair Maclean, Emily Macnaughton, Pinglawathee Madona, Mailis Maes, Laurentiu Maftei, Adhyana I.K. Mahanama, Tabitha W. Mahungu, Daniel Mair, Joshua Maksimovic, Cassandra S. Malone, Daniel Maloney, Nikos Manesis, Robin Manley, Anna Mantzouratou, Angela Marchbank, Arun Mariappan, Inigo Martincorena, Rocio T. Martinez Nunez, Alison E. Mather, Patrick Maxwell, Megan Mayhew, Tamyo Mbisa, Clare M. McCann, Shane A. McCarthy, Kathryn McCluggage, Patrick C. McClure, J.T. McCrone, Martin P. McHugh, James P. McKenna, Caoimhe McKerr, Georgina M. McManus, Claire L. McMurray, Claire McMurray, Alan McNally, Lizzie Meadows, Nathan Medd, Oliver Megram, Mirko Menegazzo, Ian Merrick, Stephen L. Michell, Michelle L. Michelsen, Mariyam Mirfenderesky, Jeremy Mirza, Julia Miskelly, Emma Moles-Garcia, Robin J. Moll, Zoltan Molnar, Irene M. Monahan, Matteo Mondani, Siddharth Mookerjee, Christopher Moore, Jonathan Moore, Nathan Moore, Catherine Moore, Helen Morcrette, Sian Morgan, Mari Morgan, Matilde Mori, Arthur Morriss, Samuel Moses, Craig Mower, Peter Muir, Afrida Mukaddas, Florence Munemo, Robert Munn, Abigail Murray, Leanne J. Murray, Darren R. Murray, Manasa Mutingwende, Richard Myers, Eleni Nastouli, Gaia Nebbia, Andrew Nelson, Charlotte Nelson, Sam Nicholls, Jenna Nichols, Roberto Nicodemi, Kyriaki Nomikou, Justin O’Grady, Sarah O'Brien, Mina Odedra, Natasha Ohemeng-Kumi, Karen Oliver, Richard J. Orton, Husam Osman, xeine O'Toole, Nicole Pacchiarini, Debra Padgett, Andrew J. Page, Emily J. Park, Naomi R. Park, Surendra Parmar, David G. Partridge, David Pascall, Amita Patel, Bindi Patel, Steve Paterson, Brendan A.I. Payne, Sharon J. Peacock, Clare Pearson, Emanuela Pelosi, Benita Percival, Jon Perkins, Malorie Perry, Malte L. Pinckert, Steven Platt, Olga Podplomyk, Manoj Pohare, Marcus Pond, Cassie F. Pope, Radoslaw Poplawski, Jessica Powell, Jennifer Poyner, Liam Prestwood, Anna Price, James R. Price, Jacqui A. Prieto, David T. Pritchard, Sophie J. Prosolek, Georgia Pugh, Monika Pusok, Oliver G. Pybus, Hannah M. Pymont, Michael A. Quail, Joshua Quick, Clara Radulescu, Jayna Raghwani, Manon Ragonnet-Cronin, Lucille Rainbow, Diana Rajan, Shavanthi Rajatileka, Newara A. Ramadan, Andrew Rambaut, John Ramble, Paul A. Randell, Paul Randell, Liz Ratcliffe, Veena Raviprakash, Mohammad Raza, Nicholas M. Redshaw, Sara Rey, Nicola Reynolds, Alex Richter, David L. Robertson, Esther Robinson, Samuel C. Robson, Fiona Rogan, Stefan Rooke, Will Rowe, Sunando Roy, Steven Rudder, Chris Ruis, Steven Rushton, Felicity Ryan, Kordo Saeed, Buddhini Samaraweera, Christine M. Sambles, Roy Sanderson, Theo Sanderson, Fei Sang, Thea Sass, Emily Scher, Garren Scott, Carol Scott, Jasveen Sehmi, Sharif Shaaban, Divya Shah, Jessica Shaw, Ekaterina Shelest, James G. Shepherd, Liz A. Sheridan, Nicola Sheriff, Lesley Shirley, John Sillitoe, Siona Silviera, David A. Simpson, Aditi Singh, Dawn Singleton, Timofey Skvortsov, Tim J. Sloan, Graciela Sluga, Ken Smith, Kim S. Smith, Perminder Smith, Darren L. Smith, Louise Smith, Colin P. Smith, Nikki Smith, Katherine L. Smollett, Luke B. Snell, Thomas Somassa, Joel Southgate, Karla Spellman, Michael H. Spencer Chapman, Lewis G. Spurgin, Moira J. Spyer, Rachael Stanley, William Stanley, Thomas D. Stanton, Igor Starinskij, Joanne Stockton, Susanne Stonehouse, Nathaniel Storey, David J. Studholme, Malur Sudhanva, Emma Swindells, Yusri Taha, Ngee Keong Tan, Julian W. Tang, Miao Tang, Ben E.W. Taylor, Joshua F. Taylor, Sarah Taylor, Ben Temperton, Kate E. Templeton, Claire Thomas, Laura Thomson, Emma C. Thomson, Alicia Thornton, Scott A.J. Thurston, John A. Todd, Rachael Tomb, Lily Tong, Gerry Tonkin-Hill, M. Estee Torok, Jaime M. Tovar-Corona, Amy Trebes, Alexander J. Trotter, Ioulia Tsatsani, Robyn Turnbull, Katherine A. Twohig, Helen Umpleby, Anthony P. Underwood, Edith E. Vamos, Tetyana I. Vasylyeva, Sreenu Vattipally, Gabrielle Vernet, Barry B. Vipond, Erik M. Volz, Sarah Walsh, Dennis Wang, Ben Warne, Joanna Warwick-Dugdale, Elizabeth Wastnedge, Joanne Watkins, Louisa K. Watson, Sheila Waugh, Hermione J. Webster, Danni Weldon, Elaine Westwick, Thomas Whalley, Helen Wheeler, Mark Whitehead, Max Whiteley, Andrew Whitwham, Claudia Wierzbicki, Nicholas J. Willford, Lesley-Anne Williams, Rebecca Williams, Cheryl Williams, Chris Williams, Charlotte A. Williams, Rachel J. Williams, Thomas Williams, Catryn Williams, Kathleen A. Williamson, Eleri Wilson-Davies, Eric Witele, Karen T. Withell, Adam A. Witney, Paige Wolverson, Nick Wong, Trudy Workman, Victoria Wright, Derek W. Wright, Tim Wyatt, Sarah Wyllie, Li Xu-McCrae, Mehmet Yavus, Geraldine Yaze, Corin A. Yeats, Gonzalo Yebra, Wen C. Yew, Gregory R. Young, Jamie Young, Alex E. Zarebski, Peijun Zhang, J. Kenneth Baillie, Malcolm G. Semple, Peter J.M. Openshaw, Gail Carson, Beatrice Alex, Petros Andrikopoulos, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Kanta Chechi, Graham S. Cooke, Annemarie B. Docherty, Gonçalo dos Santos Correia, Marc-Emmanuel Dumas, Jake Dunning, Tom Fletcher, Christopher A. Green, William Greenhalf, Julian L. Griffin, Rishi K. Gupta, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Matthew R. Lewis, Sonia Liggi, Wei Shen Lim, Lynn Maslen, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Michael Olanipekun, Anthonia Osagie, Massimo Palmarini, Carlo Palmieri, William A. Paxton, Georgios Pollakis, Nicholas Price, Clark D. Russell, Vanessa Sancho-Shimizu, Caroline J. Sands, Janet T. Scott, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Olivia V. Swann, Zoltan Takats, Panteleimon Takis, Richard S. Tedder, A.A. Roger Thompson, Ryan S. Thwaites, Maria Zambon, Hayley Hardwick, Chloe Donohue, Fiona Griffiths, Wilna Oosthuyzen, Cara Donegan, Rebecca G. Spencer, Jo Dalton, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Daniel Plotkin, James Lee, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W.A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W.S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Lisa Flaherty, Nicole Maziere, Emily Cass, Alejandra Doce Carracedo, Nicola Carlucci, Anthony Holmes, Hannah Massey, Lee Murphy, Nicola Wrobel, Sarah McCafferty, Kirstie Morrice, Alan MacLean, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Erin L. Aldera, Ana Alegria, Sam Allen, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, Sneha Basude, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Colin Berry, Nicola Best, Pieter Bothma, David Chadwick, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Phil Donnison, Sam Douthwaite, Andrew Drummond, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Mark Lyttle, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Lillian Norris, Matthew K. O'Shea, Igor Otahal, Marlies Ostermann, Mark Pais, Selva Panchatsharam, Danai Papakonstantinou, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Tim Planche, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Bobby Ruge, Brendan Ryan, Taranprit Saluja, Matthias L. Schmid, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Nick Vallotton, Rama Vancheeswaran, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Padmasayee Papineni, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wootton, Andrew Workman, Bryan Yates, and Peter Young
Subjects: Phylogenetics, Molecular biology, Immunology, Immune response, Virology, Science
Abstract: Summary: We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.
Published: 2021
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20. Impact of Female Sex on Lipid Lowering, Clinical Outcomes, and Adverse Effects in Atorvastatin Trials

Author: Hsue, Priscilla Y, Bittner, Vera A, Betteridge, John, Fayyad, Rana, Laskey, Rachel, Wenger, Nanette K, and Waters, David D
Subjects: Biomedical and Clinical Sciences, Clinical Sciences, Cardiovascular, Heart Disease, Stroke, Heart Disease - Coronary Heart Disease, Atherosclerosis, Prevention, Clinical Trials and Supportive Activities, Clinical Research, Evaluation of treatments and therapeutic interventions, 6.1 Pharmaceuticals, Atorvastatin, Coronary Artery Disease, Diabetes Mellitus, Type 2, Double-Blind Method, Female, Follow-Up Studies, Global Health, Heptanoic Acids, Humans, Incidence, Lipids, Male, Middle Aged, Prospective Studies, Pyrroles, Risk Factors, Sex Factors, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology
Abstract: The aim of this study was to evaluate the effect of atorvastatin on lipid lowering, cardiovascular (CV) events, and adverse events in women compared with men in 6 clinical trials. In the Incremental Decrease in End Points Through Aggressive Lipid Lowering (IDEAL) trial (atorvastatin 80 mg vs simvastatin 20 to 40 mg), the Treating to New Targets (TNT) trial (atorvastatin 80 vs 10 mg), the Stroke Prevention by Aggressive Reduction in Cholesterol Levels (SPARCL) trial (atorvastatin 80 mg vs placebo), and the Collaborative Atorvastatin Diabetes Study (CARDS), the Anglo-Scandinavian Cardiac Outcomes Trial (ASCOT), and the Atorvastatin Study for Prevention of Coronary Heart Disease Endpoints in Non-Insulin-Dependent Diabetes Mellitus (ASPEN) (atorvastatin 10 mg vs placebo), lipid changes on treatment were compared between genders with studies grouped by dose. The association of on-study low-density lipoprotein (LDL) cholesterol and CV events by gender was evaluated in the combined studies and the impact of gender on adverse events in each study separately. Major CV events occurred in 3,083 of 30,000 men (10.3%) and 823 of 9,173 women (9.0%). Changes in lipids were similar in women and men. Major CV events were associated with gender-specific quintiles of on-treatment LDL cholesterol for women and men. In women, LDL cholesterol was a significant predictor of stroke, but not in men. Discontinuation rates due to adverse events were higher in women in 4 of 6 trials, but in only 1 trial was a significant treatment-gender interaction seen. Myalgia rates were slightly higher in women in both statin and placebo groups. In conclusion, the response of women to atorvastatin was similar to that of men, with slightly more discontinuations due to adverse events. Higher on-treatment LDL cholesterol was significantly associated with more CV events in both genders, but the association was stronger for stroke in women and for coronary heart disease death in men.
Published: 2015

21. The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens [version 1; peer review: 2 approved]

Author: Eerik Aunin, Ulrike Böhme, Damer Blake, Alexander Dove, Michelle Smith, Craig Corton, Karen Oliver, Emma Betteridge, Michael A. Quail, Shane A. McCarthy, Jonathan Wood, Alan Tracey, James Torrance, Ying Sims, Kerstin Howe, Richard Challis, Matthew Berriman, and Adam Reid
Subjects: Medicine, Science
Abstract: We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.
Published: 2021
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22. Using de novo assembly to identify structural variation of eight complex immune system gene regions.

Author: Jia-Yuan Zhang, Hannah Roberts, David S C Flores, Antony J Cutler, Andrew C Brown, Justin P Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C Knight, John A Todd, and Gavin Band
Subjects: Biology (General), QH301-705.5
Abstract: Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable structural polymorphism of the underlying genes. Characterizing this variation is challenging due to the complexity of these loci, which contain extensive regions of paralogy, segmental duplication and high copy-number repeats, but recent progress in long-read sequencing and optical mapping techniques suggests this problem may now be tractable. Here we assess this by using long-read sequencing platforms from PacBio and Oxford Nanopore, supplemented with short-read sequencing and Bionano optical mapping, to sequence DNA extracted from CD14+ monocytes and peripheral blood mononuclear cells from a single European individual identified as HV31. We use this data to build a de novo assembly of eight genomic regions encoding four key components of the immune system, namely the human leukocyte antigen, immunoglobulins, T cell receptors, and killer-cell immunoglobulin-like receptors. Validation of our assembly using k-mer based and alignment approaches suggests that it has high accuracy, with estimated base-level error rates below 1 in 10 kb, although we identify a small number of remaining structural errors. We use the assembly to identify heterozygous and homozygous structural variation in comparison to GRCh38. Despite analyzing only a single individual, we find multiple large structural variants affecting core genes at all three immunoglobulin regions and at two of the three T cell receptor regions. Several of these variants are not accurately callable using current algorithms, implying that further methodological improvements are needed. Our results demonstrate that assessing haplotype variation in these regions is possible given sufficiently accurate long-read and associated data. Continued reductions in the cost of these technologies will enable application of these methods to larger samples and provide a broader catalogue of germline structural variation at these loci, an important step toward making these regions accessible to large-scale genetic association studies.
Published: 2021
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23. Blood Pressure Management Goals in Critically Ill Aneurysmal Subarachnoid Hemorrhage Patients in Australia and New Zealand

Author: Betteridge, Toby, Finnis, Mark, Cohen, Jeremy, Delaney, Anthony, Young, Paul, Udy, Andrew, Anstey, James, Anstey, Matthew, Barge, Deborah, Bellomo, Rinaldo, Bhardwa, Vishnu, Board, Jasmin, Brinkerhoff, Gail, Cohen, Jeremy, Cooper, David J., Delaney, Anthony, Finnis, Mark, Fitzgerald, Emily, Flower, Oliver, Healey, Paul M., Hunt, Anna, Lawrence, Cassie, Mehrtens, Jan, Newby, Lynette, Pearson, David, Raith, Eamon P., Robertson, Yvonne, Schweikert, Sacha, Starr, Therese, Tallott, Mandy, Udy, Andrew A., van der Poll, Andrew, and Young, Paul
Published: 2024
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24. Effects of statin therapy on diagnoses of new-onset diabetes and worsening glycaemia in large-scale randomised blinded statin trials: an individual participant data meta-analysis

Author: Reith, Christina, Preiss, David, Blackwell, Lisa, Emberson, Jonathan, Spata, Enti, Davies, Kelly, Halls, Heather, Harper, Charlie, Holland, Lisa, Wilson, Kate, Roddick, Alistair J, Cannon, Christopher P, Clarke, Robert, Colhoun, Helen M, Durrington, Paul N, Goto, Shinya, Hitman, Graham A, Hovingh, G Kees, Jukema, J Wouter, Koenig, Wolfgang, Marschner, Ian, Mihaylova, Borislava, Newman, Connie, Probsfield, Jeffrey L, Ridker, Paul M, Sabatine, Marc S, Sattar, Naveed, Schwartz, Gregory G, Tavazzi, Luigi, Tonkin, Andrew, Trompet, Stella, White, Harvey, Yusuf, Salim, Armitage, Jane, Keech, Anthony, Simes, John, Collins, Rory, Baigent, Colin, Barnes, Elizabeth, Fulcher, Jordan, Herrington, William G, Kirby, Adrienne, O'Connell, Rachel, Amarenco, Pierre, Arashi, Hiroyuki, Barter, Philip, Betteridge, D John, Blazing, Michael, Blauw, Gerard J, Bosch, Jackie, Bowman, Louise, Braunwald, Eugene, Bulbulia, Richard, Byington, Robert, Clearfield, Michael, Cobbe, Stuart, Dahlöf, Björn, Davis, Barry, de Lemos, James, Downs, John R, Fellström, Bengt, Flather, Marcus, Ford, Ian, Franzosi, Maria Grazia, Fuller, John, Furberg, Curt, Glynn, Robert, Goldbourt, Uri, Gordon, David, Gotto, Antonio, Jr, Grimm, Richard, Gupta, Ajay, Hawkins, C Morton, Haynes, Richard, Holdaas, Hallvard, Hopewell, Jemma, Jardine, Alan, Kastelein, John JP, Kean, Sharon, Kearney, Patricia, Kitas, George, Kjekshus, John, Knatterud, Genell, Knopp, Robert H, Koren, Michael, Krane, Vera, Landray, Martin, LaRosa, John, Latini, Roberto, Lonn, Eva, Lucci, Donata, MacFadyen, Jean, Macfarlane, Peter, MacMahon, Stephen, Maggioni, Aldo, Marchioli, Roberto, Moyé, Lemuel, Murphy, Sabina, Neil, Andrew, Nicolis, Enrico B, Packard, Chris, Parish, Sarah, Pedersen, Terje R, Peto, Richard, Pfeffer, Marc, Poulter, Neil, Pressel, Sara, Probstfield, Jeffrey, Rahman, Mahboob, Robertson, Michele, Sacks, Frank, Schmieder, Roland, Serruys, Patrick, Sever, Peter, Shaw, John, Shepherd, James, Simpson, Lara, Sleight, Peter, Smeeth, Liam, Tobert, Jonathan, Tognoni, Gianni, Varigos, John, Wanner, Christoph, Wedel, Hans, Weis, Stephen, Welch, K Michael, Wikstrand, John, Wilhelmsen, Lars, Wiviott, Stephen, Yamaguchi, Junichi, Young, Robin, and Zannad, Faiez
Abstract: Previous meta-analyses of summary data from randomised controlled trials have shown that statin therapy increases the risk of diabetes, but less is known about the size or timing of this effect, or who is at greatest risk. We aimed to address these gaps in knowledge through analysis of individual participant data from large, long-term, randomised, double-blind trials of statin therapy.
Published: 2024
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25. The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Jenny C. Dunn, Michael A. Quail, James Torrance, Ying Sims, Marcela Uliano-Silva, Richard Challis, Antony J. Morris, Keith C. Hamer, Sarah Pelan, William Chow, Philip V. Grice, Mark Blaxter, Daniel Mead, Craig Corton, Michelle Smith, Jason Skelton, Karen Oliver, Emma Betteridge, Shane A. McCarthy, Jonathan Threlfall, Jale Dolucan, and Kerstin Howe
Subjects: Streptopelia turtur, European turtle dove, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.
Published: 2021
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26. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author: Bo Meng, Steven A. Kemp, Guido Papa, Rawlings Datir, Isabella A.T.M. Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed Mohamed, Giulia Gallo, Nazia Thakur, Dami A. Collier, Petra Mlcochova, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J. Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra K. Gupta, Samuel C. Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Rich Livett, Samuel Moses, Roberto Amato, Sam Nicholls, Matthew Bull, Darren L. Smith, Jeff Barrett, David M. Aanensen, Martin D. Curran, Surendra Parmar, Dinesh Aggarwal, James G. Shepherd, Matthew D. Parker, Sharon Glaysher, Matthew Bashton, Anthony P. Underwood, Nicole Pacchiarini, Katie F. Loveson, Kate E. Templeton, Cordelia F. Langford, John Sillitoe, Thushan I. de Silva, Dennis Wang, Dominic Kwiatkowski, Andrew Rambaut, Justin O’Grady, Simon Cottrell, Matthew T.G. Holden, Emma C. Thomson, Husam Osman, Monique Andersson, Anoop J. Chauhan, Mohammed O. Hassan-Ibrahim, Mara Lawniczak, Alex Alderton, Meera Chand, Chrystala Constantinidou, Meera Unnikrishnan, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Inigo Martincorena, Erik M. Volz, Andrew J. Page, Oliver G. Pybus, Andrew R. Bassett, Cristina V. Ariani, Michael H. Spencer Chapman, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yusri Taha, Martin P. McHugh, Rebecca Dewar, Aminu S. Jahun, Claire McMurray, Sarojini Pandey, James P. McKenna, Andrew Nelson, Gregory R. Young, Clare M. McCann, Scott Elliott, Hannah Lowe, Ben Temperton, Sunando Roy, Anna Price, Sara Rey, Matthew Wyles, Stefan Rooke, Sharif Shaaban, Mariateresa de Cesare, Laura Letchford, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Myra Hosmillo, Áine O’Toole, Andrew R. Hesketh, Richard Stark, Louis du Plessis, Chris Ruis, Helen Adams, Yann Bourgeois, Stephen L. Michell, Dimitris Gramatopoulos, Jonathan Edgeworth, Judith Breuer, John A. Todd, Christophe Fraser, David Buck, Michaela John, Gemma L. Kay, Steve Palmer, Sharon J. Peacock, David Heyburn, Danni Weldon, Esther Robinson, Alan McNally, Peter Muir, Ian B. Vipond, John Boyes, Venkat Sivaprakasam, Tranprit Salluja, Samir Dervisevic, Emma J. Meader, Naomi R. Park, Karen Oliver, Aaron R. Jeffries, Sascha Ott, Ana da Silva Filipe, David A. Simpson, Chris Williams, Jane A.H. Masoli, Bridget A. Knight, Christopher R. Jones, Cherian Koshy, Amy Ash, Anna Casey, Andrew Bosworth, Liz Ratcliffe, Li Xu-McCrae, Hannah M. Pymont, Stephanie Hutchings, Lisa Berry, Katie Jones, Fenella Halstead, Thomas Davis, Christopher Holmes, Miren Iturriza-Gomara, Anita O. Lucaci, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Kathryn Ann Harris, Julianne Rose Brown, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Steven Liggett, Clive Graham, Emma Swindells, Jennifer Collins, Gary Eltringham, Sharon Campbell, Patrick C. McClure, Gemma Clark, Tim J. Sloan, Carl Jones, Jessica Lynch, Ben Warne, Steven Leonard, Jillian Durham, Thomas Williams, Sam T. Haldenby, Nathaniel Storey, Nabil-Fareed Alikhan, Nadine Holmes, Christopher Moore, Matthew Carlile, Malorie Perry, Noel Craine, Ronan A. Lyons, Angela H. Beckett, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, Robert Davies, Beth Blane, Sophia T. Girgis, Mathew A. Beale, Katherine L. Bellis, Matthew J. Dorman, Eleanor Drury, Leanne Kane, Sally Kay, Samantha McGuigan, Rachel Nelson, Liam Prestwood, Shavanthi Rajatileka, Rahul Batra, Rachel J. Williams, Mark Kristiansen, Angie Green, Anita Justice, Adhyana I.K. Mahanama, Buddhini Samaraweera, Nazreen F. Hadjirin, Joshua Quick, Radoslaw Poplawski, Leanne M. Kermack, Nicola Reynolds, Grant Hall, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Robin J. Moll, Alicia Thornton, Richard Myers, Joanne Stockton, Charlotte A. Williams, Wen C. Yew, Alexander J. Trotter, Amy Trebes, George MacIntyre-Cockett, Alec Birchley, Alexander Adams, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Ember Hilvers, Hannah Jones, Hibo Asad, Jason Coombes, Johnathan M. Evans, Laia Fina, Lauren Gilbert, Lee Graham, Michelle Cronin, Sara Kumziene-Summerhayes, Sarah Taylor, Sophie Jones, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Igor Starinskij, Chris Jackson, Marina Gourtovaia, Gerry Tonkin-Hill, Kevin Lewis, Jaime M. Tovar-Corona, Keith James, Laura Baxter, Mohammad T. Alam, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Olivia Boyd, Lily Geidelberg, Alex E. Zarebski, Jayna Raghwani, Moritz U.G. Kraemer, Joel Southgate, Benjamin B. Lindsey, Timothy M. Freeman, Jon-Paul Keatley, Joshua B. Singer, Leonardo de Oliveira Martins, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, John Danesh, Wendy Hogsden, Sahar Eldirdiri, Anita Kenyon, Jenifer Mason, Trevor I. Robinson, Alison Holmes, James Price, John A. Hartley, Tanya Curran, Alison E. Mather, Giri Shankar, Rachel Jones, Robin Howe, Sian Morgan, Elizabeth Wastenge, Michael R. Chapman, Siddharth Mookerjee, Rachael Stanley, Wendy Smith, Timothy Peto, David Eyre, Derrick Crook, Gabrielle Vernet, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Declan T. Bradley, Tim Wyatt, Charlotte Beaver, Luke Foulser, Sophie Palmer, Carol M. Churcher, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus, Frances Bolt, Francesc Coll, Lizzie Meadows, Stephen W. Attwood, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Garry P. Scarlett, Sarah Jeremiah, Nikki Smith, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Michelle Wantoch, Dorota Jamrozy, Stephanie Lo, Minal Patel, Verity Hill, Claire M. Bewshea, Sian Ellard, Cressida Auckland, Ian Harrison, Chloe Bishop, Vicki Chalker, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Richard Hopes, Patawee Asamaphan, Marc O. Niebel, Rory N. Gunson, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Holli Carden, Nicholas W. Machin, Kathryn A. Jackson, Shazaad S.Y. Ahmad, Ryan P. George, Lance Turtle, Elaine O’Toole, Joanne Watts, Cassie Breen, Angela Cowell, Adela Alcolea-Medina, Themoula Charalampous, Amita Patel, Lisa J. Levett, Judith Heaney, Aileen Rowan, Graham P. Taylor, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adam P. Westhorpe, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani, Leah Ensell, Wendy Chatterton, Monika Pusok, Ashok Dadrah, Amanda Symmonds, Graciela Sluga, Zoltan Molnar, Paul Baker, Stephen Bonner, Sarah Essex, Edward Barton, Debra Padgett, Garren Scott, Jane Greenaway, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Veena Raviprakash, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Jonathan Moore, Susanne Stonehouse, Louise Smith, Rose K. Davidson, Luke Bedford, Lindsay Coupland, Victoria Wright, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Nichola Duckworth, Sarah Walsh, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Stephen Kidd, Rebecca Williams, Laura Gifford, Kelly Bicknell, Sarah Wyllie, Allyson Lloyd, Robert Impey, Cassandra S. Malone, Benjamin J. Cogger, Nick Levene, Lynn Monaghan, Alexander J. Keeley, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Emma Betteridge, Ben W. Farr, Scott Goodwin, Michael A. Quail, Carol Scott, Lesley Shirley, Scott A.J. Thurston, Diana Rajan, Iraad F. Bronner, Louise Aigrain, Nicholas M. Redshaw, Stefanie V. Lensing, Shane McCarthy, Alex Makunin, Carlos E. Balcazar, Michael D. Gallagher, Kathleen A. Williamson, Thomas D. Stanton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Hassan Hartman, Nikos Manesis, Vineet Patel, Juan Ledesma, Katherine A. Twohig, Elias Allara, Clare Pearson, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Paul E. Brown, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Katherine L. Smollett, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Seema Nickbakhsh, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J. Webster, Chloe L. Fisher, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Gaia Nebbia, Flavia Flaviani, Alberto C. Cerda, Tammy V. Merrill, Rebekah E. Wilson, Marius Cotic, Nadua Bayzid, Thomas Thompson, Erwan Acheson, Steven Rushton, Sarah O’Brien, David J. Baker, Steven Rudder, Alp Aydin, Fei Sang, Johnny Debebe, Sarah Francois, Tetyana I. Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, Angela Marchbank, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Mari Morgan, Robert Beer, Safiah Afifi, Trudy Workman, William Fuller, Catherine Bresner, Adrienn Angyal, Luke R. Green, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Max Whiteley, James Bonfield, Christoph Puethe, Andrew Whitwham, Jennifier Liddle, Will Rowe, Igor Siveroni, Thanh Le-Viet, Amy Gaskin, Rob Johnson, Irina Abnizova, Mozam Ali, Laura Allen, Ralph Anderson, Cristina Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey Barrett, Andrew Bassett, Kristina Battleday, James Beal, Mathew Beale, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matt Berriman, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad Bronner, Tanya Brooklyn, Sarah Kay Buddenborg, Robert Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Carvalho Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, David Dodd, Sunil Dogga, Matthew Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Monika Dudek, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Pete Ellis, Ben Farr, Michael Fenton, Marcella Ferrero, Neil Flack, Howerd Fordham, Grace Forsythe, Matt Francis, Audrey Fraser, Adam Freeman, Anastasia Galvin, Maria Garcia-Casado, Alex Gedny, Sophia Girgis, James Glover, Oliver Gould, Andy Gray, Emma Gray, Coline Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul Heath, Anastasia Hernandez-Koutoucheva, Rhiannon Hobbs, Dave Holland, Sarah Holmes, Gary Hornett, Nicholas Hough, Liz Huckle, Lena Hughes-Hallet, Adam Hunter, Stephen Inglis, Sameena Iqbal, Adam Jackson, David Jackson, Carlos Jimenez Verdejo, Matthew Jones, Kalyan Kallepally, Keely Kay, Jon Keatley, Alan Keith, Alison King, Lucy Kitchin, Matt Kleanthous, Martina Klimekova, Petra Korlevic, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Stefanie Lensing, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rhona Long, Jamie Lovell, Jon Lovell, James Mack, Mark Maddison, Aleksei Makunin, Irfan Mamun, Jenny Mansfield, Neil Marriott, Matt Martin, Matthew Mayho, Jo McClintock, Sandra McHugh, Liz MapcMinn, Carl Meadows, Emily Mobley, Robin Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume G. Noell, Sarah O’Meara, Valeriu Ohan, Charles Olney, Doug Ormond, Agnes Oszlanczi, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Maggie Payne, Sharon Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Michael Quail, Richard Rance, Suzannah Rawlings, Nicholas Redshaw, Joe Reynolds, Mark Reynolds, Simon Rice, Matt Richardson, Connor Roberts, Katrina Robinson, Melanie Robinson, David Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark Rose, Luke Rudd, Ramin Sadri, Nicholas Salmon, David Saul, Frank Schwach, Phil Seekings, Alison Simms, Matt Sinnott, Shanthi Sivadasan, Bart Siwek, Dale Sizer, Kenneth Skeldon, Jason Skelton, Joanna Slater-Tunstill, Lisa Sloper, Nathalie Smerdon, Chris Smith, Christen Smith, James Smith, Katie Smith, Michelle Smith, Sean Smith, Tina Smith, Leighton Sneade, Carmen Diaz Soria, Catarina Sousa, Emily Souster, Andrew Sparkes, Michael Spencer-Chapman, Janet Squares, Robert Stanley, Claire Steed, Tim Stickland, Ian Still, Mike Stratton, Michelle Strickland, Allen Swann, Agnieszka Swiatkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark Thompson, Mark Thomson, Nicholas Thomson, Scott Thurston, Dee Toombs, Benjamin Topping, Jaime Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanova, Philip Jansen Van, Valerie Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary Ward, Charlie Weatherhogg, Niki Webb, Alan Wells, Eloise Wells, Luke Westwood, Theo Whipp, Thomas Whiteley, Georgia Whitton, Sara Widaa, Mia Williams, Mark Wilson, and Sean Wright
Subjects: SARS-CoV-2, COVID-19, antibody escape, neutralizing antibodies, infectivity, spike mutation, Biology (General), QH301-705.5
Abstract: Summary: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.
Published: 2021
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27. Health systems strengthening to arrest the global disability burden: empirical development of prioritised components for a global strategy for improving musculoskeletal health

Author: Dieter Wiek, Richard Brown, Andrew M Briggs, Saurab Sharma, James Waddell, Anthony D Woolf, Lyn March, Helen Slater, Enrique R Soriano, Kristina E Åkesson, Fiona M Blyth, Ali Mobasheri, Ben Horgan, Helen E Foster, Neil Betteridge, Joanne E Jordan, Anil Jain, Francesca Gimigliano, Nuzhat Ali, Margareta C Nordin, Shuichi Matsuda, Carmen Huckel Schneider, Sarika Parambath, James J Young, Deborah Kopansky-Giles, Swatee Mishrra, Joletta Belton, Demelash Debere, Karsten E Dreinhöfer, Laura Finucane, Scott Haldeman, Syed A Haq, Manjul Joshipura, Asgar A Kalla, Jakob Lothe, Lillian Mwaniki, Marilyn Pattison, Felipe J J Reis, and Heather Tick
Subjects: Medicine (General), R5-920, Infectious and parasitic diseases, RC109-216
Abstract: Introduction Despite the profound burden of disease, a strategic global response to optimise musculoskeletal (MSK) health and guide national-level health systems strengthening priorities remains absent. Auspiced by the Global Alliance for Musculoskeletal Health (G-MUSC), we aimed to empirically derive requisite priorities and components of a strategic response to guide global and national-level action on MSK health.Methods Design: mixed-methods, three-phase design.Phase 1: qualitative study with international key informants (KIs), including patient representatives and people with lived experience. KIs characterised the contemporary landscape for MSK health and priorities for a global strategic response.Phase 2: scoping review of national health policies to identify contemporary MSK policy trends and foci.Phase 3: informed by phases 1–2, was a global eDelphi where multisectoral panellists rated and iterated a framework of priorities and detailed components/actions.Results Phase 1: 31 KIs representing 25 organisations were sampled from 20 countries (40% low and middle income (LMIC)). Inductively derived themes were used to construct a logic model to underpin latter phases, consisting of five guiding principles, eight strategic priority areas and seven accelerators for action.Phase 2: of the 165 documents identified, 41 (24.8%) from 22 countries (88% high-income countries) and 2 regions met the inclusion criteria. Eight overarching policy themes, supported by 47 subthemes, were derived, aligning closely with the logic model.Phase 3: 674 panellists from 72 countries (46% LMICs) participated in round 1 and 439 (65%) in round 2 of the eDelphi. Fifty-nine components were retained with 10 (17%) identified as essential for health systems. 97.6% and 94.8% agreed or strongly agreed the framework was valuable and credible, respectively, for health systems strengthening.Conclusion An empirically derived framework, co-designed and strongly supported by multisectoral stakeholders, can now be used as a blueprint for global and country-level responses to improve MSK health and prioritise system strengthening initiatives.
Published: 2021
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28. The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Michael A. Quail, James Torrance, Ying Sims, Richard Challis, Sarah Pelan, Mark Blaxter, Daniel Mead, Marcela Uliano Da Silva, Angus I. Carpenter, Craig Corton, Michelle Smith, Francesca Floriana Tricomi, Jason Skelton, Karen Oliver, Emma Betteridge, Jale Doulcan, Shane A. McCarthy, Jonathan Wood, Jonathan Threlfall, and Kerstin Howe
Subjects: Arvicola amphibius, European water vole, genome sequence, chromosomal, eng, Medicine, Science
Abstract: We present a genome assembly from an individual male Arvicola amphibius (the European water vole; Chordata; Mammalia; Rodentia; Cricetidae). The genome sequence is 2.30 gigabases in span. The majority of the assembly is scaffolded into 18 chromosomal pseudomolecules, including the X sex chromosome. Gene annotation of this assembly on Ensembl has identified 21,394 protein coding genes.
Published: 2021
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29. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Author: Mark S Graham, PhD, Carole H Sudre, PhD, Anna May, MA, Michela Antonelli, PhD, Benjamin Murray, MSc, Thomas Varsavsky, MSc, Kerstin Kläser, MSc, Liane S Canas, PhD, Erika Molteni, PhD, Marc Modat, PhD, David A Drew, PhD, Long H Nguyen, MD, Lorenzo Polidori, MSc, Somesh Selvachandran, MSc, Christina Hu, MA, Joan Capdevila, PhD, Alexander Hammers, ProfPhD, Andrew T Chan, ProfMD, Jonathan Wolf, MA, Tim D Spector, ProfPhD, Claire J Steves, PhD, Sebastien Ourselin, ProfPhD, Cherian Koshy, Amy Ash, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Jessica Lynch, Stephen Kidd, Derek J Fairley, Tanya Curran, James P McKenna, Helen Adams, Christophe Fraser, Tanya Golubchik, David Bonsall, Mohammed O Hassan-Ibrahim, Cassandra S Malone, Benjamin J Cogger, Michelle Wantoch, Nicola Reynolds, Ben Warne, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Michaela John, Robert Beer, Safiah Afifi, Sian Morgan, Angela Marchbank, Anna Price, Christine Kitchen, Huw Gulliver, Ian Merrick, Joel Southgate, Martyn Guest, Robert Munn, Trudy Workman, Thomas R Connor, William Fuller, Catherine Bresner, Luke B Snell, Amita Patel, Themoula Charalampous, Gaia Nebbia, Rahul Batra, Jonathan Edgeworth, Samuel C Robson, Angela H Beckett, David M Aanensen, Anthony P Underwood, Corin A Yeats, Khalil Abudahab, Ben EW Taylor, Mirko Menegazzo, Gemma Clark, Wendy Smith, Manjinder Khakh, Vicki M Fleming, Michelle M Lister, Hannah C Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Carl Jones, Christopher Holmes, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Veena Raviprakash, Sharon Campbell, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Matthew W Loose, Nadine Holmes, Christopher Moore, Matthew Carlile, Victoria Wright, Fei Sang, Johnny Debebe, Francesc Coll, Adrian W Signell, Gilberto Betancor, Harry D Wilson, Sahar Eldirdiri, Anita Kenyon, Thomas Davis, Oliver G Pybus, Louis du Plessis, Alex E Zarebski, Jayna Raghwani, Moritz UG Kraemer, Sarah Francois, Stephen W Attwood, Tetyana I Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, M. Estee Torok, William L Hamilton, Ian G Goodfellow, Grant Hall, Aminu S Jahun, Yasmin Chaudhry, Myra Hosmillo, Malte L Pinckert, Iliana Georgana, Samuel Moses, Hannah Lowe, Luke Bedford, Jonathan Moore, Susanne Stonehouse, Chloe L Fisher, Ali R Awan, John BoYes, Judith Breuer, Kathryn Ann Harris, Julianne Rose Brown, Divya Shah, Laura Atkinson, Jack CD Lee, Nathaniel Storey, Flavia Flaviani, Adela Alcolea-Medina, Rebecca Williams, Gabrielle Vernet, Michael R Chapman, Lisa J Levett, Judith Heaney, Wendy Chatterton, Monika Pusok, Li Xu-McCrae, Darren L Smith, Matthew Bashton, Gregory R Young, Alison Holmes, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Frances Bolt, James Price, Siddharth Mookerjee, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Igor Siveroni, Rob Johnson, Olivia Boyd, Lily Geidelberg, Erik M Volz, Aileen Rowan, Graham P Taylor, Katherine L Smollett, Nicholas J Loman, Joshua Quick, Claire McMurray, Joanne Stockton, Sam Nicholls, Will Rowe, Radoslaw Poplawski, Alan McNally, Rocio T Martinez Nunez, Jenifer Mason, Trevor I Robinson, Elaine O'Toole, Joanne Watts, Cassie Breen, Angela Cowell, Graciela Sluga, Nicholas W Machin, Shazaad S Y Ahmad, Ryan P George, Fenella Halstead, Venkat Sivaprakasam, Wendy Hogsden, Chris J Illingworth, Chris Jackson, Emma C Thomson, James G Shepherd, Patawee Asamaphan, Marc O Niebel, Kathy K Li, Rajiv N Shah, Natasha G Jesudason, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Igor Starinskij, Ana da Silva Filipe, David L Robertson, Richard J Orton, Joseph Hughes, Sreenu Vattipally, Joshua B Singer, Seema Nickbakhsh, Antony D Hale, Louissa R Macfarlane-Smith, Katherine L Harper, Holli Carden, Yusri Taha, Brendan AI Payne, Shirelle Burton-Fanning, Sheila Waugh, Jennifer Collins, Gary Eltringham, Steven Rushton, Sarah O'Brien, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Kate E Templeton, Martin P McHugh, Rebecca Dewar, Elizabeth Wastenge, Samir Dervisevic, Rachael Stanley, Emma J Meader, Lindsay Coupland, Louise Smith, Clive Graham, Edward Barton, Debra Padgett, Garren Scott, Emma Swindells, Jane Greenaway, Andrew Nelson, Clare M McCann, Wen C Yew, Monique Andersson, Timothy Peto, Anita Justice, David Eyre, Derrick Crook, Tim J Sloan, Nichola Duckworth, Sarah Walsh, Anoop J Chauhan, Sharon Glaysher, Kelly Bicknell, Sarah Wyllie, Scott Elliott, Allyson Lloyd, Robert Impey, Nick Levene, Lynn Monaghan, Declan T Bradley, Tim Wyatt, Elias Allara, Clare Pearson, Husam Osman, Andrew Bosworth, Esther Robinson, Peter Muir, Ian B Vipond, Richard Hopes, Hannah M Pymont, Stephanie Hutchings, Martin D Curran, Surendra Parmar, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Meera Chand, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Alicia Thornton, Richard Myers, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Ian Harrison, Hassan Hartman, Nikos Manesis, Vineet Patel, Chloe Bishop, Vicki Chalker, Juan Ledesma, Katherine A Twohig, Matthew T.G. Holden, Sharif Shaaban, Alec Birchley, Alexander Adams, Alisha Davies, Amy Gaskin, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Catherine Moore, Chris Williams, David Heyburn, Elen De Lacy, Ember Hilvers, Fatima Downing, Giri Shankar, Hannah Jones, Hibo Asad, Jason Coombes, Joanne Watkins, Johnathan M Evans, Laia Fina, Laura Gifford, Lauren Gilbert, Lee Graham, Malorie Perry, Mari Morgan, Matthew Bull, Michelle Cronin, Nicole Pacchiarini, Noel Craine, Rachel Jones, Robin Howe, Sally Corden, Sara Rey, Sara Kumziene-SummerhaYes, Sarah Taylor, Simon Cottrell, Sophie Jones, Sue Edwards, Justin O'Grady, Andrew J Page, Alison E Mather, David J Baker, Steven Rudder, Alp Aydin, Gemma L Kay, Alexander J Trotter, Nabil-Fareed Alikhan, Leonardo de Oliveira Martins, Thanh Le-Viet, Lizzie Meadows, Anna Casey, Liz Ratcliffe, David A Simpson, Zoltan Molnar, Thomas Thompson, Erwan Acheson, Jane AH Masoli, Bridget A Knight, Sian Ellard, Cressida Auckland, Christopher R Jones, Tabitha W Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Ashok Dadrah, Amanda Symmonds, Tranprit Saluja, Yann Bourgeois, Garry P Scarlett, Katie F Loveson, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, David G Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Steven Liggett, Paul Baker, Stephen Bonner, Sarah Essex, Ronan A Lyons, Kordo Saeed, Adhyana I.K Mahanama, Buddhini Samaraweera, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Rachel J Williams, Mark Kristiansen, Sunando Roy, Charlotte A Williams, Marius Cotic, Nadua Bayzid, Adam P Westhorpe, John A Hartley, Riaz Jannoo, Helen L Lowe, Angeliki Karamani, Leah Ensell, Jacqui A Prieto, Sarah Jeremiah, Dimitris Grammatopoulos, Sarojini Pandey, Lisa Berry, Katie Jones, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Colin P Smith, Giselda Bucca, Andrew R Hesketh, Beth Blane, Sophia T Girgis, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K Gill, Joana Dias, Ellen E Higginson, Mailis Maes, Jamie Young, Leanne M Kermack, Ravi Kumar Gupta, Catherine Ludden, Sharon J Peacock, Sophie Palmer, Carol M Churcher, Nazreen F Hadjirin, Alessandro M Carabelli, Ellena Brooks, Kim S Smith, Katerina Galai, Georgina M McManus, Chris Ruis, Rose K Davidson, Andrew Rambaut, Thomas Williams, Carlos E Balcazar, Michael D Gallagher, Áine O'Toole, Stefan Rooke, Verity Hill, Kathleen A Williamson, Thomas D Stanton, Stephen L Michell, Claire M Bewshea, Ben Temperton, Michelle L Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W Harrison, Christine M Sambles, David J Studholme, Aaron R Jeffries, Alistair C Darby, Julian A Hiscox, Steve Paterson, Miren Iturriza-Gomara, Kathryn A Jackson, Anita O Lucaci, Edith E Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Lance Turtle, Sam T Haldenby, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J Webster, Thushan I de Silva, Nikki Smith, Adrienn Angyal, Benjamin B Lindsey, Danielle C Groves, Luke R Green, Dennis Wang, Timothy M Freeman, Matthew D Parker, Alexander J Keeley, Paul J Parsons, Rachel M Tucker, Rebecca Brown, Matthew Wyles, Max Whiteley, Peijun Zhang, Marta Gallis, Stavroula F Louka, Chrystala Constantinidou, Meera Unnikrishnan, Sascha Ott, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Richard Stark, Laura Baxter, Mohammad T. Alam, Paul E Brown, Dinesh Aggarwal, Alberto C Cerda, Tammy V Merrill, Rebekah E Wilson, Patrick C McClure, Joseph G Chappell, Theocharis Tsoleridis, Jonathan Ball, David Buck, John A Todd, Angie Green, Amy Trebes, George MacIntyre-Cockett, Mariateresa de Cesare, Alex Alderton, Roberto Amato, Cristina V Ariani, Mathew A Beale, Charlotte Beaver, Katherine L Bellis, Emma Betteridge, James Bonfield, John Danesh, Matthew J Dorman, Eleanor Drury, Ben W Farr, Luke Foulser, Sonia Goncalves, Scott Goodwin, Marina Gourtovaia, Ewan M Harrison, David K Jackson, Dorota Jamrozy, Ian Johnston, Leanne Kane, Sally Kay, Jon-Paul Keatley, Dominic Kwiatkowski, Cordelia F Langford, Mara Lawniczak, Laura Letchford, Rich Livett, Stephanie Lo, Inigo Martincorena, Samantha McGuigan, Rachel Nelson, Steve Palmer, Naomi R Park, Minal Patel, Liam Prestwood, Christoph Puethe, Michael A Quail, Shavanthi Rajatileka, Carol Scott, Lesley Shirley, John Sillitoe, Michael H Spencer Chapman, Scott AJ Thurston, Gerry Tonkin-Hill, Danni Weldon, Diana Rajan, Iraad F Bronner, Louise Aigrain, Nicholas M Redshaw, Stefanie V Lensing, Robert Davies, Andrew Whitwham, Jennifier Liddle, Kevin Lewis, Jaime M Tovar-Corona, Steven Leonard, Jillian Durham, Andrew R Bassett, Shane McCarthy, Robin J Moll, Keith James, Karen Oliver, Alex Makunin, Jeff Barrett, and Rory N Gunson
Subjects: Public aspects of medicine, RA1-1270
Abstract: Summary: Background: The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods: We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings: From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation: The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding: Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society.
Published: 2021
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30. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Tom Hansen, Per Gunnar Fjelldal, Sigbjørn Lien, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, William Chow, Kerstin Howe, James Torrance, Jonathan Wood, Ying Sims, Leanne Haggerty, Richard Challis, Jonathan Threlfall, Daniel Mead, Richard Durbin, and Mark Blaxter
Subjects: Medicine, Science
Abstract: We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
Published: 2021
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31. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Dan Mead, Rob Ogden, Anna Meredith, Gabriela Peniche, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Nadine Holmes, Victoria Wright, Matt Loose, Michael A. Quail, Shane A. McCarthy, Kerstin Howe, William Chow, James Torrance, Joanna Collins, Richard Challis, Richard Durbin, and Mark Blaxter
Subjects: Medicine, Science
Abstract: We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.
Published: 2021
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32. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769 [version 1; peer review: 2 approved]

Author: Kerstin Howe, Melinda Dwinell, Mary Shimoyama, Craig Corton, Emma Betteridge, Alexander Dove, Michael A. Quail, Michelle Smith, Laura Saba, Robert W. Williams, Hao Chen, Anne E. Kwitek, Shane A. McCarthy, Marcela Uliano-Silva, William Chow, Alan Tracey, James Torrance, Ying Sims, Richard Challis, Jonathan Threlfall, and Mark Blaxter
Subjects: Medicine, Science
Abstract: We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.
Published: 2021
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33. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins.

Author: Postmus, Iris, Trompet, Stella, Deshmukh, Harshal A, Barnes, Michael R, Li, Xiaohui, Warren, Helen R, Chasman, Daniel I, Zhou, Kaixin, Arsenault, Benoit J, Donnelly, Louise A, Wiggins, Kerri L, Avery, Christy L, Griffin, Paula, Feng, QiPing, Taylor, Kent D, Li, Guo, Evans, Daniel S, Smith, Albert V, de Keyser, Catherine E, Johnson, Andrew D, de Craen, Anton JM, Stott, David J, Buckley, Brendan M, Ford, Ian, Westendorp, Rudi GJ, Slagboom, P Eline, Sattar, Naveed, Munroe, Patricia B, Sever, Peter, Poulter, Neil, Stanton, Alice, Shields, Denis C, O'Brien, Eoin, Shaw-Hawkins, Sue, Chen, Y-D Ida, Nickerson, Deborah A, Smith, Joshua D, Dubé, Marie Pierre, Boekholdt, S Matthijs, Hovingh, G Kees, Kastelein, John JP, McKeigue, Paul M, Betteridge, John, Neil, Andrew, Durrington, Paul N, Doney, Alex, Carr, Fiona, Morris, Andrew, McCarthy, Mark I, Groop, Leif, Ahlqvist, Emma, Welcome Trust Case Control Consortium, Bis, Joshua C, Rice, Kenneth, Smith, Nicholas L, Lumley, Thomas, Whitsel, Eric A, Stürmer, Til, Boerwinkle, Eric, Ngwa, Julius S, O'Donnell, Christopher J, Vasan, Ramachandran S, Wei, Wei-Qi, Wilke, Russell A, Liu, Ching-Ti, Sun, Fangui, Guo, Xiuqing, Heckbert, Susan R, Post, Wendy, Sotoodehnia, Nona, Arnold, Alice M, Stafford, Jeanette M, Ding, Jingzhong, Herrington, David M, Kritchevsky, Stephen B, Eiriksdottir, Gudny, Launer, Leonore J, Harris, Tamara B, Chu, Audrey Y, Giulianini, Franco, MacFadyen, Jean G, Barratt, Bryan J, Nyberg, Fredrik, Stricker, Bruno H, Uitterlinden, André G, Hofman, Albert, Rivadeneira, Fernando, Emilsson, Valur, Franco, Oscar H, Ridker, Paul M, Gudnason, Vilmundur, Liu, Yongmei, Denny, Joshua C, Ballantyne, Christie M, Rotter, Jerome I, Adrienne Cupples, L, Psaty, Bruce M, Palmer, Colin NA, Tardif, Jean-Claude, and Colhoun, Helen M
Subjects: Welcome Trust Case Control Consortium, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Pharmacogenetics, Polymorphism, Single Nucleotide, Cholesterol, LDL, Genome-Wide Association Study, Cholesterol, LDL, Polymorphism, Single Nucleotide
Abstract: Statins effectively lower LDL cholesterol levels in large studies and the observed interindividual response variability may be partially explained by genetic variation. Here we perform a pharmacogenetic meta-analysis of genome-wide association studies (GWAS) in studies addressing the LDL cholesterol response to statins, including up to 18,596 statin-treated subjects. We validate the most promising signals in a further 22,318 statin recipients and identify two loci, SORT1/CELSR2/PSRC1 and SLCO1B1, not previously identified in GWAS. Moreover, we confirm the previously described associations with APOE and LPA. Our findings advance the understanding of the pharmacogenetic architecture of statin response.
Published: 2014

34. Very low levels of atherogenic lipoproteins and the risk for cardiovascular events: a meta-analysis of statin trials.

Author: Boekholdt, S, Hovingh, G, Mora, Samia, Arsenault, Benoit, Amarenco, Pierre, Pedersen, Terje, LaRosa, John, DeMicco, David, Simes, R, Keech, Antony, Colquhoun, David, Hitman, Graham, Betteridge, D, Clearfield, Michael, Downs, John, Colhoun, Helen, Gotto, Antonio, Ridker, Paul, Grundy, Scott, Kastelein, John, and Waters, David
Subjects: LDL-cholesterol, apolipoprotein B, meta-analysis, non–HDL-cholesterol, Atherosclerosis, Biomarkers, Cardiovascular Diseases, Global Health, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Incidence, Lipoproteins, Randomized Controlled Trials as Topic, Risk Factors
Abstract: BACKGROUND: Levels of atherogenic lipoproteins achieved with statin therapy are highly variable, but the consequence of this variability for cardiovascular disease risk is not well-documented. OBJECTIVES: The aim of this meta-analysis was to evaluate: 1) the interindividual variability of reductions in low-density lipoprotein cholesterol (LDL-C), non-high-density lipoprotein cholesterol (non-HDL-C), or apolipoprotein B (apoB) levels achieved with statin therapy; 2) the proportion of patients not reaching guideline-recommended lipid levels on high-dose statin therapy; and 3) the association between very low levels of atherogenic lipoproteins achieved with statin therapy and cardiovascular disease risk. METHODS: This meta-analysis used individual patient data from 8 randomized controlled statin trials, in which conventional lipids and apolipoproteins were determined in all study participants at baseline and at 1-year follow-up. RESULTS: Among 38,153 patients allocated to statin therapy, a total of 6,286 major cardiovascular events occurred in 5,387 study participants during follow-up. There was large interindividual variability in the reductions of LDL-C, non-HDL-C, and apoB achieved with a fixed statin dose. More than 40% of trial participants assigned to high-dose statin therapy did not reach an LDL-C target 175 mg/dl, those who reached an LDL-C 75 to 40% did not reach an LDL-C target
Published: 2014

35. Fludarabine, Cytarabine, Granulocyte Colony-Stimulating Factor, and Idarubicin With Gemtuzumab Ozogamicin Improves Event-Free Survival in Younger Patients With Newly Diagnosed AML and Overall Survival in Patients With NPM1 and FLT3 Mutations.

Author: Russell, Nigel H., Wilhelm-Benartzi, Charlotte, Othman, Jad, Dillon, Richard, Knapper, Steven, Batten, Leona M., Canham, Joanna, Hinson, Emily L., Betteridge, Sophie, Overgaard, Ulrik Malthe, Gilkes, Amanda, Potter, Nicola, Mehta, Priyanka, Kottaridis, Panagiotis, Cavenagh, Jamie, Hemmaway, Claire, Arnold, Claire, Freeman, Sylvie D., and Dennis, Mike
Published: 2024
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36. Interleukin-22 mitigates acute respiratory distress syndrome (ARDS).

Author: Sharven Taghavi, Olan Jackson-Weaver, Sarah Abdullah, Alanna Wanek, Robert Drury, Jacob Packer, Aaron Cotton-Betteridge, Juan Duchesne, Derek Pociask, and Jay Kolls
Subjects: Medicine, Science
Abstract: BackgroundThe goal of this study was to determine if IL-22:Fc would Acute Respiratory Distress Syndrome (ARDS).Summary background dataNo therapies exist for ARDS and treatment is purely supportive. Interleukin-22 (IL-22) plays an integral component in recovery of the lung from infection. IL-22:Fc is a recombinant protein with a human FC immunoglobulin that increases the half-life of IL-22.Study designARDS was induced in C57BL/6 mice with intra-tracheal lipopolysaccharide (LPS) at a dose of 33.3 or 100 ug. In the low-dose LPS group (LDG), IL-22:FC was administered via tail vein injection at 30 minutes (n = 9) and compared to sham (n = 9). In the high-dose LPS group (HDG), IL-22:FC was administered (n = 11) then compared to sham (n = 8). Euthanasia occurred after bronchioalveolar lavage (BAL) on post-injury day 4.ResultsIn the LDG, IL-22:FC resulted in decreased protein leak (0.15 vs. 0.25 ug/uL, p = 0.02). BAL protein in animals receiving IL-22:Fc in the HDG was not different. For the HDG, animals receiving IL-22:Fc had lower BAL cell counts (539,636 vs 3,147,556 cells/uL, p = 0.02). For the HDG, IL-6 (110.6 vs. 527.1 pg/mL, p = 0.04), TNF-α (5.87 vs. 25.41 pg/mL, p = 0.04), and G-CSF (95.14 vs. 659.6, p = 0.01) levels were lower in the BAL fluid of IL-22:Fc treated animals compared to sham.ConclusionsIL-22:Fc decreases lung inflammation and lung capillary leak in ARDS. IL-22:Fc may be a novel therapy for ARDS.
Published: 2021
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37. Transcriptional profiling of equine endometrium before, during and after capsule disintegration during normal pregnancy and after oxytocin-induced luteostasis in non-pregnant mares.

Author: Claudia Klein, Phoebe Bruce, Jutta Hammermueller, Tony Hayes, Brandon Lillie, and Keith Betteridge
Subjects: Medicine, Science
Abstract: The current study used RNA sequencing to determine transcriptional profiles of equine endometrium collected 14, 22, and 28 days after ovulation from pregnant mares. In addition, the transcriptomes of endometrial samples obtained 20 days after ovulation from pregnant mares, and from non-pregnant mares which displayed and failed to display extended luteal function following the administration of oxytocin, were determined and compared in order to delineate genes whose expressions depend on the presence of the conceptus as opposed to elevated progesterone alone. A mere fifty-five transcripts were differentially expressed between samples collected from mares at Day 22 and Day 28 of pregnancy. This likely reflects the longer-term exposure to a relatively constant, progesterone-dominated environment with little change in factors secreted by the conceptus that would affect endometrial gene expression. The complement system was amongst the canonical pathways significantly enriched in transcripts differentially expressed between Day 14 and Day 22/28 of pregnancy. The expression of complement components 7 and 8 was confirmed using in situ hybridization. The expression of SERPING1, an inhibitor of the complement system, was confirmed by immunohistochemistry. In line with the resumed capacity of the endometrium to produce prostaglandin, prostaglandin G/H synthase 1 was expressed at higher levels at Days 22 and 28 than at Day 14 of pregnancy. Our data suggest that this up-regulation is enhanced by the presence of the conceptus; samples obtained from mares at Day 20 of pregnancy had significantly higher levels of prostaglandin G/H synthase 1 transcript than mares with extended luteal function.
Published: 2021
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38. Clinical codes combined with procedure codes increase diagnostic accuracy of Crohn’s disease in a US Military health record

Author: Susan Hutfless, Manish Singla, Elie Al Kazzi, Benjamin Rodriguez, John Betteridge, and Steven Brant
Subjects: Diseases of the digestive system. Gastroenterology, RC799-869
Abstract: Background and aimsPrevious examinations of International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) codes to predict accuracy of diagnosis in inflammatory bowel disease have had limited chart review to confirm diagnosis. We aimed to evaluate using the ICD-9-CM for identifying Crohn’s disease (CD) in a large electronic health record (EHR) database.MethodsThis is a retrospective case-control study with a 3:1 allocation of EHRs of active duty service members diagnosed with CD from 1996 to 2012. Subjects were selected by having two ICD-9-CM codes for CD during the study period. Gastroenterologists reviewed each chart and confirmed the diagnosis of CD by analysing medication history and clinical, endoscopic, histological, and radiographic exams.Results300 cases of CD were selected; 14 cases were discarded due to lack of data, limiting our analysis to 284 subjects. Two diagnostic codes for CD had sensitivity, specificity, and positive predictive value (PPV) of 1.0, 0.53, and 0.69, respectively, for confirmed CD. If two encounters listing CD were with a gastroenterologist, the sensitivity, specificity, and PPV was 0.76, 0.81, and 0.80, respectively. If a colonoscopy was performed within 90 days of any three encounters with a CD code, the sensitivity, specificity, and PPV was 0.51, 0.94, and 0.89, respectively.ConclusionsThe poor PPV of ICD-9-CM codes in making the diagnosis of CD should be taken into consideration when interpreting results and when conducting research using such codes. Limiting these codes to those patients who have been given this diagnosis by a gastroenterologist, or to those who have had a colonoscopy near the time of diagnosis, increases the PPV.
Published: 2020
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39. Serum kidney injury molecule 1 and β2-microglobulin perform as well as larger biomarker panels for prediction of rapid decline in renal function in type 2 diabetes

Author: Colombo, Marco, Looker, Helen C., Farran, Bassam, Hess, Sibylle, Groop, Leif, Palmer, Colin N. A., Brosnan, Mary Julia, Dalton, R. Neil, Wong, Max, Turner, Charles, Ahlqvist, Emma, Dunger, David, Agakov, Felix, Durrington, Paul, Livingstone, Shona, Betteridge, John, McKeigue, Paul M., Colhoun, Helen M., and on behalf of the SUMMIT Investigators
Published: 2019
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40. mHealth Apps for Enhanced Management of Spinal Surgery Patients: A Review

Author: Michael Y. Bai, Ralph J. Mobbs, William R. Walsh, and Callum Betteridge
Subjects: surgery, spine, mHealth, smartphone, apps, Surgery, RD1-811
Abstract: mHealth (mobile health) refers to mobile technologies that aid medical and public health practices. As of February 2019, 81% of Americans own a smartphone, and mHealth applications (apps) have become increasingly common with more than 400,000 mHealth applications currently available. Advancements in mobile technology now allow us to provide personalized up-to-date information, track personal health data, remind and engage patients, and communicate in a cost-effective way. There are new opportunities for healthcare providers to integrate mHealth into clinical practice. We discuss the current scientific evidence, and research into mHealth technology.
Published: 2020
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41. Considerations for improving quality of care of patients with rheumatoid arthritis and associated comorbidities

Author: Maxime Dougados, Tore K Kvien, Anne Grete Semb, Maya H Buch, Patrick Durez, Karel Pavelka, Cem Gabay, Frank Van den Hoogen, Lars Klareskog, Mikkel Østergaard, Alison Kent, Alejandro Balsa, Magnus Sköld, Ennio Giulio Favalli, Rinie Geenen, Neil Betteridge, Guillaume Favier, Ioanna Gouni-Berthold, and Joaquim Polido Pereira
Subjects: Medicine
Abstract: Objective Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder with a global prevalence of approximately 0.5–1%. Patients with RA are at an increased risk of developing comorbidities (eg, cardiovascular disease, pulmonary disease, diabetes and depression). Despite this, there are limited recommendations for the management and implementation of associated comorbidities. This study aimed to identify good practice interventions in the care of RA and associated comorbidities.Methods A combination of primary research (180+ interviews with specialists across 12 European rheumatology centres) and secondary research (literature review of existing publications and guidelines/recommendations) were used to identify challenges in management and corresponding good practice interventions. Findings were prioritised and reviewed by a group of 18 rheumatology experts including rheumatologists, comorbidity experts, a patient representative and a highly specialised nurse.Results Challenges throughout the patient pathway (including delays in diagnosis and referral, shortage of rheumatologists, limited awareness of primary care professionals) and 18 good practice interventions were identified in the study. The expert group segmented and prioritised interventions according to three distinct stages of the disease: (1) suspected RA, (2) recent diagnosis of RA and (3) established RA. Examples of good practice interventions included enabling self-management (self-monitoring and disease management support, for example, lifestyle adaptations); early arthritis clinic; rapid access to care (online referral, triage, ultrasound-guided diagnosis); dedicated comorbidity specialists; enhanced communication with primary care (hotline, education sessions); and integrating patient registries into daily clinical practice.Conclusion Learning from implementation of good practice interventions in centres across Europe provides an opportunity to more widely improved care for patients with RA and associated comorbidities.
Published: 2020
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42. Following Manson

Author: Ellen Dillon and Tom Betteridge
Subjects: Articulatedness, Pareidolia, Peter Manson, English literature, PR1-9680
Abstract: A brief introduction to the work of Peter Manson and the papers delivered at the 2017 Glasgow symposium dedicated to his work.
Published: 2020
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43. Understanding the patient voice in gout: a quantitative study conducted in Europe

Author: Marc De Meulemeester, Elsa Mateus, Hilda Wieberneit-Tolman, Neil Betteridge, Lucy Ireland, Gudula Petersen, Nina Jeanette Maske, Tim L Jansen, and Fernando Perez-Ruiz
Subjects: gout, uric acid, urate, quality of life, general practice, patient care, surveys and questionnaires, pain, Medicine (General), R5-920
Abstract: Background: Although commonly diagnosed, gout often remains a poorly managed disease. This is partially due to a lack of awareness of the long-term effect of gout among patients and healthcare professionals. Aim: To understand unmet needs for patients and provide insight into achieving better treatment. Design & setting: A quantitative online questionnaire collected from 1100 people with gout from 14 countries within Europe. Method: Patients were recruited to complete an online survey via healthcare professional (HCP) referral, patient associations, or market research panels. Patients were included if they had been diagnosed with gout by a physician. Prior to commencement, patients were made aware that this study was sponsored by Grünenthal. The responses collected were collated and analyses were performed. Results: Patients had an average of 2.9 gout flares within a 12-month period. Although 79% of patients were satisfied with treatment, inadequate gout control was also reported by 71% of patients. Furthermore, 84% experienced moderate-to-severe pain with their most recent flare. Of those who acknowledged treatment dissatisfaction, only 24% discussed other options with their GP. Most patients reported irregular follow-up and serum uric acid (sUA) monitoring. In addition, loss of belief that more can be done was a key barrier for patients. Conclusion: Patients reported severe pain and social burden, coupled with low treatment expectation and lack of awareness of target sUA. Education around knowing and reaching sUA target is needed so that patients can receive and GPs can deliver higher quality management.
Published: 2020
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44. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Daniel Mead, Kathryn Fingland, Rachel Cripps, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Dolucan, Olga Dudchenko, Arina D. Omer, David Weisz, Erez Lieberman Aiden, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, Ying Sims, James Torrance, Alan Tracey, Kerstin Howe, Richard Challis, Richard Durbin, and Mark Blaxter
Subjects: Medicine, Science
Abstract: We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
Published: 2020
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45. The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758 [version 1; peer review: 2 approved]

Author: Dan Mead, Frank Hailer, Elisabeth Chadwick, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan Doulcan, Olga Dudchenko, Arina Omer, David Weisz, Erez Lieberman Aiden, Shane McCarthy, Kerstin Howe, Ying Sims, James Torrance, Alan Tracey, Richard Challis, Richard Durbin, and Mark Blaxter
Subjects: Medicine, Science
Abstract: We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.
Published: 2020
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46. The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788 [version 1; peer review: 2 approved]

Author: Dan Mead, Kathryn Fingland, Rachel Cripps, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Michael A. Quail, Shane A. McCarthy, Kerstin Howe, Ying Sims, James Torrance, Alan Tracey, Richard Challis, Richard Durbin, and Mark Blaxter
Subjects: Medicine, Science
Abstract: We present a genome assembly from an individual male Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
Published: 2020
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47. Investigation of myositis and scleroderma specific autoantibodies in patients with lung cancer

Author: Zoe E. Betteridge, Lynsey Priest, Robert G. Cooper, Neil J. McHugh, Fiona Blackhall, and Janine A. Lamb
Subjects: Idiopathic inflammatory myopathies, Myositis, Scleroderma, Cancer, Autoantibodies, Anti-glycyl-tRNA synthetase, Diseases of the musculoskeletal system, RC925-935
Abstract: Abstract Background The close temporal association between onset of some connective tissue diseases and cancer suggests a paraneoplastic association. Adult patients with scleroderma with anti-RNA polymerase III autoantibodies and adult patients with dermatomyositis with anti-transcriptional intermediary factor 1 (anti-TIF1) or anti-nuclear matrix protein 2 (anti-NXP2) autoantibodies have a significantly increased risk of developing cancer. Autoantibodies may serve as biomarkers for early detection of cancer and also could be relevant for prediction of responses to immune therapies. We aimed to test whether myositis and scleroderma specific or associated autoantibodies are detectable in individuals with lung cancer. Methods Serum from 60 Caucasian patients with lung cancer (30 with small cell lung cancer, 30 with non-small cell lung cancer) was screened for myositis and scleroderma specific and associated autoantibodies by radiolabelled immunoprecipitation. Results Anti-TIF1, anti-NXP2 or anti-RNA polymerase III autoantibodies were not detected in any of the 60 patients with lung cancer. Anti-glycyl-transfer RNA (tRNA) synthetase (anti-EJ) autoantibodies were detected in one patient with non-small cell lung cancer. No other known myositis or scleroderma autoantibodies were identified. Conclusions Myositis and scleroderma specific autoantibodies, including anti-TIF1, anti-NXP2 and anti-RNA polymerase III, are rare in patients with lung cancer without an autoimmune disease. We report here the first case of anti-EJ autoantibodies being detected in a patient with lung cancer without clinical or radiographic evidence of the anti-synthetase syndrome.
Published: 2018
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48. Nocebo effects and participant information leaflets: evaluating information provided on adverse effects in UK clinical trials

Author: Kirby, Nigel, Shepherd, Victoria, Howick, Jeremey, Betteridge, Sophie, and Hood, Kerenza
Published: 2020
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49. Linkage and association of haplotypes at the APOA1/C3/A4/A5 gene cluster to familial combined hyperlipidemia

Author: Eichenbaum-Voline, Sophie, Olivier, Michael, Jones, Emma L., Naoumova, Rossitza P., Jones, Bethan, Gau, Brian, Seed, Mary, Betteridge, D. John, Galton, David J., Rubin, Edward M., Scott, James, Shoulders, Carol C., and Pennacchio, Len A.
Subjects: Basic biological sciences
Abstract: Combined hyperlipidemia (CHL) is a common disorder of lipid metabolism that leads to an increased risk of cardiovascular disease. The lipid profile of CHL is characterised by high levels of atherogenic lipoproteins and low levels of high-density-lipoprotein-cholesterol. Apolipoprotein (APO) A5 is a newly discovered gene involved in lipid metabolism located within 30kbp of the APOA1/C3/A4 gene cluster. Previous studies have indicated that sequence variants in this cluster are associated with increased plasma lipid levels. To establish whether variation at the APOA5 gene contributes to the transmission of CHL, we performed linkage and linkage disequilibrium (LD) tests on a large cohort of families (n=128) with familial CHL (FCHL). The linkage data produced evidence for linkage of the APOA1/C3/A4/A5 genomic interval to FCHL (NPL = 1.7, P = 0.042). The LD studies substantiated these data. Two independent rare alleles, APOA5c.56G and APOC3c.386G of this gene cluster were over-transmitted in FCHL (P = 0.004 and 0.007, respectively), and this was associated with a reduced transmission of the most common APOA1/C3/A4/A5 haplotype (frequency 0.4425) to affected subjects (P = 0.013). The APOA5c.56G allele was associated with increased plasma triglyceride levels in FCHL probands, whereas the second, and independent, APOC3c.386G allele was associated with increased plasma triglyceride levels in FCHL pedigree founders. Thus, this allele (or an allele in LD) may mark a quantitative trait associated with FCHL, as well as representing a disease susceptibility locus for the condition. This study establishes that sequence variation in the APOA1/C3/A4/A5 gene cluster contributes to the transmission of FCHL in a substantial proportion of affected families, and that these sequence variants may also contribute to the lipid abnormalities of the metabolic syndrome, which is present in up to 40 percent of persons with cardiovascular disease.
Published: 2002

50. Perfusion by Arterial Spin labelling following Single dose Tadalafil In Small vessel disease (PASTIS): study protocol for a randomised controlled trial

Author: Mathilde M. H. Pauls, Natasha Clarke, Sarah Trippier, Shai Betteridge, Franklyn A. Howe, Usman Khan, Christina Kruuse, Jeremy B. Madigan, Barry Moynihan, Anthony C. Pereira, Debbie Rolfe, Egill Rostrup, Caroline E. Haig, Thomas R. Barrick, Jeremy D. Isaacs, and Atticus H. Hainsworth
Subjects: Tadalafil, Cerebral blood flow, Vascular cognitive impairment, Vascular dementia, Phosphodiesterase, MRI, Medicine (General), R5-920
Abstract: Abstract Background Cerebral small vessel disease is a common cause of vascular cognitive impairment in older people, with no licensed treatment. Cerebral blood flow is reduced in small vessel disease. Tadalafil is a widely prescribed phosphodiesterase-5 inhibitor that increases blood flow in other vascular territories. The aim of this trial is to test the hypothesis that tadalafil increases cerebral blood flow in older people with small vessel disease. Methods/design Perfusion by Arterial Spin labelling following Single dose Tadalafil In Small vessel disease (PASTIS) is a phase II randomised double-blind crossover trial. In two visits, 7-30 days apart, participants undergo arterial spin labelling to measure cerebral blood flow and a battery of cognitive tests, pre- and post-dosing with oral tadalafil (20 mg) or placebo. Sample size: 54 participants are required to detect a 15% increase in cerebral blood flow in subcortical white matter (p
Published: 2017
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