DNA Methylation: Bisulphite Modification and Analysis

Epigenetics describes the heritable changes in gene function that occur independently to the DNA sequence. The molecular basis of epigenetic gene regulation is complex, but essentially involves modifications to the DNA itself or the proteins with which DNA associates. The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA methylation provides instruction to gene expression machinery as to where and when the gene should be expressed. The primary target sequence for DNA methylation in mammals is 5'-CpG-3' dinucleotides (Figure 1). CpG dinucleotides are not uniformly distributed throughout the genome, but are concentrated in regions of repetitive genomic sequences and CpG "islands" commonly associated with gene promoters (Figure 1). DNA methylation patterns are established early in development, modulated during tissue specific differentiation and disrupted in many disease states including cancer. To understand the biological role of DNA methylation and its role in human disease, precise, efficient and reproducible methods are required to detect and quantify individual 5-MeCs

Evidence for Past Subduction Earthquakes at a Plate Boundary with Widespread Upper Plate Faulting: Southern Hikurangi Margin, New Zealand

At the southern Hikurangi margin, New Zealand, we use salt marsh stratigraphy, sedimentology, micropaleontology, and radiocarbon dating to document evidence of two earthquakes producing coseismic subsidence and (in one case) a tsunami over the past 1000 yrs. The earthquake at 520-470 yrs before present (B.P.) produced 0.25 +/- 0.1 m of subsidence at Big Lagoon. The earthquake at 880-800 yrs B.P. produced 0.45 +/- 0.1 m of subsidence at Big Lagoon and was accompanied by a tsunami that inundated >= 360 m inland with a probable height of >= 3.3 m. Distinguishing the effects of upper plate faulting from plate interface earthquakes is a significant challenge at this margin. We use correlation with regional upper plate paleoearthquake chronologies and elastic dislocation modeling to determine that the most likely cause of the subsidence and tsunami events is subduction interface rupture, although the older event may have been a synchronous subduction interface and upper plate fault rupture. The southern Hikurangi margin has had no significant (M > 6.5) documented subduction interface earthquakes in historic times, and previous assumptions that this margin segment is prone to rupture in large to great earthquakes were based on seismic and geodetic evidence of strong contemporary plate coupling. This is the first geologic evidence to confirm that the southern Hikurangi margin ruptures in large earthquakes. The relatively short-time interval between the two subduction earthquakes (similar to 350 yrs) is shorter than in current seismic-hazard models.GNSEQC Biennial ProjectNew Zealand Natural Hazards Research Platform and Foundation for Research Science and TechnologyInstitute for Geophysic

Exploring Engagement with Authors of Randomised Controlled Trials to Develop Recommendations to Improve Allocation Concealment Implementation and Reporting

Background: Reviews have consistently shown that allocation concealment is frequently implemented and reported suboptimally in randomised controlled trials (RCTs). This research aims to pilot engaging with authors of RCTs to explore their knowledge and understanding of allocation concealment implementation and reporting to ascertain areas and mechanisms for their improvement. Methods: Authors that published RCTs in core clinical journals in one month in 2019 were identified. Authors were invited to complete questionnaires to elicit their views and experiences on the implementation and reporting quality focussing on allocation concealment. Methodological quality of allocation concealment was evaluated in this sample by assessing adherence to the Consolidated Standards of Reporting Trials (CONSORT). Results: Reporting was suboptimal, with only 57% of allocation concealment methods reported to be implemented which were judged as adequate, with 18% using sealed envelopes and more than 40% not adequately reporting allocation methods. When exploring allocation concealment, implementation and reporting questionnaires were found to elicit a low response rate amongst authors of RCTs. Discussion: Following analysis of the themes that emerged from the questionnaires, the main recommendations to improve reporting quality are: journals need to endorse, adhere and promote reporting guidelines, a methodologist could review methodological details of publications simultaneously to peer review, envelopes as a form of allocation concealment are poorly implemented and reported, so careful review of these is required, funders need to insist on more robust allocation concealment methods are employed if the RCT setting allows, and authors need to acknowledge their responsibility for transparent reporting of RCTs

Bah humbug! Association between sending Christmas cards to trial participants and trial retention: randomised study within a trial conducted simultaneously across eight host trials

Objective To determine the effectiveness of sending Christmas cards to participants in randomised controlled trials to increase retention rate at follow-ups, and to explore the feasibility of doing a Study Within A Trial (SWAT) across multiple host trials simultaneously. Design Randomised SWAT conducted simultaneously across eight host trials. Setting Eight randomised controlled trials researching various areas including surgery and smoking cessation. Participants 3,223 participants who were still due at least one follow-up from their host randomised controlled trial. Intervention Participants were randomised (1:1, separately by each host trial) to either received a Christmas card in mid-December 2019 or to not receive a card. Main outcome measures Proportion of participants that completed their next follow-up (retention rate) within their host randomised controlled trial. Results 1469 participants (age 16-94 years; 70% (n=1033) female; 96% (813/847) white ethnicity) across the eight host randomised controlled trials were involved in the analysis (cut short owing to covid-19). No evidence was found of a difference in retention rate between the two arms for any of the host trials when analysed separately or when the results were combined (85.3% (639/749) for cards versus 85.4% (615/720) for no card; odds ratio 0.96, 95% confidence interval 0.71 to 1.29; P=0.77). No difference was observed when comparing just participants who were due a follow-up in the 30 days after receiving the card (odds ratio 0.96, 0.42 to 2.21). No evidence of a difference in time to complete the questionnaire was found (hazard ratio 1.01, 95% confidence interval 0.91 to 1.13; P=0.80). These results were robust to post hoc sensitivity analyses. The cost of this intervention was £0.76 (€0.91; $1.02) per participant, and it will have a carbon footprint of approximately 140 g CO2 equivalent per card. One benefit of this approach was the need to only submit one ethics application. Conclusions Sending Christmas cards to participants in randomised controlled trials does not increase retention. Undertaking a SWAT within multiple randomised controlled trials at the same time is, however, possible. This approach should be used more often to build an evidence base to support selection of recruitment and retention strategies. Although no evidence of a boost to retention was found, embedding a SWAT in multiple host trials simultaneously has been shown to be possible. Trial Registration SWAT 82: Sending Christmas cards to trial participants to improve retention (SWAT repository - https://www.qub.ac.uk/sites/TheNorthernIrelandNetworkforTrialsMethodologyResearch/FileStore/Filetoupload,846275,en.pdf#search=SWAT%2082

The alarms should no longer be ignored: survey of the demand, capacity and provision of adult community eating disorder services in England and Scotland before COVID-19.

This national pre-pandemic survey compared demand and capacity of adult community eating disorder services (ACEDS) with NHS England (NHSE) commissioning guidance. Thirteen services in England and Scotland responded (covering 10.7 million population). Between 2016-2017 and 2019-2020 mean referral rates increased by 18.8%, from 378 to 449/million population. Only 3.7% of referrals were from child and adolescent eating disorder services (CEDS-CYP), but 46% of patients were aged 18-25 and 54% were aged >25. Most ACEDS had waiting lists and rationed access. Many could not provide full medical monitoring, adapt treatment for comorbidities, offer assertive outreach or provide seamless transitions. For patient volume, the ACEDS workforce budget was 15%, compared with the NHSE workforce calculator recommendations for CEDS-CYP. Parity required £7 million investment/million population for the ACEDS. This study highlights the severe pressure in ACEDS, which has increased since the COVID-19 pandemic. Substantial investment is required to ensure NHS ACEDS meet national guidance, offer evidence-based treatment, reduce risk and preventable deaths, and achieve parity with CEDS-CYP

Undertaking studies within a trial to evaluate recruitment and retention strategies for RCTs : lessons learnt from the PROMETHEUS research programme

Background Randomised controlled trials (‘trials’) are susceptible to poor participant recruitment and retention. Studies Within A Trial (SWATs) are the strongest methods for testing the effectiveness of strategies to improve recruitment and retention. However, relatively few of these have been conducted. Aims PROMoting THE USE of Studies Within A Trial (PROMETHEUS) aimed to facilitate at least 25 SWATs evaluating recruitment or retention strategies. We share our experience of delivering the PROMETHEUS programme, and the lessons learnt for undertaking randomised SWATs. Design A network of 10 Clinical Trials Units (CTUs) and one primary care research centre committed to conducting randomised controlled SWATs of recruitment and/or retention strategies was established. Promising recruitment and retention strategies were identified from various sources including Cochrane systematic reviews, the SWAT Repository, and existing prioritisation exercises, which were reviewed by patient and public (PPI) members to create an initial priority list of seven recruitment and eight retention interventions. Host trial teams could apply for funding and receive support from the PROMETHEUS team to undertake SWATs. We also tested the feasibility of undertaking coordinated SWATs, across multiple host trials simultaneously. Setting CTU-based trials recruiting or following up participants in any setting in the UK were eligible. Participants CTU-based teams undertaking trials in any clinical context in the UK. Interventions Funding of up to £5,000 and support from the PROMETHEUS team to design, implement, and report SWATs. Main outcome measures Number of host trials funde

The effectiveness of a multidisciplinary intervention strategy for the treatment of symptomatic joint hypermobility in childhood:A randomised, single Centre parallel group trial (The Bendy Study)

Introduction: Joint hypermobility is common in childhood and can be associated with musculoskeletal pain and dysfunction. Current management is delivered by a multidisciplinary team, but evidence of effectiveness is limited. This clinical trial aimed to determine whether a structured multidisciplinary, multisite intervention resulted in improved clinical outcomes compared with standard care. Method: A prospective randomised, single centre parallel group trial comparing an 8-week individualised multidisciplinary intervention programme (bespoke physiotherapy and occupational therapy in the clinical, home and school environment) with current standard management (advice, information and therapy referral if deemed necessary). The primary endpoint of the study was between group difference in child reported pain from baseline to 12 months as assessed using the Wong Baker faces pain scale. Secondary endpoints were parent reported pain (100 mm visual analogue scale), parent reported function (child health assessment questionnaire), child reported quality of life (child health utility 9-dimensional assessment), coordination (movement assessment battery for children version 2) and grip strength (handheld dynamometer). Results: 119 children aged 5 to 16 years, with symptomatic hypermobility were randomised to receive an individualised multidisciplinary intervention (I) (n = 59) or standard management (S) (n = 60). Of these, 105 completed follow up at 12 months. No additional significant benefit could be shown from the intervention compared to standard management. However, there was a statistically significant improvement in child and parent reported pain, coordination and grip strength in both groups. The response was independent of the degree of hypermobility. Conclusion: This is the first randomised controlled trial to compare a structured multidisciplinary, multisite intervention with standard care in symptomatic childhood hypermobility. For the majority, the provision of education and positive interventions aimed at promoting healthy exercise and self-management was associated with significant benefit without the need for more complex interventions. Trial registration: The trial was registered prospectively with the national database at the Clinical Research Network (UKCRN Portfolio 9366). The trial was registered retrospectively with ISRCTN (ISRCTN86573140)

Genome-Wide Association Study of Alzheimer's Disease Brain Imaging Biomarkers and Neuropsychological Phenotypes in the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Dataset

Alzheimer's disease (AD) is the most frequent neurodegenerative disease with an increasing prevalence in industrialized, aging populations. AD susceptibility has an established genetic basis which has been the focus of a large number of genome-wide association studies (GWAS) published over the last decade. Most of these GWAS used dichotomized clinical diagnostic status, i.e., case vs. control classification, as outcome phenotypes, without the use of biomarkers. An alternative and potentially more powerful study design is afforded by using quantitative AD-related phenotypes as GWAS outcome traits, an analysis paradigm that we followed in this work. Specifically, we utilized genotype and phenotype data from n = 931 individuals collected under the auspices of the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD) study to perform a total of 19 separate GWAS analyses. As outcomes we used five magnetic resonance imaging (MRI) traits and seven cognitive performance traits. For the latter, longitudinal data from at least two timepoints were available in addition to cross-sectional assessments at baseline. Our GWAS analyses revealed several genome-wide significant associations for the neuropsychological performance measures, in particular those assayed longitudinally. Among the most noteworthy signals were associations in or near EHBP1 (EH domain binding protein 1; on chromosome 2p15) and CEP112 (centrosomal protein 112; 17q24.1) with delayed recall as well as SMOC2 (SPARC related modular calcium binding 2; 6p27) with immediate recall in a memory performance test. On the X chromosome, which is often excluded in other GWAS, we identified a genome-wide significant signal near IL1RAPL1 (interleukin 1 receptor accessory protein like 1; Xp21.3). While polygenic score (PGS) analyses showed the expected strong associations with SNPs highlighted in relevant previous GWAS on hippocampal volume and cognitive function, they did not show noteworthy associations with recent AD risk GWAS findings. In summary, our study highlights the power of using quantitative endophenotypes as outcome traits in AD-related GWAS analyses and nominates several new loci not previously implicated in cognitive decline

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson