Partial characterization of Agrobacterium vitis strains

Seventeen strains of Agrobacterium vitis (formerly classified A. tumefaciens biovar 3) were characterized using part of the T-DNA and virA regions of the Ti plasmid as probes. All strains except one were of the wide host range (WHR) strains and were classified into two groups depending on their ability to utilize octopine or nopaline. These WHR type oncogenic strains had homology with the limited host range type (LHR) virA gen of A. vitis but not with the WHR virA gene of A. tumefaciens. The frequency of T-DNA excision in some Agrobacterium strains was estimated with the plasmid pTMA which mimics T-DNA excision from Ti plasmid DNA. In an A. vitis strain isolated from grapevine, T-DNA excision occurred after co-cultivation with grapevine tissues, but not with acetosyringone. In contrast, in A. tumefaciens, T-DNA excision occurred after co-cultivation with acetosyringone, but not with grapevine tissue

EpiCompare: R package for the comparison and quality control of epigenomic peak files

Summary EpiCompare combines a variety of downstream analysis tools to compare, quality control and benchmark different epigenomic datasets. The package requires minimal input from users, can be run with just one line of code and provides all results of the analysis in a single interactive HTML report. EpiCompare thus enables downstream analysis of multiple epigenomic datasets in a simple, effective and user-friendly manner. Availability and Implementation EpiCompare is available on Bioconductor (≥ v3.15): https://bioconductor.org/packages/release/bioc/html/EpiCompare.html All source code is publically available via GitHub: https://github.com/neurogenomics/EpiCompare Documentation website https://neurogenomics.github.io/EpiCompare EpiCompare DockerHub repository: https://hub.docker.com/repository/docker/neurogenomicslab/epicompare Competing Interest Statement The authors have declared no competing interest

A robust, discrete-gradient descent procedure for optimisation with time-dependent PDE and norm constraints

Many physical questions in fluid dynamics can be recast in terms of norm constrained optimisation problems; which in-turn, can be further recast as unconstrained problems on spherical manifolds. Due to the nonlinearities of the governing PDEs, and the computational cost of performing optimal control on such systems, improving the numerical convergence of the optimisation procedure is crucial. Borrowing tools from the optimisation on manifolds community we outline a numerically consistent, discrete formulation of the direct-adjoint looping method accompanied by gradient descent and line-search algorithms with global convergence guarantees. We numerically demonstrate the robustness of this formulation on three example problems of relevance in fluid dynamics and provide an accompanying library SphereManOp

A randomised, multi-centre trial of total ankle replacement versus ankle arthrodesis in the treatment of patients with end stage ankle osteoarthritis (TARVA): statistical analysis plan.

BACKGROUND: The total ankle replacement versus ankle arthrodesis (TARVA) trial aims to determine which surgical procedure confers the greatest improvement in pain-free function for patients with end-stage ankle osteoarthritis. Both procedures are effective but there has not yet been a direct comparison to establish which is superior. This article describes the statistical analysis plan for this trial as an update to the published protocol. It is written prior to the end of patient follow-up, while the outcome of the trial is still unknown. DESIGN AND METHODS: TARVA is a randomised, un-blinded, parallel group trial of total ankle replacement versus ankle arthrodesis. The primary outcome is the Manchester-Oxford Foot Questionnaire walking/standing domain score at 52 weeks post-surgery. Secondary outcomes include measures of pain, social interaction, physical function, quality of life, and range of motion. We describe in detail the statistical aspects of TARVA: the outcome measures, the sample size calculation, general analysis principles including treatment of missing data, the planned descriptive statistics and statistical models, and planned subgroup and sensitivity analyses. DISCUSSION: The TARVA statistical analysis will provide comprehensive and precise information on the relative effectiveness of the two treatments. The plan will be implemented in January 2020 when follow-up for the trial is completed. TRIAL REGISTRATION: ISRCTN registry number 60672307, ClinicalTrials.gov registration number NCT02128555. Registered 1 May 2014. Recruitment started in January 2015 and ended in January 2019

Improving uptake of hepatitis B and hepatitis C testing in South Asian migrants in community and faith settings using educational interventions - a prospective descriptive study

BACKGROUND: Chronic viral hepatitis (CVH) is a leading contributor to the UK liver disease epidemic, with global migration from high-prevalence areas (e.g. South Asia-SA). Despite international guidance for testing high-risk groups in line with elimination targets, there is no consensus on how to achieve this. OBJECTIVES: (i) Feasibility of recruiting SA migrants to view an educational film on CVH (ii) Effectiveness of the film in promoting testing, knowledge of CVH (iii) Methodological issues relevant to scale-up to randomized trial. METHODS: We recruited SA migrants to view the film (intervention) in community venues (primary care, religious, community), offering dried-blood spot CVH testing immediately afterwards. Pre/post-film questionnaires assessed the interventions effectiveness. RESULTS: Two hundred and nineteen first generation migrants >18yrs (53% female) were recruited to view the film;184 (84%) underwent CVH testing (HBc Ab or HCV Ab positive, demonstrating exposure in 8.5%) at the following sites: n = 112 (51%) religious, n = 98(45%) community, and primary care, n = 9 (4%). Pre (n = 173, 79%) and post (n = 154, 70%) intervention questionnaires were completed. CONCLUSIONS: We demonstrate the feasibility of recruiting first generation migrants to participate in a community-based educational film, promoting CVH testing in this higher-risk group, confirming value of developing interventions to facilitate global WHO plan for targeted case finding, elimination and future randomized controlled trial. We highlight the importance of culturally relevant interventions including faith, and culturally sensitive settings appearing to minimize logistical issues effective at engaging minority groups and allowing ease of access to individuals 'at risk'