Characterization of two in vivo-expressesd methyltransferases of the Mycobacterium tuberculosis complex:Antigenicity and genetic regulation

Genome sequencing of Mycobacterium tuberculosis complex members has accelerated the search for new disease-control tools. Antigen mining is one area that has benefited enormously from access to genome data. As part of an ongoing antigen mining programme, we screened genes that were previously identified by transcriptome analysis as upregulated in response to an in vitro acid shock for their in vivo expression profile and antigenicity. We show that the genes encoding two methyltransferases, Mb1438c/Rv1403c and Mb1440c/Rv1404c, were highly upregulated in a mouse model of infection, and were antigenic in M. bovis-infected cattle. As the genes encoding these antigens were highly upregulated in vivo, we sought to define their genetic regulation. A mutant was constructed that was deleted for their putative regulator, Mb1439/Rv1404; loss of the regulator led to increased expression of the flanking methyltransferases and a defined set of distal genes. This work has therefore generated both applied and fundamental outputs, with the description of novel mycobacterial antigens that can now be moved into field trials, but also with the description of a regulatory network that is responsive to both in vivo and in vitro stimuli

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression

BACKGROUND: Bovine tuberculosis (bTB) is a disease with major implications for animal welfare and productivity, as well as having the potential for zoonotic transmission. In Great Britain (GB) alone, controlling bTB costs in the region of £100 million annually, with the current control scheme seemingly unable to stop the inexorable spread of infection. One aspect that may be driving the epidemic is evolution of the causative pathogen, Mycobacterium bovis. To understand the underlying genetic changes that may be responsible for this evolution, we performed a comprehensive genome-level analyses of 4 M. bovis strains that encompass the main molecular types of the pathogen circulating in GB. RESULTS: We have used a combination of genome sequencing, transcriptome analyses, and recombinant DNA technology to define genetic differences across the major M. bovis lineages circulating in GB that may give rise to phenotypic differences of practical importance. The genomes of three M. bovis field isolates were sequenced using Illumina sequencing technology and strain specific differences in gene expression were measured during in vitro growth and in ex vivo bovine alveolar macrophages using a whole genome amplicon microarray and a whole genome tiled oligonucleotide microarray. SNP/small base pair insertion and deletions and gene expression data were overlaid onto the genomic sequence of the fully sequenced strain of M. bovis 2122/97 to link observed strain specific genomic differences with differences in RNA expression. CONCLUSIONS: We show that while these strains show extensive similarities in their genetic make-up and gene expression profiles, they exhibit distinct expression of a subset of genes. We provide genomic, transcriptomic and functional data to show that synonymous point mutations (sSNPs) on the coding strand can lead to the expression of antisense transcripts on the opposing strand, a finding with implications for how we define a 'silent’ nucleotide change. Furthermore, we show that transcriptomic data based solely on amplicon arrays can generate spurious results in terms of gene expression profiles due to hybridisation of antisense transcripts. Overall our data suggest that subtle genetic differences, such as sSNPS, may have important consequences for gene expression and subsequent phenotype

How inclusive, user-centered design research can improve psychological therapies for psychosis: Development of SlowMo

Real-world implementation of psychological interventions for psychosis is poor. Barriers include therapy being insufficiently usable and useful for a diverse range of people. User-centered, inclusive design approaches could improve the usability of therapy, which may increase uptake, adherence, and effectiveness. This study aimed to optimize the usability of an existing psychological intervention, Thinking Well, which targets reasoning processes in paranoia using a basic digital interface. We conducted inclusive, user-centered design research characterized by purposive sampling of extreme users from the margins of groups, ethnographic investigation of the problem context, and iterative prototyping of solutions. The UK Design Council's double diamond method was used. This consisted of 4 phases: discover, including a case series of Thinking Well, stakeholder interviews, desk research, user profiling, system mapping, and a mood board; define, consisting of workshops to synthesize findings and generate the design brief; develop, involving concept workshops and prototype testing; and deliver, in which the final minimal viable product was storyboarded and iteratively coded. Consistent with our previous work, the Thinking Well case series showed medium to large effects on paranoia and well-being and small effects on reasoning. These were maintained at follow-up despite some participants reporting difficulties with the therapy interface. Insights from the discover phase confirmed that usability was challenged by information complexity and poor accessibility. Participants were generally positive about the potential of technology to be enjoyable, help manage paranoia, and provide tailored interpersonal support from therapists and peers, although they reported privacy and security concerns. The define phase highlighted that the therapy redesign should support monitoring, simplify information processing, enhance enjoyment and trust, promote personalization and normalization, and offer flexible interpersonal support. During the develop phase over 60 concepts were created, with 2 key concepts of thoughts visualized as bubbles and therapy as a journey selected for storyboarding. The output of the deliver phase was a minimal viable product of an innovative digital therapy, SlowMo. SlowMo works by helping people to notice their worries and fast thinking habits, and encourages them to slow down for a moment to find ways of feeling safer. A Web app supports the delivery of 8 face-to-face sessions, which are synchronized to a native mobile app. SlowMo makes use of personalization, ambient information, and visual metaphors to tailor the appeal, engagement, and memorability of therapy to a diversity of needs. Feasibility testing has been promising, and the efficacy of SlowMo therapy is now being tested in a multicentered randomized controlled trial. The study demonstrates that developments in psychological theory and techniques can be enhanced by improving the usability of the therapy interface to optimize its impact in daily life. [Abstract copyright: ©Amy Hardy, Anna Wojdecka, Jonathan West, Ed Matthews, Christopher Golby, Thomas Ward, Natalie D Lopez, Daniel Freeman, Helen Waller, Elizabeth Kuipers, Paul Bebbington, David Fowler, Richard Emsley, Graham Dunn, Philippa Garety. Originally published in JMIR Mental Health (http://mental.jmir.org), 05.12.2018.

Deep Learning for Detection and Localization of B-Lines in Lung Ultrasound

Lung ultrasound (LUS) is an important imaging modality used by emergency physicians to assess pulmonary congestion at the patient bedside. B-line artifacts in LUS videos are key findings associated with pulmonary congestion. Not only can the interpretation of LUS be challenging for novice operators, but visual quantification of B-lines remains subject to observer variability. In this work, we investigate the strengths and weaknesses of multiple deep learning approaches for automated B-line detection and localization in LUS videos. We curate and publish, BEDLUS, a new ultrasound dataset comprising 1,419 videos from 113 patients with a total of 15,755 expert-annotated B-lines. Based on this dataset, we present a benchmark of established deep learning methods applied to the task of B-line detection. To pave the way for interpretable quantification of B-lines, we propose a novel "single-point" approach to B-line localization using only the point of origin. Our results show that (a) the area under the receiver operating characteristic curve ranges from 0.864 to 0.955 for the benchmarked detection methods, (b) within this range, the best performance is achieved by models that leverage multiple successive frames as input, and (c) the proposed single-point approach for B-line localization reaches an F1-score of 0.65, performing on par with the inter-observer agreement. The dataset and developed methods can facilitate further biomedical research on automated interpretation of lung ultrasound with the potential to expand the clinical utility.Comment: 10 pages, 4 figure

Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex

Lineage 7 (L7) emerged in the phylogeny of the Mycobacterium tuberculosis complex (MTBC) subsequent to the branching of 'ancient' lineage 1 and prior to the Eurasian dispersal of 'modern' lineages 2, 3 and 4. In contrast to the major MTBC lineages, the current epidemiology suggests that prevalence of L7 is highly confined to the Ethiopian population, or when identified outside of Ethiopia, it has mainly been in patients of Ethiopian origin. To search for microbiological factors that may contribute to its restricted distribution, we compared the genome of L7 to the genomes of globally dispersed MTBC lineages. The frequency of predicted functional mutations in L7 was similar to that documented in other lineages. These include mutations characteristic of modern lineages - such as constitutive expression of nitrate reductase - as well as mutations in the VirS locus that are commonly found in ancient lineages. We also identified and characterized multiple lineage-specific mutations in L7 in biosynthesis pathways of cell wall lipids, including confirmed deficiency of methoxy-mycolic acids due to a stop-gain mutation in the mmaA3 gene that encodes a methoxy-mycolic acid synthase. We show that the abolished biosynthesis of methoxy-mycolates of L7 alters the cell structure and colony morphology on selected growth media and impacts biofilm formation. The loss of these mycolic acid moieties may change the host-pathogen dynamic for L7 isolates, explaining the limited geographical distribution of L7 and contributing to further understanding the spread of MTBC lineages across the globe

The design and testing of large bore hose used for the offshore transportation of hydrocarbons

For many years the physical design of offshore hose has relied on subjective opinion and experience only occasionally populated by factual design criteria. Similarly the testing of the same could only be described as a faint shadow of reality. It was against this background and an increasing history of hose failures that the work described by this this thesis was initiated in the form of an I .H.D project put forward by Dunlop Limited. The thesis describes the initial investigation into the problem and how this was translated into long, mediwn and short term objectives together with an action plan necessary to achieve the same. A need for objective design information was identified in the very early stag-es of the project.This precipitated the setting up and conduction of field tests, offshore Nigeria 1973, designed to monitor the forces acting on such hoses at a Single Buoy Mooring installation. In order to extend the scope of the above tests a need was highlighted for the establishment of model testing facilities aimed at studying the submarine hose system design for such terminals. Such facilities were designed, installed .and resulted in the establishment of much desired information. On the basis of the above work, a full scale test rig was designed, in order to simulate load generation on hose under laboratory conditions. The rig as designed was installed during 1976/7, following which initial hose testing has been conducted. On the basis of results to date, all indicators point to a realistic testing situation (rig and service failures relate), which should enable future hose designs to be based on scientifical fact rather than opinion