Christopher Tomlinson

The use of nanoelectronic devices in highly parallel computing systems

The continuing development of smaller electronic devices into the nanoelectronic regime offers great possibilities for the construction of highly parallel computers. This paper describes work designed to discover the best ways to take advantage of this opportunity. Simulated results are presented which indicate that improvements in clock rates of two orders of magnitude, and in packing density of three orders of magnitude, over the best current systems, should be attainable. These results apply to the class of data-parallel computers, and their attainment demands modifications to the design which are also described. Evaluation of the requirements of alternative classes of parallel architecture is currently under way, together with a study of the vitally important area of fault-tolerance.

MiMiR – an integrated platform for microarray data sharing, mining and analysis

BackgroundDespite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Mi croarray data Mi ning R esource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.ResultsA user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.ConclusionThe new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centres large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

The evolution of standards and data management practices in systems biology

A recent community survey conducted by Infrastructure for Systems Biology Europe (ISBE) informs requirements for developing an efficient infrastructure for systems biology standards, data and model management.

Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α).

Viruses that infect birds pose major threats—to the global supply of chicken, the major, universally-acceptable meat, and as zoonotic agents (e.g. avian influenza viruses H5N1 and H7N9). Controlling these viruses in birds as well as understanding their emergence into, and transmission amongst, humans will require considerable ingenuity and understanding of how different species defend themselves. The type I interferon-coordinated response constitutes the major antiviral innate defence. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals. Viruses induce interferon-stimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. This study focusses on the potentially anti-viral genes by identifying those induced just by interferon in primary chick embryo fibroblasts. Three transcriptomic technologies were exploited: RNA-seq, a classical 3′-biased chicken microarray and a high density, “sense target”, whole transcriptome chicken microarray, with each recognising 120–150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). Overall, the results are considered robust because 128 of the compiled, curated list of 193 regulated genes were detected by two, or more, of the technologies.

XperimentR: painless annotation of a biological experiment for the laboratory scientist

BackgroundToday’s biological experiments often involve the collaboration of multidisciplinary researchers utilising several high throughput ‘omics platforms. There is a requirement for the details of the experiment to be adequately described using standardised ontologies to enable data preservation, the analysis of the data and to facilitate the export of the data to public repositories. However there are a bewildering number of ontologies, controlled vocabularies, and minimum standards available for use to describe experiments. There is a need for user-friendly software tools to aid laboratory scientists in capturing the experimental information.ResultsA web application called XperimentR has been developed for use by laboratory scientists, consisting of a browser-based interface and server-side components which provide an intuitive platform for capturing and sharing experimental metadata. Information recorded includes details about the biological samples, procedures, protocols, and experimental technologies, all of which can be easily annotated using the appropriate ontologies. Files and raw data can be imported and associated with the biological samples via the interface, from either users’ computers, or commonly used open-source data repositories. Experiments can be shared with other users, and experiments can be exported in the standard ISA-Tab format for deposition in public databases. XperimentR is freely available and can be installed natively or by using a provided pre-configured Virtual Machine. A guest system is also available for trial purposes.ConclusionWe present a web based software application to aid the laboratory scientist to capture, describe and share details about their experiments.

Educating novice practitioners to detect elder financial abuse: a randomised controlled trial

BackgroundHealth and social care professionals are well positioned to identify and intervene in cases of elder financial abuse. An evidence-based educational intervention was developed to advance practitioners’ decision-making in this domain. The objective was to test the effectiveness of a decision-training educational intervention on novices’ ability to detect elder financial abuse. The research was funded by an E.S.R.C. grant reference RES-189-25-0334.MethodsA parallel-group, randomised controlled trial was conducted using a judgement analysis approach. Each participant used the World Wide Web to judge case sets at pre-test and post-test. The intervention group was provided with training after pre-test testing, whereas the control group were purely given instructions to continue with the task. 154 pre-registration health and social care practitioners were randomly allocated to intervention (n78) or control (n76). The intervention comprised of written and graphical descriptions of an expert consensus standard explaining how case information should be used to identify elder financial abuse. Participants’ ratings of certainty of abuse occurring (detection) were correlated with the experts’ ratings of the same cases at both stages of testing.ResultsAt pre-test, no differences were found between control and intervention on rating capacity. Comparison of mean scores for the control and intervention group at pre-test compared to immediate post-test, showed a statistically significant result. The intervention was shown to have had a positive moderate effect; at immediate post-test, the intervention group’s ratings had become more similar to those of the experts, whereas the control’s capacity did not improve. The results of this study indicate that the decision-training intervention had a positive effect on detection ability.ConclusionsThis freely available, web-based decision-training aid is an effective evidence-based educational resource. Health and social care professionals can use the resource to enhance their ability to detect elder financial abuse. It has been embedded in a web resource at http://www.elderfinancialabuse.co.uk.

Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women

Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.Metabolic activity of specific human gut microorganisms contributes to liver steatosis in obese women.

Effectiveness of a Decision-Training Aid on Referral Prioritization Capacity A Randomized Controlled Trial

Background. In the community mental health field, occupational therapy students lack the capacity to prioritize referrals effectively. Objective. The purpose of this study was to test the effectiveness of a clinical decision-training aid on referral prioritization capacity. Design. A double-blind, parallel-group, randomized controlled trial was conducted using a judgment analysis approach. Setting. Each participant used the World Wide Web to prioritize referral sets at baseline, immediate posttest, and 2-wk follow-up. The intervention group was provided with training after baseline testing; control group was purely given instructions to continue with the task. Participants. One hundred sixty-five students were randomly allocated to intervention (n = 87) or control (n = 81). Intervention. Written and graphical descriptions were given of an expert consensus standard explaining how referral information should be used to prioritize referrals. Measurements. Participants’ prioritization ratings were correlated with the experts’ ratings of the same referrals at each stage of testing, as well as to examine the effect on mean group scores, regression weights, and the lens model indices. Results. At baseline, no differences were found between control and intervention on rating capacity or demographic characteristics. Comparison of the difference in mean correlation baseline scores of the control and intervention group compared with immediate posttest showed a statistically significant result that was maintained at 2-wk follow-up. The effect size was classified as large. At immediate posttest and follow-up, the intervention group improved rating capacity, whereas the control group’s capacity remained poor. The results of this study indicate that the decision-training aid has a positive effect on referral prioritization capacity. Conclusions. This freely available, Web-based decision-training aid will be a valuable adjunct to the education of these novice health professionals internationally.

The propagated instruction processor

As the dimensions of electronic devices become smaller, they enter the realm of nano-electronics, where the device dimensions lie between the inter-atomic spacing (lnm) and the electron wavelength (lOnm). This offers greatly-enhanced packing density and speed of operation, but introduces the difficulty of maintaining signal quality over large distances. The paper introduces an architectural solution to this problem which is appropriate for the class of highly data-parallel computers [1,2,3]. In the propagated instruction architecture proposed here, instructions sweep across the array (and hence across the data set) in bands, one instruction following another closely. The paper examines the architectural implications of this idea, and assesses the benefits in the application area of image processing.

Defining functional interactions during biogenesis of epithelial junctions

In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases.