TcruziKB: Enabling Complex Queries for Genomic Data Exploration

We developed a novel analytical environment to aid in the examination of the extensive amount of interconnected data available for genome projects. Our focus is to enable flexibility and abstraction from implementation details, while retaining the expressivity required for post-genomic research. To achieve this goal, we associated genomics data to ontologies and implemented a query formulation and execution environment with added visualization capabilities. We use ontology schemas to guide the user through the process of building complex queries in a flexible Web interface. Queries are serialized in SPARQL and sent to servers via Ajax. A component for visualization of the results allows researchers to explore result sets in multiple perspectives to suit different analytical needs. We show a use case of semantic computing with real world data. We demonstrate facilitated access to information through expressive queries in a flexible and friendly user interface. Our system scores 90.54% in a user satisfaction evaluation with 30 subjects. In comparison with traditional genome databases, preliminary evaluation indicates a reduction of the amount of user interaction required to answer the provided sample queries

End stage renal disease and survival in people with diabetes:a national database linkage study

© The Author 2014. Published by Oxford University Press on behalf of the Association of Physicians. Funding This work was supported by the Wellcome Trust through the Scottish Health Informatics Programme (SHIP). The SHIP is collaboration between the Universities of Aberdeen, Dundee, Edinburgh, Glasgow and St Andrews and the Information Services Division of National Health Service National Service Scotland. Funding for diabetes register linkage and data extraction was provided by the Chief Scientist’s Office of the Scottish Government. The Scottish Diabetes Research Network receives financial support from National Health Services Research Scotland. The Scottish Renal Registry is funded by the Information Services Division of National Health Service National Services Scotland but relies heavily on the goodwill of the contributing renal units who spent a large amount time working with Scottish Renal Registry staff to ensure that the data held within the register are accurate and complete.Peer reviewedPublisher PD

A calculus for distrust and mistrust

Properties of trust are becoming widely studied in several applications within the computational domain. On the contrary, negative trust attribution is less well-defined and related issues are yet to be approached and resolved. We present a natural deduction calculus for trust protocols and its negative forms, distrust and mistrust. The calculus deals efficiently with forms of trust transitivity and negative trust multiplication and we briefly illustrate some possible applications

Late Miocene to early Pliocene biofacies of Wanganui and Taranaki Basins, New Zealand: Applications to paleoenvironmental and sequence stratigraphic analysis

The Matemateaonga Formation is late Miocene to early Pliocene (upper Tongaporutuan to lower Opoitian New Zealand Stages) in age. The formation comprises chiefly shellbeds, siliciclastic sandstone, and siltstone units and to a lesser extent non-marine and shallow marine conglomerate and rare paralic facies. The Matemateaonga Formation accumulated chiefly in shelf paleoenvironments during basement onlap and progradation of a late Miocene to early Pliocene continental margin wedge in the Wanganui and Taranaki Basins. The formation is strongly cyclothemic, being characterised by recurrent vertically stacked facies successions, bounded by sequence boundaries. These facies accumulated in a range of shoreface to mid-outer shelf paleoenvironments during conditions of successively oscillating sea level. This sequential repetition of facies and the biofacies they enclose are the result of sixth-order glacio-eustatic cyclicity. Macrofaunal associations have been identified from statistical analysis of macrofossil occurrences collected from multiple sequences. Each association is restricted to particular lithofacies and stratal positions and shows a consistent order and/or position within the sequences. This pattern of temporal paleoecologic change appears to be the result of lateral, facies-related shifting of broad biofacies belts, or habitat-tracking, in response to fluctuations of relative sea level, sediment flux, and other associated paleoenvironmental variables. The associations also show strong similarity in terms of their generic composition to biofacies identified in younger sedimentary strata and the modern marine benthic environment in New Zealand

Rates of referable eye disease in the Scottish National Diabetic Retinopathy Screening Programme

Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.Peer reviewedPublisher PD

Infrared Hall effect in high Tc superconductors: Evidence for non-Fermi liquid Hall scattering

Infrared (20-120 cm-1 and 900-1100 cm-1) Faraday rotation and circular dichroism are measured in high Tc superconductors using sensitive polarization modulation techniques. Optimally doped YBCO thin films are studied at temperatures down to 15 K and magnetic fields up to 8 T. At 1000 cm-1 the Hall conductivity varies strongly with temperature in contrast to the longitudinal conductivity which is nearly independent of temperature. The Hall scattering rate has a T^2 temperature dependence but, unlike a Fermi liquid, depends only weakly on frequency. The experiment puts severe constraints on theories of transport in the normal state of high Tc superconductors.Comment: 8 pages, 3 figure

Mid-infrared Hall effect in thin-film metals: Probing the Fermi surface anisotropy in Au and Cu

A sensitive mid-infrared (MIR, 900-1100 cm-1, 112-136 meV) photo-elastic polarization modulation technique is used to measure simultaneously Faraday rotation and circular dichroism in thin metal films. These two quantities determine the complex AC Hall conductivity. This novel technique is applied to study Au and Cu thin films at temperatures down to 20 K and magnetic fields up to 8 T. The Hall frequency is consistent with band theory predictions. We report the first measurement of the MIR Hall scattering rate, which is significantly lower than that derived from Drude analysis of zero magnetic field MIR transmission measurements. This difference is qualitatively explained in terms of the anisotropy of the Fermi surface in Au and Cu.Comment: 14 pages of text, 5 figure

Longitudinal assessment of symptoms and risk of SARS-CoV-2 infection in healthcare workers across 5 hospitals to understand ethnic differences in infection risk.

BACKGROUND: Healthcare workers (HCWs) have increased rates of SARS-CoV-2 infection compared with the general population. We aimed to understand ethnic differences in SARS-CoV-2 seropositivity among hospital healthcare workers depending on their hospital role, socioeconomic status, Covid-19 symptoms and basic demographics. METHODS: A prospective longitudinal observational cohort study. 1364 HCWs at five UK hospitals were studied with up to 16 weeks of symptom questionnaires and antibody testing (to both nucleocapsid and spike protein) during the first UK wave in five NHS hospitals between March 20 and July 10 2020. The main outcome measures were SARS-CoV-2 infection (seropositivity at any time-point) and symptoms. Registration number: NCT04318314. FINDINGS: 272 of 1364 HCWs (mean age 40.7 years, 72% female, 74% White, ≥6 samples per participant) seroconverted, reporting predominantly mild or no symptoms. Seropositivity was lower in Intensive Therapy Unit (ITU) workers (OR=0.44 95%CI 0.24, 0.77; p=0.0035). Seropositivity was higher in Black (compared to White) participants, independent of age, sex, role and index of multiple deprivation (OR=2.61 95%CI 1.47-4.62 p=0.0009). No association was seen between White HCWs and other minority ethnic groups. INTERPRETATION: In the UK first wave, Black ethnicity (but not other ethnicities) more than doubled HCWs likelihood of seropositivity, independent of age, sex, measured socio-economic factors and hospital role

Visualisation of trust and quality information for geospatial dataset selection and use:Drawing trust presentation comparisons with B2C e-Commerce

The evaluation of geospatial data quality and trustworthiness presents a major challenge to geospatial data users when making a dataset selection decision. Part of the problem arises from the inconsistent and patchy nature of data quality information, which makes intercomparison very difficult. Over recent years, the production and availability of geospatial data has significantly increased, facilitated by the recent explosion of Web-based catalogues, portals, standards and services, and by initiatives such as INSPIRE and GEOSS. Despite this significant growth in availability of geospatial data and the fact that geospatial datasets can, in many respects, be considered commercial products that are available for purchase online, consumer trust has to date received relatively little attention in the GIS domain. In this paper, we discuss how concepts of trust, trust models, and trust indicators (largely derived from B2C e-Commerce) apply to the GIS domain and to geospatial data selection and use. Our research aim is to support data users in more efficient and effective geospatial dataset selection on the basis of quality, trustworthiness and fitness for purpose. To achieve this, we propose a GEO label – a decision support mechanism that visually summarises availability of key geospatial data informational aspects. We also present a Web service that was developed to support generation of dynamic GEO label representations for datasets by combining producer metadata (from standard catalogues or other published locations) with structured user feedback

Cohort Profile:Scottish Diabetes Research Network Type 1 Bioresource Study (SDRNT1BIO)

No abstract available