Knowledge Exchange, Spatial Analysis & Healthy Urban Environments (KESUE): Project Report

The Knowledge Exchange, Spatial Analysis and Healthy Urban Environments (KESUE) project has extended work previously undertaken by a QUB team of inter-disciplinary researchers engaged with the Physical Activity in the Regeneration of Connswater (PARC) project (Tully et al, 2013). The PARC project focussed on parts of East Belfast to assess the health impact of the Connswater Community Greenway. The KESUE project has aimed to extend some of the tools used initially in East Belfast so that they have data coverage of all of Belfast and Derry-Londonderry. The purpose of this has been to enable the development of evidence and policy tools that link features of the built environment with physical activity in these two cities. The project has used this data to help shape policy decisions in areas such as physical activity, park management, public transport and planning.

Working with a range of local partners who part-funded the project (City Councils in Belfast and Derry-Londonderry, Public Health Agency, Belfast Healthy Cities and Department of Regional Development), this project has mapped all the footpaths in the two cities (covering 37% of the NI population) and employed this to develop evidence used in strategies related to healthy urban planning. Using Geographic Information Systems (GIS), the footpath network has been used as a basis for a wide range of policy-relevant analyses including pedestrian accessibility to public facilities, site options for new infrastructure and assessing how vulnerable groups can access services such as pharmacies. Key outputs have been Accessibility Atlases and maps showing how walkability of the built environment varies across the two cities.

In addition to generating this useful data, the project included intense engagement with potential users of the research, which has led to its continued uptake in a number of policies and strategies, creating a virtuous circle of research, implementation and feedback. The project has proved so valuable to Belfast City Council that they have now taken on one of the researchers to continue the work in-house.

The paradox of invasion: Reeves’ muntjac deer invade the British Isles from a limited number of founding females

High levels of genetic diversity and high propagule pressure are favoured by conservation biologists as the basis for successful reintroductions and ensuring the persistence of populations. However, invasion ecologists recognize the ‘paradox of invasion’, as successful species introductions may often be characterized by limited numbers of individuals and associated genetic bottlenecks. In the present study, we used a combination of high-resolution nuclear and mitochondrial genetic markers to investigate the invasion history of Reeves' muntjac deer in the British Isles. This invasion has caused severe economic and ecological damage, with secondary spread currently a concern throughout Europe and potentially globally. Microsatellite analysis based on eight loci grouped all 176 introduced individuals studied from across the species' range in the UK into one genetic cluster, and seven mitochondrial D-loop haplotypes were recovered, two of which were present at very low frequency and were related to more common haplotypes. Our results indicate that the entire invasion can be traced to a single founding event involving a low number of females. These findings highlight the fact that even small releases of species may, if ignored, result in irreversible and costly invasion, regardless of initial genetic diversity or continual genetic influx.

Covering over the cracks in conservation assessments at EU interfaces: A cross-jurisdictional ecoregion scale approach using the Eurasian otter (Lutra lutra)

Throughout the European Union, the EC Habitats Directive requires that member states undertake national surveillance of designated species. Despite biological connections between-populations across-borders, national assessments need not be co-ordinated in any way. We conducted a trans-boundary assessment of the status of Eurasian otters (Lutra lutra) aimed at providing consistency across a single biogeographical unit, i.e. the island of Ireland, comprising two states, i.e. the Republic of Ireland and the United Kingdom (Northern Ireland). Our aim was to ensure consistency with previous assessments conducted separately in each state, and permit each Government to fulfil their separate statutory reporting commitments. The species range increased by 23% from 1996–2006 and 2007–11. The population estimate of 9400 [95%CI 8700–12,200] breeding females during 2010/11 was not significantly different from 8300 [95%CI 7600–9800] breeding females established as a baseline during 1981–82. Modelling of species-habitat associations suggested that available habitat was not limiting and no putative pressures recorded at sites surveyed negatively affected species occurrence. Thus, under the statutory parameters for assessing a species’ conservation status, i.e. range, population, habitat and future prospects, the otter was judged to be in ‘Favourable’ status throughout Ireland and in both discrete political jurisdictions. Thus, we provide a trans-boundary test case for EU member states that share habitats and species across ecoregions, ensuring conservation assessment data are standardised, synchronised, spatially consistent and, therefore, biologically relevant without compromising legal and administrative autonomy within separate jurisdictions.

Magnetic Characteristics of a High-layer-number NiFe/FeMn Multilayer

We report the static & dynamic magnetic characteristics of a high-layer-number NiFe/FeMn multilayer test structure with potential applications in broadband absorber and filter devices. To allow fine control over the absorption linewidths and to understand the mechanisms governing the resonances in a tailored structure similar to that expected to be used in real world applications, the multilayer was intentionally designed to have layer thickness and interface roughness variations. Magnetometry measurements show the sample has complex hysteresis loops with features consistent with single ferromagnetic film reversals. Structural characterisation by transmission electron microscopy allows us to correlate the magnetic properties with structural features. Analysis of resonance frequencies from broadband ferromagnetic resonance measurements as a function of field magnitude and orientation provide values of the local exchange bias, rotatable anisotropy, and uniaxial anisotropy fields for specific layers in the stack and explain the observed mode softening. The linewidths of the multilayer are adjustable around the bias field, approaching twice that seen at larger fields, allowing control over the bandwidth of devices formed from the structure.

Low alanine aminotransferase levels and higher number of cardiovascular events in people with Type 2 diabetes: analysis of the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) study.

AIMS: To determine whether alanine aminotransferase or gamma-glutamyltransferase levels, as markers of liver health and non-alcoholic fatty liver disease, might predict cardiovascular events in people with Type 2 diabetes.

METHODS: Data from the Fenofibrate Intervention and Event Lowering in Diabetes study were analysed to examine the relationship between liver enzymes and incident cardiovascular events (non-fatal myocardial infarction, stroke, coronary and other cardiovascular death, coronary or carotid revascularization) over 5 years.

RESULTS: Alanine aminotransferase level had a linear inverse relationship with the first cardiovascular event occurring in participants during the study period. After adjustment, for every 1 sd higher baseline alanine aminotransferase value (13.2 U/l), the risk of a cardiovascular event was 7% lower (95% CI 4-13; P=0.02). Participants with alanine aminotransferase levels below and above the reference range 8-41 U/l for women and 9-59 U/l for men, had hazard ratios for a cardiovascular event of 1.86 (95% CI 1.12-3.09) and 0.65 (95% CI 0.49-0.87), respectively (P=0.001). No relationship was found for gamma-glutamyltransferase.

CONCLUSIONS: The data may indicate that in people with Type 2 diabetes, which is associated with higher alanine aminotransferase levels because of prevalent non-alcoholic fatty liver disease, a low alanine aminotransferase level is a marker of hepatic or systemic frailty rather than health. This article is protected by copyright. All rights reserved.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

The Application of Geophysics to a Number of Threats to Irish Soils

In its 2002 Communication "Towards a Thematic Strategy on Soil Protection" (COM 2002, 179), the Commission identified the main threats to which soils in the EU are confronted. More recently, the EU published a Thematic Strategy for Soil Protection (COM 2006, 231) as well as a proposal for a Soil Framework Directive (COM 2006, 232). The proposed directive, if implemented, will require states to identify a number of specific soil degradation processes that have occurred or are likely to occur in the near future. This project applies a number of recent geophysical developments, in addition to a range of traditional approaches, to a number of areas of Irish concern to Thematic Strategy for Soil Protection and the proposed Soil Framework Directive.