Statistical Comparison of Classifiers Applied to the Interferential Tear Film Lipid Layer Automatic Classification

The tear film lipid layer is heterogeneous among the population. Its classification depends on its thickness and can be done using the interference pattern categories proposed by Guillon. The interference phenomena can be characterised as a colour texture pattern, which can be automatically classified into one of these categories. From a photography of the eye, a region of interest is detected and its low-level features are extracted, generating a feature vector that describes it, to be finally classified in one of the target categories. This paper presents an exhaustive study about the problem at hand using different texture analysis methods in three colour spaces and different machine learning algorithms. All these methods and classifiers have been tested on a dataset composed of 105 images from healthy subjects and the results have been statistically analysed. As a result, the manual process done by experts can be automated with the benefits of being faster and unaffected by subjective factors, with maximum accuracy over 95%

Asymmetric base-pair opening drives helicase unwinding dynamics

The opening of a Watson-Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix

On Chip Implementation of a Pixel-Parallel Approach for Retinal Vessel Tree Extraction

Abstract-Retinal vessel tree extraction from angiography images play an important role not only in the medical domain, but also in biometric identification applications. From the image processing point of view, a lot of algorithms and strategies have been developed to deal with this topic. Although reliable results have been obtained, the main disadvantage in most of these proposals is still the high computation effort required. In this paper, a methodology to extract the retinal vessel tree has been developed, specially defined in terms of fine grain SIMD processing with the purpose of improving the computation time. The proposal has been implemented on the SIMD processor array chip SCAMP-3. The execution times for the main modules of the proposed algorithm have been included to show its capability

Vector-like Singlet Quarks: a Roadmap

We review the theory and phenomenology of isosinglet vector-like quarks (VLQs). In recent years, interest in VLQs has been increasing, due to their contributions to new physics effects that can be tested in experiments at LHC and High-Luminosity LHC. The similarities of models with isosinglet VLQs and the seesaw framework in the leptonic sector are pointed out. The existence of VLQs leads to flavour-changing neutral currents at tree level and deviations from unitarity of the CKM matrix, introducing rich phenomenological implications. These new effects are naturally suppressed by the masses of the new quarks, that are constrained to be above the electroweak scale. In addition, striking new effects can be achieved with the inclusion of an extra complex scalar singlet. Such a minimal extension of the SM can give rise to new sources of CP violation with profound theoretical implications, allowing for a solution to the strong CP problem and a possible explanation for the baryon asymmetry of the Universe. We list and explain strong motivations to consider this class of models. We also briefly review how models with VLQs can be matched to the SM effective field theory (SMEFT). A detailed analysis of flavour observables that can be affected by the presence of VLQs is presented. Current bounds from collider searches of VLQs are summarized. We point out that the discovery of VLQs can be within the reach of present or future colliders being planned.Comment: 109 pages, 7 figures, 7 tables. Work intended as a review. Comments, suggestions and missing references are welcome

Physical activity and health related quality of life

Copyright @ 2012 Anokye et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.BACKGROUND: Research on the relationship between Health Related Quality of Life (HRQoL) and physical activity (PA), to date, have rarely investigated how this relationship differ across objective and subjective measures of PA. The aim of this paper is to explore the relationship between HRQoL and PA, and examine how this relationship differs across objective and subjective measures of PA, within the context of a large representative national survey from England. METHODS: Using a sample of 5,537 adults (40–60 years) from a representative national survey in England (Health Survey for England 2008), Tobit regressions with upper censoring was employed to model the association between HRQoL and objective, and subjective measures of PA controlling for potential confounders. We tested the robustness of this relationship across specific types of PA. HRQoL was assessed using the summary measure of health state utility value derived from the EuroQol-5 Dimensions (EQ-5D) whilst PA was assessed via subjective measure (questionnaire) and objective measure (accelerometer- actigraph model GT1M). The actigraph was worn (at the waist) for 7 days (during waking hours) by a randomly selected sub-sample of the HSE 2008 respondents (4,507 adults – 16 plus years), with a valid day constituting 10 hours. Analysis was conducted in 2010. RESULTS: Findings suggest that higher levels of PA are associated with better HRQoL (regression coefficient: 0.026 to 0.072). This relationship is consistent across different measures and types of PA although differences in the magnitude of HRQoL benefit associated with objective and subjective (regression coefficient: 0.047) measures of PA are noticeable, with the former measure being associated with a relatively better HRQoL (regression coefficient: 0.072). CONCLUSION: Higher levels of PA are associated with better HRQoL. Using an objective measure of PA compared with subjective shows a relatively better HRQoL.This project was funded by the NIHR Health Technology Assessment programme (project number 08/72/01)

Dual origins of dairy cattle farming - evidence from a comprehensive survey of European Y-chromosomal variation

BACKGROUND: Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS: Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS: We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.Penedo, Lenstra mail

To what extent is climate change adaptation a novel challenge for agricultural modellers?

Modelling is key to adapting agriculture to climate change (CC), facilitating evaluation of the impacts and efficacy of adaptation measures, and the design of optimal strategies. Although there are many challenges to modelling agricultural CC adaptation, it is unclear whether these are novel or, whether adaptation merely adds new motivations to old challenges. Here, qualitative analysis of modellers’ views revealed three categories of challenge: Content, Use, and Capacity. Triangulation of findings with reviews of agricultural modelling and Climate Change Risk Assessment was then used to highlight challenges specific to modelling adaptation. These were refined through literature review, focussing attention on how the progressive nature of CC affects the role and impact of modelling. Specific challenges identified were: Scope of adaptations modelled, Information on future adaptation, Collaboration to tackle novel challenges, Optimisation under progressive change with thresholds, and Responsibility given the sensitivity of future outcomes to initial choices under progressive change

The effectiveness of a preferred intensity exercise programme on the mental health outcomes of young people with depression: a sequential mixed methods evaluation

<p>Abstract</p> <p>Background</p> <p>People with mental illness are more likely to suffer physical health problems than comparable populations who do not have mental illness. There is evidence to suggest that exercise, as well has having obvious physical benefits, also has positive effects on mental health. There is a distinct paucity of research testing its effects on young people seeking help for mental health issues. Additionally, it is generally found that compliance with prescribed exercise programmes is low. As such, encouraging young people to exercise at levels recommended by national guidelines may be unrealistic considering their struggle with mental health difficulties. It is proposed that an exercise intervention tailored to young people's preferred intensity may improve mental health outcomes, overall quality of life, and reduce exercise attrition rates.</p> <p>Methods/Design</p> <p>A sequential mixed methods design will be utilised to assess the effectiveness of an individually tailored exercise programme on the mental health outcomes of young people with depression. The mixed methods design incorporates a Randomised Controlled Trial (RCT), focus groups and interviews and an economic evaluation. <it>Participants: </it>158 young people (14-17 years) recruited from primary care and voluntary services randomly allocated to either the intervention group or control group. <it>Intervention group</it>: Participants will undertake a 12 week exercise programme of 12 × 60 minutes of preferred intensity aerobic exercise receiving motivational coaching and support throughout. Participants will also be invited to attend focus groups and 1-1 interviews following completion of the exercise programme to illicit potential barriers facilitators to participation. <it>Control group</it>: Participants will receive treatment as usual. <it>Primary Outcome measure</it>: Depression using the Children's Depression Inventory 2 (CDI-2). <it>Secondary Outcome measures</it>: Quality of Life (EQ-5D), physical fitness (Borg RPE scale, heart rate), incidents of self-harm, treatment received and compliance with treatment, and the cost effectiveness of the intervention. Outcome measures will be taken at baseline, post intervention and 6 month follow up.</p> <p>Discussion</p> <p>The results of this study will inform policy makers of the effectiveness of preferred intensity exercise on the mental health outcomes of young people with depression, the acceptability of such an intervention to this population and its cost effectiveness.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT01474837">NCT01474837</a></p

Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses

Champagne coat color in horses is controlled by a single, autosomal-dominant gene (CH). The phenotype produced by this gene is valued by many horse breeders, but can be difficult to distinguish from the effect produced by the Cream coat color dilution gene (CR). Three sires and their families segregating for CH were tested by genome scanning with microsatellite markers. The CH gene was mapped within a 6 cM region on horse chromosome 14 (LOD = 11.74 for θ = 0.00). Four candidate genes were identified within the region, namely SPARC [Secreted protein, acidic, cysteine-rich (osteonectin)], SLC36A1 (Solute Carrier 36 family A1), SLC36A2 (Solute Carrier 36 family A2), and SLC36A3 (Solute Carrier 36 family A3). SLC36A3 was not expressed in skin tissue and therefore not considered further. The other three genes were sequenced in homozygotes for CH and homozygotes for the absence of the dilution allele (ch). SLC36A1 had a nucleotide substitution in exon 2 for horses with the champagne phenotype, which resulted in a transition from a threonine amino acid to an arginine amino acid (T63R). The association of the single nucleotide polymorphism (SNP) with the champagne dilution phenotype was complete, as determined by the presence of the nucleotide variant among all 85 horses with the champagne dilution phenotype and its absence among all 97 horses without the champagne phenotype. This is the first description of a phenotype associated with the SLC36A1 gene