Efficient Bayesian-based Multi-View Deconvolution

Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the sam- ples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited due to the large size of the datasets. Here we present a Bayesian- based derivation of multi-view deconvolution that drastically improves the convergence time and provide a fast implementation utilizing graphics hardware.Comment: 48 pages, 20 figures, 1 table, under review at Nature Method

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role

phenosim - A software to simulate phenotypes for testing in genome-wide association studies

<p>Abstract</p> <p>Background</p> <p>There is a great interest in understanding the genetic architecture of complex traits in natural populations. Genome-wide association studies (GWAS) are becoming routine in human, animal and plant genetics to understand the connection between naturally occurring genotypic and phenotypic variation. Coalescent simulations are commonly used in population genetics to simulate genotypes under different parameters and demographic models.</p> <p>Results</p> <p>Here, we present <monospace>phenosim</monospace>, a software to add a phenotype to genotypes generated in time-efficient coalescent simulations. Both qualitative and quantitative phenotypes can be generated and it is possible to partition phenotypic variation between additive effects and epistatic interactions between causal variants. The output formats of <monospace>phenosim</monospace> are directly usable as input for different GWAS tools. The applicability of <monospace>phenosim</monospace> is shown by simulating a genome-wide association study in <it>Arabidopsis thaliana</it>.</p> <p>Conclusions</p> <p>By using the coalescent approach to generate genotypes and <monospace>phenosim</monospace> to add phenotypes, the data sets can be used to assess the influence of various factors such as demography, genetic architecture or selection on the statistical power of association methods to detect causal genetic variants under a wide variety of population genetic scenarios. <monospace>phenosim</monospace> is freely available from the authors' website <url>http://evoplant.uni-hohenheim.de</url></p

Spatiotemporal PET reconstruction using ML-EM with learned diffeomorphic deformation

Patient movement in emission tomography deteriorates reconstruction quality because of motion blur. Gating the data improves the situation somewhat: each gate contains a movement phase which is approximately stationary. A standard method is to use only the data from a few gates, with little movement between them. However, the corresponding loss of data entails an increase of noise. Motion correction algorithms have been implemented to take into account all the gated data, but they do not scale well, especially not in 3D. We propose a novel motion correction algorithm which addresses the scalability issue. Our approach is to combine an enhanced ML-EM algorithm with deep learning based movement registration. The training is unsupervised, and with artificial data. We expect this approach to scale very well to higher resolutions and to 3D, as the overall cost of our algorithm is only marginally greater than that of a standard ML-EM algorithm. We show that we can significantly decrease the noise corresponding to a limited number of gates

Learning from contract change in primary care dentistry: a qualitative study of stakeholders in the north of England

The aim of this research was to explore and synthesise learning from stakeholders (NHS dentists, commissioners and patients) approximately five years on from the introduction of a new NHS dental contract in England. The case study involved a purposive sample of stakeholders associated with a former NHS Primary Care Trust (PCT) in the north of England. Semi-structured interviews were conducted with 8 commissioners of NHS dental services and 5 NHS general dental practitioners. Three focus group meetings were held with 14 NHS dental patients. All focus groups and interviews were audio recorded and transcribed verbatim. The data were analysed using a framework approach. Four themes were identified: ‘commissioners’ views of managing local NHS dental services’; ‘the risks of commissioning for patient access’; ‘costs, contract currency and commissioning constraints’; and ‘local decision-making and future priorities’. Commissioners reported that much of their time was spent managing existing contracts rather than commissioning services. Patients were unclear about the NHS dental charge bands and dentists strongly criticised the contract's target-driven approach which was centred upon them generating ‘units of dental activity’. NHS commissioners remained relatively constrained in their abilities to reallocate dental resources amongst contracts. The national focus upon practitioners achieving their units of dental activity appeared to outweigh interest in the quality of dental care provided

Paediatric obsessive-compulsive disorder and depressive symptoms: clinical correlates and CBT treatment outcomes.

Depression frequently co-occurs with paediatric obsessive-compulsive disorder (OCD), yet the clinical correlates and impact of depression on CBT outcomes remain unclear. The prevalence and clinical correlates of depression were examined in a paediatric specialist OCD-clinic sample (N = 295; Mean = 15 [7 - 18] years, 42 % female), using both dimensional (Beck Depression Inventory-youth; n = 261) and diagnostic (Development and Wellbeing Assessment; n = 127) measures of depression. The impact of depressive symptoms and suspected disorders on post-treatment OCD severity was examined in a sub-sample who received CBT, with or without SSRI medication (N = 100). Fifty-one per-cent of patients reported moderately or extremely elevated depressive symptoms and 26 % (95 % CI: 18 - 34) met criteria for a suspected depressive disorder. Depressive symptoms and depressive disorders were associated with worse OCD symptom severity and global functioning prior to CBT. Individuals with depression were more likely to be female, have had a psychiatric inpatient admission and less likely to be attending school (ps < 0.01). OCD and depressive symptom severity significantly decreased after CBT. Depressive symptoms and depressive disorders predicted worse post-treatment OCD severity (βs = 0.19 and 0.26, ps < 0.05) but became non-significant when controlling for pre-treatment OCD severity (βs = 0.05 and 0.13, ns). Depression is common in paediatric OCD and is associated with more severe OCD and poorer functioning. However, depression severity decreases over the course of CBT for OCD and is not independently associated with worse outcomes, supporting the recommendation for treatment as usual in the presence of depressive symptoms

Knowledge generation about care-giving in the UK: a critical review of research paradigms

While discourse about care and caring is well developed in the UK, the nature of knowledge generation about care and the research paradigms that underpin it have been subjected to limited critical reflection and analysis. An overarching synthesis of evidence – intended to promote debate and facilitate new understandings – identifies two largely separate bodies of carer-related research. The first body of work – referred to as Gathering and Evaluating – provides evidence of the extent of caregiving, who provides care to whom and with what impact; it also focuses on evaluating policy and service efficacy. This type of research tends to dominate public perception about caring, influences the type and extent of policy and support for carers and attracts funding from policy and health-related sources. However, it also tends to be conceptually and theoretically narrow, has limited engagement with carers’ perspectives and adopts an atomistic purview on the care-giving landscape. The second body of work – Conceptualising and Theorising – explores the conceptual and experiential nature of care and aims to extend thinking and theory about caring. It is concerned with promoting understanding of care as an integral part of human relationships, embedded in the life course, and a product of interdependence and reciprocity. This work conceptualises care as both an activity and a disposition and foregrounds the development of an ‘ethic of care’, thereby providing a perspective within which to recognise both the challenges care-giving may present and the significance of care as a normative activity. It tends to be funded from social science sources and, while strong in capturing carers’ experiences, has limited policy and service-related purchase. Much could be gained for citizens, carers and families, and the generation of knowledge advanced, if the two bodies of research were integrated to a greater degree