Estimation of Parameters in DNA Mixture Analysis

In Cowell et al. (2007), a Bayesian network for analysis of mixed traces of DNA was presented using gamma distributions for modelling peak sizes in the electropherogram. It was demonstrated that the analysis was sensitive to the choice of a variance factor and hence this should be adapted to any new trace analysed. In the present paper we discuss how the variance parameter can be estimated by maximum likelihood to achieve this. The unknown proportions of DNA from each contributor can similarly be estimated by maximum likelihood jointly with the variance parameter. Furthermore we discuss how to incorporate prior knowledge about the parameters in a Bayesian analysis. The proposed estimation methods are illustrated through a few examples of applications for calculating evidential value in casework and for mixture deconvolution

Gaussian Belief with dynamic data and in dynamic network

In this paper we analyse Belief Propagation over a Gaussian model in a dynamic environment. Recently, this has been proposed as a method to average local measurement values by a distributed protocol ("Consensus Propagation", Moallemi & Van Roy, 2006), where the average is available for read-out at every single node. In the case that the underlying network is constant but the values to be averaged fluctuate ("dynamic data"), convergence and accuracy are determined by the spectral properties of an associated Ruelle-Perron-Frobenius operator. For Gaussian models on Erdos-Renyi graphs, numerical computation points to a spectral gap remaining in the large-size limit, implying exceptionally good scalability. In a model where the underlying network also fluctuates ("dynamic network"), averaging is more effective than in the dynamic data case. Altogether, this implies very good performance of these methods in very large systems, and opens a new field of statistical physics of large (and dynamic) information systems.Comment: 5 pages, 7 figure

Urban wind power and the private sector : community benefits, social acceptance and public engagement

Given the ambitious government targets for renewable energy generation in the UK, there has been a push by government and industry towards various types and scales of Renewable Energy Technologies (RETs). This paper explores the implications of commercial urban wind projects for local communities, drawing on a case study of proposals by ASDA to construct wind turbines in two semi-urban locations in the UK. The paper argues that community responses to the proposals were complex and varied and could not adequately be encapsulated by 'nimby' (not in my back yard) assignations. It concludes that while ASDA followed a process of consulting local people, this process highlighted the problems of the 'business as usual' approach to public engagement employed by ASDA, and assumptions made about public acceptance of RETs

Molecular characterisation of viruses from Kiwifruit

In 2003 Apple stem grooving virus was discovered in Actinidia accessions from China, being held in quarantine in Auckland. Subsequent examination of kiwifruit germplasm from the same source has detected several additional viruses, including a ~300 nm rigid rod related to Ribgrass mosaic virus (Tobamovirus), a 700-750 nm flexuous virus related to Citrus leaf blotch virus (Flexiviridae) and a novel vitivirus. Currently these viruses have not been reported from commercial kiwifruit crops in New Zealand or elsewhere. The biological properties of the viruses from kiwifruit and their phylogenetic relationships with similar viruses from other plants will be described, and the possible implications for the international movement of Actinidia germplasm are discussed

Predicting Climate-Driven Coastlines With a Simple and Efficient Multiscale Model

Ocean-basin-scale climate variability produces shifts in wave climates and water levels affecting the coastlines of the basin. Here we present a hybrid shoreline change?foredune erosion model (A COupled CrOss-shOre, loNg-shorE, and foreDune evolution model, COCOONED) intended to inform coastal planning and adaptation. COCOONED accounts for coupled longshore and cross-shore processes at different timescales, including sequencing and clustering of storm events, seasonal, interannual, and decadal oscillations by incorporating the effects of integrated varying wave action and water levels for coastal hazard assessment. COCOONED is able to adapt shoreline change rates in response to interactions between longshore transport, cross-shore transport, water level variations, and foredune erosion. COCOONED allows for the spatial and temporal extension of survey data using global data sets of waves and water levels for assessing the behavior of the shoreline at multiple time and spatial scales. As a case study, we train the model in the period 2004?2014 (11 years) with seasonal topographic beach profile surveys from the North Beach Sub-cell (NBSC) of the Columbia River Littoral Cell (Washington, USA).We explore the shoreline response and foredune erosion along 40 km of beach at several timescales during the period 1979?2014 (35 years), revealing an accretional trend producing reorientation of the beach, cross-shore accretional, and erosional periods through time (breathing) and alternating beach rotations that are correlated with climate indices.J. A. A. Antolínez and F. J. Méndez acknowledge the support of the Spanish “Ministerio de Economia y Competitividad” under Grant BIA2014-59643-R

High-sensitivity troponin I concentrations are a marker of an advanced hypertrophic response and adverse outcomes in patients with aortic stenosis

Aims: High-sensitivity cardiac troponin I (cTnI) assays hold promise in detecting the transition from hypertrophy to heart failure in aortic stenosis. We sought to investigate the mechanism for troponin release in patients with aortic stenosis and whether plasma cTnI concentrations are associated with long-term outcome. Methods and results: Plasma cTnI concentrations were measured in two patient cohorts using a high-sensitivity assay. First, in the Mechanism Cohort, 122 patients with aortic stenosis (median age 71, 67% male, aortic valve area 1.0 ± 0.4 cm2) underwent cardiovascular magnetic resonance and echocardiography to assess left ventricular (LV) myocardial mass, function, and fibrosis. The indexed LV mass and measures of replacement fibrosis (late gadolinium enhancement) were associated with cTnI concentrations independent of age, sex, coronary artery disease, aortic stenosis severity, and diastolic function. In the separate Outcome Cohort, 131 patients originally recruited into the Scottish Aortic Stenosis and Lipid Lowering Trial, Impact of REgression (SALTIRE) study, had long-term follow-up for the occurrence of aortic valve replacement (AVR) and cardiovascular deaths. Over a median follow-up of 10.6 years (1178 patient-years), 24 patients died from a cardiovascular cause and 60 patients had an AVR. Plasma cTnI concentrations were associated with AVR or cardiovascular death HR 1.77 (95% CI, 1.22 to 2.55) independent of age, sex, systolic ejection fraction, and aortic stenosis severity. Conclusions: In patients with aortic stenosis, plasma cTnI concentration is associated with advanced hypertrophy and replacement myocardial fibrosis as well as AVR or cardiovascular death

RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes

Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 ± 1 or 23 ± 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of pre-computed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing

The place of strategic environmental assessment in the privatised electricity industry

The private sector has given relatively little attention to the emergence of strategic environmental assessment (SEA); even recently privatised utilities, where SEA might be deemed particularly appropriate, and whose activities are likely to fall within the scope of the European Union SEA Directive, have shown less interest than might be expected. However, the global trend towards the privatisation of state-owned enterprises makes the adaptation of SEA towards these industries all the more pressing. This paper addresses the place that SEA might take within the electricity sector, taking the privatised UK electricity industry as an example. Particular challenges are posed by the radical restructuring of the industry, designed to introduce competitive behaviour, making the development of comprehensive SEA processes problematic, and requiring SEA to be placed in the context of corporate environmental policy and objectives.</p

aCGHViewer: A Generic Visualization Tool For aCGH data

Array-Comparative Genomic Hybridization (aCGH) is a powerful high throughput technology for detecting chromosomal copy number aberrations (CNAs) in cancer, aiming at identifying related critical genes from the affected genomic regions. However, advancing from a dataset with thousands of tabular lines to a few candidate genes can be an onerous and time-consuming process. To expedite the aCGH data analysis process, we have developed a user-friendly aCGH data viewer (aCGHViewer) as a conduit between the aCGH data tables and a genome browser. The data from a given aCGH analysis are displayed in a genomic view comprised of individual chromosome panels which can be rapidly scanned for interesting features. A chromosome panel containing a feature of interest can be selected to launch a detail window for that single chromosome. Selecting a data point of interest in the detail window launches a query to the UCSC or NCBI genome browser to allow the user to explore the gene content in the chromosomal region. Additionally, aCGHViewer can display aCGH and expression array data concurrently to visually correlate the two. aCGHViewer is a stand alone Java visualization application that should be used in conjunction with separate statistical programs. It operates on all major computer platforms and is freely available at http://falcon.roswellpark.org/aCGHview/