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

The quest for a donor: probability based methods offer help

When a patient in need of a stem cell transplant has no compatible donor within his or her closest family, and no matched unrelated donor can be found, a remaining option is to search within the patient’s extended family. This situation often arises when the patient is of an ethnic minority, originating from a country that lacks a well-developed stem cell donor program, and has HLA haplotypes that are rare in his or her country of residence. Searching within the extended family may be time-consuming and expensive, and tools to calculate the probability of a match within groups of untested relatives would facilitate the search. We present a general approach to calculating the probability of a match in a given relative, or group of relatives, based on the pedigree, and on knowledge of the genotypes of some of the individuals. The method extends previous approaches by allowing the pedigrees to be consanguineous and arbitrarily complex, with deviations from Hardy-Weinberg equilibrium. We show how this extension has a considerable effect on results, in particular for rare haplotypes. The methods are exemplified using freeware programs to solve a case of practical importance

Word frequency predicts translation asymmetry

Bilingualism studies report asymmetries in word processing across languages. Access to L2 words is slower and sensitive to semantic blocking. These observations inform influential models of bilingual processing, which propose autonomous lexicons with different processing routes. In a series of experiments, we explored an alternative hypothesis that the asymmetries are due to frequency of use. Using a within-language ‘translation’ task, involving high/low frequency (HF/LF) synonyms, we obtained parallel results to bilingual studies. Experiment 1 revealed that HF synonyms were accessed faster than LF ones. Experiment 2 showed that semantic blocking slowed retrieval only of LF synonyms, while form blocking produced powerful interference of both HF and LF words. Experiment 3 examined translation speed and sensitivity to blocking in two groups of Russian-English bilinguals who differed in frequency of use of their languages. Translation asymmetries were modulated by frequency of use. The results support an integrated lexicon model of bilingual processing

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

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

Penicillium bilaji (PB50) and phosphorus fertilizer responses of yield of wheat and barley grown on stubble and summerfallow

Non-Peer Reviewe

Transgressive coastal systems (2nd part): geometric principles of stratal preservation on gently sloping continental shelves

This study focuses on the causes and mechanisms of coastal-lithosome preservation during transgressions driven by roll-over processes of barrier migration. Using the Shoreface Translation Model, a large range of idealised coastal settings was simulated to identify the environmental conditions of stratal preservation. Preservation occurs within two broad categories of experimental conditions. The first category relates to transgressive phases evolving under relatively constant conditions in which stratal preservation takes place only if the coastal barrier experiences positive net sediment supplies. The resulting deposits show tabular geometries, have poorly differentiated internal architectures and tend to extend continuously with quite uniform thickness upslope across plain regions of the shelf. In the second category, by comparison, deposits are thicker and stratal preservation is more localised. Moreover preservation occurs as an adaptive morpho-kinematic response to environmental perturbations due to variations in: (1) the ratio of sediment supply (Vs) to accommodation generated by sea-level rise (SLR); (2) the substrate topography; (3) the morphology of the barrier profile. More specifically, changes of the ratio Vs /SLR, where SLR is an approximate surrogate for added accommodation space, directly promotes growth of the barrier (Vs /SLR >> 0) and its subsequent drowning (Vs /SLR?0). The topographic variations of the substrate may include minor irregularities as well as sudden changes in gradient that afford other types of preservation, such as local fills and residual littoral packages. Finally, barrier-profile changes inducing stratal preservation may include the reduction in barrier width and depth of surf base as well as the increment in shoreface concavity and shoreface length. Simplified methods are given for relating the geometry of preserved deposits to rates of sea-level rise and sediment supply over different shelf slopes, and for identifying the position of the shoreline at specific times. Holocene evolution of some coastal deposits from the Tuscan shelf (Italy) is presented in a morpho kinematic reconstruction to illustrate the geometric relationships for stratal preservation

Transgressive coastal systems (1st part): barrier migration processes and geometric principles

Coastal processes during transgression have been explored through morpho-kinematic simulations using the Shoreface Translation Model (STM). Our STM experiments show that the landward migration of coastal system is controlled by the rate of sea level rise (SLR), the rate of sediment supply (Vs), the shelf slope (?), and the morphology of the coastal profile (M). Additionally, the geometric relationships between shoreface and plane of translation govern three kinematic modes of coastal barrier migration: (1) roll-over, (2) hybrid, (3) encroachment. Each mode exhibits differences along the coastal profile in relation to zones of erosion (cut) and redeposition (fill) and to the consequent sediment exchanges across the profile (from the cut to the fill). Each mode produces distinctive facies architectures and specific stratigraphic position of the shoreface-ravinement surface. Environmental conditions (rates of sea-level rise, sediment supply (±), barrier morphology) and kinematic modes both control stratal preservation. Transgressive roll-over, in particular, occurs on gently sloping shelves and involves erosion along the entire shoreface and landward sediment redeposition (by overwash and tidal inlet processes). Three different types of roll-over are possible depending on the conditions of sediment supply (Vs) to the coastal cell: neutral roll-over (Vs=0 m3), which produces no effect on the shelf; depositional roll-over (Vs >0) and erosional (Vs<0) roll-over, which modify the shelf through stratal preservation and erosion, respectively. These differences are quantified in simulations by tracking parameters that principally relate to the trajectory of a ‘neutral point’ (maximum depth of shoreface erosion). The shoreface-ravinement defines the trajectory in all the transgressions and in principle is preserved in the rock record, making it a much more useful tracking point than the shoreline trajectory analysed in other studies. Coastal migration in all kinematic modes includes state-dependent inertial effects, experimentally well evident when, after a perturbation, the drivers (SLR, Vs, ?, M) are maintained constant for a long interval of time. Kinematic inertia appears as progressive geometric self-adjustments of the barrier until it acquires a shape that is stable under prevailing conditions (constant drivers). At this stage (kinematic equilibrium), which is unlikely ever to be attained in nature, simulated transgressions finally evolve with processes and geological products that remain invariant. Kinematic inertia is likely to be an additional factor that governs the real transgressions under most circumstances