HYDRA: a Java library for Markov Chain Monte Carlo

Hydra is an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use, extend, and integrate with other software tools. In this paper, we describe the problem that motivated our work, outline our goals for the Hydra pro ject, and describe the current features of the Hydra library. We then provide a step-by-step example of using Hydra to simulate from a mixture model drawn from cancer genetics, first using a variable-at-a-time Metropolis sampler and then a Normal Kernel Coupler. We conclude with a discussion of future directions for Hydra.

The well-being of British expatriate retirees in southern Europe

This article examines the personal outcomes of overseas residence in later life, by analysing some findings from the first large-scale, comparative study of the retirement of British citizens to southern Europe. Four study areas are compared: Tuscany in Italy, Malta, the Costa del Sol of Spain, and the Algarve region of Portugal. The analysis focuses on the expressed reasons for moving to and residing in the areas, the reported advantages and disadvantages, and the respondents' predictions of whether they would stay or leave in response to adverse and beneficial events. Overall the subjects give very positive reports, but there are considerable differences among the four areas. The associations of individual variation in well-being with both a person's ‘temporal commitment’ to the area and to facets of their social integration are analysed. The onset of severe incapacity, sufficient to prevent the continued running of a home, is the event most likely to cause people to leave their adopted areas of residence

License GPL-2 NeedsCompilation No Repository CRAN

Description Various R programming tools for plotting dat

Resistive state of superconducting structures with fractal clusters of a normal phase

The effect of morphologic factors on magnetic flux dynamics and critical currents in percolative superconducting structures is considered. The superconductor contains the fractal clusters of a normal phase, which act as pinning centers. The properties of these clusters are analyzed in the general case of gamma-distribution of their areas. The statistical characteristics of the normal phase clusters are studied, the critical current distribution is derived, and the dependencies of the main statistical parameters on the fractal dimension are found. The effect of fractal clusters of a normal phase on the electric field induced by the motion of the magnetic flux after the vortices have been broken away from pinning centers is considered. The voltage-current characteristics of fractal superconducting structures in a resistive state for an arbitrary fractal dimension are obtained. It is found that the fractality of the boundaries of normal phase clusters intensifies magnetic flux trapping and thereby increases the current-carrying capability of the superconductor.Comment: 15 pages with 8 figures, revtex3, alternative e-mail of author is [email protected]

Corrosion of industrial ironwork

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Bisphenol A causes reproductive toxicity, decreasesdnmt1transcription, and reduces global DNA methylation in breeding zebrafish(Danio rerio)

Bisphenol A (BPA) is a commercially important high production chemical widely used in epoxy resins and polycarbonate plastics, and is ubiquitous in the environment. Previous studies demonstrated that BPA activates estrogenic signaling pathways associated with adverse effects on reproduction in vertebrates and that exposure can induce epigenetic changes. We aimed to investigate the reproductive effects of BPA in a fish model and to document its mechanisms of toxicity. We exposed breeding groups of zebrafish (Danio rerio) to 0.01, 0.1, and 1 mg/L BPA for 15 days. We observed a significant increase in egg production, together with a reduced rate of fertilization in fish exposed to 1 mg/L BPA, associated with significant alterations in the transcription of genes involved in reproductive function and epigenetic processes in both liver and gonad tissue at concentrations representing hotspots of environmental contamination (0.1 mg/L) and above. Of note, we observed reduced expression of DNA methyltransferase 1 (dnmt1) at environmentally relevant concentrations of BPA, along with a significant reduction in global DNA methylation, in testes and ovaries following exposure to 1 mg/L BPA. Our findings demonstrate that BPA disrupts reproductive processes in zebrafish, likely via estrogenic mechanisms, and that environmentally relevant concentrations of BPA are associated with altered transcription of key enzymes involved in DNA methylation maintenance. These findings provide evidence of the mechanisms of action of BPA in a model vertebrate and advocate for its reduction in the environment.We thank the Aquatic Resources Centre technical team for support with zebrafish husbandry. This work was funded by a PhD studentship from the Fisheries Society of the British Isles (http://www.fsbi.org.uk/) and the University of Exeter (http://www.exeter.ac.uk/) to LVL and EMS. TMUW was funded by a Natural Environment Research Council CASE PhD studentship (grant no. NE/I528326/1) and the Salmon & Trout Association (http://www.salmon-trout.org/)

Dynamics of the magnetic flux trapped in fractal clusters of normal phase in a superconductor

The influence of geometry and morphology of superconducting structure on critical currents and magnetic flux trapping in percolative type-II superconductor is considered. The superconductor contains the clusters of a normal phase, which act as pinning centers. It is found that such clusters have significant fractal properties. The main features of these clusters are studied in detail: the cluster statistics is analyzed; the fractal dimension of their boundary is estimated; the distribution of critical currents is obtained, and its peculiarities are explored. It is examined thoroughly how the finite resolution capacity of the cluster geometrical size measurement affects the estimated value of fractal dimension. The effect of fractal properties of the normal phase clusters on the electric field arising from magnetic flux motion is investigated in the case of an exponential distribution of cluster areas. The voltage-current characteristics of superconductors in the resistive state for an arbitrary fractal dimension are obtained. It is revealed that the fractality of the boundaries of the normal phase clusters intensifies the magnetic flux trapping and thereby raises the critical current of a superconductor.Comment: revtex, 16 pages with 1 table and 5 figures; text and figures are improved; more detailed version with geometric probability analisys of the distribution of entry points into weak links over the perimeter of a normal phase clusters and one additional figure is published in Phys.Rev.B; alternative e-mail of author is [email protected]

Constructing living buildings: a review of relevant technologies for a novel application of biohybrid robotics

Biohybrid robotics takes an engineering approach to the expansion and exploitation of biological behaviours for application to automated tasks. Here, we identify the construction of living buildings and infrastructure as a high-potential application domain for biohybrid robotics, and review technological advances relevant to its future development. Construction, civil infrastructure maintenance and building occupancy in the last decades have comprised a major portion of economic production, energy consumption and carbon emissions. Integrating biological organisms into automated construction tasks and permanent building components therefore has high potential for impact. Live materials can provide several advantages over standard synthetic construction materials, including self-repair of damage, increase rather than degradation of structural performance over time, resilience to corrosive environments, support of biodiversity, and mitigation of urban heat islands. Here, we review relevant technologies, which are currently disparate. They span robotics, self-organizing systems, artificial life, construction automation, structural engineering, architecture, bioengineering, biomaterials, and molecular and cellular biology. In these disciplines, developments relevant to biohybrid construction and living buildings are in the early stages, and typically are not exchanged between disciplines. We, therefore, consider this review useful to the future development of biohybrid engineering for this highly interdisciplinary application.publishe

A candidate tolerance gene identified in a natural population of field voles (Microtus agrestis)

The animal immune response has hitherto been viewed primarily in the context of resistance only. However, individuals can also employ a tolerance strategy to maintain good health in the face of ongoing infection. To shed light on the genetic and physiological basis of tolerance, we use a natural population of field voles, Microtus agrestis, to search for an association between the expression of the transcription factor Gata3, previously identified as a marker of tolerance in this system, and polymorphism in 84 immune and nonimmune genes. Our results show clear evidence for an association between Gata3 expression and polymorphism in the Fcer1a gene, with the explanatory power of this polymorphism being comparable to that of other nongenetic variables previously identified as important predictors of Gata3 expression. We also uncover the possible mechanism behind this association using an existing protein–protein interaction network for the mouse model rodent, Mus musculus, which we validate using our own expression network for M. agrestis. Our results suggest that the polymorphism in question may be working at the transcriptional level, leading to changes in the expression of the Th2-related genes, Tyrosine-protein kinase BTK and Tyrosine-protein kinase TXK, and hence potentially altering the strength of the Th2 response, of which Gata3 is a mediator. We believe our work has implications for both treatment and control of infectious disease