Probabilistic methods in the analysis of protein interaction networks

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Displacement Profile of Charge Density Waves and Domain Walls at Critical Depinning

The influence of a strong surface potential on the critical depinning of an elastic system driven in a random medium is considered. If the surface potential prevents depinning completely the elastic system shows a parabolic displacement profile. Its curvature $\mathcal{C}$ exhibits at zero temperature a pronounced rhombic hysteresis curve of width $2f_c$ with the bulk depinning threshold $f_c$. The hysteresis disappears at non-zero temperatures if the driving force is changed adiabatically. If the surface depins by the applied force or thermal creep, $\mathcal{C}$ is reduced with increasing velocity. The results apply, e.g., to driven magnetic domain walls, flux-line lattices and charge-density waves.Comment: 4 pages, 2 figure

Statistical analysis of network data and evolution on GPUs: High-performance statistical computing

Network analysis typically involves as set of repetitive tasks that are particularly amenable to poor-man's parallelization. This is therefore an ideal application are for GPU architectures, which help to alleviate the tedium inherent to statistically sound analysis of network data. Here we will illustrate the use of GPUs in a range of applications, which include percolation processes on networks, the evolution of protein-protein interaction networks, and the fusion of different types of biomedical and disease data in the context of molecular interaction networks. We will pay particular attention to the numerical performance of different routines that are frequently invoked in network analysis problems. We conclude with a review over recent developments in the generation of random numbers that address the specific requirements posed by GPUs and high-performance computing needs

Stochastic Process Algebra Models of a Circadian Clock

We present stochastic process algebra models of a Circadian clock mechanism used in many biological organisms to regulate time-based behaviour. We compare modelling techniques from different modelling paradigms, PEPA and stochastic $pi$-calculus

General-Relativistic MHD for the Numerical Construction of Dynamical Spacetimes

We assemble the equations of general relativistic magnetohydrodynamics (MHD) in 3+1 form. These consist of the complete coupled set of Maxwell equations for the electromagnetic field, Einstein's equations for the gravitational field, and the equations of relativistic MHD for a perfectly conducting ideal gas. The adopted form of the equations is suitable for evolving numerically a relativistic MHD fluid in a dynamical spacetime characterized by a strong gravitational field.Comment: 8 pages; scheduled for March 10 issue of Ap

Template banks to search for compact binaries with spinning components in gravitational wave data

Gravitational waves from coalescing compact binaries are one of the most promising sources for detectors such as LIGO, Virgo and GEO600. If the components of the binary posess significant angular momentum (spin), as is likely to be the case if one component is a black hole, spin-induced precession of a binary's orbital plane causes modulation of the gravitational-wave amplitude and phase. If the templates used in a matched-filter search do not accurately model these effects then the sensitivity, and hence the detection rate, will be reduced. We investigate the ability of several search pipelines to detect gravitational waves from compact binaries with spin. We use the post-Newtonian approximation to model the inspiral phase of the signal and construct two new template banks using the phenomenological waveforms of Buonanno, Chen and Vallisneri. We compare the performance of these template banks to that of banks constructed using the stationary phase approximation to the non-spinning post-Newtonian inspiral waveform currently used by LIGO and Virgo in the search for compact binary coalescence. We find that, at the same false alarm rate, a search pipeline using phenomenological templates is no more effective than a pipeline which uses non-spinning templates. We recommend the continued use of the non-spinning stationary phase template bank until the false alarm rate associated with templates which include spin effects can be substantially reduced.Comment: 11 pages, 3 figure

Corrections and Comments on the Multipole Moments of Axisymmetric Electrovacuum Spacetimes

Following the method of Hoenselaers and Perj\'{e}s we present a new corrected and dimensionally consistent set of multipole gravitational and electromagnetic moments for stationary axisymmetric spacetimes. Furthermore, we use our results to compute the multipole moments, both gravitational and electromagnetic, of a Kerr-Newman black hole.Comment: This is a revised and corrected versio

A narrative analysis positioning HIV relative to personal (sexual) relationship challenges in an agony aunt column in the Western Cape, South Africa - Aunty Mona's "love advice".

HIV prevalence and incidence in South Africa remain high, making HIV a part of everyday life. Community narratives on HIV treatment and prevention are important and influence official and unofficial health messaging and community perceptions and understandings of HIV. We explore how contributors and the columnist of an agony aunt column position HIV relative to choices made about love, partnership, and sex over three years. We analysed all columns of an agony aunt series (Antie Mona) published between December 2012 and November 2015. The column is published in a South African, Afrikaans-language newspaper "Son", prioritising sensationalist news items. Trends were identified through narrative analysis. Data were managed in ATLAS.ti and inductive, iterative coding conducted. It was found that letters to the agony aunt rarely refer to HIV directly (less than 7%). Euphemisms such as diseases of the flesh and the great flu were more commonly used instead of HIV or AIDS. Letters addressed HIV in three ways: direct references to experiences living with HIV; direct questions about HIV prevention; and scenarios where HIV could (from a public health perspective) have been the main concern, but everyday issues took precedence. The majority of letters fell into this latter category where the writers focused on the immediate concerns of good sexual relations, problems related to love and romantic relationships, good moral behaviour of others, and issues of oppressive life conditions rather than on HIV directly. The findings illustrate that informal, public contributions to health information, such as agony aunts, are important narratives that inform popular perspectives on HIV and health. A better appreciation of this context would allow health implementers to ensure that these role players receive updated health messaging to avoid the risk of HIV-related stigma where HIV is used as a moral rod to punish perceived moral transgressions

From Screening to Synthesis: Using NVivo to Enhance Transparency in Qualitative Evidence Synthesis

Aims and objectives The aim of this qualitative evidence synthesis was to explore the experiences and perceptions of health care staff caring for people with dementia in the acute setting. This paper focuses on the methodological process of conducting framework synthesis using NVivo for each stage of the review: screening, data extraction, synthesis and critical appraisal. Background Qualitative evidence synthesis brings together many research findings in a meaningful way that can be used to guide practice and policy development. For this purpose, synthesis must be conducted in a comprehensive and rigorous way. There has been previous discussion on how using NVivo can assist in enhancing and illustrate the rigorous processes involved. Design Qualitative Framework Synthesis. Methods Twelve documents, or research reports, based on nine studies, were included for synthesis. Conclusion The benefits of using NVivo are outlined in terms of facilitating teams of researchers to systematically and rigorously synthesise findings. NVivo functions were used to conduct a sensitivity analysis. Some valuable lessons were learned and these are presented to assist and guide researchers who wish to use similar methods in future

Studies of the Earth's Deep Interior: Goals and Trends

The deep interior of planet Earth has long fascinated philosophers, scientists and fantasy writers, yet it remains inaccessible to direct scrutiny and thus largely enigmatic. Romantic notions about the interior are provocative, with crystal‐filled chambers and pitchfork‐bearing devils. However, the more scientifically based visions are just as alluring. Profound opportunities for understanding the mysteries of the inner Earth lie within reach. But it will take a concerted interdisciplinary research effort to model the total dynamic Earth system