Grid infrastructures for secure access to and use of bioinformatics data: experiences from the BRIDGES project

The BRIDGES project was funded by the UK Department of Trade and Industry (DTI) to address the needs of cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) cardiovascular functional genomics (CFG) project. Security was at the heart of the BRIDGES project and an advanced data and compute grid infrastructure incorporating latest grid authorisation technologies was developed and delivered to the scientists. We outline these grid infrastructures and describe the perceived security requirements at the project start including data classifications and how these evolved throughout the lifetime of the project. The uptake and adoption of the project results are also presented along with the challenges that must be overcome to support the secure exchange of life science data sets. We also present how we will use the BRIDGES experiences in future projects at the National e-Science Centre

Structural precursor to freezing: An integral equation study

Recent simulation studies have drawn attention to the shoulder which forms in the second peak of the radial distribution function of hard-spheres at densities close to freezing and which is associated with local crystalline ordering in the dense fluid. We address this structural precursor to freezing using an inhomogeneous integral equation theory capable of describing local packing constraints to a high level of accuracy. The addition of a short-range attractive interaction leads to a well known broadening of the fluid-solid coexistence region as a function of attraction strength. The appearence of a shoulder in our calculated radial distribution functions is found to be consistent with the broadened coexistence region for a simple model potential, thus demonstrating that the shoulder is not exclusively a high density packing effect

Sleep disturbance and serum ferritin levels associate with high impulsivity and impulse control disorders in male Parkinson\u27s Disease patients

Impulse control disorders (ICDs) occur in a subset of Parkinson’s disease (PD) patients on dopaminergic medications however there are currently no reliable markers to identify patients at risk. Sleep disturbances are more common in patients with an ICD. Serum ferritin levels have been associated with PD disease stage and progression, but have not previously been associated with impulsivity levels. The objective of this study was to determine if serum ferritin levels and sleep disturbance are associated with high traits of impulsivity and ICD in a cohort of PD patients attending a movement disorders clinic. This study assessed impulsiveness in 87 PD patients using the Barratt Impulsiveness Scale. Severity of sleep disturbance was determined using the sleep-related items of the MDS-UPDRS. Serum ferritin, iron and transferrin levels were measured in patients, as well as 36 age-matched healthy controls. Serum ferritin levels were significantly elevated in male PD patients in the high impulsivity group compared to patients in the low (p=.022) and normal range groups (p=.024) and showed a linear increase across the three groups. Sleep disturbance also demonstrated a linear trend, which was most severe in the high impulsivity group (p=.030). A subgroup of 11 male PD patients who fulfilled the DSM-5 criteria for an ICD had significantly higher ferritin levels and more severe sleep disturbance when compared with the remaining male PD cohort. Serum ferritin levels and sleep disturbance severity are highlighted as potential markers for abnormal impulsivity and ICD in PD patients

Exact factorization of correlation functions in 2-D critical percolation

By use of conformal field theory, we discover several exact factorizations of higher-order density correlation functions in critical two-dimensional percolation. Our formulas are valid in the upper half-plane, or any conformally equivalent region. We find excellent agreement of our results with high-precision computer simulations. There are indications that our formulas hold more generally.Comment: 6 pages, 3 figures. Oral presentation given at STATPHYS 23. V2: Minor additions and corrections, figures improve

Model Energy Landscapes of Low-Temperature Fluids: Dipolar Hard Spheres

An analytical model of non-Gaussian energy landscape of low-temperature fluids is developed based on the thermodynamics of the fluid of dipolar hard spheres. The entire excitation profile of the liquid, from the high temperatures to the point of ideal-glass transition, has been obtained from the Monte Carlo simulations. The fluid of dipolar hard spheres loses stability when reaching the point of ideal-glass transition transforming via a first-order transition into a columnar liquid phase of dipolar chains locally arranged in a body-centered tetragonal order.Comment: 4 pages, 3 figure

Owner perceptions of their cat's quality of life when treated with a modified University of Wisconsin-Madison protocol for lymphoma

The objectives of this study were to assess owner perceptions of their cat’s quality of life during treatment for lymphoma with a doxorubicin-containing multi-agent chemotherapy protocol, whether various health-related parameters correlated with quality of life scores, and to assess owner satisfaction with the protocol

Long wavelength structural anomalies in jammed systems

The structural properties of static, jammed packings of monodisperse spheres in the vicinity of the jamming transition are investigated using large-scale computer simulations. At small wavenumber $k$, we argue that the anomalous behavior in the static structure factor, $S(k) \sim k$, is consequential of an excess of low-frequency, collective excitations seen in the vibrational spectrum. This anomalous feature becomes more pronounced closest to the jamming transition, such that $S(0) \to 0$ at the transition point. We introduce an appropriate dispersion relation that accounts for these phenomena that leads us to relate these structural features to characteristic length scales associated with the low-frequency vibrational modes of these systems. When the particles are frictional, this anomalous behavior is suppressed providing yet more evidence that jamming transitions of frictional spheres lie at lower packing fractions that that for frictionless spheres. These results suggest that the mechanical properties of jammed and glassy media may therefore be inferred from measurements of both the static and dynamical structure factors.Comment: 8 pages, 6 figure captions. Completely revised version to appear in Phys. Rev.

UK utility data integration: overcoming schematic heterogeneity

In this paper we discuss syntactic, semantic and schematic issues which inhibit the integration of utility data in the UK. We then focus on the techniques employed within the VISTA project to overcome schematic heterogeneity. A Global Schema based architecture is employed. Although automated approaches to Global Schema definition were attempted the heterogeneities of the sector were too great. A manual approach to Global Schema definition was employed. The techniques used to define and subsequently map source utility data models to this schema are discussed in detail. In order to ensure a coherent integrated model, sub and cross domain validation issues are then highlighted. Finally the proposed framework and data flow for schematic integration is introduced

Gas-liquid critical point in ionic fluids

Based on the method of collective variables we develop the statistical field theory for the study of a simple charge-asymmetric $1:z$ primitive model (SPM). It is shown that the well-known approximations for the free energy, in particular DHLL and ORPA, can be obtained within the framework of this theory. In order to study the gas-liquid critical point of SPM we propose the method for the calculation of chemical potential conjugate to the total number density which allows us to take into account the higher order fluctuation effects. As a result, the gas-liquid phase diagrams are calculated for $z=2-4$. The results demonstrate the qualitative agreement with MC simulation data: critical temperature decreases when $z$ increases and critical density increases rapidly with $z$.Comment: 18 pages, 1 figur

SCOZA for Monolayer Films

We show the way in which the self-consistent Ornstein-Zernike approach (SCOZA) to obtaining structure factors and thermodynamics for Hamiltonian models can best be applied to two-dimensional systems such as thin films. We use the nearest-neighbor lattice gas on a square lattice as an illustrative example.Comment: 10 pages, 5 figure