Probability Models for Degree Distributions of Protein Interaction Networks

The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional form contains important clues as to underlying evolutionary processes that have shaped the network. Generally, the functional form for the degree distribution has been determined in an ad-hoc fashion, with clear power-law like behaviour often only extending over a limited range of connectivities. Here we apply formal model selection techniques to decide which probability distribution best describes the degree distributions of protein interaction networks. Contrary to previous studies this well defined approach suggests that the degree distribution of many molecular networks is often better described by distributions other than the popular power-law distribution. This, in turn, suggests that simple, if elegant, models may not necessarily help in the quantitative understanding of complex biological processes.

Towards More Accurate Molecular Dynamics Calculation of Thermal Conductivity. Case Study: GaN Bulk Crystals

Significant differences exist among literature for thermal conductivity of various systems computed using molecular dynamics simulation. In some cases, unphysical results, for example, negative thermal conductivity, have been found. Using GaN as an example case and the direct non-equilibrium method, extensive molecular dynamics simulations and Monte Carlo analysis of the results have been carried out to quantify the uncertainty level of the molecular dynamics methods and to identify the conditions that can yield sufficiently accurate calculations of thermal conductivity. We found that the errors of the calculations are mainly due to the statistical thermal fluctuations. Extrapolating results to the limit of an infinite-size system tend to magnify the errors and occasionally lead to unphysical results. The error in bulk estimates can be reduced by performing longer time averages using properly selected systems over a range of sample lengths. If the errors in the conductivity estimates associated with each of the sample lengths are kept below a certain threshold, the likelihood of obtaining unphysical bulk values becomes insignificant. Using a Monte-Carlo approach developed here, we have determined the probability distributions for the bulk thermal conductivities obtained using the direct method. We also have observed a nonlinear effect that can become a source of significant errors. For the extremely accurate results presented here, we predict a [0001] GaN thermal conductivity of 185 $\rm{W/K \cdot m}$ at 300 K, 102 $\rm{W/K \cdot m}$ at 500 K, and 74 $\rm{W/K \cdot m}$ at 800 K. Using the insights obtained in the work, we have achieved a corresponding error level (standard deviation) for the bulk (infinite sample length) GaN thermal conductivity of less than 10 $\rm{W/K \cdot m}$, 5 $\rm{W/K \cdot m}$, and 15 $\rm{W/K \cdot m}$ at 300 K, 500 K, and 800 K respectively

Improved estimation of density of states for Monte Carlo sampling via MBAR

We present a new method to calculate the density of states using the multistate Bennett acceptance ratio (MBAR) estimator. We use a combination of parallel tempering (PT) and multicanonical simulation to demonstrate the efficiency of our method in a statistical model of sampling from a two-dimensional normal mixture and also in a physical model of aggregation of lattice polymers. While MBAR has been commonly used for final estimation of thermodynamic properties, our numerical results show that the efficiency of estimation with our new approach, which uses MBAR as an intermediate step, often improves upon conventional use of MBAR. We also demonstrate that it can be beneficial in our method to use full PT samples for MBAR calculations in cases where simulation data exhibit long correlation

Identification of Novel Cetacean Poxviruses in Cetaceans Stranded in South West England

Poxvirus infections in marine mammals have been mainly reported through their clinical lesions and electron microscopy (EM). Poxvirus particles in association with such lesions have been demonstrated by EM and were previously classified as two new viruses, cetacean poxvirus 1 (CePV-1) and cetacean poxvirus 2 (CePV-2). In this study, epidermal pox lesions in cetaceans stranded in South West England (Cornwall) between 2008 and 2012 were investigated by electron microscopy and molecular analysis. PCR and sequencing of a highly conserved region within the viral DNA polymerase gene ruled out both parapoxand orthopoxviruses. Moreover, phylogenetic analysis of the PCR product clustered the sequences with those previously described as cetacean poxviruses. However, taking the close genetic distance of this gene fragment across the family of poxviridae into account, it is reasonable to postulate further, novel cetacean poxvirus species. The nucleotide similarity within each cluster (tentative species) detected ranged from 98.6% to 100%, whilst the similarity between the clusters was no more than 95%. The detection of several species of poxvirus in different cetacean species confirms the likelihood of a heterogeneous cetacean poxvirus genus, comparable to the heterogeneity observed in other poxvirus genera

Prevention is better than cure, but...: Preventive medication as a risk to ordinariness?

Preventive health remains at the forefront of public health concerns; recent initiatives, such as the NHS health check, may lead to recommendations for medication in response to the identification of 'at risk' individuals. Little is known about lay views of preventive medication. This paper uses the case of aspirin as a prophylactic against heart disease to explore views among people invited to screening for a trial investigating the efficacy of such an approach. Qualitative interviews (N=46) and focus groups (N=5, participants 31) revealed dilemmas about preventive medication in the form of clashes between norms: first, in general terms, assumptions about the benefit of prevention were complicated by dislike of medication; second, the individual duty to engage in prevention was complicated by the need not to be over involved with one's own health; third, the potential appeal of this alternative approach to health promotion was complicated by unease about the implications of encouraging irresponsible behaviour among others. Though respondents made different decisions about using the drug, they reported very similar ways of trying to resolve these conflicts, drawing upon concepts of necessity and legitimisation and the special ordinariness of the particular dru

RXTE Observations of 1A 1744-361: Correlated Spectral and Timing Behavior

We analyze Rossi X-ray Timing Explorer (RXTE) Proportional Counter Array (PCA) data of the transient low mass X-ray binary (LMXB) system 1A 1744-361. We explore the X-ray intensity and spectral evolution of the source, perform timing analysis, and find that 1A 1744-361 shows `atoll' behavior during the outbursts. The color-color diagram indicates that this LMXB was observed in a low intensity spectrally hard (low-hard) state and in a high intensity `banana' state. The low-hard state shows a horizontal pattern in the color-color diagram, and the previously reported `dipper QPO' appears only during this state. We also perform energy spectral analyses, and report the first detection of broad iron emission line and iron absorption edge from 1A 1744-361.Comment: 20 pages, 4 tables, 4 figures, accepted for publication in Ap

Dose-related effects of flavanol-rich cocoa on blood pressure

Consumption of flavanol-containing cocoa products has been shown to lower blood pressure (BP), but the minimum dose required to reduce BP is not known. This study aimed to examine the effect of three different doses of cocoa flavanols (CF) on 24-h mean arterial BP. Twenty four hour ambulatory BP (24-ABP) monitoring was performed in 32 men and 20 postmenopausal women with untreated mild hypertension (seated clinic BP >130/85 and <160/100 mm Hg). Participants were randomized and instructed to consume daily a reconstituted cocoa beverage containing 33, 372, 712 or 1052 mg day(-1) of CF for 6 weeks in a double-blind, parallel comparison. Seated clinic BP and 24-h ABP were measured at 0, 3 and 6 weeks. Seated clinic BP did not change during the study period. There were significant reductions in 24-h systolic (5.3+/-5.1 mm Hg; P=0.001), diastolic (3+/-3.2 mm Hg; P=0.002) and mean arterial BP (3.8+/-3.2 mm Hg; P=0.0004) at the 1052 mg day(-1) CF only. No reduction in BP was seen at any other dose. No evidence of dose-response was seen in this experiment. The highest dose of 1052 mg CF per day was found to significantly lower BP. These results support previous evidence for CF to lower BP, however more research is needed to establish the most effective dose and food matrix