NXFit: A program for simultaneously fitting X-ray and neutron diffraction pair-distribution functions to provide optimized structural parameters

NXFit is a program for obtaining optimized structural parameters from amorphous materials by simultaneously fitting X-ray and neutron pair-distribution functions. Partial correlation functions are generated in Q space, summed and Fourier transformed for comparison with the experimental data in r space. NXFit uses the Nelder-Mead method to vary a set of 'best guess' parameters to achieve a fit to experimentally derived data. The output parameters from NXFit are coordination number, atomic separation and disorder parameter for each atomic correlation used in the fitting process. The use of NXFit has been demonstrated by fitting both X-ray and neutron diffraction data from two quite different amorphous materials: a melt-quenched (Na2O) 0.5(P2O5)0.5glass and a (TiO2)0.18(SiO2)0.82sol-gel

Numerical simulations of immiscible fluid clusters

Accepted versio

An Unexpected Discovery in the Rich Open Cluster NGC 6819 Using XMM-Newton

We present the first study of the X-ray population of the intermediate-age rich open cluster NGC 6819 using the XMM-Newton Observatory. In the past decade, Chandra X-ray observations have shown a relationship between the X-ray population of globular clusters and their internal dynamics and encounter frequency. We investigate the role dynamics possibly play in the formation of X-ray sources in NGC 6819, and compare our results with known properties of field and globular cluster X-ray populations. We implement a multi wavelength approach to studying the X-ray sources, utilizing X-ray and UV data from XMM observations along with the wealth of photometry and radial-velocity data from the WIYN Open Cluster Study (WOCS) and the CFHT Open Cluster Survey. Within the cluster half-light radius we detect 12 X-ray sources down to a luminosity of 10^30 erg/s for cluster members. The sources include a candidate quiescent low-mass X-ray binary (qLMXB), a candidate cataclysmic variable, and two active binary systems. The presence of a qLMXB in an open cluster is previously unexpected given the known relationships between luminous X-ray sources and encounter frequency in globular clusters, and most likely has a dynamical origin.Comment: 14 pages, 11 figures, accepted for publication in the Astrophysical Journa

Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping

<p>Abstract</p> <p>Background</p> <p>The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs) mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB) method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model.</p> <p>Results</p> <p>We developed a fast empirical Bayesian LASSO (EBLASSO) method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects.</p> <p>Conclusions</p> <p>The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.</p

A Bayesian statistical analysis of behavioral facilitation associated with deep brain stimulation

Deep brain stimulation (DBS) is an established therapy for Parkinson's Disease and is being investigated as a treatment for chronic depression, obsessive compulsive disorder and for facilitating functional recovery of patients in minimally conscious states following brain injury. For all of these applications, quantitative assessments of the behavioral effects of DBS are crucial to determine whether the therapy is effective and, if so, how stimulation parameters can be optimized. Behavioral analyses for DBS are challenging because subject performance is typically assessed from only a small set of discrete measurements made on a discrete rating scale, the time course of DBS effects is unknown, and between-subject differences are often large. We demonstrate how Bayesian state-space methods can be used to characterize the relationship between DBS and behavior comparing our approach with logistic regression in two experiments: the effects of DBS on attention of a macaque monkey performing a reaction-time task, and the effects of DBS on motor behavior of a human patient in a minimally conscious state. The state-space analysis can assess the magnitude of DBS behavioral facilitation (positive or negative) at specific time points and has important implications for developing principled strategies to optimize DBS paradigms.National Institutes of Health (U.S.)(R01 MH-071847)National Institutes of Health (U.S.) (DP1 OD003646)National Institutes of Health (U.S.)(NS02172)IntElect Medical (Firm

Simulation-based optimal Bayesian experimental design for nonlinear systems

The optimal selection of experimental conditions is essential to maximizing the value of data for inference and prediction, particularly in situations where experiments are time-consuming and expensive to conduct. We propose a general mathematical framework and an algorithmic approach for optimal experimental design with nonlinear simulation-based models; in particular, we focus on finding sets of experiments that provide the most information about targeted sets of parameters. Our framework employs a Bayesian statistical setting, which provides a foundation for inference from noisy, indirect, and incomplete data, and a natural mechanism for incorporating heterogeneous sources of information. An objective function is constructed from information theoretic measures, reflecting expected information gain from proposed combinations of experiments. Polynomial chaos approximations and a two-stage Monte Carlo sampling method are used to evaluate the expected information gain. Stochastic approximation algorithms are then used to make optimization feasible in computationally intensive and high-dimensional settings. These algorithms are demonstrated on model problems and on nonlinear parameter estimation problems arising in detailed combustion kinetics.Comment: Preprint 53 pages, 17 figures (54 small figures). v1 submitted to the Journal of Computational Physics on August 4, 2011; v2 submitted on August 12, 2012. v2 changes: (a) addition of Appendix B and Figure 17 to address the bias in the expected utility estimator; (b) minor language edits; v3 submitted on November 30, 2012. v3 changes: minor edit

Obesity and caries in four-to-six year old English children: a cross-sectional study.

BACKGROUND: Obesity and caries are common conditions in childhood and can have significant implications on children's wellbeing. Evidence into their association remains conflicting. Furthermore, studies examining the ssociation between obesity and caries commonly focus on individual-level determinants. The present study aimed to examine the association between obesity and caries in young English children and to determine the impact of deprivation and area-level characteristics on the distribution of the two conditions. METHODS: This was a cross-sectional study among children in Plymouth city aged four-to-six years. Anthropometric measurements included weight and height (converted to Body Mass Index centiles and z-scores), and waist circumference. Caries was assessed by using the sum of the number of teeth that were decayed, missing or filled. A questionnaire was used to obtain information on children's demographic characteristics, oral hygiene, and dietary habits. The impact of deprivation on anthropometric variables and caries was determined using Linear and Poisson regression models, respectively. Multiple logistic regression was used to assess the association between different anthropometric measures and caries. Logistic regression models were also used to examine the impact of several demographic characteristics and health behaviours on the presence of obesity and caries. RESULTS: The total sample included 347 children aged 5.10 ± 0.31 (mean ± SD). Deprivation had a significant impact on caries and BMI z-scores (p < 0.05). Neither BMI- nor waist circumference z-scores were shown to be significantly associated with dental caries. Among the neighbourhood characteristics examined, the percentage of people dependent on benefits was found to have a significant impact on caries rates (p < 0.05). Household's total annual income was inversely related to caries risk and parental educational level affected children's tooth brushing frequency. CONCLUSIONS: No associations between any measure of obesity and caries were found. However, deprivation affected both obesity and caries, thus highlighting the need to prioritise disadvantaged children in future prevention programmes

ASPCAP: THE APOGEE STELLAR PARAMETER AND CHEMICAL ABUNDANCES PIPELINE

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) has built the largest moderately high-resolution (R ≈ 22,500) spectroscopic map of the stars across the Milky Way, and including dust-obscured areas. The APOGEE Stellar Parameter and Chemical Abundances Pipeline (ASPCAP) is the software developed for the automated analysis of these spectra. ASPCAP determines atmospheric parameters and chemical abundances from observed spectra by comparing observed spectra to libraries of theoretical spectra, using χ2 minimization in a multidimensional parameter space. The package consists of a fortran90 code that does the actual minimization and a wrapper IDL code for book-keeping and data handling. This paper explains in detail the ASPCAP components and functionality, and presents results from a number of tests designed to check its performance. ASPCAP provides stellar effective temperatures, surface gravities, and metallicities precise to 2%, 0.1 dex, and 0.05 dex, respectively, for most APOGEE stars, which are predominantly giants. It also provides abundances for up to 15 chemical elements with various levels of precision, typically under 0.1 dex. The final data release (DR12) of the Sloan Digital Sky Survey III contains an APOGEE database of more than 150,000 stars. ASPCAP development continues in the SDSS-IV APOGEE-2 survey

Biodiversity on Broadway - Enigmatic Diversity of the Societies of Ants (Formicidae) on the Streets of New York City

Each year, a larger proportion of the Earth's surface is urbanized, and a larger proportion of the people on Earth lives in those urban areas. The everyday nature, however, that humans encounter in cities remains poorly understood. Here, we consider perhaps the most urban green habitat, street medians. We sampled ants from forty-four medians along three boulevards in New York City and examined how median properties affect the abundance and species richness of native and introduced ants found on them. Ant species richness varied among streets and increased with area but was independent of the other median attributes measured. Ant assemblages were highly nested, with three numerically dominant species present at all medians and additional species present at a subset of medians. The most common ant species were the introduced Pavement ant (Tetramorium caespitum) and the native Thief ant (Solenopsis molesta) and Cornfield ant (Lasius neoniger). The common introduced species on the medians responded differently to natural and disturbed elements of medians. Tetramorium caespitum was most abundant in small medians, with the greatest edge/area ratio, particularly if those medians had few trees, whereas Nylanderia flavipes was most abundant in the largest medians, particularly if they had more trees. Many of the species encountered in Manhattan were similar to those found in other large North American cities, such that a relatively small subset of ant species probably represent most of the encounters humans have with ants in North America

A New (Old), Invasive Ant in the Hardwood Forests of Eastern North America and Its Potentially Widespread Impacts

Biological invasions represent a serious threat for the conservation of biodiversity in many ecosystems. While many social insect species and in particular ant species have been introduced outside their native ranges, few species have been successful at invading temperate forests. In this study, we document for the first time the relationship between the abundance of the introduced ant, Pachycondyla chinensis, in mature forests of North Carolina and the composition, abundance and diversity of native ant species using both a matched pair approach and generalized linear models. Where present, P. chinensis was more abundant than all native species combined. The diversity and abundance of native ants in general and many individual species were negatively associated with the presence and abundance of P. chinensis. These patterns held regardless of our statistical approach and across spatial scales. Interestingly, while the majority of ant species was strongly and negatively correlated with the abundance and presence of P. chinensis, a small subset of ant species larger than P. chinensis was either as abundant or even more abundant in invaded than in uninvaded sites. The large geographic range of this ant species combined with its apparent impact on native species make it likely to have cascading consequences on eastern forests in years to come, effects mediated by the specifics of its life history which is very different from those of other invasive ants. The apparent ecological impacts of P. chinensis are in addition to public health concerns associated with this species due to its sometimes, deadly sting