State practitioner insights into local public health challenges and opportunities in obesity prevention: a qualitative study.

IntroductionThe extent of obesity prevention activities conducted by local health departments (LHDs) varies widely. The purpose of this qualitative study was to characterize how state obesity prevention program directors perceived the role of LHDs in obesity prevention and factors that impact LHDs' success in obesity prevention.MethodsFrom June 2011 through August 2011, we conducted 28 semistructured interviews with directors of federally funded obesity prevention programs at 22 state and regional health departments. Interviews were transcribed verbatim, coded, and analyzed to identify recurring themes and key quotations.ResultsMain themes focused on the roles of LHDs in local policy and environmental change and on the barriers and facilitators to LHD success. The role LHDs play in obesity prevention varied across states but generally reflected governance structure (decentralized vs centralized). Barriers to local prevention efforts included competing priorities, lack of local capacity, siloed public health structures, and a lack of local engagement in policy and environmental change. Structures and processes that facilitated prevention were having state support (eg, resources, technical assistance), dedicated staff, strong communication networks, and a robust community health assessment and planning process.ConclusionsThese findings provide insight into successful strategies state and local practitioners are using to implement innovative (and evidence-informed) community-based interventions. The change in the nature of obesity prevention requires a rethinking of the state-local relationship, especially in centralized states

Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations

The phylogenetic likelihood function (PLF) is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection, and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory savings attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 12-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the PLF currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation

Entropic and gradient flow formulations for nonlinear diffusion

Nonlinear diffusion $\partial_t \rho = \Delta(\Phi(\rho))$ is considered for a class of nonlinearities $\Phi$. It is shown that for suitable choices of $\Phi$, an associated Lyapunov functional can be interpreted as thermodynamics entropy. This information is used to derive an associated metric, here called thermodynamic metric. The analysis is confined to nonlinear diffusion obtainable as hydrodynamic limit of a zero range process. The thermodynamic setting is linked to a large deviation principle for the underlying zero range process and the corresponding equation of fluctuating hydrodynamics. For the latter connections, the thermodynamic metric plays a central role

Carbon Monoxide Poisoning Resistance and Structural Stability of Single Atom Alloys

Platinum group metals (PGMs) serve as highly active catalysts in a variety of heterogeneous chemical processes. Unfortunately, their high activity is accompanied by a high affinity for CO and thus, PGMs are susceptible to poisoning. Alloying PGMs with metals exhibiting lower affinity to CO could be an effective strategy toward preventing such poisoning. In this work, we use density functional theory to demonstrate this strategy, focusing on highly dilute alloys of PGMs (Pd, Pt, Rh, Ir and Ni) with poison resistant coinage metal hosts (Cu, Ag, Au), such that individual PGM atoms are dispersed at the atomic limit forming single atom alloys (SAAs). We show that compared to the pure metals, CO exhibits lower binding strength on the majority of SAAs studied, and we use kinetic Monte Carlo simulation to obtain relevant temperature programed desorption spectra, which are found to be in good agreement with experiments. Additionally, we consider the effects of CO adsorption on the structure of SAAs. We calculate segregation energies which are indicative of the stability of dopant atoms in the bulk compared to the surface layer, as well as aggregation energies to determine the stability of isolated surface dopant atoms compared to dimer and trimer configurations. Our calculations reveal that CO adsorption induces dopant atom segregation into the surface layer for all SAAs considered here, whereas aggregation and island formation may be promoted or inhibited depending on alloy constitution and CO coverage. This observation suggests the possibility of controlling ensemble effects in novel catalyst architectures through CO-induced aggregation and kinetic trapping

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell

Phylogenetic inference is considered to be one of the grand challenges in Bioinformatics due to the immense computational requirements. RAxML is currently among the fastest and most accurate programs for phylogenetic tree inference under the Maximum Likelihood (ML) criterion. First, we introduce new tree search heuristics that accelerate RAxML by a factor of 2.43 while returning equally good trees. The performance of the new search algorithm has been assessed on 18 real-world datasets comprising 148 up to 4,843 DNA sequences. We then present the implementation, optimization, and evaluation of RAxML on the IBM Cell Broadband Engine. We address the problems and provide solutions pertaining to the optimization of floating point code, control flow, communication, and scheduling of multi-level parallelism on the Cel

Re(I) tricarbonyl complex of 1,10-phenanthroline-5,6-dione: DNA binding, cytotoxicity, antiinflammatory and anti-coagulant effects towards platelet activating factor

The complex fac-[Re(CO)3(phendione)Cl] (1) (where phendione = 1,10-phenanthroline-5,6-dione) has been synthesized and fully characterized by UV–visible, FTIR, and NMR techniques. The DNA binding properties of 1 are investigated by UV-spectrophotometric (melting curves), covalent binding assay, CV (cyclic voltammetry), circular dichroism (CD) and viscosity measurements. Experimental data indicate that 1 fits into the major groove without disrupting the helical structure of the B-DNA in contrast to the free phendione which intercalates within the base pairs of DNA. Upon irradiation, complex 1promotes the cleavage of plasmid pBR322 DNA from supercoiled form I to nicked form II via a proton coupled electron transfer mechanism. This comes as a result of experimental data in anaerobic/aerobic conditions and in the presence of DMSO. The biological activities of 1 and its precursors [Re(CO)5Cl] and phendione are tested towards a series of cancerous cell lines as glioblastoma (T98G), prostate cancer (PC3) and breast cancer (MCF-7) as well as platelet activating factor (PAF)-aggregation. Moreover, all the aforementioned compounds are tested for their ability to modulate PAF-basic metabolic enzyme activities in preparations of rabbit leukolytes. The in vitro experiments indicate that phendione has a better antitumor effect than cisplatin whereas [Re(CO)5Cl] is a better PAF inhibitor than both the phendione ligand and 1. Moreover, for the first time it is indicated that [Re(CO)5Cl], with a IC50 of 17 nM is comparable to the widely used PAF receptor antagonists, BN52021 and WEB2170 with IC50 of 30 and 20 nM, respectively, whereas 1 affects PAF-catabolism

Low socioeconomic status and psychological distress as synergistic predictors of mortality from stroke and coronary heart disease.

The purpose of this study was to test whether lower socioeconomic status (SES) augments the effect of psychological distress on mortality from stroke or coronary heart disease (CHD)