MEASURING ECONOMIC GROWTH IN RURAL COMMUNITIES: THE SHIFT-SHARE APPROACH

Community/Rural/Urban Development,

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.This work was supported by the National Science Foundation [grant numbers DBI-0755048, DEB-0732920, DEB-1036448, DMS-0931642, EF-0331495, EF-0905606, EF-0949453]; the National Institutes of Health [grant numbers R01-HG006139, R01-GM037841, R01-GM078985, R01-GM086887, R01-NS063897]; the Biotechnology and Biological Sciences Research Council [grant number BB/H011285/1]; the Wellcome Trust [grant number WT092807MA]; and Google Summer of Code

Label-free segmentation of co-cultured cells on a nanotopographical gradient

The function and fate of cells is influenced by many different factors, one of which is surface topography of the support culture substrate. Systematic studies of nanotopography and cell response have typically been limited to single cell types and a small set of topographical variations. Here, we show a radical expansion of experimental throughput using automated detection, measurement, and classification of co-cultured cells on a nanopillar array where feature height changes continuously from planar to 250 nm over 9 mm. Individual cells are identified and characterized by more than 200 descriptors, which are used to construct a set of rules for label-free segmentation into individual cell types. Using this approach we can achieve label-free segmentation with 84% confidence across large image data sets and suggest optimized surface parameters for nanostructuring of implant devices such as vascular stents

An Investigation of the Ionic Conductivity and Species Crossover of Lithiated Nafion 117 in Nonaqueous Electrolytes

Nonaqueous redox flow batteries are a fast-growing area of research and development motivated by the need to develop low-cost energy storage systems. The identification of a highly conductive, yet selective membrane, is of paramount importance to enabling such a technology. Herein, we report the swelling behavior, ionic conductivity, and species crossover of lithiated Nafion 117 membranes immersed in three nonaqueous electrolytes (PC, PC : EC, and DMSO). Our results show that solvent volume fraction within the membrane has the greatest effect on both conductivity and crossover. An approximate linear relationship between diffusive crossover of neutral redox species (ferrocene) and the ionic conductivity of membrane was observed. As a secondary effect, the charge on redox species modifies crossover rates in accordance with Donnan exclusion. The selectivity of membrane is derived mathematically and compared to experimental results reported here. The relatively low selectivity for lithiated Nafion 117 in nonaqueous conditions suggests that new membranes are required for competitive nonaqueous redox flow batteries to be realized. Potential design rules are suggested for the future membrane engineering work.United States. Dept. of Energy. Office of Basic Energy Sciences. Joint Center for Energy Storage Researc

Current Knowledge and Considerations Regarding Survey Refusals: Executive Summary of the AAPOR Task Force Report on Survey Refusals

The landscape of survey research has arguably changed more significantly in the past decade than at any other time in its relatively brief history. In that short time, landline telephone ownership has dropped from some 98 percent of all households to less than 60 percent; cell-phone interviewing went from a novelty to a mainstay; address-based designs quickly became an accepted method of sampling the general population; and surveys via Internet panels became ubiquitous in many sectors of social and market research, even as they continue to raise concerns given their lack of random selection. Among these widespread changes, it is perhaps not surprising that the substantial increase in refusal rates has received comparatively little attention. As we will detail, it was not uncommon for a study conducted 20 years ago to have encountered one refusal for every one or two completed interviews, while today experiencing three or more refusals for every one completed interview is commonplace. This trend has led to several concerns that motivate this Task Force. As refusal rates have increased, refusal bias (as a component of nonresponse bias) is an increased threat to the validity of survey results. Of practical concern are the efficacy and cost implications of enhanced efforts to avert initial refusals and convert refusals that do occur. Finally, though no less significant, are the ethical concerns raised by the possibility that efforts to minimize refusals can be perceived as coercive or harassing potential respondents. Indeed, perhaps the most important goal of this document is to foster greater consideration by the reader of the rights of respondents in survey research

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software

Families’ perceptions of and experiences related to a pediatric weight management program.

Objective: To examine parents' and children's perceptions of and experiences related to a Parents as Agents of Change (PAC) intervention for managing pediatric obesity. Methods: Ten families were recruited from a PAC intervention. Participants were interviewed before (10 adults and 9 children), during (9 adults and 8 children), and after (8 adults) the intervention. Results: Before the intervention, families reported goals to increase physical activity, plan and eat healthier meals, reduce screen time, and lose weight. During the intervention, families described different approaches to making behavior changes depending on who assumed responsibility (parent, child, or shared responsibility). After the intervention, group setting, goal setting, and portion size activities were viewed positively. Suggestions for improvement included engaging children and reducing intervention length. Conclusions and Implications: Practitioners delivering PAC interventions should discuss families' goals and concerns, and who is responsible for making lifestyle changes. Practical activities are valuable. The length of interventions and engagement of children should be considere

Professor W Mike Edmunds: a pioneer in applied hydrogeochemistry and champion of international collaboration

Mike Edmunds was a pioneer in modern applied hydrogeochemistry, helping to develop geochemical tools and their application to managing water resources. In a career span- ning almost 50 years, Mike made major contributions to water resource science as well as pro moting the role of chemistry in solving groundwater problems and championing the need to incorporate science into policy. There can be few hydrogeologists who travelled so extensively in order to study the vast range of groundwater environments of the world. Mike ’ s contribution to water scie nce was recognised through the many accolades he received including the Whitaker Medal in 1999, the O.E. Meinzer Award in 2009, and the Vernadsky Medal in 2010