bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attitudes to food differ between adolescent dieters and non-dieters from Otago, New Zealand, but overall food intake does not
Authors: Howe Anna S , Mandic Sandra , Parnell Winsome R , Skidmore Paula ML 
Published: May 2012

AbstractObjectiveThere is increasing pressure for adolescents to be thin and this may not always be acted upon in healthy ways; for example, certain foods or food groups may be restricted or meals skipped. As foods are not eaten in isolation it is useful to examine dietary patterns and associated psychosocial factors to better understand eating behaviour. The aim of the present study was to identify correlates of ‘dieting’ in adolescents from Otago, New Zealand.DesignA web-based survey was conducted in 2009, collecting information on food consumption and factors potentially associated with food consumption. Principal components analysis was used to investigate dietary patterns. Correlates were examined in 1329 students using multiple logistic regression analysis.SettingNineteen secondary schools in the province of Otago, New Zealand.SubjectsStudents from school years 9 and 10 (mean age 14·1 (sd 0·7) years).ResultsThere was no relationship between dieting and dietary patterns. Those not dieting were 17 % (95 % CI 7, 26 %) more likely to eat lunch and 22 % (95 % CI 3, 37 %) more likely to eat an evening meal on one more weekday than those who were dieting. Those who reported dieting were more likely to report healthiness (OR = 2·18, 95 % CI 1·11, 4·26) as an important factor when choosing food and that eating fruit and vegetables makes you better looking. No sex by dieting interaction was found.ConclusionsIn this cohort, while there was no difference in actual food consumption between dieters and non-dieters, there were significant differences in attitudes to food.
Cooking frequency may enhance survival in Taiwanese elderly
Authors: Chen Rosalind Chia-Yu , Lee Meei-Shyuan , Chang Yu-Hung , Wahlqvist Mark L 
Published: May 2012

AbstractObjectiveTo investigate the association between cooking behaviour and long-term survival among elderly Taiwanese.DesignCohort study. The duration of follow-up was the interval between the date of interview and the date of death or 31 December 2008, when censored for survivors. Information used included demographics, socio-economic status, health behaviours, cooking frequencies, physical function, cognitive function, nutrition knowledge awareness, eating out habits and food and nutrient intakes. These data were linked to death records. Cox proportional-hazards models were used to evaluate cooking frequency on death from 1999 to 2008 with related covariate adjustments.SettingElderly Nutrition and Health Survey in Taiwan, 1999–2000.SubjectsNationally representative free-living elderly people aged ≥65 years (n 1888).ResultsDuring a 10-year follow-up, 695 participants died. Those who cooked most frequently were younger, women, unmarried, less educated, non-drinkers of alcohol, non-smokers, without chewing difficulty, had spouse as dinner companion, normal cognition, who walked or shopped more than twice weekly, who ate less meat and more vegetables. Highly frequent cooking (>5 times/week, compared with never) predicted survival (hazard ratio (HR) = 0·47; 95 % CI, 0·36, 0·61); with adjustment for physical function, cognitive function, nutrition knowledge awareness and other covariates, HR was 0·59 (95 % CI, 0·41, 0·86). Women benefited more from cooking more frequently than did men, with decreased HR, 51 % v. 24 %, when most was compared with least. A 2-year delay in the assessment of survivorship led to similar findings.ConclusionsCooking behaviour favourably predicts survivorship. Highly frequent cooking may favour women more than men.
Investigation of scattering in lunar seismic coda
Authors: Blanchette‐Guertin J.‐F. , Johnson C. L. , Lawrence J. F. 
Published: May 2012

We investigate the intrinsic attenuation and scattering properties of the Moon by parameterizing the coda decay of 369 higher‐quality lunar seismograms from 72 events via their characteristic rise and decay times. We investigate any dependence of the decay times on source type, frequency, and epicentral distance. Intrinsic attenuation, scattering, and possible focusing of energy in a near‐surface, low‐velocity layer all contribute to the coda decay. Although it is not possible to quantify the exact contribution of each of these effects in the seismograms, results suggest that scattering in a near‐surface global layer dominates the records of shallow events (∼0–200 km depth), particularly at frequencies above 2 Hz, and for increasing epicentral distance. We propose that the scattering layer is the megaregolith and that energy from shallow sources encounters more scatterers as it travels longer distances in the layer, increasing the coda decay times. A size distribution of ejecta blocks that has more small‐scale than large‐scale scatterers intensifies this effect for increasing frequencies. Deep moonquakes (700–1100 km depth) exhibit no dependence of the decay time on epicentral distance. We suggest that because of their large depths and small amplitudes, deep moonquakes from any distance sample a similar region near a given receiver. Near‐station structure and geology may also control the decay times of local events, as evidenced by two natural impact records. This study provides constraints and testable hypotheses for waveform modeling of the lunar interior that includes the effects of intense scattering and shallow, low‐velocity layers.
Looking for evidence of mixing in the solar wind from 0.31 to 0.98 AU
Authors: Borovsky Joseph E. 
Published: May 2012

To determine the efficacy of turbulence in the solar wind, the amount of mixing of the solar wind plasma is quantified. If magnetohydrodynamic turbulence in the solar wind acts as does Navier‐Stokes turbulence, the chunk mixture of scalar quantities in the solar wind plasma should evolve with time. In particular, (1) the sizes of plasma chunks should decrease with distance from the Sun owing to the stretching and folding action of turbulence and (2) the occurrence distributions of passive‐scalar values in the plasma should narrow with distance from the Sun owing to homogenization. The evolution of the chunk mix is studied through the use of interface‐crossing statistics. Using Helios 1 and Helios 2 slow‐solar wind measurements from 0.31 to 0.98 AU, temporal jumps in the proton number density, proton specific entropy, and proton beta are used to locate plasma interfaces in the solar wind and the plasma chunk sizes are determined from the distances between the plasma interfaces. No evidence for the evolution of the chunk‐size distribution is seen, indicating an absence of mixing in the solar wind. The distribution of plasma density broadens by 11% with distance, the distribution of proton flux stays constant, while the distribution of proton specific entropy narrows by 14%; collectively the three distributions do not show clear evidence for evolution toward homogeneity, hence they do not show clear evidence for mixing. Implications of the lack of evidence for mixing in the solar wind are discussed.
Seasonal variation of upwelling in the Alaskan Beaufort Sea: Impact of sea ice cover
Authors: Schulze Lena M. , Pickart Robert S. 
Published: May 2012

Data from a mooring array deployed from August 2002 to September 2004 are used to characterize differences in upwelling near the shelf break in the Alaskan Beaufort Sea due to varying sea ice conditions. The record is divided into three ice seasons: open water, partial ice, and full ice. The basic response is the same in each of the seasons. Roughly 8 h after the onset of easterly winds the shelf break jet reverses, followed approximately 10 h later by upwelling of saltier water which is cold near the shelf break (Pacific Winter Water) and warm at depth (Atlantic Water). The secondary circulation at the outer shelf is, to first order, consistent with a two‐dimensional Ekman balance of offshore flow in the upper layer and onshore flow at depth. There are, however, important seasonal differences in the upwelling. Overall the response is strongest in the partial ice season and weakest in the full ice season. It is believed that these differences are dictated by the degree to which wind stress is transmitted through the pack‐ice, as the strength of the wind‐forcing was comparable over the three seasons. An EOF‐based upwelling index is constructed using information about the primary flow, secondary flow, and hydrography. The ability to predict upwelling using the wind record alone is explored, which demonstrates that 90% of easterly wind events exceeding 9.5 m s−1 drive significant upwelling. During certain periods the ice cover on the shelf became landfast, which altered the upwelling and circulation patterns near the shelf break.
Time domain waveform and azimuth variation of ionospherically reflected VLF/LF radio emissions from lightning
Authors: Jacobson Abram R. , Shao Xuan‐Min , Lay Erin 
Published: May 2012

The Earth's geomagnetic field can, in principle, cause significant magnetic‐azimuth variations of the lower ionosphere's reflection of 2–150 kHz radio waves emitted by lightning. There has been little published work on this azimuth variation, either modeled or observational. We use broadband emissions from negative cloud‐to‐ground lightning strokes to study the azimuthal variations systematically. The data are from the Los Alamos Sferic Array, operating in the United States' southern Great Plains during 2005. We compare the observations to a model of lower‐ionosphere reflection of radio waves. The model recapitulates the basic features of the time domain reflection waveforms rather well, except at the lowest frequencies. The model transfer function describing the vertical electric field at the receiver is symmetric about 90° magnetic and about 270° magnetic. Two noteworthy features of the azimuth variation are both predicted by the model, and seen in the data: First, at the lowest frequencies (<30 kHz) there is enhanced reflection for eastward propagation, relative to westward propagation. Second, at the higher frequencies (>50 kHz) there is an opposite enhancement, of the reflection for westward propagation, relative to eastward propagation. The westward enhancement at >50 kHz depends sensitively on range and is most evident in nighttime conditions, while the eastward enhancement at <30 kHz occurs at all ranges studied. Range‐dependent frequency modulations of the transfer function are the least for magnetic northward propagation (duplicated by magnetic southward).
Characterization of VAMP‐2 in the lung: implication in lung surfactant secretion
Authors: Wang Pengcheng , Howard Marcia D. , Zhang Honghao , Chintagari Narendranath Reddy , Bell Anna , Jin Nili , Mishra Amarjit , Liu Lin 
Published: May 2012

AbstractLung surfactant is crucial for reducing the surface tension of alveolar space, thus preventing the alveoli from collapse. Lung surfactant is synthesized in alveolar epithelial type II cells and stored in lamellar bodies before being released via the fusion of lamellar bodies with the apical plasma membrane. SNAREs (soluble N‐ethylmaleimide‐sensitive fusion protein‐attachment protein receptors) play an essential role in membrane fusion. We have previously demonstrated the requirement of t‐SNARE (target SNARE) proteins, syntaxin 2 and SNAP‐23 (N‐ethylmaleimide‐sensitive factor‐attachment protein 23), in regulated surfactant secretion. Here, we characterized the distribution of VAMPs (vesicle‐associated membrane proteins) in rat lung and alveolar type II cells. VAMP‐2, −3 and −8 are shown in type II cells at both mRNA and protein levels. VAMP‐2 and −8 were enriched in LB (lamellar body) fraction. Immunochemistry studies indicated that VAMP‐2 was co‐localized with the LB marker protein, LB‐180. Functionally, the cytoplasmic domain of VAMP‐2, but not VAMP‐8 inhibited surfactant secretion in type II cells. We suggest that VAMP‐2 is the v‐SNARE (vesicle SNARE) involved in regulated surfactant secretion.
Livestock infectious disease and climate change: a review of selected literature.
Authors: Heffernan C. , Salman M. , York L. 
Published: May 2012

Abstract
It is indisputable that climate is an important factor in many livestock diseases. Nevertheless, our knowledge of the impact of climate change on livestock infectious diseases is much less certain. Therefore, the aim of the article is to conduct a systematic review of the literature on the topic utilizing available retrospective data and information. Across a corpus of 175 formal publications, limited empirical evidence was offered to underpin many of the main arguments. The literature reviewed was highly polarized and often inconsistent regarding what the future may hold. Historical explorations were rare. However, identifying past drivers to livestock disease may not fully capture the extent that new and unknown drivers will influence future change. As such, our current predictive capacity is low. We offer a number of recommendations to strengthen this capacity in the coming years. We conclude that our current approach to research on the topic is limiting and unlikely to yield sufficient, actionable evidence to inform future praxis. Therefore, we argue for the creation of a reflexive, knowledge-based system, underpinned by a collective intelligence framework to support the drawing of inferences across the literature.
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform
Authors: Liu Yongchao , Schmidt Bertil , Maskell Douglas L. 
Published: May 2012

Abstract
Motivation: New high-throughput sequencing technologies have promoted the production of short reads with dramatically low unit cost. The explosive growth of short read datasets poses a challenge to the mapping of short reads to reference genomes, such as the human genome, in terms of alignment quality and execution speed.
Results: We present CUSHAW, a parallelized short read aligner based on the compute unified device architecture (CUDA) parallel programming model. We exploit CUDA-compatible graphics hardware as accelerators to achieve fast speed. Our algorithm uses a quality-aware bounded search approach based on the Burrows–Wheeler transform (BWT) and the Ferragina–Manzini index to reduce the search space and achieve high alignment quality. Performance evaluation, using simulated as well as real short read datasets, reveals that our algorithm running on one or two graphics processing units achieves significant speedups in terms of execution time, while yielding comparable or even better alignment quality for paired-end alignments compared with three popular BWT-based aligners: Bowtie, BWA and SOAP2. CUSHAW also delivers competitive performance in terms of single-nucleotide polymorphism calling for an Escherichia coli test dataset.
Availability: http://cushaw.sourceforge.net.
Contact: liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de
Supplementary information: Supplementary data are available at Bioinformatics online.
BEDOPS: high-performance genomic feature operations
Authors: Neph Shane , Kuehn M. Scott , Reynolds Alex P. , Haugen Eric , Thurman Robert E. , Johnson Audra K. , Rynes Eric , Maurano Matthew T. , Vierstra Jeff , Thomas Sean , Sandstrom Richard , Humbert Richard , Stamatoyannopoulos John A. 
Published: May 2012

Abstract
Summary: The large and growing number of genome-wide datasets highlights the need for high-performance feature analysis and data comparison methods, in addition to efficient data storage and retrieval techniques. We introduce BEDOPS, a software suite for common genomic analysis tasks which offers improved flexibility, scalability and execution time characteristics over previously published packages. The suite includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives.
Availability: http://code.google.com/p/bedops/ includes binaries, source and documentation.
Contact: sjn@u.washington.edu and jstam@u.washington.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool
Authors: James Regis A. , Rao Mitchell M. , Chen Edward S. , Goodell Margaret A. , Shaw Chad A. 
Published: May 2012

Abstract
Summary: Many important data in current biological science comprise hundreds, thousands or more individual results. These massive data require computational tools to navigate results and effectively interact with the content. Mobile device apps are an increasingly important tool in the everyday lives of scientists and non-scientists alike. These software present individuals with compact and efficient tools to interact with complex data at meetings or other locations remote from their main computing environment. We believe that apps will be important tools for biologists, geneticists and physicians to review content while participating in biomedical research or practicing medicine. We have developed a prototype app for displaying gene expression data using the iOS platform. To present the software engineering requirements, we review the model-view-controller schema for Apple's iOS. We apply this schema to a simple app for querying locally developed microarray gene expression data. The challenge of this application is to balance between storing content locally within the app versus obtaining it dynamically via a network connection.
Availability: The Hematopoietic Expression Viewer is available at http://www.shawlab.org/he_viewer. The source code for this project and any future information on how to obtain the app can be accessed at http://www.shawlab.org/he_viewer.
Contact: cashaw@bcm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CPSS: a computational platform for the analysis of small RNA deep sequencing data
Authors: Zhang Yuanwei , Xu Bo , Yang Yifan , Ban Rongjun , Zhang Huan , Jiang Xiaohua , Cooke Howard J. , Xue Yu , Shi Qinghua 
Published: May 2012

Abstract
Summary: Next generation sequencing (NGS) techniques have been widely used to document the small ribonucleic acids (RNAs) implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analysing the enormous datasets from small RNA deep sequencing approach. Herein, we present a novel web server, CPSS (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. Small RNA NGS data can be submitted to this server with analysis results being returned in two parts: (i) annotation analysis, which provides the most comprehensive analysis for small RNA transcriptome, including length distribution and genome mapping of sequencing reads, small RNA quantification, prediction of novel miRNAs, identification of differentially expressed miRNAs, piwi-interacting RNAs and other non-coding small RNAs between paired samples and detection of miRNA editing and modifications and (ii) functional analysis, including prediction of miRNA targeted genes by multiple tools, enrichment of gene ontology terms, signalling pathway involvement and protein–protein interaction analysis for the predicted genes. CPSS, a ready-to-use web server that integrates most functions of currently available bioinformatics tools, provides all the information wanted by the majority of users from small RNA deep sequencing datasets.
Availability: CPSS is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/db/cpss/index.html or http://mcg.ustc.edu.cn/sdap1/cpss/index.html.
Contact: xueyu@mail.hust.edu.cn or qshi@ustc.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Genome-scale analysis of interaction dynamics reveals organization of biological networks
Authors: Das Jishnu , Mohammed Jaaved , Yu Haiyuan 
Published: May 2012

Abstract
Summary: Analyzing large-scale interaction networks has generated numerous insights in systems biology. However, such studies have primarily been focused on highly co-expressed, stable interactions. Most transient interactions that carry out equally important functions, especially in signal transduction pathways, are yet to be elucidated and are often wrongly discarded as false positives. Here, we revisit a previously described Smith–Waterman-like dynamic programming algorithm and use it to distinguish stable and transient interactions on a genomic scale in human and yeast. We find that in biological networks, transient interactions are key links topologically connecting tightly regulated functional modules formed by stable interactions and are essential to maintaining the integrity of cellular networks. We also perform a systematic analysis of interaction dynamics across different technologies and find that high-throughput yeast two-hybrid is the only available technology for detecting transient interactions on a large scale.
Contact: haiyuan.yu@cornell.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mediational relations between 12‐Step attendance, depression and substance use in patients with comorbid substance dependence and major depression
Authors: Worley Matthew J. , Tate Susan R. , Brown Sandra A. 
Published: May 2012

AbstractAimsAmong patients with substance dependence and comorbid major depressive disorder (MDD) receiving treatment in a controlled trial, we examined if group differences in depression were mediated by 12‐Step involvement, and if the effects of 12‐Step involvement on future alcohol and drug use were mediated by reductions in depression.DesignControlled trial of Twelve‐Step facilitation (TSF) and integrated cognitive–behavioral therapy (ICBT), delivered in out‐patient groups for 6 months with adjunct pharmacotherapy.SettingOut‐patient dual diagnosis clinic in Veteran's Affairs Healthcare Center.ParticipantsVeterans (n = 209) diagnosed with alcohol, stimulant or marijuana dependence and substance‐independent MDD.MeasurementsTwelve‐Step attendance and affiliation, depression severity, percentage of days drinking and percentage of days using drugs assessed at baseline and months 3, 6 and 9.FindingsIn multi‐level analyses greater 12‐Step meeting attendance predicted lower depression and mediated the superior depression outcomes of the TSF group, explaining 24.3% of the group difference in depression. Independent of treatment group, lower depression severity predicted lower future alcohol use and mediated the effects of 12‐Step meetings, explaining 15.7% of their effects on future drinking. Controlled, lagged models indicated these effects were not confounded by current substance use, suggesting that depression had unique associations with 12‐Step meeting attendance and future drinking.ConclusionsFor patients with substance dependence and major depressive disorder, attendance at 12‐Step meetings is associated with mental health benefits that extend beyond substance use, and reduced depression could be a key mechanism whereby 12‐Step meetings reduce future drinking in this population.