bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soft drinks consumption, diet quality and BMI in a Mediterranean population
Authors: Balcells Eva , Delgado-Noguera Mario , Pardo-Lozano Ricardo , Roig-González Taïs , Renom Anna , González-Zobl Griselda , Muñoz-Ortego Juan , Valiente-Hernández Susana , Pou-Chaubron Marina , Schröder Helmut 
Published: October 2010

AbstractObjectivesEvidence of the effects of soft drinks consumption on BMI and lifestyle in adult populations is mixed and quite limited. The aim of the present study was to determine the association of soft drinks consumption with BMI and lifestyle in a representative Mediterranean population.DesignTwo independent, population-based, cross-sectional (2000 and 2005) studies. Dietary intake was assessed using a validated FFQ. Weight and height were measured.SettingGirona, Spain.SubjectsRandom sample of the 35- to 74-year-old population (3910 men and 4285 women).ResultsLess than half (41·7 %) of the population consumed soft drinks; the mean consumption was 36·2 ml/d. The prevalence of sedentary lifestyle increased with the frequency of soft drinks consumption (P= 0·025). Daily soft drinks consumption significantly increased the risk of low adherence to the Mediterranean diet (OR = 0·57, 95 % CI 0·44, 0·74v. top tertile of Mediterranean diet score). Multiple linear regression analyses, controlled for potential confounders, revealed that an increment in soft drinks consumption of 100 ml was associated with a 0·21 kg/m2increase in BMI (P= 0·001). Only implausibly low reports of energy consumption showed a null association between soft drinks consumption and BMI.ConclusionsSoft drinks consumption was not embedded in a healthy diet context and was positively associated with BMI and sedentary lifestyle in this Mediterranean population.
Recruitment of volunteers for a home-delivered meals programme serving homebound older adults: a theoretically derived programme among faith communities
Authors: Buys David R , Marler Malcolm L , Robinson Caroline O , Hamlin Christopher M , Locher Julie L 
Published: October 2010

AbstractObjectiveHome-delivered nutrition programmes that are federally subsidized by the US Administration on Aging seek to ensure that socially isolated older adults who are unable to purchase and prepare their own food have nutritious meals delivered to them regularly by both employed and volunteer staff. Unfortunately, there are long waiting lists in some neighbourhoods that are often due to a shortage of volunteers. The present paper describes a theoretically driven community-based project designed to increase volunteer participation in serving Meals on Wheels (MOW) clients.DesignA Support Team model was applied in the project wherein existing social capital among religious faith communities, and social networks within those organizations, was joined with a local MOW programme to create a sustainable meal delivery route to vulnerable homebound older adults.SettingThe programme participants were in one underserved neighbourhood in Birmingham, Alabama, an urban city in the south-eastern USA.SubjectsThe subjects under consideration are both MOW clients and volunteers. MOW clients are those individuals aged 60 years and above who qualify for the service; the volunteers are from community churches.ResultsOne volunteer route, comprising six congregations that delivered meals to sixteen homebound older adults, was created. The route served more than 2000 meals in 2006 (the year the programme began) and continues to serve clients today.ConclusionsThe programme’s successful implementation provides evidence that reliance on theory is critical in planning and developing effective community-based programme interventions.
Elias Howe, William Bradbury Ryan, and Irish Music in Nineteenth-Century Boston
Authors: WELLS PAUL F. 
Published: October 2010

AbstractRyan's Mammoth Collectionis a compendium of fiddle tunes assembled by William Bradbury Ryan. Originally published in Boston in 1883 by Elias Howe, Jr., it has remained in print in one form or another ever since. It has been used as a source of tunes by many generations of fiddlers in different stylistic traditions, but its value as a descriptive document of the repertoire of late-nineteenth-century Boston, particularly the Irish community in that city, has largely been overlooked. Ryan, rather than Capt. Francis O'Neill of Chicago, should be regarded as the first great documentarian of Irish traditional music in the United States.
No Yankee Doodling: Notable Trends and Traditional Recordings from Irish America
Authors: HITCHNER EARLE 
Published: October 2010

AbstractThe emergence of the compact disc in 1979 was regarded as the likely sales salvation of recorded music, and for many years the CD reigned supreme, generating steady, often substantial, company profits. More recently, however, the music industry has painfully slipped a disc. The CD has been in sharp decline, propelled mainly by young consumer ire over price and format inflexibility and by Internet technology available to skirt or subvert both. Irish American traditional music has not been impervious to this downward trend in sales and to other challenging trends and paradigm shifts in recording and performing. Amid the tumult, Irish American traditional music has nevertheless shown a new resilience and fresh vitality through a greater do-it-yourself, do-more-with-less spirit of recording, even for established small labels. The five recent albums of Irish American traditional music reviewed here—three of which were released by the artists themselves—exemplify a trend of their own, preserving the best of the past without slavishly replicating it. If the new mantra of music making is adapt or disappear, then Irish American traditional music, in adapting to change free of any impulse to dumb down, is assured of robustly enduring.
Direct Carbon Fuel Cells
Authors: Desclaux P. , Nürnberger S. , Stimming U. 
Published: October 2010

Direct carbon fuel cells (DCFCs) are high temperature fuel cells which offer the possibility to directly convert the chemical energy of carbon materials (e.g. coal, lignite, char, carbonized biomass) into electricity. In addition to using solid carbon fuels, higher overall efficiencies should be possible because the thermodynamic efficiency is close to 100 %. This means higher than those of conventional fuel cell types for gaseous fuels.
DCFC technology can employ three different electrolyte types: Molten carbonate electrolyte (liquid salt), molten hydroxide electrolyte (liquid salt) and solid oxide electrolyte (solid ceramic layer). Recently, also combined technologies have been developed.
In this chapter, all the concepts are described and their advantages and difficulties are discussed.
Electrolysis Using Fuel Cell Technology
Authors: Brisse A. , Schefold J. , Stoots C. , O’Brien J. 
Published: October 2010

Present global hydrogen demand is met to a large extent by fossil fuels. Hydrogen is produced via alkaline electrolysis of water only, when the required electric energy is readily available. Alternatively, hydrogen can be produced by water electrolysis with reversibly operated fuel cells, PEMFCs or SOFCs. PEM electrolysis is technologically mature with an energy-conversion efficiency (electrical-to-chemical) somewhat above the one of alkaline electrolysis (70-80%).
Higher efficiency for electrolysis is expected with increasing temperature as consequence of the decrease of the molar Gibbs energy of the reaction. This was first confirmed with the reversible operation of tubular SOFCs as solid oxide electrolyser cells (SOECs) in pioneering works in the 1980ies. With present SOFCs operated as SOECs, notably the planar cells, the theoretically predicted efficiencies are more and more approached in the experiment. State-of-the-art SOECs may be operated with and without external heat supply; already without heat supply the electrical-to-chemical energy-conversion efficiency is above the one of low temperature electrolysers. Operation cell voltages are around 1.1 to 1.3 V at 800°C at a Faradaic efficiency of 100%. The high efficiency may render the SOEC technology attractive for the storage of (intermittent) renewable energy, such as wind or solar.
In this chapter, examples for the actual state of research on SOECs as well as on SOEC stacks and systems are given, notably their current-voltage response and behaviour under long-term operation. Moreover, some development options – and potential hurdles like cell degradation – are summarised for this potentially new branch of the solid oxide cell technology.
ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations
Authors: Wright Mark H. , Tung Chih-Wei , Zhao Keyan , Reynolds Andy , McCouch Susan R. , Bustamante Carlos D. 
Published: October 2010

Abstract
Motivation: The development of new high-throughput genotyping products requires a significant investment in testing and training samples to evaluate and optimize the product before it can be used reliably on new samples. One reason for this is current methods for automated calling of genotypes are based on clustering approaches which require a large number of samples to be analyzed simultaneously, or an extensive training dataset to seed clusters. In systems where inbred samples are of primary interest, current clustering approaches perform poorly due to the inability to clearly identify a heterozygote cluster.
Results: As part of the development of two custom single nucleotide polymorphism genotyping products for Oryza sativa (domestic rice), we have developed a new genotype calling algorithm called ‘ALCHEMY’ based on statistical modeling of the raw intensity data rather than modelless clustering. A novel feature of the model is the ability to estimate and incorporate inbreeding information on a per sample basis allowing accurate genotyping of both inbred and heterozygous samples even when analyzed simultaneously. Since clustering is not used explicitly, ALCHEMY performs well on small sample sizes with accuracy exceeding 99% with as few as 18 samples.
Availability: ALCHEMY is available for both commercial and academic use free of charge and distributed under the GNU General Public License at http://alchemy.sourceforge.net/
Contact: mhw6@cornell.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
High-throughput prediction of protein antigenicity using protein microarray data
Authors: Magnan Christophe N. , Zeller Michael , Kayala Matthew A. , Vigil Adam , Randall Arlo , Felgner Philip L. , Baldi Pierre 
Published: October 2010

Abstract
Motivation: Discovery of novel protective antigens is fundamental to the development of vaccines for existing and emerging pathogens. Most computational methods for predicting protein antigenicity rely directly on homology with previously characterized protective antigens; however, homology-based methods will fail to discover truly novel protective antigens. Thus, there is a significant need for homology-free methods capable of screening entire proteomes for the antigens most likely to generate a protective humoral immune response.
Results: Here we begin by curating two types of positive data: (i) antigens that elicit a strong antibody response in protected individuals but not in unprotected individuals, using human immunoglobulin reactivity data obtained from protein microarray analyses; and (ii) known protective antigens from the literature. The resulting datasets are used to train a sequence-based prediction model, ANTIGENpro, to predict the likelihood that a protein is a protective antigen. ANTIGENpro correctly classifies 82% of the known protective antigens when trained using only the protein microarray datasets. The accuracy on the combined dataset is estimated at 76% by cross-validation experiments. Finally, ANTIGENpro performs well when evaluated on an external pathogen proteome for which protein microarray data were obtained after the initial development of ANTIGENpro.
Availability: ANTIGENpro is integrated in the SCRATCH suite of predictors available at http://scratch.proteomics.ics.uci.edu.
Contact: pfbaldi@ics.uci.edu
TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence
Authors: Davey Robert P. , James Stephen A. , Dicks Jo , Roberts Ian N. 
Published: October 2010

Abstract
Summary: TURNIP comprises a suite of Perl scripts and modules that facilitates the resolution of microheterogeneity within hard-to-assemble repetitive DNA sequences. TURNIP was originally developed for the Saccharomyces Genome Resequencing Project (SGRP) within which the ribosomal DNA (rDNA) of 36 strains of S.cerevisiae were analysed to investigate the occurrence of potential polymorphisms. Here, ‘partially resolved SNPs’, or pSNPs, as well as indels, were found to be far more prevalent than previously suspected. More generally, the TURNIP software ascertains degrees of variation between large tandem repeats within a single locus, offering insights into mechanisms of genome stability and gene conversion in any organism for which genome sequence data are available.
Availability: The TURNIP source code, results files and online help are available at http://www.ncyc.co.uk/software/turnip.html .
Contact: robert.davey@bbsrc.ac.uk
Robust relationship inference in genome-wide association studies
Authors: Manichaikul Ani , Mychaleckyj Josyf C. , Rich Stephen S. , Daly Kathy , Sale Michèle , Chen Wei-Min 
Published: October 2010

Abstract
Motivation: Genome-wide association studies (GWASs) have been widely used to map loci contributing to variation in complex traits and risk of diseases in humans. Accurate specification of familial relationships is crucial for family-based GWAS, as well as in population-based GWAS with unknown (or unrecognized) family structure. The family structure in a GWAS should be routinely investigated using the SNP data prior to the analysis of population structure or phenotype. Existing algorithms for relationship inference have a major weakness of estimating allele frequencies at each SNP from the entire sample, under a strong assumption of homogeneous population structure. This assumption is often untenable.
Results: Here, we present a rapid algorithm for relationship inference using high-throughput genotype data typical of GWAS that allows the presence of unknown population substructure. The relationship of any pair of individuals can be precisely inferred by robust estimation of their kinship coefficient, independent of sample composition or population structure (sample invariance). We present simulation experiments to demonstrate that the algorithm has sufficient power to provide reliable inference on millions of unrelated pairs and thousands of relative pairs (up to 3rd-degree relationships). Application of our robust algorithm to HapMap and GWAS datasets demonstrates that it performs properly even under extreme population stratification, while algorithms assuming a homogeneous population give systematically biased results. Our extremely efficient implementation performs relationship inference on millions of pairs of individuals in a matter of minutes, dozens of times faster than the most efficient existing algorithm known to us.
Availability: Our robust relationship inference algorithm is implemented in a freely available software package, KING, available for download at http://people.virginia.edu/∼wc9c/KING.
Contact: wmchen@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
Authors: Montojo J. , Zuberi K. , Rodriguez H. , Kazi F. , Wright G. , Donaldson S. L. , Morris Q. , Bader G. D. 
Published: October 2010

Abstract
Summary: The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses over 800 networks from six organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data.
Availability and Implementation: The GeneMANIA Cytoscape plugin is implemented in Java and is freely available at http://www.genemania.org/plugin/.
Contact: gary.bader@utoronto.ca; quaid.morris@utoronto.ca
Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity
Authors: Aggio Raphael B. M. , Ruggiero Katya , Villas-Bôas Silas Granato 
Published: October 2010

AbstractMotivation: Metabolomics is one of the most recent omics-technologies and uses robust analytical techniques to screen low molecular mass metabolites in biological samples. It has evolved very quickly during the last decade. However, metabolomics datasets are considered highly complex when used to relate metabolite levels to metabolic pathway activity. Despite recent developments in bioinformatics, which have improved the quality of metabolomics data, there is still no straightforward method capable of correlating metabolite level to the activity of different metabolic pathways operating within the cells. Thus, this kind of analysis still depends on extremely laborious and time-consuming processes.Results: Here, we present a new algorithm Pathway Activity Profiling (PAPi) with which we are able to compare metabolic pathway activities from metabolite profiles. The applicability and potential of PAPi was demonstrated using a previously published data from the yeast Saccharomyces cerevisiae. PAPi was able to support the biological interpretations of the previously published observations and, in addition, generated new hypotheses in a straightforward manner. However, PAPi is time consuming to perform manually. Thus, we also present here a new R-software package (PAPi) which implements the PAPi algorithm and facilitates its usage to quickly compare metabolic pathways activities between different experimental conditions. Using the identified metabolites and their respective abundances as input, the PAPi package calculates pathways' Activity Scores, which represents the potential metabolic pathways activities and allows their comparison between conditions. PAPi also performs principal components analysis and analysis of variance or t-test to investigate differences in activity level between experimental conditions. In addition, PAPi generates comparative graphs highlighting up- and down-regulated pathway activity.Availability: These datasets are available in http://www.4shared.com/file/hTWyndYU/extra.html and http://www.4shared.com/file/VbQIIDeu/intra.html. PAPi package is available in: http://www.4shared.com/file/s0uIYWIg/PAPi_10.htmlContact: s.villas-boas@auckland.ac.nzSupplementary information: Supplementary data are available at Bioinformatics online.
Target-align: a tool for plant microRNA target identification
Authors: Xie Fuliang , Zhang Baohong 
Published: October 2010

Abstract
Motivation: MicroRNAs (miRNAs) are important regulatory molecules. A critical step in elucidating miRNA function is identifying potential miRNA targets. However, few reliable tools have been developed for identifying miRNA targets in plants.
Results: Here, we developed a Smith–Waterman-like alignment tool in order to accurately predict miRNA targets. Dynamic programming was used to build a score matrix based on the complementarity of nucleotides in order to trace the optimal local alignments. Important parameters, such as maximum mismatches and maximum consecutive mismatches between miRNAs and their targets, were also used for filtering the optimal local alignments. Almost all of the parameters in this alignment tool can be adjusted by users. Compared to other target prediction tools, Target-align exhibits strong sensitivity and accuracy for identifying miRNA targets. More importantly, Target-align can identify multi-target sites as well potential for non-cleaved targets sites by change the default settings. Windows, web and command-line versions were developed to better serve different users.
Availability: http://www.leonxie.com/targetAlign.php.
Contact: zhangb@ecu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Pre-calculated protein structure alignments at the RCSB PDB website
Authors: Prlić Andreas , Bliven Spencer , Rose Peter W. , Bluhm Wolfgang F. , Bizon Chris , Godzik Adam , Bourne Philip E. 
Published: October 2010

AbstractSummary: With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.Availability and Implementation: A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.orgContact: andreas@sdsc.edu; pbourne@ucsd.edu
The relationship between addiction and reward bundling: an experiment comparing smokers and non‐smokers
Authors: Hofmeyr Andre , Ainslie George , Charlton Richard , Ross Don 
Published: October 2010

ABSTRACTAims Previous studies indicate that addicts show reduced preference for more delayed versus more immediate rewards compared to non‐addicts. This may reflect a lower propensity to view such decisions in terms of the larger sequences to which they typically belong (e.g. smoking is a frequently repeated act). Therefore, this study aims to test whether, in a sequence of decisions involving smaller, sooner (SS) versus larger, later (LL) rewards, suggesting or forcing people with a propensity to addiction to make the decision for the series as a whole would increase LL preference. It is hypothesized that people without a propensity to addiction should benefit less from being encouraged to think of reward sequences because they already tend to take that view.Design Thirty regular smokers (as exemplars of addicted individuals) and 30 non‐smokers chose between small short‐term and larger long‐term monetary rewards over a sequence of four decisions spaced 2 weeks apart. Subjects were divided into three groups: one who made each decision independently with no suggestion that they be considered as a series (‘free’), a group to whom it was suggested from the start that they consider each decision as part of the series (‘suggested’) and a group who were told that their very first choice in the series would be used for the remaining decisions (‘forced’). All subjects were paid the amounts they had chosen.Setting A laboratory room at the University of Cape Town (UCT).Participants UCT undergraduate volunteers.Analyses The proportion of LL choices in each subgroup was evaluated by χ2tests and a probit model.Findings Smokers increased their preference for LL rewards when ‘bundling’ of individual decisions into a sequence was either suggested or forced. This preference increased with repeated experience. Non‐smokers showed neither pattern.Conclusions The propensity of smokers to prefer small short‐term rewards over larger delayed rewards may be mitigated, over a sequence of decisions of this kind, by encouraging or forcing them to think of the sequence as a whole. If replicated, this finding may form the basis of an intervention that could attenuate the choice patterns characteristic of addiction.