bluuebunny/crossref_metadata_2025_split huggingface dataset:
A healthy trend: less food used in fundraising and as rewards and incentives in Minnesota middle and high schools
Authors: Kubik Martha Y , Farbakhsh Kian , Lytle Leslie A 
Published: October 2012

AbstractObjectiveTo assess change in the 4-year prevalence (2006–2009) of the use of food in school fundraising and as rewards and incentives for students, following implementation of federal legislation in the USA in 2006.DesignSerial cross-sectional design using trend analysis to assess school-level data collected over four consecutive years from 2006/2007 to 2009/2010.SettingMinneapolis/St. Paul, MN.SubjectsConvenience sample of middle and high schools participating in two longitudinal, aetiological studies that examined youth, their environment and obesity-related factors.ResultsA significant and sustained decrease was demonstrated in the use of low-nutrient, energy-dense foods in school fundraising activities and the use of food and food coupons as rewards and incentives by teachers and school staff.ConclusionsResults support the utility of policy and legislative action as a tool for creating healthy, sustainable environmental change.
Association of the PDYN gene with alcohol dependence and the propensity to drink in negative emotional states
Authors: Karpyak Victor M. , Winham Stacey J. , Preuss Ulrich W. , Zill Peter , Cunningham Julie M. , Walker Denise L. , Lewis Kriste A. , Geske Jennifer R. , Colby Colin L. , Abulseoud Osama A. , Hall-Flavin Daniel K. , Loukianova Larissa L. , Schneekloth Terry D. , Frye Mark A , Bazov Igor , Heit John A. , Bakalkin Georgy , Mrazek David A. , Biernacka Joanna M. 
Published: October 2012

AbstractSynthetic κ-opioid receptor (KOR) agonists induce dysphoric and pro-depressive effects and variations in the KOR (OPRK1) and prodynorphin (PDYN) genes have been shown to be associated with alcohol dependence. We genotyped 23 single nucleotide polymorphisms (SNPs) in the PDYN and OPRK1 genes in 816 alcohol-dependent subjects and investigated their association with: (1) negative craving measured by a subscale of the Inventory of Drug Taking Situations; (2) a self-reported history of depression; (3) the intensity of depressive symptoms measured by the Beck Depression Inventory-II. In addition, 13 of the 23 PDYN and OPRK1 SNPs, which were previously genotyped in a set of 1248 controls, were used to evaluate association with alcohol dependence. SNP and haplotype tests of association were performed. Analysis of a haplotype spanning the PDYN gene (rs6045784, rs910080, rs2235751, rs2281285) revealed significant association with alcohol dependence (p = 0.00079) and with negative craving (p = 0.0499). A candidate haplotype containing the PDYN rs2281285-rs1997794 SNPs that was previously associated with alcohol dependence was also associated with negative craving (p = 0.024) and alcohol dependence (p = 0.0008) in this study. A trend for association between depression severity and PDYN variation was detected. No associations of OPRK1 gene variation with alcohol dependence or other studied phenotypes were found. These findings support the hypothesis that sequence variation in the PDYN gene contributes to both alcohol dependence and the induction of negative craving in alcohol-dependent subjects.
Reversible transformation between α-oxo acids and α-amino acids on ZnS particles: a photochemical model for tuning the prebiotic redox homoeostasis
Authors: Wang Wei , Liu Xiaoyang , Yang Yanqiang , Su Wenhui 
Published: October 2012

AbstractHow prebiotic metabolic pathways could have formed is an essential question for the origins of life on early Earth. From the abiogenetic point of view, the emergence of primordial metabolism may be postulated as a continuum from Earth's geochemical processes to chemoautotrophic biochemical procedures on mineral surfaces. In the present study, we examined in detail the reversible amination of α-ketoglutarate on UV-irradiated ZnS particles under variable reaction conditions such as pH, temperature, hole scavenger species and concentrations, and different amino acids. It was observed that the reductive amination of α-ketoglutarate and the oxidative amination of glutamate were both effectively performed on ZnS surfaces in the presence and absence of a hole scavenger, respectively. Accordingly, a photocatalytic mechanism was proposed. The reversible photochemical reaction was more efficient under basic conditions but independent of temperature in the range of 30–60 °C. SO32−was more effective than S2−as the hole scavenger. Finally, we extended the glutamate dehydrogenase-like chemistry to a set of other α-amino acids and their corresponding α-oxo acids and found that hydrophobic amino acid side chains were more conducive to the reversible redox reactions. Since the experimental conditions are believed to have been prevalent in shallow water hydrothermal vent systems of early Earth, the results of this work not only suggest that the ZnS-assisted photochemical reaction can regulate the redox equilibrium between α-amino acids and α-oxo acids, but also provide a model of how prebiotic metabolic homoeostasis could have been developed and regulated. These findings can advance our understanding of the establishment of archaic non-enzymatic metabolic systems and the origins of autotrophy.
Wilhelm Wundts Wissenschaftstheorie der Psychologie
Authors: Fahrenberg Jochen 
Published: October 2012

Wilhelm Wundt entwickelte seine Wissenschaftstheorie der Psychologie–die erste überhaupt–in einem weiten theoretischen Horizont, der durch seine neurophysiologischen, psychologischen und philosophischen Arbeiten bestimmt war. Er postuliert den Prozesscharakter des Bewusstseins und gibt den Transzendenzbezug des Seelenbegriffs auf. Der Mensch als denkendes und wollendes Subjekt ist nicht in den Begriffen der Naturwissenschaften zu erfassen; die Psychologie erfordert spezielle Kategorien und eigenständige Erkenntnisprinzipien. Sie ist einerseits empirische Geisteswissenschaft, soll jedoch andererseits ihre physiologischen Grundlagen nicht ausklammern. Wundts Ansatz ist perspektivisch, er verlangt ein „komplementäres” Denken in verschiedenen Bezugssystemen und einen entsprechenden Wechsel der Methoden. Die Psychologie soll mit der Philosophie in Verbindung bleiben, um die Erkenntniskritik der unter Psychologen verbreiteten metaphysischen Voraussetzungen zu fördern.Der Versuch einer Rekonstruktion von Wundts Wissenschaftstheorie ist Bestandteil einer Rezeptionsanalyse seines Werks, über die hier nur kurz berichtet wird. Aufgrund von etwa 200 zeitgenössischen und späteren Rezensionen sowie weiterer Quellen werden Hypothesen abgeleitet, weshalb Wundt noch zu Lebzeiten vom Gründervater fast zum Außenseiter wurde.
Chronocoulometry for quantitative control of mass removal in micro-structures and sensors
Authors: Nowakowski B. K. , Smith S. T. , Pratt J. R. , Shaw G. A. 
Published: October 2012

In this work, tungsten wires have been etched in a KOH electrolyte solution. Based on the oxidation state of the electrolytic dissolution reaction's product and time integration of the Faradaic current produced during the reaction, this method is capable of providing a direct measurement of the change in mass of a structure from anodic dissolution. To assess the application of this process for controlled mass removal spanning sub-micrograms to milligrams, two experimental studies and accompanying uncertainty analyses have been undertaken. In the first of these, 5 tungsten wires of length 30 mm were used to remove mass values ranging from 50 to 350 μg. Uncertainty estimates indicate relative combined standard uncertainties of less than 0.3% in the mass changes determined from the measurement of Faradaic current. Comparison of the mass change determined using the electrolytic method, and using a precision ultra-microbalance agreed within this uncertainty. The charge-based method was then applied to modify the dynamic characteristics of a quartz tuning fork oscillator. In these experiments, tungsten fiber attached to one tine of the oscillator was etched in 5 μg increments up to 120 μg of total removed mass. In general, frequency shifts of 2.8 Hz·μg−1 were observed, indicating sub-microgram resolution for the characterization of probes based on frequency shift and charge-based mass measurement. Taken together, this study provides the basis for a precision method for determining changes in mass based on electrical measurements from an electrochemical system. The utility of this technique is demonstrated through controlled modification of the dynamic properties of a mechanical oscillator.
XiP: a computational environment to create, extend and share workflows
Authors: Nagasaki Masao , Fujita André , Sekiya Yayoi , Saito Ayumu , Ikeda Emi , Li Chen , Miyano Satoru 
Published: October 2012

Abstract
XiP (eXtensible integrative Pipeline) is a flexible, editable and modular environment with a user-friendly interface that does not require previous advanced programming skills to run, construct and edit workflows. XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed. XiP already comes with several ready-to-use pipeline flows for the most common genomic and transcriptomic analysis and ∼300 computational components.
Availability: XiP is open source, freely available under the Lesser General Public License (LGPL) and can be downloaded from http://xip.hgc.jp.
Contact: nagasaki@megabank.tohoku.ac.jp
RIP-chip enrichment analysis
Authors: Erhard Florian , Dölken Lars , Zimmer Ralf 
Published: October 2012

AbstractMotivation: RIP-chip is a high-throughput method to identify mRNAs that are targeted by RNA-binding proteins. The protein of interest is immunoprecipitated, and the identity and relative amount of mRNA associated with it is measured on microarrays. Even if a variety of methods is available to analyse microarray data, e.g. to detect differentially regulated genes, the additional experimental steps in RIP-chip require specialized methods. Here, we focus on two aspects of RIP-chip data: First, the efficiency of the immunoprecipitation step performed in the RIP-chip protocol varies in between different experiments introducing bias not existing in standard microarray experiments. This requires an additional normalization step to compare different samples and even technical replicates. Second, in contrast to standard differential gene expression experiments, the distribution of measurements is not normal. We exploit this fact to define a set of biologically relevant genes in a statistically meaningful way.Results: Here, we propose two methods to analyse RIP-chip data: We model the measurement distribution as a gaussian mixture distribution, which allows us to compute false discovery rates (FDRs) for any cut-off. Thus, cut-offs can be chosen for any desired FDR. Furthermore, we use principal component analysis to determine the normalization factors necessary to remove immunoprecipitation bias. Both methods are evaluated on a large RIP-chip dataset measuring targets of Ago2, the major component of the microRNA guided RNA-induced silencing complex (RISC). Using published HITS-CLIP experiments performed with the same cell line as used for RIP-chip, we show that the mixture modelling approach is a necessary step to remove background, which computed FDRs are valid, and that the additional normalization is a necessary step to make experiments comparable.Availability: An R implementation of REA is available on the project website (http://www.bio.ifi.lmu.de/REA) and as supplementary data file.Contact: florian.erhard@bio.ifi.lmu.deSupplementary information: Supplementary data are available at Bioinformatics online.
STAR: ultrafast universal RNA-seq aligner
Authors: Dobin Alexander , Davis Carrie A. , Schlesinger Felix , Drenkow Jorg , Zaleski Chris , Jha Sonali , Batut Philippe , Chaisson Mark , Gingeras Thomas R. 
Published: October 2012

Abstract
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases.
Results: To align our large (&gt;80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of &gt;50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80–90% success rate, corroborating the high precision of the STAR mapping strategy.
Availability and implementation: STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
Contact: dobin@cshl.edu.
A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes
Authors: Bonneville Russell , Jin Victor X. 
Published: October 2012

AbstractMotivation: Many studies have shown that epigenetic changes, such as altered DNA methylation and histone modifications, are linked to estrogen receptor α (ERα)-positive tumors and disease prognoses. Several recent studies have applied high-throughput technologies such as ChIP-seq and MBD-seq to interrogate the altered architectures of ERα regulation in tamoxifen (Tam)-resistant breast cancer cells. However, the details of combinatorial epigenetic regulation of ERα target genes in breast cancers with acquired Tam resistance have not yet been fully examined.Results: We developed a computational approach to identify and analyze epigenetic patterns associated with Tam resistance in the MCF7-T cell line as opposed to the Tam-sensitive MCF7 cell line, with the goal of understanding the underlying mechanisms of epigenetic regulatory influence on resistance to Tam treatment in breast cancer. In this study, we used ChIP-seq of ERα, RNA polymerase II, three histone modifications and MBD-seq data of DNA methylation in MCF7 and MCF7-T cells to train hidden Markov models (HMMs). We applied the Bayesian information criterion to determine that a 20-state HMM was best, which was reduced to a 14-state HMM with a Bayesian information criterion score of 1.21291 × 107. We further identified four classes of biologically meaningful states in this breast cancer cell model system, and a set of ERα combinatorial epigenetic regulated target genes. The correlated gene expression level and gene ontology analyses showed that different gene ontology terms were enriched with Tam-resistant versus sensitive breast cancer cells. Our study illustrates the applicability of HMM-based analysis of genome-wide high-throughput genomic data to study epigenetic influences on E2/ERα regulation in breast cancer.Contact: victor.jin@osumc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks
Authors: Sheppard Patrick W. , Rathinam Muruhan , Khammash Mustafa 
Published: October 2012

Abstract
Summary: SPSens is a software package for the efficient computation of stochastic parameter sensitivities of biochemical reaction networks. Parameter sensitivity analysis is a valuable tool that can be used to study robustness properties, for drug targeting, and many other purposes. However its application to stochastic models has been limited when Monte Carlo methods are required due to extremely high computational costs. SPSens provides efficient, state of the art sensitivity analysis algorithms in a single software package so that sensitivity analysis can be easily performed on stochastic models of biochemical reaction networks. SPSens implements the algorithms in C and estimates sensitivities with respect to both infinitesimal and finite perturbations to system parameters, in many cases reducing variance by orders of magnitude compared to basic methods. Included among the features of SPSens are serial and parallel command line versions, an interface with Matlab, and several example problems.
Availability: SPSens is distributed freely under GPL version 3 and can be downloaded from http://sourceforge.net/projects/spsens/. The software can be run on Linux, Mac OS X and Windows platforms.
Contact: mustafa.khammash@bsse.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Effects of a large-scale and offshore marine protected area on the demersal fish assemblage in the Southwest Atlantic
Authors: Alemany Daniela , Iribarne Oscar O. , Acha Eduardo M. 
Published: October 2012

Abstract
Alemany, D., Iribarne, O. O., and Acha, E. M. 2013. Effects of a large-scale and offshore marine protected area on the demersal fish assemblage in the Southwest Atlantic. – ICES Journal of Marine Science, 70:123–134. There are few extensive and offshore located marine protected areas (MPAs) in the world oceans and their performance is still being debated. We evaluated the effects of a large-scale offshore MPA located on the Southwest Atlantic Patagonian Shelf (43°S 63°W) on the demersal fish assemblage. Compliance of the Patagonian MPA was assessed by analysing eight years of satellite vessel monitoring system (VMS; 2000–2008) data, which showed compliance and fishing effort concentrated near the protection boundaries. MPA effects were studied by employing a five year database collected by a scientific research vessel in protected and fishing locations, before and after the MPA establishment. We assessed 152 scientific trawling stations using multivariate analysis of fish assemblage structure, fish abundance (discriminating target and non-target species), and mean size and proportion of juveniles of the target species (Argentine hake, Merluccius hubbsi). The identified MPA effects were a trend towards increasing abundance of the demersal fish assemblage, the target and non-target fish species, and hake juvenile size, and a higher proportion of juveniles aged 2+ inside the MPA. These positive trends support the case for offshore, large-scale MPAs.
Genome-Wide Analysis ofStowaway-Like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification
Authors: Yaakov Beery , Ben-David Smadar , Kashkush Khalil 
Published: October 2012

AbstractThe diversity and evolution of wheat (Triticum-Aegilops group) genomes is determined, in part, by the activity of transposable elements that constitute a large fraction of the genome (up to 90%). In this study, we retrieved sequences from publicly available wheat databases, including a 454-pyrosequencing database, and analyzed 18,217 insertions of 18 Stowaway-like miniature inverted-repeat transposable element (MITE) families previously characterized in wheat that together account for approximately 1.3 Mb of sequence. All 18 families showed high conservation in length, sequence, and target site preference. Furthermore, approximately 55% of the elements were inserted in transcribed regions, into or near known wheat genes. Notably, we observed significant correlation between the mean length of the MITEs and their copy number. In addition, the genomic composition of nine MITE families was studied by real-time quantitative polymerase chain reaction analysis in 40 accessions of Triticum spp. and Aegilops spp., including diploids, tetraploids, and hexaploids. The quantitative polymerase chain reaction data showed massive and significant intraspecific and interspecific variation as well as genome-specific proliferation and nonadditive quantities in the polyploids. We also observed significant differences in the methylation status of the insertion sites among MITE families. Our data thus suggest a possible role for MITEs in generating genome diversification and in the establishment of nascent polyploid species in wheat.
Group III-AXTHGenes of Arabidopsis Encode Predominant Xyloglucan Endohydrolases That Are Dispensable for Normal Growth
Authors: Kaewthai Nomchit , Gendre Delphine , Eklöf Jens M. , Ibatullin Farid M. , Ezcurra Ines , Bhalerao Rishikesh P. , Brumer Harry 
Published: October 2012

AbstractThe molecular basis of primary wall extension endures as one of the central enigmas in plant cell morphogenesis. Classical cell wall models suggest that xyloglucan endo-transglycosylase activity is the primary catalyst (together with expansins) of controlled cell wall loosening through the transient cleavage and religation of xyloglucan-cellulose cross links. The genome of Arabidopsis (Arabidopsis thaliana) contains 33 phylogenetically diverse XYLOGLUCAN ENDO-TRANSGLYCOSYLASE/HYDROLASE (XTH) gene products, two of which were predicted to be predominant xyloglucan endohydrolases due to clustering into group III-A. Enzyme kinetic analysis of recombinant AtXTH31 confirmed this prediction and indicated that this enzyme had similar catalytic properties to the nasturtium (Tropaeolum majus) xyloglucanase1 responsible for storage xyloglucan hydrolysis during germination. Global analysis of Genevestigator data indicated that AtXTH31 and the paralogous AtXTH32 were abundantly expressed in expanding tissues. Microscopy analysis, utilizing the resorufin β-glycoside of the xyloglucan oligosaccharide XXXG as an in situ probe, indicated significant xyloglucan endohydrolase activity in specific regions of both roots and hypocotyls, in good correlation with transcriptomic data. Moreover, this hydrolytic activity was essentially completely eliminated in AtXTH31/AtXTH32 double knockout lines. However, single and double knockout lines, as well as individual overexpressing lines, of AtXTH31 and AtXTH32 did not demonstrate significant growth or developmental phenotypes. These results suggest that although xyloglucan polysaccharide hydrolysis occurs in parallel with primary wall expansion, morphological effects are subtle or may be compensated by other mechanisms. We hypothesize that there is likely to be an interplay between these xyloglucan endohydrolases and recently discovered apoplastic exo-glycosidases in the hydrolytic modification of matrix xyloglucans.
Crystallization and preliminary crystallographic studies of the W2 domain ofDrosophila melanogastereukaryotic translation initiation factor 5C domain-containing protein
Authors: Zhao Hui , Wang Hong , Liu Huihui , Teng Maikun , Li Xu 
Published: October 2012

TheDrosophila melanogastereukaryotic translation initiation factor 5C domain-containing protein (ECP) is composed of two independently folded domains which belong to the basic leucine-zipper and W2 domain-containing protein (BZW) family. Based on the sequence similarity between the C-terminal W2 domain of ECP and some eukaryotic translation initiation factors (such as eIF2B∊, eIF4γ, eIF5etc.), ECP has been speculated to participate in the translation initiation process. Structural information on the C-terminal W2 domain of ECP would be helpful in understanding the specific cellular function of this protein. Here, the W2 domain of ECP was expressed and crystallized. Crystals grown by the hanging-drop vapour-diffusion method diffracted to 2.70 Å resolution and belonged to space groupI4, with unit-cell parametersa = b = 81.05,c= 57.44 Å. The Matthews coefficient suggested that there was one molecule per asymmetric unit in the crystal.