bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building the Eco-social State: Do Welfare Regimes Matter?
Authors: KOCH MAX , FRITZ MARTIN 
Published: June 2014

AbstractAuthors such as Dryzek, Gough and Meadowcroft have indicated that social-democratic welfare states could be in a better position to deal with development of the ‘green’ or ‘eco’ state, and the intersection of social and environmental policies, than conservative or liberal welfare regimes (synergy hypothesis). However, this hypothesis has as yet not been examined in comparative empirical research. Based on comparative empirical data from EUROSTAT, the World Bank, the OECD, the Global Footprint Network and the International Social Survey Programme, we are carrying out two research operations: First, by applying correspondence analysis, we contrast the macro-structural welfare and sustainability indicators of thirty countries and ask whether clusters largely follow the synergy hypothesis. Second, we raise the issue of whether differences in the institutional and organisational capabilities of combining welfare with environmental policies are reflected in people's attitudes and opinions. With regard to the first issue, our results suggest that there is no ‘automatic’ development of the ecostate based on already existing advanced welfare institutions. Representatives of all welfare regimes are spread across established, deadlocked, failing, emerging and endangered ecostates. As for the second issue, the results are mixed. While responses to the statements ‘economic growth always harms the environment’ and ‘governments should pass laws to make ordinary people protect the environment, even if it interferes with people's rights to make their own decisions’ did not vary according to welfare regimes, people from social-democratic countries expressed more often than average their willingness to accept cuts in their standard of living in order to protect the environment.
Variation in Standard Dutch vowels: The impact of formant measurement methods on identifying the speaker's regional origin
Authors: Van der Harst Sander , Van de Velde Hans , Van Hout Roeland 
Published: June 2014

AbstractIt is common practice in sociophonetics to measure vowel formants at one (monophthongs) or two (diphthongs) time points. This paper compares this traditional target approach with two dynamic approaches for investigating regional patterns of variation: the multiple time point approach, which measures formants at successive time points, and the regression approach, which estimates formant dynamics over time by fitting polynomial regression equations to formant contours. The speech material consisted of monosyllabic words containing all full vowels of Dutch, except for /y/. These words were read out by 160 speakers of Standard Dutch, who were distributed over four regions in the Netherlands and four regions in Flanders, Belgium. The results show that dynamic approaches outperform the target approach in uncovering regional vowel differences, which suggests that sociophonetic vowel studies that apply the target approach run the risk of overlooking important sociolinguistic patterns.
Comparing social meanings across listener and speaker groups: The indexical field of Spanish /s/
Authors: Walker Abby , García Christina , Cortés Yomi , Campbell-Kibler Kathryn 
Published: June 2014

AbstractRecent research has suggested that the contribution of individual sociolinguistic variables to the social perception of a speaker is influenced by other available information about the speaker (Campbell-Kibler, 2007; Pharao, Maegaard, Spindler Møller, & Kristiansen, 2014). Here we investigate the impact of listener awareness of regional sociolinguistic variation on sociolinguistic perception. Specifically, we compare how the social meanings attributed to word-internal, preconsonantal /s/ differ based on whether the listeners and speakers use predominantly /s/-weakening Puerto Rican Spanish or predominantly non–/s/-weakening Mexican Spanish. We find that for measures of status, Puerto Rican and Mexican listeners both show a smaller effect of /s/ when rating Puerto Rican as opposed to Mexican speakers. However, we see no effect of speaker nationality on heteronormativity, and Puerto Rican listeners and male Mexican listeners rate strong /s/ as less heteronormative across the board. Mexican female listeners, however, rate strong /s/ as more heteronormative. These results suggest that listeners integrate their own local ideologies with their understanding of regional differences when socially evaluating language variation.
MRI shows limited mixing between systemic and pulmonary circulations in foetal transposition of the great arteries: a potential cause of in utero pulmonary vascular disease
Authors: Porayette Prashob , van Amerom Joshua F.P. , Yoo Shi-Joon , Jaeggi Edgar , Macgowan Christopher K , Seed Mike 
Published: June 2014

AbstractObjectivesTo investigate the relationship between foetal haemodynamics and postnatal clinical presentation in patients with transposition of the great arteries using phase-contrast cardiovascular magnetic resonance.BackgroundA severe and irreversible form of persistent pulmonary hypertension of the newborn occurs in up to 5% of patients with transposition and remains an important cause of morbidity and mortality in these infants. Restriction at the foramen ovale and ductus arteriosus has been identified as a risk factor for the development of pulmonary hypertension, and this can now be studied with magnetic resonance imaging using a new technique called metric optimised gating.MethodsBlood flow was measured in the major vessels of four foetuses with transposition with intact ventricular septum (gestational age range: 35–38 weeks) and compared with values from 12 normal foetuses (median gestational age: 37 weeks; range: 34–40 weeks).ResultsWe found significantly reduced flows in the ductus arteriosus (p<0.01) and foramen ovale (p=0.03) and increased combined ventricular output (p=0.01), ascending aortic (p=0.001), descending aortic (p=0.03), umbilical vein (p=0.03), and aorto-pulmonary collateral (p<0.001) flows in foetuses with transposition compared with normals. The foetus with the lowest foramen ovale shunt and highest aorto-pulmonary collateral flow developed fatal pulmonary vascular disease.ConclusionsWe found limited mixing between the systemic and pulmonary circulations in a small group of late-gestation foetuses with transposition. We propose that the resulting hypoxia of the pulmonary circulation could be the driver behind increased aorto-pulmonary collateral flow and contribute to the development of pulmonary vascular disease in some foetuses with transposition.
“Rigid body rotation” of the left ventricle in hypoplastic right-heart syndrome: a case from the three-dimensional speckle-tracking echocardiographic MAGYAR-Path Study
Authors: Nemes Attila , Havasi Kálmán , Forster Tamás 
Published: June 2014

AbstractLeft ventricular twist results from the movement of two orthogonally oriented muscular bands of the helical myocardial structure, with a consequent clockwise rotation of the left ventricular base and counterclockwise rotation of the left ventricular apex. To the best of the authors’ knowledge, this is the first time that left ventricular “rigid body rotation”, the near absence of left ventricular twist in hypoplastic right-heart syndrome, has been demonstrated.
Physiological changes in blood pressure impact peripheral endothelial function during adolescence
Authors: Deda Livia , Sochett Etienne B. , Mahmud Farid H. 
Published: June 2014

AbstractReactive hyperemia index is a measure of endothelial function used to assess subclinical atherosclerosis. When evaluated in healthy adolescents, significant changes in endothelial function were correlated with advancing age, pubertal status, and blood pressure. Blood pressure was the principal contributor to reactive hyperemia index variability independent of age, lipid profile, body mass index, and/or pubertal status. Interpretation of this peripheral vascular marker should include age and maturational changes in paediatric patients.
Computational Analysis of Enhanced Magnetic Bioseparation in Microfluidic Systems with Flow-Invasive Magnetic Elements
Authors: Khashan S. A. , Alazzam A. , Furlani E. P. 
Published: June 2014

AbstractA microfluidic design is proposed for realizing greatly enhanced separation of magnetically-labeled bioparticles using integrated soft-magnetic elements. The elements are fixed and intersect the carrier fluid (flow-invasive) with their length transverse to the flow. They are magnetized using a bias field to produce a particle capture force. Multiple stair-step elements are used to provide efficient capture throughout the entire flow channel. This is in contrast to conventional systems wherein the elements are integrated into the walls of the channel, which restricts efficient capture to limited regions of the channel due to the short range nature of the magnetic force. This severely limits the channel size and hence throughput. Flow-invasive elements overcome this limitation and enable microfluidic bioseparation systems with superior scalability. This enhanced functionality is quantified for the first time using a computational model that accounts for the dominant mechanisms of particle transport including fully-coupled particle-fluid momentum transfer.
Bulk metallic glass composite with good tensile ductility, high strength and large elastic strain limit
Authors: Wu Fu-Fa , Chan K. C. , Jiang Song-Shan , Chen Shun-Hua , Wang Gang 
Published: June 2014

AbstractBulk metallic glasses exhibit high strength and large elastic strain limit but have no tensile ductility. However, bulk metallic glass composites reinforced by in-situ dendrites possess significantly improved toughness but at the expense of high strength and large elastic strain limit. Here, we report a bulk metallic glass composite with strong strain-hardening capability and large elastic strain limit. It was found that, by plastic predeformation, the bulk metallic glass composite can exhibit both a large elastic strain limit and high strength under tension. These unique elastic mechanical properties are attributed to the reversible B2↔B19′ phase transformation and the plastic-predeformation-induced complicated stress state in the metallic glass matrix and the second phase. These findings are significant for the design and application of bulk metallic glass composites with excellent mechanical properties.
The air-sea interface and surface stress under tropical cyclones
Authors: Soloviev Alexander V. , Lukas Roger , Donelan Mark A. , Haus Brian K. , Ginis Isaac 
Published: June 2014

AbstractTropical cyclone track prediction is steadily improving, while storm intensity prediction has seen little progress in the last quarter century. Important physics are not yet well understood and implemented in tropical cyclone forecast models. Missing and unresolved physics, especially at the air-sea interface, are among the factors limiting storm predictions. In a laboratory experiment and coordinated numerical simulation, conducted in this work, the microstructure of the air-water interface under hurricane force wind resembled Kelvin-Helmholtz shear instability between fluids with a large density difference. Supported by these observations, we bring forth the concept that the resulting two-phase environment suppresses short gravity-capillary waves and alters the aerodynamic properties of the sea surface. The unified wave-form and two-phase parameterization model shows the well-known increase of the drag coefficient (Cd) with wind speed, up to ~30 ms−1. Around 60 ms−1, the new parameterization predicts a local peak ofCk/Cd, under constant enthalpy exchange coefficientCk. This peak may explain rapid intensification of some storms to major tropical cyclones and the previously reported local peak of lifetime maximum intensity (bimodal distribution) in the best-track records. The bimodal distribution of maximum lifetime intensity, however, can also be explained by environmental parameters of tropical cyclones alone.
GSK3-like kinases positively modulate abscisic acid signaling through phosphorylating subgroup III SnRK2s in
Arabidopsis
Authors: Cai Zhenying , Liu Jingjing , Wang Haijiao , Yang Cangjing , Chen Yuxiao , Li Yongchi , Pan Shanjin , Dong Rui , Tang Guiliang , Barajas-Lopez Juan de Dios , Fujii Hiroaki , Wang Xuelu 
Published: June 2014

Significance
Abscisic acid (ABA) is a key stress-responsive hormone. Subgroup III Snf1-related kinase 2s (SnRK2s) are crucial positive regulators in ABA signaling pathway, but it is still not clear how SnRK2s are activated. In addition, besides ABA, some abiotic stresses can also activate SnRK2s with unknown mechanisms. Here we provide several lines of evidence to strongly support that brassinosteroid insensitive 2, a glycogen synthase kinase 3 (GSK3)-like kinase, interacts with and phosphorylates SnRK2s on specific novel sites to activate SnRK2s, which provides significant insights into the function of GSK3-like kinases in ABA signaling and transactivation of SnRK2s. Moreover, many GSK3-like kinases are regulated at transcriptional and/or posttranslational levels by many abiotic stresses, implying the presence of direct regulation of ABA signaling by other abiotic stresses.
Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies
Authors: Messih Mario Abdel , Lepore Rosalba , Marcatili Paolo , Tramontano Anna 
Published: June 2014

AbstractMotivation: Antibodies are able to recognize a wide range of antigens through their complementary determining regions formed by six hypervariable loops. Predicting the 3D structure of these loops is essential for the analysis and reengineering of novel antibodies with enhanced affinity and specificity. The canonical structure model allows high accuracy prediction for five of the loops. The third loop of the heavy chain, H3, is the hardest to predict because of its diversity in structure, length and sequence composition.Results: We describe a method, based on the Random Forest automatic learning technique, to select structural templates for H3 loops among a dataset of candidates. These can be used to predict the structure of the loop with a higher accuracy than that achieved by any of the presently available methods. The method also has the advantage of being extremely fast and returning a reliable estimate of the model quality.Availability and implementation: The source code is freely available at http://www.biocomputing.it/H3Loopred/Contact: anna.tramontano@uniroma1.itSupplementary Information: Supplementary data are available at Bioinformatics online.
Using association rule mining to determine promising secondary phenotyping hypotheses
Authors: Oellrich Anika , Jacobsen Julius , Papatheodorou Irene ,   The Sanger Mouse Genetics Project, Smedley Damian 
Published: June 2014

Abstract
Motivation: Large-scale phenotyping projects such as the Sanger Mouse Genetics project are ongoing efforts to help identify the influences of genes and their modification on phenotypes. Gene–phenotype relations are crucial to the improvement of our understanding of human heritable diseases as well as the development of drugs. However, given that there are ∼20 000 genes in higher vertebrate genomes and the experimental verification of gene–phenotype relations requires a lot of resources, methods are needed that determine good candidates for testing.
Results: In this study, we applied an association rule mining approach to the identification of promising secondary phenotype candidates. The predictions rely on a large gene–phenotype annotation set that is used to find occurrence patterns of phenotypes. Applying an association rule mining approach, we could identify 1967 secondary phenotype hypotheses that cover 244 genes and 136 phenotypes. Using two automated and one manual evaluation strategies, we demonstrate that the secondary phenotype candidates possess biological relevance to the genes they are predicted for. From the results we conclude that the predicted secondary phenotypes constitute good candidates to be experimentally tested and confirmed.
Availability: The secondary phenotype candidates can be browsed through at http://www.sanger.ac.uk/resources/databases/phenodigm/gene/secondaryphenotype/list.
Contact: ao5@sanger.ac.uk or ds5@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
EPIQ—efficient detection of SNP–SNP epistatic interactions for quantitative traits
Authors: Arkin Ya’ara , Rahmani Elior , Kleber Marcus E. , Laaksonen Reijo , März Winfried , Halperin Eran 
Published: June 2014

Abstract
Motivation: Gene–gene interactions are of potential biological and medical interest, as they can shed light on both the inheritance mechanism of a trait and on the underlying biological mechanisms. Evidence of epistatic interactions has been reported in both humans and other organisms. Unlike single-locus genome-wide association studies (GWAS), which proved efficient in detecting numerous genetic loci related with various traits, interaction-based GWAS have so far produced very few reproducible discoveries. Such studies introduce a great computational and statistical burden by necessitating a large number of hypotheses to be tested including all pairs of single nucleotide polymorphisms (SNPs). Thus, many software tools have been developed for interaction-based case–control studies, some leading to reliable discoveries. For quantitative data, on the other hand, only a handful of tools exist, and the computational burden is still substantial.
Results: We present an efficient algorithm for detecting epistasis in quantitative GWAS, achieving a substantial runtime speedup by avoiding the need to exhaustively test all SNP pairs using metric embedding and random projections. Unlike previous metric embedding methods for case–control studies, we introduce a new embedding, where each SNP is mapped to two Euclidean spaces. We implemented our method in a tool named EPIQ (EPIstasis detection for Quantitative GWAS), and we show by simulations that EPIQ requires hours of processing time where other methods require days and sometimes weeks. Applying our method to a dataset from the Ludwigshafen risk and cardiovascular health study, we discovered a pair of SNPs with a near-significant interaction (P = 2.2 × 10−13), in only 1.5 h on 10 processors.
Availability: https://github.com/yaarasegre/EPIQ
Contact: heran@post.tau.ac.il
An efficient parallel algorithm for accelerating computational protein design
Authors: Zhou Yichao , Xu Wei , Donald Bruce R. , Zeng Jianyang 
Published: June 2014

Abstract
Motivation: Structure-based computational protein design (SCPR) is an important topic in protein engineering. Under the assumption of a rigid backbone and a finite set of discrete conformations of side-chains, various methods have been proposed to address this problem. A popular method is to combine the dead-end elimination (DEE) and A* tree search algorithms, which provably finds the global minimum energy conformation (GMEC) solution.
Results: In this article, we improve the efficiency of computing A* heuristic functions for protein design and propose a variant of A* algorithm in which the search process can be performed on a single GPU in a massively parallel fashion. In addition, we make some efforts to address the memory exceeding problem in A* search. As a result, our enhancements can achieve a significant speedup of the A*-based protein design algorithm by four orders of magnitude on large-scale test data through pre-computation and parallelization, while still maintaining an acceptable memory overhead. We also show that our parallel A* search algorithm could be successfully combined with iMinDEE, a state-of-the-art DEE criterion, for rotamer pruning to further improve SCPR with the consideration of continuous side-chain flexibility.
Availability: Our software is available and distributed open-source under the GNU Lesser General License Version 2.1 (GNU, February 1999). The source code can be downloaded from http://www.cs.duke.edu/donaldlab/osprey.php or http://iiis.tsinghua.edu.cn/∼compbio/software.html.
Contact: zengjy321@tsinghua.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach
Authors: Kotera Masaaki , Tabei Yasuo , Yamanishi Yoshihiro , Muto Ai , Moriya Yuki , Tokimatsu Toshiaki , Goto Susumu 
Published: June 2014

Abstract
Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale.
Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways.
Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2014/
Contact: goto@kuicr.kyoto-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
ExSPAnder: a universal repeat resolver for DNA fragment assembly
Authors: Prjibelski Andrey D. , Vasilinetc Irina , Bankevich Anton , Gurevich Alexey , Krivosheeva Tatiana , Nurk Sergey , Pham Son , Korobeynikov Anton , Lapidus Alla , Pevzner Pavel A. 
Published: June 2014

Abstract
Next-generation sequencing (NGS) technologies have raised a challenging de novo genome assembly problem that is further amplified in recently emerged single-cell sequencing projects. While various NGS assemblers can use information from several libraries of read-pairs, most of them were originally developed for a single library and do not fully benefit from multiple libraries. Moreover, most assemblers assume uniform read coverage, condition that does not hold for single-cell projects where utilization of read-pairs is even more challenging. We have developed an exSPAnder algorithm that accurately resolves repeats in the case of both single and multiple libraries of read-pairs in both standard and single-cell assembly projects.
Availability and implementation: http://bioinf.spbau.ru/en/spades
Contact: ap@bioinf.spbau.ru