bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Influence of Traffic Signal Solutions on Self-Reported Road-Crossing Behavior
Authors: Di Stasi Leandro L. , Megías Alberto , Cándido Antonio , Maldonado Antonio , Catena Andrés 
Published: January 2015

AbstractInjury to pedestrians is a major safety hazard in many countries. Since the beginning of the last century, modern cities have been designed around the use of motor vehicles despite the unfavourable interactions between the vehicles and pedestrians. This push towards urbanization resulted in a substantial number of crashes and fatalities involving pedestrians every day, all over the world. Thus, improving the design of urban cities and townships is a pressing issue for modern society. The study presented here provides a characterization of pedestrian safety problems, with the emphasis on signalized crosswalks (i.e. traffic signal) design solutions. We tested the impact of seven different traffic light configurations (steady [green, yellow, and red], flashing [green, yellow, and red], and light off) on pedestrian self-reported road-crossing behavior, using a 11-point scale -ranging from 0 (“I never cross in this situation”) to 10 (“I always cross in this situation”). Results showed that mandatory solutions (steady green vs. steady red) are the best solutions to avoid unsafe pedestrian behaviors while crossing controlled intersections (frequency of crossing: Mgreen = 9.4 ± 1 vs. Mred = 2.6 ± 2). These findings offer important guidelines for the design of future traffic signals for encouraging a pedestrian/transit-friendly environment.
Sichtung von Bewerbungsunterlagen
Authors: Kanning Uwe Peter , Woike Janine 
Published: January 2015

In einer Studie mit 1053 Probanden wird die Frage untersucht, inwieweit soziales Engagement ein sinnvoller Indikator zur Einschätzung der sozialen Kompetenzen von Bewerbern darstellt. Es werden 17 soziale Kompetenzen berücksichtigt, die sich zu vier Faktoren zweiter Ordnung gruppieren. Sozial engagierte Personen weisen höhere Standardwerte in allen Kompetenzen aus den Bereichen der sozialen Orientierung sowie der Offensivität auf. Im Bereich der Selbststeuerung gilt dies nur einmal, für den Bereich der Reflexibilität in keinem Fall. Der lineare Zusammenhang zwischen der Intensität des Engagements und der Ausprägung der Kompetenzen ergibt nach der Herauspartialisierung demographischer Variablen (Alter, Geschlecht, Bildung) positive Zusammenhänge insbesondere in den Kompetenzbereichen der sozialen Orientierung sowie der Offensivität. Die Varianzaufklärung fällt allerdings mit 0.36 – 6.25 % eher gering aus. Die Nutzung von Informationen über das soziale Engagement der Bewerber zum Zwecke der Personalauswahl wird diskutiert. Zudem wird ein Ausblick auf die weitere Forschung gegeben.
Flow damping due to stochastization of the magnetic field
Authors: Ida K. , Yoshinuma M. , Tsuchiya H. , Kobayashi T. , Suzuki C. , Yokoyama M. , Shimizu A. , Nagaoka K. , Inagaki S. , Itoh K. ,   the LHD Experiment Group, Akiyama T. , Emoto M. , Evans T. , Dinklage A. , Du X. , Fujii K. , Goto M. , Goto T. , Hasuo M. , Hidalgo C. , Ichiguchi K. , Ishizawa A. , Jakubowski M. , Kamiya K. , Kasahara H. , Kawamura G. , Kato D. , Kobayashi M. , Morita S. , Mukai K. , Murakami I. , Murakami S. , Narushima Y. , Nunami M. , Ohdach S. , Ohno N. , Osakabe M. , Pablant N. , Sakakibara S. , Seki T. , Shimozuma T. , Shoji M. , Sudo S. , Tanaka K. , Tokuzawa T. , Todo Y. , Wang H. , Yamada H. , Takeiri Y. , Mutoh T. , Imagawa S. , Mito T. , Nagayama Y. , Watanabe K. Y. , Ashikawa N. , Chikaraishi H. , Ejiri A. , Furukawa M. , Fujita T. , Hamaguchi S. , Igami H. , Isobe M. , Masuzaki S. , Morisaki T. , Motojima G. , Nagasaki K. , Nakano H. , Oya Y. , Suzuki Y. , Sakamoto R. , Sakamoto M. , Sanpei A. , Takahashi H. , Tokitani M. , Ueda Y. , Yoshimura Y. , Yamamoto S. , Nishimura K. , Sugama H. , Yamamoto T. , Idei H. , Isayama A. , Kitajima S. , Masamune S. , Shinohara K. , Bawankar P. S. , Bernard E. , von Berkel M. , Funaba H. , Huang X. L. , Ii T. , Ido T. , Ikeda K. , Kamio S. , Kumazawa R. , Moon C. , Muto S. , Miyazawa J. , Ming T. , Nakamura Y. , Nishimura S. , Ogawa K. , Ozaki T. , Oishi T. , Ohno M. , Pandya S. , Seki R. , Sano R. , Saito K. , Sakaue H. , Takemura Y. , Tsumori K. , Tamura N. , Tanaka H. , Toi K. , Wieland B. , Yamada I. , Yasuhara R. , Zhang H. , Kaneko O. , Komori A. 
Published: January 2015

AbstractThe driving and damping mechanism of plasma flow is an important issue because flow shear has a significant impact on turbulence in a plasma, which determines the transport in the magnetized plasma. Here we report clear evidence of the flow damping due to stochastization of the magnetic field. Abrupt damping of the toroidal flow associated with a transition from a nested magnetic flux surface to a stochastic magnetic field is observed when the magnetic shear at the rational surface decreases to 0.5 in the large helical device. This flow damping and resulting profile flattening are much stronger than expected from the Rechester–Rosenbluth model. The toroidal flow shear shows a linear decay, while the ion temperature gradient shows an exponential decay. This observation suggests that the flow damping is due to the change in the non-diffusive term of momentum transport.
Visualizing cellular imaging data using PhenoPlot
Authors: Sailem Heba Z. , Sero Julia E. , Bakal Chris 
Published: January 2015

AbstractVisualization is essential for data interpretation, hypothesis formulation and communication of results. However, there is a paucity of visualization methods for image-derived data sets generated by high-content analysis in which complex cellular phenotypes are described as high-dimensional vectors of features. Here we present a visualization tool, PhenoPlot, which represents quantitative high-content imaging data as easily interpretable glyphs, and we illustrate how PhenoPlot can be used to improve the exploration and interpretation of complex breast cancer cell phenotypes.
Unravelling the physics of size-dependent dislocation-mediated plasticity
Authors: El-Awady Jaafar A. 
Published: January 2015

AbstractSize-affected dislocation-mediated plasticity is important in a wide range of materials and technologies. Here we develop a generalized size-dependent dislocation-based model that predicts strength as a function of crystal/grain size and the dislocation density. Three-dimensional (3D) discrete dislocation dynamics (DDD) simulations reveal the existence of a well-defined relationship between strength and dislocation microstructure at all length scales for both single crystals and polycrystalline materials. The results predict a transition from dislocation-source strengthening to forest-dominated strengthening at a size-dependent critical dislocation density. It is also shown that the Hall–Petch relationship can be physically interpreted by coupling with an appropriate kinetic equation of the evolution of the dislocation density in polycrystals. The model is shown to be in remarkable agreement with experiments. This work presents a micro-mechanistic framework to predict and interpret strength size-scale effects, and provides an avenue towards performing multiscale simulations without ad hoc assumptions.
PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6
Authors: Kasimova Marina A. , Zaydman Mark A. , Cui Jianmin , Tarek Mounir 
Published: January 2015

AbstractAmong critical aspects of voltage-gated potassium (Kv) channels' functioning is the effective communication between their two composing domains, the voltage sensor (VSD) and the pore. This communication, called coupling, might be transmitted directly through interactions between these domains and, as recently proposed, indirectly through interactions with phosphatidylinositol-4,5-bisphosphate (PIP2), a minor lipid of the inner plasma membrane leaflet. Here, we show how the two components of coupling, mediated by protein-protein or protein-lipid interactions, both contribute in the Kv7.1 functioning. On the one hand, using molecular dynamics simulations, we identified a Kv7.1 PIP2binding site that involves residues playing a key role in PIP2-dependent coupling. On the other hand, combined theoretical and experimental approaches have shown that the direct interaction between the segments of the VSD (S4–S5) and the pore (S6) is weakened by electrostatic repulsion. Finally, we conclude that due to weakened protein-protein interactions, the PIP2-dependent coupling is especially prominent in Kv7.1.
MicroRNA-574-3p, identified by microRNA library-based functional screening, modulates tamoxifen response in breast cancer
Authors: Ujihira T. , Ikeda K. , Suzuki T. , Yamaga R. , Sato W. , Horie-Inoue K. , Shigekawa T. , Osaki A. , Saeki T. , Okamoto K. , Takeda S. , Inoue S. 
Published: January 2015

AbstractMost primary breast cancers express estrogen receptor α and can be treated via endocrine therapy using anti-estrogens such as tamoxifen; however, acquired endocrine resistance is a critical issue. To identify tamoxifen response-related microRNAs (miRNAs) in breast cancer, MCF-7 cells infected with a lentiviral miRNA library were treated with 4-hydroxytamoxifen (OHT) or vehicle for 4 weeks and the amounts of individual miRNA precursors that had integrated into the genome were evaluated by microarray. Compared to the vehicle-treated cells, 5 ‘dropout’ miRNAs, which were downregulated in OHT-treated cells and 6 ‘retained’ miRNAs, which were upregulated in OHT-treated cells, were identified. Of the dropout miRNAs, we found that miR-574-3p expression was downregulated in clinical breast cancer tissues as compared with their paired adjacent tissues. In addition, anti-miR-574-3p reversed tamoxifen-mediated suppression of MCF-7 cell growth. Clathrin heavy chain (CLTC) was identified as a miR-574-3p target gene by in silico algorithms and luciferase reporter assay using the 3′ untranslated region of CLTC mRNA. Interestingly, loss and gain of miR-574-3p function in MCF-7 cells causes CLTC to be upregulated and downregulated, respectively. These results suggest that functional screening mediated by miRNA libraries can provide new insights into the genes essential for tamoxifen response in breast cancer.
Following the dynamics of matter with femtosecond precision using the X-ray streaking method
Authors: David C. , Karvinen P. , Sikorski M. , Song S. , Vartiainen I. , Milne C. J. , Mozzanica A. , Kayser Y. , Diaz A. , Mohacsi I. , Carini G. A. , Herrmann S. , Färm E. , Ritala M. , Fritz D. M. , Robert A. 
Published: January 2015

AbstractX-ray Free Electron Lasers (FELs) can produce extremely intense and very short pulses, down to below 10 femtoseconds (fs). Among the key applications are ultrafast time-resolved studies of dynamics of matter by observing responses to fast excitation pulses in a pump-probe manner. Detectors with sufficient time resolution for observing these processes are not available. Therefore, such experiments typically measure a sample's full dynamics by repeating multiple pump-probe cycles at different delay times. This conventional method assumes that the sample returns to an identical or very similar state after each cycle. Here we describe a novel approach that can provide a time trace of responses following a single excitation pulse, jitter-free, with fs timing precision. We demonstrate, in an X-ray diffraction experiment, how it can be applied to the investigation of ultrafast irreversible processes.
A growth model for directed complex networks with power-law shape in the out-degree distribution
Authors: Esquivel-Gómez J. , Stevens-Navarro E. , Pineda-Rico U. , Acosta-Elias J. 
Published: January 2015

AbstractMany growth models have been published to model the behavior of real complex networks. These models are able to reproduce several of the topological properties of such networks. However, in most of these growth models, the number of outgoing links (i.e., out-degree) of nodes added to the network is constant, that is all nodes in the network are born with the same number of outgoing links. In other models, the resultant out-degree distribution decays as a poisson or an exponential distribution. However, it has been found that in real complex networks, the out-degree distribution decays as a power-law. In order to obtain out-degree distribution with power-law behavior some models have been proposed. This work introduces a new model that allows to obtain out-degree distributions that decay as a power-law with an exponent in the range from 0 to 1.
Uncoupling lifespan and healthspan in
Caenorhabditis elegans
longevity mutants
Authors: Bansal Ankita , Zhu Lihua J. , Yen Kelvin , Tissenbaum Heidi A. 
Published: January 2015

Significance
Genetic and environmental manipulations have been identified that result in lifespan extension. The underlying assumption that lifespan extension would also result in an increase in healthspan is seemingly valid but infrequently examined. Here, we examined multiple pathways that modulate lifespan to investigate the relationship between lifespan extension and health. We analyzed wild-type and four long-lived mutants in an unbiased cross-sectional study with multiple assays until animals reached 80% maximum lifespan. We show lifespan and healthspan can be separated and all of the long-lived mutants extend the period of frailty as a consequence. If applied to humans, this would likely lead to unsustainable healthcare costs and demonstrates the importance of examining healthspan as opposed to lifespan for future research.
Plant functional traits and the multidimensional nature of species coexistence
Authors: Kraft Nathan J. B. , Godoy Oscar , Levine Jonathan M. 
Published: January 2015

Significance
Biologists have long understood that differences between species in traits such as bill shape or rooting depth can maintain diversity in communities by promoting specialization and reducing competition. Here we test the assumption that phenotypic differences drive the stabilizing niche differences that promote coexistence. Using advances in ecological theory and detailed experiments we quantify average fitness and stabilizing niche differences between 102 plant species pairs and relate these differences to 11 functional traits. Individual traits were correlated with fitness differences that drive competitive exclusion but not stabilizing niche differences that promote coexistence. Stabilizing niche differences could only be described by combinations of traits, representing differentiation in multiple dimensions. This challenges the simplistic use of trait patterns to infer community assembly.
Atmospheric record in the Hadean Eon from multiple sulfur isotope measurements in Nuvvuagittuq Greenstone Belt (Nunavik, Quebec)
Authors: Thomassot Emilie , O’Neil Jonathan , Francis Don , Cartigny Pierre , Wing Boswell A. 
Published: January 2015

Significance
Sulfur isotopes in ancient Earth sediments have peculiar compositions resulting from photochemical reactions of sulfur-bearing gaseous species with UV photons in the anoxic early Earth's atmosphere. High-precision measurements of sediments from distinct localities have revealed that these isotopic anomalies are sensitive to the abundances of atmospheric gases. They thus appear as promising metrics of ancient atmospheric composition. In the present study, we focus on the origin and extent of this atmospheric memory. We analyzed the multiple S-isotope compositions of some of the oldest metasediments preserved on Earth (originating from the >3.8-Ga Nuvvuagittuq Greenstone Belt, Canada) and found that this unusual atmospheric fingerprint has been present since the end of the Hadean, the earliest eon of Earth history.
Gamma irradiated chitosan and its derivatives as antioxidants for minced chicken
Authors: Abd El-Rehim Hassan A , Zahran Dalia A , El-Sawy Naeem M , Hegazy El-Sayed A , Elbarbary Ahmed M 
Published: January 2015

AbstractIonizing radiation and oxidizing agent like H2O2 were used to degrade chitosan (CS) and its derivatives; N-maleoylchitosan (NMCS), and N-phthaloylchitosan (NPhCS). The structure changes were detected using gel permeation chromatography (GPC). The results revealed that ionizing radiation degraded CS, MNCS, NPhCS and altered their molecular weights and antioxidant activity. The higher the irradiation dose, the lower the molecular weight and the higher antioxidant activity. The addition of irradiated CS and NMCS to minced chicken resulted in highly significant reduction in malondialdehyde (MDA) content (50 and 70%, respectively) if compared with the control. The irradiated NMCS toxicity study did not show strong proliferative effect at small concentrations or cytotoxic effects at higher concentrations. The obtained results suggested that CS and NMCS could be used as natural antioxidant for improving the oxidative deterioration of minced chicken during refrigerated storage.
An N-terminal region of a Myb-like protein is involved in its intracellular localization and activation of a gibberellin-inducible proteinase gene in germinated rice seeds
Authors: Sutoh Keita , Washio Kenji , Imai Ryozo , Wada Masamitsu , Nakai Tomonori , Yamauchi Daisuke 
Published: January 2015

Abstract
The expression of the gene for a proteinase (Rep1) is upregulated by gibberellins. The CAACTC regulatory element (CARE) of the Rep1 promoter is involved in the gibberellin response. We isolated a cDNA for a CARE-binding protein containing a Myb domain in its carboxyl-terminal region and designated the gene Carboxyl-terminal Myb1 (CTMyb1). This gene encodes two polypeptides of two distinctive lengths, CTMyb1L and CTMyb1S, which include or exclude 213 N-terminal amino acid residues, respectively. CTMyb1S transactivated the Rep1 promoter in the presence of OsGAMyb, but not CTMyb1L. We observed an interaction between CTMyb1S and the rice prolamin box-binding factor (RPBF). A bimolecular fluorescence complex analysis detected the CTMyb1S and RPBF complex in the nucleus, but not the CTMyb1L and RPBF complex. The results suggest that the arrangement of the transfactors is involved in gibberellin-inducible expression of Rep1.
GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome
Authors: Li Fuyi , Li Chen , Wang Mingjun , Webb Geoffrey I. , Zhang Yang , Whisstock James C. , Song Jiangning 
Published: January 2015

Abstract
Motivation: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular recognition. It is estimated that &gt;50% of the entire human proteome is glycosylated. However, it is still a significant challenge to identify glycosylation sites, which requires expensive/laborious experimental research. Thus, bioinformatics approaches that can predict the glycan occupancy at specific sequons in protein sequences would be useful for understanding and utilizing this important PTM.
Results: In this study, we present a novel bioinformatics tool called GlycoMine, which is a comprehensive tool for the systematic in silico identification of C-linked, N-linked, and O-linked glycosylation sites in the human proteome. GlycoMine was developed using the random forest algorithm and evaluated based on a well-prepared up-to-date benchmark dataset that encompasses all three types of glycosylation sites, which was curated from multiple public resources. Heterogeneous sequences and functional features were derived from various sources, and subjected to further two-step feature selection to characterize a condensed subset of optimal features that contributed most to the type-specific prediction of glycosylation sites. Five-fold cross-validation and independent tests show that this approach significantly improved the prediction performance compared with four existing prediction tools: NetNGlyc, NetOGlyc, EnsembleGly and GPP. We demonstrated that this tool could identify candidate glycosylation sites in case study proteins and applied it to identify many high-confidence glycosylation target proteins by screening the entire human proteome.
Availability and implementation: The webserver, Java Applet, user instructions, datasets, and predicted glycosylation sites in the human proteome are freely available at http://www.structbioinfor.org/Lab/GlycoMine/.
Contact: Jiangning.Song@monash.edu or James.Whisstock@monash.edu or zhangyang@nwsuaf.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis
Authors: Chen Rui , Wei Qiang , Zhan Xiaowei , Zhong Xue , Sutcliffe James S. , Cox Nancy J. , Cook Edwin H. , Li Chun , Chen Wei , Li Bingshan 
Published: January 2015

Abstract
Motivation: A major focus of current sequencing studies for human genetics is to identify rare variants associated with complex diseases. Aside from reduced power of detecting associated rare variants, controlling for population stratification is particularly challenging for rare variants. Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to eliminate spurious associations. To increase power of rare variant association analysis, gene-based collapsing methods become standard approaches for analyzing rare variants. Existing methods that extend this strategy to rare variants in families usually combine TDT statistics at individual variants and therefore lack the flexibility of incorporating other genetic models.
Results: In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH) (i.e. recessive) models as well as other complex interactions. Unlike existing methods, gTDT constructs haplotypes by transmission when possible and inherently takes into account the linkage disequilibrium among variants. Through extensive simulations we showed that type I error was correctly controlled for rare variants under all models investigated, and this remained true in the presence of population stratification. Under a variety of genetic models, gTDT showed increased power compared with the single marker TDT. Application of gTDT to an autism exome sequencing data of 118 trios identified potentially interesting candidate genes with CH rare variants.
Availability and implementation: We implemented gTDT in C++ and the source code and the detailed usage are available on the authors’ website (https://medschool.vanderbilt.edu/cgg).
Contact: bingshan.li@vanderbilt.edu or wei.chen@chp.edu
Supplementary information: Supplementary data are available at Bioinformatics online.