bluuebunny/crossref_metadata_2025_split huggingface dataset:
Holographic patterning of high-performance on-chip 3D lithium-ion microbatteries
Authors: Ning Hailong , Pikul James H. , Zhang Runyu , Li Xuejiao , Xu Sheng , Wang Junjie , Rogers John A. , King William P. , Braun Paul V. 
Published: May 2015

Significance
Microscale batteries can deliver energy at the actual point of energy usage, providing capabilities for miniaturizing electronic devices and enhancing their performance. Here, we demonstrate a high-performance microbattery suitable for large-scale on-chip integration with both microelectromechanical and complementary metal-oxide–semiconductor (CMOS) devices. Enabled by a 3D holographic patterning technique, the battery possesses well-defined, periodically mesostructured porous electrodes. Such battery architectures offer both high energy and high power, and the 3D holographic patterning technique offers exceptional control of the electrode’s structural parameters, enabling customized energy and power for specific applications.
A hypothesis to reconcile the physical and chemical unfolding of proteins
Authors: de Oliveira Guilherme A. P. , Silva Jerson L. 
Published: May 2015

Significance
A comprehensive view of protein folding is crucial for understanding how misfolding can cause neurodegenerative diseases and cancer. When using physical or chemical perturbations, NMR spectroscopy is a powerful tool to reveal a shift in the native conformation toward local intermediates that act as seeds for misfolding. Using NMR, we show that the ensemble of dry and wet molten-globule intermediates populated by high pressure is different from that found when urea is used. The dissimilar actions of urea and pressure can be summarized by their “pull” and “push” effects, respectively. By combining NMR and small-angle X-ray scattering (SAXS), we demonstrate the action of urea at the initial stages of unfolding and the dominance of a direct interaction mechanism for urea-induced protein denaturation.
A decline in prosocial language helps explain public disapproval of the US Congress
Authors: Frimer Jeremy A. , Aquino Karl , Gebauer Jochen E. , Zhu Luke (Lei) , Oakes Harrison 
Published: May 2015

Significance
Past laboratory research has shown that talking about helping others can make a positive impression upon a listener. We tested whether this basic social-cognitive phenomenon can help explain how governments gain the confidence of the public they serve. A computerized text analysis of the debates of the US Congress over the past 20 y found that the density of prosocial language strongly predicted public approval ratings 6 mo later. These results suggest that both individuals and governments can gain social approval by merely talking about cooperating and about helping others.
Circuit-dependent striatal PKA and ERK signaling underlies rapid behavioral shift in mating reaction of male mice
Authors: Goto Akihiro , Nakahara Ichiro , Yamaguchi Takashi , Kamioka Yuji , Sumiyama Kenta , Matsuda Michiyuki , Nakanishi Shigetada , Funabiki Kazuo 
Published: May 2015

Significance
Selection of actions that allow the seeking of rewards and avoidance of uncomfortable environments is a fundamental animal behavior. Here, we report an in vivo method, in which the activities of PKA and ERK were optically recorded by microendoscopy of Förster resonance energy transfer responses of biosensors in distinct D1 and D2 dopamine receptor-expressing neurons of the dorsal striatum. The PKA and ERK were coordinately but reciprocally regulated not only by rewarding and aversive stimuli but also between the two parallel projection neurons. Importantly, the cell type-specific regulation of PKA and ERK was causally linked to active and indifferent mating reactions of male mice. The dynamic modulation of PKA and ERK in the striatum underlies the selection of alternative actions.
Resilience and reactivity of global food security
Authors: Suweis Samir , Carr Joel A. , Maritan Amos , Rinaldo Andrea , D’Odorico Paolo 
Published: May 2015

Significance
The past few decades have seen an intensification of international food trade and the increase in the number of countries that depend on food imports. As an effect of the associated globalization of food, local shocks in food production, combined with the adoption of new national or regional energy and trade policies, have recently led to global food crises. Here we develop a framework to investigate the coupled global food–population dynamics, and evaluate the effect of international trade on global food security. We find that, as the dependency on trade increases, the global food system is losing resilience and is becoming increasingly unstable and susceptible to conditions of crisis.
Effect of oil droplet size on activation energy for coalescence of oil droplets in an O/W emulsion
Authors: Miyagawa Yayoi , Katsuki Kazutaka , Matsuno Ryuichi , Adachi Shuji 
Published: May 2015

Abstract
The activation energy of a reasonable order of magnitude was estimated for the coalescence of oil droplets in an O/W emulsion by formulating the balance of forces acting on a droplet that crosses over the potential barrier to coalesce with another droplet by the DLVO theory and Stokes’ law. An emulsion with smaller oil droplets was shown to be more stable.
Localized Properties of Rogue Wave for a Higher-Order Nonlinear Schrödinger Equation*
Authors: Liu Wei , Qiu De-Qin , He Jing-Song 
Published: May 2015

Abstract
In this paper, we provide determinant representation of the n-th order rogue wave solutions for a higher-order nonlinear Schrödinger equation (HONLS) by the Darboux transformation and confirm the decomposition rule of the rogue wave solutions up to fourth-order. These solutions have two parameters α and β which denote the contribution of the higher-order terms (dispersions and nonlinear effects) included in the HONLS equation. Two localized properties, i.e., length and width of the first-order rogue wave solution are expressed by above two parameters, which show analytically a remarkable influence of higher-order terms on the rogue wave. Moreover, profiles of the higher-order rogue wave solutions demonstrate graphically a strong compression effect along t-direction given by higher-order terms.
A Corresponding Lie Algebra of a Reductive homogeneous Group and Its Applications*
Authors: Zhang Yu-Feng , Wu Li-Xin , Rui Wen-Juan 
Published: May 2015

Abstract
With the help of a Lie algebra of a reductive homogeneous space G/K, where G is a Lie group and K is a resulting isotropy group, we introduce a Lax pair for which an expanding (2+1)-dimensional integrable hierarchy is obtained by applying the binormial-residue representation (BRR) method, whose Hamiltonian structure is derived from the trace identity for deducing (2+1)-dimensional integrable hierarchies, which was proposed by Tu, et al. We further consider some reductions of the expanding integrable hierarchy obtained in the paper. The first reduction is just right the (2+1)-dimensional AKNS hierarchy, the second-type reduction reveals an integrable coupling of the (2+1)-dimensional AKNS equation (also called the Davey-Stewartson hierarchy), a kind of (2+1)-dimensional Schrödinger equation, which was once reobtained by Tu, Feng and Zhang. It is interesting that a new (2+1)-dimensional integrable nonlinear coupled equation is generated from the reduction of the part of the (2+1)-dimensional integrable coupling, which is further reduced to the standard (2+1)-dimensional diffusion equation along with a parameter. In addition, the well-known (1+1)-dimensional AKNS hierarchy, the (1+1)-dimensional nonlinear Schrödinger equation are all special cases of the (2+1)-dimensional expanding integrable hierarchy. Finally, we discuss a few discrete difference equations of the diffusion equation whose stabilities are analyzed by making use of the von Neumann condition and the Fourier method. Some numerical solutions of a special stationary initial value problem of the (2+1)-dimensional diffusion equation are obtained and the resulting convergence and estimation formula are investigated.
Modulational Instability of Spinor Condensates in an Optical Lattice*
Authors: Zheng Gong-Ping , Jian Wen-Tian , Yang Ling-Ling 
Published: May 2015

Abstract
We obtain analytically the static states and corresponding collective-excitation spectra of a quasi-one-dimensional spin-1 condensate modulated by a long-wavelength optical lattice in the weak lattice limit. It is demonstrated that both ferromagnetic and antiferromagnetic condensates may exhibit dynamical instability, which agree with the results with numerical simulation. In the homogeneous limit, our results reduce to the previous results for homogeneous spinor condensates, i.e., dynamical instability can occur only for ferromagnetic interaction and an antiferromagnetic condensate is always dynamically stable.
Optimal Force Mismatch for Fluctuation-Activated Transition in a System of Two Coupled Bistable Oscillators*
Authors: Chen Han-Shuang , Huang Feng , He Gang , Shen Chuan-Sheng , Hou Zhong-Huai 
Published: May 2015

Abstract
We study the fluctuation-activated transition process in a system of two coupled forced bistable oscillators with a mismatch σ in the force constants. As the coupling strength μ is increased, the transition pathway undergoes four stages changes from a two-step process with two candidate pathways to a mixture of a two-step pathway and a one-step pathway to a one-step process with also two candidate pathways and then to a one-step process with a single pathway. Interestingly, we find that the total transition rate depends nonmonotonically on σ in the weak coupling: a maximal rate appears in an intermediate magnitude of σ. Moreover, the rate also exhibits an unexpected maximum as a function of μ. The results are in an excellent agreement with our numerical simulations by forward flux sampling.
Fast Generation of GHZ States with Bose—Einstein Condensate in a Cavity*
Authors: Zhang Gang , Zhou Jian , Xue Zheng-Yuan 
Published: May 2015

Abstract
It is shown that strong coupling of Bose—Einstein condensates to an optical cavity can be realized experimentally. With an additional driven microwave field, we show that a highly nonlinear coupling among atoms in a Bose—Einstein condensate can be induced with the assistance of the cavity mode. With such interaction, we can investigate the generation of many body entangled states. In particularly, we show that multipartite entangled GHZ states can be obtained in such architecture with current available techniques.
Photo-Detached Electron Flux Distribution in a Gradient Electric Field*
Authors: Wang De-Hua , Tang Tian-Tian 
Published: May 2015

Abstract
This paper investigates the flux distributions of the electron photo-detached from H− ion localized in a gradient electric field. In contrast with the photodetachment in the uniform electric field [Phys. Rev. A 40 (1989) 4983], where only two electron trajectories interfere at each given point on a detector, for the photodetachment in a gradient electric field, the electrons waves can travel along multiple paths from the negative ion to a given point on the detector plane, which makes the electron flux distributions on the detector plane become much complex. Using the semi-classical theory, we put forward a formula for calculating the electron flux. Our calculation results suggest that the electron flux distributions on a given detector plane is not only related to the propagation time of the detached electron, but also related to the detached electron's energy. With the increase of the detached electron's energy, the oscillating region in the electron flux distributions becomes enlarged and the oscillating structure in the flux distributions becomes much more complicated. This study will guide future experiment research on the photodetachment microscopy of the negative ions in the presence of non-uniform external fields.
Nonautonomous Vortices in (2+1)-Dimensional Graded-Index Waveguide
Authors: Lai Xian-Jing , Cai Xiao-Ou , Zhang Jie-Fang 
Published: May 2015

Abstract
With the help of self-similarity transformation, we construct and study the nonautonomous vortices with different topological charges inside a planar graded-index nonlinear waveguide, analytically, and numerically. Although these vortices are approximate, they can reflect the real properties of self-similar optical beam during a short-term propagation. Existence of these autonomous vortices require delicate balances between the system parameters such as diffraction, nonlinearity, gain, and external potential. We are concerned with some special but interesting situations, and discussing the changes of the height, width, energy, and central position of the vortices as the increase of propagation distance. Moreover, we are also interested in the azimuthal modulational instability of the system, and comparing our prediction for the modulational instability growth rates to numerical results.
Nonlinear Exact Solutions of the 2-Dimensional Rotational Euler Equations for the Incompressible Fluid*
Authors: An Hong-Li , Yang Jin-Jing , Yuen Man-Wai 
Published: May 2015

Abstract
In this paper, the Clarkson-Kruskal direct approach is employed to investigate the exact solutions of the 2-dimensional rotational Euler equations for the incompressible fluid. The application of the method leads to a system of completely solvable ordinary differential equations. Several special cases are discussed and novel nonlinear exact solutions with respect to variables x and y are obtained. It is of interest to notice that the pressure p is obtained by the second kind of curvilinear integral and the coefficients of the nonlinear solutions are solitary wave type functions like tanh(kt/2) and sech (kt/2) due to the rotational parameter k ≠ 0. Such phenomenon never appear in the classical Euler equations wherein the Coriolis force arising from the gravity and Earth's rotation is ignored. Finally, illustrative numerical figures are attached to show the behaviors that the exact solutions may exhibit.
Absorption Spectra and Refractive Index Changes of an Exciton in a Core/Shell Quantum Dot
Authors: Xie Wen-Fang 
Published: May 2015

Abstract
The absorption spectra and the refractive index changes are calculated theoretically for an exciton in a core/shell quantum dot. The advantage of our methodology is that one can investigate the influence of the repulsive core by varying two parameters in the confinement potential. The dimensionality effect of exciton quantum dots on the optical absorptions has been studied. It has been found that in the same regime, the optical absorption intensities of excitons are much smaller for the core/shell quantum dots than for the two-dimensional quantum rings. The linear and the nonlinear optical absorption coefficients and refractive index changes have been examined with the change of the confinement potential. The results show that the optical absorptions and the refractive index changes are strongly affected by the repulsive core of core/shell quantum dots. Moreover, the calculated results also reveal that as the inner radius increases, the peak values of the absorption coefficients and the refractive index changes of an exciton will show the optical Aharonov-Bohm oscillation in core/shell quantum dots.
Calculation of Half-Metal, Debye and Curie Temperatures of Co2VAl Compound: First Principles Study*
Authors: Boochani Arash , Khosravi Heidar , Khodadadi Jabbar , Solaymani Shahram , Sarmazdeh Masoud Majidiyan , Mendi Rohollah Taghavi , Elahi Sayed Mohammad 
Published: May 2015

Abstract
By FP-LAPW calculations, the structural, elastic, Debye and Curie temperatures, electronic and magnetic properties of Co2 VAl are investigated. The results indicate that Ferromagnetic (FM) phase is more stable than Anti-Ferromagnetic (AFM) and Non-magnetic (NM) ones. In addition, C11-C12 > 0, C44 > 0, and B > 0 so Co2VAl is an elastically stable material with high Debye temperature. Also, the B/G ratio exhibits a ductility behavior. The relatively high Curie temperature provides it as a favorable material for spintronic application. It's electronic and magnetic properties are studied by GGA+U approach leading to a 100% spin polarization at Fermi level.
All-magnetic control of skyrmions in nanowires by a spin wave
Authors: Zhang Xichao , Ezawa Motohiko , Xiao Dun , Zhao G P , Liu Yaowen , Zhou Yan 
Published: May 2015

Abstract
Magnetic skyrmions are topologically protected nanoscale objects, which are promising building blocks for novel magnetic and spintronic devices. Here, we investigate the dynamics of a skyrmion driven by a spin wave in a magnetic nanowire. It is found that (i) the skyrmion is first accelerated and then decelerated exponentially; (ii) it can turn L-corners with both right and left turns; and (iii) it always turns left (right) when the skyrmion number is positive (negative) in the T- and Y-junctions. Our results will be the basis of skyrmionic devices driven by a spin wave.
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
Authors: Aßhauer Kathrin P. , Wemheuer Bernd , Daniel Rolf , Meinicke Peter 
Published: May 2015

Abstract
Motivation: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data.
Results: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches.
Availability and implementation: Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/.
Contact: kasshau@gwdg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
MemGen: a general web server for the setup of lipid membrane simulation systems
Authors: Knight Christopher J. , Hub Jochen S. 
Published: May 2015

Abstract
Motivation: Molecular dynamics simulations provide atomic insight into the physicochemical characteristics of lipid membranes and hence, a wide range of force field families capable of modelling various lipid types have been developed in recent years. To model membranes in a biologically realistic lipid composition, simulation systems containing multiple different lipids must be assembled.
Results: We present a new web service called MemGen that is capable of setting up simulation systems of heterogenous lipid membranes. MemGen is not restricted to certain lipid force fields or lipid types, but instead builds membranes from uploaded structure files which may contain any kind of amphiphilic molecule. MemGen works with any all-atom or united-atom lipid representation.
Availability and implementation: MemGen is freely available without registration at http://memgen.uni-goettingen.de.
Contact: jhub@gwdg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data
Authors: Kähärä Juhani , Lähdesmäki Harri 
Published: May 2015

Abstract
Motivation: Transcription factors (TFs) are a class of DNA-binding proteins that have a central role in regulating gene expression. To reveal mechanisms of transcriptional regulation, a number of computational tools have been proposed for predicting TF-DNA interaction sites. Recent studies have shown that genome-wide sequencing data on open chromatin sites from a DNase I hypersensitivity experiments (DNase-seq) has a great potential to map putative binding sites of all transcription factors in a single experiment. Thus, computational methods for analysing DNase-seq to accurately map TF-DNA interaction sites are highly needed.
Results: Here, we introduce a novel discriminative algorithm, BinDNase, for predicting TF-DNA interaction sites using DNase-seq data. BinDNase implements an efficient method for selecting and extracting informative features from DNase I signal for each TF, either at single nucleotide resolution or for larger regions. The method is applied to 57 transcription factors in cell line K562 and 31 transcription factors in cell line HepG2 using data from the ENCODE project. First, we show that BinDNase compares favourably to other supervised and unsupervised methods developed for TF-DNA interaction prediction using DNase-seq data. We demonstrate the importance to model each TF with a separate prediction model, reflecting TF-specific DNA accessibility around the TF-DNA interaction site. We also show that a highly standardised DNase-seq data (pre)processing is a requisite for accurate TF binding predictions and that sequencing depth has on average only a moderate effect on prediction accuracy. Finally, BinDNase’s binding predictions generalise to other cell types, thus making BinDNase a versatile tool for accurate TF binding prediction.
Availability and implementation: R implementation of the algorithm is available in: http://research.ics.aalto.fi/csb/software/bindnase/.
Contact: juhani.kahara@aalto.fi
Supplementary information: Supplemental data are available at Bioinformatics online.
Interactive analysis of large cancer copy number studies with Copy Number Explorer
Authors: Newman Scott 
Published: May 2015

Abstract
Summary: Copy number abnormalities (CNAs) such as somatically-acquired chromosomal deletions and duplications drive the development of cancer. As individual tumor genomes can contain tens or even hundreds of large and/or focal CNAs, a major difficulty is differentiating between important, recurrent pathogenic changes and benign changes unrelated to the subject’s phenotype. Here we present Copy Number Explorer, an interactive tool for mining large copy number datasets. Copy Number Explorer facilitates rapid visual and statistical identification of recurrent regions of gain or loss, identifies the genes most likely to drive CNA formation using the cghMCR method and identifies recurrently broken genes that may be disrupted or fused. The software also allows users to identify recurrent CNA regions that may be associated with differential survival.
Availability and Implementation: Copy Number Explorer is available under the GNU public license (GPL-3). Source code is available at: https://sourceforge.net/projects/copynumberexplorer/
Contact: scott.newman@emory.edu