bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly-effective photocatalytic properties and interfacial transfer efficiencies of charge carriers for the novel Ag2CO3/AgX heterojunctions achieved by surface modification
Authors: Dong Hongjun , Chen Gang , Sun Jingxue , Feng Yujie , Li Chunmei , Xiong Guihong , Lv Chade
Published: February 2014

Ag2CO3/AgX heterojunctions are achieved from the surface modification of Ag2CO3 with AgX nanoparticles, which improves the photocatalytic activity and stability for dye degradation.
A copper based pillared-bilayer metal organic framework: its synthesis, sorption properties and catalytic performance
Authors: Parshamoni Srinivasulu , Sanda Suresh , Jena Himanshu Sekhar , Konar Sanjit
Published: February 2014

A copper based metal organic framework with selective, hysteretic sorption, which can act as a heterogeneous catalyst for Glaser type homo-coupling reactions.
Anti-inflammatory effect and prostate gene expression profiling of steryl ferulate on experimental rats with non-bacterial prostatitis
Authors: Hu Yinzhou , Xiong Lina , Huang Weisu , Cai Huafang , Luo Yanxi , Zhang Ying , Lu Baiyi
Published: February 2014

Steryl ferulate (SF) is a bioactive mixture extracted from rice bran and shows higher inhibitory activity against inflammation than the corresponding free sterols.
Tetramethylbithiophene in π-conjugated alternating copolymers as an effective structural component for the formation of spherical assemblies
Authors: Tong Liang , Kushida Soh , Kuwabara Junpei , Kanbara Takaki , Ishii Noriyuki , Saeki Akinori , Seki Shu , Furumi Seiichi , Yamamoto Yohei
Published: February 2014

π-Conjugated alternating copolymers containing a tetramethylbithiophene unit show a strong tendency to form well-defined, sub- to several-micrometer-sized spheres.
Novel poly(ethylene oxide monomethyl ether)-b-poly(ε-caprolactone) diblock copolymers containing a pH-acid labile ketal group as a block linkage
Authors: Petrova S. , Jäger E. , Konefał R. , Jäger A. , Venturini C. G. , Spěváček J. , Pavlova E. , Štěpánek P.
Published: February 2014

Acidic physiological conditions trigger degradation of amphiphilic block copolymers containing a ketal group as a block linkage into biocompatible degradation products.
Finite‐time stochastic stabilisation of Markovian jump non‐linear quadratic systems with partially known transition probabilities
Authors: Wei Yunliang , Zheng Wei Xing
Published: February 2014

This paper studies the problems of the finite‐time stochastic boundedness (FTSB) and stabilisation for a class of discrete‐time Markovian jump non‐linear quadratic systems with incomplete information on transition probabilities. It is shown that the FTSB of the system can be ensured under some sufficient conditions derived. As a corollary, some sufficient conditions of the finite‐time stochastic stability for the non‐linear quadratic systems without exogenous disturbance are also established. Based on these results, stabilising mode‐dependent state feedback controllers are designed for Markovian jump non‐linear quadratic systems with/without exogenous disturbance, respectively. Consequently, the finite‐time stochastic stabilisation problem is resolved. Finally, a numerical example is presented to demonstrate the effectiveness of the proposed theory.
Alternative formulations to compute the binary shape Euler number
Authors: Humberto Sossa Azuela Juan , Rubio Espino Elsa , Santiago Raúl , López Alejandro , Peña Ayala Alejandro , Cuevas Jimenez Erik V.
Published: February 2014

The authors propose two equations based on the pixel geometry and connectivity properties, which can be used to compute, efficiently, the Euler number of a binary digital image with either thick or thin boundaries. Although computing this feature, the authors’ technique extracts the underlying topological information provided by the shape pixels of the given image. The correctness of computing the Euler number using the new equations is also established theoretically. The performance of the proposed method is compared against other available alternatives. Experimental results on a large image database demonstrate that the authors technique for computing the Euler number outperforms the earlier approaches significantly in terms of the number of basic arithmetic operations needed per pixel. Both equations are specialised only for 4‐connectivity cases.
Semi‐automatic annotation samples for vehicle type classification in urban environments
Authors: Chen Zezhi , Ellis Tim
Published: February 2014

Data collection, and especially data annotation, are surprisingly time consuming and costly tasks for vehicle classification. Annotation is used to label examples of vehicles, manually outlining their shapes and assigning their correct classification, for use in classifier training and performance evaluation. This study presents a semi‐automatic approach for the annotation of the vehicle samples recorded from roadside CCTV video cameras. Vehicles are detected by using automatic image analysis and classified into four main categories: car, van, bus and motorcycle/bicycle by using a vehicle observation vector constructed from the size, the shape and the appearance features. Unsupervised K ‐means clustering is used to automatically compute an initial class label for each detected vehicle. Then, in an iterative process, the output scores of a linear support vector machines classifier are used to identify the low confidence samples, for which the annotations are considered for manual correction. Experimental results are presented for both synthetic and real datasets to demonstrate the effectiveness and the efficiency of the authors approach, which significantly reduces the time required to generate an annotated dataset. The method is general enough that it can be used in other classification problems and domains that use a manually‐created ground‐truth.
A new method of voltage and frequency control in isolated microgrids using enhanced droop controller optimized by frog algorithm
Authors: Taghizadeh Mahdi , Mardaneh Mohammad , Sha Sadeghi Mokhtar
Published: February 2014

This paper presents a new method for optimal frequency and voltage control in microgrids (MG) considering the mutual effect of line parameters on power transfer. In MGs each distributed generation (DG) has its special droop characteristics. When a load consumption change occurs in the MG, an imbalance between generation and consumption rises, thus a change occurs in the voltage and frequency of DGs according to their droop characteristics. In order to minimize oscillations of voltage and frequency, we have used optimal droop controller which is based on considering the mutual effects of transfer parameters on active and reactive powers. Since line parameters heavily affect the droop characteristics, these parameters are obtained optimally by the frog algorithm such that oscillations in voltage and frequency are minimized. In order to enhance the controlling scheme, effects of line resistance on reactive power changes and effects of line reactance on active power changes are also considered. Since enhanced droop control depends on line parameters, it cannot be implemented in large MGs; therefore, it is modeled by multi-layer perceptron neural networks. We have used the frog algorithm in order to train the perceptron network. The obtained results show satisfactory voltage and frequency control in various load level. In this paper, MGs are studied and simulated in an isolated state.
Breaking generalized covariance, classical renormalization, and boundary conditions from superpotentials
Authors: Livshits Gideon I.
Published: February 2014

Superpotentials offer a direct means of calculating conserved charges associated with the asymptotic symmetries of space-time. Yet superpotentials have been plagued with inconsistencies, resulting in nonphysical or incongruent values for the mass, angular momentum, and energy loss due to radiation. The approach of Regge and Teitelboim, aimed at a clear Hamiltonian formulation with a boundary, and its extension to the Lagrangian formulation by Julia and Silva have resolved these issues, and have resulted in a consistent, well-defined and unique variational equation for the superpotential, thereby placing it on a firm footing. A hallmark solution of this equation is the KBL superpotential obtained from the first-order Lovelock Lagrangian. Nevertheless, here we show that these formulations are still insufficient for Lovelock Lagrangians of higher orders. We present a paradox, whereby the choice of fields affects the superpotential for equivalent on-shell dynamics. We offer two solutions to this paradox: either the original Lagrangian must be effectively renormalized, or that boundary conditions must be imposed, so that space-time be asymptotically maximally symmetric. Non-metricity is central to this paradox, and we show how quadratic non-metricity in the bulk of space-time contributes to the conserved charges on the boundary, where it vanishes identically. This is a realization of the gravitational Higgs mechanism, proposed by Percacci, where the non-metricity is the analogue of the Goldstone boson.
Direct-potential-fit analyses yield improved empirical potentials for the ground $X\,^1\Sigma _g^+$XΣg+1 state of Be2
Authors: Meshkov Vladimir V. , Stolyarov Andrey V. , Heaven Michael C. , Haugen Carl , LeRoy Robert J.
Published: February 2014

We have performed new direct-potential-fit (DPF) analyses of the rotationally resolved \documentclass[12pt]{minimal}\begin{document}$A\,^1\Pi _u(v^{\prime }\break=2,3;J^{\prime }=1,2)\rightarrow X\,^1\Sigma _g^+(v^{\prime \prime }\in [0, 11];J^{\prime \prime }\in [0,3])$\end{document}AΠu1(v′=2,3;J′=1,2)→XΣg+1(v″∈[0,11];J″∈[0,3]) stimulated emission pumping spectra of Be2 [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] using two quite different analytical potential energy functions that incorporate the correct theoretically known long-range behaviour in different ways. These functions are: the damped Morse/long-range potential [R. J. Le Roy, C. C. Haugen, J. Tao, and H. Li, Mol. Phys. 109, 435 (2011)], and the Chebyshev polynomial expansion potential [L. Busevica, I. Klincare, O. Nikolayeva, M. Tamanis, R. Ferber, V. V. Meshkov, E. A. Pazyuk, and A. V. Stolyarov, J. Chem. Phys. 134, 104307 (2011)]. In contrast with the expanded Morse oscillator potential determined in the original DPF analysis of Merritt et al. [Science 324, 1548 (2009)], both of these functions unambiguously support the existence of the v″ = 11 last vibrational levels which is bound by only ∼0.5 cm−1, and they give equivalent, essentially exact predictions for this level when using the original data set which ended at v″ = 10. These empirical potentials predict an equilibrium distance of re = 2.445(5) Å and a well depth of \documentclass[12pt]{minimal}\begin{document}${\mathfrak {D}}_e=934.9(0.4)$\end{document}De=934.9(0.4) cm−1, values which agree (within the uncertainties) with the best ab initio estimates of 2.444(10) Å and 935(10) cm−1, respectively [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)].
Topology of surfaces for molecular Stark energy, alignment, and orientation generated by combined permanent and induced electric dipole interactions
Authors: Schmidt Burkhard , Friedrich Bretislav
Published: February 2014

We show that combined permanent and induced electric dipole interactions of linear polar and polarizable molecules with collinear electric fields lead to a sui generis topology of the corresponding Stark energy surfaces and of other observables – such as alignment and orientation cosines – in the plane spanned by the permanent and induced dipole interaction parameters. We find that the loci of the intersections of the surfaces can be traced analytically and that the eigenstates as well as the number of their intersections can be characterized by a single integer index. The value of the index, distinctive for a particular ratio of the interaction parameters, brings out a close kinship with the eigenproperties obtained previously for a class of Stark states via the apparatus of supersymmetric quantum mechanics.
Electronic excitation spectra of molecules in solution calculated using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model with perturbative approach
Authors: Fukuda Ryoichi , Ehara Masahiro , Cammi Roberto
Published: February 2014

A perturbative approximation of the state specific polarizable continuum model (PCM) symmetry-adapted cluster-configuration interaction (SAC-CI) method is proposed for efficient calculations of the electronic excitations and absorption spectra of molecules in solutions. This first-order PCM SAC-CI method considers the solvent effects on the energies of excited states up to the first-order with using the zeroth-order wavefunctions. This method can avoid the costly iterative procedure of the self-consistent reaction field calculations. The first-order PCM SAC-CI calculations well reproduce the results obtained by the iterative method for various types of excitations of molecules in polar and nonpolar solvents. The first-order contribution is significant for the excitation energies. The results obtained by the zeroth-order PCM SAC-CI, which considers the fixed ground-state reaction field for the excited-state calculations, are deviated from the results by the iterative method about 0.1 eV, and the zeroth-order PCM SAC-CI cannot predict even the direction of solvent shifts in n-hexane for many cases. The first-order PCM SAC-CI is applied to studying the solvatochromisms of (2,2′-bipyridine)tetracarbonyltungsten [W(CO)4(bpy), bpy = 2,2′-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC)5W(pyz)W(CO)5, pyz = pyrazine]. The SAC-CI calculations reveal the detailed character of the excited states and the mechanisms of solvent shifts. The energies of metal to ligand charge transfer states are significantly sensitive to solvents. The first-order PCM SAC-CI well reproduces the observed absorption spectra of the tungsten carbonyl complexes in several solvents.
Advantages of microsphere-assisted super-resolution imaging technique over solid immersion lens and confocal microscopies
Authors: Darafsheh Arash , Limberopoulos Nicholaos I. , Derov John S. , Walker Dennis E. , Astratov Vasily N.
Published: February 2014

We demonstrate a series of advantages of microsphere-assisted imaging over confocal and solid immersion lens microscopies including intrinsic flexibility, better resolution, higher magnification, and longer working distances. We discerned minimal feature sizes of ∼50-60 nm in nanoplasmonic arrays at the illumination wavelength λ = 405 nm. It is demonstrated that liquid-immersed, high-index (n ∼ 1.9-2.1) spheres provide a superior image quality compared to that obtained by spheres with the same index contrast in an air environment. We estimate that using transparent microspheres at deep UV wavelengths of ∼200 nm might make possible imaging of various nanostructures with extraordinary high ∼30 nm resolution.
Photo-driven oxidation of water on α-Fe2O3 surfaces: An ab initio study
Authors: Nguyen Manh-Thuong , Seriani Nicola , Piccinin Simone , Gebauer Ralph
Published: February 2014

Adopting the theoretical scheme developed by the Nørskov group [see, for example, Nørskov et al., J. Phys. Chem. B 108, 17886 (2004)], we conducted a density functional theory study of photo-driven oxidation processes of water on various terminations of the clean hematite (α-Fe2O3) (0001) surface, explicitly taking into account the strong correlation among the 3d states of iron through the Hubbard U parameter. Six best-known terminations, namely, \documentclass[12pt]{minimal}\begin{document}$\rm Fe-Fe-O_3-$\end{document} Fe − Fe −O3− (we call \documentclass[12pt]{minimal}\begin{document}$\rm S_1$\end{document}S1), \documentclass[12pt]{minimal}\begin{document}$\rm O-Fe-Fe-$\end{document}O− Fe − Fe − (\documentclass[12pt]{minimal}\begin{document}$\rm S_2$\end{document}S2), \documentclass[12pt]{minimal}\begin{document}$\rm O_2-Fe-Fe-$\end{document}O2− Fe − Fe −(\documentclass[12pt]{minimal}\begin{document}$\rm S_3$\end{document}S3), \documentclass[12pt]{minimal}\begin{document}$\rm O_3-Fe-Fe-$\end{document}O3− Fe − Fe − (\documentclass[12pt]{minimal}\begin{document}$\rm S_4$\end{document}S4), \documentclass[12pt]{minimal}\begin{document}$\rm Fe-O_3-Fe-$\end{document} Fe −O3− Fe − (\documentclass[12pt]{minimal}\begin{document}$\rm S_5$\end{document}S5), and \documentclass[12pt]{minimal}\begin{document}$\rm O-Fe-O_3-$\end{document}O− Fe −O3−(\documentclass[12pt]{minimal}\begin{document}$\rm S_6$\end{document}S6), are first exposed to water, the stability of resulting surfaces is investigated under photoelectrochemical conditions by considering different chemical reactions (and their reaction free energies) that lead to surfaces covered by O atoms or/and OH groups. Assuming that the water splitting reaction is driven by the redox potential for photogenerated holes with respect to the normal hydrogen electrode, UVB, at voltage larger than UVB, most 3-oxygen terminated substrates are stable. These results thus suggest that the surface, hydroxylated in the dark, should release protons under illumination. Considering the surface free energy of all the possible terminations shows that \documentclass[12pt]{minimal}\begin{document}$\rm O_3$\end{document}O3–\documentclass[12pt]{minimal}\begin{document}$\rm S_5$\end{document}S5 and \documentclass[12pt]{minimal}\begin{document}$\rm O_3$\end{document}O3–\documentclass[12pt]{minimal}\begin{document}$\rm S_1$\end{document}S1 are the most thermodynamically stable. While water oxidation process on the former requires an overpotential of 1.22 V, only 0.84 V is needed on the latter.
The iron lung: A device for the continuous delivery of fine particulate matter
Authors: Arnold I. J. , Berger C. , Chakrabarty R. K. , Moosmüller H. , Sharma N. , Mazzoleni C.
Published: February 2014

In aerosol research, bag-sampling techniques are commonly used for temporary storage of aerosols. They have been used for aging studies and to integrate over fluctuations in aerosol properties and concentrations. Here, we describe the design and operation of an iron lung aerosol sampler consisting of a large volume (∼277 l) drum and a conductive drum liner. This iron lung is used for the continuous delivery of fine particulate matter. Its performance for storage and sampling of fine particulate matter has been evaluated with soot from a kerosene lamp by characterizing the change of particle number and size distribution as function of time with a scanning mobility particle sizer. Changes in these properties have been shown to be smooth, demonstrating the utility of the iron lung described here.
Study on negative incident photon-to-electron conversion efficiency of quantum dot-sensitized solar cells
Authors: Li Chunhui , Wu Huijue , Zhu Lifeng , Xiao Junyan , Luo Yanhong , Li Dongmei , Meng Qingbo
Published: February 2014

Recently, negative signals are frequently observed during the measuring process of monochromatic incident photon-to-electron conversion efficiency (IPCE) for sensitized solar cells by DC method. This phenomenon is confusing and hindering the reasonable evaluation of solar cells. Here, cause of negative IPCE values is studied by taking quantum dot-sensitized solar cell (QDSC) as an example, and the accurate measurement method to avoid the negative value is suggested. The negative background signals of QDSC without illumination are found the direct cause of the negative IPCE values by DC method. Ambient noise, significant capacitance characteristics, and uncontrolled electrochemical reaction all can lead to the negative background signals. When the photocurrent response of device under monochromatic light illumination is relatively weak, the actual photocurrent signals will be covered by the negative background signals and the resulting IPCE values will appear negative. To improve the signal-to-noise ratio, quasi-AC method is proposed for IPCE measurement of solar cells with weak photocurrent response based on the idea of replacing the absolute values by the relative values.
Computer program for the sensitivity calculation of a CR-39 detector in a diffusion chamber for radon measurements
Authors: Nikezic D. , Yu K. N. , Stajic J. M.
Published: February 2014

Computer software for calculation of the sensitivity of a CR-39 detector closed in a diffusion chamber to radon is described in this work. The software consists of two programs, both written in the standard Fortran 90 programming language. The physical background and a numerical example are given. Presented software is intended for numerous researches in radon measurement community. Previously published computer programs TRACK_TEST.F90 and TRACK_VISION.F90 [D. Nikezic and K. N. Yu, Comput. Phys. Commun.174, 160 (2006); D. Nikezic and K. N. Yu, Comput. Phys. Commun.178, 591 (2008)] are used here as subroutines to calculate the track parameters and to determine whether the track is visible or not,based on the incident angle, impact energy, etching conditions, gray level, and visibility criterion. The results obtained by the software, using five different V functions,were compared with the experimental data found in the literature. Application of two functions in this software reproduced experimental data very well, while other three gave lower sensitivity than experiment.
An unattended device for high-voltage sampling and passive measurement of thoron decay products
Authors: Gierl Stefanie , Meisenberg Oliver , Haninger Thomas , Wielunski Marek , Tschiersch Jochen
Published: February 2014

An integrating measurement device for the concentration of airborne thoron decay products was designed and calibrated. It is suitable for unattended use over up to several months also in inhabited dwellings. The device consists of a hemispheric capacitor with a wire mesh as the outer electrode on ground potential and the sampling substrates as the inner electrode on +7.0 kV. Negatively charged and neutral thoron decay products are accelerated to and deposited on the sampling substrates. As sampling substrates, CR39 solid-state nuclear track detectors are used in order to record the alpha decay of the sampled decay products. Nuclide discrimination is achieved by covering the detectors with aluminum foil of different thickness, which are penetrated only by alpha particles with sufficient energy. Devices of this type were calibrated against working level monitors in a thoron experimental house. The sensitivity was measured as 9.2 tracks per Bq/m3 × d of thoron decay products. The devices were used over 8 weeks in several houses built of earthen material in southern Germany, where equilibrium equivalent concentrations of 1.4–9.9 Bq/m3 of thoron decay products were measured.
Characterization of intrinsic and induced lateral conduction in space dielectric materials
Authors: Hanna R. , Paulmier T. , Belhaj M. , Dirassen B. , Payan D. , Balcon N.
Published: February 2014

Characterization of lateral charge carrier conduction in space dielectrics is of high importance for the prediction of charging behavior and electrostatic discharges on satellites. In the present paper, a new experimental approach for the analysis of surface conduction, which is not well understood and characterized in the literature, is established and discussed. Though this method, based on the use of two Kelvin probes, we have been able to discriminate between lateral and bulk charge transports and to reveal the presence of an intrinsic lateral conductivity on Teflon® FEP irradiated with low energy electron beam. We demonstrated that lateral intrinsic conductivity is enhanced when incident current density increases and when approaching the sample surface. The experimental results are analyzed through trapping/detrapping and hopping models. Depending on radiation configuration mode, we have revealed as well the presence of a lateral conductivity that is enhanced by radiation ionization processes, and explained as well with a trapping/recombination model.
Predicting the stability of surface phases of molybdenum selenides
Authors: Roma Guido , Ghorbani Elaheh , Mirhosseini Hossein , Kiss Janos , Kühne Thomas D. , Felser Claudia
Published: February 2014

The selenization of molybdenum might become an important step in the production of nanostructures based on the layered compound MoSe2. It is already technologically relevant for the production of thin film chalcopyrite solar cells. However, the control of the process is still very poor, due to the lack of basic knowledge of the surface thermodynamics of the system. Here, we present a theoretical study on the stability of surface adlayers of Se on the Mo(110) surface, predicting surface patterns and their stability range in terms of temperature and selenium partial pressure. Our results, based on density functional theory, show that the attainable Se coverages range from 1/4 to 3/4 of a monolayer for systems in equilibrium with a gas formed of Se molecules. We provide simulated scanning tunneling microscopy images to help the experimental characterization of adsorbed surface patterns.
Magnetic hysteresis behavior and magnetic pinning in a d ferromagnet/superconductor nanostructure
Authors: Uchino Takashi , Uenaka Yuki , Soma Haruka , Sakurai Takahiro , Ohta Hitoshi
Published: February 2014

We investigate the interaction between superconductivity and defect-induced d0 ferromagnetism using a composite consisting of MgB2 and MgO nanocrystals. The composite exhibits a ferromagnetic hysteresis behavior in the temperature region from 40 to 300 K. Defective MgO nanocrystals (∼20 nm) embedded in the composite are considered to be responsible for the observed ferromagnetism. The zero field cool and field cool magnetization curves show that the superconducting transition occurs at Tc = 38.6 K, in agreement with Tc of pure MgB2. In the temperature region from Tc to 0.9Tc (∼35 K), the magnetization hysteresis curves show a superposition of ferromagnetic (F) and superconducting (S) signals. When the temperature of the system is decreased below 0.65Tc (∼25 K), the S signals dominate over the F signals. The resulting magnetic hysteresis loops are highly asymmetric and the descending filed branch is nearly flat, as predicted in the case of surface pinning. At temperatures below 0.5Tc (∼20 K), a sharp peak is developed near zero field in the magnetization hysteresis curves, implying an enhancement of superconducting vortex pinning. The observed pinning enhancement most likely results from magnetic pinning due to randomly distributed magnetic MgO grains, which yield the magnetic inhomogeneity and the related pinning potential in a length scale of ∼100 nm. Thus, the present ferromagnetic/superconducting composite provides an ideal model system that demonstrates the availability of d0 ferromagnetism as a source of magnetic potential for effective vortex pinning.
Reaction kinetics during the thermal activation of the silicon surface passivation with atomic layer deposited Al2O3
Authors: Richter Armin , Benick Jan , Hermle Martin , Glunz Stefan W.
Published: February 2014

The excellent surface passivation of crystalline silicon provided by Al2O3 requires always an activation by a thermal post-deposition treatment. In this work, we present an indirect study of the reaction kinetics during such thermal activation treatments for Al2O3 synthesized by atomic layer deposition. The study was performed for Al2O3 deposited at varying temperatures, which results in different micro-structures of the films and, in particular, different hydrogen concentrations. The effective carrier lifetime was measured sequentially as a function of the annealing time and temperature. From these data, the reaction rate Ract and the activation energy EA were extracted. The results revealed a rather constant EA in the range of 1.4 to 1.5 eV, independent of the deposition temperature. The reaction rate, however, was found to increase with decreasing deposition temperature, which correlates with an increasing amount of hydrogen being incorporated in the Al2O3 films. This is a strong indication for an interface hydrogenation that takes place during the thermal activation, which is limited by the amount of hydrogen provided by the Al2O3 layer.
Tyrosine phosphorylation of protein kinase complex BAK1/BIK1 mediates
Arabidopsis
innate immunity
Authors: Lin Wenwei , Li Bo , Lu Dongping , Chen Sixue , Zhu Ning , He Ping , Shan Libo
Published: February 2014

Significance

The innate immune response is initiated by the recognition of conserved microbial signatures via membrane-resident receptor complex. The dimerization and phosphorylation of
Arabidopsis
protein kinase complex FLS2/BAK1/BIK1 is essential to initiate and transduce immune signaling to bacterial flagellin. BIK1, a classic serine/threonine kinase, was found here to be autophosphorylated and transphosphorylated by BAK1 at multiple tyrosine residues to relay plant immune signaling. The essential function of tyrosine kinase activity of BIK1 in plants echoes the function of nonreceptor tyrosine kinases that transduce receptor tyrosine kinase signaling via dimerization and phosphorylation in metazoans. Thus, despite lack of classical tyrosine kinases, tyrosine phosphorylation is also an important regulatory mechanism to control membrane-resident receptor signaling in plants.
Multimodal metaphors in contemporary experimental literature
Authors: Gibbons Alison
Published: February 2014

Multimodal metaphor studies has hitherto neglected one key arena in the creative arts: literature. This article explores four case studies of multimodal metaphor within contemporary experimental literature. In poetry, the metaphor EMOTIONS ARE OBJECTS is discussed within Anne Carson’s (2009) accordion ‘poem in a box’, in which the poet struggles with the death of her brother; in literature, Steve Tomasula and Stephen Farrell’s (1996) fold-out fiction TOC and Mark Z. Danielewski’s (2006) novel Only Revolutions, both thematically interested in time and designed to be rotated in reading, are explored to reveal the metaphor TIME IS CIRCULAR MOTION; and in the graphic novel, analysis of Warren Ellis’ (2011) “SVK”, for which readers use a torch to reveal characters’ thoughts printed in UV ink, exposes the metaphor KNOWLEDGE IS LIGHT.

Throughout, it is shown that multimodal metaphors are generated through both the interaction of verbal and visual modes, and through a reader-user’s performative engagement with the text. Moreover, early theorisations of multimodal metaphor in which the two domains (source and target) were required to stem from different modalities, are called into question. Rather, the creative affordances of multimodal literature show such metaphors to be more integrative in nature, both cognitively and semantically.
Metaphorical creativity and recontextualization in multimodal advertisements on e-business across time
Authors: Hidalgo-Downing Laura , Kraljevic Mujic Blanca , Nuñez-Perucha Begoña
Published: February 2014

In this article we explore the creative recontextualization of JOURNEY, WAR, RACE and SPORTS metaphors and discuss their manifestations in multimodal ICT advertisements across time. Our objectives are to discuss (i) the choices of metaphors and related source domains used to describe (e)businesses in two different time periods, (ii) how the highlighting and hiding of features of the source domains remain constant or change, (iii) the relations between modes, and (iv) the discursive strategies for metaphorical creativity. The results of our analysis reflect an interesting shift in the highlighting and hiding of features of the main metaphors and related sources across the two time periods, thus revealing variations in emergent metaphors across time. We argue that these results reflect ongoing social changes which illustrate the contextual basis and motivation of metaphor as a linguistic form of action and creative communication in advertising discourse.
Amy Gladfelter: Fungi with a streak of individuality
Authors: Sedwick Caitlin
Published: February 2014

Gladfelter studies the behavior of nuclei and cytoskeletal structures in syncytia.
Discrete mixture modeling to address genetic heterogeneity in time-to-event regression
Authors: Eng Kevin H. , Hanlon Bret M.
Published: February 2014

Motivation: Time-to-event regression models are a critical tool for associating survival time outcomes with molecular data. Despite mounting evidence that genetic subgroups of the same clinical disease exist, little attention has been given to exploring how this heterogeneity affects time-to-event model building and how to accommodate it. Methods able to diagnose and model heterogeneity should be valuable additions to the biomarker discovery toolset.

Results: We propose a mixture of survival functions that classifies subjects with similar relationships to a time-to-event response. This model incorporates multivariate regression and model selection and can be fit with an expectation maximization algorithm, we call Cox-assisted clustering. We illustrate a likely manifestation of genetic heterogeneity and demonstrate how it may affect survival models with little warning. An application to gene expression in ovarian cancer DNA repair pathways illustrates how the model may be used to learn new genetic subsets for risk stratification. We explore the implications of this model for censored observations and the effect on genomic predictors and diagnostic analysis.

Availability and implementation: R implementation of CAC using standard packages is available at https://gist.github.com/programeng/8620b85146b14b6edf8f Data used in the analysis are publicly available.

Contact: kevin.eng@roswellpark.org

Supplementary information: Supplementary data are available at Bioinformatics online.
TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
Authors: Anvar Seyed Yahya , van der Gaag Kristiaan J. , van der Heijden Jaap W. F. , Veltrop Marcel H. A. M. , Vossen Rolf H. A. M. , de Leeuw Rick H. , Breukel Cor , Buermans Henk P. J. , Verbeek J. Sjef , de Knijff Peter , den Dunnen Johan T. , Laros Jeroen F. J.
Published: February 2014

Motivation: Advances in sequencing technologies and computational algorithms have enabled the study of genomic variants to dissect their functional consequence. Despite this unprecedented progress, current tools fail to reliably detect and characterize more complex allelic variants, such as short tandem repeats (STRs). We developed TSSV as an efficient and sensitive tool to specifically profile all allelic variants present in targeted loci. Based on its design, requiring only two short flanking sequences, TSSV can work without the use of a complete reference sequence to reliably profile highly polymorphic, repetitive or uncharacterized regions.

Results: We show that TSSV can accurately determine allelic STR structures in mixtures with 10% representation of minor alleles or complex mixtures in which a single STR allele is shared. Furthermore, we show the universal utility of TSSV in two other independent studies: characterizing de novo mutations introduced by transcription activator-like effector nucleases (TALENs) and profiling the noise and systematic errors in an IonTorrent sequencing experiment. TSSV complements the existing tools by aiding the study of highly polymorphic and complex regions and provides a high-resolution map that can be used in a wide range of applications, from personal genomics to forensic analysis and clinical diagnostics.

Availability and implementation: We have implemented TSSV as a Python package that can be installed through the command-line using pip install TSSV command. Its source code and documentation are available at https://pypi.python.org/pypi/tssv and http://www.lgtc.nl/tssv.

Contact:  S.Y.Anvar@lumc.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Authors: Xie Yinlong , Wu Gengxiong , Tang Jingbo , Luo Ruibang , Patterson Jordan , Liu Shanlin , Huang Weihua , He Guangzhu , Gu Shengchang , Li Shengkang , Zhou Xin , Lam Tak-Wah , Li Yingrui , Xu Xun , Wong Gane Ka-Shu , Wang Jun
Published: February 2014

Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge.

Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution.

Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/.

Contact:  xieyl@genomics.cn or bgi-soap@googlegroups.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms
Authors: Guney Emre , Garcia-Garcia Javier , Oliva Baldo
Published: February 2014

Summary: Determining genetic factors underlying various phenotypes is hindered by the involvement of multiple genes acting cooperatively. Over the past years, disease–gene prioritization has been central to identify genes implicated in human disorders. Special attention has been paid on using physical interactions between the proteins encoded by the genes to link them with diseases. Such methods exploit the guilt-by-association principle in the protein interaction network to uncover novel disease–gene associations. These methods rely on the proximity of a gene in the network to the genes associated with a phenotype and require a set of initial associations. Here, we present GUILDify, an easy-to-use web server for the phenotypic characterization of genes. GUILDify offers a prioritization approach based on the protein–protein interaction network where the initial phenotype–gene associations are retrieved via free text search on biological databases. GUILDify web server does not restrict the prioritization to any predefined phenotype, supports multiple species and accepts user-specified genes. It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies.

Availability and implementation: Available online at http://sbi.imim.es/GUILDify.php

Contact:  baldo.oliva@upf.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content
Authors: Pyatkov Maxim I. , Pankratov Anton N.
Published: February 2014

Summary: Structural analysis of long DNA fragments, including chromosomes and whole genomes, is one of the main challenges in modern bioinformatics. Here, we propose an original approach based on spectral methods and its implementation called SBARS (Spectral-Based Approach for Repeats Search. The main idea of our approach is that repeated DNA structures are recognized not within the nucleotide sequence directly but within the function derived from this sequence. This allows us to investigate nucleotide sequences on different scales and decrease time complexity for dotplot creation down to .

Availability and implementation: Pre-compiled versions for Windows and Linux and documentation are available at http://mpyatkov.github.com/sbars/.

Contact:  mpyatkov@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
SKINK: a web server for string kernel based kink prediction in α-helices
Authors: Seifert Tim , Lund Andreas , Kneissl Benny , Mueller Sabine C. , Tautermann Christofer S. , Hildebrandt Andreas
Published: February 2014

Motivation: The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. Here, we present a new web server, called SKINK, for string kernel based kink prediction. Extending our previous study, we also annotate the most probable kink position in a given α-helix sequence.

Availability and implementation: The SKINK web server is freely accessible at http://biows-inf.zdv.uni-mainz.de/skink. Moreover, SKINK is a module of the BALL software, also freely available at www.ballview.org.

Contact:  benny.kneissl@roche.com
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data
Authors: Hung Ling-Hong , Samudrala Ram
Published: February 2014

Motivation: fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project.

Results: fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco.

Availability and implementation: fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster)

Contact:  lhhung@compbio.washington.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
ADaCGH2: parallelized analysis of (big) CNA data
Authors: Diaz-Uriarte Ramon
Published: February 2014

Motivation: Studies of genomic DNA copy number alteration can deal with datasets with several million probes and thousands of subjects. Analyzing these data with currently available software (e.g. as available from BioConductor) can be extremely slow and may not be feasible because of memory requirements.

Results: We have developed a BioConductor package, ADaCGH2, that parallelizes the main segmentation algorithms (using forking on multicore computers or parallelization via message passing interface, etc., in clusters of computers) and uses ff objects for reading and data storage. We show examples of data with 6 million probes per array; we can analyze data that would otherwise not fit in memory, and compared with the non-parallelized versions we can achieve speedups of 25–40 times on a 64-cores machine.

Availability and implementation: ADaCGH2 is an R package available from BioConductor. Version 2.3.11 or higher is available from the development branch: http://www.bioconductor.org/packages/devel/bioc/html/ADaCGH2.html.

Contact:  ramon.diaz@iib.uam.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Characterizing foodweb structure to identify potential ecosystem effects of fishing in the Ross Sea, Antarctica
Authors: Pinkerton Matthew H. , Bradford-Grieve Janet M.
Published: February 2014

The potential ecosystem effects of fishing for Antarctic toothfish (Dissostichus mawsoni) in the Ross Sea region were investigated. Mixed trophic impact analysis was applied to a model of the Ross Sea foodweb and used to calculate the relative trophic importances of species and trophic groups in the system. The trophic impact of toothfish on medium-sized demersal fish was identified as the strongest top-down interaction in the system based on multiple-step analysis. This suggests a potential for a strong predation-release effect on some piscine prey of toothfish (especially grenadiers and ice-fish on the Ross Sea slope). However, Antarctic toothfish had moderate trophic importance in the Ross Sea foodweb as a whole, and the analysis did not support the hypothesis that changes to toothfish will cascade through the ecosystem by simple trophic effects. Because of limitations of this kind of analysis, cascading effects on the Ross Sea ecosystem due to changes in the abundance of toothfish cannot be ruled out, but for such changes to occur a mechanism other than simple trophic interactions is likely to be involved. Trophic importances were highest in the middle of the foodweb where silverfish and krill are known to have a key role in ecosystem structure and function. The six groups with the highest indices of trophic importance were (in decreasing order): phytoplankton, mesozooplankton, Antarctic silverfish, small demersal fish, Antarctic krill and cephalopods. Crystal krill and small pelagic fish also had high trophic importance in some analyses. Strengths and limitations of this kind of analysis are presented. In particular, it is noted that the analysis only considers trophic interactions at the spatial, temporal and ecological scale of the whole Ross Sea shelf and slope area, averaged over a typical year and in 35 trophic groups. Interference and density-dependent effects were not included in this analysis. Effects at smaller spatial and temporal scales, and effects concerning only parts of populations, were not resolved by the analysis, and this is likely to underestimate the potential risks of fishing to Weddell seals and type-C killer whales.
Embedding stock assessment within an integrated hierarchical Bayesian life cycle modelling framework: an application to Atlantic salmon in the Northeast Atlantic
Authors: Massiot-Granier Félix , Prévost Etienne , Chaput Gérald , Potter Ted , Smith Gordon , White Jonathan , Mäntyniemi Samu , Rivot Etienne
Published: February 2014

We developed a hierarchical Bayesian integrated life cycle model for Atlantic salmon that improves on the stock assessment approach currently used by ICES and provides some interesting insights about the population dynamics of a stock assemblage. The model is applied to the salmon stocks in eastern Scotland. It assimilates a 40-year (1971–2010) time-series of data compiled by ICES, including the catches in the distant water fisheries at Faroes and West Greenland and estimates of returning fish abundance. Our model offers major improvements in terms of statistical methodology for A. salmon stock assessment. Uncertainty about inferences is readily quantified in the form of Bayesian posterior distributions for parameters and abundance at all life stages, and the model could be adapted to provide projections based on the uncertainty derived from the estimation phase. The approach offers flexibility to improve the ecological realism of the model. It allows the introduction of density dependence in the egg-to-smolt transition, which is not considered in the current ICES assessment method. The results show that this modifies the inferences on the temporal dynamics of the post-smolt marine survival. In particular, the overall decrease in the marine survival between 1971 and 2010 and the sharp decline around 1988–1990 are dampened when density dependence is considered. The return rates of smolts as two-sea-winter (2SW) fish has declined in a higher proportion than return rates as one-sea-winter (1SW) fish. Our results indicate that this can be explained either by an increase in the proportion maturing as 1SW fish or by an increase in the mortality rate at sea of 2SW fish, but the data used in our analyses do not allow the likelihood of these two hypotheses to be gauged.