bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of magnetic amplification by flow constraints in turbulent liquid sodium
Authors: Nornberg M. D. , Taylor N. Z. , Forest C. B. , Rahbarnia K. , Kaplan E.
Published: May 2014

Direct measurements of the vector turbulent emf in a driven two-vortex flow of liquid sodium were performed in the Madison Dynamo Experiment [K. Rahbarnia et al., Astrophys. J. 759, 80 (2012)]. The measured turbulent emf is anti-parallel with the mean current and is almost entirely described by an enhanced resistivity, which increases the threshold for a kinematic dynamo. We have demonstrated that this enhanced resistivity can be mitigated by eliminating the largest-scale eddies through the introduction of baffles. By tailoring the flow to reduce large-scale components and control the helical pitch, we have reduced the power required to drive the impellers, doubled the magnetic flux generated by differential rotation, and increased the decay time of externally applied magnetic fields. Despite these improvements, the flows remain sub-critical to the dynamo instability due to the reemergence of turbulent fluctuations at high flow speeds.
Enhanced photovoltaic performance of nanocrystalline CdTe/ZnO solar cells using sol-gel ZnO and positive bias treatment
Authors: MacDonald B. I. , Della Gaspera E. , Watkins S. E. , Mulvaney P. , Jasieniak J. J.
Published: May 2014

The effect of doping and porosity of the n-type ZnO layer on the performance of solution-processed, sintered p-CdTe/n-ZnO nanocrystal photovoltaic (PV) devices is investigated. Amorphous sol-gel ZnO is found to be the best candidate with overall energy conversion efficiencies above 8% obtained if the ZnO is also indium doped. We demonstrate that when such PV devices are left under forward bias (in dark or light), the device efficiency values are raised to at least 9.8%, due to a substantially increased open-circuit voltage and fill-factor. This drastic enhancement is attributed to improved band alignment at the ITO/CdTe interface. The forward-bias treatment is slowly reversed over a period of days to weeks on standing under open circuit conditions, but is readily restored with further voltage treatment. The moderate processing conditions and high efficiency of such devices demonstrate that nanocrystal-based systems are a promising technology for photovoltaics.
High-resolution X-ray diffraction analysis of AlxGa1−xN/InxGa1−xN/GaN on sapphire multilayer structures: Theoretical, simulations, and experimental observations
Authors: Jana Sanjay Kumar , Mukhopadhyay Partha , Ghosh Saptarsi , Kabi Sanjib , Bag Ankush , Kumar Rahul , Biswas D.
Published: May 2014

The work presents a comparative study on the effects of In incorporation in the channel layer of AlGaN/GaN type-II heterostructures grown on c-plane sapphire by Plasma Assisted Molecular Beam Epitaxy. The structural characterizations of these samples were performed by High-Resolution X-Ray Diffraction (HRXRD), X-ray Reflectivity (XRR), Field Emission Scanning Electron Microscopy, and High Resolution Transmission Electron Microscopy. The two-dimensional electron gas in the AlGaN/GaN and AlGaN/InGaN interface was analyzed by electrochemical capacitance voltage and compared with theoretical results based on self-consistent solution of Schördinger–Poisson equations. The carrier profile shows enhanced confinement in InGaN channel (1.4393 × 1013 cm−2 compared to 1.096 × 1013 cm−2 in GaN). On the basis of HRXRD measurements, the stress-strain of the layers was examined. The c- and a-lattice parameters of the epilayers as well as in-plane and out-of plane strains were determined from the ω-2θ for symmetric scan and ω-Xθ (X represents the coupling coefficient) for asymmetric scan. Strain, tilt, and correlation lengths were calculated from Williamson–Hall plots, whereas stress was examined from modified plot of the same data assuming Uniform Stress Deformation Model. Moreover, the twist angle was measured from skew symmetric scan of (102), (103), and (105) plane along with (002) symmetric plane. The composition and strain/relaxation state of the epilayers were observed in detail by reciprocal space mapping (RSM). The symmetric (002) triple axis RSM and asymmetric (105 and 114) double axis RSM of grazing incidence and exit geometry were carried out on each sample. The defect density was measured from HRXRD curves of skew symmetric (002) and (102) reflection plane. The Al and In mole fraction and strain states of the layers were calculated by fitting the experimental curves with computer simulations and compared with theoretical findings based on elastic theory. The thicknesses of the layers and roughness of the interfaces were measured from simulation of the nominal structure by fitting with XRR experimental curves. The HRXRD measured thicknesses of the layers were further confirmed by cross sectional electron micrographs.
Nano-crystallization and magnetic mechanisms of Fe85Si2B8P4Cu1 amorphous alloy by ab initio molecular dynamics simulation
Authors: Wang Yaocen , Takeuchi Akira , Makino Akihiro , Liang Yunye , Kawazoe Yoshiyuki
Published: May 2014

Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe85Si2B8P4Cu1 amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.
Temperature dependencies of hydrogen-induced blistering of thin film multilayers
Authors: Kuznetsov A. S. , Gleeson M. A. , Bijkerk F.
Published: May 2014

We report on the influence of sample temperature on the development of hydrogen-induced blisters in Mo/Si thin-film multilayers. In general, the areal number density of blisters decreases with increasing exposure temperature, whereas individual blister size increases with exposure temperatures up to ∼200 °C but decreases thereafter. Comparison as a function of sample temperature is made between exposures to a flux containing both hydrogen ions and neutrals and one containing only neutrals. In the case of the neutral-only flux, blistering is observed for exposure temperatures ≥90 °C. The inclusion of ions promotes blister formation at <90 °C, while retarding their growth at higher temperatures. In general, ion-induced effects become less evident with increasing exposure temperature. At 200 °C, the main effect discernable is reduced blister size as compared with the equivalent neutral-only exposure. The temperature during exposure is a much stronger determinant of the blistering outcome than either pre- or post-annealing of the sample. The trends observed for neutral-only exposures are attributed to competing effects of defect density thermal equilibration and H-atom induced modification of the Si layers. Energetic ions modify the blistering via (temperature dependent) enhancement of H-mobility and re-crystallization of amorphous Si.
Optical gain characteristics in Al-rich AlGaN/AlN quantum wells
Authors: Oto Takao , Banal Ryan G. , Funato Mitsuru , Kawakami Yoichi
Published: May 2014

The optical gain characteristics of Al-rich AlGaN/AlN quantum wells (QWs) were assessed by the variable stripe length method at room temperature. An Al0.79Ga0.21N/AlN QW with a well width of 5 nm had a large optical gain of 140 cm−1. Increasing the excitation length induced a redshift due to the gain consumption and the consequent saturation of the amplified spontaneous emission. Moreover, a change in the dominant gain polarization with Al composition, which was attributed to switching of the valence band ordering of strained AlGaN/AlN QWs at Al compositions of ∼0.8, was experimentally demonstrated.
Ultra-sensitive graphene Hall elements
Authors: Huang Le , Zhang Zhiyong , Chen Bingyan , Ma Xiaomeng , Zhong Hua , Peng Lian-Mao
Published: May 2014

Hall elements were fabricated based on high quality chemical vapor deposition grown graphene, and their performance limit was explored. The as-fabricated graphene Hall element exhibits current-related sensitivity of up to 2093 V/AT under 200 μA, and magnetic resolution of around 1 mG/Hz0.5 at 3 kHz. This ultrahigh sensitivity and resolution stem from high carrier mobility, small Dirac point voltage of 3 V, and low carrier density of about 3 × 1011 cm−2 in graphene device. The current sensitivity is found to decrease with increasing current bias at large bias, and this phenomenon is attributed to the drain induced Dirac point shift effect in graphene channel.
Mechanism of force mode dip-pen nanolithography
Authors: Yang Haijun , Xie Hui , Wu Haixia , Rong Weibin , Sun Lining , Guo Shouwu , Wang Huabin
Published: May 2014

In this work, the underlying mechanism of the force mode dip-pen nanolithography (FMDPN) is investigated in depth by analyzing force curves, tapping mode deflection signals, and “Z-scan” voltage variations during the FMDPN. The operation parameters including the relative “trigger threshold” and “surface delay” parameters are vital to control the loading force and dwell time for ink deposition during FMDPN. A model is also developed to simulate the interactions between the atomic force microscope tip and soft substrate during FMDPN, and verified by its good performance in fitting our experimental data.
Improvement of graphene–metal contact resistance by introducing edge contacts at graphene under metal
Authors: Min Song Seung , Yong Kim Taek , Jae Sul One , Cheol Shin Woo , Jin Cho Byung
Published: May 2014

We report an alternative approach to lower contact resistance and extend charge transfer length by forming graphene antidot arrays under metal electrode to introduce edge contact of graphene. The edge contact resistivity of ∼2.2 × 10−9 Ω·cm2 is experimentally estimated, based on the experiment and one-dimensional equivalent circuit model, and the result agrees well with the previous theoretical report. The proposed contact module structure can open alternative ways to overcome the poor contact performance and the current crowding effect at the metal-graphene contact.
Characterization of radial turbulent fluxes in the Santander linear plasma machine
Authors: Mier J. A. , Sánchez R. , Newman D. E. , Castellanos O. F. , Anabitarte E. , Sentíes J. M. , van Milligen B. Ph.
Published: May 2014

It is shown that the statistical and correlation properties of the local turbulent flux measured at different radial locations of the cold, weakly ionized plasmas inside the Santander Linear Plasma Machine [Castellanos et al., Plasma Phys. Control. Fusion 47, 2067 (2005)] are consistent with diffusive-like transport dynamics. This is in contrast to the dynamical behavior inferred from similar measurements taken in hotter, fully ionized tokamak and stellarator edge plasmas, in which long-term correlations and other features characteristic of complex, non-diffusive transport dynamics have been reported in the past. These results may shed some light on a recent controversy regarding the possible universality of the dynamics of turbulent transport in magnetized plasmas.
An ionic liquid-gated polymer thin film transistor with exceptionally low “on” resistance
Authors: Algarni Saud A. , Althagafi Talal M. , Smith Patrick J. , Grell Martin
Published: May 2014

We report the ionic liquid (IL) gating of a solution processed semiconducting polymer, poly(2,5-bis(3-hexadecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). IL gating relies on the poor solubility of PBTTT, which requires hot chlorinated benzenes for solution processing. PBTTT, thus, resists dissolution even in IL, which otherwise rapidly dissolves semiconducting polymers. The resulting organic thin film transistors (OTFTs) display low threshold, very high carrier mobility (>3 cm2/Vs), and deliver high currents (in the order of 1 mA) at low operational voltages. Such OTFTs are interesting both practically, for the addressing of current-driven devices (e.g., organic LEDs), and for the study of charge transport in semiconducting polymers at very high carrier density.
Graphene as a surfactant for metal growth on solid surfaces: Fe on graphene/SiC(0001)
Authors: Wang Zhou-jun , Dong Aiyi , Wei Mingming , Fu Qiang , Bao Xinhe
Published: May 2014

X-ray photoelectron spectroscopic and scanning tunneling microscopic results demonstrate that annealing of Fe/carbon-rich 6H-SiC(0001) surface between 650 and 750 °C leads to Fe intercalation under the surface carbon layer. Accompanied with the metal intercalation, the carbon nanomesh surface was transformed into a graphene surface. Moreover, the formed graphene layers always float out to the topmost surface even after deposition of more than 10 monolayer Fe, acting as a surfactant. Using graphene as the surfactant may not only promote the 2D growth but also can improve the film performance considering that graphene is stable and robust.
Phase-field modeling of switchable diode-like current-voltage characteristics in ferroelectric BaTiO3
Authors: Cao Y. , Shen J. , Randall C. A. , Chen L. Q.
Published: May 2014

A self-consistent model has been proposed to study the switchable current-voltage (I-V) characteristics in Cu/BaTiO3/Cu sandwiched structure combining the phase-field model of ferroelectric domains and diffusion equations for ionic/electronic transport. The electrochemical transport equations and Ginzburg-Landau equations are solved using the Chebyshev collocation algorithm. We considered a single parallel plate capacitor configuration which consists of a single layer BaTiO3 containing a single tetragonal domain orientated normal to the plate electrodes (Cu) and is subject to a sweep of ac bias from −1.0 to 1.0 V at 25 °C. Our simulation clearly shows rectifying I-V response with rectification ratios amount to 102. The diode characteristics are switchable with an even larger rectification ratio after the polarization direction is flipped. The effects of interfacial polarization charge, dopant concentration, and dielectric constant on current responses were investigated. The switchable I-V behavior is attributed to the polarization bound charges that modulate the bulk conduction.
Domain motion modeling for hysteresis in piezoceramic materials under mechanical loading
Authors: Domenjoud Mathieu , Bustillo Julien , Lethiecq Marc
Published: May 2014

The purpose of this study is to model domain motions of piezoceramic materials under mechanical loading to reproduce their hysteretic behaviors. Evolutions of remanent strain and remanent polarization are described by bridging the characteristics of microscopic domain distribution into macroscopic behaviors. Taking into account hysteretic behavior in unpoled piezoceramics, this model calculates electric displacement and longitudinal strain as a function of uniaxial mechanical field. Good quality of the formulation is demonstrated through comparison with experimental data. In addition, results confirm our choice of one single domain evolution law to describe domain motion in piezoceramics under mechanical and electrical loading.
Synthesis, characterization and electrostatic properties of WS2 nanostructures
Authors: Fan Yinping , Hao Guolin , Luo Siwei , Qi Xiang , Li Hongxing , Ren Long , Zhong Jianxin
Published: May 2014

We report the direct growth of atomically thin WS2 nanoplates and nanofilms on the SiO2/Si (300 nm) substrate by vapor phase deposition method without any catalyst. The WS2 nanostructures were systematically characterized by optical microscopy, scanning electron microscopy, Raman microscopy and atomic force microscopy. We found that growth time and growth temperature play important roles in the morphology of WS2 nanostructures. Moreover, by using Kelvin probe force microscopy, we found that the WS2 nanoplates exhibit uniform surface and charge distributions less than 10 mV fluctuations. Our results may apply to the study of other transition metal dichalcogenides by vapor phase deposition method.
Effects of Stone-Wales and vacancy defects in atomic-scale friction on defective graphite
Authors: Sun Xiao-Yu , Wu RunNi , Xia Re , Chu Xi-Hua , Xu Yuan-Jie
Published: May 2014

Graphite is an excellent solid lubricant for surface coating, but its performance is significantly weakened by the vacancy or Stone-Wales (SW) defect. This study uses molecular dynamics simulations to explore the frictional behavior of a diamond tip sliding over a graphite which contains a single defect or stacked defects. Our results suggest that the friction on defective graphite shows a strong dependence on defect location and type. The 5-7-7-5 structure of SW defect results in an effectively negative slope of friction. For defective graphite containing a defect in the surface, adding a single vacancy in the interior layer will decrease the friction coefficients, while setting a SW defect in the interior layer may increase the friction coefficients. Our obtained results may provide useful information for understanding the atomic-scale friction properties of defective graphite.
High frequency resonant waveguide grating imager for assessing drug-induced cardiotoxicity
Authors: Ferrie Ann M. , Wu Qi , Deichmann Oberon D. , Fang Ye
Published: May 2014

We report a high-frequency resonant waveguide grating imager for assessing compound-induced cardiotoxicity. The imager sweeps the wavelength range from 823 nm to 838 nm every 3 s to identify and monitor compound-induced shifts in resonance wavelength and then switch to the intensity-imaging mode to detect the beating rhythm and proarrhythmic effects of compounds on induced pluripotent stem cell-derived cardiomyocytes. This opens possibility to study cardiovascular biology and compound-induced cardiotoxicity.
Low-energy equivalence between periodically gated graphene structures and bilayer-like gated graphene
Authors: Zubarev A. , Dragoman D.
Published: May 2014

The linear dispersion law of graphene is modified in periodically gated structures, the charge carriers acquiring a finite effective mass. We show that, in the low energy approximation, periodically gated graphene structures are equivalent, from the point of view of charge transport, to a bilayer-like gated graphene region, i.e., to a material that satisfies the same equation as bilayer graphene but with a potentially different effective mass. The hypothetic bilayer-like material becomes identical to the genuine bilayer graphene if its effective mass matches that of the latter. The effective mass, potential energy, and width of bilayer-like graphene can be identified by imposing the condition that the transmission coefficient through the bilayer-like region, computed using a transfer matrix approach, is identical to that through the periodically gated graphene structure.
Adverb use and language proficiency in young learners’ writing
Authors: Pérez-Paredes Pascual , Sánchez-Tornel María
Published: May 2014

Our research examines the use of general adverbs by learners across grades 5, 6, 9 and 10 in the International Corpus of Crosslinguistic Interlanguage (ICCI) by looking at whether this use increases with age. For our research we use data from the Polish, Spanish and Chinese components in the ICCI, in particular, those from the “food” and “money” topics. Our results show that general adverbs are more widely used as age increases. Statistically significant differences were found between grade 6 and 10 learners across all three L1 groups in terms of the frequency of use of general adverbs, which suggests that 10-graders integrate adverbs in their discourse in ways that differ from those in previous years. This study, together with Pérez-Paredes & Díez-Bedmar’s (2012), suggests that learners below grade 9 are more unlikely to use adverbs.
Pragmatic Competence and Relevance
Authors: Ifantidou Elly
Published: May 2014

This book probes into under-researched issues in L2 pragmatics. Firstly, pragmatic competence, pragmatic awareness and metapragmatic awareness are re-defined and clearly distinguished on theoretical grounds. Secondly, pragmatic competence and its manifestations are evaluated on empirical grounds by distinct criteria and validated testing measures. More importantly, genuine pragmatic inference is elicited in contexts of online interpretation where figurative speech plays a central role. Genre-specific discourse which occurs in editorials and news reports serves as a natural testbed for examining the role of advanced mind-reading abilities in developing pragmatic competence. Sperber and Wilson’s relevance theory accommodates the findings of empirical assessment and yields new insights in the cognitive procedures activated during interpretation. The comprehensive theoretical and methodological treatment of pragmatic competence makes this book of interest to researchers and students in pragmatics, L2 theory and applications, genre studies, and to those concerned with the cognitive underpinnings of communication in L2.
A “rape victim” by any other name
Authors: Hockett Jericho M. , McGraw Lora K. , Saucier Donald A.
Published: May 2014

Our purpose in this chapter was to examine the power in and behind two labels – “rape victim” and “rape survivor” – commonly applied to women who have been raped, especially in the psychological literature. Thus, we examined past theory and research pertaining to power, language, and the language of rape, including evidence regarding the self-conceptualizations of women who have been raped. We then reported four recent studies on differences in individuals’ perceptions of women who are labeled as “rape victims” versus “rape survivors”. Finally, we discussed the intrapersonal, social, and political power of rape language, and offered suggestions for application and future research.
South Tyrol's changing political system: from dissociative on the road to associative conflict resolution
Authors: Pallaver Günther
Published: May 2014

South Tyrol (Italy), with its three officially recognized language groups (Germans, Italians and Ladins), is a successful model of how a minority problem can be solved. It is based upon the principle of dissociative conflict resolution, which means separating the language groups as much as possible between themselves, as well as the principle of consociational democracy, which focuses primarily on the cooperation between the language groups’ elites. In the last few years it has been observed that while the institutional frame has not changed, society has, thereby starting to undermine the existing political and institutional system from below. This concerns mainly the ethnic division, which is being questioned more and more by civil society, as well as aspects of cooperation between the elites. As a consequence of this process, South Tyrol's autonomy is moving toward further integration, with the latter again translating into strengthening the two factors of territoriality and identity.
Pyrosequencing-based analysis of bacterial community and metabolites profiles in Korean traditional seafood fermentation: a flatfish-fermented seafood
Authors: Jung Jaejoon , Lee Se Hee , Jin Hyun Mi , Jeon Che Ok , Park Woojun
Published: May 2014

Bacterial community and metabolites were analyzed in a flatfish jeotgal, a Korean fermented seafood. Inverse relationship of pH and 16S rRNA gene copy number was identified during fermentation. Lactobacillus was the predominant bacterial genus. Increase of Firmicutes was a common characteristic shared by other fermented seafood. Fructose, glucose, and maltose were the major metabolites.
Construction of a novel secretion expression system guided by native signal peptide of PhoD in Zymomonas mobilis
Authors: Wu Bo , He Ming-Xiong , Feng Hong , Shui Zong-Xia , Tang Xiao-Yu , Hu Qi-Chun , Zhang Yi-Zheng
Published: May 2014

In the current study, three native signal peptides (SPs) from PhoC, PhoD, and ZMO0331were investigated and compared to construct novel secretion expression systems in Zymomonas mobilis. The secretion expression of target protein, α-amylase from Bacillus amyloliquefaciens (BAA), guided by PhoD’s SP resulted in more hydrolysis of starch than that by the other two SPs. Extracellular and intracellular α-amylase activities of the strain containing PhoD’s SP were also higher than the other two strains containing PhoC or ZMO0331’s SP. In addition, the evidence by alcohol dehydrogenase activity assay further confirmed that the starch hydrolysis was resulted from the secretion expression of BAA rather than the breakage of cells. Our results indicated that the SP of PhoD is able to serve as a promising candidate to assist secretion expression of heterogeneous genes in Z. mobilis. This will contribute to development of engineered Z. mobilis strains converting starch into ethanol.
Transnational feminist solidarity and lessons from the 2011 protests in Tahrir Square
Authors: Scholz Sally J.
Published: May 2014

Transnational feminist solidarity can be and has been very effective at bringing about social change in local and regional contexts. Transnational feminist activists, however, must be attentive to cultural differences in the means and methods of protest employed to challenge unjust or oppressive social and political conditions. In this article, I offer a discussion of some of the key theoretical elements of a transnational feminist solidarity. I then use the protests in Tahrir Square in 2011 to problematize transnational feminist solidarity. This exercise reveals both the power of transnational alliances and some of the obstacles – cultural, political, and gender based – that must be addressed by feminist transnational solidarity efforts.
Asymptotics of orbits of a Kolmogorov type planar vector field with a fixed Newton polygon
Authors: Berezovskaya F.
Published: May 2014

Using the Newton polygon technique we show that the orbits of a Kolmogorov type planar vector field, consisting of a finite sum of power terms, have power asymptotics while tending to the equilibria on the axes and on the boundary of the Poincaré sphere.
PhenoNet: identification of key networks associated with disease phenotype
Authors: Ben-Hamo Rotem , Gidoni Moriah , Efroni Sol
Published: May 2014

Motivation: At the core of transcriptome analyses of cancer is a challenge to detect molecular differences affiliated with disease phenotypes. This approach has led to remarkable progress in identifying molecular signatures and in stratifying patients into clinical groups. Yet, despite this progress, many of the identified signatures are not robust enough to be clinically used and not consistent enough to provide a follow-up on molecular mechanisms.

Results: To address these issues, we introduce PhenoNet, a novel algorithm for the identification of pathways and networks associated with different phenotypes. PhenoNet uses two types of input data: gene expression data (RMA, RPKM, FPKM, etc.) and phenotypic information, and integrates these data with curated pathways and protein–protein interaction information. Comprehensive iterations across all possible pathways and subnetworks result in the identification of key pathways or subnetworks that distinguish between the two phenotypes.

Availability and implementation: Matlab code is available upon request.

Contact:  sol.efroni@biu.ac.il

Supplementary information:  Supplementary Data are available at Bioinformatics online.
RNASeqGUI: a GUI for analysing RNA-Seq data
Authors: Russo Francesco , Angelini Claudia
Published: May 2014

Summary: We present RNASeqGUI R package, a graphical user interface (GUI) for the identification of differentially expressed genes across multiple biological conditions. This R package includes some well-known RNA-Seq tools, available at www.bioconductor.org. RNASeqGUI package is not just a collection of some known methods and functions, but it is designed to guide the user during the entire analysis process. RNASeqGUI package is mainly addressed to those users who have little experience with command-line software. Therefore, thanks to RNASeqGUI, they can conduct analogous analyses using this simple graphical interface. Moreover, RNASeqGUI is also helpful for those who are expert R-users because it speeds up the usage of the included RNASeq methods drastically.

Availability and implementation: RNASeqGUI package needs the RGTK2 graphical library to run. This package is open source and is freely available under General Public License at http://bioinfo.na.iac.cnr.it/RNASeqGUI/Download.

Contact:  f.russo@na.iac.cnr.it

Supplementary information:  Supplementary Data are available at Bioinformatics online.
fastGapFill: efficient gap filling in metabolic networks
Authors: Thiele Ines , Vlassis Nikos , Fleming Ronan M. T.
Published: May 2014

Motivation: Genome-scale metabolic reconstructions summarize current knowledge about a target organism in a structured manner and as such highlight missing information. Such gaps can be filled algorithmically. Scalability limitations of available algorithms for gap filling hinder their application to compartmentalized reconstructions.

Results: We present fastGapFill, a computationally efficient tractable extension to the COBRA toolbox that permits the identification of candidate missing knowledge from a universal biochemical reaction database (e.g. Kyoto Encyclopedia of Genes and Genomes) for a given (compartmentalized) metabolic reconstruction. The stoichiometric consistency of the universal reaction database and of the metabolic reconstruction can be tested for permitting the computation of biologically more relevant solutions. We demonstrate the efficiency and scalability of fastGapFill on a range of metabolic reconstructions.

Availability and implementation:   fastGapFill is freely available from http://thielelab.eu.

Contact:  ines.thiele@uni.lu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Estimating effect of environmental contaminants on women's subfecundity for the MoBa study data with an outcome-dependent sampling scheme
Authors: Ding Jieli , Zhou Haibo , Liu Yanyan , Cai Jianwen , Longnecker Matthew P.
Published: May 2014

Motivated by the need from our on-going environmental study in the Norwegian Mother and Child Cohort (MoBa) study, we consider an outcome-dependent sampling (ODS) scheme for failure-time data with censoring. Like the case-cohort design, the ODS design enriches the observed sample by selectively including certain failure subjects. We present an estimated maximum semiparametric empirical likelihood estimation (EMSELE) under the proportional hazards model framework. The asymptotic properties of the proposed estimator were derived. Simulation studies were conducted to evaluate the small-sample performance of our proposed method. Our analyses show that the proposed estimator and design is more efficient than the current default approach and other competing approaches. Applying the proposed approach with the data set from the MoBa study, we found a significant effect of an environmental contaminant on fecundability.
Varying Responses to Common Shocks and Complex Cross-Sectional Dependence: Dynamic Multilevel Modeling with Multifactor Error Structures for Time-Series Cross-Sectional Data
Authors: Pang Xun
Published: May 2014

Multifactor error structures utilize factor analysis to deal with complex cross-sectional dependence in Time-Series Cross-Sectional data caused by cross-level interactions. The multifactor error structure specification is a generalization of the fixed-effects model. This article extends the existing multifactor error models from panel econometrics to multilevel modeling, from linear setups to generalized linear models with the probit and logistic links, and from assuming serial independence to modeling the error dynamics with an autoregressive process. I develop Markov Chain Monte Carlo algorithms mixed with a rejection sampling scheme to estimate the multilevel multifactor error structure model with apth-order autoregressive process in linear, probit, and logistic specifications. I conduct several Monte Carlo studies to compare the performance of alternative specifications and approaches with varying degrees of data complication and different sample sizes. The Monte Carlo studies provide guidance on when and how to apply the proposed model. An empirical application sovereign default demonstrates how the proposed approach can accommodate a complex pattern of cross-sectional dependence and helps answer research questions related to units' sensitivity or vulnerability to systemic shocks.
Finance and the Preservation of Wealth
*
Authors: Gennaioli Nicola , Shleifer Andrei , Vishny Robert
Published: May 2014

We introduce the model of asset management developed in Gennaioli, Shleifer, and Vishny (“Money Doctors,” Journal of Finance , forthcoming 2015) into a Solow-style neoclassical growth model with diminishing returns to capital. Savers rely on trusted intermediaries to manage their wealth (claims on capital stock), who can charge fees above costs to trusting investors. In this model, the ratio of financial income to GDP increases with the ratio of aggregate wealth to GDP. Both rise along the convergence path to steady state growth. We examine several further implications of the model for management fees, unit costs of finance, and the consequences of shocks to trust and to the capital stock.
Synergistic effect of fluconazole and doxycycline against Candida albicans biofilms resulting from calcium fluctuation and downregulation of fluconazole-inducible efflux pump gene overexpression
Authors: Gao Yuan , Li Hui , Liu Shuyuan , Zhang Xiang , Sun Shujuan
Published: May 2014

Candida albicans biofilms are intrinsically resistant to antimicrobial agents. Previous work demonstrated that the antifungal activity of fluconazole against C. albicans biofilms is notably enhanced by doxycycline. In order to explore the synergistic mechanism of fluconazole and doxycycline, we investigated the changes of efflux pump gene expression, intracellular calcium concentration and cell cycle distribution after drug intervention in this study. The expression levels of CDR1, CDR2 and MDR1 were determined by real-time PCR, and the results showed that fluconazole alone could stimulate the high expression of CDR1, CDR2 and MDR1, and the combination of doxycycline and fluconazole downregulated the gene overexpression induced by fluconazole. Intracellular calcium concentration was determined using Fluo-3/AM by observing the fluorescence with flow cytometry. A calcium fluctuation, which started 4 h and peaked 8 h after the treatment with fluconazole, was observed. The combined drugs also initiated a calcium fluctuation after 4 h treatment and showed a peak at 16 h, and the peak was higher than that stimulated by fluconazole alone. The cell cycle was measured using flow cytometry. Fluconazole alone and the combined drugs both induced a reduction in the percentages of S-phase cells and an elevation in the percentages of cells in the G2/M phase. The results of this research showed that the synergism of fluconazole and doxycycline against C. albicans biofilms is associated with blockade of the efflux pump genes CDR1, CDR2 and MDR1, and stimulation of high intracellular calcium concentration. The findings of this study are of great significance in the search for new antifungal mechanisms.
The Putative E3 Ubiquitin Ligase ECERIFERUM9 Regulates Abscisic Acid Biosynthesis and Response during Seed Germination and Postgermination Growth in Arabidopsis
Authors: Zhao Huayan , Zhang Huoming , Cui Peng , Ding Feng , Wang Guangchao , Li Rongjun , Jenks Matthew A. , Lü Shiyou , Xiong Liming
Published: May 2014

The ECERIFERUM9 (CER9) gene encodes a putative E3 ubiquitin ligase that functions in cuticle biosynthesis and the maintenance of plant water status. Here, we found that CER9 is also involved in abscisic acid (ABA) signaling in seeds and young seedlings of Arabidopsis (Arabidopsis thaliana). The germinated embryos of the mutants exhibited enhanced sensitivity to ABA during the transition from reversible dormancy to determinate seedling growth. Expression of the CER9 gene is closely related to ABA levels and displays a similar pattern to that of ABSCISIC ACID-INSENSITIVE5 (ABI5), which encodes a positive regulator of ABA responses in seeds. cer9 mutant seeds exhibited delayed germination that is independent of seed coat permeability. Quantitative proteomic analyses showed that cer9 seeds had a protein profile similar to that of the wild type treated with ABA. Transcriptomics analyses revealed that genes involved in ABA biosynthesis or signaling pathways were differentially regulated in cer9 seeds. Consistent with this, high levels of ABA were detected in dry seeds of cer9. Blocking ABA biosynthesis by fluridone treatment or by combining an ABA-deficient mutation with cer9 attenuated the phenotypes of cer9. Whereas introduction of the abi1-1, abi3-1, or abi4-103 mutation could completely eliminate the ABA hypersensitivity of cer9, introduction of abi5 resulted only in partial suppression. These results indicate that CER9 is a novel negative regulator of ABA biosynthesis and the ABA signaling pathway during seed germination.
Connecting heterogeneous single slip to diffraction peak evolution in high-energy monochromatic X-ray experiments
Authors: Pagan Darren C. , Miller Matthew P.
Published: May 2014

A forward modeling diffraction framework is introduced and employed to identify slip system activity in high-energy diffraction microscopy (HEDM) experiments. In the framework, diffraction simulations are conducted on virtual mosaic crystals with orientation gradients consistent with Nye's model of heterogeneous single slip. Simulated diffraction peaks are then compared against experimental measurements to identify slip system activity. Simulation results compared against diffraction data measuredin situfrom a silicon single-crystal specimen plastically deformed under single-slip conditions indicate that slip system activity can be identified during HEDM experiments.
Stoichiometries and affinities of interacting proteins from concentration series of solution scattering data: decomposition by least squares and quadratic optimization
Authors: Chandola Himanshu , Williamson Tim E. , Craig Bruce A. , Friedman Alan M. , Bailey-Kellogg Chris
Published: May 2014

In studying interacting proteins, complementary insights are provided by analyzing both the association model (the stoichiometry and affinity constants of the intermediate and final complexes) and the quaternary structure of the resulting complexes. Many current methods for analyzing protein interactions either give a binary answer to the question of association and no information about quaternary structure or at best provide only part of the complete picture. Presented here is a method to extract both types of information from X-ray or neutron scattering data for a series of equilibrium mixtures containing the initial components at different concentrations. The method determines the association pathway and constants, along with the scattering curves of the individual members of the mixture, so as to best explain the scattering data for the mixtures. The derived curves then enable reconstruction of the intermediate and final complexes. Using simulated solution scattering data for four hetero-oligomeric complexes with different structures, molecular weights and association models, it is demonstrated that this method accurately determines the simulated association model and scattering profiles for the initial components and complexes. Recognizing that experimental mixtures contain static contaminants and nonspecific complexes with the lowest affinities (inter-particle interference) as well as the desired specific complex(es), a new analytical method is also employed to extend this approach to evaluating the association models and scattering curves in the presence of static contaminants, testing both a nonparticipating monomer and a large homo-oligomeric aggregate. It is demonstrated that the method is robust to both random noise and systematic noise from such contaminants, and the treatment of nonspecific complexes is discussed. Finally, it is shown that this method is applicable over a large range of weak association constants typical of specific but transient protein–protein complexes.
Position-dependent shear-induced austenite–martensite transformation in double-notched TRIP and dual-phase steel samples
Authors: Blondé Romain , Jimenez-Melero Enrique , Ponnusami Sathiskumar A. , Zhao Lie , Schell Norbert , Brück Ekkes , van der Zwaag Sybrand , van Dijk Niels
Published: May 2014

While earlier studies on transformation-induced-plasticity (TRIP) steels focused on the determination of the austenite-to-martensite decomposition in uniform deformation or thermal fields, the current research focuses on the determination of the local retained austenite-to-martensite transformation behaviour in an inhomogeneous yet carefully controlled shear-loaded region of double-notched TRIP and dual-phase (DP) steel samples. A detailed powder analysis has been performed to simultaneously monitor the evolution of the phase fraction and the changes in average carbon concentration of metastable austenite together with the local strain components in the constituent phases as a function of the macroscopic stress and location with respect to the shear band. The metastable retained austenite shows a mechanically induced martensitic transformation in the localized shear zone, which is accompanied by an increase in average carbon concentration of the remaining austenite due to a preferred transformation of the austenite grains with the lowest carbon concentration. At the later deformation stages the geometry of the shear test samples results in the development of an additional tensile component. The experimental strain field within the probed sample area is in good agreement with finite element calculations. The strain development observed in the low-alloyed TRIP steel with metastable austenite is compared with that of steels with the same chemical composition containing either no austenite (a DP grade) or stable retained austenite (a TRIP grade produced at a long bainitic holding time). The transformation of metastable austenite under shear is a complex interplay between the local microstructure and the evolving strain fields.
HELIX: a new modular nucleic acid crystallization screen
Authors: Viladoms Julia , Parkinson Gary N.
Published: May 2014

Crystallization of nucleic acids remains a bottleneck to their structural characterization by X-ray crystallography. A new 96-well-format initial screen for nucleic acids, called HELIX, has been developed at UCL School of Pharmacy, London, on the basis of a detailed analysis of the crystallization conditions from 1450 nucleic acid structures deposited in the Protein Data Bank (PDB), combined with observations and experience acquired in the authors' nucleic acids crystallography laboratory during the crystallization of DNA/RNA quadruplexes and ligand complexes. Despite using traditional buffers, precipitants and salts, the resulting modular screen is designed to offer a variety of approaches to enhance successful crystallization of oligonucleotides with a diverse range of topologies, sequences and molecular weights. HELIX includes a set of 24 conditions divided into four sets that can be mixed (inter- and intra-set) to provide a customizable orthogonal screening tool for experienced users, termed VariX. Additionally, mindful of synchrotron anomalous data collection, cacodylate buffers are avoided in the formulations and an optimized cryocrystallization module is included. This article reviews the crystallization trends and data derived from the PDB and discusses the HELIX screen layout, formulation and results from in-house crystallization trials.
Spectral modulation of higher harmonic spontaneous emission from an optical klystron
Authors: Sei Norihiro , Ogawa Hiroshi , Yamada Kawakatsu , Koike Masaki , Ohgaki Hideaki
Published: May 2014

Higher harmonics of spontaneous emission from an optical klystron have been observed. The modulation factor of the spontaneous emission spectrum for the higher harmonics can be described by considering the observation system. When the dispersive gap of the optical klystron was fixed, the microstructure interval of the spontaneous emission spectrum at a certain resonant wavelength became narrower as the order of the higher harmonic became larger. Some unique characteristics of the higher harmonics have been clarified, and these studies are likely to contribute to the development of free-electron lasers using higher harmonics of an optical klystron in the shorter-wavelengths region.
A tunable wedge-shaped absorber for hard X-ray synchrotron applications
Authors: Krywka C. , Brix M. , Müller M.
Published: May 2014

The concept of a concave aluminium wedge-shaped absorber for hard X-ray synchrotron beamlines is presented. Unlike the commonly used absorber types (fixed-thickness absorber sheets or binary exchangers of individual fixed absorbers), this concept allows a compact system, controlled with a single linear positioner, and provides a wide attenuation range as well as a precise tunability over a large energy range. Data were recorded at the Nanofocus Endstation of the MINAXS beamline, PETRA III, Hamburg, Germany.
Molecular and supramolecular ionic aggregates HxOyzin organic and organometallic crystalline hydrates
Authors: Bernal Ivan , Watkins Steven F.
Published: May 2014

Ionic aggregates of the form HxOyz(z≠ 0) have been characterized during an analysis of 245 crystal structures extracted from the Cambridge Structural Database [Allen (2002).Acta Cryst.B58, 380–388]. A systematic nomenclature is proposed for these species. Three modes of hydrogen bonding are described, characterized in part by the distance between contiguous O atoms: normal (NHB; O...O = 2.6–3.0 Å), charge assisted (CAHB; O...O = 2.5 Å) and molecular (MHB; O...O = 2.4 Å). The three modes are consistent with previous reports, our experimental results, and quantum-chemical-optimized geometries and energetics. No evidence is presented concerning the possible existence or stability of these aggregates in solution. Rather, emphasis is placed on the necessity in crystal structure analysis to develop thoroughly existing hydrogen-bonded networks, ignorance of which can lead to erroneous crystal structure models and other physico-chemical data associated with composition and charge balance.
Structure of a His170Tyr mutant of thermostable pNPPase fromGeobacillus stearothermophilus
Authors: Shen Tiantian , Guo Zheng , Ji Chaoneng
Published: May 2014

Using directed evolution based on random mutagenesis and heat-treated selection, a thermostable His170Tyr mutant ofGeobacillus stearothermophilusthermostablep-nitrophenylphosphatase (TpNPPase) was obtained. The temperature at which the His170Tyr mutant lost 50% of its activity (T1/2) was found to be 4.40 K higher than that of wild-type TpNPPase, and the melting temperature of the His170Tyr mutant increased by 2.39 K. The crystal structure of the His170Tyr mutant was then determined at 2.0 Å resolution in the presence of a sodium ion and a sulfate ion in the active site. The cap domain of chainBshows a half-closed conformation. The hydrophobic side chain of the mutated residue, the hydroxyphenyl group, forms a hydrophobic contact with the methyl group of Ala166. This hydrophobic interaction was found using theProtein Interactions Calculator(PIC) web server with an interaction distance of 4.6 Å, and might be a key factor in the thermostabilization of the His170Tyr mutant. This study potentially offers a molecular basis for both investigation of the catalytic mechanism and thermostable protein engineering.