bluuebunny/crossref_metadata_2025 huggingface dataset:
Questioning the Secular-Religious Cleavage in Palestinian Politics: Comparing Fatah and Hamas
Authors: Løvlie Frode
Published: October 2013

Following the 2007 war between Fatah and Hamas, Palestinian politics appears to have followed the regional trend where the competition between secularism and Islamism is developing into a major political cleavage. Through comparisons of the two movements' ideologies, however, the article questions the relevance of this religious-secular cleavage to explaining Palestinian factional politics. Fatah — the traditional hegemon in Palestinian politics and previously staunchly secularist — has turned increasingly religious in response to the spread of Islamism. Hamas for its part has shed its overly religious rhetoric, absolutist territorial claims, and insistence on a violent solution to the Palestinian problem, in tandem with the deradicalization of the Palestinian population. In finding that both movements have moved toward the center of the political spectrum to maximize support, the article concludes that their rivalry is best understood as a competition for the median voter rather than as an indication of political polarization.
Optimal Designs for Event History Analysis
Authors: Moerbeek Mirjam , Jóźwiak Katarzyna
Published: October 2013

The aim of event history analysis is to study the occurrence and timing of events, such as premature psychotherapy termination or drinking onset, and to relate the probability of event occurrence to relevant covariates. In the social sciences, the timing of the event is often measured discretely by using time intervals, which implies the exact timing of event occurrence is unknown. The optimal number of subjects and time intervals need to be decided upon in the design stage of a trial with discrete-time survival endpoints. This paper shows how the optimal design depends on the underlying survival function and the costs to include a subject relative to the costs to take a measurement. Furthermore, the effects of attrition on the optimal design are studied. An example on drinking onset illustrates the proposed methodology.
An investigation of mixing in a three-stream turbulent jet
Authors: Rowinski David H. , Pope Stephen B.
Published: October 2013

Mixing models are required to account for the effects of molecular diffusion in probability density function (PDF) methods for reacting flows, and these models entail one of the greatest sources of modeling uncertainty in PDF calculations. In this work, we perform PDF calculations of a turbulent coaxial jet using both Reynolds-Averaged Navier-Stokes (RANS) and Large Eddy Simulation (LES) based methods. The configuration of the coaxial jet comes from a recently developed experiment, in which the conditional diffusion and scalar dissipation rate of two conserved scalars are measured. These measurements present the unique opportunity to compare directly the conditional diffusion implied by PDF mixing models to the measured conditional diffusion. In the RANS-PDF calculations, three classic mixing models are evaluated: Interaction by Exchange with the Mean (IEM), Modified Curl (MC), and Euclidean Minimum Spanning Tree (EMST). Though calculations with all three mixing models yield time-averaged mean and RMS statistics of the two scalars in good agreement with the experimental measurements, the joint PDFs of the two scalars show a wide variability from the measurements. The EMST mixing model is unique in that it produces compositions which lie very close to the slow manifold identified in the experimental work. Next, LES calculations of the same flow are performed, and the dissipation rate and conditional diffusion are calculated. The resolved scalar dissipation rate is found to be in good agreement with the experimental data, but depends strongly on the resolution; the total dissipation rate from the RANS-PDF and LES calculations indicates significantly larger scalar dissipation rates than those measured experimentally. Finally, LES-PDF calculations of the same flow yield joint PDFs in very good agreement with the experimental data. The attenuation of variance production model is introduced and tested in this flow: this new model is found to yield calculations of improved accuracy in LES-PDF calculations on coarse grids.
Effect of antenna size on electron kinetics in inductively coupled plasmas
Authors: Lee Hyo-Chang , Chung Chin-Wook
Published: October 2013

Spatially resolved measurements of electron energy distribution functions (EEDFs) are investigated in inductively coupled plasmas with two planar antenna coils. When the plasma is sustained by the antenna with a diameter of 18 cm, the nonlocal kinetics is preserved in the argon gas pressure range from 2 mTorr to 20 mTorr. However, electron kinetics transit from nonlocal kinetics to local kinetics in discharge sustained by the antenna coil with diameter 34 cm. The results suggest that antenna size as well as chamber length are important parameters for the transition of the electron kinetics. Spatial variations of plasma potential, effective electron temperature, and EEDF in terms of total electron energy scale are also presented.
Kinetic modeling of the Townsend breakdown in argon
Authors: Macheret S. O. , Shneider M. N.
Published: October 2013

Kinetic modeling of the Townsend breakdown in argon was performed in the “forward-back” approximation. The kinetic model was found to adequately describe the left branch of the Paschen curve, and the important role of ionization by fast ions and atoms near the cathode, as well as the increase in secondary emission coefficient in strong electric fields described in the literature, was confirmed. The modeling also showed that the electron energy distribution function develops a beam of high-energy electrons and that the runaway effect, i.e., the monotonic increase of the mean electron energy with the distance from the cathode, occurs at the left branch of the Paschen curve.
On plasma rotation induced by waves in tokamaks
Authors: Guan Xiaoyin , Dodin I. Y. , Qin Hong , Liu Jian , Fisch N. J.
Published: October 2013

The momentum conservation for resonant wave-particle interactions, now proven rigorously and for general settings, is applied to explain in simple terms how tokamak plasma is spun up by the wave momentum perpendicular to the dc magnetic field. The perpendicular momentum is passed through resonant particles to the dc field and, giving rise to the radial electric field, is accumulated as a Poynting flux; the bulk plasma is then accelerated up to the electric drift velocity proportional to that flux, independently of collisions. The presence of this collisionless acceleration mechanism permits varying the ratio of the average kinetic momentum absorbed by the resonant-particle and bulk distributions depending on the orientation of the wave vector. Both toroidal and poloidal forces are calculated, and a fluid model is presented that yields the plasma velocity at equilibrium.
Ultraviolet spectroscopy of fundamental lignin subunits: Guaiacol, 4-methylguaiacol, syringol, and 4-methylsyringol
Authors: Dean Jacob C. , Navotnaya Polina , Parobek Alexander P. , Clayton Rachel M. , Zwier Timothy S.
Published: October 2013

Ultraviolet spectroscopy of the G- and S-type lignin subunits, guaiacol (G) and syringol (S), along with their para-methylated derivatives 4-methylguaiacol (4-MG) and 4-methylsyringol (4-MS), has been carried out in the cold, isolated environment of a supersonic jet. The excitation spectra and dispersed fluorescence (DFL) spectra of G and 4-MG show strong S0-S1 origins and Franck-Condon activity involving both the ring modes typical of aromatic derivatives, and the four lowest frequency out-of-plane modes (a″) and lowest in-plane mode (a′) involving the OH and OCH3 groups. The four low-frequency out-of-plane modes undergo extensive Duschinsky mixing between the ground and excited state. In 4-MG, combination bands involving methyl rotor levels with out-of-plane modes appeared with surprisingly high intensity, indicating a high degree of hindered rotor-vibration coupling in both S0 and S1. These mixing effects accompany the change in geometry upon π−π* electronic excitation going from a planar ground state to a non-planar excited state. Time-dependent density functional theory (TDDFT M05-2X/6-311++G(d,p)) calculations predict a geometric distortion along the out-of-plane oxygen flapping coordinate, yielding a double minimum potential in S1 with a barrier to planarity of 195 cm−1 in G. The excitation spectrum of S and 4-MS showed a much higher degree of spectral congestion and a larger geometry change evident by a shifted intensity distribution peaking ∼300 cm−1 above the electronic origin. TDDFT calculations predict a larger geometry change in S compared with G, with the OH and H-bonded methoxy groups displaced in opposite directions above/below the ring plane. Dispersed fluorescence from all S1 excited state levels in S/4-MS yield only broad emission peaking far to the red of the excitation wavelength (−4500 cm−1). Several hypotheses regarding the source of this broad, redshifted emission were tested, but the cause remains unclear. p-Methylation was found to significantly redshift the UV absorption in both 4-MG and 4-MS, and methyl rotor transitions were assigned in both allowing for the determination of the shape and barrier heights of their respective potentials. These results provide a foundation for the discrimination of G- and S-chromophores in lignin oligomers, and demonstrate the potential for site-selective absorption.
Phase transition and magneto-electric coupling of BiFeO3–YMnO3 multiferroic nanoceramics
Authors: Narayan Tripathy Satya , Mishra K. K. , Sen S. , Mishra B. G. , Pradhan Dhiren K. , Palai R. , Pradhan Dillip K.
Published: October 2013

We report the crystal structure, dielectric, magnetic, and magneto-electric properties of (1−x) BiFeO3-xYMnO3 (0.00 ≤ x ≤ 0.2) multiferroic nanoceramics prepared by auto-combustion technique. YMnO3 substitution is found to induce a structural phase transition from R3c to R3c+Pbnm after x ≈ 0.1 using Rietveld refinement technique. Field emission scanning electron micrographs show decrease in grain size with increase in YMnO3 content. The dielectric permittivity and loss tangent are found to be increased with composition x. The anomalies noticed from the temperature dependent dielectric analysis reveal the signature of magneto-electric coupling in the system. A decrease in magnetic ordering temperature as a function of composition is found from dielectric study. At room temperature, the dielectric permittivity of all the YMnO3 modified samples decrease with increasing magnetic field. The maximum value of magneto-electric coupling coefficient (ε(H)-ε(0))/ε(0) is found to be ∼ −5.5% at H = 2 T for x = 0.2. The behaviour of the magnetic hysteresis loop observed at room temperature suggests the suppression of space modulated spin structure.
Numerical study of the effect of normalised window size, sampling frequency, and noise level on short time Fourier transform analysis
Authors: Ota T. A.
Published: October 2013

Photonic Doppler velocimetry, also known as heterodyne velocimetry, is a widely used optical technique that requires the analysis of frequency modulated signals. This paper describes an investigation into the errors of short time Fourier transform analysis. The number of variables requiring investigation was reduced by means of an equivalence principle. Error predictions, as the number of cycles, samples per cycle, noise level, and window type were varied, are presented. The results were found to be in good agreement with analytical models.
Numerical study of atomic production rate in hydrogen negative ion sources with the effect of non-equilibrium electron energy distribution function
Authors: Shibata T. , Kashiwagi M. , Inoue T. , Hatayama A. , Hanada M.
Published: October 2013

Spatial non-uniformity of the dissociative hydrogen atom (H0) production has been investigated in a large negative ion source (JAEA 10 A source) with the electron energy distribution function (EEDF) obtained by a Monte-Carlo simulation code for electron transport in 3D3V (three dimensional real and velocity) space. It has been shown that the H0 production rate becomes larger in the upper region (one side in the longitudinal direction) of the source chamber. This spatial non-uniformity of the H0 production profile is mainly explained by the non-equilibrium features of the EEDF in the upper region, i.e., the EEDF consists of thermal electron component with kinetic energy ε < 25 eV and fast electron component with energy ε > 25 eV in the upper region, while the EEDF mainly consists of only thermal electrons in the bottom region. These characteristics for the EEDF and the energy dependence of cross-sections for dissociation and dissociative ionization processes lead to the non-uniform profile of the H0 production. The above numerical results of the spatial H0 non-uniformity are validated and confirmed by comparisons with those by spectroscopic measurement. It has been clarified that the non-equilibrium (fast electron) component of the EEDF has a large contribution to the non-uniformity of the H0 production rate.
Enhanced conformational sampling using enveloping distribution sampling
Authors: Lin Zhixiong , van Gunsteren Wilfred F.
Published: October 2013

To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.710/12-helix and a left-handed 314-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.
Total molecular photoionization cross-sections by algebraic diagrammatic construction-Stieltjes-Lanczos method: Benchmark calculations
Authors: Ruberti M. , Yun R. , Gokhberg K. , Kopelke S. , Cederbaum L. S. , Tarantelli F. , Averbukh V.
Published: October 2013

In [K. Gokhberg, V. Vysotskiy, L. S. Cederbaum, L. Storchi, F. Tarantelli, and V. Averbukh, J. Chem. Phys. 130, 064104 (2009)] we introduced a new \documentclass[12pt]{minimal}\begin{document}$\mathscr {L}^{2}$\end{document}L2ab initio method for the calculation of total molecular photoionization cross-sections. The method is based on the ab initio description of discretized photoionized molecular states within the many-electron Green's function approach, known as algebraic diagrammatic construction (ADC), and on the application of Stieltjes-Chebyshev moment theory to Lanczos pseudospectra of the ADC electronic Hamiltonian. Here we establish the accuracy of the new technique by comparing the ADC-Lanczos-Stieltjes cross-sections in the valence ionization region to the experimental ones for a series of eight molecules of first row elements: HF, NH3, H2O, CO2, H2CO, CH4, C2H2, and C2H4. We find that the use of the second-order ADC technique [ADC(2)] that includes double electronic excitations leads to a substantial systematic improvement over the first-order method [ADC(1)] and to a good agreement with experiment for photon energies below 80 eV. The use of extended second-order ADC theory [ADC(2)x] leads to a smaller further improvement. Above 80 eV photon energy all three methods lead to significant deviations from the experimental values which we attribute to the use of Gaussian single-electron bases. Our calculations show that the ADC(2)-Lanczos-Stieltjes technique is a reliable and efficient ab initio tool for theoretical prediction of total molecular photo-ionization cross-sections in the valence region.
Quantum transport through single and multilayer icosahedral fullerenes
Authors: Lovey Daniel A. , Romero Rodolfo H.
Published: October 2013

We use a tight-binding Hamiltonian and Green functions methods to calculate the quantum transmission through single-wall fullerenes and bilayered and trilayered onions of icosahedral symmetry attached to metallic leads. The electronic structure of the onion-like fullerenes takes into account the curvature and finite size of the fullerenes layers as well as the strength of the intershell interactions depending on to the number of interacting atom pairs belonging to adjacent shells. Misalignment of the symmetry axes of the concentric iscosahedral shells produces breaking of the level degeneracies of the individual shells, giving rise some narrow quasi-continuum bands instead of the localized discrete peaks of the individual fullerenes. As a result, the transmission function for non symmetrical onions is rapidly varying functions of the Fermi energy. Furthermore, we found that most of the features of the transmission through the onions are due to the electronic structure of the outer shell with additional Fano-like antiresonances arising from coupling with or between the inner shells.
Electronic and transport properties of zintl phase AeMg2Pn2, Ae = Ca,Sr,Ba, Pn = As,Sb,Bi in relation to Mg3Sb2
Authors: Singh David J. , Parker David
Published: October 2013

First principles calculations of the electronic structure and transport properties of Zintl phase AeMg2Pn2, Ae = Ca,Sr,Ba, Pn = As,Sb,Bi compounds and Mg3Sb2 are reported. These are discussed in relation to the thermoelectric performance of the compounds and specifically the optimization of carrier concentration. It is found that there are several promising compositions and that the materials that have been studied to date are not fully optimized in terms of carrier concentration and may not ultimately be the best thermoelectrics in this family. We additionally report optical properties and show that there are significant differences among the compounds arising from differences in electronic structure and that these differences should be accessible to experiment. This provides a way to test the trends observed here.
Cellulose as biodegradable high-k dielectric layer in organic complementary inverters
Authors: Petritz A. , Wolfberger A. , Fian A. , Irimia-Vladu M. , Haase A. , Gold H. , Rothländer T. , Griesser T. , Stadlober B.
Published: October 2013

We report on the natural source based and biodegradable material cellulose on Al2O3 as ultrathin hybrid high-k dielectric layer for applications in green electronics. Dielectric films of 16 nm cellulose (ε ≈ 8.4) and 8 nm Al2O3 (ε ≈ 9) exhibit low leakage currents up to electric fields of 1.5 MV/cm. Pentacene and C60 based organic thin film transistors show a well-balanced performance with operation voltages around 2 V. They are implemented in complementary inverters with excellent switching behavior, a small-signal gain up to 60 and with exceptionally high and balanced noise margin values of 82% at ultralow operation voltage (VDD = 2.5 V).
Effect of laser beam filamentation on coexisting stimulated Raman and Brillouin scattering
Authors: Sharma R. P. , Vyas Ashish , Kishor Singh Ram
Published: October 2013

This paper presents the study of stimulated Raman scattering (SRS) and stimulated Brillouin scattering (SBS) when both of these processes are coexisting and pump laser beam initial power is more than filamentation threshold. On account of the ponderomotive nonlinearity, the pump laser beam gets filamented, and both the scattering processes (SRS and SBS) get affected. Simultaneous presence of SRS and SBS (five wave interaction case) also affect the pump filamentation process due to pump depletion. Both the scattering processes (SRS and SBS) are enhanced due to filamentation of laser beam. Results are also compared with the three wave interaction case (either SRS or SBS) with and without filamentation.
Linear stability and nonlinear dynamics of the fishbone mode in spherical tokamaks
Authors: Wang Feng , Fu G. Y. , Breslau J. A. , Liu J. Y.
Published: October 2013

Extensive linear and nonlinear simulations have been carried out to investigate the energetic particle-driven fishbone instability in spherical tokamak plasmas with weakly reversed q profile and the qmin slightly above unity. The global kinetic-MHD hybrid code M3D-K is used. Numerical results show that a fishbone instability is excited by energetic beam ions preferentially at higher qmin values, consistent with the observed appearance of the fishbone before the “long-lived mode” in MAST and NSTX experiments. In contrast, at lower qmin values, the fishbone tends to be stable. In this case, the beam ion effects are strongly stabilizing for the non-resonant kink mode. Nonlinear simulations show that the fishbone saturates with strong downward frequency chirping as well as radial flattening of the beam ion distribution. An (m, n) = (2, 1) magnetic island is found to be driven nonlinearly by the fishbone instability, which could provide a trigger for the (2, 1) neoclassical tearing mode sometimes observed after the fishbone instability in NSTX.
Structural, electronic, and optical properties of Cu3-V-VI4 compound semiconductors
Authors: Shi Tingting , Yin Wan-Jian , Al-Jassim Mowafak , Yan Yanfa
Published: October 2013

Cu-V-VII chalcogenide semiconductors have recently been considered promising earth-abundant solar cell materials. Using first-principles density-functional theory with hybrid functional, we have studied the structural, electronic, and optical properties of Cu3-V-VI4 compounds. We find that Cu3PS4 and Cu3PSe4 prefer energetically the enargite structure, whereas other compounds favor the famatinite structure. The Cu3-V-VI4 family exhibits bandgaps ranging from 0.88 eV to 2.51 eV, revealing the potentials for both single junction and multijunction solar cell applications. The calculated bandgaps for Cu3-V-VI4 compounds are in good agreement with the available theoretical and experimental results.
Surface effects on stability of nanorings under uniform pressure
Authors: Hashemi Roohollah , Avazmohammadi Reza
Published: October 2013

In this work, we study the effect of surface stress on the stability behavior of a circular ring with nano dimensions under uniform pressure. It is known that the surface elasticity and residual surface tension can have significant effects on the mechanical behavior of the nano-sized structures. Taking both effects into account, we present an analytical expression for the smallest critical radial load acting on the nanoring. It is shown that, depending on surface mechanical properties of the nanoring, these effects can stabilize or destabilize the nanoring under uniform pressure. The results, in this work, are expected to provide informative predictions on characterizing the stability behavior of nano elements used in nanostructured devices.
Mechanism of stress relaxation in (0001) InGaN/GaN via formation of V-shaped dislocation half-loops
Authors: Lobanova A. V. , Kolesnikova A. L. , Romanov A. E. , Karpov S. Yu. , Rudinsky M. E. , Yakovlev E. V.
Published: October 2013

From the analysis of available experimental data, we suggest a mechanism of stress relaxation in strained (0001) InGaN/GaN layers, assuming formation of V-shaped edge-type dislocation half-loops. An energy-balance approach is applied to estimate the critical thickness of the InGaN layer resulting in generation of the V-shaped half-loops. The computed dependence of the critical thickness on the InGaN composition agrees well with the literature data reported for single-layer InGaN/GaN heterostructures.
Full counting statistics of a quantum dot doped with a single magnetic impurity
Authors: Zhang Hong-Wei , Xue Hai-Bin , Nie Yi-Hang
Published: October 2013

The full counting statistics of electron transport through a quantum dot (QD) doped with a single magnetic impurity weakly coupled to one ferromagnetic (F) and one normal-metal lead (N) is studied based on an efficient particle-number-resolved master equation. We demonstrate that the current noise properties depend sensitively on whether the source-electrode is the ferromagnetic lead and the type of exchange coupling between the conduction electron and magnetic impurity spin. For the F-QD-N system, namely, the ferromagnetic lead as source electrode and the normal-metal lead as drain one, the super-Poissonian noise in the anti-ferromagnetic coupling case can appear; whereas for the ferromagnetic coupling case the super-Poissonian noise does not appear. As for the N-QD-F system, the super-Poissonian noise in the ferromagnetic coupling case can appear in a relatively large bias voltage range; while for the anti-ferromagnetic coupling case, the super-Poissonian noise appears only in a relatively small bias voltage range. These super-Poissonian noise characteristics can be used to reveal the type of exchange coupling between the conduction electron and magnetic impurity spin, and can be qualitatively attributed to the spin-blockade mechanism and the effective competition between fast and slow transport channels.
Feminicidio, Narcoviolence, and Gentrification in Ciudad Juárez: The Feminist Fight
Authors: Wright Melissa W
Published: October 2013

The fight against impunity continues along Mexico's border, especially in the industrial hub of Ciudad Juárez. In the 1990s feminists brought this fight to international attention as they launched a transnational justice movement against feminicidio, the killing of women with impunity. In this paper I create a feminist and Marxist frame to show that there is much to be learned from the fight against feminicidio for the ongoing struggles in a border city that is now also notorious for juvenicidio, the killing of youth with impunity, which is occurring in relation to the Mexican government's declaration of war against organized crime. By situating these justice struggles within a context of North American securitization and neoliberal gentrification along the Mexico—US border, I argue that the feminist fight against impunity exposes the synergy of symbolic and material processes within the drug war. And I argue that this synergy seeks to generate value through the extermination of whole populations, especially of working poor women and their families in this border city today.
Co-expression of xerophyte Zygophyllum xanthoxylum ZxNHX and ZxVP1-1 enhances salt and drought tolerance in transgenic Lotus corniculatus by increasing cations accumulation
Authors: Bao Ai-Ke , Wang Yan-Wen , Xi Jie-Jun , Liu Chen , Zhang Jin-Lin , Wang Suo-Min
Published: October 2013

Lotus corniculatus L. is an important legume for forage, but is sensitive to salinity and drought. To develop salt- and drought-resistant L. corniculatus, ZxNHX and ZxVP1-1 genes encoding tonoplast Na+/H+ antiporter and H+-pyrophosphatase (H+-PPase) from a succulent xerophyte Zygophyllum xanthoxylum L., which is well adapted to arid environments through accumulating Na+ in its leaves, were transferred into this forage. We obtained the transgenic lines co-expressing ZxNHX and ZxVP1-1 genes (VX) as well as expressing ZxVP1-1 gene alone (VP). Compared with wild-type, both VX and VP transgenic lines grew better at 200 mM NaCl, and also exhibited higher tolerance and faster recovery from water-deficit stress: these performances were associated with more Na+, K+ and Ca2+ accumulation in their leaves and roots, which caused lower leaf solute potential and thus retained more water. Moreover, the transgenic lines maintained lower relative membrane permeability and higher net photosynthesis rate under salt or water-deficit stress. These results indicate that expression of tonoplast Na+/H+ antiporter and H+-PPase genes from xerophyte enhanced salt and drought tolerance of L. corniculatus. Furthermore, compared with VP, VX showed higher shoot biomass, more cations accumulation, higher water retention, lesser cell membrane damage and higher photosynthesis capacity under salt or water-deficit condition, suggesting that co-expression of ZxVP1-1 and ZxNHX confers even greater performance to transgenic L. corniculatus than expression of the single ZxVP1-1.
Assessment of cultivated and wild, weedy rice lines to concurrent changes in CO2 concentration and air temperature: determining traits for enhanced seed yield with increasing atmospheric CO2
Authors: Ziska Lewis H. , Tomecek Martha B. , Gealy David R.
Published: October 2013

Although several studies have examined intra-specific variability in growth and yield to projected atmospheric CO2 concentration, [CO2], few have considered concurrent increases in air temperature and [CO2], and none have compared the relative responses of cultivated and wild, weedy crop lines. In the current study we quantified the growth and seed yield response of three cultivated (‘Rondo’, ‘Clearfield 161’, ‘M204’) and one wild (red) rice line (‘Stuttgart-S’ or ‘Stg-S’), grown at ambient or +200 µmol mol–1 [CO2] at one of three day/night temperatures (29/21, 31/23 or 33/25°C). Averaged among all cultivars, [CO2] increased biomass and seed yield, but conversely, increasing air temperature reduced the [CO2] response of both parameters. Among the cultivated and weedy rice tested, ‘Rondo’ and ‘Stg-S’ showed significant increases in aboveground biomass and seed yield with elevated [CO2] at 29/21°C; however, only ‘Stg-S’, the weedy rice line, demonstrated a significant increase with [CO2] at all growth temperatures. A regression analysis for this line indicated that the relative increase in seed yield with [CO2] and air temperature was positively associated with panicle and tiller number, but negatively correlated with the percentage of immature seed. An analysis of all lines indicated that the ratio of tiller production between CO2 treatments at 30 days after sowing (DAS) was a significant predictor of seed yield response to increasing [CO2] for all temperatures. These results suggest that: (i) inclusion of wild lines may broaden genotypic or phenotypic variation and assist in selection to temperature/[CO2]; and (ii) early differences in tiller formation may be an effective means to facilitate screening for CO2 sensitive rice genotypes.
A penalized Bayesian approach to predicting sparse protein–DNA binding landscapes
Authors: Levinson Matthew , Zhou Qing
Published: October 2013

Motivation: Cellular processes are controlled, directly or indirectly, by the binding of hundreds of different DNA binding factors (DBFs) to the genome. One key to deeper understanding of the cell is discovering where, when and how strongly these DBFs bind to the DNA sequence. Direct measurement of DBF binding sites (BSs; e.g. through ChIP-Chip or ChIP-Seq experiments) is expensive, noisy and not available for every DBF in every cell type. Naive and most existing computational approaches to detecting which DBFs bind in a set of genomic regions of interest often perform poorly, due to the high false discovery rates and restrictive requirements for prior knowledge.

Results: We develop SparScape, a penalized Bayesian method for identifying DBFs active in the considered regions and predicting a joint probabilistic binding landscape. Using a sparsity-inducing penalization, SparScape is able to select a small subset of DBFs with enriched BSs in a set of DNA sequences from a much larger candidate set. This substantially reduces the false positives in prediction of BSs. Analysis of ChIP-Seq data in mouse embryonic stem cells and simulated data show that SparScape dramatically outperforms the naive motif scanning method and the comparable computational approaches in terms of DBF identification and BS prediction.

Availability and implementation: SparScape is implemented in C++ with OpenMP (optional at compilation) and is freely available at ‘www.stat.ucla.edu/∼zhou/Software.html’ for academic use.

Contact:  zhou@stat.ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Correction for Seymour Benzer. 15 October 1921 — 30 November 2007
Authors: Greenspan Ralph J.
Published: October 2013

Biogr. Mems Fell. R. Soc.
58
, 23–32 (2012; Published online 18 July 2012) (
http://dx.doi.org/10.1098/rsbm.2012.0031
)

We regret that on page 26 the election of Guido Pontecorvo to the Royal Society is incorrectly referred to as ‘(ForMemRS 1955)’; this should read ‘(FRS 1955)’.
Regulated IRE1-dependent decay pathway is activated during Japanese encephalitis virus-induced unfolded protein response and benefits viral replication
Authors: Bhattacharyya Sankar , Sen Utsav , Vrati Sudhanshu
Published: October 2013

Japanese encephalitis virus (JEV) infection-induced encephalitis causes extensive death or long-term neurological damage, especially among children, in south and south-east Asia. Infection of mammalian cells has shown induction of an unfolded protein response (UPR), presumably leading to programmed cell death or apoptosis of the host cells. UPR, a cellular response to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) lumen, is initiated by three ER-lumen-resident sensors (PERK, IRE1 and ATF6), and involves transcriptional and translational regulation of the expression of several genes. The sensor IRE1 possesses an intrinsic RNase activity, activated through homo-dimerization and autophosphorylation during UPR. Activated IRE1 performs cytoplasmic cleavage of Xbp1u transcripts, thus facilitating synthesis of XBP1S transcription factor, in addition to cleavage of a cohort of cellular transcripts, the later initiating the regulated IRE1-dependent decay (RIDD) pathway. In this study, we report the initiation of the RIDD pathway in JEV-infected mouse neuroblastoma cells (Neuro2a) and its effect on viral infection. Activation of the RIDD pathway led to degradation of known mouse cell target transcripts without showing any effect on JEV RNA despite the fact that both when biochemically purified showed significant enrichment in ER membrane-enriched fractions. Additionally, inhibition of the IRE1 RNase activity by STF083010, a specific drug, diminished viral protein levels and reduced the titre of the virus produced from infected Neuro2a cells. The results present evidence for the first report of a beneficial effect of RIDD activation on the viral life cycle.
Molecular basis of telomere syndrome caused by CTC1 mutations
Authors: Chen Liuh-Yow , Majerská Jana , Lingner Joachim
Published: October 2013

Mutations in CTC1 lead to the telomere syndromes Coats Plus and dyskeratosis congenita (DC), but the molecular mechanisms involved remain unknown. CTC1 forms with STN1 and TEN1 a trimeric complex termed CST, which binds ssDNA, promotes telomere DNA synthesis, and inhibits telomerase-mediated telomere elongation. Here we identify CTC1 disease mutations that disrupt CST complex formation, the physical interaction with DNA polymerase α-primase (polα-primase), telomeric ssDNA binding in vitro, accumulation in the nucleus, and/or telomere association in vivo. While having diverse molecular defects, CTC1 mutations commonly lead to the accumulation of internal single-stranded gaps of telomeric DNA, suggesting telomere DNA replication defects as a primary cause of the disease. Strikingly, mutations in CTC1 may also unleash telomerase repression and telomere length control. Hence, the telomere defect initiated by CTC1 mutations is distinct from the telomerase insufficiencies seen in classical forms of telomere syndromes, which cause short telomeres due to reduced maintenance of distal telomeric ends by telomerase. Our analysis provides molecular evidence that CST collaborates with DNA polα-primase to promote faithful telomere DNA replication.
Calorie restriction and sirtuins revisited
Authors: Guarente Leonard
Published: October 2013

Calorie or dietary restriction (CR) has attracted attention because it is the oldest and most robust way to extend rodent life span. The idea that the nutrient sensors, termed sirtuins, might mediate effects of CR was proposed 13 years ago and has been challenged in the intervening years. This review addresses these challenges and draws from a great body of new data in the sirtuin field that shows a systematic redirection of mammalian physiology in response to diet by sirtuins. The prospects for drugs that can deliver at least a subset of the benefits of CR seems very real.
Molecular replacement: tricks and treats
Authors: Abergel Chantal
Published: October 2013

Molecular replacement is the method of choice for X-ray crystallographic structure determination provided that suitable structural homologues are available in the PDB. Presently, there are ∼80 000 structures in the PDB (8074 were deposited in the year 2012 alone), of which ∼70% have been solved by molecular replacement. For successful molecular replacement the model must cover at least 50% of the total structure and the Cαr.m.s.d. between the core model and the structure to be solved must be less than 2 Å. Here, an approach originally implemented in theCaspRserver (http://www.igs.cnrs-mrs.fr/Caspr2/index.cgi) based on homology modelling to search for a molecular-replacement solution is discussed. How the use of as much information as possible from different sources can improve the model(s) is briefly described. The combination of structural information with distantly related sequences is crucial to optimize the multiple alignment that will define the boundaries of the core domains. PDB clusters (sequences with ≥30% identical residues) can also provide information on the eventual changes in conformation and will help to explore the relative orientations assumed by protein subdomains. Normal-mode analysis can also help in generating series of conformational models in the search for a molecular-replacement solution. Of course, finding a correct solution is only the first step and the accuracy of the identified solution is as important as the data quality to proceed through refinement. Here, some possible reasons for failure are discussed and solutions are proposed using a set of successful examples.
Application of theAMPLEcluster-and-truncate approach to NMR structures for molecular replacement
Authors: Bibby Jaclyn , Keegan Ronan M. , Mayans Olga , Winn Martyn D. , Rigden Daniel J.
Published: October 2013

AMPLEis a program developed for clustering and truncatingab initioprotein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models.Rosettaremodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on usingAMPLEare provided.
An estimated 5% of new protein structures solved today represent a new Pfam family
Authors: Mistry Jaina , Kloppmann Edda , Rost Burkhard , Punta Marco
Published: October 2013

High-resolution structural knowledge is key to understanding how proteins function at the molecular level. The number of entries in the Protein Data Bank (PDB), the repository of all publicly available protein structures, continues to increase, with more than 8000 structures released in 2012 alone. The authors of this article have studied how structural coverage of the protein-sequence space has changed over time by monitoring the number of Pfam families that acquired their first representative structure each year from 1976 to 2012. Twenty years ago, for every 100 new PDB entries released, an estimated 20 Pfam families acquired their first structure. By 2012, this decreased to only about five families per 100 structures. The reasons behind the slower pace at which previously uncharacterized families are being structurally covered were investigated. It was found that although more than 50% of current Pfam families are still without a structural representative, this set is enriched in families that are small, functionally uncharacterized or rich in problem features such as intrinsically disordered and transmembrane regions. While these are important constraints, the reasons why it may not yet be time to give up the pursuit of a targeted but more comprehensive structural coverage of the protein-sequence space are discussed.
Thulium nickel/lithium distannide, TmNi1−xLixSn2(x= 0.035)
Authors: Stetskiv Andrij , Tarasiuk Ivan , Misztal Renata , Pavlyuk Volodymyr
Published: October 2013

The quaternary thulium nickel/lithium distannide, TmNi1−xLixSn2(x= 0.035), crystallizes in the orthorhombic LuNiSn2structure type. The asymmetric unit contains three Tm sites, six Sn sites, two Ni sites and one Ni/Li site [relative occupancies = 0.895 (8):0.185 (8)]. Site symmetries are .m. for all atoms. The 17-, 18- and 19-vertex distorted pseudo-Frank–Kasper polyhedra are typical for all Tm atoms. Four Sn atoms are enclosed in a 12-vertex deformed cubooctahedron, and another Sn atom is enclosed in a pentagonal prism with three added atoms. A tricapped trigonal prism is typical for a further Sn atom. The coordination number for all Ni atoms and Ni/Li statistical mixtures is 12 (fourcapped trigonal prism [Ni/LiTm5Sn5]). Tm atoms form the base of a prism and Ni/Li atoms are at the centres of the side faces of an [SnTm6Ni/Li3] prism. These isolated prisms are implemented into three-dimensional-nets built out of Sn atoms. Electronic structure calculations using TB-LMTO-ASA suggest that the Tm and Ni/Li atoms form positively chargedn[TmNi/Li]m+polycations which compensate the negative charge of 2n[Sn]m−polyanions. Analysis of the interatomic distances and electronic structure calculations indicate the dominance of a metallic type of bonding.
4,4′-Oxybis(2,6-dimethylpyridinium) bis(trifluoromethanesulfonate)
Authors: Stubbs Amanda W. , Golen James A. , Rheingold Arnold L. , Manke David R.
Published: October 2013

In the asymmetric unit of the title salt, C14H18N2O2+·2CF3O3S−, the components are linked by two N—H...O and one C—H...O hydrogen bonds. The dipyridinium salt demonstrates a skew conformation based upon C—O—C—C torsion angles of 61.5 (3) and 15.1 (4)°. A C—O—C angle of 119.3 (2)° and C—O bond distances of 1.364 (3) and 1.389 (3) Å are consistent with other dipyridyl ethers. The planes of the pyridyl rings exhibit a twist angle of 67.89 (8)°. One of the trifluoromethanesulfonate ions shows disorder of the F atoms [in a 0.52 (7):0.48 (7) occupancy ratio] and an O atom [0.64 (8):0.36 (8) occupancy ratio]. In the crystal, the components are linked by C—H...O interactions, which form chains along [101].
Multi-shot printing of conductive tracks using a dry carbon nanotube ink
Authors: Wright Andrew
Published: October 2013

Purpose

– Wearable electronics is an emerging technology predicted to become a 50B$ industry by 2018. Components and circuits will be highly integrated into clothing and other apparel. One crucial factor is the need for highly robust, flexible printed circuit tracks with sufficiently high electrical conductivity. The fact that metal-based tracks tend to suffer from fatigue failure has driven the development of alternative materials. The paper aims to discuss these issues.

Design/methodology/approach

– Alternative materials are organic conductors and carbon nanotubes. The latter has a great flexibility and intrinsic strength. While nanotubes can be solubilised and printed using ink-jet techniques, this usually requires polymer additives. The paper has therefore sought to develop a novel solvent-free dry-ink.

Findings

– The paper has found that it is possible to directly transfer from a nanotube growth substrate, via a hard print stamp head, onto a flexible rubber substrate and that one loading of the stamp can give many individual prints before exhaustion: the dry-ink stamp face effectively de-layers by a set amount each time a print is made. Many consecutive, highly consistent and uniform prints can be made using this approach. When printed onto natural rubber, the printed tracks are very robust and can be stretched to 100 per cent strain without permanent damage. The electrical conductivity can be improved by a simple alcohol treatment to consolidate the fibers and by iodine doping reaching 38 S · cm−1.

Originality/value

– The findings offer an economical way to print highly robust electrically conductive tracks of carbon nanotubes directly onto flexible substrates.
“Tuning” the body of the classical musician
Authors: Gabor Elena
Published: October 2013

Purpose

– The purpose of this paper was to investigate the role of the body in the vocational anticipatory socialization (VAS) processes of classical musicians.

Design/methodology/approach

– Using grounded theory, the paper analyzed semi-structured interviews with 48 musicians (27 children; 21 parents) to understand how classical musicians’ bodies intermediate the meaning of work. The Aristotelian concepts of potentiality and actuality frame this study.

Findings

– The paper reveals that: “tuning” bodies is as important as tuning instruments (body as object of work), and diseases, occupational injuries, and accidents pose challenges to both health and performance (body as obstacle).

Research limitations/implications

– Theoretically, the paper contributes the notion that phases of VAS are fused not just through cognitive and relational processes, but also through embodied learning for classical musicians.

Practical implications

– At the practical level, the paper reminds that the body is an important source of vocational socialization information.

Originality/value

– The paper is filling a gap in organizational literature, which has under addressed the materiality of the body.