bluuebunny/crossref_metadata_2025 huggingface dataset:
Attentional Adjustment to Conflict Strength
Authors: Wendt Mike , Kiesel Andrea , Geringswald Franziska , Purmann Sascha , Fischer Rico
Published: October 2013

Current models of cognitive control assume gradual adjustment of processing selectivity to the strength of conflict evoked by distractor stimuli. Using a flanker task, we varied conflict strength by manipulating target and distractor onset. Replicating previous findings, flanker interference effects were larger on trials associated with advance presentation of the flankers compared to simultaneous presentation. Controlling for stimulus and response sequence effects by excluding trials with feature repetitions from stimulus administration (Experiment 1) or from the statistical analyses (Experiment 2), we found a reduction of the flanker interference effect after high-conflict predecessor trials (i.e., trials associated with advance presentation of the flankers) but not after low-conflict predecessor trials (i.e., trials associated with simultaneous presentation of target and flankers). This result supports the assumption of conflict-strength-dependent adjustment of visual attention. The selective adaptation effect after high-conflict trials was associated with an increase in prestimulus pupil diameter, possibly reflecting increased cognitive effort of focusing attention.
Hsp90 Inhibitors in Clinic
Authors: Avsar Emin
Published: October 2013

Hsp90 has been extensively studied as a viable oncogenic target since 1985, when it was first shown that targeting Hsp90 results in anti-neoplastic effects. Early clinical development was hindered by the fact that both geldanamycin and radicicol, the first biologically occurring compounds shown to inhibit Hsp90, were too toxic for use in the clinic. This limitation was overcome by the development of the first-generation geldanamycin-based compounds, which entered into clinic in 2003. Although, these first-generation compounds showed clinical limitation of use due to hepatotoxicity, development of newer Hsp90 inhibitors have shown early promise. Herein we will review the current landscape of Hsp90 inhibitors.
On the rising motion of a drop in stratified fluids
Authors: Bayareh M. , Doostmohammadi A. , Dabiri S. , Ardekani A. M.
Published: October 2013

The rising dynamics of a deformable drop in a linearly stratified fluid is numerically obtained using a finite-volume/front-tracking method. Our results show that the drag coefficient of a spherical drop in a stratified fluid enhances as \documentclass[12pt]{minimal}\begin{document}$C_{d,s}/C_{d,h}-1\sim Fr_d^{-2.86}$\end{document}Cd,s/Cd,h−1∼Frd−2.86 for drop Froude numbers in the range of 4 < Frd < 16. The role of the deformability of the drop on the temporal evolution of the motion is investigated along with stratification and inertial effects. We also present the important role of stratification on the transient rising motion of the drop. It is shown that a drop can levitate in the presence of a vertical density gradient. The drop undergoes a fading oscillatory motion around its neutrally buoyant position except for high viscosity ratio drops where the oscillation occurs around a density level lighter than the neutral buoyancy level. In addition, a detailed characterization of the flow signature of a rising drop in a linearly stratified fluid including the buoyancy induced vortices and the resultant buoyant jet is presented.
Simulation based planning of surgical interventions in pediatric cardiology
Authors: Marsden Alison L.
Published: October 2013

Hemodynamics plays an essential role in the progression and treatment of cardiovascular disease. However, while medical imaging provides increasingly detailed anatomical information, clinicians often have limited access to hemodynamic data that may be crucial to patient risk assessment and treatment planning. Computational simulations can now provide detailed hemodynamic data to augment clinical knowledge in both adult and pediatric applications. There is a particular need for simulation tools in pediatric cardiology, due to the wide variation in anatomy and physiology in congenital heart disease patients, necessitating individualized treatment plans. Despite great strides in medical imaging, enabling extraction of flow information from magnetic resonance and ultrasound imaging, simulations offer predictive capabilities that imaging alone cannot provide. Patient specific simulations can be used for in silico testing of new surgical designs, treatment planning, device testing, and patient risk stratification. Furthermore, simulations can be performed at no direct risk to the patient. In this paper, we outline the current state of the art in methods for cardiovascular blood flow simulation and virtual surgery. We then step through pressing challenges in the field, including multiscale modeling, boundary condition selection, optimization, and uncertainty quantification. Finally, we summarize simulation results of two representative examples from pediatric cardiology: single ventricle physiology, and coronary aneurysms caused by Kawasaki disease. These examples illustrate the potential impact of computational modeling tools in the clinical setting.
Circulation based models for Boussinesq gravity currents
Authors: Borden Zachary , Meiburg Eckart
Published: October 2013

In addition to the conservation of mass and horizontal momentum, existing analytical models of gravity currents traditionally require an assumption about the conservation or loss of energy along specific streamlines for closure. Here, we show that the front velocity of gravity currents can be predicted as a function of their height from mass and momentum balances alone by considering the evolution of interfacial vorticity. This approach does not require information on the pressure field and therefore avoids the need for the energy conservation arguments invoked by earlier models. Predictions by the new theory are shown to be in close agreement with results from numerical simulations. We also discuss the influence of downstream mixing on the front velocity predicted by this theory.
Linear transport of domain walls confined to propagating 1-D potential wells
Authors: Negotia M. , Hodges M. P. P. , Bryan M. T. , Fry P. W. , Im M.-Y. , Fischer P. , Allwood D. A. , Hayward T. J.
Published: October 2013

We present a method of controllably propagating domain walls (DWs) in magnetic nanowires over extended linear distances by confining them to geometrically defined energy minima. Using simple models, magnetic transmission soft x-ray microscopy and magneto-optic Kerr effect measurements, we show that the technique allows DWs to be moved at arbitrary, user-defined velocities and be positioned with micrometer precision. Our approach is expected to be of utility in applications where the precise transport and positioning of DWs take precedent over the absolute speed of propagation, for example, where the fields produced by DWs are used to trap and transport magnetized particles.
Motional heterogeneity in human acetylcholinesterase revealed by a non-Gaussian model for elastic incoherent neutron scattering
Authors: Peters Judith , Kneller Gerald R.
Published: October 2013

We study the dynamical transition of human acetylcholinesterase by analyzing elastic neutron scattering data with a simulation gauged analytical model that goes beyond the standard Gaussian approximation for the elastic incoherent structure factor [G. R. Kneller and K. Hinsen, J. Chem. Phys. 131, 045104 (2009)]. The model exploits the whole available momentum transfer range in the experimental data and yields not only a neutron-weighted average of the atomic mean square position fluctuations, but also an estimation for their distribution. Applied to the neutron scattering data from human acetylcholinesterase, it reveals a strong increase of the motional heterogeneity at the two transition temperatures T = 150 K and T = 220 K, respectively, which can be located with less ambiguity than with the Gaussian model. We find that the first transition is essentially characterized by a change in the form of the elastic scattering profile and the second by a homogeneous increase of all motional amplitudes. These results are in agreement with previous combined experimental and simulation studies of protein dynamics, which attribute the first transition to an onset of methyl rotations and the second to more unspecific diffusion processes involving large amplitude motions.
Fluctuation driven height reduction of crosslinked polymer brushes: A Monte Carlo study
Authors: Lang M. , Hoffmann M. , Dockhorn R. , Werner M. , Sommer J.-U.
Published: October 2013

We study the changes in the conformations of brushes upon the addition of crosslinks between the chains using the bond fluctuation model. The Flory-Rehner model applied to uniaxially swollen networks predicts a collapse for large degrees of crosslinking q proportional to q−1/3 in disagreement with our simulation data. We show that the height reduction of the brushes is driven by monomer fluctuations in a direction perpendicular to the grafting plane and not due to network elasticity. We observe that the impact of crosslinking is different for reactions between monomers of the same or on different chains. If the length reduction of the effective chain length due to both types of reactions is accounted for in a function β(q), the height of the brush can be derived from a Flory approach for the equilibrium brush height leading to H(q) ≈ Hbβ(q)1/3, whereby Hb denotes the height of the non-crosslinked brush.
Light emission despite doubly-forbidden radiative transitions in AlP/GaP quantum wells: Role of localized states
Authors: Bhuyan Sumi , Mondal Richarj , Khatua Pradip , Semtsiv Mykhaylo , Masselink W. T. , Léotin Jean , Pal Bipul , Bansal Bhavtosh
Published: October 2013

The GaP/AlP/GaP heterostructure has an indirect gap both in real as well as momentum space, making the first order radiative recombination doubly forbidden. Nevertheless, we have observed relatively efficient emission from these structures. This paper comprehensively studies the origin of this improved light emission through a detailed analysis of the photoluminescence (PL) spectra. Our observations suggest that localized excitons within the acceptor states in GaP close to the heterostructure interface are enough for efficient light emission in these structures, doing away with the need for more complicated structures (superlattices or neighboring confinement structures). This real space localization of holes, close to the interface, apart from increasing the wave function overlap, also relaxes the delta-function momentum selection rule. Independent experimental evidence for this assertion comes from (i) the PL spectrum at high excitation power where transitions from both the localized as well as extended states are independently observed, (ii) the observation that extended states emission has the expected band-bending-induced blue-shift with increase in excitation power, whereas the localized states do not, (iii) observation of phonon replicas for PL from localized states, and (iv) observation of persistent photoconductivity at low temperature. Finally, we propose a simple analytical model that accounts for both the type-II nature as well as the indirect bandgap to explain the improvement of radiative recombination efficiency with increased localization. The experimental observations are reproduced within an order of magnitude. The model is very general and it also provides a framework to study the optical properties of other such (type-II and/or indirect gap) heterostructures.
Energy harvesting from electric power lines employing the Halbach arrays
Authors: He Wei , Li Ping , Wen Yumei , Zhang Jitao , Lu Caijiang , Yang Aichao
Published: October 2013

This paper proposes non-invasive energy harvesters to scavenge alternating magnetic field energy from electric power lines. The core body of a non-invasive energy harvester is a linear Halbach array, which is mounted on the free end of a piezoelectric cantilever beam. The Halbach array augments the magnetic flux density on the side of the array where the power line is placed and significantly lowers the magnetic field on the other side. Consequently, the magnetic coupling strength is enhanced and more alternating magnetic field energy from the current-carrying power line is converted into electrical energy. An analytical model is developed and the theoretical results verify the experimental results. A power of 566 μW across a 196 kΩ resistor is generated from a single wire, and a power of 897 μW across a 212 kΩ resistor is produced from a two-wire power cord carrying opposite currents at 10 A. The harvesters employing Halbach arrays for a single wire and a two-wire power cord, respectively, exhibit 3.9 and 3.2 times higher power densities than those of the harvesters employing conventional layouts of magnets. The proposed devices with strong response to the alternating currents are promising to be applied to electricity end-use environment in electric power systems.
Application of recent double-hybrid density functionals to low-lying singlet-singlet excitation energies of large organic compounds
Authors: Meo F. Di , Trouillas P. , Adamo C. , Sancho-García J. C.
Published: October 2013

The present work assesses some recently developed double-hybrid density functionals (B2π-PLYP, PBE0-DH, and PBE0-2) using linear-response Tamm-Dancoff Time-Dependent Density Functional Theory. This assessment is achieved against experimentally derived low-lying excitation energies of large organic dyes of recent interest, including some excitations dominated by charge-transfer transitions. Comparisons are made with some of the best-performing methods established from the literature, such as PBE0 or B3LYP hybrid or the recently proposed B2-PLYP and B2GP-PLYP double-hybrid models, to ascertain their quality and robustness on equal footing. The accuracy of parameter-free or empirical forms of double-hybrid functionals is also briefly discussed. Generally speaking, it turns out that double-hybrid expressions always provide more accurate estimates than corresponding hybrid methods. Double-hybrid functionals actually reach averaged accuracies of 0.2 eV, that can be admittedly considered close to any intended accuracy limit within the present theoretical framework.
Shock response of single crystal and nanocrystalline pentaerythritol tetranitrate: Implications to hotspot formation in energetic materials
Authors: Cai Y. , Zhao F. P. , An Q. , Wu H. A. , Goddard W. A. , Luo S. N.
Published: October 2013

We investigate shock response of single crystal and nanocrystalline pentaerythritol tetranitrate (PETN) with a coarse-grained model and molecular dynamics simulations, as regards mechanical hotspot formation in the absence or presence of grain boundaries (GBs). Single crystals with different orientations, and columnar nanocrystalline PETN with regular hexagonal, irregular hexagonal, and random GB patterns, are subjected to shock loading at different shock strengths. In single crystals, shock-induced plasticity is consistent with resolved shear stress calculations and the steric hindrance model, and this deformation leads to local heating. For regular-shaped hexagonal columnar nanocrystalline PETN, different misorientation angles lead to activation of different/same slip systems, different deformation in individual grains and as a whole, different GB friction, different temperature distributions, and then, different hotspot characteristics. Compared to their regular-shaped hexagonal counterpart, nanocrystalline PETN with irregular hexagonal GB pattern and that with random GBs, show deformation and hotspot features specific to their GBs. Driven by stress concentration, hotspot formation is directly related to GB friction and GB-initiated crystal plasticity, and the exact deformation is dictated by grain orientations and resolved shear stresses. GB friction alone can induce hotspots, but the hotspot temperature can be enhanced if it is coupled with GB-initiated crystal plasticity, and the slip of GB atoms has components out of the GB plane. The magnitude of shearing can correlate well with temperature, but the slip direction of GB atoms relative to GBs may play a critical role. Wave propagation through varying microstructure may also induce differences in stress states (e.g., stress concentrations) and loading rates, and thus, local temperature rise. GB-related friction and plasticity induce local heating or mechanical hotspots, which could be precursors to chemical hotspot formation related to initiation in energetic materials, in the absence of other, likely more effective, means for hotspot formation such as void collapse.
Conduction and relaxation mechanisms in bismuth doped La2Mo2O9 ionic conductors
Authors: Paul T. , Ghosh A.
Published: October 2013

Oxygen ion conduction and relaxation mechanisms in bismuth substituted La2Mo2O9 have been reported in this paper. The phase transition observed in La2Mo2O9 is suppressed in bismuth substituted samples, and the cubic β form is stabilized at room temperature. A transition of the dc anionic conductivity from low temperature Arrhenius type to high temperature Arrhenius type has been observed in La2Mo2O9. However, for bismuth doped samples the dc anionic conductivity shows a transition from Arrhenius behavior at low temperatures to Vogel-Tamman-Fulcher in the high temperature regime. The frequency dependence of the ac conductivity shows a power law behavior. The ac conductivity remains constant in low frequency region but shows dispersion at the crossover frequency. The crossover frequency shifted towards higher value with the increase of temperature. The dimensionality of the conduction space does not change with bismuth doping. The scaling behavior of the conductivity spectra for different temperatures and compositions indicates that dynamics of oxygen ions is independent of temperatures and compositions.
Communication: Ultrafast vibrational dynamics of hydrogen bond network terminated at the air/water interface: A two-dimensional heterodyne-detected vibrational sum frequency generation study
Authors: Singh Prashant Chandra , Nihonyanagi Satoshi , Yamaguchi Shoichi , Tahara Tahei
Published: October 2013

Ultrafast vibrational dynamics of hydrogen bond network at the air/water interface is revealed by two-dimensional heterodyne-detected vibrational sum frequency generation (2D HD-VSFG) spectroscopy. Three diagonal peaks are clearly observed in the 2D HD-VSFG spectrum, which correspond to the negative and positive hydrogen-bonded OH stretch bands and the positive “free” OH stretch band in the steady-state HD-VSFG spectrum. A diagonally elongated bleaching lobe of the hydrogen-bonded OH at 0 ps indicates that it is partly inhomogeneously broadened. This diagonal elongation vanishes in a few hundred femtoseconds, implying the ultrafast spectral diffusion in the hydrogen-bonded OH band. Off-diagonal cross peaks between each OH oscillator are clearly observed instantaneously within the time resolution of 0.2 ps, suggesting that they are vibrationally coupled through anharmonicity and/or energy transfer.
Note: Four-port microfluidic flow-cell with instant sample switching
Authors: MacGriff Christopher A. , Wang Shaopeng , Tao Nongjian
Published: October 2013

A simple device for high-speed microfluidic delivery of liquid samples to a surface plasmon resonance sensor surface is presented. The delivery platform is comprised of a four-port microfluidic cell, two ports serve as inlets for buffer and sample solutions, respectively, and a high-speed selector valve to control the alternate opening and closing of the two outlet ports. The time scale of buffer/sample switching (or sample injection rise and fall time) is on the order of milliseconds, thereby minimizing the opportunity for sample plug dispersion. The high rates of mass transport to and from the central microfluidic sensing region allow for SPR-based kinetic analysis of binding events with dissociation rate constants (kd) up to 130 s−1. The required sample volume is only 1 μL, allowing for minimal sample consumption during high-speed kinetic binding measurement.
Improved stability of amorphous zinc tin oxide thin film transistors using molecular passivation
Authors: Rajachidambaram M. S. , Pandey A. , Vilayurganapathy S. , Nachimuthu P. , Thevuthasan S. , Herman G. S.
Published: October 2013

The role of back channel surface chemistry on amorphous zinc tin oxide (ZTO) bottom gate thin film transistors (TFTs) has been characterized by positive bias-stress measurements and x-ray photoelectron spectroscopy. Positive bias-stress turn-on voltage shifts for ZTO-TFTs were significantly reduced by passivation of back channel surfaces with self-assembled monolayers of n-hexylphosphonic acid when compared to ZTO-TFTs with no passivation. These results indicate that adsorption of molecular species on the exposed back channel of ZTO-TFTs strongly influence observed turn-on voltage shifts, as opposed to charge injection into the dielectric or trapping due to oxygen vacancies.
Background limited ultraviolet photodetectors of solar-blind ultraviolet detection
Authors: Li Xiang , Zhu Chenxin , Zhu Xi , Xu Zhihuang , Zhuang Xinxin , Ji Xiaoli , Yan Feng
Published: October 2013

The background noise in solar-blind ultraviolet (UV) detectors from the solar-irradiance leakage photons has been compared with the detector noise from the dark current. It has been found that the background noise is the deterministic limiting factor in solar-blind UV photodetection. The detector performance of background limited ultraviolet photodetector limit and the ultimate signal fluctuation limit are therefore proposed. It proves to be an effective method for device optimization by suppressing the declining tails above 285 nm in the response curves. The absorptive spectral filter requirement has been discussed for common solar-blind UV detectors to achieve the detectivity improvement.
In situ gas analysis for high pressure applications using property measurements
Authors: Moeller J. , Span R. , Fieback T.
Published: October 2013

As the production, distribution, and storage of renewable energy based fuels usually are performed under high pressures and as there is a lack of in situ high pressure gas analysis instruments on the market, the aim of this work was to develop a method for in situ high pressure gas analysis of biogas and hydrogen containing gas mixtures. The analysis is based on in situ measurements of optical, thermo physical, and electromagnetic properties in gas mixtures with newly developed high pressure sensors. This article depicts the calculation of compositions from the measured properties, which is carried out iteratively by using highly accurate equations of state for gas mixtures. The validation of the method consisted of the generation and measurement of several mixtures, of which three are presented herein: a first mixture of 64.9 mol. % methane, 17.1 mol. % carbon dioxide, 9 mol. % helium, and 9 mol. % ethane at 323 K and 423 K in a pressure range from 2.5 MPa to 17 MPa; a second mixture of 93.0 mol. % methane, 4.0 mol. % propane, 2.0 mol. % carbon dioxide, and 1.0 mol. % nitrogen at 303 K, 313 K, and 323 K in a pressure range from 1.2 MPa to 3 MPa; and a third mixture of 64.9 mol. % methane, 30.1 mol. % carbon dioxide, and 5.0 mol. % nitrogen at 303 K, 313 K, and 323 K in a pressure range from 2.5 MPa to 4 MPa. The analysis of the tested gas mixtures showed that with measured density, velocity of sound, and relative permittivity the composition can be determined with deviations below 1.9 mol. %, in most cases even below 1 mol. %. Comparing the calculated compositions with the generated gas mixture, the deviations were in the range of the combined uncertainty of measurement and property models.
Graphene/polydimethylsiloxane nanocomposite strain sensor
Authors: Wang Bo , Lee Bong-Kee , Kwak Min-Joo , Lee Dong-Weon
Published: October 2013

The objective of this research is to fabricate graphene nanopowder composites based on polydimethylsiloxane (PDMS) and to characterize the gauge factor of the graphene/PDMS composites for the use of strain sensors. The fabrication of graphene/PDMS composites can be accomplished by simple sonication and micro molding processes. We found that the measured gauge factors strongly depend on the concentration of graphene flakes in the composites. Obtained gauge factor of the graphene/PDMS composite strain sensor reached about 233 at a graphene concentration of 8.33 vol.%, which was measured within a strain range of 2%.
Coherent transverse-optical phonon generation induced by lattice defects in nitrogen-ion-implanted GaAs
Authors: Kim J. S. , Ryu H. C. , Kim S. H. , Kim H. , Rho H. , Kim Y. J. , Lim Y. S. , Yee K. J.
Published: October 2013

We describe our observation of coherent phonon oscillations of X-point zone-boundary transverse-optical (TO) mode, TO(X), in nitrogen-ion-implanted GaAs that has been annealed at high temperatures. With the TO(X) mode being forbidden from the Raman selection rule in pure zinc-blende GaAs, the lattice defects have provided additional momentum for phonon generation. Annealing-induced structural modifications were demonstrated through X-ray diffraction, transmission electron microscopy, and Raman scattering measurements. The polarization dependence of the TO(X) mode was compared with that of the longitudinal optical mode, and the temperature dependence of the TO(X) phonon dephasing was also investigated.
Experimental study of self magnetic pinch diode as flash radiography source at 4 megavolt
Authors: Etchessahar Bertrand , Maisonny Rémi , Toury Martial , Hourdin Laurent , Bicrel Béatrice , Cassany Bruno , Desanlis Thierry , Voisin Luc , Cartier Frédéric , Cartier Stéphanie , D'Almeida Thierry , Delbos Christophe , Garrigues Alain , Plouhinec Damien , Ritter Sandra , Sol David , Zucchini Frédéric , Caron Michel
Published: October 2013

The Self Magnetic Pinch (SMP) diode is a potential high-brightness X-ray source for high voltage generators (2–10 MV) that has shown good reliability for flash radiography applications [D. D. Hinchelwood et al., “High power self-pinch diode experiments for radiographic applications” IEEE Trans. Plasma Sci. 35(3), 565–572 (2007)]. We have studied this diode at about 4 MV, driven by the ASTERIX generator operated at the CEA/GRAMAT [G. Raboisson et al., “ASTERIX, a high intensity X-ray generator,” in Proceedings of the 7th IEEE Pulsed Power Conference (1989), pp. 567–570]. This generator, made up of a capacitor bank and a Blumlein line, was initially designed to test the behavior of electronic devices under irradiation. In our experiments, the vacuum diode is modified in order to set up flash radiographic diodes. A previous set of radiographic experiments was carried out on ASTERIX with a Negative Polarity Rod Pinch (NPRP) diode [B. Etchessahar et al., “Study and optimization of negative polarity rod pinch diode as flash radiography source at 4.5 MV,” Phys. Plasmas 19(9), 093104 (2012)]. The SMP diode which is examined in the present study provides an alternative operating point on the same generator and a different radiographic performance: 142 ± 11 rad at 1 m dose (Al) for a 3.46 ± 0.42 mm spot size (1.4× FWHM of the LSF). This performance is obtained in a reproducible and robust nominal configuration. However, several parametric variations were also tested, such as cathode diameter and anode/cathode gap. They showed that an even better performance is accessible after optimization, in particular, a smaller spot size (<3 mm). Numbers of electrical, optical, and X-ray diagnostics have been implemented in order to gain more insight in the diode physics and to optimize it further. For the first time in France, visible and laser imaging of the SMP diode has been realized, from a radial point of view, thus, providing key information on the electrode plasmas evolution, responsible for the gap closure.
The macroscopic polarization effect on thermal conductivity of binary nitrides
Authors: Sahoo S. K. , Sahoo B. K. , Sahoo S.
Published: October 2013

We theoretically investigate the effect of macroscopic polarization on phonon thermal conductivity of wurtzite (WZ) binary nitrides (AlN, GaN and InN). Our results show that macroscopic polarization contributes to the effective elastic constant of the wurtzite nitrides and modifies the phonon group velocity, Debye frequency, and Debye temperature. Using revised phonon velocity and Debye temperature, different phonon scattering rates and combined scattering rate are calculated as functions of the phonon frequency at room temperature. We estimate phonon thermal conductivity of binary nitrides using these modified parameters. The theoretical analysis shows that up to a certain temperature (different for AlN, GaN, and InN) the polarization effect acts as ill effect and reduces the thermal conductivity. However, after this temperature, the thermal conductivity is significantly enhanced by the polarization effect. The revised thermal conductivity at room temperature is found to be increased by 12% in GaN, 18% in InN and 20% in case of AlN due to macroscopic polarization, i.e., maximum polarization effect is observed in AlN and minimum in GaN. The method we have developed can be used for calculation of thermal energy in the active region of nitride optoelectronic devices.
High ferromagnetic transition temperature in multiferroic BiFe0.95Ni0.05O3 compound
Authors: Yoo Y. J. , Hwang J. S. , Lee Y. P. , Park J. S. , Kang J.-H. , Kim J. , Lee B. W. , Seo M. S.
Published: October 2013

We have prepared BiFe0.95Ni0.05O3 by the standard solid-state reaction and rapid sintering. The structural analysis by x-ray diffraction for BiFe0.95Ni0.05O3 shows rhombohedral perovskite structure (R3c), and lattice constants a and c of BiFe0.95Ni0.05O3 are slightly increased as compared to those of BiFeO3. The Raman studies present the increase of oxygen vacancy by the Ni2+ substitution. The magnetic properties of BiFe0.95Ni0.05O3 are greatly improved, owing to the enhanced ferromagnetic interaction caused by the Fe/Ni coupling. BiFe0.95Ni0.05O3 sample is ferromagnetic with a cluster-glass state unlike the antiferromagnetic BiFeO3-based compounds.
Control of the quantum interference in a superconducting qubit system
Authors: Ying Hao , Luo Da-Wei , Xu Jing-Bo
Published: October 2013

We propose a scheme to control quantum interference pattern in a system of a superconducting qubit coupled to its own data bus by applying a controllable time-dependent electromagnetic field. It is shown that the quantum interference induced by the initial phase difference is closely related to the quantum correlations between two superconducting qubits which are coupled to their own data bus and the geometric discord can also be increased by applying the controllable electromagnetic field.
Micro-textures for efficient light trapping and improved electrical performance in thin-film nanocrystalline silicon solar cells
Authors: Tan Hairen , Psomadaki Efthymia , Isabella Olindo , Fischer Marinus , Babal Pavel , Vasudevan Ravi , Zeman Miro , Smets Arno H. M.
Published: October 2013

Micro-textures with large opening angles and smooth U-shape are applied to nanocrystalline silicon (nc-Si:H) solar cells. The micro-textured substrates result in higher open-circuit-voltage (Voc) and fill-factor (FF) than nano-textured substrates. For thick solar cells, high Voc and FF are maintained. Particularly, the Voc only drops from 564 to 541 mV as solar cell thickness increases from 1 to 5 μm. The improvement in electrical performance of solar cells is ascribed to the growth of dense nc-Si:H layers free from defective filaments on micro-textured substrates. Thereby, micromorph tandem solar cells with an initial efficiency of 13.3%, Voc = 1.464 V, and FF = 0.759 are obtained.
Transport properties of single TiO2 nanotubes
Authors: Stiller Markus , Barzola-Quiquia José , Lorite Israel , Esquinazi Pablo , Kirchgeorg Robin , Albu Sergiu P. , Schmuki Patrik
Published: October 2013

We investigated the electric transport properties of single TiO2 nanotubes separated from an anodic titania nanotube array. The temperature dependence of the resistance measured with the conventional four point method of all investigated samples show a Mott variable range hopping behavior. The results obtained with two contacts indicate the existence of a potential barrier between the Cr/Au contacts and samples surfaces, which influence is clearly observable at temperatures <150 K. Impedance spectroscopy in the frequency range of 40 Hz to 1 MHz carried out at room temperature indicates that the electronic transport of these polycrystalline tubes is dominated by the grain cores.
Analysis of small vertical wind turbine having H-Darrieus blades with stall delay model
Authors: Tai Feng-Zhu , Yun Teak-Han , Kang Ki-Weon , Lee Jang-Ho
Published: October 2013

Several models, about the power performance prediction for the Darrieus wind turbines, have been developed during the last decades. Among these models, an enhanced multiple stream tubes model, LDWT (Lee-Darrieus Wind Turbine model) for Darrieus wind turbine blade with experimental aerofoil characteristics showed simple, fast, and precise results, without time consuming, of solving Reynolds Averaged Navier-Stokes equation for the complex air flow passing through rotational blade. Recent interest has been paid on the straight Darrieus rotor blade (H-Darrieus rotor) because of its several advantages over the curved blades. However, few reports cover its power performance prediction model. In this paper, the LDWT was extended into the H-Darrieus rotor with 2-dimensional experimental data and stall delay model. From results for the high solidity H-Darrieus rotor, LDWT underestimate the test data without stall delay model, but it shows dramatically well matching with test data when stall delaying is calculated additionally in the model. Therefore, it is shown that the model with stall delaying can be used for the design and analysis of H-type vertical wind turbine blade without solving of Navier-Stokes equation.
High power terahertz quantum cascade lasers with symmetric wafer bonded active regions
Authors: Brandstetter Martin , Deutsch Christoph , Krall Michael , Detz Hermann , MacFarland Donald C. , Zederbauer Tobias , Andrews Aaron M. , Schrenk Werner , Strasser Gottfried , Unterrainer Karl
Published: October 2013

We increased the active region/waveguide thickness of terahertz quantum cascade lasers with semi-insulating surface plasmon waveguides by stacking two symmetric active regions on top of each other, via a direct wafer bonding technique. In this way, we enhance the generated optical power in the cavity and the mode confinement. We achieved 470 mW peak output power in pulsed mode from a single facet at a heat sink temperature of 5 K and a maximum operation temperature of 122 K. Furthermore, the devices show a broad band emission spectrum over a range of 420 GHz, centered around 3.9 THz.
EZH2 is essential for development of mouse preimplantation embryos
Authors: Huang Xian-Ju , Wang Xuguang , Ma Xueshan , Sun Shao-Chen , Zhou Xiaolong , Zhu Chengcheng , Liu Honglin
Published: October 2013

Enhancer of zeste homologue 2 (Ezh2) is essential for the development of the early mouse preimplantation embryo. Loss of Ezh2 results in embryonic lethality in mice. Ezh2-deficient embryos display impaired outgrowth potential, defective establishment of Ezh2-null embryonic stem (ES) cells and adherence and differentiation of the trophoblast layer into giant cells. We investigated if Ezh2 controls the fate of embryos at an earlier stage by treating with cycloheximide (CHX) or microinjecting short interfering RNA (siRNA) to restrict embryonic Ezh2 expression during preimplantation. CHX inhibited de novo EZH2 protein synthesis in zygotes, suggesting that EZH2 requires de novo synthesis during post-fertilisation stages. We found that loss of Ezh2 at the pronuclear stage caused severe growth retardation and reduced blastocyst formation. Expression of the pluripotency-associated markers Oct4, Sox2 and Nanog were significantly decreased in embryos that had been injected with Ezh2 siRNA. In addition, Ezh2 loss induced upregulated expression of genes related to the differentiation of germ layers, including Gata6, Hoxb1 and Hand1. Finally, apoptosis was increased in the blastocyst embryos with Ezh2 knockdown. Modification of histone H3-Lysine 27 de-methylation and tri-methylation (H3K27me2/3) was strongly reduced in Ezh2 siRNA embryos. We conclude that Ezh2 is essential for early preimplantation embryo development through the regulation of epigenetic modification and apoptosis.
Transcript processing and export kinetics are rate-limiting steps in expressing vertebrate segmentation clock genes
Authors: Hoyle Nathaniel P. , Ish-Horowicz David
Published: October 2013

Significance

This paper describes in vivo measurements of the kinetics of transcript processing and export for endogenous genes in mouse and chick embryos. It shows that transcript export is unexpectedly slow, even slower than splicing, and relates its finding to rate-limiting steps that would contribute to the molecular oscillator that drives segmentation in vertebrate embryos. It also relates them to interspecies differences in clock period.
Inferring the soybean (Glycine max) microRNA functional network based on target gene network
Authors: Xu Yungang , Guo Maozu , Liu Xiaoyan , Wang Chunyu , Liu Yang
Published: October 2013

Motivation: The rapid accumulation of microRNAs (miRNAs) and experimental evidence for miRNA interactions has ushered in a new area of miRNA research that focuses on network more than individual miRNA interaction, which provides a systematic view of the whole microRNome. So it is a challenge to infer miRNA functional interactions on a system-wide level and further draw a miRNA functional network (miRFN). A few studies have focused on the well-studied human species; however, these methods can neither be extended to other non-model organisms nor take fully into account the information embedded in miRNA–target and target–target interactions. Thus, it is important to develop appropriate methods for inferring the miRNA network of non-model species, such as soybean (Glycine max), without such extensive miRNA-phenotype associated data as miRNA-disease associations in human.

Results: Here we propose a new method to measure the functional similarity of miRNAs considering both the site accessibility and the interactive context of target genes in functional gene networks. We further construct the miRFNs of soybean, which is the first study on soybean miRNAs on the network level and the core methods can be easily extended to other species. We found that miRFNs of soybean exhibit a scale-free, small world and modular architecture, with their degrees fit best to power-law and exponential distribution. We also showed that miRNA with high degree tends to interact with those of low degree, which reveals the disassortativity and modularity of miRFNs. Our efforts in this study will be useful to further reveal the soybean miRNA–miRNA and miRNA–gene interactive mechanism on a systematic level.

Availability and implementation: A web tool for information retrieval and analysis of soybean miRFNs and the relevant target functional gene networks can be accessed at SoymiRNet: http://nclab.hit.edu.cn/SoymiRNet.

Contact:  maozuguo@hit.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Parallel Tempering algorithm for probabilistic sampling and multimodal optimization
Authors: Sambridge Malcolm
Published: October 2013

Non-linear inverse problems in the geosciences often involve probabilistic sampling of multimodal density functions or global optimization and sometimes both. Efficient algorithmic tools for carrying out sampling or optimization in challenging cases are of major interest. Here results are presented of some numerical experiments with a technique, known as Parallel Tempering, which originated in the field of computational statistics but is finding increasing numbers of applications in fields ranging from Chemical Physics to Astronomy. To date, experience in use of Parallel Tempering within earth sciences problems is very limited. In this paper, we describe Parallel Tempering and compare it to related methods of Simulated Annealing and Simulated Tempering for optimization and sampling, respectively. A key feature of Parallel Tempering is that it satisfies the detailed balance condition required for convergence of Markov chain Monte Carlo (McMC) algorithms while improving the efficiency of probabilistic sampling. Numerical results are presented on use of Parallel Tempering for trans-dimensional inversion of synthetic seismic receiver functions and also the simultaneous fitting of multiple receiver functions using global optimization. These suggest that its use can significantly accelerate sampling algorithms and improve exploration of parameter space in optimization. Parallel Tempering is a meta-algorithm which may be used together with many existing McMC sampling and direct search optimization techniques. It's generality and demonstrated performance suggests that there is significant potential for applications to both sampling and optimization problems in the geosciences.
Disruptive camouflage impairs object recognition
Authors: Webster Richard J. , Hassall Christopher , Herdman Chris M. , Godin Jean-Guy J. , Sherratt Thomas N.
Published: October 2013

Whether hiding from predators, or avoiding battlefield casualties, camouflage is widely employed to prevent detection. Disruptive coloration is a seemingly well-known camouflage mechanism proposed to function by breaking up an object's salient features (for example their characteristic outline), rendering objects more difficult to recognize. However, while a wide range of animals are thought to evade detection using disruptive patterns, there is no direct experimental evidence that disruptive coloration impairs recognition. Using humans searching for computer-generated moth targets, we demonstrate that the number of edge-intersecting patches on a target reduces the likelihood of it being detected, even at the expense of reduced background matching. Crucially, eye-tracking data show that targets with more edge-intersecting patches were looked at for longer periods prior to attack, and passed-over more frequently during search tasks. We therefore show directly that edge patches enhance survivorship by impairing recognition, confirming that disruptive coloration is a distinct camouflage strategy, not simply an artefact of background matching.
Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques
Authors: Gobet Angélique , Boetius Antje , Ramette Alban
Published: October 2013

Changes in richness and bacterial community structure obtained via 454 Massively Parallel Tag Sequencing (MPTS) and Automated Ribosomal Intergenic Analysis (ARISA) were systematically compared to determine whether and how the ecological knowledge obtained from both molecular techniques could be combined. We evaluated community changes over time and depth in marine coastal sands at different levels of taxonomic resolutions, sequence corrections and sequence abundances. Although richness over depth layers or sampling dates greatly varied [∼ 30% and 70–80% new operational taxonomic units (OTU) between two samples with ARISA and MPTS respectively], overall patterns of community variations were similar with both approaches. Alpha‐diversity estimated by ARISA‐derived OTU was most similar to that obtained from MPTS‐derived OTU defined at the order level. Similar patterns of OTU replacement were also found with MPTS at the family level and with 20–25% rare types removed. Using ARISA or MPTS datasets with lower resolution, such as those containing only resident OTU, yielded a similar set of significant contextual variables explaining bacterial community changes. Hence, ARISA as a rapid and low‐cost fingerprinting technique represents a valid starting point for more in‐depth exploration of community composition when complemented by the detailed taxonomic description offered by MPTS.
Borrelia chilensis, a new member of theBorrelia burgdorferisensu lato complex that extends the range of this genospecies in theSouthernHemisphere
Authors: Ivanova Larisa B. , Tomova Alexandra , González‐Acuña Daniel , Murúa Roberto , Moreno Claudia X. , Hernández Claudio , Cabello Javier , Cabello Carlos , Daniels Thomas J. , Godfrey Henry P. , Cabello Felipe C.
Published: October 2013

Borrelia burgdorferisensu lato (s.l.), transmitted byIxodesspp. ticks, is the causative agent ofLyme disease. AlthoughIxodesspp. ticks are distributed in bothNorthern andSouthernHemispheres, evidence for the presence ofB. burgdorferis.l. inSouthAmerica apart fromUruguay is lacking. We now report the presence of culturable spirochetes with flat‐wave morphology and borrelialDNAin endemicIxodes stilesiticks collected inChile from environmental vegetation and long‐tailed rice rats (Oligoryzomys longicaudatus). Cultured spirochetes and borrelialDNAin ticks were characterized by multilocus sequence typing and by sequencing five other loci (16Sand 23Sribosomal genes, 5S–23Sintergenic spacer,flaB,ospC). Phylogenetic analysis placed this spirochete as a new genospecies within theLyme borreliosis group. Its plasmid profile determined by polymerase chain reaction and pulsed‐field gel electrophoresis differed from that ofB. burgdorferi B31A3. We propose naming this newSouthAmerican member of theLyme borreliosis groupB. chilensis VA1 in honor of its country of origin.
Software platforms to facilitate reconstructing genome‐scale metabolic networks
Authors: Hamilton Joshua J. , Reed Jennifer L.
Published: October 2013

System‐level analyses of microbial metabolism are facilitated by genome‐scale reconstructions of microbial biochemical networks. A reconstruction provides a structured representation of the biochemical transformations occurring within an organism, as well as the genes necessary to carry out these transformations, as determined by the annotated genome sequence and experimental data. Network reconstructions also serve as platforms for constraint‐based computational techniques, which facilitate biological studies in a variety of applications, including evaluation of network properties, metabolic engineering and drug discovery. Bottom‐up metabolic network reconstructions have been developed for dozens of organisms, but until recently, the pace of reconstruction has failed to keep up with advances in genome sequencing. To address this problem, a number of software platforms have been developed to automate parts of the reconstruction process, thereby alleviating much of the manual effort previously required. Here, we review four such platforms in the context of established guidelines for network reconstruction. While many steps of the reconstruction process have been successfully automated, some manual evaluation of the results is still required to ensure a high‐quality reconstruction. Widespread adoption of these platforms by the scientific community is underway and will be further enabled by exchangeable formats across platforms.