bluuebunny/crossref_metadata_2025 huggingface dataset:
Low Mach number fluctuating hydrodynamics of multispecies liquid mixtures
Authors: Donev Aleksandar , Nonaka Andy , Bhattacharjee Amit Kumar , Garcia Alejandro L. , Bell John B.
Published: March 2015

We develop a low Mach number formulation of the hydrodynamic equations describing transport of mass and momentum in a multispecies mixture of incompressible miscible liquids at specified temperature and pressure, which generalizes our prior work on ideal mixtures of ideal gases [Balakrishnan et al., “Fluctuating hydrodynamics of multispecies nonreactive mixtures,” Phys. Rev. E 89 013017 (2014)] and binary liquid mixtures [Donev et al., “Low mach number fluctuating hydrodynamics of diffusively mixing fluids,” Commun. Appl. Math. Comput. Sci. 9(1), 47-105 (2014)]. In this formulation, we combine and extend a number of existing descriptions of multispecies transport available in the literature. The formulation applies to non-ideal mixtures of arbitrary number of species, without the need to single out a “solvent” species, and includes contributions to the diffusive mass flux due to gradients of composition, temperature, and pressure. Momentum transport and advective mass transport are handled using a low Mach number approach that eliminates fast sound waves (pressure fluctuations) from the full compressible system of equations and leads to a quasi-incompressible formulation. Thermal fluctuations are included in our fluctuating hydrodynamics description following the principles of nonequilibrium thermodynamics. We extend the semi-implicit staggered-grid finite-volume numerical method developed in our prior work on binary liquid mixtures [Nonaka et al., “Low mach number fluctuating hydrodynamics of binary liquid mixtures,” arXiv:1410.2300 (2015)] and use it to study the development of giant nonequilibrium concentration fluctuations in a ternary mixture subjected to a steady concentration gradient. We also numerically study the development of diffusion-driven gravitational instabilities in a ternary mixture and compare our numerical results to recent experimental measurements [Carballido-Landeira et al., “Mixed-mode instability of a miscible interface due to coupling between Rayleigh–Taylor and double-diffusive convective modes,” Phys. Fluids 25, 024107 (2013)] in a Hele-Shaw cell. We find that giant nonequilibrium fluctuations can trigger the instability but are eventually dominated by the deterministic growth of the unstable mode, in both quasi-two-dimensional (Hele-Shaw) and fully three-dimensional geometries used in typical shadowgraph experiments.
Comment on “A model for phosphate glass topology considering the modifying ion sub-network” [J. Chem. Phys. 140, 154501 (2014)]
Authors: Sidebottom David L.
Published: March 2015

In a recent paper, Hermansen, Mauro, and Yue [J. Chem. Phys. 140, 154501 (2014)] applied the temperature-dependent constraint theory to model both the glass transition temperature, Tg, and fragility, m, of a series of binary alkali phosphate glasses of the form R2OxP2O51−x, where R represents an alkali species. Key to their success seems to be the retention of linear constraints between the alkali ion (R+) and the non-bridging oxygens near Tg, which allows the model to mimic a supposed minimum for both Tg(x) and m(x) located near x = 0.2. However, the authors have overlooked several recent studies that clearly show there is no minimum in m(x). We argue that the retention of the alkali ion constraints at these temperatures is unjustified and question whether the model calculations can be revised to meet the actual experimental data. We also discuss alternative interpretations for the fragility based on two-state thermodynamics that can accurately account for its compositional dependence.
Differential cross sections for electron impact excitation of the electronic bands of phenol
Authors: Neves R. F. C. , Jones D. B. , Lopes M. C. A. , Nixon K. L. , da Silva G. B. , Duque H. V. , de Oliveira E. M. , da Costa R. F. , Varella M. T. do N. , Bettega M. H. F. , Lima M. A. P. , Ratnavelu K. , García G. , Brunger M. J.
Published: March 2015

We report results from a joint theoretical and experimental investigation into electron scattering from the important organic species phenol (C6H5OH). Specifically, differential cross sections (DCSs) have been measured and calculated for the electron-impact excitation of the electronic states of C6H5OH. The measurements were carried out at energies in the range 15–40 eV, and for scattered-electron angles between 10∘ and 90∘. The energy resolution of those experiments was typically ∼80 meV. Corresponding Schwinger multichannel method with pseudo-potentials calculations, with and without Born-closure, were also performed for a sub-set of the excited electronic-states that were accessed in the measurements. Those calculations were conducted at the static exchange plus polarisation (SEP)-level using a minimum orbital basis for single configuration interaction (MOBSCI) approach. Agreement between the measured and calculated DCSs was typically fair, although to obtain quantitative accord, the theory would need to incorporate even more channels into the MOBSCI.
Nonadiabatic nuclear dynamics of the ammonia cation studied by surface hopping classical trajectory calculations
Authors: Belyaev Andrey K. , Domcke Wolfgang , Lasser Caroline , Trigila Giulio
Published: March 2015

The Landau–Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn–Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.
The effect of non-uniform mass loading on the linear, temporal development of particle-laden shear layers
Authors: Senatore Giacomo , Davis Sean , Jacobs Gustaaf
Published: March 2015

The effect of non-uniformity in bulk particle mass loading on the linear development of a particle-laden shear layer is analyzed by means of a stochastic Eulerian-Eulerian model. From the set of governing equations of the two-fluid model, a modified Rayleigh equation is derived that governs the linear growth of a spatially periodic disturbance. Eigenvalues for this Rayleigh equation are determined numerically using proper conditions at the co-flowing gas and particle interface locations. For the first time, it is shown that non-uniform loading of small-inertia particles (Stokes number (St) <0.2) may destabilize the inviscid mixing layer development as compared to the pure-gas flow. The destabilization is triggered by an energy transfer rate that globally flows from the particle phase to the gas phase. For intermediate St (1 < St < 10), a maximum stabilizing effect is computed, while at larger St, two unstable modes may coexist. The growth rate computations from linear stability analysis are verified numerically through simulations based on an Eulerian-Lagrangian (EL) model based on the inviscid Euler equations and a point particle model. The growth rates found in numerical experiments using the EL method are in very good agreement with growth rates from the linear stability analysis and validate the destabilizing effect induced by the presence of particles with low St.
Compressed exponential decays in correlation experiments: The influence of temperature gradients and convection
Authors: Gabriel Jan , Blochowicz Thomas , Stühn Bernd
Published: March 2015

In a wide range of soft materials, correlation experiments using laser light or partially coherent X-rays report the so called compressed exponential correlation functions, i. e., decays c(t) ∝ exp(−(t/τ)β) with β > 1. In many cases, this is related to the relaxation of inner stresses, but in some systems, the source of such a phenomenon is still poorly understood. We performed multi speckle-dynamic light scattering experiments in a system of polystyrene spheres in supercooled propanediol. At low temperatures, compressed exponential decays are observed in a multispeckle experiment, in agreement with the literature findings in similar systems. At the same time, due to the particular geometry of our setup, the speckle pattern shows indication for convection in the sample due to a slight temperature gradient across the sample cuvette mounted in a cold finger cryostat. These effects increase with decreasing temperature and after a temperature jump. In some cases it can be corrected for by assuming convective flow at constant velocity. Such corrections reduce or remove compressed exponential behavior in our experiment.
Relationships between the surface electronic and chemical properties of doped 4d and 5d late transition metal dioxides
Authors: Xu Zhongnan , Kitchin John R.
Published: March 2015

Density functional theory calculations were performed to elucidate the underlying physics describing the adsorption energies on doped late transition metal dioxide rutiles. Adsorption energies of atomic oxygen on doped rutiles MD-MHO2, where transition metal MD is doped into MHO2, were expressed in terms of a contribution from adsorption on the pure oxide of the dopant MD and perturbations to this adsorption energy caused by changing its neighboring metal cations and lattice parameters to that of the host oxide MHO2, which we call the ligand and strain effects, respectively. Our analysis of atom projected density of states revealed that the t2g-band center had the strongest correlation with adsorption energies. We show that charge transfer mediated shifts to the t2g-band center describe the ligand effect, and the radii of the atomic orbitals of metal cations can predict the magnitude and direction of this charge transfer. Strain produces systematic shifts to all features of the atom projected density of states, but correlations between the strain effect and the electronic structure were dependent on the chemical identity of the metal cation. The slope of these correlations can be related to the idealized d-band filling. This work elucidates the underlying physics describing adsorption on doped late transition metal oxides and establishes a foundation for models that use known chemical properties for the prediction of reactivity.
A new Preisach type hysteresis model of high temperature superconductors
Authors: Duan Nana , Xu Weijie , Wang Shuhong , Zhu Jianguo , Guo Youguang
Published: March 2015

This paper presents a new Preisach type hysteresis model for the high temperature superconductor. This model requires only the limiting hysteresis loop as the input data, and for this model, the limiting hysteresis loop is first separated into two limiting M−H loops based on the mechanisms, which can then be modeled by two separate modified Preisach algorithms. The area integrations of the Preisach distribution functions are determined only based on the limiting M−H loops. The validity and accuracy of this model is confirmed by comparing the simulation and experiment results of Bi-2223 and YBa2Cu3Ox superconducting tapes with external magnetic fields.
New X-ray insight into oxygen intercalation in epitaxial graphene grown on 4H-SiC(0001)
Authors: Kowalski G. , Tokarczyk M. , Dąbrowski P. , Ciepielewski P. , Możdżonek M. , Strupiński W. , Baranowski J. M.
Published: March 2015

Efficient control of intercalation of epitaxial graphene by specific elements is a way to change properties of the graphene. Results of several experimental techniques, such as X-ray photoelectron spectroscopy, micro-Raman mapping, reflectivity, attenuated total reflection, X-ray diffraction, and X-ray reflectometry, gave a new insight into the intercalation of oxygen in the epitaxial graphene grown on 4H-SiC(0001). These results confirmed that oxygen intercalation decouples the graphene buffer layer from the 4H-SiC surface and converts it into the graphene layer. However, in contrast to the hydrogen intercalation, oxygen does not intercalate between carbon planes (in the case of few layer graphene) and the interlayer spacing stays constant at the level of 3.35–3.32 Å. Moreover, X-ray reflectometry showed the presence of an oxide layer having the thickness of about 0.8 Å underneath the graphene layers. Apart from the formation of the nonuniform thin oxide layer, generation of defects in graphene caused by oxygen was also evidenced. Last but not least, water islands underneath defected graphene regions in both intercalated and non-intercalated samples were most probably revealed. These water islands are formed in the case of all the samples stored under ambient laboratory conditions. Water islands can be removed from underneath the few layer graphene stacks by relevant thermal treatment or by UV illumination.
Acoustic non-diffracting Airy beam
Authors: Lin Zhou , Guo Xiasheng , Tu Juan , Ma Qingyu , Wu Junru , Zhang Dong
Published: March 2015

The acoustic non-diffracting Airy beam as its optical counterpart has unique features of self-bending and self-healing. The complexity of most current designs handicaps its applications. A simple design of an acoustic source capable of generating multi-frequency and broad-band acoustic Airy beam has been theoretically demonstrated by numerical simulations. In the design, a piston transducer is corrugated to induce spatial phase variation for transducing the Airy function. The piston's surface is grooved in a pattern that the width of each groove corresponds to the half wavelength of Airy function. The resulted frequency characteristics and its dependence on the size of the piston source are also discussed. This simple design may promote the wide applications of acoustic Airy beam particularly in the field of medical ultrasound.
Study of the effects of metalloid elements (P, C, B) on Fe-based amorphous alloys by ab initio molecular dynamics simulations
Authors: Zhang Wenbiao , Li Qiang , Duan Haiming
Published: March 2015

In order to understand the effects of the metalloid elements M (M: P, C, B) on the atomic structure, glass formation ability (GFA) and magnetic properties of Fe-based amorphous alloys, Fe80P13C7, Fe80P14B6 and Fe80B14C6 amorphous alloys are chosen to study through first-principle simulations in the present work. The atomic structure characteristic of the three amorphous alloys is investigated through the pair distribution functions (PDFs) and Voronoi Polyhedra (VPs) analyses. The PDFs and VPs analyses suggest that the GFA of the three alloys dropped in the order of Fe80P13C7, Fe80P14B6, and Fe80B14C6, which is well consistent with the experimental results. The density of state (DOS) of the three amorphous alloys is calculated to investigate their magnetic properties. Based on the DOS analysis, the average magnetic moment of Fe atom in Fe80P13C7 and Fe80P14B6 amorphous alloys can be estimated to be 1.71 μB and 1.70 μB, respectively, which are in acceptable agreement with the experimental results. However, the calculated average magnetic moment of Fe atom in Fe80B14C6 amorphous alloy is about 1.62 μB, which is far less than the experimental result.
Integrated polymer micro-ring resonators for optical sensing applications
Authors: Girault Pauline , Lorrain Nathalie , Poffo Luiz , Guendouz Mohammed , Lemaitre Jonathan , Carré Christiane , Gadonna Michel , Bosc Dominique , Vignaud Guillaume
Published: March 2015

Micro-resonators (MR) have become a key element for integrated optical sensors due to their integration capability and their easy fabrication with low cost polymer materials. Nowadays, there is a growing need on MRs as highly sensitive and selective functions especially in the areas of food and health. The context of this work is to implement and study integrated micro-ring resonators devoted to sensing applications. They are fabricated by processing SU8 polymer as core layer and PMATRIFE polymer as lower cladding layer. The refractive index of the polymers and of the waveguide structure as a function of the wavelength is presented. Using these results, a theoretical study of the coupling between ring and straight waveguides has been undertaken in order to define the MR design. Sub-micronic gaps of 0.5 μm to 1 μm between the ring and the straight waveguides have been successfully achieved with UV (i-lines) photolithography. Different superstrates such as air, water, and aqueous solutions with glucose at different concentrations have been studied. First results show a good normalized transmission contrast of 0.98, a resonator quality factor around 1.5 × 104 corresponding to a coupling ratio of 14.7%, and ring propagation losses around 5 dB/cm. Preliminary sensing experiments have been performed for different concentrations of glucose; a sensitivity of 115 ± 8 nm/RIU at 1550 nm has been obtained with this couple of polymers.
Energy barriers for bit-encoding states based on 360° domain walls in ultrathin ferromagnetic nanorings
Authors: Muratov C. B. , Osipov V. V. , Vanden-Eijnden E.
Published: March 2015

A numerical thermal stability study of the bit-encoding states in a proposed multi-level magnetic storage element based on an ultrathin ferromagnetic nanoring is presented. The material parameters and the ring dimensions for which there are five distinct metastable magnetization configurations separated by energy barriers exceeding 50kBT at room temperature are identified. The results are obtained, using the string method for the study of rare events to locate the transition states separating the metastable states and to identify the most likely thermally activated pathways.
Thickness- and temperature-dependent magnetodynamic properties of yttrium iron garnet thin films
Authors: Haidar M. , Ranjbar M. , Balinsky M. , Dumas R. K. , Khartsev S. , Åkerman J.
Published: March 2015

The magnetodynamical properties of nanometer-thick yttrium iron garnet films are studied using ferromagnetic resonance as a function of temperature. The films were grown on gadolinium gallium garnet substrates by pulsed laser deposition. First, we found that the damping coefficient increases as the temperature increases for different film thicknesses. Second, we found two different dependencies of the damping on film thickness: at room temperature, the damping coefficient increases as the film thickness decreases, while at T = 8 K, we find the damping to depend only weakly on the thickness. We attribute this behavior to an enhancement of the relaxation of the magnetization by impurities or defects at the surfaces.
The glass-forming ability of model metal-metalloid alloys
Authors: Zhang Kai , Liu Yanhui , Schroers Jan , Shattuck Mark D. , O’Hern Corey S.
Published: March 2015

Bulk metallic glasses (BMGs) are amorphous alloys with desirable mechanical properties and processing capabilities. To date, the design of new BMGs has largely employed empirical rules and trial-and-error experimental approaches. Ab initio computational methods are currently prohibitively slow to be practically used in searching the vast space of possible atomic combinations for bulk glass formers. Here, we perform molecular dynamics simulations of a coarse-grained, anisotropic potential, which mimics interatomic covalent bonding, to measure the critical cooling rates for metal-metalloid alloys as a function of the atomic size ratio σS/σL and number fraction xS of the metalloid species. We show that the regime in the space of σS/σL and xS where well-mixed, optimal glass formers occur for patchy and LJ particle mixtures, coincides with that for experimentally observed metal-metalloid glass formers. Thus, our simple computational model provides the capability to perform combinatorial searches to identify novel glass-forming alloys.
Osmotic self-propulsion of slender particles
Authors: Schnitzer Ory , Yariv Ehud
Published: March 2015

We consider self-diffusiophoresis of axisymmetric particles using the continuum description of Golestanian et al. [“Designing phoretic micro-and nano-swimmers,” New J. Phys. 9, 126 (2007)], where the chemical reaction at the particle boundary is modelled by a prescribed distribution of solute absorption and the interaction of solute molecules with that boundary is represented by diffusio-osmotic slip. With a view towards modelling of needle-like particle shapes, commonly employed in experiments, the self-propulsion problem is analyzed using slender-body theory. For a particle of length 2L, whose boundary is specified by the axial distribution κ(z) of cross-sectional radius, we obtain the approximation −μ2DL∫−LLj(z)dκ(z)dz dz for the particle velocity, wherein j(z) is the solute-flux distribution, μ the diffusio-osmotic slip coefficient, and D the solute diffusivity. This approximation can accommodate discontinuous flux distributions, which are commonly used for describing bimetallic particles; it agrees strikingly well with the numerical calculations of Popescu et al. [“Phoretic motion of spheroidal particles due to self-generated solute gradients,” Eur. Phys. J. E: Soft Matter Biol. Phys. 31, 351–367 (2010)], performed for spheroidal particles.
Inherent room temperature ferromagnetism and dopant dependent Raman studies of PbSe, Pb1−xCuxSe, and Pb1−xNixSe
Authors: Gayner Chhatrasal , Kar Kamal K.
Published: March 2015

Polycrystalline lead selenide (PbSe) doped with copper (Cu) and nickel (Ni) was prepared to understand its magnetic behaviour and Raman activity. The processing conditions, influence of dopants (magnetically active and non-active) and their respective compositions on the magnetic properties and Raman active mode were studied. A surprising/anomalous room temperature ferromagnetism (hysteresis loop) is noticed in bulk diamagnetic PbSe, which is found to be natural or inherent characteristic of material, and depends on the crystallite size, dopant, and developed strain due to dopant/defects. The magnetic susceptibility (−1.71 × 10−4 emu/mol Oe) and saturated magnetic susceptibility (−2.74 × 10−4 emu/mol Oe) are found to be higher than the earlier reported value (diamagnetic: −1.0 × 10−4 emu/mol Oe) in bulk PbSe. With increase of Cu concentration (2% to 10%) in PbSe, the saturated magnetic susceptibility decreases from −1.22 × 10−4 to −0.85 × 10−4 emu/mol Oe. Whereas for Ni dopant, the saturated magnetic susceptibility increases to −2.96 × 10−4 emu/mol Oe at 2% Ni doped PbSe. But it further decreases with dopant concentration. In these doped PbSe, the shifting of longitudinal (LO) phonon mode was also studied by the Raman spectroscopy. The shifting of LO mode is found to be dopant dependent, and the frequency shift of LO mode is associated with the induced strain that created by the dopants and vacancies. This asymmetry in LO phonon mode (peak shift and shape) may be due to the intraband electronic transition of dopants. The variation in magnetic susceptibility and Raman shifts are sensitive to crystallite size, nature of dopant, concentration of dopants, and induced strain due to dopants.
Dynamics of the phase formation process upon the low temperature selenization of Cu/In-multilayer stacks
Authors: Oertel M. , Ronning C.
Published: March 2015

Phase reactions occurring during a low temperature selenization of thin In/Cu-multilayer stacks were investigated by ex-situ x-ray diffraction (XRD) and energy dispersive x-ray spectroscopy (EDS). Therefore, dc-sputtered In/Cu-multilayers onto molybdenum coated soda lime glass were selenized in a high vacuum system at temperatures between 260 and 340 °C with different dwell times and selenium supply. The combination of the results of the phase analysis by XRD and the measurements of the in-depth elemental distribution by EDS allowed a conclusion on the occurring reactions within the layer depth. We found two CuInSe2 formation processes depending on the applied temperature. Already, at a heater temperature of 260 °C, the CuInSe2 formation can occur by the reaction of Cu2−xSe with In4Se3 and Se. At 340 °C, CuInSe2 is formed by the reaction of Cu2−xSe with InSe and Se. Because both reactions need additional selenium, the selenium supply during the selenization can shift the reaction equilibria either to the metal binaries side or to the CuInSe2 side. Interestingly, a lower selenium supply shifts the equilibrium to the CuInSe2 side, because the amount of selenium incorporated into the metallic layer is higher for a lower selenium supply. Most likely, a larger number of grain boundaries are the reason for the stronger selenium incorporation. The results of the phase formation studies were used to design a two stage selenization process to get a defined structure of an indium selenide- and a copper selenide-layer at low temperatures as the origin for a controlled interdiffusion to form the CuInSe2-absorber-layer at higher temperatures. The approach delivers a CuInSe2 absorber which reach total area efficiencies of 11.8% (13.0% active area) in a CuInSe2-thin-film solar cell. A finished formation of CuInSe2 at low temperature was not observed in our experiments but is probably possible for longer dwell times.
Low temperature (150 °C) fabrication of high-performance TiO2 films for dye-sensitized solar cells using ultraviolet light and plasma treatments of TiO2 paste containing organic binder
Authors: Zen Shungo , Inoue Yuki , Ono Ryo
Published: March 2015

Dye-sensitized solar cells (DSSCs) require annealing of TiO2 photoelectrodes at 450 °C to 550 °C. However, such high-temperature annealing is unfavorable because it limits the use of materials that cannot withstand high temperatures, such as plastic substrates. In our previous paper, a low-temperature annealing technique of TiO2 photoelectrodes using ultraviolet light and dielectric barrier discharge treatments was proposed to reduce the annealing temperature from 450 °C to 150 °C for a TiO2 paste containing an organic binder. Here, we measure the electron diffusion length in the TiO2 film, the amount of dye adsorption on the TiO2 film, and the sheet resistance of a glass substrate of samples manufactured with the 150 °C annealing method, and we discuss the effect that the 150 °C annealing method has on those properties of DSSCs.
GaSb-based composite quantum wells for laser diodes operating in the telecom wavelength range near 1.55-μm
Authors: Cerutti L. , Castellano A. , Rodriguez J.-B. , Bahri M. , Largeau L. , Balocchi A. , Madiomanana K. , Lelarge F. , Patriarche G. , Marie X. , Tournié E.
Published: March 2015

We have investigated in detail the material, optical, and lasing properties of innovative GaInSb/AlInSb composite quantum wells (CQWs). The CQWs are confined by AlGaAsSb barrier layers, and a monolayer-thin AlInSb barrier layer has been inserted within the GaInSb QWs in order to achieve lasing emission within the telecom window. High-resolution X-ray diffraction, transmission electron microscopy, and photoluminescence spectroscopies reveal high structural quality of the samples. Inserting AlInSb layers allows wider QWs, and thus higher gain-material volume and CQW/optical mode overlap. This translates into better laser performances. Near room temperature, a threshold current of 85 mA and an output power of ∼30 mW/uncoated-facet under continuous wave operation are demonstrated at 1.55 μm with 10 μm × 1 mm laser diodes.
Uniaxial and tensile strained germanium nanomembranes in rolled-up geometry by polarized Raman scattering spectroscopy
Authors: Guo Qinglei , Zhang Miao , Xue Zhongying , Zhang Jing , Wang Gang , Chen Da , Mu Zhiqiang , Huang Gaoshan , Mei Yongfeng , Di Zengfeng , Wang Xi
Published: March 2015

We present a rolled-up approach to form Ge microtubes and their array by rolling-up hybrid Ge/Cr nanomembranes, which is driven by the built-in stress in the deposited Cr layer. The study of Raman intensity as a function of the angle between the crystal-axis and the polarization-direction of the scattered light, i.e., polarized Raman measurement reveals that the strain state in Ge tube is uniaxial and tensile, and can reach a maximal value 1.0%. Both experimental observations and theoretical calculations suggest that the uniaxial-tensile strain residual in the rolled-up Ge tubes correlates with their tube diameters, which can be tuned by the thicknesses of the Cr layers deposited. Using the polarized Raman scattering spectroscopy, our study provides a comprehensive analysis of the strain state and evolution in self-rolled-up nano/micro-tubes.
Modification of inkjet printer for polymer sensitive layer preparation on silicon-based gas sensors
Authors: Li Tianjian , Dong Ying , Yuan Dengpeng , Liu Yujin
Published: March 2015

Inkjet printing is a versatile, low cost deposition technology with the capabilities for the localized deposition of high precision, patterned deposition in a programmable way, and the parallel deposition of a variety of materials. This paper demonstrates a new method of modifying the consumer inkjet printer to prepare polymer-sensitive layers on silicon wafer for gas sensor applications. A special printing tray for the modified inkjet printer to support a 4-inch silicon wafer is designed. The positioning accuracy of the deposition system is tested, based on the newly modified printer. The experimental data show that the positioning errors in the horizontal direction are negligibly small, while the positioning errors in the vertical direction rise with the increase of the printing distance of the wafer. The method for making suitable ink to be deposited to form the polymer-sensitive layer is also discussed. In the testing, a solution of 0.1 wt% polyvinyl alcohol (PVA) was used as ink to prepare a sensitive layer with certain dimensions at a specific location on the surface of the silicon wafer, and the results prove the feasibility of the methods presented in this article.
The Processing Speed of Scene Categorization at Multiple Levels of Description: The Superordinate Advantage Revisited
Authors: Banno Hayaki , Saiki Jun
Published: March 2015

Recent studies have sought to determine which levels of categories are processed first in visual scene categorization and have shown that the natural and man-made superordinate-level categories are understood faster than are basic-level categories. The current study examined the robustness of the superordinate-level advantage in a visual scene categorization task. A go/no-go categorization task was evaluated with response time distribution analysis using an ex-Gaussian template. A visual scene was categorized as either superordinate or basic level, and two basic-level categories forming a superordinate category were judged as either similar or dissimilar to each other. First, outdoor/ indoor groups and natural/man-made were used as superordinate categories to investigate whether the advantage could be generalized beyond the natural/man-made boundary. Second, a set of images forming a superordinate category was manipulated. We predicted that decreasing image set similarity within the superordinate-level category would work against the speed advantage. We found that basic-level categorization was faster than outdoor/indoor categorization when the outdoor category comprised dissimilar basic-level categories. Our results indicate that the superordinate-level advantage in visual scene categorization is labile across different categories and category structures.
Important sources of variation to be considered when using fin clips as a surrogate for muscle in trophic studies using stable isotopes
Authors: Galván David E. , Funes Manuela , Liberoff Ana L. , Botto Florencia , Iribarne Oscar O.
Published: March 2015

White muscle is the prevalent tissue for C and N stable isotope analysis in fish, requiring the death of the fish or biopsy procedures that could lead to infections or severe damage. Given that caudal fin-clipping does not seriously affect growth or condition, the present study assessed the suitability of caudal fin tissue as replacement for muscle tissue in trophic studies. Clips of caudal fin were a useful non-lethal surrogate of muscle samples in four studied reef-fish (Diplodus argenteus, Pagrus pagrus, Acanthistius patachonicus and Pinguipes brasilianus). Fin clips were easy to collect in quantities adequate for mass spectrometry analyses and had C:N ratios similar to those of white muscle with low lipid content. However, results showed that fin-muscle correction models should be specific and sampling design should be conducted to reduce spatial and temporal variation. Moreover, species-specific correction factors may not be valid for other populations of the same species if the presumed range of δX values differ from the population used to estimate the correction models. Results also showed that the fin-muscle relationship could vary with size. Thus, unless a non-ecological meaningful fin-muscle correlation with body size was previously identified, correction models should be estimated sampling a representative size range and fin samples should be used with caution to study size-related trophodynamics.
A field evaluation of a new molecular-based point-of-care test for chlamydia and gonorrhoea in remote Aboriginal health services in Australia
Authors: Causer Louise M. , Hengel Belinda , Natoli Lisa , Tangey Annie , Badman Steven G. , Tabrizi Sepehr N. , Whiley David , Ward James , Kaldor John M. , Guy Rebecca J.
Published: March 2015

Background Point-of-care (POC) tests could be important public health tools in settings with treatment delays and high rates of sexually transmissible infections (STIs). Use is limited due to suboptimal performance. The performance and ease-of-use of a new molecular-based POC test for simultaneous detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) was assessed, alongside two single-organism immunochromatographic tests (ICT). Methods: The evaluation occurred between May 2012 and March 2013 during community STI screens in two remote Aboriginal health services. Urine was tested with the GeneXpert®CT/NG and if sufficient volume, also with Diaquick CT and Gonorrhoea Card. The gold standard comparison was laboratory nucleic acid amplification testing (NAAT). Operational characteristics were also assessed. Results: Among 198 samples, GeneXpert CT sensitivity and specificity was 100% [95% confidence intervals (CI): 75.9–100] and 99.5% (95% CI: 96.5–100), and NG was 100% (95% CI: 96.5–100) and 100% (95% CI: 97.5–100), respectively. Among a sample subset, Diaquick CT (n = 104) sensitivity and specificity was 27.3% (95% CI: 7.3–60.7) and 66.7% (95% CI: 12.5–98.2), and Gonorrhoea Card (n = 29), was 66.7% (95% CI: 12.5–98.2) and 76.9% (95% CI: 56.0–90.2), respectively. GeneXpert required 1 mL of urine, four steps, 1 min specimen preparation and 90 min to result. ICTs required 15 mL of urine, eight steps, 18 min preparation and 10–15 min to result. Conclusion: The accuracy and operational benefits of GeneXpert CT/NG make it very suitable in these settings where delays to treatment are encountered.
Let’s talk about sex: gender norms and sexual health in English schools
Authors: Jamal Farah , Bonell Chris , Wooder Kai , Blake Simon
Published: March 2015

The sexual health of young people in England is an urgent public health concern. While interventions to address young people’s sexual health have focussed on knowledge, skills and contraception access, amazingly none in the UK has explicitly addressed the effects of the social hierarchies of gender and gendered behavioural ideals that shape young people’s sexual expectations, attitudes and behaviour. The lack of attention to gender is a persistent gap in health research, practice and policy. A rigorous evaluation of such an intervention package would go some way to building an evidence base for challenging gender norms, which appear to be strongly associated with adverse sexual health outcomes.
The role of social science in the governance and management of wildland fire
Authors: Bosomworth Karyn , Handmer John , Thornton Richard
Published: March 2015

Global social-economic and environmental changes are increasing the challenges of wildfire risk management. Addressing these challenges requires perspectives beyond knowledge of the bio-physical dynamics of fire. This Special Section provides some such perspectives, including safety, children's understanding of the risk, indigenous knowledge of fire, and ‘shared responsibility’. Each paper highlights important challenges and ideas for fire management.
The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc
Authors: Sun Xiao-Xin , He Xia , Yin Li , Komada Masayuki , Sears Rosalie C. , Dai Mu-Shui
Published: March 2015

Significance

c-Myc is ubiquitinated by SCF
Fbw7
and appears to be degraded mainly in the nucleolus, where it acts as a master regulator of ribosomal biogenesis. However, deubiquitination regulation of c-Myc in the nucleolus is previously unknown. Here, we found that ubiquitin-specific protease 36 (USP36), a nucleolar ubiquitin-specific protease, interacts with and deubiquitinates c-Myc in the nucleolus. It also interacts with Fbw7γ but not Fbw7α, yet it abolishes c-Myc degradation mediated by either Fbw7γ or Fbw7α. Ablation of USP36 reduced c-Myc levels and severely inhibited cancer cell proliferation. USP36 is overexpressed in a subset of human breast and lung cancers. Thus, our study reveals USP36 as a novel deubiquitinating enzyme controlling c-Myc’s nucleolar degradation, adding a missing and end-point regulator into the c-Myc degradation pathway.
Recombination in diverse maize is stable, predictable, and associated with genetic load
Authors: Rodgers-Melnick Eli , Bradbury Peter J. , Elshire Robert J. , Glaubitz Jeffrey C. , Acharya Charlotte B. , Mitchell Sharon E. , Li Chunhui , Li Yongxiang , Buckler Edward S.
Published: March 2015

Significance

Meiotic recombination is known to vary over 1,000-fold in many eukaryotic organisms, including maize. This regional genomic variation has enormous consequences for plant breeders, who rely on meiotic cross-overs to fine-map quantitative traits and introgress favorable alleles. Deleterious mutations are also predicted to accumulate preferentially within low-recombination regions, particularly within historically outcrossing species, such as maize. Here, we show that meiotic recombination is predictable across diverse crosses based on several genomic features of the reference genome. We demonstrate that the extant patterns of recombination are historically stable and tied to variation in the number of deleterious mutations. The ability of plant breeders to exploit recombination to purge segregating deleterious alleles will determine the efficacy of future crop improvement.
Permafrost carbon−climate feedback is sensitive to deep soil carbon decomposability but not deep soil nitrogen dynamics
Authors: Koven Charles D. , Lawrence David M. , Riley William J.
Published: March 2015

Significance

As the climate warms, the carbon balance of arctic ecosystems will respond in two opposing ways: Plants will grow faster, leading to a carbon sink, while thawing permafrost will lead to decomposition and loss of soil carbon. However, thawing permafrost also releases nitrogen that fertilizes plant growth, offsetting some carbon losses. The balance of these processes determines whether these ecosystems will act as a stabilizing or destabilizing feedback to climate change. We show that this balance is determined by the rate at which permafrost carbon decomposes as it thaws, and that the stabilizing effects of nitrogen from permafrost is weaker than the destabilizing carbon losses from those soil layers.
Functionally conserved architecture of hepatitis C virus RNA genomes
Authors: Mauger David M. , Golden Michael , Yamane Daisuke , Williford Sara , Lemon Stanley M. , Martin Darren P. , Weeks Kevin M.
Published: March 2015

Significance

Plus-sense RNA viruses cause diverse pathologies in humans. Viral RNA genomes are selected to encode information both in their primary sequences and in their higher-order tertiary structures required to replicate and to evade host immune responses. We interrogated the physical structures of three evolutionarily divergent hepatitis C virus (HCV) RNA genomes using high-throughput chemical probing and found, along with all previously known RNA-structure–based regulatory elements, diverse previously uncharacterized structures that impact viral replication. We also characterized strategies by which the HCV genomic RNA structure masks detection by innate immune sensors. This structure-first strategy for comparative analysis of genome-wide RNA structure can be broadly applied to understand the contributions of higher-order genome structure to viral replication and pathogenicity.
L-selectin shedding is activated specifically within transmigrating pseudopods of monocytes to regulate cell polarity in vitro
Authors: Rzeniewicz Karolina , Newe Abigail , Rey Gallardo Angela , Davies Jessica , Holt Mark R. , Patel Ashish , Charras Guillaume T. , Stramer Brian , Molenaar Chris , Tedder Thomas F. , Parsons Maddy , Ivetic Aleksandar
Published: March 2015

Significance

During an inflammatory response, L-selectin, an immune cell-specific adhesion molecule, guides monocytes from the bloodstream toward the surrounding extravascular environment (termed “transmigration”). We show, under conditions that mimic blood flow, that L-selectin is proteolytically cleaved (or shed) exclusively within leading migratory fronts (pseudopods) of actively transmigrating monocytes. Calmodulin/L-selectin interaction, which acts to block shedding, is lost through Ser phosphorylation of the L-selectin cytoplasmic tail, occurring specifically within transmigrating pseudopods. Blocking L-selectin shedding specifically during transmigration increases pseudopod numbers, leading to defective front/back polarity that is essential for migration. These findings are the first to report, to our knowledge, an extended role for L-selectin in regulating morphological changes in leukocytes that are required for migration.
Methane transport from the active layer to lakes in the Arctic using Toolik Lake, Alaska, as a case study
Authors: Paytan Adina , Lecher Alanna L. , Dimova Natasha , Sparrow Katy J. , Kodovska Fenix Garcia-Tigreros , Murray Joseph , Tulaczyk Slawomir , Kessler John D.
Published: March 2015

Significance

Methane, a greenhouse gas, contributes to global warming. We show that methane-rich water from the seasonally thawed active layer in the Arctic flows into Toolik Lake, Alaska. This may be an important previously unrecognized conduit for methane transport and emissions in Arctic lakes. The controls on methane input from the active layer are fundamentally different than those affecting methane production within lakes, and the response of these processes to climate and environmental change is also distinct. The accuracy of predictions of methane emissions and ultimately the extent of climate change that can be expected in the Arctic depend on a better understanding of methane dynamics in the region, including the controls over methane production and transport processes within the active layer.
Regulation of Nrf2 signaling and longevity in naturally long-lived rodents
Authors: Lewis Kaitlyn N. , Wason Emily , Edrey Yael H. , Kristan Deborah M. , Nevo Eviatar , Buffenstein Rochelle
Published: March 2015

Significance

Both genetically altered and naturally long-lived mammals are more resistant to toxic compounds that may cause cancer and age-associated diseases than their shorter-lived counterparts. The mechanisms by which this stress resistance occurs remain elusive. We found that longer-lived rodent species had markedly higher levels of signaling activity of the multifunctional regulator nuclear factor erythroid 2-related factor (Nrf2) and that this increase in cytoprotective signaling appeared to be due to species differences in Kelch-like ECH-Associated Protein 1 (Keap1) and β-transducin repeat-containing protein (βTrCP) regulation of Nrf2 activity. Both of these negative regulators of Nrf2-signaling activity are significantly lower in longer-lived species. By targeting the proteins that regulate Nrf2 rather than Nrf2 itself, we may be able to identify new therapies that impact aging and age-associated diseases such as cancer.
Conserved role of Sonic Hedgehog in tonotopic organization of the avian basilar papilla and mammalian cochlea
Authors: Son Eun Jin , Ma Ji-Hyun , Ankamreddy Harinarayana , Shin Jeong-Oh , Choi Jae Young , Wu Doris K. , Bok Jinwoong
Published: March 2015

Significance

Sound frequency discrimination is crucial for daily activities throughout the animal kingdom. This process begins at the auditory peripheral organ known as the organ of Corti in mammals and basilar papilla in birds. This frequency tuning is facilitated by specific anatomical and physiological properties, including gradual changes in the shape of the mechanosensory hair cells and the total number of stereocilia per hair cell along the cochlea. Unlike in birds, the molecular mechanism(s) that establishes this tonotopic organization is not known in mammals. In this study, we provide in vivo evidence that Sonic Hedgehog signaling mediates regional identity of the developing cochlea in both mammals and birds, and this regional identity prefigures the tonotopic organization in the basilar papilla.
Endocytic proteins drive vesicle growth via instability in high membrane tension environment
Authors: Walani Nikhil , Torres Jennifer , Agrawal Ashutosh
Published: March 2015

Significance

Biological cells are engaged in an incessant uptake of macromolecules for nutrition and inter- and intracellular communication; this entails significant local bending of the plasma membrane and formation of cargo-carrying vesicles executed by a designated set of membrane-deforming proteins. The energetic cost incurred in forming vesicles is directly related to the stressed state of the membrane and, hence, that of the cell. In this study, we reveal a protein-induced “snap-through instability” that offsets tension and drives vesicle growth during clathrin-mediated endocytosis, the main pathway for the transport of macromolecules into cells. Because these proteins (actin and BAR proteins) are involved in other interfacial rearrangements in cells, the predicted instability could be at play in cells at-large.
A TOCA/CDC-42/PAR/WAVE functional module required for retrograde endocytic recycling
Authors: Bai Zhiyong , Grant Barth D.
Published: March 2015

Significance

Endosomes are membrane-bound organelles that are required for the sorting of membrane-associated proteins and lipids. Once integral membrane proteins reach the endosomal system they can be sent to the lysosome for degradation, recycled to the plasma membrane, or recycled to the Golgi apparatus. Here we provide insight into the molecules that mediate a poorly understood route to the Golgi from recycling endosomes. The mediators of this transport step that we identified include the membrane-binding and -bending TOCA proteins, the small GTPase CDC-42, associated polarity proteins PAR-6 and PKC-3/atypical protein kinase C, and the WAVE actin nucleation complex. Many transmembrane proteins likely use this same transport mechanism.