bluuebunny/crossref_metadata_2025 huggingface dataset:
Dual analyzer system for surface analysis dedicated for angle-resolved photoelectron spectroscopy at liquid surfaces and interfaces
Authors: Niedermaier Inga , Kolbeck Claudia , Steinrück Hans-Peter , Maier Florian
Published: April 2016

The investigation of liquid surfaces and interfaces with the powerful toolbox of ultra-high vacuum (UHV)-based surface science techniques generally has to overcome the issue of liquid evaporation within the vacuum system. In the last decade, however, new classes of liquids with negligible vapor pressure at room temperature—in particular, ionic liquids (ILs)—have emerged for surface science studies. It has been demonstrated that particularly angle-resolved X-ray Photoelectron Spectroscopy (ARXPS) allows for investigating phenomena that occur at gas-liquid and liquid-solid interfaces on the molecular level. The results are not only relevant for IL systems but also for liquids in general. In all of these previous ARXPS studies, the sample holder had to be tilted in order to change the polar detection angle of emitted photoelectrons, which restricted the liquid systems to very thin viscous IL films coating a flat solid support. We now report on the concept and realization of a new and unique laboratory “Dual Analyzer System for Surface Analysis (DASSA)” which enables fast ARXPS, UV photoelectron spectroscopy, imaging XPS, and low-energy ion scattering at the horizontal surface plane of macroscopically thick non-volatile liquid samples. It comprises a UHV chamber equipped with two electron analyzers mounted for simultaneous measurements in 0° and 80° emission relative to the surface normal. The performance of DASSA on a first macroscopic liquid system will be demonstrated.
Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT
Authors: Baruah Tunna , Garnica Amanda , Paggen Marina , Basurto Luis , Zope Rajendra R.
Published: April 2016

We study the electronic structure of C60 fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Our results show that all functionalized fullerenes with an exception of the C60-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C60 fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C61-butyric acid methyl ester (PCBM)-P3MT complex.
Coupled cluster Green function: Model involving single and double excitations
Authors: Bhaskaran-Nair Kiran , Kowalski Karol , Shelton William A.
Published: April 2016

In this paper, we report on the development of a parallel implementation of the coupled-cluster (CC) Green function formulation (GFCC) employing single and double excitations in the cluster operator (GFCCSD). A key aspect of this work is the determination of the frequency dependent self-energy, Σ(ω). The detailed description of the underlying algorithm is provided, including approximations used that preserve the pole structure of the full GFCCSD method, thereby reducing the computational costs while maintaining an accurate character of methodology. Furthermore, for systems with strong local correlation, our formulation reveals a diagonally dominate block structure where as the non-local correlation increases, the block size increases proportionally. To demonstrate the accuracy of our approach, several examples including calculations of ionization potentials for benchmark systems are presented and compared against experiment.
Femtosecond time-resolved impulsive stimulated Raman spectroscopy using sub-7-fs pulses: Apparatus and applications
Authors: Kuramochi Hikaru , Takeuchi Satoshi , Tahara Tahei
Published: April 2016

We describe details of the setup for time-resolved impulsive stimulated Raman spectroscopy (TR-ISRS). In this method, snapshot molecular vibrational spectra of the photoreaction transients are captured via time-domain Raman probing using ultrashort pulses. Our instrument features transform-limited sub-7-fs pulses to impulsively excite and probe coherent nuclear wavepacket motions, allowing us to observe vibrational fingerprints of transient species from the terahertz to 3000-cm−1 region with high sensitivity. Key optical components for the best spectroscopic performance are discussed. The TR-ISRS measurements for the excited states of diphenylacetylene in cyclohexane are demonstrated, highlighting the capability of our setup to track femtosecond dynamics of all the Raman-active fundamental molecular vibrations.
Weyl-von Neumann-Berg theorem for quaternionic operators
Authors: G Ramesh
Published: April 2016

We prove the Weyl-von Neumann-Berg theorem for right linear operators (not necessarily bounded) in a quaternionic Hilbert space: Let N be a right linear normal (need not be bounded) operator in a quaternionic separable infinite dimensional Hilbert space H. Then for a given ϵ > 0, there exists a compact operator K with K<ϵ and a diagonal operator D on H such that N = D + K.
Dynamics of the two-spin spin-boson model with a common bath
Authors: Deng Tianrui , Yan Yiying , Chen Lipeng , Zhao Yang
Published: April 2016

Dynamics of the two-spin spin-boson model in the presence of Ohmic and sub-Ohmic baths is investigated by employing a multitude of the Davydov D1 trial states, also known as the multi-D1 Ansatz. Its accuracy in dynamics simulations of the two-spin SBM is improved significantly over the single D1 Ansatz, especially in the weak to moderately strong coupling regime. Validity of the multi-D1 Ansatz for various coupling strengths is also systematically examined by making use of the deviation vector which quantifies how faithfully the trial state obeys the Schrödinger equation. The time evolution of population difference and entanglement has been studied for various initial conditions and coupling strengths. Careful comparisons are carried out between our approach and three other methods, i.e., the time-dependent numerical renormalization group (TD-NRG) approach, the Bloch-Redfield theory, and a method based on a variational master equation. For strong coupling, the multi-D1 trial state yields consistent results as the TD-NRG approach in the Ohmic regime while the two disagree in the sub-Ohmic regime, where the multi-D1 trial state is shown to be more accurate. For weak coupling, the multi-D1 trial state agrees with the two master-equation methods in the presence of both Ohmic and sub-Ohmic baths, but shows considerable differences with the TD-NRG approach in the presence of a sub-Ohmic bath, calling into question the validity of the TD-NRG results at long times in the literature.
Effect of interfacial excess oxygen on positive-bias temperature stress instability of self-aligned coplanar InGaZnO thin-film transistors
Authors: Oh Saeroonter , Baeck Ju Heyuck , Bae Jong Uk , Park Kwon-Shik , Kang In Byeong
Published: April 2016

We investigated the impact of excess oxygen on positive bias temperature stress (PBTS) instability of self-aligned coplanar amorphous InGaZnO thin-film transistors. We focus on the interface region which is compositionally differentiated from the bulk material on each side. The threshold voltage shift under PBTS is proportional to the extracted density of interface trap states that act as electron traps. The density of interface trap states is extracted from capacitance-voltage measurements with monochromatic light of varying wavelengths. We introduce a figure-of-merit that quantifies the amount of excess oxygen relative to the metal cation composition in the interface region. Minimization of interfacial excess oxygen from 112.4% to 101.2% reduces the density of interface trap states by a factor of 2.77, resulting in improvement of PBTS instability from a threshold voltage shift value of 4.42 V to 0.35 V.
Theoretical study of vibrational energy transfer of free OH groups at the water-air interface
Authors: Zheng Renhui , Wei Wenmei , Sun Yuanyuan , Song Kai , Shi Qiang
Published: April 2016

Recent experimental studies have shown that the vibrational dynamics of free OH groups at the water-air interface is significantly different from that in bulk water. In this work, by performing molecular dynamics simulations and mixed quantum/classical calculations, we investigate different vibrational energy transfer pathways of free OH groups at the water-air interface. The calculated intramolecular vibrational energy transfer rate constant and the free OH bond reorientation time scale agree well with the experiment. It is also found that, due to the small intermolecular vibrational couplings, the intermolecular vibrational energy transfer pathway that is very important in bulk water plays a much less significant role in the vibrational energy relaxation of the free OH groups at the water-air interface.
Magnetic nanoscopic correlations in the crossover between a superspin glass and a superferromagnet
Authors: Alba Venero D. , Rogers S. E. , Langridge S. , Alonso J. , Fdez-Gubieda M. L. , Svalov A. , Fernández Barquín L.
Published: April 2016

Collective behaviors in which the magnetic response depends not only on the individual constituents but also on their interactions are an area of active research. We have produced a paradigmatic system where DC magnetron sputtered FexAg100–x (x = 15, 35) nanogranular films exhibit a crossover between a superspin glass (SSG) state and a superferromagnetism (SFM), where direct exchange interactions overcome the frustration. The systems have been studied by non-linear susceptibility (NLS) and small angle neutron scattering (SANS). The NLS measurements were carried out between 2 and 300 K, in the absence of a biasing magnetic field, with frequencies spanning two decades. These measurements shed light on the complex nature of the interactions and the intricate relationship between direct exchange and long range magnetic interactions. The use of SANS allows us to estimate qualitatively the lengthscale of the magnetic correlations, and therefore identify a clear difference between the collective “supermagnetic” states (i.e., SSG and SFM) while establishing links between the structure and the magnetic interactions.
Effect of temperature variations on equilibrium distances in levitating parallel dielectric plates interacting through Casimir forces
Authors: Esteso Victoria , Carretero-Palacios Sol , Míguez Hernán
Published: April 2016

We study at thermal equilibrium the effect of temperature deviations around room temperature on the equilibrium distance (deq) at which thin films made of Teflon, silica, or polystyrene immersed in glycerol levitate over a silicon substrate due to the balance of Casimir, gravity, and buoyancy forces. We find that the equilibrium nature (stable or unstable) of deq is preserved under temperature changes, and provide simple rules to predict whether the new equilibrium position will occur closer to or further from the substrate at the new temperature. These rules depend on the static permittivities of all materials comprised in the system (ε0(m)) and the equilibrium nature of deq. Our designed dielectric configuration is excellent for experimental observation of thermal effects on the Casimir force indirectly detected through the tunable equilibrium distances (with slab thickness and material properties) in levitation mode.
Simulations of Coulomb systems with slab geometry using an efficient 3D Ewald summation method
Authors: dos Santos Alexandre P. , Girotto Matheus , Levin Yan
Published: April 2016

We present a new approach to efficiently simulate electrolytes confined between infinite charged walls using a 3d Ewald summation method. The optimal performance is achieved by separating the electrostatic potential produced by the charged walls from the electrostatic potential of electrolyte. The electric field produced by the 3d periodic images of the walls is constant inside the simulation cell, with the field produced by the transverse images of the charged plates canceling out. The non-neutral confined electrolyte in an external potential can be simulated using 3d Ewald summation with a suitable renormalization of the electrostatic energy, to remove a divergence, and a correction that accounts for the conditional convergence of the resulting lattice sum. The new algorithm is at least an order of magnitude more rapid than the usual simulation methods for the slab geometry and can be further sped up by adopting a particle–particle particle–mesh approach.
Intense radiative heat transport across a nano-scale gap
Authors: Budaev Bair V. , Ghafari Amin , Bogy David B.
Published: April 2016

In this paper, we analyze the radiative heat transport in layered structures. The analysis is based on our prior description of the spectrum of thermally excited waves in systems with a heat flux. The developed method correctly predicts results for all known special cases for both large and closing gaps. Numerical examples demonstrate the applicability of our approach to the calculation of the radiative heat transport coefficient across various layered structures.
Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions
Authors: Hager Robert , Chang C. S.
Published: April 2016

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steep edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. A new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.
Investigating flow patterns and related dynamics in multi-instability turbulent plasmas using a three-point cross-phase time delay estimation velocimetry scheme
Authors: Brandt C. , Thakur S. C. , Tynan G. R.
Published: April 2016

Complexities of flow patterns in the azimuthal cross-section of a cylindrical magnetized helicon plasma and the corresponding plasma dynamics are investigated by means of a novel scheme for time delay estimation velocimetry. The advantage of this introduced method is the capability of calculating the time-averaged 2D velocity fields of propagating wave-like structures and patterns in complex spatiotemporal data. It is able to distinguish and visualize the details of simultaneously present superimposed entangled dynamics and it can be applied to fluid-like systems exhibiting frequently repeating patterns (e.g., waves in plasmas, waves in fluids, dynamics in planetary atmospheres, etc.). The velocity calculations are based on time delay estimation obtained from cross-phase analysis of time series. Each velocity vector is unambiguously calculated from three time series measured at three different non-collinear spatial points. This method, when applied to fast imaging, has been crucial to understand the rich plasma dynamics in the azimuthal cross-section of a cylindrical linear magnetized helicon plasma. The capabilities and the limitations of this velocimetry method are discussed and demonstrated for two completely different plasma regimes, i.e., for quasi-coherent wave dynamics and for complex broadband wave dynamics involving simultaneously present multiple instabilities.
Transparency of the strong shock-compressed diamond for 532 nm laser light
Authors: Zhang Zhiyu , Zhao Yang , Yang Jiamin
Published: April 2016

An optical reflectivity and transmissivity model for the shock-compressed diamond is established and used to calculate the optical reflectivity and transmissivity of the diamond under different shock compressions. The simulated results indicate that the reflection occurs at the shock front and does not depend on the thickness of the compressed diamond, but the transmissivity decreases with the thickness. The simulated reflectivity is consistent with the experimental results in the literature, which validates the model. It is shown that the diamond keeps transparent when the shock pressure is lower than 2.00 Mbar, and becomes opaque but does not reflect the probe laser as the shock pressure increases from 2.00 Mbar to 4.60 Mbar and reflects the probe laser markedly when the shock pressure is higher than 4.60 Mbar.
Ion temperature gradient mode driven solitons and shocks
Authors: Zakir U. , Adnan Muhammad , Haque Q. , Qamar Anisa , Mirza Arshad M.
Published: April 2016

Ion temperature gradient (ITG) driven solitons and shocks are studied in a plasma having gradients in the equilibrium number density and equilibrium ion temperature. In the linear regime, it is found that the ion temperature and the ratio of the gradient scale lengths, ηi=Ln/LT, affect both the real frequency and the growth rate of the ITG driven wave instability. In the nonlinear regime, for the first time we derive a Korteweg de Vries-type equation for the ITG mode, which admits solitary wave solution. It is found that the ITG mode supports only compressive solitons. Further, it is noticed that the soliton amplitude and width are sensitive to the parameter ηi=Ln/LT. Second, in the presence of dissipation in the system, we obtain a Burger type equation, which admits the shock wave solution. This work may be useful to understand the low frequency electrostatic modes in inhomogeneous electron-ion plasma having density and ion temperature gradients. For illustration, the model has been applied to tokamak plasma.
Observations of zonal flows in electrode biasing experiments on the Joint Texas Experimental tokamak
Authors: Shen H. G. , Lan T. , Chen Z. P. , Kong D. F. , Zhao H. L. , Wu J. , Sun X. , Liu A. D. , Xie J. L. , Li H. , Ding W. X. , Liu W. D. , Yu C. X. , Xu M. , Sun Y. , Liu H. , Wang Z. J. , Zhuang G. ,   J-TEXT Team
Published: April 2016

Zonal flows (ZFs) are observed during the electrode biasing (EB) high confinement mode (H-mode) using Langmuir probe arrays on the edge of J-TEXT tokamak. The long-distance correlation characteristics of floating potentials and interactions with turbulence are studied. During positive biasing H-mode, either the geodesic acoustic mode or low frequency ZF increases. Strong suppression of radial transport by ZFs is found in the low frequency region. The components of the radial particle flux without and with EB are compared in the frequency domain. The interaction between ZFs and ambient turbulence is also discussed. The results show that the rate of ZFs' shear is comparable with that of E×B shear, suggesting that ZFs could be the trigger of the biasing H-mode.
Beam-plasma instability in charged plasma in the absence of ions
Authors: Dubinov Alexander E. , Petrik Alexey G. , Kurkin Semen A. , Frolov Nikita S. , Koronovskii Alexey A. , Hramov Alexander E.
Published: April 2016

We report on the possibility of the beam-plasma instability development in the system with electron beam interacting with the single-component hot electron plasma without ions. As considered system, we analyse the interaction of the low-current relativistic electron beam (REB) with squeezed state in the high-current REB formed in the relativistic magnetically insulated two-section vircator drift space. The numerical analysis is provided by means of 3D electromagnetic simulation in CST Particle Studio. We have conducted an extensive study of characteristic regimes of REB dynamics determined by the beam-plasma instability development in the absence of ions. As a result, the dependencies of instability increment and wavelength on the REB current value have been obtained. The considered process brings the new mechanism of controlled microwave amplification and generation to the device with a virtual cathode. This mechanism is similar to the action of the beam-plasma amplifiers and oscillators.
Ultra-sensitive atomic magnetometer for studying magnetization fields produced by hyperpolarized helium-3
Authors: Zou Sheng , Zhang Hong , Chen Xi-yuan , Chen Yao , Lu Ji-xi , Hu Zhao-hui , Shan Guang-cun , Quan Wei , Fang Jian-cheng
Published: April 2016

An ingenious approach to acquire the absolute magnetization fields produced by polarized atoms has been presented in this paper. The method was based on detection of spin precession signal of the hyperpolarized helium-3 with ultra-sensitive atomic magnetometer of potassium by referring to time-domain analysis. At first, dynamic responses of the mixed spin ensembles in the presence of variant external magnetic fields have been analyzed by referring to the Bloch equation. Subsequently, the relevant equipment was established to achieve the functions of hyperpolarizing helium-3 and detecting the precession of spin-polarized noble gas. By analyzing the transient response of the magnetometer in time domain, we obtained the relevant damping ratio and natural frequency. When the value of damping ratio reached the maximum value of 0.0917, the combined atomic magnetometer was in equilibrium. We draw a conclusion from the steady response: the magnetization fields of the polarized electrons and the hyperpolarized nuclei were corresponding 16.12 nT and 90.74 nT. Under this situation, the nuclear magnetization field could offset disturbing magnetic fields perpendicular to the orientation of the electronic polarization, and it preserved the electronic spin staying in a stable axis. Therefore, the combined magnetometer was particularly attractive for inertial measurements.
Formation of snowflake domains during fast cooling of lithium tantalate crystals
Authors: Shur V. Ya. , Kosobokov M. S. , Mingaliev E. A. , Kuznetsov D. K. , Zelenovskiy P. S.
Published: April 2016

Formation of the original dendrite snowflake-shape domains during fast cooling after heating above phase transition temperature by pulse laser irradiation was revealed in congruent lithium tantalate crystals. The effect was attributed to polarization reversal under the action of spatially nonuniform pyroelectric field. Two stages of the domain shape evolution at the surface were separated: (1) growth of circular domains by sideways motion of the domain walls and (2) backswitching leading to formation of the snowflake domains. The simulated spatial distribution of the pyroelectric field in regular two-dimensional structure was used for an explanation of the obtained results. The backswitching process in the surface layer has been attributed to change of the sign of the pyroelectric field at the domain wall. The snowflake domain shape is caused by the formation of isolated nanodomain fingers and hampering of their merging.
An alternative experimental approach to produce rare-earth-doped SiOx films
Authors: Zanatta A. R.
Published: April 2016

Rare-earth (RE) doped silicon-oxide (SiOx) films were prepared by sputtering a combined Si + RE2O3 target with argon ions. The study comprised the neodymium (Nd) and samarium (Sm) rare-earth species and the Si + RE2O3 targets were obtained by partially covering a solid disc of Si with area-defined thin layers of Nd2O3 or Sm2O3 powders. The films were investigated by energy-dispersive x-ray, Raman scattering, optical transmission, and photo-luminescence measurements. According to the experimental results, in the as-deposited form, the films were amorphous and presented RE and oxygen concentrations that scaled with the RE2O3 target area. Additional compositional-structural changes were obtained by thermal annealing the films under a flow of oxygen. Within these changes, one can mention: increase of oxygen concentration, optical bandgap widening, partial Si crystallization, and the development of RE-related light emission. The main aspects associated to the production and structural-optical properties of the films, as determined either by the deposition conditions or by the annealing treatments, are presented and discussed in detail.
Improvement of optical quality of semipolar (112¯2) GaN on m-plane sapphire by in-situ epitaxial lateral overgrowth
Authors: Monavarian Morteza , Izyumskaya Natalia , Müller Marcus , Metzner Sebastian , Veit Peter , Can Nuri , Das Saikat , Özgür Ümit , Bertram Frank , Christen Jürgen , Morkoç Hadis , Avrutin Vitaliy
Published: April 2016

Among the major obstacles for development of non-polar and semipolar GaN structures on foreign substrates are stacking faults which deteriorate the structural and optical quality of the material. In this work, an in-situ SiNx nano-network has been employed to achieve high quality heteroepitaxial semipolar (112¯2) GaN on m-plane sapphire with reduced stacking fault density. This approach involves in-situ deposition of a porous SiNx interlayer on GaN that serves as a nano-mask for the subsequent growth, which starts in the nanometer-sized pores (window regions) and then progresses laterally as well, as in the case of conventional epitaxial lateral overgrowth (ELO). The inserted SiNx nano-mask effectively prevents the propagation of defects, such as dislocations and stacking faults, in the growth direction and thus reduces their density in the overgrown layers. The resulting semipolar (112¯2) GaN layers exhibit relatively smooth surface morphology and improved optical properties (PL intensity enhanced by a factor of 5 and carrier lifetimes by 35% to 85% compared to the reference semipolar (112¯2) GaN layer) which approach to those of the c-plane in-situ nano-ELO GaN reference and, therefore, holds promise for light emitting and detecting devices.
Three-dimensional buoyancy-driven convection structures in thermohaline stratification
Authors: Gong Ye-Jun , Luo Ying-Ying , Zhan Jie-Min
Published: April 2016

We report on three-dimensional convection structures in thermohaline stratification with the high Rayleigh number RaT = 7 ⋅ 107, the diffusion ratio δ = 0.01 and various initial density stability ratios R = 0.5, 0.8, and 1.1. According to the classification of buoyancy-driven instability in the parameter space (R, δ), the three cases are referred to follow the Rayleigh-Taylor (RT) mode, the mixed mode (MM) and the diffusive-layer convection (DCL) mode, respectively. Whether the shape of the peak is a finger under the RT mode or a spike under the MM/DLC mode, the 3D view of the interface is likely to be a rolling mountain with a doughnut-shaped vortex around the peak and a banded vortex above the ridge. The doughnut-shaped vortex is maintained around the peak if its growth continues under RT convection; otherwise, the vortex sheds off and moves upward from the peak under the DLC mode. Additionally, we have observed the previously unreported vortex stratification by the contact interface due to the differential diffusion effect.
Vacancy enhanced formation and phase transition of Cu-rich precipitates in α - iron under neutron irradiation
Authors: Lv G. C. , Zhang H. , He X. F. , Yang W. , Su Y. J.
Published: April 2016

In this paper, we employed both molecular statics and molecular dynamics simulation methods to investigate the role of vacancies in the formation and phase transition of Cu-rich precipitates in α-iron. The results indicated that vacancies promoted the diffusion of Cu atoms to form Cu-rich precipitates. After Cu-rich precipitates formed, they further trapped vacancies. The supersaturated vacancy concentration in the Cu-rich precipitate induced a shear strain, which triggered the phase transition from bcc to fcc structure by transforming the initial bcc (110) plane into fcc (111) plane. In addition, the formation of the fcc-twin structure and the stacking fault structure in the Cu-rich precipitates was observed in dynamics simulations.
Mapping physiological G protein-coupled receptor signaling pathways reveals a role for receptor phosphorylation in airway contraction
Authors: Bradley Sophie J. , Wiegman Coen H. , Iglesias Max Maza , Kong Kok Choi , Butcher Adrian J. , Plouffe Bianca , Goupil Eugénie , Bourgognon Julie-Myrtille , Macedo-Hatch Timothy , LeGouill Christian , Russell Kirsty , Laporte Stéphane A. , König Gabriele M. , Kostenis Evi , Bouvier Michel , Chung Kian Fan , Amrani Yassine , Tobin Andrew B.
Published: April 2016

Significance

Studies in transfected cells have established that G protein-coupled receptors (GPCRs) activate a number of intracellular signaling pathways; however, which of these pathways are physiologically important is unclear. Here, we use a genetically engineered mouse to demonstrate a novel role for M3-muscarinic acetylcholine receptor (M3-mAChR) phosphorylation in airway constriction, with implications for human respiratory disease, including asthma and chronic obstructive pulmonary disease. Combining this finding with other M3-mAChR physiological responses, we generate a map of responses that are downstream of G protein-dependent signaling or receptor phosphorylation-dependent signaling. Such a map predicts the outcome of biased GPCR drugs designed to drive receptor signaling preferentially toward pathways that improve therapeutic efficacy while minimizing toxic/adverse outcomes and provides a fundamental approach to the rational design of next-generation GPCR-based therapies.
Towards a broader approach to the community interpreter’s role
Authors: Kaczmarek Lukasz
Published: April 2016

The community interpreter’s role has been described in various ways, associating it with labels (Roberts 1997), tasks (Pöchhacker 2000), dynamic positioning (Mason 2009), and the interpreter’s relative (in)visibility (Angelelli 2004). Increasingly, conceptions of role are seen not as static and absolute, but as related to the differing (and subjective) viewpoints of the various participants involved. This study uses semi-structured interviews, conducted immediately after five interpreter-mediated encounters (four medical, one legal), to examine: (1) how participants in each encounter differ in their comments on the interpreter, and (2) whether the resulting perspective on the interpreter’s role is related to each respondent’s specific conversational goal on the occasion in question. Twenty-six excerpts from the interviews are discussed: all three participants (service provider, service user, interpreter) were interviewed in three cases, while the interpreter was unavailable for interview in one case and the service recipient in another. The interpreted meetings and subsequent interviews took place in London and Manchester, the languages involved being English (service providers) and Polish (service recipients). The various respondents seemed to differ in their perceptions of the interpreter’s role, ostensibly reflecting their own conversational goals, but not necessarily in line with their status as service provider, service recipient or interpreter.
Influence of organic and mineral-based conventional fertilization practices on nutrient levels, anti-proliferative activities and quality of sweet red peppers following cold storage
Authors: Elmann Anat , Garra Ausaid , Alkalai-Tuvia Sharon , Fallik Elazar
Published: April 2016

The demand for organic food products has increased over the last decades; however, the health effects of organically grown products are controversial and knowledge about how different fertilization regimes affect nutritionally and health relevant components is still limited. The aim of the present study was to determine the effect of organic and conventional mineral-based fertilizers on the quality of sweet red peppers. The parameters tested were anti-proliferative activity against cancer cells and the concentrations of antioxidants, flavonoids, phenolics, and vitamin C. The decay incidence, percentage of weight loss, and total soluble solids (TSS) content were also evaluated. The different parameters were tested in fresh peppers immediately after harvest and after cold storage. Our results show that the anti-proliferative activity of pepper extracts against colon cancer cells is similar in fresh organically and conventionally fertilized sweet red peppers. While in conventionally fertilized peppers the extent of the anti-proliferative activity was not affected by long storage, stored organic peppers lost 50% of their inhibitory activity. We also found that the levels of antioxidants, polyphenols, flavonoids, and vitamin C, as well as the general quality of the peppers were not significantly affected by the different fertilization practices nor by long storage.
Unique techniques developed in Israel for short- and long-term storage of table grapes
Authors: Lichter Amnon , Kaplunov Tatiana , Zutahy Yohanan , Lurie Susan
Published: April 2016

Gray mold caused byBotrytis cinereaand rachis browning due to desiccation are the two main factors that reduce table grape quality after harvest. For over 90 years treatments with the gas sulfur dioxide (SO2) have been in use to control decay. In Israel, two methods have been developed for grape storage: one for short-term storage and shipping, and one for extended storage of late ripening cultivars. The first is based on storage in cardboard boxes without liners, which shortens the forced air cooling time due to the reduction in packaging material. After cooling the pallets are wrapped around with linear low density polyethylene to contain the SO2and the humidity. The second method involves storage in plastic boxes with modification of commercially available dual release SO2pads, so that the pads release a continuous low rate of SO2for a long period of over 4 months in cold storage. In this case as well, the pallet is wrapped on all sides in order to maintain the level of SO2and high humidity. Moreover, for late season grapes, we established the efficacy of a postharvest disinfection treatment with ethanol in order to reduce the inoculum load before extended storage and to clean the grapes from accumulation of dust particles. These techniques allow prolonged storage for more than 3 months with minimal decay development combined with retention of grape quality.
The dominance of quenching through cosmic times
Authors: Renzini Alvio
Published: April 2016

The evolution with cosmic time of the star formation rate density (SFRD) and of the main-sequence star formation rate–stellar mass relations are two well-established observational facts. In this Letter, the implications of these two relations combined are analytically explored, showing that quenching of star formation must start already at very early cosmic times and the quenched fraction then dominates ever since over the star-forming one. Thus, a simple picture of the cosmic evolution of the global SFRD is derived, in terms of the interplay between star formation and its quenching.
Inferring the distances of fast radio bursts through associated 21-cm absorption
Authors: Margalit Ben , Loeb Abraham
Published: April 2016

The distances of fast radio burst (FRB) sources are currently unknown. We show that the 21-cm absorption line of hydrogen can be used to infer the redshifts of FRB sources, and determine whether they are Galactic or extragalactic. We calculate a probability of ∼10 per cent for the host galaxy of an FRB to exhibit a 21-cm absorption feature of equivalent width ≳10 km s−1. Arecibo, along with several future radio observatories, should be capable of detecting such associated 21-cm absorption signals for strong bursts of ≳several Jy peak flux densities.
Biphasic growth dynamics duringCaulobacter crescentusdivision
Authors: Banerjee Shiladitya , Lo Klevin , Daddysman Matthew K. , Selewa Alan , Kuntz Thomas , Dinner Aaron R. , Scherer Norbert F.
Published: April 2016

Cell size is specific to each species and impacts their ability to function. While various phenomenological models for cell size regulation have been proposed, recent work in bacteria have demonstrated anaddermodel, in which a cell increments its size by a constant amount between each division. However, the coupling between cell size, shape and constriction, remain poorly understood. Here, we investigate size control and the cell cycle dependence of bacterial growth, using multigenerational cell growth and shape data for singleCaulobacter crescentuscells. Our analysis reveals a biphasic mode of growth:a relative timerphase before constriction where cell growth is correlated to its initial size, followed by apure adderphase during constriction. Cell wall labeling measurements reinforce this biphasic model: a crossover from uniform lateral growth to localized septal growth is observed. We present a mathematical model that quantitatively explains this biphasicmixermodel for cell size control.
Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data
Authors: Weber Lukas M. , Robinson Mark D.
Published: April 2016

Recent technological developments in high-dimensional flow cytometry and mass cytometry (CyTOF) have made it possible to detect expression levels of dozens of protein markers in thousands of cells per second, allowing cell populations to be characterized in unprecedented detail. Traditional data analysis by “manual gating” can be inefficient and unreliable in these high-dimensional settings, which has led to the development of a large number of automated analysis methods. Methods designed for unsupervised analysis use specialized clustering algorithms to detect and define cell populations for further downstream analysis. Here, we have performed an up-to-date, extensible performance comparison of clustering methods for high-dimensional flow and mass cytometry data. We evaluated methods using several publicly available data sets from experiments in immunology, containing both major and rare cell populations, with cell population identities from expert manual gating as the reference standard. Several methods performed well, includingFlowSOM, X-shift, PhenoGraph, Rclusterpp, andflowMeans. Among these,FlowSOMhad extremely fast runtimes, making this method well-suited for interactive, exploratory analysis of large, high-dimensional data sets on a standard laptop or desktop computer. These results extend previously published comparisons by focusing on high-dimensional data and including new methods developed for CyTOF data. R scripts to reproduce all analyses are available from GitHub (https://github.com/lmweber/cytometry-clustering-comparison), and pre-processed data files are available from FlowRepository (FR-FCM-ZZPH), allowing our comparisons to be extended to include new clustering methods and reference data sets.
Fate of glair glands and spawning behaviour in unmated crayfish: a comparison between gonochoristic slough crayfish and parthenogenetic marbled crayfish
Authors: Vogt Günter
Published: April 2016

In the period before spawning, freshwater crayfish females develop glair glands on the underside of the pleon. These glands produce the mucus for a transient tent-like structure in which the eggs are fertilized and attached to the pleopods. Long-term observation of females of the bisexually reproducing slough crayfish,Procambarus fallax, kept in captivity revealed that glair glands developed in late winter and late summer of each year independent of the presence of males. However, in contrast to mated females unmated females did neither form a fertilization tent nor spawn. Their glair glands persisted for an unusually long period of time and disappeared only during the next moult. Apparently, females use information on sperm availability to either reproduce or save the resources. Marbled crayfish,Procambarus virginalis, a parthenogenetic descendant of slough crayfish, developed glair glands in approximately the same periods of the year but spawned despite of the absence of mating. These findings indicate that on their way from gonochorism to parthenogenesis regulation of glair gland activity and spawning has been decoupled from mating. Therefore, the species pairProcambarus fallax/Procambarus virginalisseems to be particularly suitable to investigate the physiological, molecular and genetic mechanisms underlying spawning in freshwater crayfish.
Evidence and role for bacterial mucin degradation in cystic fibrosis airway disease
Authors: Flynn Jeffrey M. , Niccum David , Dunitz Jordan M. , Hunter Ryan C.
Published: April 2016

Chronic respiratory infections are composed of complex microbial communities that incite persistent inflammation and airway damage. Despite the high density of bacteria that colonize the airways, nutrient sources that sustain bacterial growthin vivoare unknown. Here we examine the role of respiratory mucins in the ecological dynamics of the cystic fibrosis lung microbiota. WhileP. aeruginosawas unable to efficiently utilize mucins, saliva-derived anaerobes stimulated the growth of opportunistic pathogens when provided mucins as the sole carbon source. The fermentative metabolisms of these oral anaerobes generated amino acids and short chain fatty acids (propionate and acetate) during mucin enrichmentin vitro,which were also found within expectorated sputum from CF patients. The significance of these findings was supported byin vivo P. aeruginosagene expression, which revealed a heightened response to propionate. Given that propionate is exclusively derived from bacterial fermentation, these data support a central role for mucin fermentation in the carbon flux of the lower airways. More specifically, commensal oral bacteria may contribute to airway disease by degrading mucins, in turn providing nutrients for pathogens otherwise unable to obtain carbon in the lung.
PALADIN:Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data
Authors: Westbrook Anthony , Ramsdell Jordan , Aggarwal Taruna , Normington Louisa , Bergeron R. Daniel , Thomas W. Kelley , MacManes Matthew
Published: April 2016

Whole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. Presently, we lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN—a novel modification of Burrows-Wheeler Aligner that provides more accurate alignment and orders-of-magnitude improved efficiency by directly mapping in protein space.
A Transcriptional Lineage of the EarlyC. elegansEmbryo
Authors: Tintori Sophia C. , Nishimura Erin Osborne , Golden Patrick , Lieb Jason D. , Goldstein Bob
Published: April 2016

HIGHLIGHTS

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RNA-seq on each cell of the earlyC. elegansembryo complements the known lineage

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We measured the zygotic activation specific to each unique cell of the embryo

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We identified genes that are functionally redundant and critical for development

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We created an interactive online data visualization tool for exploring the data

eTOC BLURB

C. elegansis a powerful model for development, with an invariant and completely described cell lineage. To enrich this resource, we performed single-cell RNA-seq on each cell of the embryo through the 16-cell stage. Zygotic genome activation is differential between cell types. We identified hundreds of candidates for partially redundant genes, and verified one such set as critical for development. We created an interactive online data visualization tool to invite others to explore our dataset.

During embryonic development, cells must establish fates, morphologies and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell’s fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify the abundance of every mRNA transcript in each cell of theC. elegansembryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify critical developmental genes previously unappreciated because of their partial redundancy. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fates of each cell, describes at a cellular resolution the mRNA landscape that guides development.
Immune DNA signature of T-cell infiltration in breast tumor exomes
Authors: Levy Eric , Marty Rachel , Garate-Calderon Valentina , Woo Brian , Dow Michelle , Armisen Ricardo , Carter Hannah , Harismendy Olivier
Published: April 2016

Tumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deepTCRBsequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839TCRBclonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes.
High performance Schottky diodes based on indium-gallium-zinc-oxide
Authors: Zhang Jiawei , Xin Qian , Song Aimin
Published: April 2016

Indium-gallium-zinc-oxide (IGZO) Schottky diodes exhibit excellent performance in comparison with conventional devices used in future flexible high frequency electronics. In this work, a high performance Pt IGZO Schottky diode was presented by using a new fabrication process. An argon/oxygen mixture gas was introduced during the deposition of the Pt layer to reduce the oxygen deficiency at the Schottky interface. The diode showed a high barrier height of 0.92 eV and a low ideality factor of 1.36 from the current–voltage characteristics. Even the radius of the active area was 0.1 mm, and the diode showed a cut-off frequency of 6 MHz in the rectifier circuit. Using the diode as a demodulator, a potential application was also demonstrated in this work.
Neuron-specific SALM5 limits inflammation in the CNS via its interaction with HVEM
Authors: Zhu Yuwen , Yao Sheng , Augustine Mathew M. , Xu Haiying , Wang Jun , Sun Jingwei , Broadwater Megan , Ruff William , Luo Liqun , Zhu Gefeng , Tamada Koji , Chen Lieping
Published: April 2016

The SALM5-HVEM interaction limits inflammation and contributes to immune privilege in the CNS.