bluuebunny/crossref_metadata_2025 huggingface dataset:
Chiral selectivity of amino acid adsorption on chiral surfaces—The case of alanine on Pt
Authors: Franke J.-H. , Kosov D. S.
Published: February 2015

We study the binding pattern of the amino acid alanine on the naturally chiral Pt surfaces Pt(531), Pt(321), and Pt(643). These surfaces are all vicinal to the {111} direction but have different local environments of their kink sites and are thus a model for realistic roughened Pt surfaces. Alanine has only a single methyl group attached to its chiral center, which makes the number of possible binding conformations computationally tractable. Additionally, only the amine and carboxyl group are expected to interact strongly with the Pt substrate. On Pt(531), we study the molecule in its pristine as well as its deprotonated form and find that the deprotonated one is more stable by 0.47 eV. Therefore, we study the molecule in its deprotonated form on Pt(321) and Pt(643). As expected, the oxygen and nitrogen atoms of the deprotonated molecule provide a local binding “tripod” and the most stable adsorption configurations optimize the interaction of this “tripod” with undercoordinated surface atoms. However, the interaction of the methyl group plays an important role: it induces significant chiral selectivity of about 60 meV on all surfaces. Hereby, the L-enantiomer adsorbs preferentially to the Pt(321)S and Pt(643)S surfaces, while the D-enantiomer is more stable on Pt(531)S. The binding energies increase with increasing surface density of kink sites, i.e., they are largest for Pt(531)S and smallest for Pt(643)S.
Boundary regularized integral equation formulation of Stokes flow
Authors: Sun Q. , Klaseboer E. , Khoo B. C. , Chan D. Y. C.
Published: February 2015

Single-phase Stokes flow problems with prescribed boundary conditions can be formulated in terms of a boundary regularized integral equation that is completely free of singularities that exist in the traditional formulation. The usual mathematical singularities that arise from using the fundamental solution in the conventional boundary integral method are removed by subtracting a related auxiliary flow field, w, that can be constructed from one of many known fundamental solutions of the Stokes equation. This approach is exact and does not require the introduction of additional cutoff parameters. The numerical implementation of this boundary regularized integral equation formulation affords considerable savings in coding effort with improved numerical accuracy. The high accuracy of this formulation is retained even in problems where parts of the boundaries may almost be in contact.
Measurement of spherical and cylindrical power in ophthalmic lenses based in the change of lateral amplification
Authors: Mendoza-Villegas P. G. , Trujillo-Schiaffino G. , Salas Peimbert D. P. , Anguiano-Morales M. , Corral-Martínez L. F. , Garduño-Wilches I. A.
Published: February 2015

In this article, we present a new technique to measure spherical and cylindrical power in ophthalmic lenses. This method is based in the change of lateral amplification produced by an optical system when introducing an ophthalmic lens. Ophthalmic lens power is calculated by considering the change in image size from a reference object and its own image seen through the ophthalmic lens. Mathematical analysis is presented along with the experimental setup and the obtained results. Several algorithms were applied to the obtained results as a method to compensate the error in order to fit into ISO 8598 specifications.
Origin of molecular conformational stability: Perspectives from molecular orbital interactions and density functional reactivity theory
Authors: Liu Shubin , Schauer Cynthia K.
Published: February 2015

To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability.
Liquid-phase-deposited siloxane-based capping layers for silicon solar cells
Authors: Veith-Wolf Boris , Wang Jianhui , Hannu-Kuure Milja , Chen Ning , Hadzic Admir , Williams Paul , Leivo Jarkko , Karkkainen Ari , Schmidt Jan
Published: February 2015

We apply non-vacuum processing to deposit dielectric capping layers on top of ultrathin atomic-layer-deposited aluminum oxide (AlOx) films, used for the rear surface passivation of high-efficiency crystalline silicon solar cells. We examine various siloxane-based liquid-phase-deposited (LPD) materials. Our optimized AlOx/LPD stacks show an excellent thermal and chemical stability against aluminum metal paste, as demonstrated by measured surface recombination velocities below 10 cm/s on 1.3 Ωcm p-type silicon wafers after firing in a belt-line furnace with screen-printed aluminum paste on top. Implementation of the optimized LPD layers into an industrial-type screen-printing solar cell process results in energy conversion efficiencies of up to 19.8% on p-type Czochralski silicon.
Temperature dependence of Brillouin light scattering spectra of acoustic phonons in silicon
Authors: Olsson Kevin S. , Klimovich Nikita , An Kyongmo , Sullivan Sean , Weathers Annie , Shi Li , Li Xiaoqin
Published: February 2015

Electrons, optical phonons, and acoustic phonons are often driven out of local equilibrium in electronic devices or during laser-material interaction processes. The need for a better understanding of such non-equilibrium transport processes has motivated the development of Raman spectroscopy as a local temperature sensor of optical phonons and intermediate frequency acoustic phonons, whereas Brillouin light scattering (BLS) has recently been explored as a temperature sensor of low-frequency acoustic phonons. Here, we report the measured BLS spectra of silicon at different temperatures. The origins of the observed temperature dependence of the BLS peak position, linewidth, and intensity are examined in order to evaluate their potential use as temperature sensors for acoustic phonons.
High-frequency magnetic properties of [FeCo/FeCo-SiO2]n multilayered films deposited on flexible substrate
Authors: Zhang L. , Zhu W. B. , Zheng H. Y. , Bi L. , Wang X. , Han M. G. , Lu H. P. , Xie J. L. , Deng L. J.
Published: February 2015

A series of 120 nm [FeCo/FeCo-SiO2]n multilayer thin films with different FeCo layer thicknesses (T = 10–40 nm) and fixed FeCo-SiO2 layer thickness (20 nm) were deposited on flexible substrate (Mylar) by controlling the sputtering time under applied magnetic field. The magnetic properties of the multilayer thin films were investigated. The experimental results showed that the multilayer thin films had obvious in-plane uniaxial magnetic anisotropy, which can be adjusted in a broad range by changing the thickness of FeCo layer. In addition, good soft magnetic performance was obtained. The coercivity in the easy axis Hce of the multilayer films with the T = 10 nm, 20 nm, 30 nm, and 40 nm was 5 Oe, 25 Oe, 10 Oe, and 8 Oe, respectively. In frequency-dependent permeability spectra measurement, two resonance peaks of complex permeability spectrum were observed, especially for T = 20 nm, which can be attributed to the complicated magnetic structure of FeCo and FeCo-SiO2 layer. By introducing multilayers with different effect anisotropy field, one can broaden the absorption peak while maintaining the high permeability, which would open the way for their potential applications as wide-band microwave absorber.
Intrinsic evolutions of dielectric function and electronic transition in tungsten doping Ge2Sb2Te5 phase change films discovered by ellipsometry at elevated temperatures
Authors: Guo S. , Ding X. J. , Zhang J. Z. , Hu Z. G. , Ji X. L. , Wu L. C. , Song Z. T. , Chu J. H.
Published: February 2015

Tungsten (W) doping effects on Ge2Sb2Te5 (GSTW) phase change films with different concentrations (3.2, 7.1, and 10.8%) have been investigated by variable-temperature spectroscopic ellipsometry. The dielectric functions from 210 K to 660 K have been evaluated with the aid of Tauc-Lorentz and Drude dispersion models. The analysis of Tauc gap energy (Eg) and partial spectral weight integral reveal the correlation between optical properties and local structural change. The order degree increment and chemical bond change from covalent to resonant should be responsible for band gap narrowing and electronic transition enhancement during the phase change process. It is found that the elevated crystalline temperature for GSTW can be related to improved disorder degree. Furthermore, the shrinkage of Eg for GSTW should be attributed to the enhanced metallicity compared with undoped GST.
Grain-grain interaction in stationary dusty plasma
Authors: Lampe Martin , Joyce Glenn
Published: February 2015

We present a particle-in-cell simulation study of the steady-state interaction between two stationary dust grains in uniform stationary plasma. Both the electrostatic force and the shadowing force on the grains are calculated explicitly. The electrostatic force is always repulsive. For two grains of the same size, the electrostatic force is very nearly equal to the shielded electric field due to a single isolated grain, acting on the charge of the other grain. For two grains of unequal size, the electrostatic force on the smaller grain is smaller than the isolated-grain field, and the force on the larger grain is larger than the isolated-grain field. In all cases, the attractive shadowing force exceeds the repulsive electrostatic force when the grain separation d is greater than an equilibrium separation d0. d0 is found to be between 6λD and 9λD in all cases. The binding energy is estimated to be between 19 eV and 900 eV for various cases.
Ordinary mode instability associated with thermal ring distribution
Authors: Hadi F. , Yoon P. H. , Qamar A.
Published: February 2015

The purely growing ordinary (O) mode instability driven by excessive parallel temperature anisotropy has recently received renewed attention owing to its potential applicability to the solar wind plasma. Previous studies of O mode instability have assumed either bi-Maxwellian or counter-streaming velocity distributions. For solar wind plasma trapped in magnetic mirror-like geometry such as magnetic clouds or in the vicinity of the Earth's collisionless bow shock environment, however, the velocity distribution function may possess a loss-cone feature. The O-mode instability in such a case may be excited for cyclotron harmonics as well as the purely growing branch. The present paper investigates the O-mode instability for plasmas characterized by the parallel Maxwellian distribution and perpendicular thermal ring velocity distribution in order to understand the general stability characteristics.
Small and arbitrary shock structures in spin 1/2 magnetohydrodynamic quantum plasma
Authors: Sahu Biswajit , Choudhury Sourav , Sinha Anjana
Published: February 2015

The shock structures in spin-1/2 quantum plasma, in the presence of magnetic diffusivity, are studied in the framework of the quantum magnetohydrodynamic model. Linear dispersion relation for the system is carried out analytically, and the results are plotted numerically for several values of the plasma parameters. Numerical analysis for arbitrary amplitude waves is carried out, whereas for waves of small amplitude, the reductive perturbation technique is applied to obtain the Korteweg-de Vries-Burgers equation. Both the analyses are observed to give the same qualitative picture. Most importantly, the different plasma parameters are found to play significant roles in determining the nature of the shock waves. The parametric ranges for which monotonic shock and oscillatory shock solutions are observed, are found analytically.
Controlling hollow relativistic electron beam orbits with an inductive current divider
Authors: Swanekamp S. B. , Richardson A. S. , Angus J. R. , Cooperstein G. , Hinshelwood D. D. , Ottinger P. F. , Rittersdorf I. M. , Schumer J. W. , Weber B. V. , Zier J. C.
Published: February 2015

A passive method for controlling the trajectory of an intense, hollow electron beam is proposed using a vacuum structure that inductively splits the beam's return current. A central post carries a portion of the return current (I1), while the outer conductor carries the remainder (I2). An envelope equation appropriate for a hollow electron beam is derived and applied to the current divider. The force on the beam trajectory is shown to be proportional to (I2-I1), while the average force on the envelope (the beam width) is proportional to the beam current Ib = (I2 + I1). The values of I1 and I2 depend on the inductances in the return-current path geometries. Proper choice of the return-current geometries determines these inductances and offers control over the beam trajectory. Solutions using realistic beam parameters show that, for appropriate choices of the return-current-path geometry, the inductive current divider can produce a beam that is both pinched and straightened so that it approaches a target at near-normal incidence with a beam diameter that is on the order of a few mm.
Neutral Vlasov kinetic theory of magnetized plasmas
Authors: Tronci Cesare , Camporeale Enrico
Published: February 2015

The low-frequency limit of Maxwell equations is considered in the Maxwell-Vlasov system. This limit produces a neutral Vlasov system that captures essential features of plasma dynamics, while neglecting radiation effects. Euler-Poincaré reduction theory is used to show that the neutral Vlasov kinetic theory possesses a variational formulation in both Lagrangian and Eulerian coordinates. By construction, the new model recovers all collisionless neutral models employed in plasma simulations. Then, comparisons between the neutral Vlasov system and hybrid kinetic-fluid models are presented in the linear regime.
Ionospheric very low frequency transmitter
Authors: Kuo Spencer P.
Published: February 2015

The theme of this paper is to establish a reliable ionospheric very low frequency (VLF) transmitter, which is also broad band. Two approaches are studied that generate VLF waves in the ionosphere. The first, classic approach employs a ground-based HF heater to directly modulate the high latitude ionospheric, or auroral electrojet. In the classic approach, the intensity-modulated HF heater induces an alternating current in the electrojet, which serves as a virtual antenna to transmit VLF waves. The spatial and temporal variations of the electrojet impact the reliability of the classic approach. The second, beat-wave approach also employs a ground-based HF heater; however, in this approach, the heater operates in a continuous wave mode at two HF frequencies separated by the desired VLF frequency. Theories for both approaches are formulated, calculations performed with numerical model simulations, and the calculations are compared to experimental results. Theory for the classic approach shows that an HF heater wave, intensity-modulated at VLF, modulates the electron temperature dependent electrical conductivity of the ionospheric electrojet, which, in turn, induces an ac electrojet current. Thus, the electrojet becomes a virtual VLF antenna. The numerical results show that the radiation intensity of the modulated electrojet decreases with an increase in VLF radiation frequency. Theory for the beat wave approach shows that the VLF radiation intensity depends upon the HF heater intensity rather than the electrojet strength, and yet this approach can also modulate the electrojet when present. HF heater experiments were conducted for both the intensity modulated and beat wave approaches. VLF radiations were generated and the experimental results confirm the numerical simulations. Theory and experimental results both show that in the absence of the electrojet, VLF radiation from the F-region is generated via the beat wave approach. Additionally, the beat wave approach generates VLF radiations over a larger frequency band than by the modulated electrojet.
The different roles of contact materials between oxidation interlayer and doping effect for high performance ZnO thin film transistors
Authors: Xu Lei , Huang Chun-Wei , Abliz Ablat , Hua Yang , Liao Lei , Wu Wen-Wei , Xiao Xiangheng , Jiang Changzhong , Liu Wei , Li Jinchai
Published: February 2015

To improve the performance of ZnO thin film transistors (TFTs) by using appropriate metal contacts, the different roles of contact materials between oxidation interlayer and doping effect are investigated. With careful characterization, an oxidation interlayer has been verified at the interface between ZnO film and Al or Ti contact, which is suggested to be responsible for contact resistance and thermal reliability. On the other hand, it is observed that the doping effect is the main reason for the Sn or Cu contact characteristics. The superior contact using Sn is due to an oxidation-free interface, donor doping effect, and a low barrier height. By using a metal contact with a high Gibbs free energy, the metal layer would hardly consume oxygen from channel layer during sputtering and easily form no oxidation interlayer. Thus, choosing a metal contact is important when fabricating high-performance metal-oxide TFTs for flat-panel displays.
Self-consistent simulation of radio frequency multipactor on micro-grooved dielectric surface
Authors: Cai Libing , Wang Jianguo , Cheng Guoxin , Zhu Xiangqin , Xia Hongfu
Published: February 2015

The multipactor plays a key role in the surface breakdown on the feed dielectric window irradiated by high power microwave. To study the suppression of multipactor, a 2D electrostatic PIC-MCC simulation code was developed. The space charge field, including surface deposited charge and multipactor electron charge field, is obtained by solving 2D Poisson's equation in time. Therefore, the simulation is self-consistent and does not require presetting a fixed space charge field. By using this code, the self-consistent simulation of the RF multipactor on the periodic micro-grooved dielectric surface is realized. The 2D space distributions of the multipactor electrons and space charge field are presented. From the simulation results, it can be found that only half slopes have multipactor discharge when the slope angle exceeds a certain value, and the groove presents a pronounced suppression effect on the multipactor.
Laser-induced ultrafast demagnetization time and spin moment in ferromagnets: First-principles calculation
Authors: Zhang G. P. , Si M. S. , George Thomas F.
Published: February 2015

When a laser pulse excites a ferromagnet, its spin undergoes a dramatic change. The initial demagnetization process is very fast. Experimentally, it is found that the demagnetization time is related to the spin moment in the sample. In this study, we employ the first-principles method to directly simulate such a process. We use the fixed spin moment method to change the spin moment in ferromagnetic nickel, and then we employ the Liouville equation to couple the laser pulse to the system. We find that in general the dependence of demagnetization time on the spin moment is nonlinear: It decreases with the spin moment up to a point, after which an increase with the spin moment is observed, followed by a second decrease. To understand this, we employ an extended Heisenberg model, which includes both the exchange interaction and spin-orbit coupling. The model directly links the demagnetization rate to the spin moment itself and demonstrates analytically that the spin relaxes more slowly with a small spin moment. A future experimental test of our predictions is needed.
Irreversible electrical manipulation of magnetization on BiFeO3-based heterostructures
Authors: Xu Qingyu , Xu Zhenyu , He Maocheng , Cao Yanqiang , Du Jun
Published: February 2015

We prepared several heterostructures, Co/Bi0.90La0.10FeO3 on surface oxidized Si or (111) SrTiO3 and NiFe/Bi0.90La0.10FeO3 on (001) SrTiO3 substrates using LaNiO3 as bottom electrode. With different strategies of voltage application, the exchange bias field HE decreased with increasing voltage irreversibly for all the heterostructures at room temperature. The chemical state at the NiFe/Bi0.90La0.10FeO3 interface was studied by X-ray photoelectron spectroscopy before and after the electrical manipulation. The oxidization of the metallic ferromagnetic layer at interface after the electrical manipulation has been confirmed, which might explain the irreversibility.
Laser parametric instability experiments of a 3ω, 15 kJ, 6-ns laser pulse in gas-filled hohlraums at the Ligne d'Intégration Laser facility
Authors: Rousseaux C. , Huser G. , Loiseau P. , Casanova M. , Alozy E. , Villette B. , Wrobel R. , Henry O. , Raffestin D.
Published: February 2015

Experimental investigation of stimulated Raman (SRS) and Brillouin (SBS) scattering have been obtained at the Ligne-d'Intégration-Laser facility (LIL, CEA-Cesta, France). The parametric instabilities (LPI) are driven by firing four laser beamlets (one quad) into millimeter size, gas-filled hohlraum targets. A quad delivers energy on target of 15 kJ at 3ω in a 6-ns shaped laser pulse. The quad is focused by means of 3ω gratings and is optically smoothed with a kinoform phase plate and with smoothing by spectral dispersion-like 2 GHz and/or 14 GHz laser bandwidth. Open- and closed-geometry hohlraums have been used, all being filled with 1-atm, neo-pentane (C5H12) gas. For SRS and SBS studies, the light backscattered into the focusing optics is analyzed with spectral and time resolutions. Near-backscattered light at 3ω and transmitted light at 3ω are also monitored in the open geometry case. Depending on the target geometry (plasma length and hydrodynamic evolution of the plasma), it is shown that, at maximum laser intensity about 9 × 1014 W/cm2, Raman reflectivity noticeably increases up to 30% in 4-mm long plasmas while SBS stays below 10%. Consequently, laser transmission through long plasmas drops to about 10% of incident energy. Adding 14 GHz bandwidth to the laser always reduces LPI reflectivities, although this reduction is not dramatic.
Interactions of nonlinear electron-acoustic solitary waves with vortex electron distribution
Authors: Demiray Hilmi
Published: February 2015

In the present work, based on a one dimensional model, we consider the head-on-collision of nonlinear electron-acoustic waves in a plasma composed of a cold electron fluid, hot electrons obeying a trapped/vortex-like distribution, and stationary ions. The analysis is based on the use of extended Poincare, Lighthill-Kuo method [C. H. Su and R. M. Mirie, J. Fluid Mech. 98, 509 (1980); R. M. Mirie and C. H. Su, J. Fluid Mech. 115, 475 (1982)]. It is shown that, for the first order approximation, the waves propagating in opposite directions are characterized by modified Korteweg-de Vries equations. In contrary to the results of previous investigations on this subject, we showed that the phase shifts are functions of both amplitudes of the colliding waves. The numerical results indicate that the waves with larger amplitude experience smaller phase shifts. Such a result seems to be plausible from physical considerations.
Interplay of electron correlations and localization in disordered β-tantalum films: Evidence from dc transport and spectroscopic ellipsometry study
Authors: Kovaleva N. N. , Chvostova D. , Bagdinov A. V. , Petrova M. G. , Demikhov E. I. , Pudonin F. A. , Dejneka A.
Published: February 2015

We report the dc transport (5 K ≲ T ≲ 380 K) and spectroscopic ellipsometry (0.8 eV ≤ hν ≤ 8.5 eV, T ≃ 300 K) study of β-Ta films prepared by rf sputtering deposition as a function of their thickness in the range 2.5 nm ≲ d ≲ 200 nm. The dc transport of the β-Ta films with a thickness d ≳ 25 nm is characterized by negative temperature coefficient of resistivity (TCR) caused by localization effects peculiar of highly disordered metals. Their dielectric function spectra display non-metallic-like behavior due to the presence of the pronounced band at 2 eV. We found that with increasing TCR absolute value, specifying elevated degree disorder, the optical spectral weight (SW) of free charge carriers decreases. The associated SW is recovered in the range of Mott-Hubbard transitions, indicating the mechanism of localization enhancement by electronic correlations in disordered metals.
Prevention of ion flux lateral inhomogeneities in large area capacitive radio frequency plasmas via the electrical asymmetry effect
Authors: Schüngel Edmund , Mohr Sebastian , Schulze Julian , Czarnetzki Uwe
Published: February 2015

The ion flux is measured spatially resolved along the substrate surface in dual-frequency large area capacitive discharges operated in H2 at 150 Pa. One electrode is driven by 40.68 MHz and/or 81.36 MHz. The dependence of the ion flux profile on the applied voltage waveform is investigated experimentally and by a two-dimensional model. The results show that lateral inhomogeneities caused by standing wave effects can be eliminated based on the electrical asymmetry effect, i.e., by tuning the phase shift between the two applied frequencies. This approach solves one of the major problems in plasma processing of large substrates.
Did Zipf Anticipate Spatial Connectivity Structures?
Authors: Reggiani Aura , Nijkamp Peter
Published: February 2015

An avalanche of empirical studies has addressed the validity of the rank-size rule (or Zipf's law) in a multicity context in many countries. Under which conditions (eg, sample size, spatial scale) this ‘law’ holds remains as yet largely underinvestigated, while spatial network constellations also deserve more attention. Against this background, we investigate the relationship between network connectivity and the rank-size rule (or Zipf's law) in an urban economic network constellation. In particular, we address the following methodological issues: (i) the (aggregate) behavioural foundation underlying the rank-size rule (Zipf's law) in the light of spatial-economic network theories (eg, entropy maximization, spatial interaction theory); (ii) the nature of the analytical relationship between social-spatial network analysis and the rank-size rule (Zipf's law). We argue that the rank-size rule is compatible with conventional economic foundations of spatial network models. We test the sensitivity of rank-size rules for changes in scale, functional forms, time periods, and connectivity structures. Our application uses an extensive spatiotemporal panel database on the evolution of the urban population in Germany. We test the relevance of the rank-size rule (Zipf's law), and—in parallel—the related ‘socioeconomic’ connectivity in these urban networks. In particular, we will show that Zipf's law (ie, with the rank-size coefficient equal to 1) is only valid under particular conditions of the sample size.
Distributed Attraction: The Effects of Street Network Connectivity upon the Distribution of Retail Frontage in the City of Buenos Aires
Authors: Scoppa Martin D , Peponis John
Published: February 2015

The City of Buenos Aires has a radial street plan, regular blocks, and a clear central place. On the basis of an analysis of the city's GIS database, we show that measures describing the syntax of its street network have a significant relationship with commercial frontage density, over and above the impact of central business district attraction. These results are obtained while controlling for the effects of population and employment density, distance from public transportation stations, and zoning. Our findings support a hypothesis that emerges from recent literature, namely, that commercial uses are subject to the distributed attraction exercised by the street network, and according to the syntax of street network connectivity. Among the variables describing the street network, those that measure how direct the connection of a street segment is to the rest of the street network, have the greatest explanatory power on the distribution of commercial frontage density. Street width and the extent to which a street segment lies on the shortest routes between all pairs of potential origins and destinations (whether by metric distance or by direction changes), have less influence. Interactions between variables indicate that the effects of spatial syntax in determining the distribution of commercial frontage density by street segment are stronger when variables accounting for other attractors (population and employment density, proximity to metrostations or proximity to other shops in the surrounding area) assume higher values.
Recent Advances in the Development of Sigma-1 Receptor Ligands
Authors: Manohar Madhura , Banister Samuel D. , Beinat Corinne , O'Brien-Brown James , Kassiou Michael
Published: February 2015

The existence of two distinct sigma (σ) receptor subtypes was established in the early 1990s. Sigma-1 and sigma-2 receptors (S1Rs and S2Rs, respectively) were shown to possess distinct molecular size, anatomical distribution, and ligand discrimination. S2R is overexpressed in numerous human cancers, and has therapeutic potential for the imaging and treatment of certain tumours. In contrast, S1R is more broadly involved in a wide variety of central nervous system (CNS) diseases including motor disorders, memory deficits, depression, schizophrenia, anxiety, pain, drug addiction, and many more. Since the human S1R was cloned in 1996, numerous high affinity ligands with excellent selectivity for S1R have been developed. This review focuses on recent developments in the generation of structurally diverse S1R-selective ligands and novel therapeutic candidates targeting S1Rs.
Landscape scale survey of indicators of soil health in grazing systems
Authors: Damsma K. M. , Rose M. T. , Cavagnaro T. R.
Published: February 2015

In a broad-scale survey across pasture-based grazing systems in south-eastern Victoria, soil biological and chemical properties were measured in an effort to establish baseline levels for commonly used indicators of soil health. Although soil properties were highly variable among sites and biological properties were difficult to predict, total soil C was found to be closely associated with soil cation exchange capacity (CEC). Importantly, the strength and nature of relationships between soil properties differed among soil textural classes. We also measured a range of soil and vegetation properties in a small number of patches of remnant vegetation and their adjacent grazed pastures. This was done in an effort to assess the sensitivity of these measures when used on samples collected from strongly contrasting land-use types. Although some factors, such as mycorrhizal colonisation of roots and soil C, did differ between the two land-use types, other factors measured in this study did not. Together, the findings of this survey provide baseline information on the landscape scale for commonly used indicators of soil health. The study explores relationships between these soil properties and assesses how they differ between two strongly contrasting land-use types. The results are discussed in the context of monitoring soil and vegetation attributes relevant to soil health.
Rhetorical dissonance of unsynchronized voices
Authors: Darwish Ali , Orero Pilar
Published: February 2015

Voice-over as an audiovisual translation modality has traditionally been described for its rendering of the truth or its faithfulness. The manipulation and deviation from the original text through translation has already been the object of study in documentaries. This paper looks at the translation of TV news through voice-over. Technical and content infidelities are rendering the broadcast actualities into sexed up copies of the original, which for all intents and purposes are in sheer contravention of what translation is for as a faithful reproduction of the original and of objective and factual news reporting.
The effects of the translator’s visibility in news voice-over is re-examined and the physical presence of the translator/voice talent is analyzed. This paper argues that the visibility of the translator in this instance pushes the boundaries of mediation beyond mere technicalities towards a sociopolitical sphere of reasoning and rationality by editorial policy makers.
The paper also argues that synchronicity of voice-overs stemming from the rhetorical features of the voice-over styles of delivery and the idiosyncrasies of the voices creates dissonance and renders the original message with a degree of infelicities that undermine the long-celebrated standards of objectivity and neutrality. Consequently, this paper underscores the invisibility of the translator in this mode of translation mediation.
Parameterizing mental model ascription across intelligent agents
Authors: McShane Marjorie
Published: February 2015

Mental model ascription – also called mindreading – is the process of inferring the mental states of others, which happens as a matter of course in social interactions. But although ubiquitous, mindreading is presumably a highly variable process: people mindread to different extents and with different results. We hypothesize that human mindreading ability relies on a large number of personal and contextual features: the inherent abilities of specific individuals, their current physical and mental states, their knowledge of the domain of discourse, their familiarity with the interlocutor, the risks associated with an incorrect assessment of intent, and so on. This paper presents a theory of mindreading that models diverse artificial intelligent agents using an inventory of parameters and value sets that represent traits of humans and features of discourse contexts. Examples are drawn from Maryland Virtual Patient, a prototype system that will permit medical trainees to diagnose and treat cognitively modeled virtual patients with the optional assistance of a virtual tutor. Since real patients vary greatly with respect to physiological and cognitive features, so must a society of virtual patients. Modeling such variation is one of the goals of the overall OntoAgent program of research and development.
Abductive understanding of dialogues about joint activities
Authors: Langley Pat , Meadows Ben , Gabaldon Alfredo , Heald Richard
Published: February 2015

This paper examines the task of understanding dialogues in terms of the mental states of the participating agents. We present a motivating example that clarifies the challenges this problem involves and then outline a theory of dialogue interpretation based on abductive inference of these unobserved beliefs and goals, incremental construction of explanations, and reliance on domain-independent knowledge. After this, we describe UMBRA, an implementation of the theory that embodies these assumptions. We report experiments with the system that demonstrate its ability to accurately infer the conversants’ mental states even when some speech acts are unavailable. We conclude by reviewing related research on dialogue and discussing avenues for future study.
Modeling inference of mental states
Authors: Meijering Ben , Taatgen Niels A. , van Rijn Hedderik , Verbrugge Rineke
Published: February 2015

Behavior oftentimes allows for many possible interpretations in terms of mental states, such as goals, beliefs, desires, and intentions. Reasoning about the relation between behavior and mental states is therefore considered to be an effortful process. We argue that people use simple strategies to deal with high cognitive demands of mental state inference. To test this hypothesis, we developed a computational cognitive model, which was able to simulate previous empirical findings: In two-player games, people apply simple strategies at first. They only start revising their strategies when these do not pay off. The model could simulate these findings by recursively attributing its own problem solving skills to the other player, thus increasing the complexity of its own inferences. The model was validated by means of a comparison with findings from a developmental study in which the children demonstrated similar strategic developments.
Gramaticalización y tradiciones discursivas
Authors: Garcés Gómez María Pilar
Published: February 2015

This article examines the evolution of the adverbial phraseen efecto(in truth) and of the adverbefectivamente(truly), which while originating from a common semantic base, have followed different evolutionary processes. Eventually, they have come to share a common function as discursive markers to indicate a confirmation of the discursive message or a reinforcement of an assertion.

Our goal is to describe the evolution of the acquisition process for the discursive value of these forms. We also analyze whether these changes are the results of a grammaticalization process and we describe the impact of discursive traditions in the incorporation of certain values. Finally, we show how this evolution is influenced by the paradigm changes caused by the incorporation, elimination or modification of the various lexical units in these forms through out the different stages in their development.
Un romance al tono de “Caballero de armas blancas” más otras obras devotas
Authors: Rovira i Cerdà Helena
Published: February 2015

We study and edit a poetic chapbook of the Biblioteca Nacional de España, whose current signature is [R/41101]. Although, through a copy of the Duke of T’Serclaes of Tilly, this issue was already known by several bibliographers since the nineteenth century, the whereabouts of the original of this Sevillian noble had been ignored for decades and might well be the same which now belongs to the aforementioned Biblioteca Nacional. For the first time, we offer a complete description of this chapbook, with the reference to some hitherto unknown works.
Thyroid hormone signaling controls hair follicle stem cell function
Authors: Contreras-Jurado Constanza , Lorz Corina , García-Serrano Laura , Paramio Jesus M. , Aranda Ana
Published: February 2015

Observations in thyroid patients and experimental animals show that the skin is an important target for the thyroid hormones. We previously showed that deletion in mice of the thyroid hormone nuclear receptors TRα1 and TRβ (the main thyroid hormone–binding isoforms) results in impaired epidermal proliferation, hair growth, and wound healing. Stem cells located at the bulges of the hair follicles are responsible for hair cycling and contribute to the regeneration of the new epidermis after wounding. Therefore a reduction in the number or function of the bulge stem cells could be responsible for this phenotype. Bulge cells show increased levels of epigenetic repressive marks, can retain bromodeoxyuridine labeling for a long time, and have colony-forming efficiency (CFE) in vitro. Here we demonstrate that mice lacking TRs do not have a decrease of the bulge stem cell population. Instead, they show an increase of label-retaining cells (LRCs) in the bulges and enhanced CFE in vitro. Reduced activation of stem cells leading to their accumulation in the bulges is indicated by a strongly reduced response to mobilization by 12- O-tetradecanolyphorbol-13-acetate. Altered function of the bulge stem cells is associated with aberrant activation of Smad signaling, leading to reduced nuclear accumulation of β-catenin, which is crucial for stem cell proliferation and mobilization. LRCs of TR-deficient mice also show increased levels of epigenetic repressive marks. We conclude that thyroid hormone signaling is an important determinant of the mobilization of stem cells out of their niche in the hair bulge. These findings correlate with skin defects observed in mice and alterations found in human thyroid disorders.
Spatiotemporal dynamics of membrane remodeling and fusion proteins during endocytic transport
Authors: Arlt Henning , Auffarth Kathrin , Kurre Rainer , Lisse Dominik , Piehler Jacob , Ungermann Christian
Published: February 2015

Organelles of the endolysosomal system undergo multiple fission and fusion events to combine sorting of selected proteins to the vacuole with endosomal recycling. This sorting requires a consecutive remodeling of the organelle surface in the course of endosomal maturation. Here we dissect the remodeling and fusion machinery on endosomes during the process of endocytosis. We traced selected GFP-tagged endosomal proteins relative to exogenously added fluorescently labeled α-factor on its way from the plasma membrane to the vacuole. Our data reveal that the machinery of endosomal fusion and ESCRT proteins has similar temporal localization on endosomes, whereas they precede the retromer cargo recognition complex. Neither deletion of retromer nor the fusion machinery with the vacuole affects this maturation process, although the kinetics seems to be delayed due to ESCRT deletion. Of importance, in strains lacking the active Rab7-like Ypt7 or the vacuolar SNARE fusion machinery, α-factor still proceeds to late endosomes with the same kinetics. This indicates that endosomal maturation is mainly controlled by the early endosomal fusion and remodeling machinery but not the downstream Rab Ypt7 or the SNARE machinery. Our data thus provide important further understanding of endosomal biogenesis in the context of cargo sorting.
CENP-32 is required to maintain centrosomal dominance in bipolar spindle assembly
Authors: Ohta Shinya , Wood Laura , Toramoto Iyo , Yagyu Ken-Ichi , Fukagawa Tatsuo , Earnshaw William C.
Published: February 2015

Centrosomes nucleate spindle formation, direct spindle pole positioning, and are important for proper chromosome segregation during mitosis in most animal cells. We previously reported that centromere protein 32 (CENP-32) is required for centrosome association with spindle poles during metaphase. In this study, we show that CENP-32 depletion seems to release centrosomes from bipolar spindles whose assembly they had previously initiated. Remarkably, the resulting anastral spindles function normally, aligning the chromosomes to a metaphase plate and entering anaphase without detectable interference from the free centrosomes, which appear to behave as free asters in these cells. The free asters, which contain reduced but significant levels of CDK5RAP2, show weak interactions with spindle microtubules but do not seem to make productive attachments to kinetochores. Thus CENP-32 appears to be required for centrosomes to integrate into a fully functional spindle that not only nucleates astral microtubules, but also is able to nucleate and bind to kinetochore and central spindle microtubules. Additional data suggest that NuMA tethers microtubules at the anastral spindle poles and that augmin is required for centrosome detachment after CENP-32 depletion, possibly due to an imbalance of forces within the spindle.
Application of clinical text data for phenome-wide association studies (PheWASs)
Authors: Hebbring Scott J. , Rastegar-Mojarad Majid , Ye Zhan , Mayer John , Jacobson Crystal , Lin Simon
Published: February 2015

Motivation: Genome-wide association studies (GWASs) are effective for describing genetic complexities of common diseases. Phenome-wide association studies (PheWASs) offer an alternative and complementary approach to GWAS using data embedded in the electronic health record (EHR) to define the phenome. International Classification of Disease version 9 (ICD9) codes are used frequently to define the phenome, but using ICD9 codes alone misses other clinically relevant information from the EHR that can be used for PheWAS analyses and discovery.

Results: As an alternative to ICD9 coding, a text-based phenome was defined by 23 384 clinically relevant terms extracted from Marshfield Clinic’s EHR. Five single nucleotide polymorphisms (SNPs) with known phenotypic associations were genotyped in 4235 individuals and associated across the text-based phenome. All five SNPs genotyped were associated with expected terms (P < 0.02), most at or near the top of their respective PheWAS ranking. Raw association results indicate that text data performed equivalently to ICD9 coding and demonstrate the utility of information beyond ICD9 coding for application in PheWAS.

Contact: hebbring.scott@mcrf.mfldclin.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Evolutionary profiles improve protein–protein interaction prediction from sequence
Authors: Hamp Tobias , Rost Burkhard
Published: February 2015

Motivation: Many methods predict the physical interaction between two proteins (protein-protein interactions; PPIs) from sequence alone. Their performance drops substantially for proteins not used for training.

Results: Here, we introduce a new approach to predict PPIs from sequence alone which is based on evolutionary profiles and profile-kernel support vector machines. It improved over the state-of-the-art, in particular for proteins that are sequence-dissimilar to proteins with known interaction partners. Filtering by gene expression data increased accuracy further for the few, most reliably predicted interactions (low recall). The overall improvement was so substantial that we compiled a list of the most reliably predicted PPIs in human. Our method makes a significant difference for biology because it improves most for the majority of proteins without experimental annotations.

Availability and implementation: Implementation and most reliably predicted human PPIs available at https://rostlab.org/owiki/index.php/Profppikernel.

Contact:  rost@in.tum.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
‘Ce qui est coupé repousse’: Jean Genet, Héléne Cixous, the Wound, and the Poetics of Omission
Authors: Fleishman Ian Thomas
Published: February 2015

This article explores the thematic and structural significance of the figure of the wound to Jean Genet's
Pompes funèbres
(1947) and Hélène Cixous's
Souffles
(1975). With reference to the differences between editions of
Pompes funèbres
and through a detailed genetic study of the hitherto unexamined manuscripts of
Souffles
(Cixous's direct response to Genet's novel), the article demonstrates how (self-)censorship becomes constitutive of narrative as such — of its deconstruction and its reconfiguration. By revealing how the later drafts of Cixous's book operate to conceal its poignant autobiographical origin, and playing with the author's ambiguous assertion that ‘Ce qui est coupé repousse’, the article exposes omission as a productive textual strategy.