bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy of vacancy formation in the continuum matter model
Authors: Khrapak A. G. , Khrapak S. A.
Published: May 2013

The quantum energy spectrum of the oscillating spherical void in solids is calculated within the continuum matter model. It is suggested that the ground state of the oscillating void corresponds to the vacancy in real crystals. The dependence of the vacancy formation energy on the shear modulus, density, pressure, and surface tension is determined. The obtained results are used to estimate the properties of vacancies in solid Ar. The possibility of using the obtained results to estimate the properties of vacancies in liquid melts is discussed.
Dynamics of vortex assisted metal condensation in superfluid helium
Authors: Popov Evgeny , Mammetkuliyev Muhammet , Eloranta Jussi
Published: May 2013

Laser ablation of copper and silver targets immersed in bulk normal and superfluid 4He was studied through time-resolved shadowgraph photography. In normal fluid, only a sub-millimeter cavitation bubble is created and immediate formation of metal clusters is observed within a few hundred microseconds. The metal clusters remain spatially tightly focused up to 15 ms, and it is proposed that this observation may find applications in particle image velocimetry. In superfluid helium, the cavitation bubble formation process is distinctly different from the normal fluid. Due to the high thermal conductivity and an apparent lag in the breakdown of superfluidity, about 20% of the laser pulse energy was transferred directly into the liquid and a large gas bubble, up to several millimeters depending on laser pulse energy, is created. The internal temperature of the gas bubble is estimated to exceed 9 K and the following bubble cool down period therefore includes two separate phase transitions: gas–normal liquid and normal liquid–superfluid. The last stage of the cool down process was assigned to the superfluid lambda transition where a sudden formation of large metal clusters is observed. This is attributed to high vorticity created in the volume where the gas bubble previously resided. As shown by theoretical bosonic density functional theory calculations, quantized vortices can trap atoms and dimers efficiently, exhibiting static binding energies up to 22 K. This, combined with hydrodynamic Bernoulli attraction, yields total binding energies as high as 35 K. For larger clusters, the static binding energy increases as a function of the volume occupied in the liquid to minimize the surface tension energy. For heliophobic species an energy barrier develops as a function of the cluster size, whereas heliophilics show barrierless entry into vortices. The present theoretical and experimental observations are used to rationalize the previously reported metal nanowire assembly in both superfluid bulk liquid helium and helium droplets, both of which share the common element of a rapid passage through the lambda point. The origin of vorticity is tentatively assigned to the Zurek-Kibble mechanism. Implications of the large gas bubble formation by laser ablation to previous experiments aimed at implanting atomic and dimeric species in bulk superfluid helium are also discussed, and it is proposed that the developed visualization method should be used as a diagnostic tool in such experiments to avoid measurements in dense gaseous environments.
Isolated catalyst sites on amorphous supports: A systematic algorithm for understanding heterogeneities in structure and reactivity
Authors: Goldsmith Bryan R. , Sanderson Evan D. , Bean Daniel , Peters Baron
Published: May 2013

Methods for modeling catalytic sites on amorphous supports lag far behind methods for modeling catalytic sites on metal surfaces, zeolites, and other crystalline materials. One typical strategy for amorphous supports uses cluster models with arbitrarily chosen constraints to model the rigid amorphous support, but these constraints arbitrarily influence catalyst site activity. An alternative strategy is to use no constraints, but this results in catalytic sites with unrealistic flexibility. We present a systematic ab initio method to model isolated active sites on insulating amorphous supports using small cluster models. A sequential quadratic programming framework helps us relate chemical properties, such as the activation energy, to active site structure. The algorithm is first illustrated on an empirical valence bond model energy landscape. We then use the algorithm to model an off-pathway kinetic trap in olefin metathesis by isolated Mo sites on amorphous SiO2. The cluster models were terminated with basis set deficient fluorine atoms to mimic the properties of an extended silica framework. We also discuss limitations of the current algorithm formulation and future directions for improvement.
Thermal conductivity inhibition in phonon engineered core-shell cross-section modulated Si/Ge nanowires
Authors: Nika Denis L. , Cocemasov Alexandr I. , Crismari Dmitrii V. , Balandin Alexander A.
Published: May 2013

We have shown theoretically that a combination of cross-section modulation and acoustic mismatch in the core-shell Si/Ge nanowires can lead to a drastic reduction of the thermal conductivity. Our calculations, which utilized two different models–five-parameter Born-von Karman and six-parameter valence force field—for the lattice vibrations, indicate that the room temperature thermal conductivity of Si/Ge cross-section modulated nanowires is almost three orders of magnitude lower than that of bulk Si. Thermal flux in the modulated nanowires is suppressed by an order of magnitude in comparison with generic Si nanowires. The effect is explained by modification of the phonon spectra in modulated nanowires leading to decrease of the phonon group velocities and localization of certain phonon modes in narrow or wide nanowire segments. The thermal conductivity inhibition is achieved in nanowires without additional surface roughness and, thus, potentially reducing degradation of the electron transport. Our results suggest that the acoustically mismatched cross-section modulated nanowires are promising candidates for thermoelectric applications.
Statistically testing the validity of analytical and computational approximations to the chemical master equation
Authors: Jenkinson Garrett , Goutsias John
Published: May 2013

The master equation is used extensively to model chemical reaction systems with stochastic dynamics. However, and despite its phenomenological simplicity, it is not in general possible to compute the solution of this equation. Drawing exact samples from the master equation is possible, but can be computationally demanding, especially when estimating high-order statistical summaries or joint probability distributions. As a consequence, one often relies on analytical approximations to the solution of the master equation or on computational techniques that draw approximative samples from this equation. Unfortunately, it is not in general possible to check whether a particular approximation scheme is valid. The main objective of this paper is to develop an effective methodology to address this problem based on statistical hypothesis testing. By drawing a moderate number of samples from the master equation, the proposed techniques use the well-known Kolmogorov-Smirnov statistic to reject the validity of a given approximation method or accept it with a certain level of confidence. Our approach is general enough to deal with any master equation and can be used to test the validity of any analytical approximation method or any approximative sampling technique of interest. A number of examples, based on the Schlögl model of chemistry and the SIR model of epidemiology, clearly illustrate the effectiveness and potential of the proposed statistical framework.
On an integrable discretisation of the Ablowitz-Ladik hierarchy
Authors: Zullo Federico
Published: May 2013

Following the general results on the relationships about Bäcklund transformations (BTs) and exact discretisation given in a previous work [Zullo, F., “Bäcklund transformations and Hamiltonian flows” J. Phys. A: Math. Theor. 46, 145203 (2013)10.1088/1751-8113/46/14/145203], we consider the Ablowitz-Ladik hierarchy and a corresponding family of BTs. After discussing the boundary conditions, we show how to get explicit transformations. The Hamiltonian properties of the maps and of the discrete flows are examined. The conditions on the parameters of the map giving exact discretisations are discussed. Finally, analytical and numerical examples are given.
The Poisson realization of $\mathfrak {so}(2, 2k+2)$so(2,2k+2) on magnetic leaves and generalized MICZ-Kepler problems
Authors: Meng Guowu
Published: May 2013

Let \documentclass[12pt]{minimal}\begin{document}${\mathbb {R}}^{2k+1}_*={\mathbb {R}}^{2k+1}\setminus \lbrace \vec{0}\rbrace$\end{document}R*2k+1=R2k+1∖{0⃗} (k ⩾ 1) and π: \documentclass[12pt]{minimal}\begin{document}${\mathbb {R}}^{2k+1}_*\rightarrow \mathrm{S}^{2k}$\end{document}R*2k+1→S2k be the map sending \documentclass[12pt]{minimal}\begin{document}$\vec{r}\in {\mathbb {R}}^{2k+1}_*$\end{document}r⃗∈R*2k+1 to \documentclass[12pt]{minimal}\begin{document}${\vec{r}\over |\vec{r}|}\in \mathrm{S}^{2k}$\end{document}r⃗|r⃗|∈S2k. Denote by \documentclass[12pt]{minimal}\begin{document}$P\rightarrow {\mathbb {R}}^{2k+1}_*$\end{document}P→R*2k+1 the pullback by π of the canonical principal SO(2k)-bundle SO(2k + 1) → S2k. Let \documentclass[12pt]{minimal}\begin{document}$E_\sharp \rightarrow {\mathbb {R}}^{2k+1}_*$\end{document}E♯→R*2k+1 be the associated co-adjoint bundle and \documentclass[12pt]{minimal}\begin{document}$E^\sharp \rightarrow T^*{\mathbb {R}}^{2k+1}_*$\end{document}E♯→T*R*2k+1 be the pullback bundle under projection map \documentclass[12pt]{minimal}\begin{document}$T^*{\mathbb {R}}^{2k+1}_*\break \rightarrow {\mathbb {R}}^{2k+1}_*$\end{document}T*R*2k+1→R*2k+1. The canonical connection on SO(2k + 1) → S2k turns E♯ into a Poisson manifold. The main result here is that the real Lie algebra \documentclass[12pt]{minimal}\begin{document}$\mathfrak {so}(2, 2k+2)$\end{document}so(2,2k+2) can be realized as a Lie subalgebra of the Poisson algebra \documentclass[12pt]{minimal}\begin{document}$(C^\infty (\mathcal {O}^\sharp ), \lbrace , \rbrace )$\end{document}(C∞(O♯),{,}), where \documentclass[12pt]{minimal}\begin{document}$\mathcal {O}^\sharp$\end{document}O♯ is a symplectic leave of E♯ of special kind. Consequently, in view of the earlier result of the author, an extension of the classical MICZ Kepler problems to dimension 2k + 1 is obtained. The Hamiltonian, the angular momentum, the Lenz vector, and the equation of motion for this extension are all explicitly worked out.
Application of SixNy:Hz (SiN) as index matching layer in a-Si:H thin film solar cells
Authors: Bhal Singh Chandra , Bhattacharya Sekhar , Singh Vandana , Balaji Bhargav P. , Sarkar Surajit , Bhavanasi Venkateswarlu , Ahmad Nafis
Published: May 2013

The difference in refractive indices of glass substrate and transparent conducting oxide (TCO) electrode causes optical reflection in thin film solar cells, which results in lower absorption of light for devices. An anti-reflection layer between glass and TCO is required to reduce the loss of light due to optical reflection. Silicon nitride (SixNy:Hz) films have shown antireflection property. The refractive index of SixNy:Hz films can be engineered by changing the silicon or nitrogen content in the film. Here, we report the optimization of refractive index of SixNy:Hz to achieve a value between refractive index of glass (1.5) and TCO film (2.0). SixNy:Hz films have been deposited in a RF-plasma enhanced chemical vapour deposition system operating at a frequency of 13.56 MHz. The substrate temperature was fixed at 300 °C. Fourier transform infrared analysis has been used to determine the nature of Si-N, N-H, and Si-H bonding in the films. Refractive index of films has been measured using spectroscopic ellipsometer. The optical reflectance and transmission of SixNy:Hz and SixNy:Hz/TCO layers have been measured using UV/VIS spectrometer. The gas flow rate ratio of N2/SiH4 has been varied from 235 to 470. Decrease in transmittance of SixNy:Hz/TCO layer is observed with increase in silicon concentration in the film. Refractive index of SixNy:Hz also increased with an increase of the silicon content in the films. The reflectance of TCO films has been decreased from 15% to 8% when SixNy:Hz film is incorporated between glass substrate and TCO film. An improvement of around 20% has been observed in current density of solar cells having SixNy:Hz film as refractive index matching layer with refractive index 1.83. Thus, SixNy:Hz film as refractive index matching layer can be used to improve the solar cells device efficiency.
Optical-resolution photoacoustic microscopy by use of a multimode fiber
Authors: Papadopoulos Ioannis N. , Simandoux Olivier , Farahi Salma , Pierre Huignard Jean , Bossy Emmanuel , Psaltis Demetri , Moser Christophe
Published: May 2013

We demonstrate Optical-Resolution Photoacoustic Microscopy (OR-PAM), where the optical field is focused and scanned using Digital Phase Conjugation through a multimode fiber. The focus is scanned across the field of view using digital means, and the acoustic signal induced is collected by a transducer. Optical-resolution photoacoustic images of a knot made by two absorptive wires are obtained and we report on resolution smaller than 1.5 μm across a 201 μm × 201 μm field of view. The use of a multimode optical fiber for the optical excitation part can pave the way for miniature endoscopes that can provide optical-resolution photoacoustic images at large optical depth.
Optical response of DyN
Authors: Azeem M. , Ruck B. J. , Do Le Binh , Warring H. , Trodahl H. J. , Strickland N. M. , Koo A. , Goian V. , Kamba S.
Published: May 2013

We report measurements of the optical response of polycrystalline DyN thin films. The frequency-dependent complex refractive index in the near IR-visible-near UV was determined by fitting reflection/transmission spectra. In conjunction with resistivity measurements, these identify DyN as a semiconductor with an optical energy gap of 1.2 eV. When doped with nitrogen vacancies it shows free carrier absorption and a blue-shifted gap associated with the Moss-Burstein effect. The refractive index of 2.0 ± 0.1 depends only weakly on energy. Far infrared reflectivity data show a polar phonon of frequency 280 cm−1 and a dielectric strength of Δε=20.
Ion-beam-induced bending of freestanding amorphous nanowires: The importance of the substrate material and charging
Authors: Cui Ajuan , Fenton J. C. , Li Wuxia , Shen Tiehan H. , Liu Zhe , Luo Qiang , Gu Changzhi
Published: May 2013

Ion-beam irradiation offers great flexibility and controllability in the construction of freestanding nanostructures with multiple advanced functionalities. Here, we present and discuss the bending of free-standing nanowires, against, towards, and ultimately parallel to a flux of directional ion irradiation. Bending components both along and perpendicular to the incident ion beam were observed, and the bending behavior was found to depend both on the ion beam scanning strategy and on the conductivity of the supporting substrate. This behavior is explained by an ion-irradiation-related electrostatic interaction. Our findings suggest the prospect of exploiting this technique to engineer 3D nanostructures for advanced applications.
Surface and interfacial reaction study of InAs(100)-crystalline oxide interface
Authors: Zhernokletov D. M. , Laukkanen P. , Dong H. , Galatage R. V. , Brennan B. , Yakimov M. , Tokranov V. , Kim J. , Oktyabrsky S. , Wallace R. M.
Published: May 2013

A crystalline oxide film on InAs(100) is investigated with in situ monochromatic x-ray photoelectron spectroscopy and low energy electron diffraction before and after in situ deposition of Al2O3 by atomic layer deposition (ALD) as well as upon air exposure. The oxidation process leads to arsenic and indium trivalent oxidation state formation. The grown epitaxial oxide-InAs interface is stable upon ALD reactor exposure; however, trimethyl aluminum decreases oxidation states resulting in an unreconstructed surface. An increase in oxide concentration is also observed upon air exposure suggesting the crystalline oxide surface is unstable.
Separating positive and negative magnetoresistance for polyaniline-silicon nanocomposites in variable range hopping regime
Authors: Gu Hongbo , Guo Jiang , Sadu Rakesh , Huang Yudong , Haldolaarachchige Neel , Chen Daniel , Young David P. , Wei Suying , Guo Zhanhu
Published: May 2013

This letter reports on unique room temperature organic magnetoresistance (OMAR) in the disordered polyaniline/silicon polymer nanocomposites in the variable range hopping regime. A transition from positive to negative OMAR was observed around 5.5 T. The theoretical analysis revealed that both wave-function shrinkage model and forward interference model contributed to the positive OMAR and only forward interference model was responsible for the observed negative OMAR. The obtained positive OMAR is well explained by the introduced localization length a0, density of states at the Fermi level (N(EF)), and average hopping length Rhop; and the negative OMAR is interpreted by the quantum interference effect.
Low-temperature crystallization of high performance Pb0.4Sr0.6TiO3 films compatible with the current silicon-based microelectronic technology
Authors: Li Kui , Rémiens Denis , Dong Xianlin , Costecalde Jean , Sama Nossikpendou , Li Tao , Du Gang , Chen Ying , Wang Genshui
Published: May 2013

This investigation presents a simple approach to realize the low temperature crystallization of Pb0.4Sr0.6TiO3 thin films at 400 °C by taking advantage of well controlled lead excess and kinetic-driving-force compensated thermodynamics crystalline via sputtering deposition. The thin films prepared at low temperature show fine-grained micro-structure because of the suppressed grain growth, furthermore, the intrinsic dielectric response can be modulated by the distinct level of crystallinity. The film processed at 450 °C exhibited a dielectric constant of 435 and high figure merit of 130 at 400 kV/cm, superior ferroelectric property, and stable performance with temperature and frequency.
Swelling of cellular solids: From conventional to re-entrant honeycombs
Authors: Rafsanjani Ahmad , Derome Dominique , Guyer Robert A. , Carmeliet Jan
Published: May 2013

We find that, in two-dimensional periodic cellular solids, the hygro-expansion properties of the cell wall and the geometrical configurations of the lattice determine the effective swelling behavior of the medium. In this letter, we present the associated phase diagram for the swelling anisotropy of conventional and re-entrant honeycomb morphologies. The presented results are obtained numerically from a finite element based computational upscaling scheme. We show how the pattern of anisotropy in swelling behavior of cellular materials reverses when swelling is more important across or along the cell walls.
Tunneling magnetoresistance from non-collinear alignment of magnetization in Fe/GaAlAs/GaMnAs magnetic tunnel junctions
Authors: Yoo Taehee , Khym Sungwon , Lee Hakjoon , Lee Sangyeop , Lee Sanghoon , Liu Xinyu , Furdyna Jacek K. , Uk Lee Dong , Kyu Kim Eun
Published: May 2013

Tunneling magnetoresistance (TMR) observed in Fe/GaAlAs/GaMnAs magnetic tunnel junctions depends strongly on relative configuration of magnetizations in the GaMnAs and Fe layers. Using a series of field orientations, we show that non-collinear alignments of magnetization in this structure occur when the magnetic field is applied away from the easy axes of the magnetic layers; and we find that the values of TMR observed for non-collinear spin configurations are very different from those of collinear configurations. The observed behavior suggests the possibility of using this effect for multivalued magnetic memory devices.
Surface photovoltage analyses of Cu(In,Ga)S2/CdS and Cu(In,Ga)S2/In2S3 photovoltaic junctions
Authors: Merdes S. , Osterloh F. , Sáez-Araoz R. , Klaer J. , Klenk R. , Dittrich T.
Published: May 2013

Spectrally dependent surface photovoltage measurements were performed with repetitive regime on Cu(In,Ga)S2 absorbers and on Cu(In,Ga)S2/CdS and Cu(In,Ga)S2/In2S3 junctions. The results are correlated to current-voltage investigations of the respective completed solar cells. The measurements show the presence of a space charge region in the bare Cu(In,Ga)S2 absorbers due to a high density of surface states. It is found that deposition of CdS increases the band bending whereas deposition of In2S3 does not change it.
Communication: Existence of the doubly excited state that mediates the photoionization of azulene
Authors: Piecuch Piotr , Hansen Jared A. , Staedter David , Faure Stéphane , Blanchet Valérie
Published: May 2013

We use the high-level electronic structure computations based on the equation-of-motion coupled-cluster (EOMCC) theory to show that the previously postulated [V. Blanchet et al., J. Chem. Phys. 128, 164318 (2008)10.1063/1.2913167] doubly excited state of azulene, located below the ionization threshold and mediating the 1 + 2′ multi-photon ionization that leads to a Rydberg fingerprint, exists. This supports the crucial role of doubly excited states in the Rydberg fingerprint spectroscopy, while demonstrating the usefulness of EOMCC methods in capturing such states.
Revealing the tunable twinning/detwinning behavior in 25 nm Cu/Au multilayers
Authors: Yan J. W. , Zhang G. P.
Published: May 2013

Stability of nanotwins during plastic deformation is an important factor to control plasticity of nanotwinned metals. Based on transmission electron microscopy observations of the 25 nm Cu/Au multilayers deformed by indentation, we found that the nanotwins in the Cu and the Au layers have different stabilities through twinning/detwinning. The mechanism-based criterion for the stability of the nanotwins under applied stress proposed here reveals that the tunable twinning/detwinning ability is related to the residual stress in the nanolayered material. The present results may provide a clue for the modulation of plasticity of nanotwinned multilayers through the nanotwin stability.
A stochastic programming approach for optimal microgrid economic operation under uncertainty using 2m + 1 point estimate method
Authors: Mohammadi Sirus , Mozafari Babak , Soleymani Soodabeh
Published: May 2013

By increasing concern over climate change and the security of energy supplies, wind power and photovoltaic are emerging as important sources of electrical energy throughout the world. The wind speed at a given location is continuously varying. There are changes in the annual mean wind speed from year to year (annual), changes with season (seasonal), with passing weather systems (synoptic), on a daily basis (diurnal), and from second to second (turbulence). Common sense tells us that irradiation varies regionally, with the changing seasons, and hourly with the daily variation of the sun's evaluation. This paper proposes a new method for optimal management of MicroGrids under uncertain environments. In this study, the 2m + 1 point estimate method is used to model the uncertainty in the load demands, the market prices, and the electric power generation of the wind farms and the photovoltaic systems. The Weibull, Beta, and normal distributions are used to handle the uncertain input variables in this study. Moreover, a Self-Adaptive Bee Swarm Optimization algorithm is presented to achieve an optimal-operational planning with regard to the cost minimization. In the proposed framework, four different moving patterns are suggested in order to make an adaptive and robust optimization algorithm for different problems with different fitness landscape. In the devised method, each bee self-adaptively chooses one of the proposed moving patterns according to a probability model to update its position. The proposed probability model is based on the ability of each strategy to generate more optimal solutions in the past generations. The efficiency of the method is validated on a typical microgrid.
Layer-by-layer processed polymer solar cells with self-assembled electron buffer layer
Authors: Li Hui , Qi Zhe , Wang Jizheng
Published: May 2013

Layer-by-layer (LL) process is attracting more and more interests in fabricating polymer solar cells (PSCs) due to its potential advantage in realizing p-i-n like structure. Meanwhile self-organization of electron buffer layer (EBL) is drawing increasing attention. Here, we combined the two and LL processed P3HT:PCBM (poly(3-hexylthiophene):phenyl-C61-butyric acid methyl ester) PSCs with self-assembled PEGN-C60 (poly(ethylene glycol) modified [60]fullerene) EBL. Power conversion efficiency of 4.40% was achieved, considerably higher than that of the traditional P3HT:PCBM bulk-heterojunction device, which is 3.84%. The result demonstrates that the approach we developed here could be very useful in fabricating high-performance PSCs.
Evolution of microstructure and magnetoresistive properties of (La0.65Sr0.35)0.8Mn1.2O3±Δ ceramics sintered at 800-1500 °C
Authors: Novokhatska A. , Akimov G. , Prylypko S. , Revenko Yu. , Burkhovetsky V.
Published: May 2013

An effect of microstructure on magnetoresistive properties of manganite ceramics (La0.65Sr0.35)0.8Mn1.2O3±Δ with superstoichiometric manganese has been studied after sintering in the temperature range of 800–1500 °C. Increase in sintering temperature to 1400 °C, an enormous growth of grains, densification of material, and rise in magnetoresistance peak from 1% to 4.8% are observed. At the same time, sintering at 1500 °C leads to a sharp increase in the grain size more than 100 μm, release of excess manganese on grain boundaries, and almost two times magnetoresistance peak rise. We propose that such radical changes are due to the presence of superstoichiometric manganese which plays a crucial role in the formation of ceramics microstructure and properties.
Structural diversity of the wood of temperate species of Acacia s.s. (Leguminosae: Mimosoideae)
Authors: Whinder Frances , Clarke Kerri L. , Warwick Nigel W. M. , Gasson Peter E.
Published: May 2013

Acacia s.s. comprises approximately 1020 species (i.e. just under one-third of all mimosoid legumes) and is almost entirely restricted to, although widespread, on the Australian continent. We investigated variation in the wood anatomy of 12 species from temperate New South Wales in a study concentrating on four recognised taxonomic sections (Botrycephalae, Juliflorae, Phyllodineae and Plurinerves), to elucidate which characteristics are consistent within the sections, having removed climatic effect as much as possible. The sections had great utility in species identification, whereas none of the wood characters reflected the hypothesised phylogeny of the genus. The main consistent difference among species was in ray width (uniseriate versus 1–3 cells wide). All species had distinct growth rings. The vessels had alternate vestured pitting and simple perforation plates. Fibres were generally thick-walled, and many fibres had a gelatinous inner wall (tension wood fibres) and were inconsistently distributed. Axial parenchyma was mainly paratracheal, ranging from vasicentric to confluent and varied greatly in abundance. Prismatic crystals were usually present in chambered fibres and axial parenchyma strands, and also varied in abundance. The variation in these qualitative characters obscures taxonomic differences, but may allow inferences to be made about environmental adaptation.
Cetrimonium Nalidixate as a Multifunctional Inhibitor to Combat Biofilm Formation and Microbiologically Influenced Corrosion
Authors: Seter Marianne , Thomson Melanie J. , Chong Alison , MacFarlane Douglas R. , Forsyth Maria
Published: May 2013

Microbial infection of surfaces and the formation of biofilms is a pervasive problem that appears in diverse fields from medical implants to corrosion of marine structures. We show here, for the first time, the multifunctional inhibitory effects of an environmentally friendly organic salt, cetrimonium nalidixate, a dual active compound based on concepts emerging from the active ionic liquids field. This salt when incorporated into a polyurethane coating leads to complete inhibition of microbiologically influenced corrosion in the presence of several bacteria strains commonly found in marine environments.
Morphological and molecular genetic variability analyses of Saudi lucerne (Medicago sativa L.) landraces
Authors: Al-Faifi Sulieman A. , Migdadi Hussein M. , Al-doss Abedallah , Ammar Megahed H. , El-Harty Ehab H. , Khan Muhammad Altaf. , Matlob Muhammad Javed , Alghamdi Salem S.
Published: May 2013

Collection and characterisation of genetic resources are required for the development of new cultivars. We analysed genetic diversity among 18 non-dormant lucerne (alfalfa, Medicago sativa L.) accessions including ten local ecotypes and eight introduced accessions at morphological and molecular levels using sequence-related amplified polymorphism (SRAP) primers. Standardised canonical discrimination functions for the investigated morphological traits showed that the first function (explaining 75% of total variability among accessions) was strongly influenced by leaflet shape, stipule shape, and the peduncle : petiole length ratio. The 16 SRAP primer pair combinations generated 677 differently sized SRAP fragments (peaks), of which 665 (98.3%) were polymorphic across all 18 accessions. We detected high levels of polymorphism (average polymorphic information content value = 0.96, average of 42.3 polymorphic fragments per primer pair). Based on morphological and SRAP data, local accessions tended to group together in the same cluster or formed individual clusters. Clusters of local accessions at high similarity sometimes correlated with their collection site (Qasemi-2 and Qasemi-3) on molecular analysis. Results of cluster analysis based on SRAP showed no significant correlation with morphological characters based on the Mantel test (r = 0.04).This inconsistent clustering of accessions could be due to the allelic variation (presumably) in a small number of genes (24 traits) contributing to morphological characterisation, while the 677 SRAP fragments (loci) are assumed to be relatively widely distributed across the genome. The wide geographical distribution of lucerne populations across different environments may provide good genetic resources for breeding purposes. SRAP analysis was effective to study genetic variability of non-dormant lucerne. This information will be helpful in assessing selections for lucerne breeding programs to develop new cultivars adapted to harsh environmental conditions.
Curves, dynamical systems, and weighted point counting
Authors: Cornelissen Gunther
Published: May 2013

Suppose
X
is a (smooth projective irreducible algebraic) curve over a finite field
k
. Counting the number of points on
X
over all finite field extensions of
k
will not determine the curve uniquely. Actually, a famous theorem of Tate implies that two such curves over
k
have the same zeta function (i.e., the same number of points over all extensions of
k
) if and only if their corresponding Jacobians are isogenous. We remedy this situation by showing that if, instead of just the zeta function, all Dirichlet
L
-series of the two curves are equal via an isomorphism of their Dirichlet character groups, then the curves are isomorphic up to “Frobenius twists”, i.e., up to automorphisms of the ground field. Because
L
-series count points on a curve in a “weighted” way, we see that weighted point counting determines a curve. In a sense, the result solves the analogue of the isospectrality problem for curves over finite fields (also know as the “arithmetic equivalence problem”): It states that a curve is determined by “spectral” data, namely, eigenvalues of the Frobenius operator of
k
acting on the cohomology groups of all ℓ-adic sheaves corresponding to Dirichlet characters. The method of proof is to show that this is equivalent to the respective class field theories of the curves being isomorphic as dynamical systems, in a sense that we make precise.
Serotonin signaling in the brain of adult female mice is required for sexual preference
Authors: Zhang Shasha , Liu Yan , Rao Yi
Published: May 2013

A role for serotonin in male sexual preference was recently uncovered by our finding that male mutant mice lacking serotonin have lost sexual preference. Here we show that female mouse mutants lacking either central serotonergic neurons or serotonin prefer female over male genital odors when given a choice, and displayed increased female–female mounting when presented either with a choice of a male and a female target or only with a female target. Pharmacological manipulations and genetic rescue experiments showed that serotonin is required in adults. Behavioral changes caused by deficient serotonergic signaling were not due to changes in plasma concentrations of sex hormones. We demonstrate that a genetic manipulation reverses sexual preference without involving sex hormones. Our results indicate that serotonin controls sexual preference.
Mantle wedge infiltrated with saline fluids from dehydration and decarbonation of subducting slab
Authors: Kawamoto Tatsuhiko , Yoshikawa Masako , Kumagai Yoshitaka , Mirabueno Ma. Hannah T. , Okuno Mitsuru , Kobayashi Tetsuo
Published: May 2013

Slab-derived fluids play an important role in heat and material transfer in subduction zones. Dehydration and decarbonation reactions of minerals in the subducting slab have been investigated using phase equilibria and modeling of fluid flow. Nevertheless, direct observations of the fluid chemistry and pressure–temperature conditions of fluids are few. This report describes CO
2
-bearing saline fluid inclusions in spinel-harzburgite xenoliths collected from the 1991 Pinatubo pumice deposits. The fluid inclusions are filled with saline solutions with 5.1 ± 1.0% (wt) NaCl-equivalent magnesite crystals, CO
2
-bearing vapor bubbles, and a talc and/or chrysotile layer on the walls. The xenoliths contain tremolite amphibole, which is stable in temperatures lower than 830 °C at the uppermost mantle. The Pinatubo volcano is located at the volcanic front of the Luzon arc associated with subduction of warm oceanic plate. The present observation suggests hydration of forearc mantle and the uppermost mantle by slab-derived CO
2
-bearing saline fluids. Dehydration and decarbonation take place, and seawater-like saline fluids migrate from the subducting slab to the mantle wedge. The presence of saline fluids is important because they can dissolve more metals than pure H
2
O and affect the chemical evolution of the mantle wedge.
Principles of parametric estimation in modeling language competition
Authors: Zhang Menghan , Gong Tao
Published: May 2013

It is generally difficult to define reasonable parameters and interpret their values in mathematical models of social phenomena. Rather than directly fitting abstract parameters against empirical data, we should define some concrete parameters to denote the sociocultural factors relevant for particular phenomena, and compute the values of these parameters based upon the corresponding empirical data. Taking the example of modeling studies of language competition, we propose a language diffusion principle and two language inheritance principles to compute two critical parameters, namely the impacts and inheritance rates of competing languages, in our language competition model derived from the Lotka–Volterra competition model in evolutionary biology. These principles assign explicit sociolinguistic meanings to those parameters and calculate their values from the relevant data of population censuses and language surveys. Using four examples of language competition, we illustrate that our language competition model with thus-estimated parameter values can reliably replicate and predict the dynamics of language competition, and it is especially useful in cases lacking direct competition data.
Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain α-ketoacid dehydrogenase kinase
Authors: Tso Shih-Chia , Qi Xiangbing , Gui Wen-Jun , Chuang Jacinta L. , Morlock Lorraine K. , Wallace Amy L. , Ahmed Kamran , Laxman Sunil , Campeau Philippe M. , Lee Brendan H. , Hutson Susan M. , Tu Benjamin P. , Williams Noelle S. , Tambar Uttam K. , Wynn R. Max , Chuang David T.
Published: May 2013

The branched-chain amino acids (BCAAs) leucine, isoleucine, and valine are elevated in maple syrup urine disease, heart failure, obesity, and type 2 diabetes. BCAA homeostasis is controlled by the mitochondrial branched-chain α-ketoacid dehydrogenase complex (BCKDC), which is negatively regulated by the specific BCKD kinase (BDK). Here, we used structure-based design to develop a BDK inhibitor, (
S
)-α-chloro-phenylpropionic acid [(
S
)-CPP]. Crystal structures of the BDK-(
S
)-CPP complex show that (
S
)-CPP binds to a unique allosteric site in the N-terminal domain, triggering helix movements in BDK. These conformational changes are communicated to the lipoyl-binding pocket, which nullifies BDK activity by blocking its binding to the BCKDC core. Administration of (
S
)-CPP to mice leads to the full activation and dephosphorylation of BCKDC with significant reduction in plasma BCAA concentrations. The results buttress the concept of targeting mitochondrial BDK as a pharmacological approach to mitigate BCAA accumulation in metabolic diseases and heart failure.
Genetic confirmation for a central role for TNFα in the direct action of thyroid stimulating hormone on the skeleton
Authors: Sun Li , Zhu Ling-Ling , Lu Ping , Yuen Tony , Li Jianhua , Ma Risheng , Baliram Ramkumarie , Moonga Surinder S. , Liu Peng , Zallone Alberta , New Maria I. , Davies Terry F. , Zaidi Mone
Published: May 2013

Clinical data showing correlations between low thyroid-stimulating hormone (TSH) levels and high bone turnover markers, low bone mineral density, and an increased risk of osteoporosis-related fractures are buttressed by mouse genetic and pharmacological studies identifying a direct action of TSH on the skeleton. Here we show that the skeletal actions of TSH deficiency are mediated, in part, through TNFα. Compound mouse mutants generated by genetically deleting the
Tnf
α
gene on a
Tshr

−/−

(homozygote) or
Tshr

+/−

(heterozygote) background resulted in full rescue of the osteoporosis, low bone formation, and hyperresorption that accompany TSH deficiency. Studies using ex vivo bone marrow cell cultures showed that TSH inhibits and stimulates TNFα production from macrophages and osteoblasts, respectively. TNFα, in turn, stimulates osteoclastogenesis but also enhances the production in bone marrow of a variant TSHβ. This locally produced TSH suppresses osteoclast formation in a negative feedback loop. We speculate that TNFα elevations due to low TSH signaling in human hyperthyroidism contribute to the bone loss that has traditionally been attributed solely to high thyroid hormone levels.
Lipolytic System of the Tomato PathogenFusarium oxysporumf. sp.lycopersici
Authors: Bravo-Ruiz Gustavo , Ruiz-Roldán Carmen , Roncero M. Isabel G.
Published: May 2013

The lipolytic profile of Fusarium oxysporum f. sp lycopersici was studied by in silico search and biochemical enzyme activity analyses. Twenty-five structural secreted lipases were predicted based on the conserved pentapeptide Gly-X-Ser-X-Gly-, characteristic of fungal lipases, and secretion signal sequences. Moreover, a predicted lipase regulatory gene was identified in addition to the previously characterized ctf1. The transcription profile of thirteen lipase genes during tomato plant colonization revealed that lip1, lip3, and lip22 were highly induced between 21 and 96 h after inoculation. Deletion mutants in five lipase genes (lip1, lip2, lip3, lip5, and lip22) and in the regulatory genes ctf1 and ctf2 as well as a Δctf1Δctf2 double mutant were generated. Quantitative reverse transcription-polymerase chain reaction expression analyses of structural lipase genes in the Δctf1, Δctf2, and Δctf1Δctf2 mutants indicated the existence of a complex lipase regulation network in F. oxysporum. The reduction of total lipase activity, as well as the severely reduced virulence of the Δctf1, Δctf2, and Δctf1Δctf2 mutants, provides evidence for an important role of the lipolytic system of this fungus in pathogenicity.
A Distinct Strain of Tomato leaf curl Sudan virus Causes Tomato Leaf Curl Disease in Oman
Authors: Khan A. J. , Akhtar S. , Singh A. K. , Briddon R. W.
Published: May 2013

Tomato leaf curl disease (ToLCD) is a significant constraint for tomato production in the Sultanate of Oman. The disease in the north of the country has previously been shown to be caused by the monopartite begomoviruses (family Geminiviridae) Tomato yellow leaf curl virus and Tomato leaf curl Oman virus. Many tomato plants infected with these two viruses were also found to harbor a symptom enhancing betasatellite. Here an analysis of a virus isolated from tomato exhibiting ToLCD symptoms originating from south and central Oman is reported. Three clones of a monopartite begomovirus were obtained. One of the clones was shown to be infectious to tomato and Nicotiana benthamiana and to induce symptoms typical of ToLCD. Analysis of the cloned sequences show them to correspond to isolates of Tomato leaf curl Sudan virus (ToLCSDV), a virus that occurs in Sudan and Yemen. However, the sequences showed less than 93% nucleotide sequence identity to previously characterized ToLCSDV isolates, indicating that the viruses represent a distinct strain of the species, for which we propose the name “Oman” strain (ToLCSDV-OM). Closer analysis of the sequences showed them to differ from their closest relative, the “Tobacco” strain of ToLCSDV originating from Yemen, in three regions of the genome. This suggests that the divergence of the “Oman” and “Tobacco” strains has occurred due to recombination. Surprisingly, ToLCSDV-OM was not found to be associated with a betasatellite, even though the isolates of the other ToLCSDV strains have been shown to be. The significance of these findings and the possible reasons for the distinct geographic distributions of the tomato-infecting begomoviruses within Oman are discussed.
Identification of a New Enamovirus Associated with Citrus Vein Enation Disease by Deep Sequencing of Small RNAs
Authors: Vives Mari Carmen , Velázquez Karelia , Pina José Antonio , Moreno Pedro , Guerri José , Navarro Luis
Published: May 2013

To identify the causal agent of citrus vein enation disease, we examined by deep sequencing (Solexa-Illumina) the small RNA (sRNA) fraction from infected and healthy Etrog citron plants. Our results showed that virus-derived sRNAs (vsRNAs): (i) represent about 14.21% of the total sRNA population, (ii) are predominantly of 21 and 24 nucleotides with a biased distribution of their 5′ nucleotide and with a clear prevalence of those of (+) polarity, and (iii) derive from all the viral genome, although a prominent hotspot is present at a 5′-proximal region. Contigs assembled from vsRNAs showed similarity with luteovirus sequences, particularly with Pea enation mosaic virus, the type member of the genus Enamovirus. The genomic RNA (gRNA) sequence of a new virus, provisionally named Citrus vein enation virus (CVEV), was completed and characterized. The CVEV gRNA was found to be single-stranded, positive-sense, with a size of 5,983 nucleotides and five open reading frames. Phylogenetic comparisons based on amino acid signatures of the RNA polymerase and the coat protein clearly classifies CVEV within the genus Enamovirus. Dot-blot hybridization and reverse transcription-polymerase chain reaction tests were developed to detect CVEV in plants affected by vein enation disease. CVEV detection by these methods has already been adopted for use in the Spanish citrus quarantine, sanitation, and certification programs.
Genetic Variability, Evolution, and Biological Effects of Grapevine fanleaf virus Satellite RNAs
Authors: Gottula J. , Lapato D. , Cantilina K. , Saito S. , Bartlett B. , Fuchs M.
Published: May 2013

Large satellite RNAs (type B satRNAs) of Grapevine fanleaf virus (GFLV) from the genus Nepovirus, family Secoviridae were identified in a naturally infected vineyard and a grapevine germplasm collection. These GFLV satRNA variants had a higher nucleotide sequence identity with satRNAs of Arabis mosaic virus (ArMV) strains NW and J86 (93.8 to 94.6%) than with the satRNA of GFLV strain F13 and those of other ArMV strains (68.3 to 75.0%). Phylogenetic analyses showed no distinction of GFLV and ArMV satRNAs with respect to the identity of the helper virus. Seven stretches of 8 to 15 conserved nucleotides (I-VII) were identified in the 5′ region of subgroup A nepovirus genomic RNAs GFLV, ArMV, and Grapevine deformation virus) and nepovirus type B satRNAs, including previously reported motif I, suggesting that large satRNAs might have originated from recombination between an ancestral subgroup A nepovirus RNA and an unknown RNA sequence with the 5′ region acting as a putative cis-replication element. A comparative analysis of two GFLV strains carrying or absent of satRNAs showed no discernable effect on virus accumulation and symptom expression in Chenopodium quinoa, a systemic herbaceous host. This work sheds light on the origin and biological effects of large satRNAs associated with subgroup A nepoviruses.
Are men better than women at acoustic size judgements?
Authors: Charlton Benjamin D. , Taylor Anna M. , Reby David
Published: May 2013

Formants are important phonetic elements of human speech that are also used by humans and non-human mammals to assess the body size of potential mates and rivals. As a consequence, it has been suggested that formant perception, which is crucial for speech perception, may have evolved through sexual selection. Somewhat surprisingly, though, no previous studies have examined whether sexes differ in their ability to use formants for size evaluation. Here, we investigated whether men and women differ in their ability to use the formant frequency spacing of synthetic vocal stimuli to make auditory size judgements over a wide range of fundamental frequencies (the main determinant of vocal pitch). Our results reveal that men are significantly better than women at comparing the apparent size of stimuli, and that lower pitch improves the ability of both men and women to perform these acoustic size judgements. These findings constitute the first demonstration of a sex difference in formant perception, and lend support to the idea that acoustic size normalization, a crucial prerequisite for speech perception, may have been sexually selected through male competition. We also provide the first evidence that vocalizations with relatively low pitch improve the perception of size-related formant information.
Shedding light on moths: shorter wavelengths attract noctuids more than geometrids
Authors: Somers-Yeates Robin , Hodgson David , McGregor Peter K. , Spalding Adrian , ffrench-Constant Richard H.
Published: May 2013

With moth declines reported across Europe, and parallel changes in the amount and spectra of street lighting, it is important to understand exactly how artificial lights affect moth populations. We therefore compared the relative attractiveness of shorter wavelength (SW) and longer wavelength (LW) lighting to macromoths. SW light attracted significantly more individuals and species of moth, either when used alone or in competition with LW lighting. We also found striking differences in the relative attractiveness of different wavelengths to different moth groups. SW lighting attracted significantly more Noctuidae than LW, whereas both wavelengths were equally attractive to Geometridae. Understanding the extent to which different groups of moth are attracted to different wavelengths of light will be useful in determining the impact of artificial light on moth populations.