bluuebunny/crossref_metadata_2025 huggingface dataset:
Model-independent quantitative measurement of nanomechanical oscillator vibrations using electron-microscope linescans
Authors: Wang Huan , Fenton J. C. , Chiatti O. , Warburton P. A.
Published: July 2013

Nanoscale mechanical resonators are highly sensitive devices and, therefore, for application as highly sensitive mass balances, they are potentially superior to micromachined cantilevers. The absolute measurement of nanoscale displacements of such resonators remains a challenge, however, since the optical signal reflected from a cantilever whose dimensions are sub-wavelength is at best very weak. We describe a technique for quantitative analysis and fitting of scanning-electron microscope (SEM) linescans across a cantilever resonator, involving deconvolution from the vibrating resonator profile using the stationary resonator profile. This enables determination of the absolute amplitude of nanomechanical cantilever oscillations even when the oscillation amplitude is much smaller than the cantilever width. This technique is independent of any model of secondary-electron emission from the resonator and is, therefore, applicable to resonators with arbitrary geometry and material inhomogeneity. We demonstrate the technique using focussed-ion-beam–deposited tungsten cantilevers of radius ∼60–170 nm inside a field-emission SEM, with excitation of the cantilever by a piezoelectric actuator allowing measurement of the full frequency response. Oscillation amplitudes approaching the size of the primary electron-beam can be resolved. We further show that the optimum electron-beam scan speed is determined by a compromise between deflection of the cantilever at low scan speeds and limited spatial resolution at high scan speeds. Our technique will be an important tool for use in precise characterization of nanomechanical resonator devices.
Inverse effect of magnetostriction in magnetoelectric laminates
Authors: Auslender M. , Liverts E. , Zadov B. , Elmalem A. , Zhdanov A. , Grosz A. , Paperno E.
Published: July 2013

We introduce the notion of inverse effect of magnetostriction for magnetostrictive-piezoelectric heterostructures and study this effect theoretically and experimentally. It is shown that the inverse effect of magnetostriction may crucially contribute to the mechanism of magnetoelectric coupling. It is shown that the studied effect essentially modifies the saturation magnetostriction of the whole structure as compared to its magnetic phase bulk and also induces an additional magnetic anisotropy. Our consideration provides useful insight into the fundamental issue of strain-mediated magnetoelectric coupling. Understanding this effect may lead to its utilization in original experimental concepts and the improvement of the ME coupling.
Reference Correlation of the Viscosity of Squalane from 273 to 373 K at 0.1 MPa
Authors: Comuñas M. J. P. , Paredes X. , Gaciño F. M. , Fernández J. , Bazile J. P. , Boned C. , Daridon J. L. , Galliero G. , Pauly J. , Harris K. R. , Assael M. J. , Mylona S. K.
Published: July 2013

The paper presents a new reference correlation for the viscosity of squalane at 0.1 MPa. The correlation should be valuable as it is the first to cover a moderately high viscosity range, from 3 to 118 mPa s. It is based on new viscosity measurements carried out for this work, as well as other critically evaluated experimental viscosity data from the literature. The correlation is valid from 273 to 373 K at 0.1 MPa. The average absolute percentage deviation of the fit is 0.67, and the expanded uncertainty, with a coverage factor k = 2, is 1.5%.
Non-spherical bubble dynamics of underwater explosions in a compressible fluid
Authors: Wang Q. X.
Published: July 2013

This paper is concerned with the bubble dynamics of underwater explosion in a compressible liquid flow whose Mach number, based on characteristic liquid velocities, is O(10−1). We will study this phenomenon based on weakly compressible theory using the method of matched asymptotic expansions. As a result, the inner flow near the bubble to second order is described by Laplace's equation with the compressible effects appearing only in the far field condition. The problem can thus be modelled approximately using the boundary integral method. Validations are performed against the Keller equation for spherical bubbles and available experimental data for “small-charge” explosions for non-spherical bubbles under the action of buoyancy. The computation traces jet impact, the transition of the bubble from a singly connected to a doubly connected form, and the recombining of a doubly connected to a singly connected form, and the further repeated transitions. The computational result of the bubble shapes correlates well with experimental data to the end of the second oscillation. The first collapse, which we call the “principal collapse,” is the most severe in terms of energy loss. The damping of the bubble oscillation is alleviated by the buoyancy effects and reduced with the buoyancy parameter.
Evolution of conductive network and properties of nanorod/polymer composite under tensile strain
Authors: Feng Yancong , Ning Nanying , Zhang Liqun , Tian Ming , Zou Hua , Mi Jianguo
Published: July 2013

In this work, the conductive network, probability, and percolation threshold of nanorod/polymer composites under tensile strain are investigated using the molecular dynamics simulation. The internal interactions, including polymer−polymer, polymer−nanorod, and nanorod−nanorod interactions, are taken into account in simulations. In particular, the influence of polymer induced depletion force on the orientation of nanorods is analyzed. Under a constant strain, the conductive stability firstly declines and then rises with the increasing concentration of fillers, and the minimum corresponds to the percolation threshold. As strain increases, the result exhibits a strong anisotropy in the stability of conductive property.
Incorporating headgroup structure into the Poisson-Boltzmann model of charged lipid membranes
Authors: Wang Muyang , Chen Er-Qiang , Yang Shuang , May Sylvio
Published: July 2013

Charged lipids often possess a complex headgroup structure with several spatially separated charges and internal conformational degrees of freedom. We propose a headgroup model consisting of two rod-like segments of the same length that form a flexible joint, with three charges of arbitrary sign and valence located at the joint and the two terminal positions. One terminal charge is firmly anchored at the polar-apolar interface of the lipid layer whereas the other two benefit from the orientational degrees of freedom of the two headgroup segments. This headgroup model is incorporated into the mean-field continuum Poisson-Boltzmann formalism of the electric double layer. For sufficiently small lengths of the two rod-like segments a closed-form expression of the charging free energy is calculated. For three specific examples—a zwitterionic headgroup with conformational freedom and two headgroups that carry an excess charge—we analyze and discuss conformational properties and electrostatic free energies.
A quantitative measure for protein conformational heterogeneity
Authors: Lyle Nicholas , Das Rahul K. , Pappu Rohit V.
Published: July 2013

Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.
Hellenic renewable energy policies and energy performance of residential buildings using solar collectors for domestic hot water production in Greece
Authors: Balaras C. A. , Dascalaki E. G. , Droutsa P. , Kontoyiannidis S.
Published: July 2013

Total final energy consumption in Hellenic buildings reached 6.5 × 106 tons of oil equivalent (Mtoe) or 34.2% of the total (2010), of which 4.6 Mtoe in residential buildings. National implementation of the European Directive on the energy performance of buildings (EPBD) in Greece since 2010 is the first coordinated attempt to improve the energy performance of Hellenic buildings. In this framework, as of 2011, new buildings have an annual solar fraction of 60% for sanitary hot water production from solar thermal systems. Efforts are currently underway to comply with the EPBD recast so that by the end of the decade, all new buildings are nearly zero-energy buildings and that the very low amount of energy required should be covered to a very significant extent by energy from renewable energy sources (RESs). At the same time, the unprecedented financial crisis and escalating energy costs in Greece have reemphasized the need to explore the opportunities of renewables and energy conservation measures (ECMs). This paper reviews the relevant RES policies and status, with an emphasis to the Hellenic buildings. Using Hellenic typical residential buildings, the national requirements, and methodologies, this work quantifies the benefits of using solar thermal collectors to cover 100% of the domestic hot water demand. The results illustrate that, even as a single action, this popular ECM can improve the energy class of existing residential buildings and in some cases even reach an energy class-B, which is the minimum requirement for new buildings. Combining with other cost effective ECMs and exploiting RES for space heating and cooling can help building owners to not simply comply with new regulations but most important reduce the operational cost of buildings while maintaining a comfortable indoor thermal environment.
Diameter dependence of polarization resolved reflectance from vertical silicon nanowire arrays: Evidence of tunable absorption
Authors: Khorasaninejad M. , Patchett S. , Sun J. , O N. , Saini S. S.
Published: July 2013

Vertical silicon nanowire arrays of different diameters ranging from 90 nm to 190 nm with a pitch of 400 nm are fabricated. Nanowires are arranged in a square lattice and have a length of 1 μm. Polarization resolved reflectances from these nanowire arrays are measured and significant differences are observed for the reflectance characteristics of the s- and p-polarized beams. A narrow wavelength band of increased absorption is reported by analyzing the reflectance using the finite difference time domain method. The center wavelength of this band shifts toward higher wavelengths as the diameter of the nanowires increases achieving tunable absorption spectra within the nanowires. The wavelength band shifts at a rate of approximately 3.3 nm with every 1 nm increment in diameter. The increased absorption is achieved due to modal excitation and near-field coupling between the nanowires.
Absolute spectral characterization of silicon barrier diode: Application to soft X-ray fusion diagnostics at Tore Supra
Authors: Vezinet D. , Mazon D. , Malard P.
Published: July 2013

This paper presents an experimental protocol for absolute calibration of photo-detectors. Spectral characterization is achieved by a methodology that unlike the usual line emissions-based method, hinges on the Bremsstrahlung radiation of a Soft X-Ray (SXR) tube only. Although the proposed methodology can be applied virtually to any detector, the application presented in this paper is based on Tore Supra's SXR diagnostics, which uses Silicon Surface Barrier Diodes. The spectral response of these n-p junctions had previously been estimated on a purely empirical basis. This time, a series of second-order effects, like the spatial distribution of the source radiated power or multi-channel analyser non linearity, are taken into account to achieve accurate measurements. Consequently, a parameterised physical model is fitted to experimental results and the existence of an unexpected dead layer (at least 5 μm thick) is evidenced. This contribution also echoes a more general on-going effort in favour of long-term quality of passive radiation measurements on Tokamaks.
Linear and nonlinear optical properties of ZnO/ZnS and ZnS/ZnO core shell quantum dots: Effects of shell thickness, impurity, and dielectric environment
Authors: Zeng Zaiping , Garoufalis Christos S. , Terzis Andreas F. , Baskoutas Sotirios
Published: July 2013

In the present work, we investigated theoretically the linear, nonlinear, and total absorption coefficients and refractive index changes associated with intersubband transitions in ZnO/ZnS core shell quantum dot (CSQD) and ZnS/ZnO inverted CSQD (ICSQD), emphasizing on the influence of the shell thickness, impurity, and dielectric environment. The effect of the polarization charges due to the possible existence of the dielectric mismatch between the system and its surrounding matrix is considered. The electronic structures are numerically calculated by employing the potential morphing method in the framework of effective mass approximation. We find that in both impurity-free CSQD and ICSQD, increasing the shell thickness red shifts significantly the threshold energy and enhances drastically the nonlinear absorption coefficients and all the refractive index changes, independently on the dielectric environments. Similar behaviour has also been observed in most of the cases studied when the impurity is displaced from the core center to the shell center. In contrast, comparing to a dielectrically homogeneous system, dispersing the systems into a matrix with a lower dielectric constant blue shifts all the peak positions of the absorption coefficients and refractive index changes. However, the corresponding magnitudes (in absolute value) are substantially reduced. Finally, we find that the nonlinear properties are more sensitive to the external perturbations, while at a weak radiation intensity, the variation of the total quantities is generally dominated by that of the corresponding linear terms.
Effect of electron beam misalignments on the gyrotron efficiency
Authors: Dumbrajs O. , Nusinovich G. S.
Published: July 2013

The theory describing the operation of gyrotrons with tilted and shifted electron beams has been developed. Effects of the tilt and shift are studied for a 1 MW, 170 GHz gyrotron, which is presently under development in Europe for electron cyclotron resonance plasma heating and current drive in the International Thermonuclear Experimental Reactor. It is shown that one should expect significant deterioration of gyrotron operation in such gyrotrons when the tilt angle exceeds 0.4°–0.5° and the parallel shift of the beam axis with respect to the axis of a microwave circuit is larger than 0.4–0.5 mm. At the same time, simultaneous tilting and shifting in a proper manner can mitigate this deteriorating effect.
Note: Molecular architecture dependent hydrogen-bonded motifs, entropy change, and dielectric permittivity of alcohols
Authors: Johari G. P.
Published: July 2013

Our previous studies showed that the static permittivity, ɛs, of some octanol isomers first increased on cooling, then decreased, and finally increased rapidly, and ɛs monotonically increased on compression such that the local minimum in ɛs vanished. Thus, while ɛs is the same at different temperatures and pressures, the density differs. To reconcile these findings with thermodynamic requirements, we propose that hydrogen bonded ring-dimers of near zero dipole moment that form on initial cooling and decrease ɛs, open to form linear-dimers on further cooling (or pressurizing). The H and O atoms at the terminals of the linear dimer form hydrogen bonds with the existing monomers and linear chains, thus extending the length of the H-bonded chains. This mechanism agrees with the enthalpy and entropy of formation of ring-dimer and linear-chain motifs.
Resonant and non-resonant microwave absorption as a probe of the magnetic dynamics and switching in spin valves
Authors: Timopheev A. A. , Sobolev N. A. , Pogorelov Y. G. , Talalaevskij A. V. , Teixeira J. M. , Cardoso S. , Freitas P. P. , Kakazei G. N.
Published: July 2013

We use the resonant and non-resonant microwave absorption to probe the dynamic and static magnetic parameters of weakly coupled spin valves. The sample series include spin valve structures with varying thickness of the non-magnetic metallic spacer and reference samples comprised only a free or fixed magnetic layer. Beside the common resonance absorption peaks, the observed microwave spectra present step-like features with hysteretic behavior. The latter effect is a direct manifestation of the interlayer coupling between the ferromagnetic layers and provides two static magnetic parameters, the switching field and coercivity of the fixed layer. The analysis of the microwave absorption spectra under in-plane rotation of the applied magnetic field at different spacer thicknesses permits a deeper insight in the magnetic interactions in this system as compared to the conventional magnetometry. We combine the standard Smit-Beljers formalism for the angular dependence of the resonance fields with a Landau-Lifshitz-Gilbert dynamics extended to describe in detail the intensity of microwave absorption in the spin valves. In this way, we extract a set of parameters for each layer including the effective magnetization and anisotropy, exchange bias and interlayer coupling, as well as Gilbert damping. The model reproduces well the experimental findings, both qualitatively and quantitatively, and the estimated parameters are in a reasonable agreement with the values known from the literature. The proposed theoretical treatment can be adopted for other multilayered dynamic systems as, e.g., spin-torque oscillators.
Theoretical investigation of acoustic wave devices based on different piezoelectric films deposited on silicon carbide
Authors: Fan Li , Zhang Shu-yi , Ge Huan , Zhang Hui
Published: July 2013

Performances of acoustic wave (AW) devices based on silicon carbide (SiC) substrates are theoretically studied, in which two types of piezoelectric films of ZnO and AlN deposited on 4H-SiC and 3C-SiC substrates are adopted. The phase velocities (PV), electromechanical coupling coefficients (ECC), and temperature coefficients of frequency (TCF) for three AW modes (Rayleigh wave, A0 and S0 modes of Lamb wave) often used in AW devices are calculated based on four types of configurations of interdigital transducers (IDTs). It is found that that the ZnO piezoelectric film is proper for the AW device operating in the low-frequency range because a high ECC can be realized using a thin ZnO film. The AlN piezoelectric film is proper for the device operating in the high-frequency range in virtue of the high PV of AlN, which can increase the finger width of the IDT. Generally, in the low-frequency Lamb wave devices using ZnO piezoelectric films with small normalized thicknesses of films to wavelengths hf/λ, thin SiC substrates can increase ECCs but induce high TCFs simultaneously. In the high-frequency device with a large hf/λ, the S0 mode of Lamb wave based on the AlN piezoelectric film deposited on a thick SiC substrate exhibits high performances by simultaneously considering the PV, ECC, and TCF.
Transport properties of two-dimensional electrons through multiple magnetic barriers
Authors: Zhang X. W. , Mou S. Y. , Dai B.
Published: July 2013

Transport properties of 2-dimensional electron system in a varying magnetic flied are investigated theoretically by a transfer matrix technique. The exact magnetic field profiles and the corresponding vector potentials are presented instead of simulated ones. The results show that several transmission domains are formed and each domain contains (N−1)-fold resonance splitting which fully depends on the number of magnetic barriers N. The computed conductance also exhibits rich transfer properties. Three peaks are observed in the low energy range. With the increasing of N, the conductance curves tend to coincide with each other as the tilting angle of magnetization relative to z direction equals to π/2, while the conductance curves shift downwards for other θ. All of our calculations reveal the important features of electron tunneling through multiple magnetic barriers.
Terahertz-infrared spectra of the rare-earth scandate DyScO3 single crystal
Authors: Komandin G. A. , Zhukova E. S. , Torgashev V. I. , Boris A. V. , Boris A. A. , Motovilova E. A. , Prokhorov A. S. , Kadyrov L. S. , Gorshunov B. P. , Dressel M.
Published: July 2013

Terahertz and infrared spectra of the optical response of DyScO3 single crystal are measured at temperatures from 5 K to 300 K for two different polarizations E‖[1¯01] and E‖[010], i.e., along the two crystallographic directions of the DyScO3 substrates used for growing of thin films and heterostructures. Detailed reference data on the terahertz dielectric characteristics of the DyScO3 substrate are presented. We discuss the mechanisms responsible for electromagnetic absorption. Phonon spectra are analyzed along with the results of group-theoretical analysis of the crystal structure. Besides phonon modes, additional resonance absorptions are found and assigned to the electronic transitions between Kramers doublets in the three lowest-energy terms of the Dy3+ ion.
Evidence for viscous flow nature in Zr60Al15Ni25 metallic glass subjected to cold rolling
Authors: Yan Zhijie , Hao Weixin , Hu Yong , Song Kaikai , Stoica Mihai , Scudino Sergio , Eckert Jürgen
Published: July 2013

The microstructure changes of Zr60Al15Ni25 metallic glass upon cold rolling and their influences on the thermally induced crystallization kinetics are investigated. The results show that atomic redistribution occurs within the localized zones in the glassy matrix, resulting from the softening of the shear modulus, which retards the crystallization behaviors during the subsequent heating. The present work provides direct evidence for the viscous flow nature in a metallic glass subjected to plastic deformation, during which the softened zones act as potential shear transformation zones.
Monoenergetic collimated nano-Coulomb electron beams driven by crossed laser beams
Authors: Wang Jingwei , Murakami M. , Weng S. M. , Ruhl H. , Luan Shixia , Yu Wei
Published: July 2013

Monoenergetic collimated electron acceleration by two crossed laser beams is investigated through an analytical model and particle-in-cell simulations. Electron bunches with a total charge of order nano-Coulombs are accelerated by the axial electric field formed by the crossed laser beams to nearly 760 MeV with an energy spread of 2.7%. The transverse components of both electric and magnetic fields vanish along the axis, making the electron beam highly collimated. This acceleration scheme appears promising in producing high quality electron beams.
Effects of humidity on performance of electric-double-layer oxide-based thin-film transistors gated by nanogranular SiO2 solid electrolyte
Authors: Guo Li-Qiang , Yang Yuan-Yuan , Zhu Li-Qiang , Wu Guo-Dong , Zhou Ju-Mei , Zhang Hong-Liang
Published: July 2013

Electric-double-layer oxide-based thin-film transistors gated by nanogranular SiO2 solid electrolyte have been fabricated at room temperature. The effects of humidity on performances are investigated. At the relative humidity of 65 %, the measured capacitance is 10 μF/cm2, and the device shows Ion/off ratio of 8.93 × 107, field-effect mobility of 5.9 cm2/Vs. As relative humidity declines, the measured capacitance decreases, which gives rise to the degradation in performance. Especially, at the relative humidity of 0 %, the capacitance of 0.01 μF/cm2 is measured, so the device cannot be turned off. The reason may be that humidity can promote H2O molecules to permeate into solid electrolyte, which can cause charges accumulation.
Molecular beam epitaxial growth of Bi2Te3 and Sb2Te3 topological insulators on GaAs (111) substrates: a potential route to fabricate topological insulator p-n junction
Authors: Zeng Zhaoquan , Morgan Timothy A. , Fan Dongsheng , Li Chen , Hirono Yusuke , Hu Xian , Zhao Yanfei , Lee Joon Sue , Wang Jian , Wang Zhiming M. , Yu Shuiqing , Hawkridge Michael E. , Benamara Mourad , Salamo Gregory J.
Published: July 2013

High quality Bi2Te3 and Sb2Te3 topological insulators films were epitaxially grown on GaAs (111) substrate using solid source molecular beam epitaxy. Their growth and behavior on both vicinal and non-vicinal GaAs (111) substrates were investigated by reflection high-energy electron diffraction, atomic force microscopy, X-ray diffraction, and high resolution transmission electron microscopy. It is found that non-vicinal GaAs (111) substrate is better than a vicinal substrate to provide high quality Bi2Te3 and Sb2Te3 films. Hall and magnetoresistance measurements indicate that p type Sb2Te3 and n type Bi2Te3 topological insulator films can be directly grown on a GaAs (111) substrate, which may pave a way to fabricate topological insulator p-n junction on the same substrate, compatible with the fabrication process of present semiconductor optoelectronic devices.
Structural enhancement of ZnO on SiO2 for photonic applications
Authors: Ruth Marcel , Meier Cedrik
Published: July 2013

Multi-layer thin films are often the basis of photonic devices. Zinc oxide (ZnO) with its excellent optoelectronic properties can serve as a high quality emitter in structures like microdisks or photonic crystals. Here, we present a detailed study on the enhancement of the structural properties of low-temperature MBE grown ZnO on silica (SiO2). By thermal annealing a grain coalescence of the initially polycrystalline layer leads to an enhancement of the electronic structure, indicated by a blue shift of the photoluminescence (PL) signal maximum. Oxygen atmosphere during the annealing process prevents the creation of intrinsic defects by out-diffusion. Pre-annealing deposited SiO2 capping layers instead obstruct the recrystallization and lead to less intense emission. While thin capping layers partially detach from the ZnO film at high temperatures and cause higher surface roughness and the weakest emission, thicker layers remain smoother and exhibit a significantly stronger photoluminescence.
Helmholtz Illusion Makes you Look Fit Only When you are Already Fit, But not for Everyone
Authors: Ashida Hiroshi , Kuraguchi Kana , Miyoshi Kiyofumi
Published: July 2013

A square filled with horizontal stripes is perceived as thinner than one with vertical stripes (Helmholtz illusion). This is not consistent with a common belief that horizontally striped clothing makes a person look fatter, and studies on this problem have shown inconsistent results. Here, we demonstrate three factors that could have complicated the issue. First, the Helmholtz effect is stronger for a thin figure than for a fat one, with possible reversal for the latter. Second, we found large variability across participants, suggesting dependence on features to attend. Third, there was strong hysteresis as to the order of testing fat and thin figures, suggesting the effect of surrounding people in daily life. There can be yet other factors, but we should note that this apparently simple case of application of a geometrical illusion in daily perception should be taken as a rather complex phenomenon.
FT genes and regulation of flowering in the legume Medicago truncatula
Authors: Putterill Joanna , Zhang Lulu , Yeoh Chin Chin , Balcerowicz Martin , Jaudal Mauren , Gasic Erika Varkonyi
Published: July 2013

Flowering time is an important contributor to plant productivity and yield. Plants integrate flowering signals from a range of different internal and external cues in order to flower and set seed under optimal conditions. Networks of genes controlling flowering time have been uncovered in the flowering models Arabidopsis, wheat, barley and rice. Investigations have revealed important commonalities such as FT genes that promote flowering in all of these plants, as well as regulators that are unique to some of them. FT genes also have functions beyond floral promotion, including acting as floral repressors and having a complex role in woody polycarpic plants such as vines and trees. However, much less is known overall about flowering control in other important groups of plants such as the legumes. This review discusses recent efforts to uncover flowering-time regulators using candidate gene approaches or forward screens for spring early flowering mutants in the legume Medicago truncatula. The results highlight the importance of a Medicago FT gene, FTa1, in flowering-time control. However, the mechanisms by which FTa1 is regulated by environmental signals such as long days (photoperiod) and vernalisation (winter cold) appear to differ from Arabidopsis.
Fruit thinning affects photosynthetic activity, carbohydrate levels, and shoot and fruit development of olive trees grown under semiarid conditions
Authors: Haouari Afef , Van Labeke Marie-Christine , Steppe Kathy , Mariem Fethi Ben , Braham Mohamed , Chaieb Mohamed
Published: July 2013

Olive (Olea europaea L.) production is marked by annual oscillations as trees alternate from high to low crop loads in successive years. Gas exchanges and carbohydrate content of leaves and fruits in olive tree (O. europaea cv. Besbassi) were monitored at pit hardening and fruit ripening. After fruit set, three crop loads were applied (100%, 50% and 25% of the initial fruit load) by manual thinning. Severe fruit thinning reduced photosynthesis, stomatal conductance and intercellular CO2 concentration. Crop load had no significant effect on chlorophyll fluorescence parameters. The reduction of 75% of the initial crop load favoured the accumulation of starch in leaves and soluble sugars in leaves and fruits. The reduction in initial fruit load had a significant positive effect on the current year’s shoot elongation and on inflorescence number the following spring. To increase the fruit size, a strong thinning (75%) was necessary, which coincided with the highest shoot vigour. Moderate thinning (50%) hardly affected leaf carbohydrate content and fruit size, but photosynthetic capacity was only limited at fruit ripening.
An Iranian Woman's Memoir on the Iran–Iraq War: The Production and Reception of Da
Authors: Nanquette Laetitia
Published: July 2013

Da (Mother): Memoirs of Seyyedeh Zahra Hoseini, as Recorded by Seyyedeh A‘zam Hoseini was published by Sureh-ye Mehr, the official publisher of the Artistic Center of the Islamic Development Organization, in 2008. According to the publishers, it became the biggest seller in the shortest period in Iranian publishing history. This article analyzes the conditions of production, distribution and reception of that work, and compares it to the canon of other contemporary Iranian war narratives. It argues that the unusually wide and varied reception of a traditional discourse of sacrifice, nationalism and revolutionary fervor was facilitated by the fashionable format of the woman's memoir, in addition to a formidable propaganda machine.
A Giambelli formula for classical 𝐺/𝑃 spaces
Authors: Tamvakis Harry
Published: July 2013

LetGGbe a classical complex Lie group,PPany parabolic subgroup ofGG, andG/PG/Pthe corresponding partial flag variety. We prove an explicit combinatorial Giambelli formula which expresses an arbitrary Schubert class inH∗(G/P)\mathrm {H}^*(G/P)as a polynomial in certain special Schubert class generators. Our formula extends to one that applies to the torus-equivariant cohomology ring ofG/PG/Pand to the setting of symplectic and orthogonal degeneracy loci.
A new framework for computational protein design through cost function network optimization
Authors: Traoré Seydou , Allouche David , André Isabelle , de Givry Simon , Katsirelos George , Schiex Thomas , Barbe Sophie
Published: July 2013

Motivation: The main challenge for structure-based computational protein design (CPD) remains the combinatorial nature of the search space. Even in its simplest fixed-backbone formulation, CPD encompasses a computationally difficult NP-hard problem that prevents the exact exploration of complex systems defining large sequence-conformation spaces.

Results: We present here a CPD framework, based on cost function network (CFN) solving, a recent exact combinatorial optimization technique, to efficiently handle highly complex combinatorial spaces encountered in various protein design problems. We show that the CFN-based approach is able to solve optimality a variety of complex designs that could often not be solved using a usual CPD-dedicated tool or state-of-the-art exact operations research tools. Beyond the identification of the optimal solution, the global minimum-energy conformation, the CFN-based method is also able to quickly enumerate large ensembles of suboptimal solutions of interest to rationally build experimental enzyme mutant libraries.

Availability: The combined pipeline used to generate energetic models (based on a patched version of the open source solver Osprey 2.0), the conversion to CFN models (based on Perl scripts) and CFN solving (based on the open source solver toulbar2) are all available at http://genoweb.toulouse.inra.fr/∼tschiex/CPD

Contacts:  thomas.schiex@toulouse.inra.fr or sophie.barbe@insa-toulouse.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
A comparative analysis of algorithms for somatic SNV detection in cancer
Authors: Roberts Nicola D. , Kortschak R. Daniel , Parker Wendy T. , Schreiber Andreas W. , Branford Susan , Scott Hamish S. , Glonek Garique , Adelson David L.
Published: July 2013

Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm.

Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates.

Availability: Data accession number SRA081939, code at http://code.google.com/p/snv-caller-review/

Contact:  david.adelson@adelaide.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Naive binning improves phylogenomic analyses
Authors: Bayzid Md Shamsuzzoha , Warnow Tandy
Published: July 2013

Motivation: Species tree estimation in the presence of incomplete lineage sorting (ILS) is a major challenge for phylogenomic analysis. Although many methods have been developed for this problem, little is understood about the relative performance of these methods when estimated gene trees are poorly estimated, owing to inadequate phylogenetic signal.

Results: We explored the performance of some methods for estimating species trees from multiple markers on simulated datasets in which gene trees differed from the species tree owing to ILS. We included *BEAST, concatenated analysis and several ‘summary methods’: BUCKy, MP-EST, minimize deep coalescence, matrix representation with parsimony and the greedy consensus. We found that *BEAST and concatenation gave excellent results, often with substantially improved accuracy over the other methods. We observed that *BEAST’s accuracy is largely due to its ability to co-estimate the gene trees and species tree. However, *BEAST is computationally intensive, making it challenging to run on datasets with 100 or more genes or with more than 20 taxa. We propose a new approach to species tree estimation in which the genes are partitioned into sets, and the species tree is estimated from the resultant ‘supergenes’. We show that this technique improves the scalability of *BEAST without affecting its accuracy and improves the accuracy of the summary methods. Thus, naive binning can improve phylogenomic analysis in the presence of ILS.

Contact:  tandy@cs.utexas.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pulmonary Blood Flow Increases in Damaged Regions Directly after Acid Aspiration in Rats
Authors: Richter Torsten , Bergmann Ralf , Knels Lilla , Hofheinz Frank , Kasper Michael , Deile Martin , Pietzsch Jens , Ragaller Maximilian , Koch Thea
Published: July 2013

Background:

After gastric aspiration events, patients are at risk of pulmonary dysfunction and the development of severe acute lung injury and acute respiratory distress syndrome, which may contribute to the development of an inflammatory reaction. The authors’ aim in the current study was to investigate the role of the spatial distribution of pulmonary blood flow in the pathogenesis of pulmonary dysfunction during the early stages after acid aspiration.

Methods:

The authors analyzed the pulmonary distribution of radiolabeled microspheres in normal (n = 6) and injured (n = 12) anesthetized rat lungs using positron emission tomography, computed tomography, and histological examination.

Results:

Injured regions demonstrate increased pulmonary blood flow in association with reduced arterial pressure and the deterioration of arterial oxygenation. After acid aspiration, computed tomography scans revealed that lung density had increased in the injured regions and that these regions colocalized with areas of increased blood flow. The acid was instilled into the middle and basal regions of the lungs. The blood flow was significantly increased to these regions compared with the blood flow to uninjured lungs in the control animals (middle region: 1.23 [1.1; 1.4] (median [25%; 75%]) vs. 1.04 [1.0; 1.1] and basal region: 1.25 [1.2; 1.3] vs. 1.02 [1.0; 1.05], respectively). The increase in blood flow did not seem to be due to vascular leakage into these injured areas.

Conclusions:

The data suggest that 10 min after acid aspiration, damaged areas are characterized by increased pulmonary blood flow. The results may impact further treatment strategies, such as drug targeting.
Conserving tropical biodiversity via strategic spatiotemporal harvest planning
Authors: Ramage Benjamin S. , Marshalek Elaina C. , Kitzes Justin , Potts Matthew D.
Published: July 2013

Tropical timber production forests have the potential to harbour many species, but landscape‐level management strategies for minimizing extinctions are lacking.

To develop relevant conservation guidelines, we investigated how harvest plans with different spatiotemporal patterns affected the persistence of sessile species with different traits and preharvest characteristics. We confronted this problem via an individual‐based simulation model.

We explored several harvest plans with different levels of spatiotemporal aggregation, but equivalent total harvest area, and found that extinction probabilities for each plan varied with species traits and predisturbance characteristics. Most notably, plans with large contiguous harvest units yielded particularly high extinction probabilities for dispersal‐limited habitat specialists with clustered preharvest distributions. Differences between plans were small for some types of species, but highly aggregated plans yielded the highest extinction rates for all extinction‐prone groups.

Synthesis and applications. Our simulations suggest that reducing the size of contiguous harvest units, even while total harvest area remains constant, may reduce extinction rates in tropical production forests (assuming that road‐related threats can be effectively managed). Our findings have important implications for tropical conservation efforts and also provide general insight into the compositional effects of disturbances with different spatiotemporal characteristics.
Adapting to conversation with semantic dementia: using enactment as a compensatory strategy in everyday social interaction
Authors: Kindell Jacqueline , Sage Karen , Keady John , Wilkinson Ray
Published: July 2013

Background

Studies to date in semantic dementia have examined communication in clinical or experimental settings. There is a paucity of research describing the everyday interactional skills and difficulties seen in this condition.

Aims

To examine the everyday conversation, at home, of an individual with semantic dementia.

Methods & Procedures

A 71‐year‐old man with semantic dementia and his wife were given a video camera and asked to record natural conversation in the home situation with no researcher present. Recordings were also made in the home environment, with the individual with semantic dementia in conversation with a member of the research team. Conversation analysis was used to transcribe and analyse the data. Recurring features were noted to identify conversational patterns.

Outcomes & Results

Analysis demonstrated a repeated practice by the speaker with semantic dementia of acting out a diversity of scenes (enactment). As such, the speaker regularly used direct reported speech along with paralinguistic features (such as pitch and loudness) and non‐vocal communication (such as body posture, pointing and facial expression) as an adaptive strategy to communicate with others in conversation.

Conclusions & Implications

This case shows that while severe difficulties may be present on neuropsychological assessment, relatively effective communicative strategies may be evident in conversation. A repeated practice of enactment in conversation allowed this individual to act out, or perform what he wanted to say, allowing him to generate a greater level of meaningful communication than his limited vocabulary alone could achieve through describing the events concerned. Such spontaneously acquired adaptive strategies require further attention in both research and clinical settings in semantic dementia and analysis of interaction in this condition, using conversation analysis, may be helpful.
Phonological therapy in jargon aphasia: effects on naming and neologisms
Authors: Bose Arpita
Published: July 2013

Background

Jargon aphasia is one of the most intractable forms of aphasia with limited recommendation on amelioration of associated naming difficulties and neologisms. The few naming therapy studies that exist in jargon aphasia have utilized either semantic or phonological approaches, but the results have been equivocal. Moreover, the effect of therapy on the characteristics of neologisms is less explored.

Aims

This study investigates the effectiveness of a phonological naming therapy (i.e. phonological component analysis—PCA) on picture‐naming abilities and on quantitative and qualitative changes in neologisms for an individual with jargon aphasia (FF).

Methods & Procedures

FF showed evidence of jargon aphasia with severe naming difficulties and produced a very high proportion of neologisms. A single‐subject multiple probe design across behaviours was employed to evaluate the effects of PCA therapy on the accuracy for three sets of words. In therapy, a phonological components analysis chart was used to identify five phonological components (i.e. rhymes, first sound, first sound associate, final sound and number of syllables) for each target word. Generalization effects—change in per cent accuracy and error pattern—were examined comparing pre‐ and post‐therapy responses on the Philadelphia Naming Test, and these responses were analysed to explore the characteristics of the neologisms. The quantitative change in neologisms was measured by change in the proportion of neologisms from pre‐ to post‐therapy and the qualitative change was indexed by the phonological overlap between target and neologism.

Outcomes & Results

As a consequence of PCA therapy, FF showed a significant improvement in his ability to name the treated items. His performance in maintenance and follow‐up phases remained comparable with his performance during the therapy phases. Generalization to other naming tasks did not show a change in accuracy, but distinct differences in error pattern (an increase in proportion of real word responses and a decrease in proportion of neologisms) were observed. Notably, the decrease in neologisms occurred with a corresponding trend for increase in the phonological similarity between the neologisms and the targets.

Conclusions & Implications

This study demonstrated the effectiveness of a phonological therapy for improving naming abilities and reducing the amount of neologisms in an individual with severe jargon aphasia. The positive outcome of this research is encouraging, as it provides evidence for effective therapies for jargon aphasia and also emphasizes that use of the quality and quantity of errors may provide a sensitive outcome measure to determine therapy effectiveness, in particular for client groups who are difficult to treat.
Globalization, Threat and Religious Freedom
Authors: Ben-Nun Bloom Pazit , Arikan Gizem , Sommer Udi
Published: July 2013

While arguably central to the human experience, religion is a largely understudied component of social life and of politics. The comparative literature on religion and politics is limited in scope, and offers mostly descriptions of trends. We know, for example, that restrictions on freedom of religion are on the rise worldwide. In our theoretical framework, the recently higher universal levels of globalization combine with other sources of threat to account for the trend away from religious freedom. As threat to the majority religion increases, due to globalization and an increasing number of minority religions, freedom of religion is on the decline. Data for two decades from 147 nations are used to test hypotheses. Time-series cross-sectional and mediation models estimated at different levels of analysis with data from two independent sources confirm that threat systematically accounts for changes in religious freedom, with globalization playing a key role.