bluuebunny/crossref_metadata_2025 huggingface dataset:
A new control strategy to suppress the tower vibrations of variable speed wind turbines
Authors: Mohammadi E. , Fadaeinedjad R. , Moallem M.
Published: May 2014

In this paper, an adaptive internal model based controller is presented for suppressing the tower vibrations in variable speed wind turbines. Wind turbines have a dedicated current and power control module for the second operation region of the machine, where the machine works below the rated wind speed, and a pitch controller for the third operation region of the machine, where the machine works above the rated wind speed. The current and power controllers are designed to maximize the captured power below the rated wind speed, whereas the pitch controller is designed to limit the rotation speed and generated power above the rated wind speed. The pitch controller can further be used to suppress the mechanical tower vibration. Since the vibration frequencies of a tower are not exactly specified in the real turbines, the proposed method, which is based on the behavior of an internal model in an error feedback system, utilizes an algorithm to identify the vibration frequency followed by cancelling the vibration signal. Four different software packages including FAST, TurbSim, AeroDyn, and Simulink are integrated and used for simulation studies. Furthermore, performance of the controller is investigated in normal and fault ride through conditions. The results indicate accurate and proper performance of the controller in terms of identification of the tower vibration frequency and its suppression.
Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method
Authors: Ovchinnikov Victor , Karplus Martin
Published: May 2014

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.
Spin-polarized hydrogen Rydberg time-of-flight: Experimental measurement of the velocity-dependent H atom spin-polarization
Authors: Broderick Bernadette M. , Lee Yumin , Doyle Michael B. , Chernyak Vladimir Y. , Vasyutinskii Oleg S. , Suits Arthur G.
Published: May 2014

We have developed a new experimental method allowing direct detection of the velocity dependent spin-polarization of hydrogen atoms produced in photodissociation. The technique, which is a variation on the H atom Rydberg time-of-flight method, employs a double-resonance excitation scheme and experimental geometry that yields the two coherent orientation parameters as a function of recoil speed for scattering perpendicular to the laser propagation direction. The approach, apparatus, and optical layout we employ are described here in detail and demonstrated in application to HBr and DBr photolysis at 213 nm. We also discuss the theoretical foundation for the approach, as well as the resolution and sensitivity we achieve.
Atomistic simulation study of short pulse laser interactions with a metal target under conditions of spatial confinement by a transparent overlayer
Authors: Karim Eaman T. , Shugaev Maxim , Wu Chengping , Lin Zhibin , Hainsey Robert F. , Zhigilei Leonid V.
Published: May 2014

The distinct characteristics of short pulse laser interactions with a metal target under conditions of spatial confinement by a solid transparent overlayer are investigated in a series of atomistic simulations. The simulations are performed with a computational model combining classical molecular dynamics (MD) technique with a continuum description of the laser excitation, electron-phonon equilibration, and electronic heat transfer based on two-temperature model (TTM). Two methods for incorporation of the description of a transparent overlayer into the TTM-MD model are designed and parameterized for Ag-silica system. The material response to the laser energy deposition is studied for a range of laser fluences that, in the absence of the transparent overlayer, covers the regimes of melting and resolidification, photomechanical spallation, and phase explosion of the overheated surface region. In contrast to the irradiation in vacuum, the spatial confinement by the overlayer facilitates generation of sustained high-temperature and high-pressure conditions near the metal-overlayer interface, suppresses the generation of unloading tensile wave, decreases the maximum depth of melting, and prevents the spallation and explosive disintegration of the surface region of the metal target. At high laser fluences, when the laser excitation brings the surface region of the metal target to supercritical conditions, the confinement prevents the expansion and phase decomposition characteristic for the vacuum conditions leading to a gradual cooling of the hot compressed supercritical fluid down to the liquid phase and eventual solidification. The target modification in this case is limited to the generation of crystal defects and the detachment of the metal target from the overlayer.
Equation-of-motion coupled cluster perturbation theory revisited
Authors: Eriksen Janus J. , Jørgensen Poul , Olsen Jeppe , Gauss Jürgen
Published: May 2014

The equation-of-motion coupled cluster (EOM-CC) framework has been used for deriving a novel series of perturbative corrections to the coupled cluster singles and doubles energy that formally converges towards the full configuration interaction energy limit. The series is based on a Møller-Plesset partitioning of the Hamiltonian and thus size extensive at any order in the perturbation, thereby remedying the major deficiency inherent to previous perturbation series based on the EOM-CC ansatz.
Sequence-dependent theory of oligonucleotide hybridization kinetics
Authors: Marimuthu Karthikeyan , Chakrabarti Raj
Published: May 2014

A theoretical approach to the prediction of the sequence and temperature-dependent rate constants for oligonucleotide hybridization reactions has been developed based on the theory of relaxation kinetics. One-sided and two-sided melting reaction mechanisms for oligonucleotide hybridization reactions have been considered, analyzed, modified, and compared to select a physically consistent as well as robust model for prediction of the relaxation times of DNA hybridization reactions that agrees with the experimental evidence. The temperature- and sequence-dependent parameters of the proposed model have been estimated using available experimental data. The relaxation time model that we developed has been combined with the nearest neighbor model of hybridization thermodynamics to estimate the temperature- and sequence-dependent rate constants of an oligonucleotide hybridization reaction. The model-predicted rate constants are compared to experimentally determined rate constants for the same oligonucleotide hybridization reactions. Finally, we consider a few important applications of kinetically controlled DNA hybridization reactions.
Spin–orbit interaction mediated molecular dissociation
Authors: Kokkonen E. , Löytynoja T. , Jänkälä K. , Kettunen J. A. , Heinäsmäki S. , Karpenko A. , Huttula M.
Published: May 2014

The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr2) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.
Pathway structure determination in complex stochastic networks with non-exponential dwell times
Authors: Li Xin , Kolomeisky Anatoly B. , Valleriani Angelo
Published: May 2014

Analysis of complex networks has been widely used as a powerful tool for investigating various physical, chemical, and biological processes. To understand the emergent properties of these complex systems, one of the most basic issues is to determine the structure and topology of the underlying networks. Recently, a new theoretical approach based on first-passage analysis has been developed for investigating the relationship between structure and dynamic properties for network systems with exponential dwell time distributions. However, many real phenomena involve transitions with non-exponential waiting times. We extend the first-passage method to uncover the structure of distinct pathways in complex networks with non-exponential dwell time distributions. It is found that the analysis of early time dynamics provides explicit information on the length of the pathways associated to their dynamic properties. It reveals a universal relationship that we have condensed in one general equation, which relates the number of intermediate states on the shortest path to the early time behavior of the first-passage distributions. Our theoretical predictions are confirmed by extensive Monte Carlo simulations.
Strong field ionization rates simulated with time-dependent configuration interaction and an absorbing potential
Authors: Krause Pascal , Sonk Jason A. , Schlegel H. Bernhard
Published: May 2014

Ionization rates of molecules have been modeled with time-dependent configuration interaction simulations using atom centered basis sets and a complex absorbing potential. The simulations agree with accurate grid-based calculations for the ionization of hydrogen atom as a function of field strength and for charge resonance enhanced ionization of \documentclass[12pt]{minimal}\begin{document}${\rm H}_2^+$\end{document}H2+ as the bond is elongated. Unlike grid-based methods, the present approach can be applied to simulate electron dynamics and ionization in multi-electron polyatomic molecules. Calculations on HCl+ and HCO+ demonstrate that these systems also show charge resonance enhanced ionization as the bonds are stretched.
Metacomposite characteristics and their influential factors of polymer composites containing orthogonal ferromagnetic microwire arrays
Authors: Luo Y. , Peng H. X. , Qin F. X. , Ipatov M. , Zhukova V. , Zhukov A. , Gonzalez J.
Published: May 2014

The microwave properties of glass-fibers reinforced polymer composite embedded with an orthogonal array of Fe77Si10B10C3 microwires have been investigated. The composites containing orthogonal wire arrays display a remarkable transmission window in the frequency band of 1 to 6 GHz under zero external magnetic field indicating an intrinsic double-negative-index characteristic. The polymer matrices have proved to exert a synergistic effect on the microwave properties, which is responsible for the disappearance of the transmission windows when Ek is perpendicular to the glass fiber direction. The plasma frequency of the orthogonal microwire array composite is higher than that of the parallel microwire array with identical wire spacing; this could be attributed to the enhanced microwire-wave interaction induced by the axial electrical components on the additional layer of perpendicular wires. All these features make this new kind of orthogonal microwire composites promising for potential cloaking and sensing applications.
Atmospheric pressure plasma jet with high-voltage power supply based on piezoelectric transformer
Authors: Babij Michał , Kowalski Zbigniew W. , Nitsch Karol , Silberring Jerzy , Gotszalk Teodor
Published: May 2014

The dielectric barrier discharge plasma jet, an example of the nonthermal atmospheric pressure plasma jet (APPJ), generates low-temperature plasmas that are suitable for the atomization of volatile species and can also be served as an ionization source for ambient mass and ion mobility spectrometry. A new design of APPJ for mass spectrometry has been built in our group. In these plasma sources magnetic transformers (MTs) and inductors are typically used in power supplies but they present several drawbacks that are even more evident when dealing with high-voltage normally used in APPJs. To overcome these disadvantages, high frequency generators with the absence of MT are proposed in the literature. However, in the case of miniaturized APPJs these conventional power converters, built of ferromagnetic cores and inductors or by means of LC resonant tank circuits, are not so useful as piezoelectric transformer (PT) based power converters due to bulky components and small efficiency. We made and examined a novel atmospheric pressure plasma jet with PT supplier served as ionization source for ambient mass spectrometry, and especially mobile spectrometry where miniaturization, integration of components, and clean plasma are required. The objective of this paper is to describe the concept, design, and implementation of this miniaturized piezoelectric transformer-based atmospheric pressure plasma jet.
Superconductivity in the system MoxCyGazOδ prepared by focused ion beam induced deposition
Authors: Weirich P. M. , Schwalb C. H. , Winhold M. , Huth M.
Published: May 2014

We have prepared the new amorphous superconductor MoxCyGazOδ with a maximum critical temperature Tc of 3.8 K by the direct-write nano-patterning technique of focused (gallium) ion beam induced deposition (FIBID) using Mo(CO)6 as precursor gas. From a detailed analysis of the temperature-dependent resistivity and the upper critical field, we found clear evidence for proximity of the samples to a disorder-induced metal-insulator transition. We observed a strong dependence of Tc on the deposition parameters and identified clear correlations between Tc, the localization tendency visible in the resistance data and the sample composition. By an in-situ feedback-controlled optimization process in the FIB-induced growth, we were able to identify the beam parameters which lead to samples with the largest Tc-value and sharpest transition into the superconducting state.
Interactions of mobile helium clusters with surfaces and grain boundaries of plasma-exposed tungsten
Authors: Hu Lin , Hammond Karl D. , Wirth Brian D. , Maroudas Dimitrios
Published: May 2014

We report results of atomistic computations for the interactions of small mobile helium clusters (Hen) with free surfaces and grain boundaries (GBs) in tungsten toward development of continuum drift-diffusion-reaction models for the dynamics of mobile helium clusters in plasma-exposed tungsten. Molecular-statics (MS) simulations based on reliable many-body interatomic potentials are carried out for Hen (1 ≤ n ≤ 7) clusters near sinks to obtain the potential energy profiles of the Hen clusters as a function of the clusters' center-of-mass distance from a sink. Sinks investigated include surfaces, GBs, and regions in the vicinity of junctions where GBs intersect free surfaces. Elastic interaction potentials based on elastic inclusion theory provide an excellent description of the MS results for the cluster-sink interactions. The key parameter in the elastic models is the sink segregation strength, which is found to increase with increasing cluster size. Such cluster-sink interactions are responsible for the migration of small helium clusters by drift and for helium segregation on surfaces and grain boundaries in tungsten. Such helium segregation on sinks is observed in large-scale molecular-dynamics simulations of helium aggregation in model polycrystalline tungsten at 933 K upon helium implantation.
Comprehensive study of the effect of the irradiation temperature on the behavior of cubic zirconia
Authors: Debelle A. , Channagiri J. , Thomé L. , Décamps B. , Boulle A. , Moll S. , Garrido F. , Behar M. , Jagielski J.
Published: May 2014

Cubic zirconia single-crystals (yttria-stabilized zirconia (YSZ)) have been irradiated with 4 MeV Au2+ ions in a broad fluence range (namely from 5 × 1012 to 2 × 1016 cm−2) and at five temperatures: 80, 300, 573, 773, and 1073 K. Irradiated samples have been characterized by Rutherford backscattering spectroscopy in channeling mode, X-ray diffraction and transmission electron microscopy techniques in order to determine the disordering kinetics. All experimental results show that, whatever is the irradiation temperature, the damage build-up follows a multi-step process. In addition, the disorder level at high fluence is very similar for all temperatures. Thus, no enhanced dynamic annealing process is observed. On the other hand, transitions in the damage accumulation process occur earlier in fluence with increasing temperature. It is shown that temperature as low as 573 K is sufficient to accelerate the disordering process in ion-irradiated YSZ.
Weibel instability for a streaming electron, counterstreaming e-e, and e-p plasmas with intrinsic temperature anisotropy
Authors: Ghorbanalilu M. , Sadegzadeh S. , Ghaderi Z. , Niknam A. R.
Published: May 2014

The existence of Weibel instability for a streaming electron, counterstreaming electron-electron (e-e), and electron-positron (e-p) plasmas with intrinsic temperature anisotropy is investigated. The temperature anisotropy is included in the directions perpendicular and parallel to the streaming direction. It is shown that the beam mean speed changes the instability mode, for a streaming electron beam, from the classic Weibel to the Weibel-like mode. The analytical and numerical solutions approved that Weibel-like modes are excited for both counterstreaming e-e and e-p plasmas. The growth rates of the instabilities in e-e and e-p plasmas are compared. The growth rate is larger for e-p plasmas if the thermal anisotropy is small and the opposite is true for large thermal anisotropies. The analytical and numerical solutions are in good agreement only in the small parallel temperature and wave number limits, when the instability growth rate increases linearly with normalized wave number kc∕ωp.
Influence of Gaussian white noise on the frequency-dependent first nonlinear polarizability of doped quantum dot
Authors: Ganguly Jayanta , Ghosh Manas
Published: May 2014

We investigate the profiles of diagonal components of frequency-dependent first nonlinear (βxxx and βyyy) optical response of repulsive impurity doped quantum dots. We have assumed a Gaussian function to represent the dopant impurity potential. This study primarily addresses the role of noise on the polarizability components. We have invoked Gaussian white noise consisting of additive and multiplicative characteristics (in Stratonovich sense). The doped system has been subjected to an oscillating electric field of given intensity, and the frequency-dependent first nonlinear polarizabilities are computed. The noise characteristics are manifested in an interesting way in the nonlinear polarizability components. In case of additive noise, the noise strength remains practically ineffective in influencing the optical responses. The situation completely changes with the replacement of additive noise by its multiplicative analog. The replacement enhances the nonlinear optical response dramatically and also causes their maximization at some typical value of noise strength that depends on oscillation frequency.
Reactive, anomalous compression in shocked polyurethane foams
Authors: Dattelbaum Dana M. , Coe Joshua D. , Kiyanda Charles B. , Gustavsen Richard L. , Patterson Brian M.
Published: May 2014

We present the results of plate impact experiments performed on 30%–75% porous, polymeric methylene diphenyl diisocyanate polyurethane foams. The combination of new data with those previously obtained on full-density material was used to calibrate complete equations-of-state under both inert and chemically reactive frameworks. Description of unreacted polyurethane was based on a combination of Hayes and P-α models, whereas its decomposition products were predicted via free energy minimization under the assumption of chemical and thermodynamic equilibrium. Correspondence of experiment and theory suggests that polyurethane at all densities decomposes when shocked above some threshold pressure, and that this threshold falls dramatically as a function of initial porosity. The shock locus of foams at 50% or less of theoretical maximum density was found “anomalous” in the sense that final volumes increased with pressure. We attribute this anomaly to chemical decomposition of the initial matrix to a mixture of small-molecule fluids and bulk carbon (graphite or diamond, depending on the initial density).
Magnetic states and ferromagnetic resonance in geometrically frustrated arrays of multilayer ferromagnetic nanoparticles ordered on triangular lattices
Authors: Mironov V. L. , Skorohodov E. V. , Blackman J. A.
Published: May 2014

We present a theoretical investigation of magnetostatic interaction effects in geometrically frustrated arrays of anisotropic one-layer and multilayer ferromagnetic nanoparticles arranged in different spatially configured systems with triangular symmetry. The peculiarities of the magnetization reversal and microwave excitation of such systems are discussed. We show that the use of multilayer stacks significantly expands the opportunities to create magnetically frustrated systems due to additional interlayer interaction. In particular, the interlayer coupling leads to the considerable splitting of the ferromagnetic resonance (FMR) spectrum. In addition, the magnetizing and remagnetizing of the two- and three-layer systems induce transitions between different states with ferromagnetic, antiferromagnetic, or mixed ferromagnetic-antiferromagnetic interlayer ordering that are accompanied by dramatic changes of FMR spectra. These effects can be potentially used in developing field controlled tunable microwave devices.
Creation and physical aspects of luminescent patterns using helium ion microscopy
Authors: Veligura Vasilisa , Hlawacek Gregor , Jahn Uwe , van Gastel Raoul , Zandvliet Harold J. W. , Poelsema Bene
Published: May 2014

The helium ion microscope provides a sub-nanometer size He+ ion beam which can be employed for materials modification. We demonstrate how material properties can be tuned in a helium ion microscope with very high precision using, as an example, the modification of the luminescence properties of a sodium chloride crystal. Although the beam size is extremely small, the actually affected sample volume is much bigger due to collision cascades. We have directly measured the diameter of the interaction volume of the 35 keV He+ beam with a sodium chloride crystal using ionoluminescence. The experimental results are compared to stopping and range of ions in matter simulations and calculations of the point spread function.
The effect of boundaries on the ion acoustic beam-plasma instability in experiment and simulation
Authors: Rapson Christopher , Grulke Olaf , Matyash Konstantin , Klinger Thomas
Published: May 2014

The ion acoustic beam-plasma instability is known to excite strong solitary waves near the Earth's bow shock. Using a double plasma experiment, tightly coupled with a 1-dimensional particle-in-cell simulation, the results presented here show that this instability is critically sensitive to the experimental conditions. Boundary effects, which do not have any counterpart in space or in most simulations, unavoidably excite parasitic instabilities. Potential fluctuations from these instabilities lead to an increase of the beam temperature which reduces the growth rate such that non-linear effects leading to solitary waves are less likely to be observed. Furthermore, the increased temperature modifies the range of beam velocities for which an ion acoustic beam plasma instability is observed.
Efficient tristable resistive memory based on single layer graphene/insulating polymer multi-stacking layer
Authors: Wu Chaoxing , Li Fushan , Guo Tailiang
Published: May 2014

Tristable resistive memories based on single layer graphene (SLG)/insulating polymer multi-stacking layer were fabricated. By using the traditional transfer method, the chemical vapor deposition-synthesized SLG serving as charging layers were combined with poly(methyl methacrylate) (PMMA) layers and polystyrene (PS) layers to form charge traps with various depth. Based on the PS/SLG/PMMA/SLG/PMMA multi-stacking layer, the devices exhibited efficient tristable memory performances. The ratios as large as 104 between different resistive states were maintained for a retention time of more than 104 s. The operation mechanisms of stepping-charging in the multi-stacking layer for the tristable resistive switching were proposed on the basis of the current-voltage analysis.
Tunable eigenmodes of coupled magnetic vortex oscillators
Authors: Hänze Max , Adolff Christian F. , Weigand Markus , Meier Guido
Published: May 2014

We study the magnetization dynamics of coupled vortices in arrays of Permalloy disks via analytical calculations and scanning transmission x-ray microscopy. The Thiele approach is used to derive linear equations of motion of the vortices. Thereby, vortex motions following a nanosecond field pulse are described by a superposition of eigenmodes that depend on the vortex polarizations. Eigenmodes are calculated for a specific polarization pattern of a 3 × 3 vortex array. With magnetic field pulses distinct oscillations are excited and imaged in space and time. The calculated eigenmodes precisely describe the measured oscillations.
Infrared selective emitters with thin films of polar materials
Authors: Narayanaswamy Arvind , Mayo Jeff , Canetta Carlo
Published: May 2014

Selective thermal emitters are materials which emit in narrow wavelength bands, unlike blackbody emitters which emit uniformly over all wavelengths. Materials with tailored emission/absorption characteristics can be useful for applications in energy conversion, energy conservation, chemical, and bio-chemical sensing. In this paper, we show that thin films of polar dielectric materials can act as selective emitters in two frequency bands on either side of the restrahlen band(s) of the polar material due to multiple reflections within the thin films.
Enhanced stimulated emission in ZnO thin films using microdisk top-down structuring
Authors: Nomenyo K. , Gadallah A.-S. , Kostcheev S. , Rogers D. J. , Lérondel G.
Published: May 2014

Microdisks were fabricated in zinc oxide (ZnO) thin films using a top-down approach combining electron beam lithography and reactive ion etching. These microdisk structured thin films exhibit a stimulated surface emission between 3 and 7 times higher than that from a reference film depending on the excitation power density. Emission peak narrowing, reduction in lasing threshold and blue-shifting of the emission wavelength were observed along with enhancement in the emitted intensity. Results indicate that this enhancement is due to an increase in the internal quantum efficiency combined with an amplification of the stimulated emission. An analysis in terms of waveguiding is presented in order to explain these effects. These results demonstrate that very significant gains in emission can be obtained through conventional microstructuration without the need for more onerous top-down nanostructuration techniques.
Total ionizing dose effect of γ-ray radiation on the switching characteristics and filament stability of HfOx resistive random access memory
Authors: Fang Runchen , Gonzalez Velo Yago , Chen Wenhao , Holbert Keith E. , Kozicki Michael N. , Barnaby Hugh , Yu Shimeng
Published: May 2014

The total ionizing dose (TID) effect of gamma-ray (γ-ray) irradiation on HfOx based resistive random access memory was investigated by electrical and material characterizations. The memory states can sustain TID level ∼5.2 Mrad (HfO2) without significant change in the functionality or the switching characteristics under pulse cycling. However, the stability of the filament is weakened after irradiation as memory states are more vulnerable to flipping under the electrical stress. X-ray photoelectron spectroscopy was performed to ascertain the physical mechanism of the stability degradation, which is attributed to the Hf-O bond breaking by the high-energy γ-ray exposure.
Transition of the polarization switching from extrinsic to intrinsic in the ultrathin polyvinylidene fluoride homopolymer films
Authors: Wang J. L. , Liu B. L. , Zhao X. L. , Tian B. B. , Zou Y. H. , Sun S. , Shen H. , Sun J. L. , Meng X. J. , Chu J. H.
Published: May 2014

Polyvinylidene fluoride homopolymer thin films have been prepared by the Langmuir-Blodgett technique, and their electrical properties have comprehensively been studied. The polyvinylidene fluoride homopolymer films show better ferroelectricity with higher polarization and higher breakdown electric field than that of the poly(vinylidene fluoride-trifluoroethylene) copolymer films. Inspection on the thickness dependence of the coercive field of the polyvinylidene fluoride films suggests an extrinsic polarization switching occurs in the thickness range from 200 to 45 nm, and a non-extrinsic switching is observed in the range between 45 and 11 nm, which is ascribed to the transition range from extrinsic to intrinsic switching.
Intense optical second harmonic generation from centrosymmetric nanocrystalline para-nitroaniline
Authors: Isakov Dmitry V. , Belsley Michael S. , de Matos Gomes Etelvina , Gonçalves Hugo , Schellenberg Peter , Almeida Bernardo G.
Published: May 2014

We demonstrate an approach that uses normally centrosymmetric, but highly polarizable organic molecules of para-nitroaniline (p-NA) as very efficient second harmonic generator (SHG) for near infra-red light. The approach is based on an effective manipulation of the nanocrystalline size and their assembly into a highly orientated mesocrystalline structures. The resulting mesocrystalline form of p-NA consists of multiple nanocrystals with common orientation, providing a set of surfaces with highly aligned molecules forming a head-to-tail polar arrangement. The second harmonic generation efficiency from this arrangement of mesocrystalline nanostructures is comparable to that from the conventional non-centrosymmetric organic crystals. The experimental results indicate that a very strong second-order nonlinear response can be obtained from small D-π-A organic molecules with elevated molecular hyperpolarizabilities even if these molecules tend to crystallize in centrosymmetric structures.
Representing inequality in language
Authors: Schulze Rainer
Published: May 2014

Using large, computerized corpora, this study aims to provide lexico-grammatical evidence for patterns or constructions in language pertaining to domains such as “power”, “dominance”, “inequality” or “status”. The study will specifically focus on the verbal uses of brook and countenance, lemmas that are pivotal to the domains in question and whose semantic and pragmatic meanings will be associated with discourses of inequality and supremacy, subordination and authorization. The verbal lemmas will turn out less as markers of energy transfer (as might be expected from the prototypical constructional meaning of transitive clauses in which they ordinarily occur) than as markers of perceived social implications, with a clear focus on the constructing and representational nature of their uses. In addition to offering a contribution to language-dependent “dominance”, “inequality”, “power”, “status” research, this paper will also demonstrate the indispensable use of corpus-linguistic methods within a predominantly functional framework (drawing its main inspirations from current research in neo-Firthian linguistics, Frame Semantics and Cognitive Linguistics in particular).
Power eliciting elements at the semantic-pragmatic interface
Authors: Marx Konstanze
Published: May 2014

Power, in this article, is to be understood as an instrument of force that is imposed purposely in order to influence, affect or persuade others. The question here is whether such power is due to aggressive expressions (lexical level) or to context-dependent aspects (discourse level) that become relevant when insulting persons via new media. I will distinguish between “cyberbullying” as an attempt to hurt a person’s feelings directly via personal SMS or email and “virtual character assassination attempts” that include third parties as an audience. Potential readers not directly involved are considered a constitutive eliciting element of power. It is assumed that their existence is even more important and effective (in terms of strengthening the perpetrator’s power) than aggressive language.
Powerless language
Authors: Pishwa Hanna
Published: May 2014

This paper brings together two different approaches to the analysis of hedges. They are viewed in linguistics as procedural cues relating to the propositional or phrasal contents and their cognitive counterparts. In social psychology, they are interpreted at an interpersonal level as powerlessness markers attributing lack of control and power to the speaker. A comparison of these approaches resulted in the finding that some usages of hedges can be interpreted as unintended interpersonal implicatures weakening speaker traits and persuasive force. A further function is intentional and strategic as in political speech. A third usage is appropriate fuzziness caused by hedges, whereby the hedged expression exhibits accuracy higher than an explicit statement.
A true authoritarian type
Authors: Donahue John
Published: May 2014

To convey authority in a document, people choose specific typefaces (or fonts). Studies find that repeating a message makes it more persuasive, and that different typefaces lead to different associations. Also, statements are more memorable when written in harder-to-read typefaces; yet more believable for easier-to-read ones. In each of the two present experiments, surveys measuring authoritarianism were written in various typefaces. The first experiment sought evaluations of groups such as the army and police. The second experiment included subject matters like illegal wiretapping by the F.B.I. The results suggested participants had more positive views for authoritarian groups and more likely supported morally questionable actions when the surveys were written in an easy-to-read typeface.
Language, normativity and power
Authors: Motschenbacher Heiko
Published: May 2014

The present paper aims to shed light on how social actors orient to sexual normativity in their talk. It relates normativity to (Foucauldian) notions of discourse and power, arguing that local linguistic negotiations of sexuality are generally shaped by a competition between dominant and marginalized discourses. The empirical section focusses on how sexual normativity is linguistically constructed in conversations related to objectophilia, a form of sexual desire that is clearly non-normative. The data consists of telephone calls from the German radio phone-in show Domian. It is shown how speakers co-construct sexual normativity in general as well as more specific forms of it such as humano-normativity and heteronormativity. It can be seen that even the construction of non-normative desires is predominantly structured by normative sexuality discourses.
Inserted rest period resensitizes MC3T3-E1 cells to fluid shear stress in a time-dependent manner via F-actin-regulated mechanosensitive channel(s)
Authors: Gong Xiaoyuan , Fan Yijuan , Zhang Yinxin , Luo Chunhua , Duan Xiaojun , Yang Liu , Pan Jun
Published: May 2014

The underlying cellular mechanism of anabolic effect recovered by inserting rest is not fully understood. In this work, we studied the role of F-actin regulated mechanosensitive channel(s) re-activation in mechanosensitivity modulation in vitro. Results showed that steady fluid shear stress (sFSS) stimulation with 30-min rest period was more potential in increasing alkalinephosphatase (ALP) activity than 10 and 0-min rest periods, and insertion of 30 min, but not 0 or 10 min, recovered the [Ca2+]i transient and contribution of the mechanosensitive channel(s). During the rest period, F-actin experienced polymerization (0–10 min), followed by depolymerization (10–30 min); inhibition of F-actin polymerization/depolymerization significantly increased/decreased the [Ca2+]i transient, as well as the contribution of the mechanosensitive channel(s) in subsequent sFSS stimulation. Our results demonstrated that the long rest period between sFSS loadings recruited [Ca2+]i transient via F-actin depolymerization-induced reactivation of mechanosensitive channel(s), suggesting that F-actin-regulated cellular stiffness could account for the decreased anabolic response during continuous mechanical loading in bone cells.
Increased microRNA-223 in Helicobacter pylori-associated gastric cancer contributed to cancer cell proliferation and migration
Authors: Ma Lianjun , Chen Yan , Zhang Bin , Liu Guifeng
Published: May 2014

Dysregulation of microRNA-223 (miR-223) was associated with gastric cancer (GC), in which Helicobacter pylori (H. pylori) played important roles. However, the mechanism of relationships between miR-223 and H. pylori-associated GC was largely undiscovered. Here, we found the overexpression of miR-223 was related with H. pylori positive infection in vivo and in vitro in GC by relative quantification of qRT-PCR. Upregulated miR-223 was responsible for the poorer prognosis of GC with H. pylori positive, also. The result indicated not only overexpression of miR-223 stimulated the proliferation by CCK-8 assays and colony formation of H. pylori associated GC cells, but also migration and invasion by scratch assay and transwell invasion assays in vitro. Above all, all our data declared H. pylori infection played an important role in developing GC according to overexpression of miR-223, which increased cancer cell proliferation and migration.
Presence of osteoinductive factors in bovine colostrum
Authors: Mussano Federico , Bartorelli Cusani Alberto , Brossa Alessia , Carossa Stefano , Bussolati Gianni , Bussolati Benedetta
Published: May 2014

New approaches in the treatment of skeletal defects may benefit from the use of soluble biological factors. We previously standardized a derivative of bovine colostrum (SBCD), deprived of casein and fat and rich in cytokines. In the present study, we tested its possible use as an adjuvant in bone healing. SBCD contained factors involved in stromal cell stimulation and differentiation and induced cytokine production from stimulated mesenchymal stem cells (MSCs). In vitro, SBCD promoted proliferation, migration and, in association with osteogenic factors, osteogenic differentiation of osteoblastic and MSCs. In in vivo experiments of subcutaneous Matrigel injection in mice, SBCD plus hydroxyapatite, but not hydroxyapatite nor SBCD alone, induced recruitment of macrophages and stromal cells. After 60 days, plugs containing SBCD and hydroxyapatite were densely calcified and diffusely positive for osteocalcin, supporting the occurrence of an early osteogenic process. These results indicate that SBCD is a rich source of factors with osteoinductive properties.
Epigenetic Modifications: Basic Mechanisms and Role in Cardiovascular Disease (2013 Grover Conference Series)
Authors: Loscalzo Joseph , Handy Diane E.
Published: May 2014

Epigenetics refers to heritable traits that are not a consequence of DNA sequence. Three classes of epigenetic regulation exist: DNA methylation, histone modification, and noncoding RNA action. In the cardiovascular system, epigenetic regulation affects development, differentiation, and disease propensity or expression. Defining the determinants of epigenetic regulation offers opportunities for novel strategies for disease prevention and treatment.
Homotopy type theory and Voevodsky’s univalent foundations
Authors: Pelayo Álvaro , Warren Michael
Published: May 2014

Recent discoveries have been made connecting abstract homotopy theory and the field of type theory from logic and theoretical computer science. This has given rise to a new field, which has been christened homotopy type theory. In this direction, Vladimir Voevodsky observed that it is possible to model type theory using simplicial sets and that this model satisfies an additional property, called the Univalence Axiom, which has a number of striking consequences. He has subsequently advocated a program, which he calls univalent foundations, of developing mathematics in the setting of type theory with the Univalence Axiom and possibly other additional axioms motivated by the simplicial set model. Because type theory possesses good computational properties, this program can be carried out in a computer proof assistant. In this paper we give an introduction to homotopy type theory in Voevodsky’s setting, paying attention to both theoretical and practical issues. In particular, the paper serves as an introduction to both the general ideas of homotopy type theory as well as to some of the concrete details of Voevodsky’s work using the well-known proof assistant Coq. The paper is written for a general audience of mathematicians with basic knowledge of algebraic topology; the paper does not assume any preliminary knowledge of type theory, logic, or computer science. Because a defining characteristic of Voevodsky’s program is that the Coq code has fundamental mathematical content, and many of the mathematical concepts which are efficiently captured in the code cannot be explained in standard mathematical English without a lengthy detour through type theory, the later sections of this paper (beginning with Section \ref{sec2}) make use of code; however, all notions are introduced from the beginning and in a self-contained fashion.
SAMBLASTER: fast duplicate marking and structural variant read extraction
Authors: Faust Gregory G. , Hall Ira M.
Published: May 2014

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.

Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results.

Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster.

Contact:  imh4y@virginia.edu
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition
Authors: Chatterjee Saikat , Koslicki David , Dong Siyuan , Innocenti Nicolas , Cheng Lu , Lan Yueheng , Vehkaperä Mikko , Skoglund Mikael , Rasmussen Lars K. , Aurell Erik , Corander Jukka
Published: May 2014

Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.

Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.

Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.

Contact: sach@kth.se
Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy
Authors: Kim Jihye , Vasu Vihas T. , Mishra Rangnath , Singleton Katherine R. , Yoo Minjae , Leach Sonia M. , Farias-Hesson Eveline , Mason Robert J. , Kang Jaewoo , Ramamoorthy Preveen , Kern Jeffrey A. , Heasley Lynn E. , Finigan James H. , Tan Aik Choon
Published: May 2014

Motivation: Non–small-cell lung cancer (NSCLC) is the leading cause of cancer death in the United States. Targeted tyrosine kinase inhibitors (TKIs) directed against the epidermal growth factor receptor (EGFR) have been widely and successfully used in treating NSCLC patients with activating EGFR mutations. Unfortunately, the duration of response is short-lived, and all patients eventually relapse by acquiring resistance mechanisms.

Result: We performed an integrative systems biology approach to determine essential kinases that drive EGFR-TKI resistance in cancer cell lines. We used a series of bioinformatics methods to analyze and integrate the functional genetics screen and RNA-seq data to identify a set of kinases that are critical in survival and proliferation in these TKI-resistant lines. By connecting the essential kinases to compounds using a novel kinase connectivity map (K-Map), we identified and validated bosutinib as an effective compound that could inhibit proliferation and induce apoptosis in TKI-resistant lines. A rational combination of bosutinib and gefitinib showed additive and synergistic effects in cancer cell lines resistant to EGFR TKI alone.

Conclusions: We have demonstrated a bioinformatics-driven discovery roadmap for drug repurposing and development in overcoming resistance in EGFR-mutant NSCLC, which could be generalized to other cancer types in the era of personalized medicine.

Availability and implementation: K-Map can be accessible at: http://tanlab.ucdenver.edu/kMap.

Contact:  aikchoon.tan@ucdenver.edu or finiganj@njhealth.org

Supplementary information:  Supplementary Data are available at Bioinformatics online.