bluuebunny/crossref_metadata_2025 huggingface dataset:
Environmental effects on noble-gas hydrides: HXeBr, HXeCCH, and HXeH in noble-gas and molecular matrices
Authors: Tsuge Masashi , Lignell Antti , Räsänen Markku , Khriachtchev Leonid
Published: November 2013

Noble-gas hydrides HNgY (Ng is a noble-gas atom and Y is an electronegative group) are sensitive probes of local environment due to their relatively weak bonding and large dipole moments. We experimentally studied HXeBr in Ar, Kr, and N2 matrices, HXeCCH in Ne and N2 matrices, and HXeH in an N2 matrix. These are the first observations of noble-gas hydrides in an N2 matrix. An N2 matrix strongly increases the H–Xe stretching frequency of HXeBr and HXeCCH with respect to a Ne matrix, which is presumably due to a strong interaction between the HNgY dipole moment and quadrupole moments of the surrounding lattice N2 molecules. The spectral shift of HXeBr in an N2 matrix is similar to that in a CO2 matrix, which is a rather unexpected result because the quadrupole moment of CO2 is about three times as large as that of N2. The H–Xe stretching frequencies of HXeBr and HXeCCH in noble-gas matrices show a trend of ν(Ne) < ν(Xe) < ν(Kr) < ν(Ar), which is a non-monotonous function of the dielectric constants of the noble-gas solids. The MP2(full) calculations of HXeBr and HXeCCH with the polarizable continuum model as well as the CCSD(T) calculations of the HXeBr···Ng and HXeCCH···Ng (Ng = Ne, Ar, Kr, and Xe) complexes cannot fully explain the experimental observations. It is concluded that more sophisticated computational models should be used to describe these experimental findings.
A picture of dilute solution behavior of polymers through polyelectrolyte simulation
Authors: Yamakawa Hiromi , Yoshizaki Takenao , Ida Daichi
Published: November 2013

A Monte Carlo (MC) study is made of the persistence length q and the binary cluster integral β (or the excluded-volume strength B) for polyelectrolytes by the use of the discrete Kratky–Porod wormlike chain with hard-core-effective Debye–Hückel electrostatic pair potentials. The quantity q is determined from the initial decay rate of the bond correlation function after preliminary confirmation of the validity of this procedure using the chain with Lennard–Jones pair potentials. The quantity B is determined from the mean-square radius of gyration along with q by the use of the quasi-two-parameter (QTP) excluded-volume theory. They are evaluated for two model cases of polyelectrolytes, sodium hyaluronate as an example of semiflexible polymers and poly(sodium 4-styrenesulfonate) as a typical example of flexible polymers, both in aqueous sodium chloride. The behavior of MC data so obtained for q and B as functions of added salt concentration c is examined in detail, comparing them with the Odijk–Skolnick–Fixman theory of q and the Fixman–Skolnick (FS) theory of B and also with literature experimental data. In particular, the MC values of B are in almost complete agreement with the FS theory for large c, although the latter still overestimates B somewhat for small c. The values of B themselves and also the validity of the QTP theory in general are discussed in comparison with the case of nonionic polymers.
Multi-component symmetry-projected approach for molecular ground state correlations
Authors: Jiménez-Hoyos Carlos A. , Rodríguez-Guzmán R. , Scuseria Gustavo E.
Published: November 2013

The symmetry-projected Hartree–Fock ansatz for the electronic structure problem can efficiently account for static correlation in molecules, yet it is often unable to describe dynamic correlation in a balanced manner. Here, we consider a multi-component, systematically improvable approach, that accounts for all ground state correlations. Our approach is based on linear combinations of symmetry-projected configurations built out of a set of non-orthogonal, variationally optimized determinants. The resulting wavefunction preserves the symmetries of the original Hamiltonian even though it is written as a superposition of deformed (broken-symmetry) determinants. We show how short expansions of this kind can provide a very accurate description of the electronic structure of simple chemical systems such as the nitrogen and the water molecules, along the entire dissociation profile. In addition, we apply this multi-component symmetry-projected approach to provide an accurate interconversion profile among the peroxo and bis(μ-oxo) forms of [Cu2O2]2+, comparable to other state-of-the-art quantum chemical methods.
Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems
Authors: Li Jun , Jiang Bin , Guo Hua
Published: November 2013

A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resulting in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.
Cross-over between central and non-central conservative effective forces in a modulated colloidal fluid
Authors: Chaudhuri Chhanda Basu , Chakrabarty Srabani , Chakrabarti J.
Published: November 2013

We study by Monte Carlo simulations the effective forces between two particles dispersed in a two-dimensional colloidal fluid, modulated in one direction by a spatially periodic external potential. When the modulation strength exceeds the strength of interaction between the dispersed and dispersing particles, the anisotropic effective forces, show cross-over between central and non-central nature, although the effective forces remain conservative. The non-central nature of the effective forces depends on the orientation of the separation vector between the dispersed particles with respect to the modulation direction.
Influence of thermal history on the photostructural changes in glassy As15S85 studied by Raman scattering and ab initio calculations
Authors: Kolar J. , Strizik L. , Kohoutek T. , Wagner T. , Voyiatzis G. A. , Chrissanthopoulos A. , Yannopoulos S. N.
Published: November 2013

Photostructural changes—the hallmark of non-crystalline chalcogenides—are in essence the basis of a number of photoinduced effects, i.e., changes of their physical properties, which are exploited in a variety of applications, especially in photonics and optoelectronics. Despite the vast number of investigations of photostructural changes, there is currently lack of systematic studies on how the thermal history, which affects glass structure, modifies the extent of photostructural changes. In this article, we study the role of thermal history on photostructural changes in glassy As15S85. This particular sulfur-rich composition has been chosen based on the colossal photostructural response it exhibits under near-band gap light irradiation, which inherently originates from its nanoscale phase-separated nature. To control the thermal history, the glass was quenched to various temperatures and each of these quenched products was annealed under four different conditions. Off-resonant Raman scattering was used to study the equilibrium study of each product. Structural changes of interest involve changes of the sulfur atoms participating into S8 rings and Sn chains. Their ratio was found to depend on quenching/annealing conditions. Near-band gap light was used to perturb the rings-to-chain ratio and at the same time to record these changes through Raman scattering, revealing an intricate behavior of photostructural changes. Ab initio calculations were employed to determine the stability of various sulfur clusters/molecules thus aiding the correlation of the particular photo-response of glassy As15S85 with its structural constituents.
Magnetic microbead transport during resistive pulse sensing
Authors: Willmott Geoff R. , Fisk Matthew G. , Eldridge James
Published: November 2013

Tunable resistive pulse sensing (TRPS) experiments have been used to quantitatively study the motion of 1 μm superparamagnetic beads in a variable magnetic field. Closed-form theory has been developed to interpret the experiments, incorporating six particle transport mechanisms which depend on particle position in and near a conical pore. For our experiments, calculations indicate that pressure-driven flow dominates electrophoresis and magnetism by a factor of ∼100 in the narrowest part of the pore, but that magnetic force should dominate further than ∼1 mm from the membrane. As expected, the observed resistive pulse rate falls as the magnet is moved closer to the pore, while the increase in pulse duration suggests that trajectories in the half space adjacent to the pore opening are important. Aggregation was not observed, consistent with the high hydrodynamic shear near the pore constriction and the high magnetization of aggregates. The theoretical approach is also used to calculate the relative importance of transport mechanisms over a range of geometries and experimental conditions extending well beyond our own experiments. TRPS is emerging as a versatile form of resistive pulse sensing, while magnetic beads are widely used in biotechnology and sensing applications.
Simulation study on the structure of rod-coil-rod triblock copolymer and nanoparticle mixture within slit
Authors: Huang Jian-Hua , Fan Zhong-Xiang , Luo Meng-Bo
Published: November 2013

Self-assembly structures of rod-coil-rod ABA triblock copolymer and nanoparticle mixture within a slit are simulated by dissipative particle dynamics method. Results show that the structures are dependent on the rigidity of the rod block kθ, the interaction between the rod block and slit awA, the fraction of rod block fA, and the slit height H. With an increase in kθ, we observe a transition from parallel lamellae to hexagonal cylinders. While with the increase in awA, the parallel lamellae at small kθ and hexagonal cylinders at large kθ change to perpendicular lamellae at large awA close to aAs. At last, we present a phase diagram of structure with respect to fA and H at large kθ.
Optical mode confinement and selection in single-crystal sapphire fibers by formation of nanometer scale cavities with hydrogen ion implantation
Authors: Spratt William , Huang Mengbing , Murray Thomas , Xia Hua
Published: November 2013

The excellent material properties of single crystal sapphire fibers promise great advantages in applications related to harsh environment optical sensing, high laser power delivery, and high-resolution/sensitivity optical spectroscopy. However, the lack of viable cladding for confining light propagation in sapphire fibers with negligible transmission loss has restricted their practical applications. Despite great efforts in engineering either a low-refractive-index cladding layer or highly reflective mirror layer as sapphire fiber surface coatings, confining light propagation within sapphire fibers remains difficult in practice since such surface coatings fail to function due to increased thermal stress and fast erosion in environments with extremely high temperatures (>1000 °C) and chemically reactive species/gases. Here, we demonstrate a method for creating nanoscale cavities/voids in sapphire as effective fiber cladding structures that are thermally robust even at 1700 °C using hydrogen ion implantation. Material analysis of implanted sapphire crystals indicates that such nanoscale cavities play a key role in reducing the refractive index in sapphire crystals.
Performance of large arrays of point absorbing direct-driven wave energy converters
Authors: Engström J. , Eriksson M. , Göteman M. , Isberg J. , Leijon M.
Published: November 2013

Future commercial installation of wave energy plants using point absorber technology will require clusters of tens up to several hundred devices, in order to reach a viable electricity production. Interconnected devices also serve the purpose of power smoothing, which is especially important for devices using direct-driven power take off. The scope of this paper is to evaluate a method to optimize wave energy farms in terms of power production, economic viability, and resources. In particular, the paper deals with the power variation in a large array of point-absorbing direct-driven wave energy converters, and the smoothing effect due to the number of devices and their hydrodynamic interactions. A few array geometries are compared and 34 sea states measured at the Lysekil research site at the Swedish west coast are used in the simulations. Potential linear flow theory is used with full hydrodynamic interactions between the buoys. It is shown that the variance in power production depends crucially on the geometry of the array and the number of interacting devices, but not significantly on the energy period of the waves.
Highly conductive n-AlxGa1−xN layers with aluminum mole fractions above 80%
Authors: Mehnke Frank , Wernicke Tim , Pingel Harald , Kuhn Christian , Reich Christoph , Kueller Viola , Knauer Arne , Lapeyrade Mickael , Weyers Markus , Kneissl Michael
Published: November 2013

Silicon doping of AlxGa1−xN layers with high aluminum mole fractions (0.8 < x < 1) was studied. The AlGaN:Si layers were pseudomorphically grown by metalorganic vapor phase epitaxy on low defect density epitaxially laterally overgrown AlN/sapphire templates. The effects of SiH4/III ratio and aluminum content on the resistivity, the carrier concentration, and the mobility have been investigated. By variation of the SiH4/III ratio during the growth of AlxGa1−xN:Si layers, a recorded low resistivity of Al0.81Ga0.19N:Si was obtained with 0.026 Ω cm. The resistivity increases exponentially with increasing aluminum content to 3.35 Ω cm for Al0.96Ga0.04N, and the optimum SiH4/III ratio is shifted towards lower values. Hall effect measurements show that the increase of the resistivity with increasing aluminum mole fraction is mainly caused by a decrease of the carrier density. The optimized Al0.81Ga0.19N:Si exhibits a carrier concentration of 1.5 × 1019 cm−3 and a mobility of the carriers of 16.5 cm2 V−1 s−1.
Influence of grain size at first monolayer on bias-stress effect in pentacene-based thin film transistors
Authors: Zhang Yiwei , Li Dexing , Jiang Chao
Published: November 2013

Threshold voltage shift under applied gate voltage is a key factor characterizing stability of organic thin-film transistors (OTFTs), while the physical mechanism is still controversial. In this study, we systematically examined the initial growth of pentacene polycrystalline films under different growth rates. Bias stress performance of the fabricated pentacene-based OTFTs was found to be highly related to the initial gain size of the pentacene films. Larger grain size at the first deposition layer led to smaller threshold voltage shift. The quantitative correlation can be described by a two-dimensional microscopic mobility model relating to the grains and grain boundaries.
Interlayer exchange coupled composite free layer for CoFeB/MgO based perpendicular magnetic tunnel junctions
Authors: Singh Amritpal , Schwarm Samuel , Mryasov Oleg , Gupta Subhadra
Published: November 2013

We have investigated the effect of Ta insertion thickness on perpendicular magnetic anisotropy (PMA) in [Co/Pt multi-layers]/Ta/CoFeB (Hard/Soft) composite free layer. For insertions less than 0.6 nm thick, the ferromagnetic exchange was strong enough to switch the two layers together. The exchange turned from ferromagnetic to anti-ferromagnetic in nature for Ta insertion thickness above 0.7 nm. We observed increase in PMA with increasing Ta insertion thickness. It was noticed that this increase in PMA was caused by the enhancement of CoFeB/MgO interface anisotropy. The interface anisotropy increased by more than 0.9 erg/cm2 as the Ta insertion thickness increased from 0 nm to 0.5 nm. The Hk value for the composite free layer with 0.5 nm thick Ta insertion is around 11 kOe leading to a high thermal stability factor, estimated around 152 for 20 nm nano-dots.
Parameter estimation and optimal scheduling algorithm for a mathematical model of intermittent androgen suppression therapy for prostate cancer
Authors: Guo Qian , Lu Zhichang , Hirata Yoshito , Aihara Kazuyuki
Published: November 2013

We propose an algorithm based on cross-entropy to determine parameters of a piecewise linear model, which describes intermittent androgen suppression therapy for prostate cancer. By comparing with clinical data, the parameter estimation for the switched system shows good fitting accuracy and efficiency. We further optimize switching time points for the piecewise linear model to obtain a feasible therapeutic schedule. The simulation results of therapeutic effect are superior to those of previous strategy.
Determination of the direct to indirect bandgap transition composition in AlxIn1−xP
Authors: Beaton D. A. , Christian T. , Alberi K. , Mascarenhas A. , Mukherjee K. , Fitzgerald E. A.
Published: November 2013

AlxIn1−xP semiconductor alloys grown by metalorganic chemical vapor deposition on InGaAs graded buffer layers with varied aluminum compositions that span the transition from a direct to indirect semiconductor alloy are explored. The direct and indirect band gap transitions are observed in a single AlxIn1−xP sample with 40.8% allowing for a precise determination of the direct-indirect cross-over composition, xc. The direct and indirect nature of observed luminescence peaks is verified using time-resolved photoluminescence. At low temperatures, xc is determined to be 40.5% at a corresponding direct band gap energy of 2.34 eV.
Simultaneous determination of porosity, tortuosity, viscous and thermal characteristic lengths of rigid porous materials
Authors: Fellah Z. E. A. , Sadouki M. , Fellah M. , Mitri F. G. , Ogam E. , Depollier C.
Published: November 2013

We present an improved method for the characterization of air-saturated porous materials by simultaneous measurement of porosity, tortuosity, viscous, and thermal characteristic lengths via ultrasonic transmission only. The proposed method is based on a temporal model of the direct and inverse scattering problem for the transient ultrasonic waves in a homogeneous isotropic slab of rigid porous material. The advantage of the proposed method is that the four parameters are determined simultaneously using just transmitted experimental waves from a porous material saturated by one gas (air). In addition, no relationship is assumed between the two characteristic lengths.
Long-range ferromagnetic order induced by a donor impurity band exchange in SnO2:Er3+ nanoparticles
Authors: Aragón F. H. , Chitta V. A. , Coaquira J. A. H. , Hidalgo P. , Brito H. F.
Published: November 2013

In this work, the structural and magnetic properties of Er-doped SnO2 (SnO2:Er) nanoparticles are reported. The SnO2:Er nanoparticles have been synthesized by a polymer precursor method with Er content from 1.0% to 10.0%. X-ray diffraction results indicate the formation of only the rutile-type structure in all samples. The estimated mean crystallite size shows a decrease from ∼10 to ∼4 nm when the Er content is increased from 1.0% to 10.0%. The particle size values have been corroborated by transmission electron microscopy technique. The thermal dependence of the magnetization is consistent with the 3+ oxidation state of erbium ions for all samples. A strong paramagnetic-like behavior coexisting with a ferromagnetic phase has been determined for samples with Er content below 5.0%. Above this concentration, only a paramagnetic behavior has been determined. Isothermal magnetization curves are consistent with the occurrence of long-range ferromagnetic order mediated by donor electrons forming bound magnetic polarons which overlap to produce a spin-split impurity band.
Viscosity-dependent drain current noise of AlGaN/GaN high electron mobility transistor in polar liquids
Authors: Fang J. Y. , Lee G. Y. , Chyi J. I. , Hsu C. P. , Kang Y. W. , Fang K. C. , Kao W. L. , Yao D. J. , Hsu C. H. , Huang Y. F. , Chen C. C. , Li S. S. , Yeh J. A. , Ren F. , Wang Y. L.
Published: November 2013

The drain current fluctuation of ungated AlGaN/GaN high electron mobility transistors (HEMTs) measured in different fluids at a drain-source voltage of 0.5 V was investigated. The HEMTs with metal on the gate region showed good current stability in deionized water, while a large fluctuation in drain current was observed for HEMTs without gate metal. The fluctuation in drain current for the HEMTs without gate metal was observed and calculated as standard deviation from a real-time measurement in air, deionized water, ethanol, dimethyl sulfoxide, ethylene glycol, 1,2-butanediol, and glycerol. At room temperature, the fluctuation in drain current for the HEMTs without gate metal was found to be relevant to the dipole moment and the viscosity of the liquids. A liquid with a larger viscosity showed a smaller fluctuation in drain current. The viscosity-dependent fluctuation of the drain current was ascribed to the Brownian motions of the liquid molecules, which induced a variation in the surface dipole of the gate region. This study uncovers the causes of the fluctuation in drain current of HEMTs in fluids. The results show that the AlGaN/GaN HEMTs may be used as sensors to measure the viscosity of liquids within a certain range of viscosity.
Epitaxial lift-off of quantum dot enhanced GaAs single junction solar cells
Authors: Bennett Mitchell F. , Bittner Zachary S. , Forbes David V. , Rao Tatavarti Sudersena , Phillip Ahrenkiel S. , Wibowo Andree , Pan Noren , Chern Kevin , Hubbard Seth M.
Published: November 2013

InAs/GaAs strain-balanced quantum dot (QD) n-i-p solar cells were fabricated by epitaxial lift-off (ELO), creating thin and flexible devices that exhibit an enhanced sub-GaAs bandgap current collection extending into the near infrared. Materials and optical analysis indicates that QD quality after ELO processing is preserved, which is supported by transmission electron microscopy images of the QD superlattice post-ELO. Spectral responsivity measurements depict a broadband resonant cavity enhancement past the GaAs bandedge, which is due to the thinning of the device. Integrated external quantum efficiency shows a QD contribution to the short circuit current density of 0.23 mA/cm2.
Cathode fall measurement in a dielectric barrier discharge in helium
Authors: Hao Yanpeng , Zheng Bin , Liu Yaoge
Published: November 2013

A method based on the “zero-length voltage” extrapolation is proposed to measure cathode fall in a dielectric barrier discharge. Starting, stable, and discharge-maintaining voltages were measured to obtain the extrapolation zero-length voltage. Under our experimental conditions, the “zero-length voltage” gave a cathode fall of about 185 V. Based on the known thickness of the cathode fall region, the spatial distribution of the electric field strength in dielectric barrier discharge in atmospheric helium is determined. The strong cathode fall with a maximum field value of approximately 9.25 kV/cm was typical for the glow mode of the discharge.
Trial-to-trial, uncertainty-based adjustment of decision boundaries in visual categorization
Authors: Qamar Ahmad T. , Cotton R. James , George Ryan G. , Beck Jeffrey M. , Prezhdo Eugenia , Laudano Allison , Tolias Andreas S. , Ma Wei Ji
Published: November 2013

Significance

Categorization is an important part of perception and cognition. For example, an animal must successfully categorize a disturbing sound as being due to the wind or to a predator. Computationally, categorization amounts to applying decision boundaries to noisy stimulus measurements. Here, we examine how these decision boundaries change as the quality of the sensory evidence varies unpredictably from trial to trial. We show that both humans and monkeys adjust their decision boundaries from trial to trial, often near-optimally. We further show how a neural network can perform this computation near-optimally. Our results might lead to a better understanding of categorization.
Facework strategies and the achievement of multiple goals in a court martial cross-examination in the film A Few Good Men
Authors: del Saz-Rubio Maria Milagros , Gregori-Signes Carmen
Published: November 2013

Following recent trends of research into television and film language that is being undertaken in various sub-disciplines of linguistics (Piazza et al. 2011), this article describes the nature of the interaction that takes place in the cross-examination of Colonel Jessep in the film ‘A Few Good Men’. The dialogue is from the last scene of the film and it exemplifies how the attorney manages to get the truth out of an uncooperative witness. It is not, however, only the outcome of the interaction itself that is of interest, but the process through which this is reached. By analyzing in detail the facework strategies enacted by the participants in the interaction towards themselves and others (Goffman 1967; Penman 1990), as well as the conspicuous intrusions of social factors, such as power and social status, into language structure (Brown and Levinson 1987, 179), we hope to have proved that there is more to this type of discourse than the mere exchange of information (Lakoff 1989). This is partly due to its confrontational nature and to its being multifunctional with regard to goals. Underlying the analysis is the intention to illustrate how the careful and crafted use and manipulation of language is context- and goal(s)-dependent and lies at the heart of the negotiation of our communicative goals. The dialogue analyzed illustrates how a miscalculated assessment of one’s rights and obligations in a specific type of communicative activity (Levinson 1992) can prove fatal and negatively influence our own portrayal as (in)competent speakers.
Rhetoric in times of crises
Authors: Molthagen-Schnöring Stefanie
Published: November 2013

In the current climate of financial crisis many people do not trust banks anymore. In reaction to this financial institutions change marketing techniques and try to convince their shareholders that their money is well invested. This article examines an advertising spot by the Commerzbank and the editorial by the CEO of the Commerzbank in the annual report 2012. The main focus of the analysis lies on the communicative strategies used to build or rebuild trust. Therefore, the model of the Dialogic Action Game as developed by Weigand is used as a theoretical foundation as it allows a comprehensive view on communication embedded in its cultural environment.
Dialogue features in football articles over a period of fifty years
Authors: Lundin Barbro
Published: November 2013

In this diachronic study of dialogic features in football, articles from three different sports events have been focused: The World Cups 1958, 1974 and the Euro Cup 2004. This period of almost 50 years distinguishes itself as a time period when new channels for communication have emerged: television, Internet, computer-mediated communication. This has made it possible to bridge the gulf between the communicators. Dialogue features such as questions, directives, addressing the readers with you (second person singular) and using an inclusive we are numerous in the football articles studied. The articles show an increasing tendency to address the readers with you in the articles from Euro 2004. Moreover, the sports writers refer to given responses from readers in the articles from 2004.
Epistemic modals
Authors: Vecsey Zoltán
Published: November 2013

In recent years, the standard account of epistemic modal discourse has been criticized from two directions. Expressivists and dynamic semanticists argue that simple epistemic modal sentences should be understood as non-truth-conditional. Relativists hold that the truth values of epistemic modal sentences are determined by the features of their contexts of assessment. I argue below that one can integrate the core insights of these critical stances without falling into contradiction.
One man’s norm is another’s metaphor
Authors: Sampson Geoffrey
Published: November 2013

Patrick Hanks sees linguistic approaches to word meaning as divided between two unattractive extremes. Generative theories, such as were pioneered by Katz and Fodor (1963) and pursued recently e.g. by Wierzbicka (1996), attempt to capture meanings with an apparatus of quasi-mathematical rules and universal semantic primitives which is unequal to reflecting the messy realities revealed by empirical corpus studies. On the other hand, the doctrine of linguistic creativity advanced by Sampson (1980, 2001) is unduly defeatist in denying the possibility of scientific analysis. Hanks argues that theoretical linguistics and practical lexicography should both embrace an intermediate position which distinguishes between high-frequency “norms” of usage and rare “exploitations”. This allows linguists and lexicographers to produce scientific lexical description while nevertheless acknowledging messy variability.
Turkey's humanitarian diplomacy: objectives, challenges and prospects
Authors: Davutoğlu Ahmet
Published: November 2013

Actors who endeavor to withstand the rapid stream of history need to adapt to new developments and changing environments. Turkey's foreign policy, with its regional and international dimensions, is a reflection of such a search for adaptation to the new international climate. Turkey's status in international relations has risen in recent years, thanks to its new foreign policy. To comprehend the multidimensional proactive foreign policy of Turkey, we need to consider new analytical approaches and concepts. Any analysis of Turkey's foreign policy requires thinking in novel ways, through which we can move beyond the current deadlocks and vicious circles in this area of study. One of the key explanatory principles of Turkish foreign policy - probably the most significant one in this period – is “humanitarian diplomacy”.
Social Constructionism and Dramatherapy: Creating Alternative Discourses
Authors: Milioni Daphne
Published: November 2013

This paper attempts to explore aspects of social constructionist theory and epistemology, as these relate to Dramatherapy theory, practice and research, with particular emphasis on the issue of interpretation as it arises in these areas.
Acceptability of a Computerized Brief Intervention for Alcohol among Abstinent but At-Risk Pregnant Women
Authors: Pollick Sarah A. , Beatty Jessica R. , Sokol Robert J. , Strickler Ronald C. , Chang Grace , Svikis Dace S. , Tzilos Golfo K. , Ondersma Steven J.
Published: November 2013

Background

Limitations in time and training have hindered widespread implementation of alcohol-based interventions in prenatal clinics. Also, despite the possibility of underreporting or relapse, many at-risk women report that they quit drinking after pregnancy confirmation so that interventions focusing on current drinking may seem unnecessary. The Computerized Brief Intervention for Alcohol Use in Pregnancy (C-BIAP) was designed to (a) be implemented via a handheld device in prenatal clinics, and (b) use a modified brief intervention strategy with women who screen at-risk but report no current drinking.

Methods

The authors administered the C-BIAP to 18 T-ACE (Tolerance, Annoyance, Cut Down, and Eye Opener)-positive pregnant African American women who provided quantitative and qualitative feedback.

Results

The C-BIAP received high ratings of acceptability; qualitative feedback was also positive overall and suggested good acceptance of abstinence themes.

Conclusions

Technology may be a feasible and acceptable method for brief intervention delivery with pregnant women who do not report current drinking.
Sequence alignment visualization in HTML5 without Java
Authors: Gille Christoph , Birgit Weyand , Gille Andreas
Published: November 2013

Motivation: Java has been extensively used for the visualization of biological data in the web. However, the Java runtime environment is an additional layer of software with an own set of technical problems and security risks. HTML in its new version 5 provides features that for some tasks may render Java unnecessary.

Results: Alignment-To-HTML is the first HTML-based interactive visualization for annotated multiple sequence alignments. The server side script interpreter can perform all tasks like (i) sequence retrieval, (ii) alignment computation, (iii) rendering, (iv) identification of a homologous structural models and (v) communication with BioDAS-servers. The rendered alignment can be included in web pages and is displayed in all browsers on all platforms including touch screen tablets. The functionality of the user interface is similar to legacy Java applets and includes color schemes, highlighting of conserved and variable alignment positions, row reordering by drag and drop, interlinked 3D visualization and sequence groups. Novel features are (i) support for multiple overlapping residue annotations, such as chemical modifications, single nucleotide polymorphisms and mutations, (ii) mechanisms to quickly hide residue annotations, (iii) export to MS-Word and (iv) sequence icons.

Conclusion: Alignment-To-HTML, the first interactive alignment visualization that runs in web browsers without additional software, confirms that to some extend HTML5 is already sufficient to display complex biological data. The low speed at which programs are executed in browsers is still the main obstacle. Nevertheless, we envision an increased use of HTML and JavaScript for interactive biological software.

Availability and implementation: Under GPL at: http://www.bioinformatics.org/strap/toHTML/.

Contact:  christoph.gille@charite.de
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
Authors: May Ali , Pool René , van Dijk Erik , Bijlard Jochem , Abeln Sanne , Heringa Jaap , Feenstra K. Anton
Published: November 2013

Motivation: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein–protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure.

Results: We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR–pMHC complex and the MP1–p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein–protein interaction strength.

Availability and implementation: The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

Contact: k.a.feenstra@vu.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data
Authors: Kovacheva Violeta N. , Khan Adnan M. , Khan Michael , Epstein David B. A. , Rajpoot Nasir M.
Published: November 2013

Motivation: New bioimaging techniques have recently been proposed to visualize the colocation or interaction of several proteins within individual cells, displaying the heterogeneity of neighbouring cells within the same tissue specimen. Such techniques could hold the key to understanding complex biological systems such as the protein interactions involved in cancer. However, there is a need for new algorithmic approaches that analyze the large amounts of multi-tag bioimage data from cancerous and normal tissue specimens to begin to infer protein networks and unravel the cellular heterogeneity at a molecular level.

Results: The proposed approach analyzes cell phenotypes in normal and cancerous colon tissue imaged using the robotically controlled Toponome Imaging System microscope. It involves segmenting the 4',6-diamidino-2-phenylindole-labelled image into cells and determining the cell phenotypes according to their protein–protein dependence profile. These were analyzed using two new measures, Difference in Sums of Weighted cO-dependence/Anti-co-dependence profiles (DiSWOP and DiSWAP) for overall co-expression and anti-co-expression, respectively. These novel quantities were extracted using 11 Toponome Imaging System image stacks from either cancerous or normal human colorectal specimens. This approach enables one to easily identify protein pairs that have significantly higher/lower co-expression levels in cancerous tissue samples when compared with normal colon tissue.

Availability and implementation:  http://www2.warwick.ac.uk/fac/sci/dcs/research/combi/research/bic/diswop.

Contact:  v.n.kovacheva@warwick.ac.uk or Nasir.Rajpoot@ieee.org

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Protein-driven inference of miRNA–disease associations
Authors: Mørk Søren , Pletscher-Frankild Sune , Palleja Caro Albert , Gorodkin Jan , Jensen Lars Juhl
Published: November 2013

Motivation: MicroRNAs (miRNAs) are a highly abundant class of non-coding RNA genes involved in cellular regulation and thus also diseases. Despite miRNAs being important disease factors, miRNA–disease associations remain low in number and of variable reliability. Furthermore, existing databases and prediction methods do not explicitly facilitate forming hypotheses about the possible molecular causes of the association, thereby making the path to experimental follow-up longer.

Results: Here we present miRPD in which miRNA–Protein–Disease associations are explicitly inferred. Besides linking miRNAs to diseases, it directly suggests the underlying proteins involved, which can be used to form hypotheses that can be experimentally tested. The inference of miRNAs and diseases is made by coupling known and predicted miRNA–protein associations with protein–disease associations text mined from the literature. We present scoring schemes that allow us to rank miRNA–disease associations inferred from both curated and predicted miRNA targets by reliability and thereby to create high- and medium-confidence sets of associations. Analyzing these, we find statistically significant enrichment for proteins involved in pathways related to cancer and type I diabetes mellitus, suggesting either a literature bias or a genuine biological trend. We show by example how the associations can be used to extract proteins for disease hypothesis.

Availability and implementation: All datasets, software and a searchable Web site are available at http://mirpd.jensenlab.org.

Contact:  lars.juhl.jensen@cpr.ku.dk or gorodkin@rth.dk
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program
Authors: Ghahremanpour Mohammad Mehdi , Arab Seyed Shahriar , Aghazadeh Saman Biook , Zhang Jin , van der Spoel David
Published: November 2013

Motivation: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule. Moreover, the lipid composition and their distribution are functionally important. As a result, there is a necessity to prepare more realistic lipid membranes containing different types of lipids at physiological concentrations.

Results: To automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields, we provided MemBuilder as a web-based graphical user interface.

Availability and implementation: MemBuilder is a free web server available from www.membuilder.org.

Contact:  sh.arab@modares.ac.ir
In silico site of metabolism prediction for human UGT-catalyzed reactions
Authors: Peng Jianlong , Lu Jing , Shen Qiancheng , Zheng Mingyue , Luo Xiaomin , Zhu Weiliang , Jiang Hualiang , Chen Kaixian
Published: November 2013

Motivation: The human uridine diphosphate-glucuronosyltransferase enzyme family catalyzes the glucuronidation of the glycosyl group of a nucleotide sugar to an acceptor compound (substrate), which is the most common conjugation pathway that serves to protect the organism from the potential toxicity of xenobiotics. Moreover, it could affect the pharmacological profile of a drug. Therefore, it is important to identify the metabolically labile sites for glucuronidation.

Results: In the present study, we developed four in silico models to predict sites of glucuronidation, for four major sites of metabolism functional groups, i.e. aliphatic hydroxyl, aromatic hydroxyl, carboxylic acid or amino nitrogen, respectively. According to the mechanism of glucuronidation, a series of ‘local’ and ‘global’ molecular descriptors characterizing the atomic reactivity, bonding strength and physical–chemical properties were calculated and selected with a genetic algorithm-based feature selection approach. The constructed support vector machine classification models show good prediction performance, with the balanced accuracy ranging from 0.88 to 0.96 on test set. For further validation, our models can successfully identify 84% of experimentally observed sites of metabolisms for an external test set containing 54 molecules.

Availability and implementation: The software somugt based on our models is available at www.dddc.ac.cn/adme/jlpeng/somugt_win32.zip.

Contact: xmluo@simm.ac.cn or myzheng@mail.shcnc.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
The impact of freeze-out on collapsing molecular clouds
Authors: Hocuk S. , Cazaux S. , Spaans M.
Published: November 2013

Atoms and molecules, and in particular CO, are important coolants during the evolution of interstellar star-forming gas clouds. The presence of dust grains, which allow many chemical reactions to occur on their surfaces, strongly impacts the chemical composition of a cloud. At low temperatures, dust grains can lock up species from the gas phase which freeze out and form ices. In this sense, dust can deplete important coolants. Our aim is to understand the effects of freeze-out on the thermal balance and the evolution of a gravitationally bound molecular cloud. For this purpose, we perform 3D hydrodynamical simulations with the adaptive mesh code flash. We simulate a gravitationally unstable cloud under two different conditions, with and without grain surface chemistry. We let the cloud evolve until one free-fall time is reached and track the thermal evolution and the abundances of species during this time. We see that at a number density of 104 cm−3 most of the CO molecules are frozen on dust grains in the run with grain surface chemistry, thereby depriving the most important coolant. As a consequence, we find that the temperature of the gas rises up to ∼25 K. The temperature drops once again due to gas–grain collisional cooling when the density reaches a few × 104 cm−3. We conclude that grain surface chemistry not only affects the chemical abundances in the gas phase, but also leaves a distinct imprint in the thermal evolution that impacts the fragmentation of a star-forming cloud. As a final step, we present the equation of state of a collapsing molecular cloud that has grain surface chemistry included.
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems
Authors: Fonfara Ines , Le Rhun Anaïs , Chylinski Krzysztof , Makarova Kira S. , Lécrivain Anne-Laure , Bzdrenga Janek , Koonin Eugene V. , Charpentier Emmanuelle
Published: November 2013

The CRISPR-Cas-derived RNA-guided Cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. The DNA-targeting mechanism of the type II CRISPR-Cas system involves maturation of tracrRNA:crRNA duplex (dual-RNA), which directs Cas9 to cleave invading DNA in a sequence-specific manner, dependent on the presence of a Protospacer Adjacent Motif (PAM) on the target. We show that evolution of dual-RNA and Cas9 in bacteria produced remarkable sequence diversity. We selected eight representatives of phylogenetically defined type II CRISPR-Cas groups to analyze possible coevolution of Cas9 and dual-RNA. We demonstrate that these two components are interchangeable only between closely related type II systems when the PAM sequence is adjusted to the investigated Cas9 protein. Comparison of the taxonomy of bacterial species that harbor type II CRISPR-Cas systems with the Cas9 phylogeny corroborates horizontal transfer of the CRISPR-Cas loci. The reported collection of dual-RNA:Cas9 with associated PAMs expands the possibilities for multiplex genome editing and could provide means to improve the specificity of the RNA-programmable Cas9 tool.
Nucleotide selection by the Y-family DNA polymerase Dpo4 involves template translocation and misalignment
Authors: Brenlla Alfonso , Markiewicz Radoslaw P. , Rueda David , Romano Louis J.
Published: November 2013

Y-family DNA polymerases play a crucial role in translesion DNA synthesis. Here, we have characterized the binding kinetics and conformational dynamics of the Y-family polymerase Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) using single-molecule fluorescence. We find that in the absence of dNTPs, the binary complex shuttles between two different conformations within ∼1 s. These data are consistent with prior crystal structures in which the nucleotide binding site is either occupied by the terminal base pair (preinsertion conformation) or empty following Dpo4 translocation by 1 base pair (insertion conformation). Most interestingly, on dNTP binding, only the insertion conformation is observed and the correct dNTP stabilizes this complex compared with the binary complex, whereas incorrect dNTPs destabilize it. However, if the n+1 template base is complementary to the incoming dNTP, a structure consistent with a misaligned template conformation is observed, in which the template base at the n position loops out. This structure provides evidence for a Dpo4 mutagenesis pathway involving a transient misalignment mechanism.