bluuebunny/crossref_metadata_2025 huggingface dataset:
The numerical detection of the Arnold web and its use for long-term diffusion studies in conservative and weakly dissipative systems
Authors: Guzzo Massimiliano , Lega Elena
Published: June 2013

The celebrated KAM and Nekhoroshev theorems provide essential informations about the long term dynamics of quasi–integrable Hamiltonian systems. In particular, long–term instability of the action variables can be observed only in the so–called Arnold web, which is the complement in the phase–space of all KAM invariant tori, and only on the very long times which depend exponentially on an inverse power of the perturbation parameter. Though the structure of the Arnold's web was clearly explained already on Arnold's 1963 article, its numerical detection with a precision sufficient to reveal exponentially slow diffusion of the actions through the web itself has become possible only in the last decade with the extensive computation of dynamical indicators. In this paper, we first review the detection method that allowed us to compute the Arnold web, and then we discuss its use to study the long–term diffusion through the web itself. We also show that the Arnold web of a quasi–integrable Hamiltonian system is useful to track the diffusion of orbits of weakly dissipative perturbations of the same Hamiltonian system.
High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects
Authors: Avila Kerstin , Hof Björn
Published: June 2013

A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101–106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities.
Fluorescence correlation spectroscopy of repulsive systems: Theory, simulation, and experiment
Authors: Feng Ligang , Yang Jingfa , Zhao Jiang , Wang Dapeng , Koynov Kaloian , Butt Hans-Jürgen
Published: June 2013

The theoretical basis of fluorescence correlation spectroscopy (FCS) for repulsive systems, such as charged colloids or macromolecules, has been further expanded and developed. It is established that the collective correlation function can no longer be fitted using the theoretical model of non-interacting systems. Also, it is discovered that the collective correlation function can be divided into two parts: a self-part and a distinct-part, named as the self-correlation and cross-correlation function, respectively. The former indicates the self-diffusion of objects, while the latter describes mutual interactions. Dual-color fluorescence cross-correlation spectroscopy provides the direct measurements of the two parts. The particle concentration and mean squared displacement of single particles can be deduced from the self-correlation function, while the correlation volume between particles can be approximated from the cross-correlation function. In the case of charged colloids, the Debye length of the solution and particle surface charge number can be fitted from the cross-correlation function. These theoretical results are successfully proven using Brownian dynamics simulations and preliminary FCS experiments for model charged colloidal systems.
Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose
Authors: Markutsya Sergiy , Devarajan Ajitha , Baluyut John Y. , Windus Theresa L. , Gordon Mark S. , Lamm Monica H.
Published: June 2013

A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-Iα microfiber are considered. Using the force matching method, effective coarse-grained forces are derived from all-atom trajectories. Performance of the coarse-grained models is evaluated by comparing the intrachain radial distribution functions with those obtained using the all-atom reference data. The all-atom simulation reveals a double peak in the radial distribution function for sites within each glucose residue that arises from the distinct conformations sampled by the primary alcohol group in the glucose residues. The three-site and four-site coarse-grained models have sufficient degrees of freedom to predict this double peak while the one-site and two-site models do not. This is the first time that coarse-grained models have been shown to reproduce such subtle, yet important, molecular features in a polysaccharide chain. The relative orientations between glucose residues along the polysaccharide chain are evaluated and it is found that the four-site coarse-grained model is best at reproducing the glucose-glucose conformations observed in the all-atom simulation. The success of the four-site coarse-grained model underscores the importance of decoupling the pyranose ring from the oxygen atom in the glycosidic bond when developing all-atom to coarse-grained mapping schemes for polysaccharides.
Diffusion of hydrogen fluoride in solid parahydrogen
Authors: Ooe Hiroki , Miyamoto Yuki , Kuma Susumu , Kawaguchi Kentarou , Nakajima Kyo , Nakano Itsuo , Sasao Noboru , Tang Jian , Taniguchi Takashi , Yoshimura Motohiko
Published: June 2013

We studied diffusion of hydrogen fluoride (HF) in solid parahydrogen (pH2) around 4 K. Diffusion rates were determined from time dependence of FT-IR spectra of HF monomers. The absorption of HF monomers shows temporal decay due to dimerization reaction via diffusion. It was found that the rates are affected by the sample temperature, the initial HF concentration, and annealing of samples. The observed non-Arrhenius-type temperature dependence suggests that the diffusion is dominated by a quantum tunneling process, that is, “quantum diffusion.” Deceleration of the diffusion in condensed samples and acceleration in annealed samples were also observed. These results can be attributed to the fact that lower periodicity of samples due to impurities or defects suppresses the quantum tunneling. It seems to be difficult to explain the observed dependences by three possible diffusion mechanisms, exchange of chemical bonds, direct cyclic exchange, and exchange with mobile vacancy. Therefore, we propose a hypothetical mechanism by exchange of vacancies originating from quantum effect.
Witten Laplacian method for generalized models of Kac type
Authors: Lo Assane
Published: June 2013

We first study the exponential decay of correlations for classical models of Kac type. Using recent results [J. Jon, “On spectral properties of Witten-Laplacians, their range of projections and Brascamp-Lieb inequality,” Integral Equ. Oper. Theory 36(3), 288–324 (2000)10.1007/BF01213926] about the Witten Laplacians, we improve the bounds obtained [A. Lo, “Witten Laplacian methods for the decay of correlations,” J. Stat. Phys. 132(2), 355–396 (2008)10.1007/s10955-008-9547-6] to justify the conjecture that the critical point in the (d+1)-dimensional Kac model is given by βc = 1/4d. We also provide a new approach for proving the exponential decay of the usual truncated correlations which is more direct than the existing ones in the sense that it does not use any cluster type expansions.
Random matrix models, double-time Painlevé equations, and wireless relaying
Authors: Chen Yang , Haq Nazmus S. , McKay Matthew R.
Published: June 2013

This paper gives an in-depth study of a multiple-antenna wireless communication scenario in which a weak signal received at an intermediate relay station is amplified and then forwarded to the final destination. The key quantity determining system performance is the statistical properties of the signal-to-noise ratio (SNR) γ at the destination. Under certain assumptions on the encoding structure, recent work has characterized the SNR distribution through its moment generating function, in terms of a certain Hankel determinant generated via a deformed Laguerre weight. Here, we employ two different methods to describe the Hankel determinant. First, we make use of ladder operators satisfied by orthogonal polynomials to give an exact characterization in terms of a “double-time” Painlevé differential equation, which reduces to Painlevé V under certain limits. Second, we employ Dyson's Coulomb fluid method to derive a closed form approximation for the Hankel determinant. The two characterizations are used to derive closed-form expressions for the cumulants of γ, and to compute performance quantities of engineering interest.
Bounds on the critical line via transfer matrix methods for an Ising model coupled to causal dynamical triangulations
Authors: Hernandez J. C. , Suhov Y. , Yambartsev A. , Zohren S.
Published: June 2013

We introduce a transfer matrix formalism for the (annealed) Ising model coupled to two-dimensional causal dynamical triangulations. Using the Krein-Rutman theory of positivity preserving operators we study several properties of the emerging transfer matrix. In particular, we determine regions in the quadrant of parameters β, μ > 0 where the infinite-volume free energy converges, yielding results on the convergence and asymptotic properties of the partition function and the Gibbs measure.
Viscous liquid films on a porous vertical cylinder: Dynamics and stability
Authors: Ding Zijing , Wong Teck Neng , Liu Rong , Liu Qiusheng
Published: June 2013

In this paper, liquid films flowing down a porous vertical cylinder were investigated by an integral boundary layer model. Linear stability and nonlinear evolution were studied. Linear stability results of the integral boundary layer model were in good agreement with the linearized Navier-Stokes equations which indicated that the permeability of the porous medium enhanced the instability of the flow system. The growth rate and cut-off wave number increased with increasing the permeability and the Reynolds number. Linear stability analysis showed that the system was more unstable for a larger Reynolds number Re. Nonlinear studies showed that, for a very small Re, the film evolved with time while a saturated state was not observed. In addition, it was observed that the film ruptured when the permeability parameter β > 0, and the rupture time decreased with increasing β. However, for a moderate Reynolds number, a small finite harmonic disturbance evolved to a saturated traveling wave. Further investigation was conducted on the droplet-like wave solution. Results showed that the wave speed increased as the permeability parameter increased.
A simplified 461-nm laser system using blue laser diodes and a hollow cathode lamp for laser cooling of Sr
Authors: Shimada Yosuke , Chida Yuko , Ohtsubo Nozomi , Aoki Takatoshi , Takeuchi Makoto , Kuga Takahiro , Torii Yoshio
Published: June 2013

We develop a simplified light source at 461 nm for laser cooling of Sr without frequency-doubling crystals but with blue laser diodes. An anti-reflection coated blue laser diode in an external cavity (Littrow) configuration provides an output power of 40 mW at 461 nm. Another blue laser diode is used to amplify the laser power up to 110 mW by injection locking. For frequency stabilization, we demonstrate modulation-free polarization spectroscopy of Sr in a hollow cathode lamp. The simplification of the laser system achieved in this work is of great importance for the construction of transportable optical lattice clocks.
Nanoscale anisotropic Nd-Fe-B particles with high coercivity prepared by attrition milling
Authors: Wehrenberg C. , Daniil M. , Willard M. , Zande B. , Sankar S. , Thadhani N.
Published: June 2013

Nanoscale Nd-Fe-B particles were fabricated with room temperature coercivity of 4.9 kOe by attrition (stirred media) milling. For longer milling times, more than 80% of the particles were less than 500 nm diameter, and 50–200 nm particles can be selected by a decanting process. Anisotropy was demonstrated by field alignment, as shown by creation of strong texture in x-ray diffraction (XRD) patterns. Limited peak broadening in XRD patterns indicates that attrition milling produces less deformation and amorphous material than high-energy milling. Compared to other magnetic nanoparticles, the higher coercivity is attributed to limited plastic deformation and larger sized particles.
Validity of rigid band approximation of PbTe thermoelectric materials
Authors: Takagiwa Yoshiki , Pei Yanzhong , Pomrehn Gregory , Jeffrey Snyder G.
Published: June 2013

The tuning of carrier concentration through chemical doping is very important for the optimization of thermoelectric materials. Traditionally, a rigid band model is used to understand and guide doping in such semiconductors, but it is not clear whether such an approximation is valid. This letter focuses on the changes in the electronic density of states (DOS) near the valence band maximum for different p-type dopants (Na, K, Tl, or vacancy on Pb site) maintaining the high symmetry of the NaCl structure. Na- and K-doped, and vacancy-introduced PbTe show a clear rigid-band like change in DOS unlike that concluded from supercell based calculations.
Carrier-tunable magnetism of graphene with single-atom vacancy
Authors: Lei Shulai , Li Bin , Kan Erjun , Huang Jing , Li Qunxiang , Yang Jinlong
Published: June 2013

We explore the carrier doping effect on magnetic properties of defective graphene with single-atom vacancy by performing spin-polarized density functional theory calculations. Theoretical results show that both hole and electron dopings can effectively modify the local magnetic moments. Besides, we also demonstrate that hole doping can greatly enhance the magnetic coupling, increasing the critical temperature of magnetism, which is absent in electron doping case. The coupling enhanced mechanism can be well understood by the different variation trends of pz-derived states around the Fermi level under hole doping. Thus, our results provide a practical way to tune the magnetism of defective graphene.
Localized ohmic contact through a passivation dielectric for solar cell rear surface design
Authors: Western Ned J. , Sung Andrew , Wenham Stuart R. , Bremner Stephen P.
Published: June 2013

We report the demonstration of a method for forming localized ohmic contact through dielectric passivation layers, via a laser doped region, with no etching prior to metal deposition. A simple bench top voltage source contacted to the gate and bulk of a test Metal-Insulator-Semiconductor device facilitates localized heating leading to ohmic contact formation. The surface passivation qualities of the dielectrics are preserved away from the contact region using this method, as hard dielectric breakdown is restricted to the laser doped region. This is a potential technique for precisely contacting rear surface of high efficiency solar cells.
Transport properties in FeSe0.5Te0.5 nanobridges
Authors: Wu C. H. , Chang W. C. , Jeng J. T. , Wang M. J. , Li Y. S. , Chang H. H. , Wu M. K.
Published: June 2013

FeSeTe nanobridges of different widths have been fabricated on MgO substrates using focused ion beams. These nanobridges exhibit the Josephson effects. The current-voltage curves of junctions with 248–564 nm wide follow the resistively and capacitatively shunted junction model. Shapiro steps under microwave radiation were clearly observed in these nanobridges. The products of the critical current and normal state resistance (IcRn) are remarkably high. The temperature dependence of IcRn product followed the Ambegaokar-Baratoff (A-B) relation. The value of energy gap of FeSeTe calculated from the A-B relation is 3.5kBTc. The nanobridge junctions have a strong potential for high frequency applications.
Effects of controllable biaxial strain on the Raman spectra of monolayer graphene prepared by chemical vapor deposition
Authors: Jie Wenjing , Yu Hui Yeung , Zhang Yang , Ping Lau Shu , Hao Jianhua
Published: June 2013

Controllable biaxial strain is delivered to monolayer graphene prepared by chemical vapor deposition via applying an electric field to the underlying piezoelectric [Pb(Mg1/3Nb2/3)O3]0.7-[PbTiO3]0.3 substrate. The effects of tunable strain on the Raman spectra of graphene are investigated in reversible and real-time manners. Such strain can result in a blue shift in 2D band of graphene. The calculations based on the Grüneisen parameter identify the actual biaxial strain to graphene, leading to a continuous 2D band shift, which is detected during the retention of bias voltage. The physical mechanism behind this unique Raman behavior is discussed.
Enhanced antiferroelectric stability and electric-field-induced strain properties in rare earth-modified Pb(Zr0.63Sn0.26Ti0.11)O3 ceramics
Authors: Zhang Qingfeng , Yang Tongqing , Zhang Yangyang , Wang Jinfei , Yao Xi
Published: June 2013

Pb0.97Ln0.02(Zr0.63Sn0.26Ti0.11)O3 ceramics with large electrically induced strain were fabricated by doping the base composition with rare earth ions. The enhancement of strain was because the substitution of rare earth ions for Pb2+ could decrease the tolerance factor of the ceramics and improve the stability of antiferroelectric phase. In addition, it was found that the electrically induced strain increased as the measuring frequency decreased; this was attributed to more complete domain reversal at the low frequency. The maximum electrically induced strain of 0.66% was obtained in Pb0.97Sm0.02(Zr0.63Sn0.26Ti0.11)O3 ceramics at the frequency 1 Hz.
Alternating and direct current field effects on the structure-property relationships in Na0.5Bi0.5TiO3-x%BaTiO3 textured ceramics
Authors: Ge Wenwei , Maurya Deepam , Li Jiefang , Priya Shashank , Viehland D.
Published: June 2013

The influence of alternating (ac) and direct current (dc) fields on the structural and dielectric properties of [001]PC textured Na0.5Bi0.5TiO3-7%BaTiO3 (NBT-7%BT) ceramics has been investigated. X-ray diffraction measurements revealed that the depolarization at temperature Td in poled samples resulted from a tetragonal → pseudo-cubic transition on heating. Moderate ac drive and dc bias had opposite influences on Td: ac drive decreased the Td, whereas dc bias increased it. These investigations suggested an effective method to expand the working temperature range of NBT-x%BT textured ceramics to a high temperature.
A comparison of ZnO films deposited on indium tin oxide and soda lime glass under identical conditions
Authors: Deka Angshuman , Nanda Karuna Kar
Published: June 2013

ZnO films have been grown via a vapour phase transport (VPT) on soda lime glass (SLG) and indium-tin oxide (ITO) coated glass. ZnO film on ITO had traces of Zn and C which gives them a dark appearance while that appears yellowish-white on SLG. X-ray photoelectron spectroscopy studies confirm the traces of C in the form of C–O. The photoluminescence studies reveal a prominent green luminescence band for ZnO film on ITO.
Quantifying the relationship between temperature regulation in the ear and floret development stage in wheat (Triticum aestivum L.) under heat and drought stress
Authors: Steinmeyer Frederick T. , Lukac Martin , Reynolds Matthew P. , Jones Hannah E.
Published: June 2013

Thermal imaging is a valuable tool for the clarification of gas exchange dynamics between a plant and its environment. The presence of stomata in wheat (Triticum aestivum L.) glumes and awns offers an opportunity to assess the photosynthetic activity of ears up to and during flowering. Knowledge of the spatial and temporal thermodynamics of the wheat ear may provide insight into interactions between floret developmental stage (FDS), temperature depression (TD) and ambient environment, with potential to use these as high-throughput screening tools for breeders. A controlled environment study was conducted using six spring wheat genotypes of the elite recombinant inbred line Seri–Babax. Average ear temperature was recorded using a hand-held infrared camera and gas exchange was measured by enclosing ears in a custom-built cuvette. FDS was monitored and recorded daily throughout the study. Plants were grown in pots and exposed to a combination of two temperature and two water regimes. In the studied wheat lines, TD varied from 0.1°C to 0.6°C according to the level of stress imposed. The results indicated that TD does not occur at FDS F3, the peak of active flowering, but during the stages before pollen release and stigma maturity (F1–F2). These findings suggest that ear temperature during the early stages of anthesis, before pollen release and full extension of the stigma, are likely to be the most relevant for identifying heat stress tolerant genotypes.
Relic bilby (Macrotis lagotis) refuge burrows: assessment of potential contribution to a rangeland restoration program
Authors: Chapman Tamra F.
Published: June 2013

In harsh, resource-limited rangelands, plants and other structures, such as animal burrows, can ameliorate extreme microclimate conditions and increase resource availability for other species. The aim of this study was to determine whether relic bilby (Macrotis lagotis) refuge burrows had the potential to contribute to a rangeland restoration program by moderating microclimate and accumulating resources. During the day, the burrows maintained significantly higher relative humidity than control microsites. At night, temperature was significantly higher and humidity was significantly lower in the burrows than the control microsites. Both temperature and humidity were also significantly less variable in the burrows. There was some overlap between burrows and control microsites in soil chemistry, but burrows were significantly higher in soil moisture, pH(CaCl2), exchangeable magnesium, exchangeable potassium, mineral nitrogen, and total cation exchange capacity, and significantly lower in bio-available aluminium. Soils in burrows contained three times more mineral nitrogen, which has been previously shown to increase plant diversity and abundance in the presence of additional moisture. These results suggest the relic bilby burrows could potentially provide more suitable habitats for the establishment and productivity of other species by moderating microclimates, accumulating nutrients and soil moisture, and ameliorating the potentially detrimental effects of bio-available aluminium.
Towards a lexicogrammatical pattern in Swedish crime novels
Authors: Klös Marie-Christine
Published: June 2013

The success of Swedish crime novels has been noted and discussed at length. Much of this commentary refers to a salient characteristic atmosphere which seems to be a common feature of most if not all Scandinavian crime novels. In this paper the potential of some recurring lexicogrammatical features to construct this characteristically gloomy and sombre atmosphere is presented and discussed. It will be shown that the vague feeling of unease which is perceived while reading these fictional texts is linguistically attestable. The analysis is conducted within the framework of M.A.K. Halliday’s systemic-functional grammar (SFG) which will be applied to three contemporary Swedish crime novels by different authors. One of the main goals is to illustrate by what means the authors instantiate perceptions and extra-linguistic phenomena in their fictional worlds.
Semantic variations of the French verb voir and the discourse system in Louis-Ferdinand Céline’s Rigodon
Authors: Lorda Clara Ubaldina
Published: June 2013

Using Culioli’s Theory of Enunciative Operations and Notional Domains as its starting point, this paper presents a unified characterisation of the French verb voir and its variations. These variations are then related to its enunciative nuances. I argue that voir is used profusely by Céline in his last novel Rigodon and plays a significant role in the book’s discourse system. From the beginning of the narrative, voir appears as the core of a brilliant meta-narrative metaphor setting the tone and tying together the entire story. I conclude that, throughout the novel, different forms of this verb are either attributed to the narrator or to the main character (which are in fact both incarnations of the author himself). This strategy helps to enhance the sense of immediate presence in the narration and results in a permanent dialogue with the reader.
The dialogics of metaphor and simile in Elizabeth Bowen’s The Last September
Authors: Kind Julia
Published: June 2013

Metaphors and similes characterise Elizabeth Bowen’s writing. Despite frequent claims that this contributes to the lexical, grammatical and syntactic irregularities of her style and hence makes her writing difficult to understand, I show that her metaphors, similes and literal descriptions in a selected passage from The Last September function within conventional linguistic structures. While my analysis of metaphors and similes is conducted with reference to Bakhtin’s essay “Discourse in the Novel”, I use Martin and Rose’s model of Discourse Analysis (2007) and Steen’s study of metaphor in literature (1999) as practical tools for my analysis of the text. I discuss how ‘dialogic’ linguistic and pragmatic processes (in a Bakhtinian sense) influence the emergence of metaphorical meaning in Bowen’s novel and examine how the linguistic structures governing literal and metaphorical elements of description give rise to cognitive patterns which in turn serve to establish the novel’s theme by connecting the protagonist with her fictional setting in a meaningful way.
Words between reality and fiction
Authors: Weigand Edda
Published: June 2013

The transition from reality to fiction can be best illustrated by analysing autobiographies which claim to describe the life of the author. Essentially they are based on memories, which poses the question whether what is being remembered really happened in this way. In what respect do ‘real’ stories differ from ‘literary’ or ‘fictional’ ones? Several literary autobiographies are analysed and contrasted with popular autobiographies. Are there special literary devices by which we can recognize that a story is intended to be fictional? According to Searle there is ‘no textual property that will identify a stretch of discourse as a work of fiction’. The paper discusses Searle’s position and identifies an interesting textual difference in the way persons are introduced in fiction. Even if there is no sharp division between fiction and non-fiction, there are a few verbal and cognitive means of the game which enable us to recognize how the text is intended.
Boundary values of the Thurston pullback map
Authors: Lodge Russell
Published: June 2013

For any Thurston map with exactly four postcritical points, we present an algorithm to compute the Weil-Petersson boundary values of the corresponding Thurston pullback map. This procedure is carried out for the Thurston map

f
(
z
)
=

3

z
2

2

z
3

+
1

f(z)=\frac {3z^2}{2z^3+1}

originally studied by Buff, et al. The dynamics of this boundary map are investigated and used to solve the analogue of Hubbard’s Twisted Rabbit problem for

f
f

.
Local, cell-nonautonomous feedback regulation of myosin dynamics patterns transitions in cell behavior: a role for tension and geometry?
Authors: Saravanan Surat , Meghana C. , Narasimha Maithreyi
Published: June 2013

How robust patterns of tissue dynamics emerge from heterogeneities, stochasticities, and asynchronies in cell behavior is an outstanding question in morphogenesis. A clear understanding of this requires examining the influence of the behavior of single cells on tissue patterning. Here we develop single-cell manipulation strategies to uncover the origin of patterned cell behavior in the amnioserosa during Drosophila dorsal closure. We show that the formation and dissolution of contractile, medial actomyosin networks previously shown to underlie pulsed apical constrictions in the amnioserosa are apparently asynchronous in adjacent cells. We demonstrate for the first time that mechanical stresses and Rho1 GTPase control myosin dynamics qualitatively and quantitatively, in amplitude and direction, both cell autonomously and nonautonomously. We then demonstrate that interfering with myosin-dependent contractility in single cells also influences pulsed constrictions cell nonautonomously. Our results suggest that signals and stresses can feedback regulate the amplitude and spatial propagation of pulsed constrictions through their influence on tension and geometry. We establish the relevance of these findings to native closure by showing that cell delamination represents a locally patterned and collective transition from pulsed to unpulsed constriction that also relies on the nonautonomous feedback control of myosin dynamics.
Hsp90 cochaperones p23 and FKBP4 physically interact with hAgo2 and activate RNA interference–mediated silencing in mammalian cells
Authors: Pare Justin M. , LaPointe Paul , Hobman Tom C.
Published: June 2013

Argonaute proteins and small RNAs together form the RNA-induced silencing complex (RISC), the central effector of RNA interference (RNAi). The molecular chaperone Hsp90 is required for the critical step of loading small RNAs onto Argonaute proteins. Here we show that the Hsp90 cochaperones Cdc37, Aha1, FKBP4, and p23 are required for efficient RNAi. Whereas FKBP4 and p23 form a stable complex with hAgo2, the function of Cdc37 in RNAi appears to be indirect and may indicate that two or more Hsp90 complexes are involved. Our data also suggest that p23 and FKBP4 interact with hAgo2 before small RNA loading and that RISC loading takes place in the cytoplasm rather than in association with RNA granules. Given the requirement for p23 and FKBP4 for efficient RNAi and that these cochaperones bind to hAgo2, we predict that loading of hAgo2 is analogous to Hsp90-mediated steroid hormone receptor activation. To this end, we outline a model in which FKBP4, p23, and Aha1 cooperatively regulate the progression of hAgo2 through the chaperone cycle. Finally, we propose that hAgo2 and RNAi can serve as a robust model system for continued investigation into the Hsp90 chaperone cycle.
Pathview: an R/Bioconductor package for pathway-based data integration and visualization
Authors: Luo Weijun , Brouwer Cory
Published: June 2013

Summary: Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines.

Availability: The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/.

Contact:  luo_weijun@yahoo.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data
Authors: Beltrame Luca , Bianco Luca , Fontana Paolo , Cavalieri Duccio
Published: June 2013

Summary: Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher’s test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway expression, leading to the identification of differentially regulated pathways in a dataset of choice.

Availability and implementation: Pathway Processor 2.0 is available as a web service at http://compbiotoolbox.fmach.it/pathwayProcessor/. Sample datasets to test the functionality can be used directly from the application.

Contact:  duccio.cavalieri@fmach.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploration of conformational transition pathways from coarse-grained simulations
Authors: Sfriso Pedro , Hospital Adam , Emperador Agustí , Orozco Modesto
Published: June 2013

Motivation: A new algorithm to trace conformational transitions in proteins is presented. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell Demon molecular dynamics and essential dynamics. The method, which shows an unprecedented computational efficiency, is able to trace a wide range of known experimental transitions. Contrary to simpler methods our strategy does not introduce distortions in the chemical structure of the protein and is able to reproduce well complex non-linear conformational transitions. The method, called GOdMD, can easily introduce additional restraints to the transition (presence of ligand, known intermediate, known maintained contacts, …) and is freely distributed to the community through the Spanish National Bioinformatics Institute (http://mmb.irbbarcelona.org/GOdMD).

Availability: Freely available on the web at http://mmb.irbbarcelona.org/GOdMD.

Contact:  modesto.orozco@irbbarcelona.org or modesto@mmb.pcb.ub.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identification of the YfgF MASE1 domain as a modulator of bacterial responses to aspartate
Authors: Lacey Melissa , Agasing Agnieshka , Lowry Rebecca , Green Jeffrey
Published: June 2013

Complex 3′-5′-cyclic diguanylic acid (c-di-GMP) responsive regulatory networks that are modulated by the action of multiple diguanylate cyclases (DGC; GGDEF domain proteins) and phosphodiesterases (PDE; EAL domain proteins) have evolved in many bacteria. YfgF proteins possess a membrane-anchoring domain (MASE1), a catalytically inactive GGDEF domain and a catalytically active EAL domain. Here, sustained expression of the
Salmonella enterica
spp. Enterica ser. Enteritidis YfgF protein is shown to mediate inhibition of the formation of the aspartate chemotactic ring on motility agar under aerobic conditions. This phenomenon was c-di-GMP-independent because it occurred in a
Salmonella
strain that lacked the ability to synthesize c-di-GMP and also when PDE activity was abolished by site-directed mutagenesis of the EAL domain. YfgF-mediated inhibition of aspartate chemotactic ring formation was impaired in the altered redox environment generated by exogenous
p-
benzoquinone. This ability of YfgF to inhibit the response to aspartate required a motif,
213
Lys-Lys-Glu
215
, in the predicted cytoplasmic loop between trans-membrane regions 5 and 6 of the MASE1 domain. Thus, for the first time the function of a MASE1 domain as a redox-responsive regulator of bacterial responses to aspartate has been shown.
Molecular genotyping of Acinetobacter spp. isolated in Arizona, USA, using multilocus PCR and mass spectrometry
Authors: Sarovich Derek S. , Colman Rebecca E. , Price Erin P. , Massire Christian , Von Schulze Alex T. , Waddell Victor , Anderson Shoana M. , Ecker David J. , Liguori Andrew P. , Engelthaler David M. , Sampath Rangarajan , Keim Paul , Eshoo Mark W. , Wagner David M.
Published: June 2013

Acinetobacter spp. are a diverse group of Gram-negative bacteria frequently implicated in nosocomial infections. Genotypic methods have been instrumental in studying Acinetobacter, but few offer high resolution, rapid turnaround time, technical ease and high inter-laboratory reproducibility, which has hampered understanding of disease incidence, transmission patterns and diversity within this genus. Here, we further evaluated multilocus PCR electrospray ionization/mass spectrometry (PCR/ESI-MS), a method that is simple and robust, and provides both species characterization and strain-level resolution of Acinetobacter spp. on a single platform. We examined 125 Acinetobacter isolates from 21 hospitals, laboratories and medical centres spanning four counties in Arizona, USA, using PCR/ESI-MS. We compared PCR/ESI-MS with an in-house amplified fragment length polymorphism (AFLP) genotyping scheme. PCR/ESI-MS demonstrated that Acinetobacter spp. from Arizonan hospitals had similar species and strain distributions to other US civilian hospitals. Furthermore, we showed that the PCR/ESI-MS and AFLP genotypes were highly congruent, with the former having the advantages of robust inter-laboratory reproducibility, rapid turnaround time and simple experimental set-up and data analysis. PCR/ESI-MS is an effective and high-throughput platform for strain typing of Acinetobacter baumannii and for identification of other Acinetobacter spp., including the emerging nosocomial pathogens Acinetobacter pittii and Acinetobacter nosocomialis.
Extended-spectrum β-lactamases in Enterobacteriaceae isolated in Brazil carry distinct types of plasmid-mediated quinolone resistance genes
Authors: Viana André L. M. , Cayô Rodrigo , Avelino Cassia C. , Gales Ana C. , Franco Marília C. , Minarini Luciene A. R.
Published: June 2013

One hundred and six nalidixic acid-resistant Enterobacteriaceae isolates from two Brazilian hospitals isolated from June to October 2010 were evaluated to characterize the co-existence of plasmid-mediated quinolone resistant (PMQR) and extended-spectrum β-lactamase (ESBL) determinants. The qnr genetic environment was determined by PCR and sequencing. Conjugation and hybridization experiments determined whether qnr-carrying plasmids were self-transferable. The aac(6′)-Ib-cr and qepA genes were also screened. Thirteen qnr-like genes (12.3 %) were identified, with qnrB1 the most common, followed by qnrS1, qnrB2 and qnrB19. No qnrA, qnrC, qnrD or qepA determinant was detected. All qnr-positive strains possessed chromosomal substitutions in gyrase- and topoisomerase-encoding genes and four harboured a aac(6′)-Ib-cr gene. The co-production of bla
CTX-M was observed in ten qnr-positive strains. These results indicate the dissemination of PMQR genes shown in clinical isolates from Brazil, and their co-existence with ESBL genes emphasizes the complexity of plasmid-mediated resistance determinants among Enterobacteriaceae.
Genetic characteristics of bla
NDM-1-positive plasmid in Citrobacter
freundii isolate separated from a clinical infectious patient
Authors: Du Xiao-Xing , Wang Jian-Feng , Fu Ying , Zhao Feng , Chen Yan , Wang Hai-Ping , Yu Yun-Song
Published: June 2013

This study reports an infectious case involving an NDM-1-producing Citrobacter
freundii and further explored the potential threat of the bla
NDM-1 gene by analysing the characteristics of the NDM-1-encoding plasmid sequence. A bla
NDM-1-positive C. freundii with high resistance to carbapenems was separated from a clinical patient suffering from a urinary tract infection. S1 nuclease-based plasmid analysis followed by Southern blot hybridization, a conjugation experiment and electrotransformation confirmed that the bla
NDM-1 gene was located on a plasmid. High-throughput sequencing of the bla
NDM-1-postive plasmid (pCFNDM-CN) showed that it was a 54 kb IncX-type plasmid and contained a backbone region and a variable region with two β-lactamase genes (bla
NDM-1 and bla
SHV-12). The NDM-1 composite transposon in the variable region was surrounded by IS26 and IS5-truncated ISAba125, and shared a high sequence similarity to the bla
NDM-1 surrounding structure in Acinetobacter spp. Our research suggested that the NDM-1 composite transposon might play an essential role in mobilization of the bla
NDM-1 gene from Acinetobacter spp. to Enterobacteriaceae.
Detection of clonal KPC-2-producing Klebsiella pneumoniae ST258 in Korea during nationwide surveillance in 2011
Authors: Yoo Jung Sik , Kim Hye Mee , Yoo Jae Il , Yang Ji Woo , Kim Hwa Su , Chung Gyung Tae , Lee Yeong Seon
Published: June 2013

This study analysed the characteristics and genetic similarity of recent Klebsiella pneumoniae carbapenemase (KPC-2)-producing Klebsiella pneumoniae isolates from Korea. Recent laboratory surveillance detected an increase in carbapenemase-producing Enterobacteriaceae in Korea. A total of 6 KPC-2-producing K. pneumoniae were identified from 277 Enterobacteriaceae clinical isolates. All were sequence type (ST) 258 and they had the same pulsotype. They had high MICs for carbapenems and multi-drug resistance. TEM-1, SHV-11 and OXA type β-lactamases were detected in all isolates, whereas CTX-M type β-lactamases and plasmid-mediated AmpC β-lactamase (PABL) were not present. A conjugation experiment failed, but bla
KPC-2-harbouring plasmids from the six isolates were used to transform Escherichia coli DH5-α by electroporation. Each of the transformants harboured a bla
KPC-2-positive approximately 95 kb plasmid, which was typed in the IncFII incompatibility group and co-harboured TEM-1 and OXA-9 β-lactamases. They shared the same restriction profile. This study confirms the emergence of clonal ST258 KPC-2-producing K. pneumoniae in some regions of Korea.
The cytomegalovirus egress proteins pUL50 and pUL53 are translocated to the nuclear envelope through two distinct modes of nuclear import
Authors: Schmeiser Cathrin , Borst Eva , Sticht Heinrich , Marschall Manfred , Milbradt Jens
Published: June 2013

The nucleocytoplasmic export of cytomegaloviral capsids is regulated by formation of a multi-component nuclear egress complex (NEC), essentially based on viral proteins pUL50 and pUL53. In this study, the generation of recombinant human cytomegaloviruses, expressing tagged versions of pUL50 and pUL53, enabled the investigation of NEC formation in infected primary fibroblasts. For these recombinant viruses, a wild-type-like mode of pUL50–pUL53 interaction and recruitment of both proteins to the nuclear envelope could be demonstrated. Importantly, pUL50 was translocated from an initial cytoplasmic distribution to the nuclear rim, whereas pUL53 accumulated in the nucleus before attaining overall rim colocalization with pUL50. Specified experimental settings illustrated that pUL50 and pUL53 were subject to different pathways of intracellular trafficking. Importantly, a novel nuclear localization signal (NLS) could be identified and functionally verified for pUL53 (amino acids 18–27), whereas no NLS was present in pUL50. Analysis of amino acid replacement mutants further illustrated the differential modes of nuclear import of the two essential viral egress proteins. Taken together, our findings suggest a combination of classical nuclear import (pUL53) and interaction-mediated recruitment (pUL50) as the driving forces for core NEC formation and viral nuclear egress.
Processing of projections containing phase contrast in laboratory micro-computerized tomography imaging
Authors: Zápražný Zdenko , Korytár Dušan , Mikulík Petr , Áč Vladimír
Published: June 2013

Free-space-propagation-based imaging belongs to several techniques for achieving phase contrast in the hard X-ray range. The basic precondition is to use an X-ray beam with a high degree of coherence. Although the best sources of coherent X-rays are synchrotrons, spatially coherent X-rays emitted from a sufficiently small spot of laboratory microfocus or sub-microfocus sources allow the transfer of some of the modern imaging techniques from synchrotrons to laboratories. Spatially coherent X-rays traverse a sample leading to a phase shift. Beam deflection induced by the local change of refractive index may be expressed as a dark–bright contrast on the edges of the object in an X-ray projection. This phenomenon of edge enhancement leads to an increase in spatial resolution of X-ray projections but may also lead to unpleasant artefacts in computerized tomography unless phase and absorption contributions are separated. The possibilities of processing X-ray images of lightweight objects containing phase contrast using phase-retrieval methods in laboratory conditions are tested and the results obtained are presented. For this purpose, simulated and recorded X-ray projections taken from a laboratory imaging system with a microfocus X-ray source and a high-resolution CCD camera were processed and a qualitative comparison of results was made.
Nonlinear continuum growth model of multiscale reliefs as applied to rigorous analysis of multilayer short-wave scattering intensity. I. Gratings
Authors: Goray Leonid , Lubov Maxim
Published: June 2013

It is shown that taking into proper account certain terms in the nonlinear continuum equation of thin-film growth makes it applicable to the simulation of the surface of multilayer gratings with large boundary profile heights and/or gradient jumps. The proposed model describes smoothing and displacement of Mo/Si and Al/Zr boundaries of gratings grown on Si substrates with a blazed groove profile by magnetron sputtering and ion-beam deposition. Computer simulation of the growth of multilayer Mo/Si and Al/Zr gratings has been conducted. Absolute diffraction efficiencies of Mo/Si and Al/Zr gratings in the extreme UV range have been found within the framework of boundary integral equations applied to the calculated boundary profiles. It has been demonstrated that the integrated approach to the calculation of boundary profiles and of the intensity of short-wave scattering by multilayer gratings developed here opens up a way to perform studies comparable in accuracy to measurements with synchrotron radiation, at least for known materials and growth techniques.