bluuebunny/crossref_metadata_2025 huggingface dataset:
The classical equation of state of fully ionized plasmas
Authors: Eisa Dalia Ahmed
Published: April 2011

The aim of this paper is to calculate the analytical form of the equation of state until the third virial coefficient of a classical system interacting via an effective potential of fully Ionized Plasmas. The excess osmotic pressure is represented in the forms of a convergent series expansions in terms of the plasma Parameter $\mu _{ab} = {{{e_a e_b \chi } \over {DKT}}}$μab=eaebχDKT, where χ2 is the square of the inverse Debye radius. We consider only the thermal equilibrium plasma.
Magnetic properties of the Co/Alq3 interface
Authors: Venkatesan M. , Tokuc H. , Burke Franklyn , Szulczewski G. , Coey J. M. D.
Published: April 2011

A method is described for measuring the magnetic integrity of ferromagnetic/organic interfaces that involves measuring the magnetic moment per unit area of bilayers with different ferromagnet thicknesses. The method is first used to determine the thickness of the oxide passivation layer on Co and Co90Fe10 (3.0 and 1.6 nm, respectively). The Alq3/Co interface is rather sharp, with roughness confined to about 3 monolayers of Co at the interface. The Co/Alq3 interface seems to be much rougher, with a dead layer that is several nanometers thick, However, this layer can be eliminated by capping the Alq3 layer with Al, so the dead layer is attributed to oxidation of the cobalt surface through the organic. The interface sharpness is improved when a 1 nm layer of LiF is inserted between Co and Alq3.
Elementary cuspoid catastrophes as the models of phenomenological equations of state
Authors: Tatarenko Alexander V.
Published: April 2011

The suggested earlier approach based on the equation of state expressed as the equilibrium surface of cuspoid catastrophes has been expanded and developed. The family of equations of state with arbitrary critical point degeneracy has been obtained. In other words, the order of a partial derivative of pressure with respect to volume at the critical point has become an arbitrary assigned variable. This, in turn, has led to more realistic, as compared to the classic case, behaviour of fluid in the immediate vicinity of the critical point. The critical exponents became functions of the degree of critical point degeneracy. By suitable selection of the degree of degeneracy it is possible to obtain the preset values of critical exponents. A simple nonanalytic equation of state has been obtained. This equation allows us to describe some non-classical phenomena in the vicinity of critical point liquid-gas without using scaling. The same equation holds in the ideal gas area without using crossover. One more implication arising from the suggested approach is a singularity in the equations of state – endpoint of gas-liquid equilibrium at low pressures.
Boundary layer receptivity to free-stream turbulence and surface roughness over a swept flat plate
Authors: Kurian Thomas , Fransson Jens H. M. , Alfredsson P. Henrik
Published: April 2011

An experimental study of the receptivity of disturbances and their subsequent development into a three-dimensional boundary layer has been carried out. The three-dimensional boundary layer was set up using a flat plate with a swept leading edge and a pressure gradient using a displacement body at the ceiling of the test section. Low level free-stream turbulence was generated with five different screens and was shown to generate traveling crossflow modes for all but the lowest turbulence level, i.e., for Tu>0.2%, where instead a stationary crossflow disturbance dominated. Stationary crossflow disturbances were triggered by small cylindrical roughness elements arranged in an array. For high enough roughness Reynolds number (Rek) stationary disturbances growing exponentially were seen and their amplitude seems to scale with Rek2.3.
Low Reynolds number flow over a square cylinder with a splitter plate
Authors: Mat Ali Mohamed Sukri , Doolan Con J. , Wheatley Vincent
Published: April 2011

Flows over a square cylinder of side length D with and without a splitter plate are numerically investigated at a Reynolds number of 150. The length of the splitter plate is varied systematically from L=0.5D to L=6D so the sensitivity of the flow structure to the inclusion of the splitter plate can be inspected. It is found that the splitter plate introduces a strong hydrodynamic interaction to the near wake of the cylinder and the length of the plate affects significantly the flow structure. The behavior of the flow can be grouped into three regimes. For short plate lengths (0≲L≲D), the free shear layers are convected further downstream before rolling up when the plate length is increased. For intermediate plate lengths (1.25D≲L≲4.75D), a secondary vortex is clearly visible around the trailing edge of the splitter plate and the shear layers begin to roll up closer to the trailing edge. For long plate lengths (L≳5D), a regime is observed in which the free shear layers reattach to the splitter plate. The study also proposes the minimum wake half-width as the length scale for a possible universal Strouhal number, which is found to be valid for 0≤L≤4D.
Strange attractors and their periodic repetition
Authors: Wang Qiudong , Oksasoglu Ali
Published: April 2011

In this paper, we present some important findings regarding a comprehensive characterization of dynamical behavior in the vicinity of two periodically perturbed homoclinic solutions. Using the Duffing system, we illustrate that the overall dynamical behavior of the system, including strange attractors, is organized in the form of an asymptotic invariant pattern as the magnitude of the applied periodic forcing approaches zero. Moreover, this invariant pattern repeats itself with a multiplicative period with respect to the magnitude of the forcing. This multiplicative period is an explicitly known function of the system parameters. The findings from the numerical experiments are shown to be in great agreement with the theoretical expectations.
Electrospinning jets and nanofibrous structures
Authors: Garg Koyal , Bowlin Gary L.
Published: April 2011

Electrospinning is a process that creates nanofibers through an electrically charged jet of polymer solution or melt. This technique is applicable to virtually every soluble or fusible polymer and is capable of spinning fibers in a variety of shapes and sizes with a wide range of properties to be used in a broad range of biomedical and industrial applications. Electrospinning requires a very simple and economical setup but is an intricate process that depends on several molecular, processing, and technical parameters. This article reviews information on the three stages of the electrospinning process (i.e., jet initiation, elongation, and solidification). Some of the unique properties of the electrospun structures have also been highlighted. This article also illustrates some recent innovations to modify the electrospinning process. The use of electrospun scaffolds in the field of tissue engineering and regenerative medicine has also been described.
Long-range interactions between an atom in its ground S state and an open-shell linear molecule
Authors: Skomorowski Wojciech , Moszynski Robert
Published: April 2011

Theory of long-range interactions between an atom in its ground S state and a linear molecule in a degenerate state with a nonzero projection of the electronic orbital angular momentum is presented. It is shown how the long-range coefficients can be related to the first and second-order molecular properties. The expressions for the long-range coefficients are written in terms of all components of the static and dynamic multipole polarizability tensor, including the nondiagonal terms connecting states with the opposite projection of the electronic orbital angular momentum. It is also shown that for the interactions of molecules in excited states that are connected to the ground state by multipolar transition moments additional terms in the long-range induction energy appear. All these theoretical developments are illustrated with the numerical results for systems of interest for the sympathetic cooling experiments: interactions of the ground state Rb(2S) atom with CO(3Π), OH(2Π), NH(1Δ), and CH(2Π) and of the ground state Li(2S) atom with CH(2Π).
Toward an axiomatic formulation of noncommutative quantum field theory
Authors: Chaichian M. , Mnatsakanova M. N. , Nishijima K. , Tureanu A. , Vernov Yu. S.
Published: April 2011

We propose new Wightman functions as vacuum expectation values of products of field operators in the noncommutative space–time. These Wightman functions involve the ⋆-product among the fields, compatible with the twisted Poincaré symmetry of the noncommutative quantum field theory (NC QFT). In the case of only space–space noncommutativity (θ0i = 0), we prove the CPT theorem using the noncommutative form of the Wightman functions. We also show that the spin-statistics theorem, demonstrated for the simplest case of a scalar field, holds in NC QFT within this formalism.
Electrochromic properties of large-area and high-density arrays of transparent one-dimensional β-Ta2O5 nanorods on indium-tin-oxide thin-films
Authors: Devan Rupesh S. , Gao Shun-Yu , Ho Wei-Der , Lin Jin-Han , Ma Yuan-Ron , Patil Pramod S. , Liou Yung
Published: April 2011

We report on the synthesis, crystalline structure, and electrochromic properties of transparent one-dimensional (1D) orthorhombic (β) Ta2O5 nanorods grown in a large-area high-density array. The transparent 1D β-Ta2O5 nanorod array was synthesized on a conducting indium-tin-oxide thin-film via hot-filament metal-oxide vapor deposition. The array contained ∼1900 β-Ta2O5 nanorods per square micrometer, which were on average, ∼17 nm wide and ∼300 nm long. The good coloration/bleaching cycles, large ion-diffusion coefficient (∼2.35×10−8 cm2/s), and high reversibility (∼79.8%) demonstrate that the 1D β-Ta2O5 nanorods to be a potential electrochromic material for electrochromic devices or smart windows.
Microfluidic formulation of pectin microbeads for encapsulation and controlled release of nanoparticles
Authors: Ogończyk D. , Siek M. , Garstecki P.
Published: April 2011

We report a method for formulation of pectin microbeads using microfluidics. The technique uses biocompatible ingredients and allows for controlled external gelation with hydrogen and calcium ions delivered from an organic phase of rapeseed oil. This method allows for encapsulation of nanoparticles into the microparticles of gel and for control of the rate of their release.
Photoionization of fixed-in-space molecules by partially polarized light
Authors: Kuznetsov V. V. , Semenov S. K. , Cherepkov N. A.
Published: April 2011

A general equation for the three-dimensional angular distribution of photoelectrons ejected from fixed-in-space molecules of any symmetry by light of arbitrary polarization is derived. The state of the light polarization is described by the Stokes parameters. The equation is also valid for photoionization of polarized atoms and aligned or oriented rotating molecules. In the particular case of linear molecules the three-dimensional angular distribution of photoelectrons is fully characterized by five two-dimensional angular distributions. Simple ways to determine experimentally these two-dimensional functions are mentioned. The application of general equations is illustrated by a numerical example of photoionization of the C K-shell of CO molecule in the region of the σ* shape resonance.
Electronic transport in Pd nanocluster devices
Authors: Ayesh A. I.
Published: April 2011

Palladium nanoclusters with an average diameter of 6.7 nm are prepared by magnetron sputtering and inert gas condensation technique. The nanoclusters are deposited between a pair of electrodes defined by optical lithography to create the device. The electronic transport in the devices is investigated by systematic current-voltage measurements. It is demonstrated through fitting the conductance-temperature profile into a conductance model that the conductance in the device is dominated by tunneling. The fitting provides meaningful physical parameters such as the number of nanoclusters within the conduction path, and it shows that some of the nanoclusters are fused together.
Diffusion process of excitons in the wetting layer and their trapping by quantum dots in sparsely spaced InAs quantum dot systems
Authors: Ohmori M. , Vitushinskiy P. , Sakaki H.
Published: April 2011

Photoluminescence (PL) characteristics have been systematically studied in a set of novel InAs quantum dot (QD) systems, where the average interdot distance is set in the range between 2 and 20 μm by controlling the self-assembled growth on GaAs. By investigating the ratio of the PL intensity of QDs to that of the wetting layer (WL), the diffusion of excitons in the WL and their subsequent trapping by QDs are examined. It is found that the diffusion length LD of excitons is about 0.45 μm at 11 K, but increases with temperature, reaching 4 μm at 60 K.
Coherent vibrational energy transfer along a peptide helix
Authors: Kobus Maja , Nguyen Phuong H. , Stock Gerhard
Published: April 2011

To measure the transport of vibrational energy along a peptide helix, Hamm and co-workers [J. Phys. Chem. B 112, 9091 (2008)] performed time-resolved vibrational experiments, which showed that the energy transport rate increases by at least a factor of 4, when a localized C=O mode of the peptide instead of an attached chromophore is excited. This finding raises the question if coherent excitonic energy transfer between the C=O modes may be of importance for the overall energy transport in peptides. With this idea in mind, nonequilibrium molecular dynamics simulations as well as quantum–classical calculations are performed, which qualitatively reproduce the experimental findings. Moreover, the latter model (an exciton Hamiltonian whose matrix elements depend on the instantaneous positions of the peptide and solvent atoms) indeed exhibits the signatures of coherent quantum energy transport, at least within the first few picoseconds and at low temperatures. The origin of the observed decoherence, the absence of vibrational self-trapping, and the possibility of quantum interference between various transport paths are discussed in some detail.
Comment on “Two definitions of the hopping time in a confined fluid of finite particles” [J. Chem. Phys. 129, 154117 (2008)]
Authors: Mon K. K.
Published: April 2011

To resolve the disagreement between two calculations for the hopping time divergence exponent of two diffusing hard disks in a narrow channel, Kalinay and Percus propose that the definitions of the hopping time used in the two calculations are not equivalent, which resulted in different exponents. The first is the mean first passage time (MFPT) and is related to the survival probability function S(t) at long time. Bowles, Mon, and Percus solve an approximate Fick–Jacobs equation to produce a MFPT exponent of −3/2. The second is defined by Kalinay and Percus in terms of the short time relaxation of S(t). Kalinay and Percus claim that Mon and Percus used the short time relaxation of the survival function to obtain an exponent of −2 in the numerical solution of the diffusion equation. This is not an accurate description of the Mon and Percus method. To the contrary, the method of Mon and Percus is designed to extract the longest relaxation time constant. In this comment, I discuss this misunderstanding of Kalinay and Percus and show that the explanation for the disagreement with the approximate Fick–Jacob equation predictions is not in the difference of the definitions for the hopping time.
Party Polarization: Congressional Divergence on Environmental Policy from 1970–2008
Authors: Tanger Shaun M. , Laband David N. , Zeng Peng
Published: April 2011

We investigate empirically the importance of a conjectured linkage between economic conditions and increasing party divergence with respect to national-level environmental policy in the US. Using data from 1970–2008, we find that increases in the rate of unemployment are associated with increases in divergence between the two parties with respect to voting on environmental legislation; a result that is consistent for both the House and Senate. We also report evidence of a positive relationship between party divergence on environmental legislation and real per capita income (inflation) in the House (Senate).
Novel model of a AlGaN/GaN high electron mobility transistor based on an artificial neural network*
Authors: Cheng Zhi-Qun , Hu Sha , Liu Jun , Zhang Qi-Jun
Published: April 2011

In this paper we present a novel approach to modeling AlGaN/GaN high electron mobility transistor (HEMT) with an artificial neural network (ANN). The AlGaN/GaN HEMT device structure and its fabrication process are described. The circuit-based Neuro-space mapping (neuro-SM) technique is studied in detail. The EEHEMT model is implemented according to the measurement results of the designed device, which serves as a coarse model. An ANN is proposed to model AlGaN/GaN HEMT based on the coarse model. Its optimization is performed. The simulation results from the model are compared with the measurement results. It is shown that the simulation results obtained from the ANN model of AlGaN/GaN HEMT are more accurate than those obtained from the EEHEMT model.
Finite element approximations in a non-Lipschitz domain: Part II
Authors: Acosta Gabriel , Armentano María
Published: April 2011

In a paper by R. Durán, A. Lombardi, and the authors (2007) the finite element method was applied to a non-homogeneous Neumann problem on a cuspidal domain

Ω
⊂

R

2

\Omega \subset \mathbb {R}^2

, and quasi-optimal order error estimates in the energy norm were obtained for certain graded meshes. In this paper, we study the error in the

L
2

L^2

norm obtaining similar results by using graded meshes of the type considered in that paper. Since many classical results in the theory Sobolev spaces do not apply to the domain under consideration, our estimates require a particular duality treatment working on appropriate weighted spaces.

On the other hand, since the discrete domain

Ω
h

\Omega _h

verifies

Ω
⊂

Ω
h

\Omega \subset \Omega _h

, in the above-mentioned paper the source term of the Poisson problem was taken equal to

0
0

outside

Ω
\Omega

in the variational discrete formulation. In this article we also consider the case in which this condition does not hold and obtain more general estimates, which can be useful in different problems, for instance in the study of the effect of numerical integration, or in eigenvalue approximations.
Acoustic surveys confirm the high-density areas of harbour porpoises found by satellite tracking
Authors: Sveegaard Signe , Teilmann Jonas , Berggren Per , Mouritsen Kim N. , Gillespie Douglas , Tougaard Jakob
Published: April 2011

Sveegaard, S., Teilmann, J., Berggren, P., Mouritsen, K. N., Gillespie, D., and Tougaard, J. 2011. Acoustic surveys confirm the high-density areas of harbour porpoises found by satellite tracking. – ICES Journal of Marine Science, 68: 929–936. The population status of the harbour porpoise (Phocoena phocoena) has long been of concern in European waters. Consequently, the European Commission (EC) Habitats Directive obligates all EC member states to designate marine protected areas (MPAs) for harbour porpoises before 2012. These will be designated areas having the greatest density of porpoises. However, little is known about comparability between the monitoring methods used to examine porpoise distribution and density, and conflicting results may arise, especially when considering their varying sample size and temporal and spatial scales. Here, vessel-based acoustic surveys are seen as an independent method of testing the temporal and spatial permanence of previously identified areas of high density of harbour porpoises found by satellite-tracking them in inner Danish waters. Based on six acoustic surveys, a strong spatial accord was found between the number of acoustic detections of harbour porpoises and their density distribution obtained from 10 years of satellite tracking. The results confirm the presence and permanence of areas of high density of porpoises and validate the two methods for identifying and monitoring future MPAs for the species.
Evidence that a chaperone–usher-like pathway of Myxococcus xanthus functions in spore coat formation
Authors: Leng Xiaoyan , Zhu Wei , Jin Jing , Mao Xiaohua
Published: April 2011

Many bacteria use the chaperone–usher (CU) secretion pathway to assemble on their surfaces typical or atypical fimbrial organelles. Four consecutive genes of Myxococcus xanthus DK1622, MXAN3885–3882, were predicted to constitute an operon encoding a CU-like system involved in the assembly of the spore coat; however, experimental evidence supporting this hypothesis was lacking. In this study, co-transcription of MXAN3885–3883 was verified, and we found that this operon was expressed 12–15 h after initiation of M. xanthus development under conditions of stringent starvation. The MXAN3885 protein, which is highly homologous to, but expressed earlier than, the spore coat protein U of another M. xanthus strain, DZF1, was present mainly on the outer surface of myxospores. Inactivation of MXAN3883, encoding a putative outer membrane usher, inhibited assembly of MXAN3885 protein on spore surfaces and caused certain morphological alterations in the spore coat. Hence, the CU-like pathway in M. xanthus indeed functions in spore coat biogenesis. Based on chaperone amino acid sequence comparisons, our analysis suggests that the structural basis of the M. xanthus CU-like pathway for spore coat assembly may be different from that of most surface structures assembled by classical CU systems.
SKIP counteracts p53-mediated apoptosis via selective regulation of p21Cip1 mRNA splicing
Authors: Chen Yupeng , Zhang Lirong , Jones Katherine A.
Published: April 2011

The Ski-interacting protein SKIP/SNW1 functions as both a splicing factor and a transcriptional coactivator for induced genes. We showed previously that transcription elongation factors such as SKIP are dispensable in cells subjected to DNA damage stress. However, we report here that SKIP is critical for both basal and stress-induced expression of the cell cycle arrest factor p21Cip1. RNAi chromatin immunoprecipitation (RNAi-ChIP) and RNA immunoprecipitation (RNA-IP) experiments indicate that SKIP is not required for transcription elongation of the gene under stress, but instead is critical for splicing and p21Cip1 protein expression. SKIP interacts with the 3′ splice site recognition factor U2AF65 and recruits it to the p21Cip1 gene and mRNA. Remarkably, SKIP is not required for splicing or loading of U2AF65 at other investigated p53-induced targets, including the proapoptotic gene PUMA. Consequently, depletion of SKIP induces a rapid down-regulation of p21Cip1 and predisposes cells to undergo p53-mediated apoptosis, which is greatly enhanced by chemotherapeutic DNA damage agents. ChIP experiments reveal that SKIP is recruited to the p21Cip1, and not PUMA, gene promoters, indicating that p21Cip1 gene-specific splicing is predominantly cotranscriptional. The SKIP-associated factors DHX8 and Prp19 are also selectively required for p21Cip1 expression under stress. Together, these studies define a new step that controls cancer cell apoptosis.
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells
Authors: Min Irene M. , Waterfall Joshua J. , Core Leighton J. , Munroe Robert J. , Schimenti John , Lis John T.
Published: April 2011

Transitions between pluripotent stem cells and differentiated cells are executed by key transcription regulators. Comparative measurements of RNA polymerase distribution over the genome's primary transcription units in different cell states can identify the genes and steps in the transcription cycle that are regulated during such transitions. To identify the complete transcriptional profiles of RNA polymerases with high sensitivity and resolution, as well as the critical regulated steps upon which regulatory factors act, we used genome-wide nuclear run-on (GRO-seq) to map the density and orientation of transcriptionally engaged RNA polymerases in mouse embryonic stem cells (ESCs) and mouse embryonic fibroblasts (MEFs). In both cell types, progression of a promoter-proximal, paused RNA polymerase II (Pol II) into productive elongation is a rate-limiting step in transcription of ∼40% of mRNA-encoding genes. Importantly, quantitative comparisons between cell types reveal that transcription is controlled frequently at paused Pol II's entry into elongation. Furthermore, “bivalent” ESC genes (exhibiting both active and repressive histone modifications) bound by Polycomb group complexes PRC1 (Polycomb-repressive complex 1) and PRC2 show dramatically reduced levels of paused Pol II at promoters relative to an average gene. In contrast, bivalent promoters bound by only PRC2 allow Pol II pausing, but it is confined to extremely 5′ proximal regions. Altogether, these findings identify rate-limiting targets for transcription regulation during cell differentiation.
The Scuttle Fly Megaselia abdita (Phoridae): A Link between Drosophila and Mosquito Development
Authors: Rafiqi Ab. Matteen , Lemke Steffen , Schmidt-Ott Urs
Published: April 2011

INTRODUCTION

The insect order Diptera (true flies) has great potential in evolutionary developmental biology, featuring the “fruit fly,” Drosophila melanogaster, one of the best-studied genetic model systems in developmental biology, and many human disease vectors (e.g., mosquitoes, blackflies, sandflies, tsetse flies). However, the embryos of only a few dipteran species are currently amenable to efficient functional analyses of developmental genes. As described here, the phorid fly Megaselia abdita has been used as model in evolutionary developmental biology and has been an important species in forensic studies.
Production of SIV Vectors for Gene Delivery
Authors: Verhoeyen Els , Cosset François-Loïc , Nègre Didier
Published: April 2011

INTRODUCTION

The acquisition of vectors suitable for in vivo gene delivery has been a recurrent theme in gene therapy research. Several challenging hurdles must be overcome to reach this goal. First, the vectors must be prepared at high titers. Second, to avoid inactivation, the gene-transfer vectors should not be recognized by the host immune system. Third, the vectors should be able to replicate and to express a transgene in cells that are nonproliferating or slowly proliferating, a predominant situation in vivo. Lentiviral vectors derived from simian immunodeficiency virus (SIV) are similar to those derived from human immunodeficiency virus (HIV-1 or HIV-2) in that they can insert transgenes in nonproliferating cells. It is becoming clear, however, that SIV vectors perform better than HIV-1 vectors in simian cells, and thus may be a valid alternative to HIV-1-based vectors in the early phases of the clinical testing of lentiviral vectors in nonhuman primate models. This protocol describes the production of SIV vector particles and the assay used to measure transduction efficiency. Included also are methods for detecting replication-competent retroviruses (RCRs) and testing the putative mobilization of the green fluorescent protein (GFP)-containing SIV vector. The percentage of GFP-positive cells is determined by fluorescence-activated cell sorting (FACS). These safety assays make use of sMAGI target cells that are permissive to SIVmac251 replication and harbor a stably integrated lacZ transcription unit driven by the SIV/HIV tat-inducible HIV-1 long terminal repeat (LTR).
Megaselia abdita: Preparing Embryos for Injection: Figure 1.
Authors: Rafiqi Ab. Matteen , Lemke Steffen , Schmidt-Ott Urs
Published: April 2011

INTRODUCTION

This protocol describes the handling ofMegaselia abditaembryos from staged egg depositions prior to injection.
Imaging Techniques for Measuring the Materials Properties of Cells
Authors: Kasza Karen E. , Vader David , Köster Sarah , Wang Ning , Weitz David A.
Published: April 2011

INTRODUCTION

The “materials properties” of a biological material include its composition and microscopic structure and the relationship between its structure and its mechanical properties. For living cells, the motor-driven internal motion also significantly impacts the properties, even independently of any remodeling of the cell structure that can occur. These materials properties dictate the passive mechanical response of the material to an applied force. The mechanical properties of cells and tissues are essential for their function and health and affect how cells actively respond to mechanical force in important biological processes, ranging from motility to differentiation and morphogenesis. The mechanical properties of bulk tissues can be determined by traditional rheological techniques that measure the force required to stretch, compress, or shear macroscopic tissue. However, individual cells are too small to be measured by such methods and have highly heterogeneous structures; thus techniques are required that can probe soft materials at the micrometer scale. A variety of microrheological techniques, developed to determine the materials properties of cells, reveal that living cells have materials properties that are quite unusual compared with common inert materials. Cells are active, nonequilibrium materials with a highly nonlinear elasticity. This article presents a subset of microrheological techniques that involve optical imaging of micrometer-sized probes on or within individual cells, describes how to analyze probe motions, and discusses limitations of the techniques.
BSSB:BLASTServer for Structural Biologists
Authors: Uthayakumar Muthukumarasamy , Sowmiya Govindhan , Sabarinathan Radhakrishnan , Udayaprakash N. , Kirti Vaishnavi M. , Sekar Kanagaraj
Published: April 2011

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processingBLASToutput, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed toolBLASTServer for Structural Biologists (BSSB), which maps aBLASToutput onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject protein is represented using a three-color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three-dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence–structure correlation. Furthermore, the additional structure-level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.
RPS: Repeats in Protein Sequences
Authors: Babu Venkatesh , Uthayakumar M. , Kirti Vaishnavi M. , Senthilkumar R. , Shankar M. , Archana C. , Sathya Priya S. , Sekar Kanagaraj
Published: April 2011

Repeats are two or more contiguous segments of amino acid residues that are believed to have arisen as a result of intragenic duplication, recombination and mutation events. These repeats can be utilized for protein structure prediction and can provide insights into the protein evolution and phylogenetic relationship. Therefore, to aid structural biologists and phylogeneticists in their research, a computing resource (a web server and a database), Repeats in Protein Sequences (RPS), has been created. Using RPS, users can obtain useful information regarding identical, similar and distant repeats (of varying lengths) in protein sequences. In addition, users can check the frequency of occurrence of the repeats in sequence databases such as the Genome Database, PIR and SWISS-PROT and among the protein sequences available in the Protein Data Bank archive. Furthermore, users can view the three-dimensional structure of the repeats using the Java visualization plug-inJmol. The proposed computing resource can be accessed over the World Wide Web at http://bioserver1.physics.iisc.ernet.in/rps/.
Advances in theEXPO2009systematic decomposition procedure: an atom-matching-based figure of merit
Authors: Altomare Angela , Cuocci Corrado , Giacovazzo Carmelo , Moliterni Anna , Rizzi Rosanna
Published: April 2011

Ab initiocrystal structure determination from powder diffraction data is not yet a straightforward process: it is strongly disrupted by the low quality of the estimated Bragg reflection intensities. In a two-stage method the integrated intensities calculated from a powder pattern are immediately submitted to direct methods to obtain phases. The larger the accuracy of the integrated intensities, the more efficient the phasing process. A systematic decomposition procedure was introduced in theEXPO2004program to improve the efficiency of the phasing process. The disadvantage of this approach is that a large number of feasible trial structures are generated, among which the correct solution must be recognized. A new procedure is described aiming at introducing strategies to reduce the total number of trials to explore by defining an appropriate figure of merit able to regroup trial structures into different batches, each element of a batch sharing a high percentage of atoms with the other elements of the same batch. The new figure of merit, implemented in an updated version ofEXPO2009, is able to discriminate non-solutions from promising trials, corresponding to incomplete or rough models which evolve, after refinement, into the correct solution.
Communication patterns in antenatal diabetes care: an explorative and descriptive study of midwife‐led consultations
Authors: Risa Christina F , Lidén Eva , Friberg Febe
Published: April 2011

Aim.  To explore and describe the verbal communication patterns in antenatal consultations between pregnant women with diabetes and their midwives.

Background.  Few studies have focused on the efficacy of communication during consultations between midwives and their clients, especially in a high‐risk context.

Design.  An explorative and descriptive study of antenatal consultations between midwives and their clients at four antenatal diabetes clinics in Norway.

Methods.  Thematic analysis was used to study verbal communication in ten woman–midwife consultations that were audio recorded and transcribed. The analysis was based on the following questions: (1) who talks and to what degree? (2) What are the topics discussed and who is the initiator? and (3) What characterises the dialogue in the consultations?

Results.  The results suggest that there was a predominantly medical focus in the consultations, with the communication style characterised by a combination of informal and formal talk. The consultations were structured into three phases, each with its own conversation style.

Conclusions.  The communication patterns adopted appeared to limit the opportunities of mothers‐to‐be to express freely any concerns. It is suggested that a larger degree of openness to the emotional and psychological aspects of pregnancy should be incorporated into the consultations. To take advantage of the different competencies in this multidisciplinary diabetes team, the contribution of the midwife to this specialised antenatal care should be both recognised and defined.

Relevance to clinical practice.  Awareness of each midwife’s own communication style, as well as their attentiveness to a woman’s implicit concerns, is required for the satisfactory support and understanding of the individual pregnant woman. It is necessary to support midwives in the continuous development of their communication skills, a task that should be included as part of midwifery education and undertaken by practitioners in the clinical environment.
Analysis of RNA localization and metabolism in single live bacterial cells: achievements and challenges
Authors: Broude Natalia E.
Published: April 2011

Studies of gene expression at the single cell level in live bacterial cells represent a new and fertile area of research providing real‐time, spatially specified information that cannot be obtained by techniques relying on large cell populations. Before recently, most single‐cell studies have been concerned with gene expression at the protein level and explored the spatiotemporal localization and dynamics of different bacterial proteins. However, to fully understand the complex process of gene expression, it is necessary to visualize and quantify RNA molecules in the cellular environment. The first studies analysing the kinetics of RNA transcription and the distribution of RNA in single bacterial cells in real time have recently been reported. Here, I discuss the methods allowing RNA detection in living bacterial cells, the results on RNA kinetics and RNA localization, and the challenges for future research in this area.
What is the proximate cause for size‐dependent ecophysiological differences in vascular epiphytes?
Authors: Zotz G. , Schmidt G. , Mikona C.
Published: April 2011

Size‐related variation in physiological parameters as diverse as photosynthetic capacity, abscisic acid relationships or the relative water deficit at stomatal closure have been reported for a large number of vascular epiphytes, but the proximate mechanism behind these observations has not been identified. We test four possible reasons for size‐related changes in photosynthetic capacity, leaf‐N content and specific leaf area: (i) plant size itself, (ii) plant age or developmental stage, (iii) previous nutrition, or (iv) previous water regime. A suite of study species and approaches were used: a ‘natural experiment’ with the orchid Polystachya foliosa; an experimental field study with another orchid, Dimerandra emarginata; and a study under controlled conditions with the tank bromeliad, Vriesea sanguinolenta. Neither size, age nor differences in water supply caused differences in leaf N and photosynthetic capacity, while low supply of nutrients yielded, and high supply with nutrients completely removed, size‐related trends. The observed size‐related trends are thus a consequence of in situ differences in nutrient acquisition. Arguably, the improved nutrient status of larger plants under natural conditions results from larger tanks, holding moisture for increasingly longer intervals, which allows longer periods of decomposition of detritus and of nutrient uptake.
Salicylic acid negatively affects the response to salt stress in pea plants
Authors: Barba‐Espín G. , Clemente‐Moreno M. J. , Álvarez S. , García‐Legaz M. F. , Hernández J. A. , Díaz‐Vivancos P.
Published: April 2011

We studied the effect of salicylic acid (SA) treatment on the response of pea plants to salinity. Sodium chloride (NaCl)‐induced damage to leaves was increased by SA, which was correlated with a reduction in plant growth. The content of reduced ascorbate and glutathione in leaves of salt‐treated plants increased in response to SA, although accumulation of the respective oxidised forms occurred. An increase in hydrogen peroxide also occurred in leaves of salt‐exposed plants treated with SA. In the absence of NaCl, SA increased ascorbate peroxidase (APX; 100 μm) and glutathione‐S transferase (GST; 50 μm) activities and increased catalase (CAT) activity in a concentration‐dependent manner. Salinity decreased glutathione reductase (GR) activity, but increased GST and CAT activity. In salt‐stressed plants, SA also produced changes in antioxidative enzymes: 100 μm SA decreased APX but increased GST. Finally, a concentration‐dependent increase in superoxide dismutase (SOD) activity was induced by SA treatment in salt‐stressed plants. Induction of PR‐1b was observed in NaCl‐stressed plants treated with SA. The treatment with SA, as well as the interaction between salinity and SA treatment, had a significant effect on PsMAPK3 expression. The expression of PsMAPK3 was not altered by 70 mm NaCl, but was statistically higher in the absence than in the presence of SA. Overall, the results show that SA treatment negatively affected the response of pea plants to NaCl, and this response correlated with an imbalance in antioxidant metabolism. The data also show that SA treatment could enhance the resistance of salt‐stressed plants to possible opportunistic pathogen attack, as suggested by increased PR‐1b gene expression.
P2 receptor antagonists prevent synaptic failure and extracellular signal‐regulated kinase1/2 activation induced by oxygen and glucose deprivation in rat CA1 hippocampus in vitro
Authors: Traini Chiara , Pedata Felicita , Cipriani Sara , Mello Tommaso , Galli Andrea , Giovannini Maria Grazia , Cerbai Francesca , Volpini Rosaria , Cristalli Gloria , Pugliese Anna Maria
Published: April 2011

To investigate the role of purinergic P2 receptors under ischemia, we studied the effect of P2 receptor antagonists on synaptic transmission and mitogen‐activated protein kinase (MAPK) activation under oxygen and glucose deprivation (OGD) in rat hippocampal slices. The effect of the P2 antagonists pyridoxalphosphate‐6‐azophenyl‐2′,4′‐disulfonate (PPADS, unselective, 30 μm), N 6‐methyl‐2′‐deoxyadenosine‐3′,5′‐bisphosphate (MRS2179, selective for P2Y1 receptor, 10 μm), Brilliant Blue G (BBG, selective for P2X7 receptor, 1 μm), and 5‐[[[(3‐phenoxyphenyl)methyl][(1S)‐1,2,3,4‐tetrahydro‐1‐naphthalenyl]amino]carbonyl]‐1,2,4‐benzenetricarboxylic acid (A‐317491, selective for P2X3 receptor, 10 μm), and of the newly synthesized P2X3 receptor antagonists 2‐amino‐9‐(5‐iodo‐2‐isopropyl‐4‐methoxybenzyl)adenine (PX21, 1 μm) and 2‐amino‐9‐(5‐iodo‐2‐isopropyl‐4‐methoxybenzyl)‐N 6‐methyladenine (PX24, 1 μm), on the depression of field excitatory postsynaptic potentials (fEPSPs) and anoxic depolarization (AD) elicited by 7 min of OGD were evaluated. All antagonists significantly prevented these effects. The extent of CA1 cell injury was assessed 3 h after the end of 7 min of OGD by propidium iodide staining. Substantial CA1 pyramidal neuronal damage, detected in untreated slices exposed to OGD injury, was significantly prevented by PPADS (30 μm), MRS2179 (10 μm), and BBG (1 μm). Western blot analysis showed that, 10 min after the end of the 7 min of OGD, extracellular signal‐regulated kinase (ERK)1/2 MAPK activation was significantly increased. MRS2179, BBG, PPADS and A‐317491 significantly counteracted ERK1/2 activation. Hippocampal slices incubated with the ERK1/2 inhibitors 1,4‐diamino‐2,3‐dicyano‐1,4‐bis(2‐aminophenylthio)butadiene (U0126, 10 μm) and α‐[amino[(4‐aminophenyl)thio]methylene]‐2‐(trifluoromethyl) benzeneacetonitrile (SL327, 10 μm) showed significant fEPSP recovery after OGD and delayed AD, supporting the involvement of ERK1/2 in neuronal damage induced by OGD. These results indicate that subtypes of hippocampal P2 purinergic receptors have a harmful effect on neurotransmission in the CA1 hippocampus by participating in AD appearance and activation of ERK1/2.
Predicted effect of climate change on the invasibility and distribution of the Western corn root‐worm
Authors: Aragón Pedro , Lobo Jorge M.
Published: April 2011

Insect pests, biological invasions and climate change are considered to represent major threats to biodiversity, ecosystem functioning, agriculture and forestry. Deriving hypothesis of contemporary and/or future potential distributions of insect pests and invasive species is becoming an important tool for predicting the spatial structure of potential threats.

The western corn rootworm (WCR) Diabrotica virgifera virgifera LeConte is a pest of maize in North America that has invaded Europe in recent years, resulting in economic costs in terms of maize yields in both continents. The present study aimed to estimate the dynamics of potential areas of invasion by the WCR under a climate change scenario in the Northern Hemisphere. The areas at risk under this scenario were assessed by comparing, using complementary approaches, the spatial projections of current and future areas of climatic favourability of the WCR. Spatial hypothesis were generated with respect to the presence records in the native range of the WCR and physiological thresholds from previous empirical studies.

We used a previously developed protocol specifically designed to estimate the climatic favourability of the WCR. We selected the most biologically relevant climatic predictors and then used multidimensional envelope (MDE) and Mahalanobis distances (MD) approaches to derive potential distributions for current and future climatic conditions.

The results obtained showed a northward advancement of the upper physiological limit as a result of climate change, which might increase the strength of outbreaks at higher latitudes. In addition, both MDE and MD outputs predict the stability of climatic favourability for the WCR in the core of the already invaded area in Europe, which suggests that this zone would continue to experience damage from this pest in Europe.
Management, Organizational Justice and Emotional Exhaustion among Chinese Migrant Workers: Evidence from two Manufacturing Firms
Authors: Frenkel Stephen J. , Li Min , Restubog Simon Lloyd D.
Published: April 2011

This article explores how Human Resource (HR) policies and practices influence employee perceptions of organizational justice, which in turn impacts employee emotions and feelings of emotional exhaustion. Using structural equation modelling and based on employee survey data drawn from two manufacturing organizations, we find that a strong HR system — perceived by workers as distinctive, attractive and consistently implemented — fosters perceptions of distributive, procedural and interactive justice. However, only distributive injustice leads to negative emotions and emotional exhaustion. This is explained by reference to the cultural and institutional context (China), status (migrant) and type of workers (semi‐skilled, manual) included in the study. We discuss the theoretical and practical implications that arise from these findings.
Emerging scientific opportunities for junior neurologists in the European Federation of Neurological Societies
Authors: Sztriha L. K. , Struhal W. , Varga E. T. , Brainin M. , Gilhus N. E. , Waldemar G. , Sipido E. , Müller E. , Sellner J.
Published: April 2011

Close collaboration between the European Association of Young Neurologists and Trainees (EAYNT) and the European Federation of Neurological Societies (EFNS) has lead to the introduction of various scientific opportunities for young neurologists at an international level. These include participation in the activities of the Scientist Panels, inclusive of workshop proposals for future congresses, task forces, guideline development and abstract reviewing. Furthermore, the EFNS acknowledges scientific contribution by junior colleagues with congress bursaries and the Uschi Tschabitscher Prize. The EAYNT, in cooperation with the EFNS, is devoted to promote the involvement of talented junior neurologists in the shaping of European neurology in the future.
Association of incompleteness of the anterior part of the circle of Willis with the occurrence of lacunes in the basal ganglia
Authors: Miyazawa N. , Shinohara T. , Yamagata Z.
Published: April 2011

Background and purpose:  This study investigated whether incompleteness of the anterior part of the circle of Willis affects the occurrence of lacunes in the basal ganglia.

Methods:  One thousand and seventy‐seven healthy individuals examined by magnetic resonance (MR) imaging and MR angiography were divided into eight subgroups according to our new classification.

Results:  Logistic regression analysis demonstrated that healthy individuals with incompleteness of the anterior circle of Willis had significantly higher frequency of lacunes [odds ratio (OR): 2.121, 95% confidence interval (CI): 1.477–3.108; or OR: 2.46, 95% CI: 1.377–4.384 in cases without or with fetal type posterior communicating artery, respectively] and higher numbers of lacunes (P < 0.001 or P < 0.001 in cases without or with fetal type posterior communicating artery, respectively) compared to patients with complete circle of Willis.

Conclusions:  Incompleteness of the anterior part of the circle of Willis significantly affected the occurrence of lacunes.