bluuebunny/crossref_metadata_2025 huggingface dataset:
Tailored Gauss quadratures, a promising route for an efficient evaluation of multicenter integrals over B functions
Authors: Rebabti A. , Ghomari R. , Bouferguene A.
Published: May 2009

In the framework of the Fourier integral transform, complicated multicenter integrals, e.g., three-center nuclear attraction and exchange integrals, over B functions involve a multiple integral (double or triple), the innermost of which is a Hankel transform of an exponentially decreasing term. Because of the oscillatory nature of the Hankel transform and the order in which it occurs in the definition of multicenter integrals, i.e., innermost, an efficient evaluation of such a quantity requires highly performant algorithms. In this context, extrapolation techniques emerged, during the past decade, as a possible solution to the problem of evaluating the oscillating semi-infinite integral. With a view to improving the efficiency of future algorithms, this contribution introduces a new technique for the evaluation of the oscillating integral by means of a tailored Gaussian quadrature. Using the case of three-center nuclear attraction integrals as a working example, it is shown that the new approach allows the semi-infinite integral to be evaluated accurately if not exactly. Further, when the roots and weights of the quadrature are available, a complexity analysis of our algorithm shows encouraging results compared to nonlinear extrapolation techniques.
Phase coexistence in melting aluminum clusters
Authors: Cao Baopeng , Starace Anne K. , Judd Oscar H. , Jarrold Martin F.
Published: May 2009

The internal energy distributions for melting aluminum cluster cations with 100, 101, 126, and 127 atoms have been investigated using multicollision induced dissociation. The experimental results can be best fit with a statistical thermodynamic model that incorporates only fully solidlike and fully liquidlike clusters so that the internal energy distributions become bimodal during melting. This result is consistent with computer simulations of small clusters, where rapid fluctuations between entirely solidlike and entirely liquidlike states occur during the phase change. To establish a bimodal internal energy distribution, the time between the melting and freezing transitions must be longer than the time required for equilibration of the energy distribution (which is estimated to be around 1–2 μs under our conditions). For Al100+ and Al101+, the results indicate that this criterion is largely met. However, for Al126+ and Al127+, it appears that the bimodal energy distributions are partly filled in, suggesting that either the time between the melting and freezing transitions is comparable to the equilibration time or that the system starts to switch to macroscopic behavior where the phase change occurs with the two phases in contact.
Nature of doped a-Si:H/c-Si interface recombination
Authors: De Wolf Stefaan , Kondo Michio
Published: May 2009

Doped hydrogenated amorphous silicon (a-Si:H) films of only a few nanometer thin find application in a-Si:H/crystalline silicon heterojunction solar cells. Although such films may yield a field effect at the interface, their electronic passivation properties are often found to be inferior, compared to those of their intrinsic counterparts. In this article, based on H2 effusion experiments, the authors argue that this phenomenon is caused by Fermi energy dependent Si–H bond rupture in the a-Si:H films, for either type of doping. This results in the creation of Si dangling bonds, counteracting intentional doping of the a-Si:H matrix, and lowering the passivation quality.
High efficiency of graded index photonic crystal as an input coupler
Authors: Cakmak Atilla Ozgur , Colak Evrim , Caglayan Humeyra , Kurt Hamza , Ozbay Ekmel
Published: May 2009

A graded index photonic crystal (GRIN PC) configuration was placed at the input side of a photonic crystal waveguide (PCW) in order to efficiently couple the light waves into the waveguide. We compared the transmission efficiencies of light in the absence and presence of the GRIN PC structure. We report a significant improvement in coupling when the GRIN PC is incorporated with the PCW. The intensity profiles were obtained by carrying out the experiments at microwave frequencies. Finite difference time domain based simulations were found to be in good agreement with our experimental results.
Updated references for the structural, electronic, and vibrational properties of TiO2(B) bulk using first-principles density functional theory calculations
Authors: Ben Yahia Mouna , Lemoigno Frédéric , Beuvier Thomas , Filhol Jean-Sébastien , Richard-Plouet Mireille , Brohan Luc , Doublet Marie-Liesse
Published: May 2009

To get updated references on the structural, electronic, and vibration properties of the metastable TiO2(B) compound, infrared and Raman spectra of TiO2(B) are computed within the density functional theory framework and all active modes are assigned. Phonons and their possible coupling with the macroscopic electric fields resulting from the long-range interactions of instantaneous local dipoles (due to nuclear vibrations) in polar solids are taken into account through supercell calculations and longitudinal optical-transversal optical splitting corrections. Full structural relaxations using conventional density functional theory and hybrid functionals with localized Gaussian-type orbitals or plane-wave basis sets reveal a similar deviation of the local Ti environment compared to the TiO2(B) structural refinements reported so far. Such deviations are shown to be significant from those computed for anatase using the same method, thus yielding distinguishable spectroscopic responses for the two polymorphs.
Resonant Raman scattering contribution to attenuation of x rays at energies in lower vicinity of the K-shell ionization threshold of some elements
Authors: Kumar Sanjeev , Sharma Veena , Kumar Sunil , Alrakabi Muhanad , Mehta D. , Singh Nirmal
Published: May 2009

Attenuation of the x rays and γ rays in the T22i, N41b, T69m, Y70b, and L71u elements have been measured with special emphasis for the x ray energies (Ein) in lower vicinity of the K shell ionization threshold (BK) of the element. The incident photon beam is obtained from decay of the F55e, A241m, and C57o radioisotopes, and fluorescence of the V23, Y70b, L71u, W74, O76s, and T90h targets excited by the x rays and γ rays from the radioisotopes. The measurements were performed using energy dispersive setups involving Ge detectors. The measured attenuation coefficients agree with the available theoretical values except at the photon energies with (BK-Ein) less than or nearly equal to the K-shell width (ΓK), where significant positive deviations as large as factor of 2 have been observed. In view of reliability of the available theoretical cross sections for the photoionization and the photon scattering processes, the magnitude of positive alteration at the photon energy in lower vicinity of the ionization threshold is attributed to the K shell resonant Raman scattering (RRS) process and the corresponding cross sections have been deduced. Possible matrix effects in the energy dispersive x ray spectrometry due to RRS are also discussed.
Device model for graphene bilayer field-effect transistor
Authors: Ryzhii V. , Ryzhii M. , Satou A. , Otsuji T. , Kirova N.
Published: May 2009

We present an analytical device model for a graphene bilayer field-effect transistor (GBL-FET) with a graphene bilayer as a channel and with back and top gates. The model accounts for the dependences of the electron and hole Fermi energies as well as energy gap in different sections of the channel on the bias back-gate and top-gate voltages. Using this model, we calculate the dc and ac source-drain currents and the transconductance of GBL-FETs with both ballistic and collision dominated electron transport as functions of structural parameters, the bias back-gate and top-gate voltages, and the signal frequency. It is shown that there are two threshold voltages, Vth,1 and Vth,2, so that the dc current versus the top-gate voltage relation markedly changes depending on whether the section of the channel beneath the top gate (gated section) is filled with electrons, depleted, or filled with holes. The electron scattering leads to a decrease in the dc and ac currents and transconductances, whereas it weakly affects the threshold frequency. As demonstrated, the transient recharging of the gated section by holes can pronouncedly influence the ac transconductance resulting in its nonmonotonic frequency dependence with a maximum at fairly high frequencies.
Fine structural splitting and exciton spin relaxation in single InAs quantum dots
Authors: Dou X. M. , Sun B. Q. , Xiong Y. H. , Niu Z. C. , Ni H. Q. , Xu Z. Y.
Published: May 2009

We have studied the exciton spin dynamics in single InAs quantum dots (QDs) with different exciton fine structural splitting (FSS) by transient luminescence measurements. We have established the correlation between exciton spin relaxation rate and the energy splitting of the FSS when FSS is nonzero and found that the spin relaxation rate in QD increases with a slope of 8.8×10−4 ns−1 μeV−1. Theoretical analyses based on the phonon-assisted relaxations via the deformation potential give a reasonable interpretation of the experimental results.
Reliability characterization of stress-induced charge trapping in HfO2 by electrostatic discharge impulse stresses
Authors: Chen Chun-Heng , Hwang Huey-Liang , Chiu Fu-Chien
Published: May 2009

The charge trapping characteristics of HfO2 dielectric under the electrostatic discharge (ESD) high-field current impulses were studied. It is found that the charge trapping phenomenon is different from that of the conventional dc stress. The results show the interface-trapped charges are built at the low stress regime, but the positive oxide-trapped charges are rapidly built up while increasing the stress voltage, which eventually dominates the oxide breakdown. The origin of the positive oxide-trapped charges at the medium stress regime is most likely the hole trapping. At high stress regime, the main contribution of the positive oxide-trapped charges results from the electric-field enhanced defect generation. Using the Fowler derivative method, the degradation characteristics of HfO2 oxides under the ESD stress are investigated. Compared with SiO2, the severer ESD-induced charge trapping in HfO2 dielectric is observed which can be elucidated by the inherent bonding nature of metal oxide.
Efficiency limits of Si/SiO2 quantum well solar cells from first-principles calculations
Authors: Kirchartz Thomas , Seino Kaori , Wagner Jan-Martin , Rau Uwe , Bechstedt Friedhelm
Published: May 2009

In order to investigate the applicability of new photovoltaic absorber materials, we show how to use first-principles calculations combined with device simulations to determine the efficiency limits of solar cells made from SiO2/Si superlattices and from coaxial ZnO/ZnS nanowires. Efficiency limits are calculated for ideal systems according to the Shockley–Queisser theory but also for more realistic devices with finite mobilities, nonradiative lifetimes, and absorption coefficients. Thereby, we identify the critical values for mobility and lifetime that are required for efficient single junction as well as tandem solar cells.
Direct evidence for orientational flip-flop of water molecules at charged interfaces: A heterodyne-detected vibrational sum frequency generation study
Authors: Nihonyanagi Satoshi , Yamaguchi Shoichi , Tahara Tahei
Published: May 2009

Complex χ(2) spectra of air/water interfaces in the presence of charged surfactants were measured by heterodyne-detected broadband vibrational sum frequency generation spectroscopy for the first time. In contrast to the neat water surface, the signs of χ(2) for two broad OH bands are the same in the presence of the charged surfactants. The obtained χ(2) spectra clearly showed flip-flop of the interfacial water molecules which is induced by the opposite charge of the head group of the surfactants. With the sign of β(2) theoretically obtained, the absolute orientation, i.e., up/down orientation, of water molecules at the charged aqueous surfaces was uniquely determined by the relation between the sign of χ(2) and the molecular orientation angle. Water molecules orient with their hydrogen up at the negatively charged aqueous interface whereas their oxygen up at the positively charged aqueous interface.
Electromechanical stability of dielectric elastomer
Authors: Leng Jinsong , Liu Liwu , Liu Yanju , Yu Kai , Sun Shouhua
Published: May 2009

Electromechanical instability may occur in dielectric elastomer films due to the coupling between mechanical forces and electric fields. According to Zhao and Suo [Appl. Phys. Lett. 91, 061921 (2007)], free-energy in any form, which consists of elastic strain energy and electric energy, can be used to analyze the electromechanical stability of dielectric elastomer. By taking the permittivity as a variable depending on the deformation in a free energy function, a relationship is established among critical nominal electric field, critical real electric field, nominal stress, and principal stretch ratios. The accurate expressions of these parameters are presented for a special equal biaxial stretch case. All the results obtained by utilizing the single material constant neo-Hookean elastic strain energy model coincide with the conclusions by Zhao and Suo.
Nonmonotonic incommensurability effects in lamellar-in-lamellar self-assembled multiblock copolymers
Authors: Kriksin Yury A. , Erukhimovich Igor Ya. , Smirnova Yuliya G. , Khalatur Pavel G. , ten Brinke Gerrit
Published: May 2009

Using the self-consistent-field theory numerical procedure we find that the period D of the lamellar-in-lamellar morphology formed in symmetric multiblock copolymer melts AmN/2(BN/2AN/2)nBmN/2 at intermediate segregations changes nonmonotonically with an increase in the relative tail length m. Therewith D reveals, as a function of the Flory χ-parameter, a drastic change in the vicinity of the internal structure formation, which can be both a drop and a rise, depending on the value of m. It is argued that the unusual behavior found is a particular case of a rather general effect of the incommensurability between the two length scales that characterize the system under consideration.
The nonlinear dielectric behavior of water: Comparisons of various approaches to the nonlinear dielectric increment
Authors: Fulton Robert L.
Published: May 2009

A number of connections between the first nonlinear dielectric increment and dipole correlation functions have been proposed over a large span of years. These range from the Langevin–Debye approach, the use of cavity and reaction fields, a cavity free formulation, to modified Langevin–Debye approaches. Comparisons of the predictions of a number of these approaches, together with results of molecular dynamics simulations and an experimental result, are given. The relations include those by Booth and by Kielich based on the use of cavity and reaction fields as traditionally used in the determination of such connections but also including a partial correction by Booth for some ignored nonlinear effects, those by Sandberg and Edholm and by Jha and Freed based on the use of a Langevin–Debye type of approach, and one based on a cavity free non-Langevin–Debye formulation that automatically includes all nonlinear effects to the appropriate order. The local structures of water used for the determination of the pertinent correlation functions are chosen to be given by the Bernal–Fowler model, by a modification of the Berna–Fowler model, and by the Onsager approximation. In the limit of ϵ⪢ϵ∞, the cavity free connection gives results for the first nonlinear decrements 36% larger than the decrement obtained by Booth, irrespective of the model used for the dipole correlation functions. The inclusion of ϵ∞ is found to decrease the decrements by about 4%. Using parameters deduced from the requirement that the Kirkwood–Fröhlich connection give the experimental value of ϵ, the Booth uncorrected expression for the dielectric decrement using the modified Bernal–Fowler model is found to give good agreement with the simulations of Yeh and Berkowitz, while the cavity free result is too large. Using the Bernal–Fowler model for the local structure of water, the cavity free expression gives good agreement with the simulation results, the partially corrected Booth expression gives reasonable agreement, while the Booth uncorrected expression is too small. Comparisons to the experimental value of the nonlinear coefficient of (1.00±0.15)×10−15 m2/V2 as found by Kołodziej et al. are also made. Using the Bernal–Fowler model, the calculated nonlinear coefficients divided by 10−15 m2/V2 are as follows: Booth, 0.82; Booth including partial corrections for nonlinear effects on the cavity and reaction fields, 0.99; Kielich, 0.83; cavity free, 1.12; and modified Langevin–Debye, 2.93. The partially corrected Booth value shows the best fit, with the cavity free value next best but still within the cited error range. If the slope of the line given by Kołodziej et al. is used as the measure of the nonlinear increment, the experimental value is 1.10×10−15 m2/V2, similar to the corrected Booth and remarkably similar to the cavity free result.
Observation of surface structure of 1-butyl-3-methylimidazolium hexafluorophosphate using high-resolution Rutherford backscattering spectroscopy
Authors: Ohno Atsushi , Hashimoto Hiroki , Nakajima Kaoru , Suzuki Motofumi , Kimura Kenji
Published: May 2009

The surface structure of 1-butyl-3-methylimidazolium hexafluorophosphate is studied by high-resolution Rutherford backscattering spectroscopy (HRBS) at room temperature. Elemental depth profiles are derived from the observed HRBS spectrum through spectrum simulation. While the obtained carbon profile has a sharp peak at the surface, the nitrogen profile shows a broader peak at a depth ∼0.3 nm. These observations indicate that the butyl chain protrudes from the bulk liquid to the vacuum at the surface. The profiles of phosphorous and fluorine also have a broad peak at almost the same depth as the nitrogen profile, indicating that the anions are located near the imidazolium rings. These results are in good agreement with recent molecular dynamics simulations.
The structural force arising from magnetic interactions in polydisperse ferrofluids
Authors: Wang Anrong , Li Jian , Gao Rongli
Published: May 2009

Ionic ZnFe2O4 is a weak magnetic ferrofluid with different particle sizes (a polydisperse ferrofluid), in which the dipolar coupling constant λ is less than 2. By comparing the reduced magnetization curves and initial magnetic susceptibilities of ferrofluids with different particle volume fractions ϕ, it is found that there are field-induced attractive interactions between the colloidal particles, which make them aggregate; this interaction decreases with ϕ. The dipolar coupling constant is so small that particle aggregation cannot be induced by magnetic interaction alone. Thus, it can be concluded from the experimental results that a nonmagnetic attractive interaction is stimulated during the magnetization process for ferrofluids. Using a model based on “large” and “small” particles (the bidisperse model), this nonmagnetic interaction can be explained as a field-induced structural force. This force is enhanced following magnetic interactions between the large particles as the applied magnetic field increases. The field-induced structural force is similar to a depletion force and can also arise in strong magnetic ferrofluids (λ>2) with polydisperse particle sizes under an applied external magnetic field.
Study on single-transverse mode output of high-power flat He–Ne laser
Authors: Ling Yi-Ming
Published: May 2009

The multimode output power of He–Ne lasers with a flat discharge tube can be enhanced by increasing the transverse size of the discharge tube. By using an N-type fold optical resonator, the high-power flat He–Ne laser tube can give the output in the lower-order mode. Inserting a limiting-mode circular-hole diaphragm into the N-type fold optical resonator, the lower-order modes are suppressed gradually with the reduction in its aperture. The high-power flat He–Ne laser tube of 1.4 m discharge length can achieve above 80 mW of the single-transverse mode output power using an N-type fold optical resonator with a limiting-mode circular-hole diaphragm of 4 mm aperture. Its output characteristics and laser mode patterns are investigated experimentally. The experimental method is introduced and its results are discussed briefly in this paper.
A physical parametrization of coupled transverse dynamics based on generalized Courant–Snyder theory and its applications
Authors: Qin Hong , Davidson Ronald C.
Published: May 2009

A physical parametrization of coupled transverse dynamics is developed by generalizing the Courant–Snyder (CS) theory for one degree of freedom to the case of coupled transverse dynamics with two degrees of freedom. The four basic components of the original CS theory, i.e., the envelope equation, phase advance, transfer matrix, and CS invariant, all have their counterparts with remarkably similar expressions in the generalized theory. Applications of the new theory are given. It is discovered that the stability of coupled dynamics is completely determined by the generalized phase advance.
Polarization mode dispersion emulation using polarization maintaining fibers: Fixed root-mean-square differential group delay but varying second-order polarization mode dispersion
Authors: Musara Vitalis , Wu Lorinda , Pelaelo Gaoboelwe , Leitch Andrew W. R.
Published: May 2009

We report on a polarization mode dispersion (PMD) emulator with a fixed root-mean-square differential group delay (RMS-DGD) but varying second-order PMD (SO-PMD) using only a combination of polarization maintaining fibers and a polarization controller. The SO-PMD control mechanism is not completely in real time. Besides controlling the mean PMD values of the emulator, simultaneous adjustments in the maximum and minimum values of PMD statistics can be performed. We therefore illustrate irregular fluctuations that occur around the RMS-DGD due to SO-PMD. This novel design can be used to further show the impact of a high first-order PMD segment on the DGD and SO-PMD statistical distributions that might occur in an optical network system.
Dissipation in quasi-two-dimensional flowing foams
Authors: Raufaste Christophe , Foulon Amandine , Dollet Benjamin
Published: May 2009

The dissipation between two-dimensional (2D) monolayers of bubbles, the so-called quasi-2D foams, and a wall is investigated in two setups: a “liquid pool” system, where the foam is confined between a soap solution and a glass coverslip, and a Hele-Shaw cell, where the foam occupies the narrow gap between two plates. This experimental study reports dissipation measurements for mobile gas/liquid interfaces (free shear boundary condition) over a large range of parameters: in the liquid pool system, velocity and bubble area; in the Hele-Shaw cell, velocity and liquid fraction. The effect of the latter quantity is measured for the first time over more than three orders of magnitude. A full comparison between our results and other experimental studies is proposed and enables to rescale all measurements on a single master curve. It shows that for mobile gas/liquid interfaces, the existing models systematically underestimate the dissipation in flowing foams. This is quantified by a discrepancy factor ξ, ratio of the experimental dissipation measurements to the theoretical predictions, which scales as ξ=1.4(RP/A)−0.5 with RP the Plateau border radius and A the bubble area, showing that the discrepancy is higher for dry foams.
Structural transformations of nitrogen adsorbed on graphite: Monte Carlo studies of spatial heterogeneity in multilayer system
Authors: Golebiowska M. , Firlej L. , Kuchta B. , Fabianski R.
Published: May 2009

We present numerical Monte Carlo studies of nitrogen multilayers adsorbed on the basal plane of graphite. The analysis is focused on the system spatial heterogeneity and its influence on structures and phase transitions. The simulations have been carried out for surface coverage from monolayer to four layers, in canonical ensemble, in the temperature range from 5 to 100 K. An intricate phase situation is observed due to the competition between intermolecular and N2-graphite interactions. The commensurate monolayer is stabilized by the graphite corrugation. The multilayer commensurate structure is only metastable at low temperatures. Its stable structure is triangular, 1.08 times denser than the commensurate one stabilized by the N2–N2 interactions. The multilayer structure is strongly spatially nonuniform, the individual layer structure changes from herringbone in the first layer to pinwheel arrangement in the fourth one. Two structural phase transitions, orientational order-disorder, and melting, are observed in each layer. Their mechanism and transition temperatures show strong variations depending on the position of the layer and the number of layers in the system.
Metal-oxide-semiconductor field-effect-transistors on indium phosphide using HfO2 and silicon passivation layer with equivalent oxide thickness of 18 Å
Authors: Chen Yen-Ting , Zhao Han , Yum Jung Hwan , Wang Yanzhen , Lee Jack C.
Published: May 2009

In this letter, we demonstrate the electrical properties of metal-oxide-semiconductor capacitors and metal-oxide-semiconductor field-effect transistors (MOSFETs) on InP using atomic layer deposited HfO2 gate dielectric and a thin silicon interface passivation layer (Si IPL). Compared with single HfO2, the use of Si IPL results in better interface quality with InP substrate, as illustrated by smaller frequency dispersion and reduced hysteresis. MOSFETs with Si IPL show much higher drive current and transconductance, improved subthreshold swing, interface-trap density and gate leakage current with equivalent oxide thickness scaling down to 18 Å.
The Unintended Segregation of Transnational Students in Central Melbourne
Authors: Fincher Ruth , Shaw Kate
Published: May 2009

Links between the rapid growth of tertiary students resident in a city and that city's gentrification have recently been proposed in a UK-based literature about ‘studentification’. These analyses frame student subjectivity, identity, and experience in particular ways—students are agents of urban change, propelling shifts in neighbourhood housing and entertainment submarkets in a manner that local host communities often resent. Consideration of the experiences of the students themselves, through the effects of the host society and the city on them, is less common. Based on research conducted in Melbourne, we focus on transnational students, who are seen as consumers for a major export industry. We use the voices of transnational students recently arrived in the city to make the claim that an unintended sociospatial segregation of these students is occurring, largely driven by institutional practices. Students' agency is fundamentally affected by their institutional context, which determines the conditions of their entry to Australia and to university there, their housing, and, to a remarkable degree, their opportunities for social interaction.
A trans-membrane segment inside the ribosome exit tunnel triggers RAMP4 recruitment to the Sec61p translocase
Authors: Pool Martin R.
Published: May 2009

Membrane protein integration occurs predominantly at the endoplasmic reticulum and is mediated by the translocon, which is formed by the Sec61p complex. The translocon binds to the ribosome at the polypeptide exit site such that integration occurs in a cotranslational manner. Ribosomal protein Rpl17 is positioned such that it contacts both the ribosome exit tunnel and the surface of the ribosome near the exit site, where it is intimately associated with the translocon. The presence of a trans-membrane (TM) segment inside the ribosomal exit tunnel leads to the recruitment of RAMP4 to the translocon at a site adjacent to Rpl17. This suggests a signaling function for Rpl17 such that it can recognize a TM segment inside the ribosome and triggers rearrangements of the translocon, priming it for subsequent TM segment integration.
Intermediate filaments exchange subunits along their length and elongate by end-to-end annealing
Authors: Çolakoğlu Gülsen , Brown Anthony
Published: May 2009

Actin filaments and microtubules lengthen and shorten by addition and loss of subunits at their ends, but it is not known whether this is also true for intermediate filaments. In fact, several studies suggest that in vivo, intermediate filaments may lengthen by end-to-end annealing and that addition and loss of subunits is not confined to the filament ends. To test these hypotheses, we investigated the assembly dynamics of neurofilament and vimentin intermediate filament proteins in cultured cells using cell fusion, photobleaching, and photoactivation strategies in combination with conventional and photoactivatable fluorescent fusion proteins. We show that neurofilaments and vimentin filaments lengthen by end-to-end annealing of assembled filaments. We also show that neurofilaments and vimentin filaments incorporate subunits along their length by intercalation into the filament wall with no preferential addition of subunits to the filament ends, a process which we term intercalary subunit exchange.
The structural and functional coupling of two molecular machines, the ribosome and the translocon
Authors: Johnson Arthur E.
Published: May 2009

Ribosomes synthesizing secretory and membrane proteins are bound to translocons at the membrane of the endoplasmic reticulum (ER). Both the ribosome and translocon are complex macromolecular machines whose structural and functional interactions are poorly understood. A new study by Pool (Pool, M.R. 2009. J. Cell Biol. 185:889–902) has now shown that the structure of the translocon is dictated by the identity of the protein being synthesized by the ribosome, thereby demonstrating that the two macromolecular machines are structurally coupled for functional purposes. The study also identifies an unexpected component in the apparent molecular linkage that connects the two machines, a discovery that shows the current view of translocon structure is oversimplified.
Genetic modification of flux for flux prediction of mutants
Authors: Zhao Quanyu , Kurata Hiroyuki
Published: May 2009

Motivation: Gene deletion and overexpression are critical technologies for designing or improving the metabolic flux distribution of microbes. Some algorithms including flux balance analysis (FBA) and minimization of metabolic adjustment (MOMA) predict a flux distribution from a stoichiometric matrix in the mutants in which some metabolic genes are deleted or non-functional, but there are few algorithms that predict how a broad range of genetic modifications, such as over- and underexpression of metabolic genes, alters the phenotypes of the mutants at the metabolic flux level.

Results: To overcome such existing limitations, we develop a novel algorithm that predicts the flux distribution of the mutants with a broad range of genetic modification, based on elementary mode analysis. It is denoted as genetic modification of flux (GMF), which couples two algorithms that we have developed: modified control effective flux (mCEF) and enzyme control flux (ECF). mCEF is proposed based on CEF to estimate the gene expression patterns in genetically modified mutants in terms of specific biological functions. GMF is demonstrated to predict the flux distribution of not only gene deletion mutants, but also the mutants with underexpressed and overexpressed genes in Escherichia coli and Corynebacterium glutamicum. This achieves breakthrough in the a priori flux prediction of a broad range of genetically modified mutants.

Contact:  kurata@bio.kyutech.ac.jp

Supplementary information:  Supplementary file and programs are available at Bioinformatics online or http://www.cadlive.jp.
NTAP: for NimbleGen tiling array ChIP-chip data analysis
Authors: He Kun , Li Xueyong , Zhou Junli , Deng Xing-Wang , Zhao Hongyu , Luo Jingchu
Published: May 2009

Summary:NTAP is designed to analyze ChIP-chip data generated by the NimbleGen tiling array platform and to accomplish various pattern recognition tasks that are useful especially for epigenetic studies. The modular design of NTAP makes the data processing highly customizable. Users can either use NTAP to perform the full process of NimbleGen tiling array data analysis, or choose post-processing modules in NTAP to analyze pre-processed epigenetic data generated by other platforms. The output of NTAP can be saved in standard GFF format files and visualized in GBrowse.

Availability and Implementation:The source code of NTAP is freely available at http://ntap.cbi.pku.edu.cn/. It is implemented in Perl and R and can be used on Linux, Mac and Windows platforms.

Contact:  ntap@mail.cbi.pku.edu.cn; luojc@pku.edu.cn; hekun78@gmail.com
Intractable cardiogenic shock in stress cardiomyopathy with left ventricular outflow tract obstruction: is extra‐corporeal life support the best treatment?
Authors: Bonacchi Massimo , Maiani Massimo , Harmelin Guy , Sani Guido
Published: May 2009

We report the use of extra‐corporeal cardiopulmonary support (ECLS), in a case of complicating refractory severe cardiogenic shock, in a patient with Tako‐tsubo cardiomyopathy (TC). Tako‐tsubo cardiomyopathy syndrome is characterized by left ventricular (LV) wall motion abnormalities, usually without coronary artery disease, mimicking the diagnosis of acute coronary syndrome. This ventricular dysfunction is typically reversible in the acute phase, though it can progress into refractory cardiogenic shock with limited therapeutic options available. Here, we report for the first time in a Tako‐tsubo patient with refractory cardiogenic shock, the use of ECLS treatment in order to unload the heart, sustain circulation and end‐organ perfusion, and promote potential ventricular recovery. Extra‐corporeal life support allowed inotropic drug weaning while maintaining end‐organ function and supported the patient until myocardial recovery. The patient recovered completely, and a normal LV ejection fraction was documented by 2D echocardiography on day 7. From our experience, ECLS can be an appropriate treatment for severe refractory cardiogenic shock in patients with TC. Extra‐corporeal life support was an effective ultimate solution.
Clinical trial: extended treatment duration of peginterferon‐alpha2b plus ribavirin for 72 and 96 weeks in hepatitis C genotype 1‐infected late responders
Authors: NAGAKI M. , SHIMIZU M. , SUGIHARA J. I. , TOMITA E. , SANO C. , NAIKI T. , KIMURA K. , AMANO K. , SAKAI T. , NINOMIYA M. , KOJIMA T. , KATSUMURA N. , FUJIMOTO M. , MORIWAKI H.
Published: May 2009

Background  The benefits of prolonging peginterferon and ribavirin after 48 weeks of treatment to maximize sustained virological responses (SVR) in hepatitis C virus (HCV) genotype 1‐infected patients remain to be understood.

Aim  To investigate whether extended treatment longer than 72 weeks may be superior to 72‐week treatment.

Methods  A total of 120 treatment‐naïve or retreated patients with HCV genotype 1 were treated with peginterferon‐alpha‐2b (1.5 μg/kg/week) plus weight‐based ribavirin. We had 34 late responders, in whom HCV RNA first became undetectable at week 12–48, and randomized them into three groups receiving standard‐dose peginterferon‐alpha‐2b plus low‐dose ribavirin (200 mg/day) for extended 24 weeks (group A), receiving low‐dose peginterferon‐alpha‐2b (0.75 μg/kg/week) plus low‐dose ribavirin for extended 48 weeks (group B) or no extended treatment (group C), and evaluated the outcome according to their virological response.

Results  Multivariate analysis showed that the treatment for 96 weeks was identified as a significant, independent factor associated with SVR in HCV genotype 1‐infected late responders in comparison with group A [odds ratio (OR), 10.002; P = 0.080] and group C (OR, 17.748; P = 0.025).

Conclusion  Extending the treatment duration from 48 weeks to 96 weeks improves SVR rates in genotype 1‐infected patients with late virological response to peginterferon‐alpha‐2b and ribavirin.
Endoscopic band ligation could decrease recurrent bleeding in Mallory–Weiss syndrome as compared to haemostasis by hemoclips plus epinephrine
Authors: LECLEIRE S. , ANTONIETTI M. , IWANICKI‐CARON I. , DUCLOS A. , RAMIREZ S. , BEN‐SOUSSAN E. , HERVÉ S. , DUCROTTÉ P.
Published: May 2009

Background  Mallory–Weiss syndrome (MWS) with active bleeding at endoscopy may require endoscopic haemostasis the modalities of which are not well‐defined.

Aim  To compare the efficacy of endoscopic band ligation vs. hemoclip plus epinephrine (adrenaline) in bleeding MWS.

Methods  From 2001 to 2008, 218 consecutive patients with a MWS at endoscopy were hospitalized in our Gastrointestinal Bleeding Unit. In 56 patients (26%), an endoscopic haemostasis was required because of active bleeding. Band ligation was performed in 29 patients (Banding group), while hemoclip application plus epinephrine injection was performed in 27 patients (H&E group). Treatment efficacy and early recurrent bleeding were retrospectively compared between the two groups.

Results  Primary endoscopic haemostasis was achieved in all patients. Recurrent bleeding occurred in 0% in Banding group vs. 18% in H&E group (P = 0.02). The use of hemoclips plus epinephrine (OR = 3; 95% CI = 1.15–15.8) and active bleeding at endoscopy (OR = 1.9; 95% CI = 1.04–5.2) were independent predictive factors of early recurrent bleeding.

Conclusions  Haemostasis by hemoclips plus epinephrine was an independent predictive factor of rebleeding. This result suggests that band ligation could be the first choice endoscopic treatment for bleeding MWS, but requires further prospective assessment.
A prostaglandin D2receptor antagonist modifies experimental asthma in sheep
Authors: Shichijo M. , Arimura A. , Hirano Y. , Yasui K. , Suzuki N. , Deguchi M. , Abraham W. M.
Published: May 2009

BackgroundProstaglandin (PG) D2is the major cylooxygenase metabolite released by mast cells upon allergen stimulation, and elicits responses through either the prostanoid DP1 receptor and/or the chemoattractant receptor homologous molecule expressed on T‐helper type 2 (Th2) cells (CRTH2/DP2). Experimental evidence suggests that stimulation of one or both these receptors contributes to asthma pathophysiology.

ObjectiveThe aim of this study was to test the hypothesis that the prostanoid DP1 receptor contributes to asthma pathophysiology by determining the efficacy of an orally active antagonist for this receptor, S‐5751, on allergen‐induced bronchoconstriction, airway hyperresponsiveness (AHR) and cellular inflammation in the sheep model of asthma.

MethodsPGD2‐induced cyclic adenosine monophosphate (cAMP) production in platelet‐rich plasma was used to establish thein vitroefficacy of S‐5751.In vivo, sheep naturally allergic toAscaris suumwere challenged with an aerosolized antigen with and without S‐5751 treatment (given 4 days before and for 6 days after the challenge).

ResultsS‐5751 inhibited PGD2‐induced cAMP production in platelet‐rich plasma with an IC50value of 0.12 μm. S‐5751 at 30 mg/kg, but not at 3 mg/kg, reduced the early bronchoconstriction and inhibited the late bronchoconstriction. AHR and inflammatory cell infiltration in bronchoalveolar lavage fluid at days 1 and 7 were also inhibited with the 30 mg/kg dose. The responses observed with S‐5751 at 30 mg/kg were comparable with those with montelukast treatment (0.15 mg/kg, twice a day, intravenous); however, S‐5751 did not block inhaled leukotrieneD4‐induced broncoconstriction.

ConclusionProstanoid DP1 receptor inhibition may represent an alternative target for asthma therapy.
The non‐proteolytic house dust mite allergen Der p 2 induce NF‐κB and MAPK dependent activation of bronchial epithelial cells
Authors: Österlund C. , Grönlund H. , Polovic N. , Sundström S. , Gafvelin G. , Bucht A.
Published: May 2009

Background
House dust mites (HDM) are well‐known as a source of indoor aeroallergens and for causing allergic airway diseases. Some proteolytic HDM allergens are known to activate respiratory epithelial cells to produce pro‐inflammatory mediators, while there is limited knowledge regarding such activity among non‐proteolytic HDM allergens.

Objective
To investigate whether Der p 2, a major non‐proteolytic allergen of Dermatophagoides pteronyssinus, activates respiratory epithelial cells to produce mediators involved in asthma pathogenesis and to elucidate the mechanism of such activation.

Methods
The human bronchial epithelial cell line BEAS‐2B, normal human bronchial epithelial (NHBE) cells and the alveolar epithelial cell line A549 were exposed to recombinant Der p 2. Following exposure, we analysed a panel of soluble mediators and cell adhesion receptors involved in asthma pathogenesis by promoting recruitment, survival and binding of inflammatory cells. The involvement of nuclear factor (NF)‐κB and mitogen‐activated protein kinases (MAPKs) was studied using specific inhibitors.

Results
Der p 2 activated bronchial BEAS‐2B and NHBE cells, but not alveolar A549 cells. In BEAS‐2B cells Der p 2 induced dose‐dependent up‐regulation in both mRNA level and protein secretion of granulocyte‐macrophage colony‐stimulating factor, IL‐6, IL‐8, monocyte‐chemotactic protein‐1 and macrophage inflammatory protein‐3α. Secretion as well as surface expression of intercellular adhesion molecule (ICAM)‐1 was also up‐regulated, which was associated with increased adhesion of monocytes to the epithelial cells. The release of cytokines and chemokines was regulated by NF‐κB and MAPK activation in different ways, while expression of ICAM‐1 was solely dependent on NF‐κB activation.

Conclusion
These results show that Der p 2 activates respiratory epithelial cells, indicating that this non‐proteolytic allergen, in addition to its immunogenic properties, can aggravate respiratory airway disease by adjuvant‐like activation of the lung epithelium.
More is not necessarily better: the impact of limiting and excessive nutrients on herbivore population growth rates
Authors: ZEHNDER CARALYN B. , HUNTER MARK D.
Published: May 2009

Abstract 1. The body tissues of insect herbivores contain higher concentrations of nitrogen and phosphorus than do their host plants, leading to an elemental mismatch that can limit herbivore growth, fecundity and ultimately influence population dynamics. While low nutrient availability can limit herbivore growth and reproduction, nutrient levels that exceed an organism’s nutritional requirements, i.e. an organisms’ threshold elemental ratio, can also decrease performance.

2. We conducted a laboratory experiment to examine the impacts of nitrogen and phosphorus additions on population growth rates of a phloem‐feeding insect herbivore.

3. Herbivore per capita population growth rates were highest at intermediate foliar nitrogen concentrations, indicating a performance cost on the highest nitrogen foliage. While there was no direct effect of foliar phosphorus concentration on insect performance, there was a strong and unexpected indirect effect. High soil phosphorus availability increased both foliar nitrogen concentrations and aphid tissue nitrogen, resulting in low population growth rates when both soil nitrogen and phosphorus availabilities were high.

4. In this study, experimental increases in foliar nitrogen levels led to a decrease in herbivore performance suggesting that excessive nutrient levels can limit herbivore population growth rates.
Impact of body fat mass extent on cardiac autonomic alterations in women
Authors: Sztajzel J. , Golay A. , Makoundou V. , Lehmann T. N. O. , Barthassat V. , Sievert K. , Pataky Z. , Assimacopoulos‐Jeannet F. , Bobbioni‐Harsch E.
Published: May 2009

Background  Obesity has been associated with significant abnormalities of the cardiac autonomic regulation. However, the precise impact of increasing body weight on cardiac autonomic function and the metabolic and hormonal contributors to these changes are presently unclear. The aim of our study was to explore in subjects with increasing values of body mass index (BMI) the alterations of cardiac autonomic function and to establish the potential role of various metabolic and hormonal contributors to these alterations.

Materials and methods  We investigated time and frequency domain heart rate variability (HRV) parameters taken from 24‐h Holter recordings, and several anthropometric, metabolic and hormonal parameters (plasma glucose, insulin, triglycerides, free fatty acids, leptin and adiponectin) in 68 normoglycaemic and normotensive women (mean age of 40 ± 3 years), subdivided according to their BMI into 15 normal body weight (controls), 15 overweight, 18 obese and 20 morbidly obese.

Results  Heart rate was increased and HRV was decreased in the morbidly obese group as compared with controls. In overall population, a negative association linked body fat mass (FM) to HRV indices. None of the metabolic and hormonal parameters were significantly related to the HRV indices, after they were adjusted for the body FM.

Conclusions  Morbidly obese, normoglycaemic and normotensive young women have increased HR and low HRV, indicating an abnormal cardiac autonomic function and representing a risk factor for adverse cardiovascular events. A decrease of HRV parameters is associated with a progressive increase of body FM. Other metabolic and hormonal factors, characterising obesity, do not show an independent influence on these HRV alterations.
Effect of guar gum on the rheological, thermal and textural properties of soybean β‐conglycinin gel
Authors: Zhu Jian‐Hua , Yang Xiao‐Quan , Ahmad Ijaz , Jiang Yueming , Wang Xiao‐Yuan , Wu Lei‐Yan
Published: May 2009

The effect of guar gum, a non‐gelling neutral polysaccharide, on the thermal gelation of soybean β‐conglycinin was analysed using the dynamic oscillatory rheological measurement, differential scanning calorimetry and texture profile analysis. The endothermic peak temperature of β‐conglycinin in the presence of 0.5% guar gum was about 89.1 °C. However, the endothermic peaks shifted to higher temperatures as the guar gum concentration increased from 0.05% to 0.5%, which could be attributed to the thermodynamic incompatibility with guar gum, resulting in a promoted aggregation of the thermally denatured β‐conglycinin. Furthermore, the elastic modulus increased with increasing concentration of guar gum, with a less frequency dependence. In addition, the springiness, cohesiveness and fracturability enhanced but the hardness decreased, as the guar gum concentration increased. The study demonstrated that incorporation of guar gum improved markedly the thermal and functional properties of soybean β‐conglycinin thermal‐induced gel, which can help better to design new food formulations.