bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformational and vibrational study of platinum(II) anticancer drugs: cis-diamminedichloroplatinum (II) as a case study
Authors: Amado Ana M. , Fiuza Sónia M. , Marques Maria P. M. , Batista de Carvalho Luis A. E.
Published: November 2007

A conformational and vibrational analysis of cisplatin [cis-diamminedichloro-platinum(II)] (cDDP) is reported. Several theory methods (from Hartree-Fock to Møller-Plesset and density functional theory) combined with different all-electron basis sets are evaluated, in view of determining the best suited strategy for accurately representing this molecule. This choice is based on the best compromise between accuracy and computational requirements. Different scaling models of the cDDP vibrational modes were tested for obtaining the best scaling factors to be used in this type of inorganic systems. The structural parameters and vibrational results predicted by the calculations are compared with the corresponding experimental data, namely, x-ray structure, and Raman and inelastic neutron scattering spectra. Finally, a complete assignment of the cDDP vibrational spectra is presented.
Photoinduced bimolecular electron transfer kinetics in small unilamellar vesicles
Authors: Choudhury Sharmistha Dutta , Kumbhakar Manoj , Nath Sukhendu , Pal Haridas
Published: November 2007

Photoinduced electron transfer (ET) from N,N-dimethylaniline to some coumarin derivatives has been studied in small unilamellar vesicles (SUVs) of the phospholipid, DL-α-dimyristoyl-phosphatidylcholine, using steady-state and time-resolved fluorescence quenching, both below and above the phase transition temperature of the vesicles. The primary interest was to examine whether Marcus inversion [H. Sumi and R. A. Marcus, J. Chem. Phys. 84, 4894 (1986)] could be observed for the present ET systems in these organized assemblies. The influence of the topology of SUVs on the photophysical properties of the reactants and consequently on their ET kinetics has also been investigated. Absorption and fluorescence spectral data of the coumarins in SUVs and the variation of their fluorescence decays with temperature indicate that the dyes are localized in the bilayer of the SUVs. Time-resolved area normalized emission spectra analysis, however, reveals that the dyes are distributed in two different microenvironments in the SUVs, which we attribute to the two leaflets of the bilayer, one toward bulk water and the other toward the inner water pool. The microenvironments in the two leaflets are, however, not indicated to be that significantly different. Time-resolved anisotropy decays were biexponential for all the dyes in SUVs, and this has been interpreted in terms of the compound motion model according to which the dye molecules can experience a fast wobbling-in-cone type of motion as well as a slow overall rotating motion of the cone containing the molecule. The expected bimolecular diffusion-controlled rates in SUVs, as estimated by comparing the microviscosities in SUVs (determined from rotational correlation times) and that in acetonitrile solution, are much slower than the observed fluorescence quenching rates, suggesting that reactant diffusion (translational) does not play any role in the quenching kinetics in the present systems. Accordingly, clear inversions are observed in the correlation of the fluorescence quenching rate constants kq with the free energy change, ΔG0 of the reactions. However, the coumarin dyes, C152 and C481 (cf. Scheme 1), show unusually high kq values and high activation barriers, which is not expected from Marcus ET theory. This unusual behavior is explained on the basis of participation of the twisted intramolecular charge transfer states of these two dyes in the ET kinetics.
Local hybrid functionals: An assessment for thermochemical kinetics
Authors: Kaupp Martin , Bahmann Hilke , Arbuznikov Alexei V.
Published: November 2007

Local hybrid functionals with position-dependent exact-exchange admixture are a new class of exchange-correlation functionals in density functional theory that promise to advance the available accuracy in many areas of application. Local hybrids with different local mixing functions (LMFs) governing the position dependence are validated for the heats of formation of the extended G3/99 set, and for two sets of barriers of hydrogen-transfer and heavy-atom transfer reactions (HTBH38 and NHTBH38 databases). A simple local hybrid Lh-SVWN with only Slater and exact exchange plus local correlation and a one-parameter LMF, g(r)=b(τW(r)∕τ(r)), performs best and provides overall mean absolute errors for thermochemistry and kinetics that are a significant improvement over standard state-of-the-art global hybrid functionals. In particular, this local hybrid functional does not suffer from the systematic deterioration that standard functionals exhibit for larger molecules. In contrast, local hybrids based on generalized gradient approximation exchange tend to give rise to nonintuitive LMFs, and no improved functionals have been obtained along this route. The LMF is a real-space function and thus can be analyzed in detail. We use, in particular, graphical analyses to rationalize the performance of different local hybrids for thermochemistry and reaction barriers.
eneSurfactant effects associated with Te-doped InPAs alloys
Authors: Cederberg J. G. , Lee S. R.
Published: November 2007

We examine the effects of heavy Te doping on strain-relaxed InPAs alloys grown on InP using metal-organic chemical vapor deposition. Compared to Si doping, Te doping of InPAs substantially reduces film roughness at high dopant concentrations (∼1×1019cm−3). Unlike similar Si concentrations, high Te concentrations also suppress the incorporation of As into InPAs. An analysis of depth profiles of Te, As, and P from secondary-ion mass spectrometry further reveals the segregation of 0.6 ML of Te on the InPAs surface during growth. We infer that surfactant effects produced by the segregated Te cause the observed changes in surface morphology and As incorporation.
6
j
symbols duality relations
Authors: Freidel L. , Noui K. , Roche Ph.
Published: November 2007

It is known that the Fourier transformation of the square of (6j) symbols has a simple expression in the case of su(2) and Uq(su(2)) when q is a root of unit. The aim of the present work is to unravel the algebraic structure behind these identities. We show that the double cross product construction H1⋈H2 of two Hopf algebras and the bi-cross-product construction H2*⧑H1 are the Hopf algebra structures behind these identities by analyzing different examples. We study the case where D=H1⋈H2 is equal to the group algebra of ISU(2), SL(2,C) and where D is a quantum double of a finite group of SU(2) and of Uq(su(2)) when q is real.
Dust charge fluctuation instability in a dusty plasma with equilibrium density and magnetic field inhomogeneities
Authors: Salimullah M. , Shah H. A. , Murtaza G.
Published: November 2007

Dust charge fluctuation instability in a dusty plasma in the presence of equilibrium density and external/ambient static magnetic field inhomogeneities has been examined in detail. The plasma ions acquire a uniform drift speed due to the equilibrium magnetic field gradient. For strongly magnetized electrons and ions, the dust charge fluctuation effect is contributed dominantly by ion dynamics. This results in an instability when the ion drift speed exceeds the perpendicular phase velocity of the waves under consideration.
A new multichannel interferometer system on HL-2A
Authors: Zhou Y. , Deng Z. C. , Liu Z. T. , Yi J. , Tang Y. W. , Gao B. Y. , Tian C. L. , Li Y. G. , Ding X. T.
Published: November 2007

A new multichannel HCN interferometer has been developed on HL-2A tokamak, which is characterized by two techniques: (1) the wave-guide HCN laser with cavity length of 6m to increase the optical resource power and (2) high response room temperature waveguide Schottky diode detectors to obtain good beat signal. The space resolution is 7cm by the use of focusing metal mirrors mounted on the vacuum chamber and a compensated optical system. In the 2006 experiment campaign, this new interferometer has been applied for plasma density profile and density sawtooth measurement.
Novel impedance cell for low conductive liquids: Determination of bulk and interface contributions
Authors: Becchi Marta , Callegaro Luca , Durbiano Francesca , D’Elia Vincenzo , Strigazzi Alfredo
Published: November 2007

A plane capacitor cell with variable gap has been designed in order to detect the complex permittivity of low conductive liquids (up to 500μS∕cm) and the impedance of the sample-electrode interface. The novelty of the cell consists of the simultaneous presence of the field uniformity ensured by a guard ring, an adjustable gap between 300μm and 6.75mm (the electrode axial motion avoiding any rotation), and the immersion of the capacitor in the sample reservoir. The size of the capacitor electrodes and the gap values have been tested via the capacitance detection of the in-air cell at 1kHz. The sample measurements have been performed by scanning the frequency range between 15Hz and 2MHz at four different capacitor gap values. In the paper a method to directly extract the bulk complex permittivity and the interface impedance versus frequency is presented. It is based on the assumption that the interface contribution is independent of the electrode gap, as confirmed (within the measurement accuracy) from measurements on all samples investigated. As samples of interest, we have chosen two certified electrolytic conductivity standards, KCl aqueous solutions having conductivity traceable to SI units; and two polymer latex aqueous dispersions of microspheres. Regarding KCl solutions, the conductivity measurements are compatible with the reference values within the specified uncertainty; the measured permittivities are consistent with the literature. For all samples, we have recovered the expected result that the interface impedance mainly affects the low frequency range (f<10kHz).
The electrical and interfacial properties of metal-high-k oxide-semiconductor field effect transistors with CeO2∕HfO2 laminated gate dielectrics
Authors: Chang Ingram Yin-ku , Chen Chun-Heng , Chiu Fu-Chien , Lee Joseph Ya-min
Published: November 2007

Metal-oxide-semiconductor field-effect transistors with CeO2∕HfO2 laminated gate dielectrics were fabricated. The transistors have a subthreshold slope of 74.9mV/decade. The interfacial properties were measured using gated diodes. The surface state density Dit was 9.78×1011cm−2eV−1. The surface-recombination velocity (s0) and the minority carrier lifetime in the field-induced depletion region (τ0,FIJ) measured from the gated diode were about 6.11×103cm∕s and 1.8×10−8s, respectively. The effective capture cross section of surface state (σs) extracted using the subthreshold-swing measurement and the gated diode was about 7.69×10−15cm2. The effective electron mobility of CeO2∕HfO2 laminated gated transistors was determined to be 212cm2∕Vs.
Extending the collisional fluid equations into the long mean-free-path regime in toroidal plasmas. IV. Banana regime
Authors: Shaing K. C.
Published: November 2007

In Part I [Phys. Fluids B 2, 1190 (1990)] and Part II [Phys. Plasmas 12, 082508 (2005)], it was emphasized that the equilibrium plasma viscous forces when applied for the magnetohydrodynamic (MHD) modes are only rigorously valid at the mode rational surface where m−nq=0. Here, m is the poloidal mode number, n is the toroidal mode number, and q is the safety factor. This important fact has been demonstrated explicitly by calculating the viscous forces in the plateau regime in Parts I and II. Here, the effective viscous forces in the banana regime are calculated for MHD modes by solving the linear drift kinetic equation that is driven by the plasma flows first derived in Part I. At the mode rational surface, the equilibrium plasma viscous forces are reproduced. However, it is found that away from the mode rational surface, the viscous forces for MHD modes decrease, a behavior similar to that observed in the viscous forces for the plateau regime. The proper form of the momentum equation that is appropriate for the modeling of the MHD modes is also discussed.
Factors affecting performance of dispenser photocathodes
Authors: Moody Nathan A. , Jensen Kevin L. , Feldman Donald W. , Montgomery Eric J. , O’Shea Patrick G.
Published: November 2007

Usable lifetime has long been a limitation of high efficiency photocathodes in high average current accelerator applications such as free electron lasers, where poor vacuum conditions and high incident laser power contribute to early degradation in electron beam emission. Recent progress has been made in adapting well known thermionic dispenser techniques to photocathodes, resulting in a dispenser photocathode whose photosensitive surface coating of cesium can be periodically replenished to extend effective lifetime. This article details the design and fabrication process of a prototype cesium dispenser photocathode and describes in detail the dominant factors affecting its performance: activation procedure, surface cleanliness, temperature, and substrate microstructure.
Low-q resonances, transport barriers, and secondary electrostatic convective cells
Authors: McDevitt C. J. , Diamond P. H.
Published: November 2007

Recent experimental observations have suggested key characteristics of internal transport barrier (ITB) formation near low-q surfaces in off-axis minimum-q (OAMq) discharges. These observations identify mean profile flattening localized to the low-q surface as a transition precursor in the absence of observable magnetic field perturbations. This observation suggests an electrostatic model of ITB formation which accounts for strong transport in the immediate vicinity of the low-q surface, as well as the formation of an ITB nearby the surface. Here, a low-m electrostatic convective cell driven by modulational instability of the background drift wave turbulence is discussed in the context of ITB formation near low-q resonances in OAMq discharges. Unlike pure m=n=0 zonal flows, convective cells are capable of intense mixing localized around low-q resonant surfaces, thus relaxing ∇T and ∇n profiles at the k∙B=0 resonance. However, nearby, but off the low-q resonant surface the magnitude of convective cell shear is maximal, providing an effective means of triggering a transport barrier there. Field line bending coupled with collisional viscosity are found to strongly damp the intensity of the vortical flows except in the case of weak magnetic shear. Furthermore, collisionless nonlinear saturation mechanisms such as nonlinear wave trapping are largely circumvented due to the strong mixing of the convective cell. This suggests that low-m convective cells may play a key role in the regulation of turbulent transport near low-q resonances for OAMq discharges.
Angular distribution of carbon ion flux in a nanotube array during the plasma process by the Monte Carlo technique
Authors: Levchenko I. , Ostrikov K. , Keidar M. , Vladimirov S. V.
Published: November 2007

Angular distribution of microscopic ion fluxes around nanotubes arranged into a dense ordered pattern on the surface of the substrate is studied by means of multiscale numerical simulation. The Monte Carlo technique was used to show that the ion current density is distributed nonuniformly around the carbon nanotubes arranged into a dense rectangular array. The nonuniformity factor of the ion current flux reaches 7 in dense (5×1018m−3) plasmas for a nanotube radius of 25nm, and tends to 1 at plasma densities below 1×1017m−3. The results obtained suggest that the local density of carbon adatoms on the nanotube side surface, at areas facing the adjacent nanotubes of the pattern, can be high enough to lead to the additional wall formation and thus cause the single- to multiwall structural transition, and other as yet unexplained nanoscience phenomena.
Trace formula for systems with spin from the coherent state propagator
Authors: Ribeiro A. D. , de Aguiar M. A. M. , de Toledo Piza A. F. R.
Published: November 2007

We present a detailed derivation of the trace formula for a general Hamiltonian with two degrees of freedom where one of them is canonical and the other a spin. Our derivation starts from the semiclassical formula for the propagator in a basis formed by the product of a canonical and a spin coherent states and is valid in the limit ℏ→0, j→∞ with jℏ constant. The trace formula, obtained by taking the trace and the Fourier transform of the coherent state propagator, is compared to others found in the literature.
Nanoscale thick layer transfer of hydrogen-implanted wafer by using polycrystalline silicon sacrificial layer
Authors: Lee T.-H. , Huang C.-H. , Yang Y. Y. , Suryasindhu T. , Li P. W.
Published: November 2007

This article presents a sacrificial layer method of forming a nanoscale thick silicon-on-insulator thin film, avoiding the channeling effect of implantation and eliminating a subsequent thinning process. However, because of the light mass of hydrogen, it is difficult with the implantation technique to have a shallow implant depth for splitting a layer at a thickness less than 100nm by a traditional Smart-Cut® process. This study proves that using a polycrystalline-Si layer as a sacrificial layer in the initial implantation step can easily define a silicon transfer layer down to a thickness of tens of nanometers.
Growth and optical properties of KTa1−xNbxO3 thin films grown by pulsed laser deposition on MgO substrates
Authors: Rousseau A. , Guilloux-Viry M. , Dogheche E. , Bensalah M. , Remiens D.
Published: November 2007

Perovskitelike KTa1−xNbxO3 (KTN, x ranging from 0 to 1) thin films were grown on (100)MgO substrates using pulsed laser deposition. X-ray diffraction analyses evidenced the epitaxial growth of the films along the (100) orientation. The optical properties of KTN planar waveguides were characterized by prism coupling for determination of ordinary and extraordinary refractive indices nTE and nTM (transverse electric and transverse magnetic). The influence of Nb content was also investigated relative to the films’ indices. The film behavior and the substrate-to-layer interface were directly qualified from the measured optical data using the experimental and theoretical approach (iWKB) (inverse Wentzel-Kramers-Brillouin). The results showed a change in the refractive index profile at the interface, which may be related to the existence of structural defects.
Deep saturation of junction voltage at large forward current of light-emitting diodes
Authors: Feng L. F. , Li D. , Zhu C. Y. , Wang C. D. , Cong H. X. , Zhang G. Y. , Du W. M.
Published: November 2007

The dependences of series resistance, ideality factor, and junction voltage of light-emitting diodes (LEDs) on applied voltage or current were characterized accurately using alternating current (ac) behavior combined with I-V plot (acIV method). The deep saturation of junction voltage and simultaneous decrease of ideality factor of LEDs at large forward current, which imply the pinning of quasi-Fermi levels, were observed. Comparing with our recent study of the similar phenomenon of laser diodes, in which the junction voltage jumps abruptly to a saturated value at lasing threshold, the changes of junction voltage of LEDs are gradual. In addition, the decrease of series resistance with the increasing current and the negative capacitance effect of LEDs were also investigated.
Complex impedance spectroscopy of alkali impurities in as-grown, irradiated and annealed quartz
Authors: Devautour-Vinot S. , Cambon O. , Prud’homme N. , Giuntini J. C. , Boy J.-J. , Cibiel G.
Published: November 2007

This work compares the dielectric relaxation properties of different crystalline quartz materials, according to their source (natural or synthetics). It is shown that these relaxation properties are due to a hopping process of alkaline (Li+, Na+, and K+) impurities located near [Al–O4]5− tetrahedra. A detailed analysis, in terms of the distribution function of the dielectric loss peak, allowed us to perfectly distinguish the different types of as-grown quartz. We show that (i) the natural quartz has less stable M+ charge carriers than the synthetic materials and that (ii) the homogeneity of the M+ trapping sites, created by the [Al–O4]5− tetrahedra, strongly depends on the crystal growth conditions. These features were then studied using quartz samples with different treatment conditions: as-grown, irradiated, or annealed at high temperature. We propose that the irradiation greatly facilitates the M+ relaxation, by creating additional low energy M+ hosting sites, whose number depends on the source of the quartz crystals. We also show that for 100krad irradiation, the saturation state of the defects is already reached for all the materials under consideration. Finally, we propose that the irradiation followed by annealing at 450°C improves the M+ stability and homogeneity in quartz materials, compared with the as-grown materials, this trend being much more relevant for the natural than for the synthetic quartz.
Optical properties of epitaxial SrHfO3 thin films grown on Si
Authors: Sousa M. , Rossel C. , Marchiori C. , Siegwart H. , Caimi D. , Locquet J.-P. , Webb D. J. , Germann R. , Fompeyrine J. , Babich K. , Seo J. W. , Dieker Ch.
Published: November 2007

The perovskite SrHfO3 can be a potential candidate among the high-permittivity materials for gate oxide replacement in future metal-oxide semiconductor field-effect transistor technology. Thin films of SrHfO3 were grown by molecular beam epitaxy and compared with SrTiO3 films. Their optical properties were investigated using spectroscopic ellipsometry and analyzed with respect to their structural properties characterized by x-ray diffractometry, atomic force microscopy, and transmission electron microscopy. A band gap of Eg=6.1±0.1eV is measured optically, which renders this material better suited for gate dielectric applications than SrTiO3 with Eg∼3.4eV. At similar equivalent oxide thickness, SrHfO3 also exhibits lower gate leakage current than SrTiO3 does.
Strain-induced transconductance enhancement by pattern dependent oxidation in silicon nanowire field-effect transistors
Authors: Seike A. , Tange T. , Sugiura Y. , Tsuchida I. , Ohta H. , Watanabe T. , Kosemura D. , Ogura A. , Ohdomari I.
Published: November 2007

Transconductance (gm) enhancement in n-type and p-type nanowire field-effect-transistors (nwFETs) is demonstrated by introducing controlled tensile strain into channel regions by pattern dependent oxidation (PADOX). Values of gm are enhanced relative to control devices by a factor of 1.5 in p-nwFETs and 3.0 in n-nwFETs. Strain distributions calculated by a three-dimensional molecular dynamics simulation reveal predominantly horizontal tensile stress in the nwFET channels. The Raman lines in the strain controlled devices display an increase in the full width at half maximum and a shift to lower wavenumber, confirming that gm enhancement is due to tensile stress introduced by the PADOX approach.
Impact of axial strain on drain current of carbon-nanotube field-effect transistors with doped junctions
Authors: Uchida Ken , Saitoh Masumi
Published: November 2007

The effect of axial strain on the performance of carbon-nanotube field-effect transistors with doped junctions is studied. When the diameter of carbon nanotubes (CNTs) is less than 1.5nm, the decrease of the off-current by axial strain occurs together with the decrease of on-current. However, if the diameter of CNTs is larger than 1.5nm, axial strain is effective for decreasing off-current while enhancing the on-current at the same time. The decrease of off-current is due to the opening of the bandgap by axial strain, whereas the increase of on-current is attributable to current flowing through the first excited state.
Global melting of Zr57Ti5Ni8Cu20Al10 bulk metallic glass under microcompression
Authors: Cheng Sheng , Wang Xun-Li , Choo Hahn , Liaw Peter K.
Published: November 2007

Global melting was observed in micron-sized pillar samples tested under microcompression. In addition to a higher strength that was reproduced in samples with different sizes, a large plastic strain was also observed prior to the final fracture, as compared to bulk counterparts. The global melting was a result of the final fracture as evidenced by the acoustic emission at the end of the microcompression. However, the increased strain rate and large plastic strain might have contributed to the temperature increase prior to the fracture.
Origin of visible luminescence in hydrogenated amorphous silicon nitride
Authors: Hao H. L. , Wu L. K. , Shen W. Z. , Dekkers H. F. W.
Published: November 2007

We present a detailed investigation on the origin of the room-temperature visible luminescence in hydrogenated amorphous silicon nitride films. In combination with Raman spectroscopy and high resolution transmission electron microscopy, we demonstrate clearly that the red light emission originates from amorphous silicon quantum dots. On the basis of the redshift of peak position, narrowing of bandwidth, and temperature quenching of luminescence, we attribute the green emission to the bandtail recombination of carriers. In addition, the blue luminescence is assigned to the silicon-related defects according to the analysis for the gap states in silicon nitride.
Low electron mobility of field-effect transistor determined by modulated magnetoresistance
Authors: Tauk R. , Łusakowski J. , Knap W. , Tiberj A. , Bougrioua Z. , Azize M. , Lorenzini P. , Sakowicz M. , Karpierz K. , Fenouillet-Beranger C. , Cassé M. , Gallon C. , Boeuf F. , Skotnicki T.
Published: November 2007

Room temperature magnetotransport experiments were carried out on field-effect transistors in magnetic fields up to 10 T. It is shown that measurements of the transistor magnetoresistance and its first derivative with respect to the gate voltage allow the derivation of the electron mobility in the gated part of the transistor channel, while the access/contact resistances and the transistor gate length need not be known. We demonstrate the potential of this method using GaN and Si field-effect transistors and discuss its importance for mobility measurements in transistors with nanometer gate length.
Nanosecond-range measurements of imprint effect for Pt∕IrO2∕Pb(Zr0.4Ti0.6)O3∕IrO2∕Pt thin-film capacitors
Authors: Jiang A. Q. , Lin Y. Y. , Tang T. A.
Published: November 2007

The determination of the coercive voltage from the height of domain-switching current plateau in ferroelectric thin films provides the liability to estimate the coercive-voltage shift with imprint time shortly on the order of polarization-reversal time. The voltage shift exhibits a linear time dependence in a logarithmic scale above an initial time (∼1μs), below which the voltage is nearly constant. The modeling of imprint on the basis of the interfacial charge injection at different stressing voltages strongly supports Schottky emission as a dominant mechanism, instead of Frenkel-Poole emission and Fowler-Nordheim tunneling.
Gene expression profiling of Hereford Shorthorn cattle following challenge with Boophilus microplus tick larvae
Authors: Wang Y. H. , Reverter A. , Kemp D. , McWilliam S. M. , Ingham A. , Davis C. A. , Moore R. J. , Lehnert S. A.
Published: November 2007

The ability of cattle to resist tick infestations is partly genetically determined. In order to better define the nature of Bos taurus resistance to the cattle tick Boophilus microplus, skin gene expression was studied using a cattle skin derived cDNA microarray. Expression profiles were determined in skin biopsies sampled from three highly tick resistant animals (HR) and two animals with lower tick resistance (LR) at time 0, immediately before challenge, and again 24 h after challenge. The analysis of the resulting expression data addressed two biological questions: first, for any animal exposed to ticks, which genes are differentially expressed in the 24 h following challenge; and second, which genes are differentially expressed between animals of high and low resistance at 24 h after challenge? In total, 214 genes were found to be differentially expressed in response to larval challenge across all the animals. Seventy-two genes were upregulated and 76 were downregulated at 24 h after challenge. Genes with significantly altered gene expression levels following tick infestation were predominantly keratin genes or mitochondrial genes, as well as odorant binding protein (OBP) and Bos taurus major allergen BDA20. In addition, we identified 66 genes with differential expression between HR and LR animals at 24 h. Of these, genes representing the extracellular matrix and immunoglobulin gene expression pathways were overrepresented. Three differentially expressed genes, OBP, Bos taurus major allergen BDA20 and dendritic cell protein HFL-B5 were further analysed by quantitative reverse transcription PCR (qRT-PCR). The qRT-PCR assay results closely mirrored the expression profiles found in the microarray experiment.
Human β-defensin-3 activates professional antigen-presenting cells via Toll-like receptors 1 and 2
Authors: Funderburg Nicholas , Lederman Michael M. , Feng Zhimin , Drage Michael G. , Jadlowsky Julie , Harding Clifford V. , Weinberg Aaron , Sieg Scott F.
Published: November 2007

There is increasing evidence that innate and adaptive immune responses are intimately linked. This linkage is in part mediated through the recognition of conserved microbial products by Toll-like receptors (TLRs). Detection of microbial products by TLRs can result in induction of inflammatory cytokines and activation of professional antigen-presenting cells, thereby enhancing adaptive immune responses. Here, we show that human β-defensin-3 (hBD-3), an innate antimicrobial peptide, can induce expression of the costimulatory molecules CD80, CD86, and CD40, on monocytes and myeloid dendritic cells in a TLR-dependent manner. Activation of monocytes by hBD-3 is mediated by interaction with TLRs 1 and 2, resulting in signaling that requires myeloid differentiating factor 88 and results in IL-1 receptor-associated kinase-1 phosphorylation. In studies with HEK cells engineered to express various TLRs, we show that activation of NF-κB by hBD-3 depends on the expression of both TLR1 and TLR2. Thus, human TLR signaling is not restricted to recognition of microbial patterns but also can be initiated by host-derived peptides such as hBD-3.
Measurement of bond vector orientations in invisible excited states of proteins
Authors: Vallurupalli Pramodh , Hansen D. Flemming , Stollar Elliott , Meirovitch Eva , Kay Lewis E.
Published: November 2007

The focus of structural biology is on studies of the highly populated, ground states of biological molecules; states that are only sparsely and transiently populated are more difficult to probe because they are invisible to most structural methods. Yet, such states can play critical roles in biochemical processes such as ligand binding, enzyme catalysis, and protein folding. A description of these states in terms of structure and dynamics is, therefore, of great importance. Here, we present a method, based on relaxation dispersion NMR spectroscopy of weakly aligned molecules in a magnetic field, that can provide such a description by direct measurement of backbone amide bond vector orientations in transient, low populated states that are not observable directly. Such information, obtained through the measurement of residual dipolar couplings, has until now been restricted to proteins that produce observable spectra. The methodology is applied and validated in a study of the binding of a target peptide to an SH3 domain from the yeast protein Abp1p and subsequently used in an application to protein folding of a mutational variant of the Fyn SH3 domain where
1
H-
15
N dipolar couplings of the invisible unfolded state of the domain are obtained. The approach, which can be used to obtain orientational restraints at other sites in proteins as well, promises to significantly extend the available information necessary for providing a site-specific characterization of structural properties of transient, low populated states that have to this point remained recalcitrant to detailed analysis.
Guarding the gates of Europe: A typological analysis of immigration attitudes across 21 countries
Authors: Green Eva G. T.
Published: November 2007

With data from the European Social Survey (N = 36,602), individual patterns of three immigration attitudes, referred to as gatekeeping attitudes, were investigated within and across 21 European national contexts. Gatekeeping attitudes, akin to blatant and subtle forms of xenophobia, designate the level of endorsement of different admission standards set for immigrants entering European countries, as well as of expulsion criteria for immigrants transgressing norms and laws. A K‐means cluster analysis, performed on national majority members' scores of endorsement of individual (e.g., language and working skills) and categorical (e.g., skin colour, religion) entry criteria and individual expulsion criteria (e.g., criminal act, long‐term unemployment), yielded a typology of three constrained combinations of these dimensions. Strict gatekeepers favoured all criteria, lenient gatekeepers opposed all criteria, whereas individualist gatekeepers favoured individual and opposed categorical criteria. Membership in typology groups was predicted with a generalized prejudiced attitude construct, social status, and personal contact with immigrants. Lenient gatekeepers were less homophobic, had a higher education level, felt financially less vulnerable, and had more immigrant friends than strict gatekeepers. Individualist gatekeepers held an intermediate position. Variability was observed in all countries, despite the prevalence of a typology group within a given country. Strict gatekeepers were common among participants from Southern and Eastern European nations, lenient gatekeepers in Scandinavian countries, and individualist gatekeepers in Western European countries. Cross‐national differences are discussed in light of European immigration history and policies.
The interplay between values, acculturation and adaptation: A study on Turkish‐Belgian adolescents
Authors: Güngör Derya
Published: November 2007

Although there is a bulk of evidence for the relations between values, acculturation, and adaptation, the interrelations between these key concepts of the acculturation literature have not yet been investigated simultaneously. The present study proposes a model connecting value orientations (separatedness and conformity) to adaptation outcomes (sociocultural and psychological). Furthermore, this link was hypothesized to be strengthened by an indirect relationship where acculturation strategies (culture maintenance and culture adoption) would relate certain values to certain aspects of adaptation. The model was tested on 287 Turkish‐Belgian adolescents with an average age of 16.27 years (SD = 1.86 years). SEM analysis confirmed the hypothesized indirect links underlining the crucial role of acculturation strategies as mediators in the adaptation process. Separatedness predicted sociocultural adaptation via culture adoption whereas conformity impacted psychological adaptation via culture maintenance. In addition, separatedness predicted poorer psychological adaptation. Results were discussed with reference to inverse benefits and costs of individualism and collectivism.
Afghanistan and the Opium World Market: Poppy Production and Trade
Authors: Kreutzmann Hermann
Published: November 2007

The Afghan poppy cultivation is presented here as a case in point to exemplify the linkages between external influences and local effects. World market and power relations have influenced cultivation patterns, processing, and trafficking. At the same time, poppy cultivation pinpoints an internal development which is strongly linked to deteriorating state control, warlordism, and regional power politics. Opium production has served as a major source of revenue for the upholding of disparate political structures which reflect the present political map of Afghanistan. Poppy cultivation in Afghanistan gained a substantial push during the last quarter century, from an annual production of 200 tons in 1979 to 4,200 tons in 2004, making use of former development efforts in creating irrigated oases in Helmand and Nangarhar. Prices rose after the Taliban's 2001 ban on production, raising farmers' incomes substantially and turning opium into an unrivalled cash crop. Fairly new production zones have been added in recent times; for example, Badakhshan—the stronghold of the Northern Alliance—has gained the third position with major increases in the last few years. Afghanistan's poppy cultivation and opium production has to be interpreted in terms of globalization and fragmentation. Drug trafficking affects the neighboring states, namely, Iran, Tajikistan, and Pakistan, as they function as consumer markets as well as trade routes for contraband drugs heading towards the West. Consequently, the Afghan poppy cultivation is interpreted in a holistic manner.
Islam and Ethnic Conflict: Hypotheses and Post-Communist Illustrations*
Authors: Horowitz Shale
Published: November 2007

The end of the Cold War drew increasing attention to ongoing and new ethnic conflicts—particularly because many of the high-profile new conflicts broke out amid the ruins of communism. Since 11 September 2001 there has been even more discussion about whether and how Islam contributes to international and civilizational conflict. However, there has been little work attempting to understand whether Islam plays any distinctive role in ethnic conflicts. Much work on ethnic conflict assumes that Islam is just one possible component of ethnic and national identities, and that it has no distinctive influence. Others examine whether Islam always has a similar impact on ethnic conflict—typically based upon identifying states or minority groups as having majority Muslim populations.
Looking over our shoulders: critical thinking and ontological insecurity in higher education
Authors: Jones Anna
Published: November 2007

This paper examines the changing landscape of higher education from the perspective of teaching academics. Critical thinking has been seen as one of the central facets of the academic identity and so this paper uses the notion of critical thinking as a lens through which to explore
this changing identity. It argues that the professional identity of the academic is in a state of flux, which has caused uncertainty regarding the academic role, its freedoms and responsibilities. The particular focus here is on teaching and the changes occurring in this arena. The paper reports
the findings of a qualitative study based on in-depth interviews with academic staff across five disciplines from two Australian universities. In the modern university, the pressures of accountability to a range of stakeholders, both internal and external, are changing the face of university
teaching.
The potential of threshold concepts: an emerging framework for educational research and practice
Authors: Lucas Ursula , Mladenovic Rosina
Published: November 2007

This paper explores the notion of a 'threshold concept' and discusses its possible implications for higher education research and practice. Using the case of introductory accounting as an illustration, it is argued that the idea of a threshold concept provides an emerging theoretical
framework for a 're-view' of educational research and practice. It is argued that this re-view both demands and supports several forms of dialogue about educational research and practice: within the disciplines (between lecturers and between lecturers and students) and between lecturers and
educational developers. Finally, it is suggested that, rather than representing a research field in its own right, the threshold concepts framework may act as a catalyst, drawing together a variety of fields of research in a productive educative framework.
Conflicting philosophies of inclusion: the contestation of knowledge in widening participation
Authors: Sheeran Yanina , Brown B. J. , Baker Sally
Published: November 2007

This paper explores the conflicting philosophies within the widening participation debate. Two categories of inclusive educators are identified, 'meritocrats' and 'democrats'. Among the democratic educators, a subgroup, 'transformative' educators, exists, which seeks to invoke changes
in society and the education system. The positions taken by some of these authors are weakened by their neglect of sociological theory. For the debate to progress and for inclusion to be successful, a renewed understanding of sociological theory is needed. This will help those contributing
to the debate to grasp fully the political and economic constraints on students and institutions that have limited inclusion.
On the same wavelength but tuned to different frequencies? Perceptions of academic and admissions staff in England and Wales on the articulation between 14–19 education and training and higher education
Authors: Wilde Stephanie , Wright Susannah
Published: November 2007

This paper examines the views of staff at higher education institutions on how well 14–19 education and training prepares young people for higher education (HE) study. It draws upon research involving focus groups with approximately 250 academic and admissions staff at 21 higher
education institutions in England and Wales. The data collection was conducted between February and June 2005. The paper presents their perceptions of the articulation between 14–19 education and training and higher education. It examines their perceptions of the preparedness of young
people to enter HE, and their preparedness to engage with HE. The evidence presented suggests an urgent need for more effective communication between the respective actors and institutions in 14–19 education and training and HE, particularly with regard to approaches to learning.
Conditions of detention and the deterioration of juveniles’ health: An evidence of ill‐treatment in Rio de Janeiro
Authors: Novis Roberta
Published: November 2007

This paper demonstrates that the health of juveniles in deprivation of liberty in Rio de Janeiro, Brazil, deteriorates while in detention and that conditions of detention are the major catalyst for offenders’ declining health status. The environment is conducive to the propagation and contamination of health‐related problems such as skin, respiratory, dental, and ear illness and viruses and parasitic infections. The paper concludes that at the moment, both inmates and the environment are disease carriers, deteriorating juveniles’ health status.
GEIGER: investigating evolutionary radiations
Authors: Harmon Luke J. , Weir Jason T. , Brock Chad D. , Glor Richard E. , Challenger Wendell
Published: November 2007

Summary: GEIGER is a new software package, written in the R language, to describe evolutionary radiations. GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Additionally, GEIGER's simulation algorithms can be used to analyze the statistical power of comparative approaches.

Availability: This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.

Contact:  lukeh@uidaho.edu
Computing topological parameters of biological networks
Authors: Assenov Yassen , Ramírez Fidel , Schelhorn Sven-Eric , Lengauer Thomas , Albrecht Mario
Published: November 2007

Summary: Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. NetworkAnalyzer can be applied to both directed and undirected networks and also contains extra functionality to construct the intersection or union of two networks. It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user.

Availability: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org

Contact:  mario.albrecht@mpi-inf.mpg.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Text processing through Web services: calling Whatizit
Authors: Rebholz-Schuhmann Dietrich , Arregui Miguel , Gaudan Sylvain , Kirsch Harald , Jimeno Antonio
Published: November 2007

Motivation: Text-mining (TM) solutions are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of resources (e.g. available controlled vocabularies), with the amount of literature to be processed (e.g. about 17 million documents in PubMed) and with the demands of the user community (e.g. different methods for fact extraction). These demands motivated the development of a server-based solution for literature analysis.

Whatizit is a suite of modules that analyse text for contained information, e.g. any scientific publication or Medline abstracts. Special modules identify terms and then link them to the corresponding entries in bioinformatics databases such as UniProtKb/Swiss-Prot data entries and gene ontology concepts. Other modules identify a set of selected annotation types like the set produced by the EBIMed analysis pipeline for proteins. In the case of Medline abstracts, Whatizit offers access to EBI's in-house installation via PMID or term query. For large quantities of the user's own text, the server can be operated in a streaming mode (http://www.ebi.ac.uk/webservices/whatizit).

Contact: rebholz@ebi.ac.uk
Epigenetic alteration of the Wnt inhibitory factor‐1 promoter occurs early in the carcinogenesis of Barrett's esophagus
Authors: Clément Geneviève , Guilleret Isabelle , He Biao , Yagui‐Beltrán Adam , Lin Yu‐Ching , You Liang , Xu Zhidong , Shi Yihui , Okamoto Junichi , Benhattar Jean , Jablons David
Published: November 2007

The role of Wnt antagonists in the carcinogenesis of esophageal adenocarcinoma (EAC) remains unclear. We hypothesized that downregulation of the Wnt inhibitory factor‐1 (WIF‐1) might be involved in the neoplastic progression of Barrett's esophagus (BE). We analyzed the DNA methylation status of the WIF‐1 promoter in normal, preneoplastic, and neoplastic samples from BE patients and in EAC cell lines. We investigated the role of WIF‐1 on EAC cell growth and the chemosensitization of the cells to cisplatin. We found that silencing of WIF‐1 correlated with promoter hypermethylation. EAC tissue samples showed higher levels of WIF‐1 methylation compared to the matched normal epithelium. In addition, we found that WIF‐1 hypermethylation was more frequent in BE samples from patients with EAC than in BE samples from patients who had not progressed to EAC. Restoration of WIF‐1 in cell lines where WIF‐1 was methylation‐silenced resulted in growth suppression. Restoration of WIF‐1 could sensitize the EAC cells to the chemotherapy drug cisplatin. Our results suggest that silencing of WIF‐1 through promoter hypermethylation is an early and common event in the carcinogenesis of BE. Restoring functional WIF‐1 might be used as a new targeted therapy for the treatment of this malignancy. (Cancer Sci 2008; 99: 46–53)