bluuebunny/crossref_metadata_2025 huggingface dataset:
Electro-optic bistability in organosiloxane bimesogenic liquid crystals
Authors: Gardiner D. J. , Davenport C. J. , Newton J. , Coles H. J.
Published: June 2006

In this paper we report the electro-optic characterization of two homologous series of low molar mass bimesogenic siloxane-containing liquid crystals. The materials used have two alkoxycyanobiphenyl mesogenic units with variable alkyl chain joined by a two- or five-siloxane moiety and all exhibit stable smectic A mesophases over wide temperature ranges (up to 100°C wide). Due to their inherent ruggedness these materials have potential for use in polarizer-free, bistable, scattering display and storage devices. The bistable modes are at low and high frequencies. The low frequency mode (write) is a highly scattering focal conic texture resulting from electrohydrodynamic instabilities while the high frequency mode (erase) is a clear state due to dielectric reorientation of the material. Both modes are preserved upon removal of the applied electric field. We present threshold voltages as a function of temperature, frequency, and cell thickness and response times as a function of voltage for each of the bistable modes. We find reduced threshold voltages (5⩽Vth⩽12V∕μm) and response times that are strongly dependent on applied voltage (50ms⩽τ⩽10s). These operating conditions would suggest that these materials are particularly suitable for slow update, large area, low power information panels and displays.
Ultraviolet and visible upconversion luminescence in Nd3+-doped oxyfluoride glasses and glass ceramics obtained by different preparation methods
Authors: Méndez-Ramos J. , Abril M. , Martín I. R. , Rodríguez-Mendoza U. R. , Lavín V. , Rodríguez V. D. , Núñez P. , Lozano-Gorrín A. D.
Published: June 2006

Ultraviolet and visible upconversion emissions under infrared excitation have been obtained and compared in Nd3+-doped oxyfluoride glasses and glass ceramics prepared by different methods. The mechanisms involved in such processes have been analyzed. A spectroscopy study comparing absorption and upconversion excitation spectra has been carried out in order to discern in each case the mechanism involved in the origin of the upconversion emissions, i.e., two- or three-photon involved excited state absorption or energy transfer processes. The shape of the absorption and emission spectra and the relative upconversion efficiencies have been compared and explained taking into account the final distribution of the luminescent ions in the glassy and nanocrystalline phases.
The influence of lateral composition modulation on the photoluminescence of tensile strained InGaAs quantum wells at room temperature
Authors: Czaban J. A. , Thompson D. A.
Published: June 2006

In some cases, it is important to consider the influence that lateral composition modulation has on room temperature photoluminescence spectra. It is shown that for tensile strained InGaAs quantum wells, there is enough composition fluctuation that occurs spontaneously during growth to have an observable effect on room temperature spectra. The photoluminescence at room temperature shows different characteristics depending on the in-plane polarization of the emission, and these differences can be traced back to transitions in the In-rich regions at low temperature.
Dielectric properties of Ba0.6Sr0.4TiO3 thin films deposited by mist plasma evaporation using aqueous solution precursor
Authors: Huang Hui , Shi Peng , Wang Minqiang , Yao Xi , Tan O. K.
Published: June 2006

Mist plasma evaporation (MPE) technique has been developed to deposit Ba0.6Sr0.4TiO3 (BST) thin films on SiO2∕Si and Pt∕Ti∕SiO2∕Si substrates at atmospheric pressure using metal nitrate aqueous solution as precursor. MPE is characterized by the injection of liquid reactants into thermal plasma where the source materials in the droplets are evaporated by the high temperature of the thermal plasma. Nanometer-scale clusters are formed in the tail flame of the plasma, and then deposited and rearranged on the substrate at a lower temperature. Due to the high temperature annealing process of the thermal plasma before deposition, well-crystallized BST films were deposited at substrate temperature of 630°C. The dielectric constant and dielectric loss of the film at 100kHz are 715 and 0.24, respectively. Due to the good crystallinity of the BST films deposited by MPE, high dielectric tunability up to 39.3% is achieved at low applied electric field of 100kVcm−1.
Normal-directional and normal-hemispherical reflectances of micron- and submicron-sized powder beds at 633 and 790nm
Authors: Gusarov A. V. , Bentefour E. H. , Rombouts M. , Froyen L. , Glorieux C. , Kruth J.-P.
Published: June 2006

A conic pyroelectric detector is employed to measure the effective reflectances of powder beds of metals, SiC, WC, and graphite. The experimental results are compared with numerical solutions of the radiation transfer equation in a half-infinite homogeneous body with effective radiative properties. The effective albedo and phase function are theoretically estimated by the model of opaque particles with specularly or diffusely reflecting surfaces in the assumption of geometrical optics. The studied powder beds with particles of several tens of microns in diameter are generally described by the model where specular reflection by particle surfaces is assumed corresponding to refraction and extinction indices of materials in the dense form. The model does not apply to semitransparent particles of SiC. The powder beds of submicron particles of SiC and WC are highly agglomerated and consist of clusters of particles with diameters of several tens of microns. A submicron powder bed is found to be considerably less reflective than a micron-sized powder bed of the same material. This is described by the model where the agglomerates of submicron particles are treated as large particles with diffusely reflecting surfaces. The effective normal-hemispherical reflectance of a micron-sized powder bed correlates with the hemispherical reflectance of dense material. The observed differences between the experiment and the model can be explained by a systematic error at calibration, oxidation of materials, and diffraction effects.
A molecular kinetic model for the optical emission spectroscopy technique in inductively coupled nitrogen plasma
Authors: Zhu Xi-Ming , Pu Yi-Kang
Published: June 2006

A molecular kinetic model used for the line-ratio technique of optical emission spectroscopy to determine electron temperature in an inductively coupled nitrogen plasma is investigated in the pressure range 0.4–100mTorr. Using the electron temperature and electron density measured by a Langmuir probe, the calculated line ratios are found to be in agreement with those measured by a spectrometer. Using this model, the relative contribution of various kinetic processes to the particle balance is analyzed over the whole pressure range.
Chaotic behavior of nonlinearly coupled electrostatic and electromagnetic modes in electron-positron-ion magnetoplasma with equilibrium flows
Authors: Azeem M. , Mirza Arshad M.
Published: June 2006

A new set of nonlinear equations has been derived to study the temporal behavior of low frequency electrostatic and electromagnetic ion-temperature-gradient driven modes in an electron-positron-ion (e-p-i) magnetoplasma. The temporal behavior of the nonlinear mode coupling equations, under certain conditions, are governed by the coupled equations, which are the generalization of Lorenz and Stenflo type equations, admitting chaotic behavior. The linear stability of the generalized Lorenz-Stenflo system of equations is also presented for electrostatic and electromagnetic cases. The results of present investigation should be useful to understand the nonlinear properties of electromagnetic/electrostatic waves in an e-p-i magnetoplasma.
Plasma-sheath transition in the kinetic Tonks-Langmuir model
Authors: Riemann K.-U.
Published: June 2006

The famous Tonks-Langmuir model of a plane symmetric discharge is supplemented by a kinetic theory of the plasma-sheath transition on the “intermediate scale.” The mathematical structure of the transition is identical to that found for the collision dominated charge exchange model [K.-U. Riemann, J. Phys. D: Appl. Phys. 36, 2811 (2003)]. It reveals the significance of the asymptotic sheath edge and clarifies the role of the kinetic Bohm criterion. From the matching conditions an approximation for the plasma eigenvalue problem is obtained that is correct up to terms of the order λD∕L. Matched asymptotic potential curves are constructed and compared with numerical solutions. They show an excellent agreement, exceeding by far the expected range of validity in λD∕L.
Speed and shape of dust acoustic solitary waves with variable dust charge and two temperature ions
Authors: Das Brindaban , Chatterjee Prasanta
Published: June 2006

Dust acoustic solitary waves are investigated on the nonlinear, unmagnetized homogeneous dust ion electron plasma with variable dust charge and two temperature ions. The Sagdeev’s pseudopotential is determined in terms of ud, the dust ion speed. It is found that there exists a critical value of ud, beyond which the solitary waves cease to exist. This critical value of ud depends on other plasma parameters also.
Propagation of radially localized helicon waves in longitudinally nonuniform plasmas
Authors: Arefiev Alexey V. , Breizman Boris N.
Published: June 2006

A gradient in the plasma density across the guiding magnetic field can support a low-frequency radially localized helicon (RLH) wave in a plasma column. If the radial density gradient changes along the magnetic field, this wave can undergo reflection and also excite conventional whistlers. This paper presents calculations of the corresponding reflection coefficient, including the effect of whistler radiation. It is shown that a sharp longitudinal density drop causes a nearly complete reflection of the RLH wave. The longitudinal wavelength of the excited whistlers is much greater than that of the RLH wave, and, as a result, only a small fraction of the RLH wave energy is transferred to the whistlers.
Modeling the effect of toroidal plasma rotation on drift-magnetohydrodynamic modes in tokamaks
Authors: Chapman I. T. , Sharapov S. E. , Huysmans G. T. A. , Mikhailovskii A. B.
Published: June 2006

A new code, MISHKA-F (Flow), has been developed as an extension of the ideal magneto-hydrodynamic (MHD) code MISHKA-1 [Mikhailovskii et al., Plasma Phys. Rep. 23, 844 (1997)] in order to investigate the linear MHD stability of ideal and resistive eigenmodes with respect to the effects of toroidal rotation in tokamaks in general toroidal geometry with the ion diamagnetic drift effect taken into account. Benchmark test results of the MISHKA-F code show good agreement with analytic theory [A. B. Mikhailovskii and S. E. Sharapov, Plasma Phys. Controlled Fusion 42, 57 (2000)] for the stability limits of the ideal n∕m=1∕1 internal kink mode. The combined stabilizing effects of the ion diamagnetic drift frequency, ω*i, and the toroidal flow shear are also studied. The ω*i stabilization of the internal kink mode is found to be more effective at finite flow shear. Finite-n ballooning modes are studied in plasmas with the toroidal flow shear effect included. The stabilization of the ballooning modes by toroidal rotation is found to agree well with earlier predictions [Webster et al., Phys. Plasmas 11, 2135 (2004)]. The effect of high flow shear is analyzed for a sawtoothing discharge typical in the Mega Ampère Spherical Tokamak (MAST) [Sykes et al., Nucl. Fusion 41, 1423 (2001)]. It is found that the ideal n=1 internal kink mode can be stabilized by toroidal rotation at values observed experimentally.
Nonlinear inward particle flux component in trapped electron mode turbulence
Authors: Terry P. W. , Gatto R.
Published: June 2006

Trapped electron turbulence is shown to have a significant inward particle flux component associated with nonlinear deviations of the density-potential cross correlation from the quasilinear value. The cross correlation is altered because the density advection nonlinearity mixes a linearly stable eigenmode with the eigenmode of the instability. The full nonlinear flux is evaluated by solving spectrum balance equations in a complete basis spanning the fluctuation space. An ordered expansion for small collisionality, perpendicular wave number, and temperature/density-gradient instability threshold parameter enables an analytic solution for a weakly driven regime. The solution quantifies the role of zonal modes on transport via their saturation of the turbulence under intensely anisotropic transfer. The inward transport is neither diffusive nor convective, but is driven by temperature gradient and enhanced by flat density gradients. It is slightly smaller than the outwardly directed flux associated with the growing eigenmode, making the flux a small fraction of the quasilinear value.
Two-stream instability for a longitudinally compressing charged particle beam
Authors: Startsev Edward A. , Davidson Ronald C.
Published: June 2006

The electrostatic two-stream instability for a cold, longitudinally compressing charged particle beam propagating through a background plasma has been investigated both analytically and numerically. Small-signal coupled equations describing the evolution of the perturbations are derived, and the asymptotic solutions are obtained. The results are confirmed by direct numerical solution of the linearized fluid equations. It is found that the longitudinal beam compression strongly modifies the space-time development of the instability. In particular, the dynamic compression leads to a significant reduction in the growth rate of the two-stream instability compared to the case without an initial velocity tilt.
Perpendicularly propagating electromagnetic modes in a strongly magnetized hot plasma with non-Maxwellian distribution function
Authors: Zaheer S. , Murtaza G. , Shah H. A.
Published: June 2006

Electromagnetic modes (ordinary and extraordinary) for strongly magnetized plasma are studied and their damping factors γor and γex are calculated using non-Maxwellian velocity distribution function. It is observed that for moderate values of the spectral indices r and q [used in (r,q) distribution functions], both the damping decrements show substantial change. As the value of the spectral index r increases for a fixed value of q, the damping increases for the O mode but decreases for the X mode. In the limiting case of r=0, q→∞, the damping factors reduce to the standard Maxwellian values.
Measurement of the charge transfer efficiency of electrons clocked on superfluid helium
Authors: Sabouret G. , Lyon S. A.
Published: June 2006

Electrons floating on the surface of liquid helium are possible qubits for quantum information processing. Varying electric potentials do not modify spin states, which allows their transport on helium using a charge-coupled device (CCD)-like array of underlying gates. This scheme depends on an efficient intergate electron transfer and on the absence of electron traps. We will present a measurement of the charge transfer efficiency (CTE) of electrons clocked back and forth above a short CCD-like structure. The CTE obtained at low clocking frequencies is 0.999 with an electron density of about 4electrons∕μm2. We find no evidence for deep electron trapping.
Design of an extremely stable low-temperature ultrahigh vacuum scanning tunneling microscope
Authors: Koslowski B. , Dietrich Ch. , Tschetschetkin A. , Ziemann P.
Published: June 2006

The design and performance of a scanning tunneling microscope operated under ultrahigh vacuum conditions and at low temperature are presented. It allows operating temperatures between 6K to at least 30K as well as safe and fast tip/sample transfers. Novel design features resulted in an extremely stable instrument with a noise level of only 0.2pmrms in the frequency range of 0.5–500Hz despite a relatively noisy laboratory environment. To demonstrate this behavior, results of test measurements performed on Au(111) and Nb(110) samples are presented.
Surface determination of the air-earth electrical current density using co-located sensors of different geometry
Authors: Bennett A. J. , Harrison R. G.
Published: June 2006

A vertical conduction current flows in the atmosphere as a result of the global atmospheric electric circuit. The current at the surface consists of the conduction current and a locally generated displacement current, which are often approximately equal in magnitude. A method of separating the two currents using two collectors of different geometry is investigated. The picoammeters connected to the collectors have a RC time constant of approximately 3s, permitting the investigation of higher frequency air-earth current changes than previously achieved. The displacement current component of the air-earth current derived from the instrument agrees with calculations using simultaneous data from a co-located fast response electric field mill. The mean value of the nondisplacement current measured over 9h was 1.76±0.002pAm−2.
Ferroelectric properties of nanocrystalline barium titanate ceramics
Authors: Deng Xiangyun , Wang Xiaohui , Wen Hai , Chen Liangliang , Chen Lei , Li Longtu
Published: June 2006

Dense nanocrystalline BaTiO3 ceramics with the average grain size of 20nm obtained by spark plasma sintering were investigated. The dielectric data show a ferroelectric to paraelectric phase transition with a maximum permittivity of ≈930 at 115°C and at 1kHz. The polarization-reversal characteristics and the local ferroelectric switching behavior were measured; the typical piezoelectric hysteresis loops were recorded. The present results provide experimental evidence, indicating that if a critical grain size exists for ferroelectricity it is less than 20nm for polycrystalline BaTiO3 ceramics.
Dependence of saturation effects on electron confinement and injector doping in GaAs∕Al0.45Ga0.55As quantum-cascade lasers
Authors: Höfling S. , Jovanović V. D. , Indjin D. , Reithmaier J. P. , Forchel A. , Ikonić Z. , Vukmirović N. , Harrison P. , Mirčetić A. , Milanović V.
Published: June 2006

We report on a detailed experimental and theoretical analysis of the role of injector doping density on both the threshold current density (Jth) and the saturation current density (Jsat), determining the dynamic range of the quantum cascade lasers. The experimental results were obtained from two growth series of λ≈9μm GaAs∕Al0.45Ga0.55As quantum-cascade lasers based on single and double phonon resonance depopulation mechanisms. We derive a quasilinear dependence of Jth on the injector doping density of both designs for doping range as wide as (4–10)×1011cm−2. Despite threshold current increase the faster rise of saturation current with doping results in an enhanced dynamic range for injector doping up to ∼8×1011cm−2. For higher doping levels, Jsat itself saturates. Furthermore, our investigations yield that single phonon resonance devices exhibit clear current saturation simultaneously with a decrease of the optical power, whereas two phonon resonance devices show only power saturation, which we attribute to increased leakage currents. These deteriorate the laser performance of the latter design at higher operational temperatures.
Electrical properties of a single electrochemically template-synthesized polypyrrole nanowire
Authors: Shen Jiaoyan , Chen Zhaojia , Wang Nanlin , Yan Hongliang , Shi Gaoquan , Jin Aizi , Gu Changzhi
Published: June 2006

The electrical properties of a single conducting polypyrrole nanowire, template-synthesized by electrochemical polymerization of pyrrole, were directly measured by the four-terminal technique. Two pairs of microelectrodes were deposited by the focused ion beam system. It is found that the resistivity of the measured nanowire lies in the insulating regime and it follows the one-dimensional Mott variable range hopping model in the temperature range of 77–300K. The conductivity of several segments of another single polypyrrole nanowire was also measured by a multiterminal configuration at room temperature, and it is found that the conductivity is not uniform even on the same nanowire.
Zinc oxide nanodonut prepared by vapor-phase transport process
Authors: Chao Liang-Chiun , Chiang Ping-Chang , Yang Shih-Hsuan , Huang Jian-Wei , Liau Chung-Chi , Chen Jyh-Shin , Su Chien-Ying
Published: June 2006

Zinc oxide nanodonuts have been synthesized using vapor-phase transport method. Zinc oxide powder, graphite powder, and erbium oxide powder were mixed with a molar ratio of 1:1:0.2 and heated at 1050°C in a flowing argon environment. Perfectly donut-shaped nanostructures with outer diameters ranging from 450to850nm were observed. The inner diameter of the zinc oxide donut varies from 75to95nm and the vertical distance from the highest point to the lowest point vary from 85to130nm. The composition of the nanodonut was analyzed using Auger electron spectroscopy and was found to be mainly of zinc oxide. Diffusion of silicon into the zinc oxide layer was confirmed by secondary ion mass spectroscopy.
Laser noise reduction in air
Authors: Béjot Pierre , Kasparian Jérôme , Salmon Estelle , Ackermann Roland , Gisin Nicolas , Wolf Jean-Pierre
Published: June 2006

Fluctuations of the white-light supercontinuum produced by ultrashort laser pulses in self-guided filaments (spatiotemporal solitons) in air are investigated. We demonstrate that correlations exist within the white-light supercontinuum, and that they can be used to significantly reduce the laser intensity noise by filtering the spectrum. More precisely, the fundamental wavelength is anticorrelated with the wings of the continuum, while conjugated wavelength pairs on both sides of the continuum are strongly correlated. Spectral filtering of the continuum reduces the laser intensity noise by 1.2dB, showing that fluctuations are rejected to the edges of the spectrum.
International Family Migration and Differential Labour-Market Participation in Great Britain: Is There a ‘Gender Gap’?
Authors: Smith Darren P , Bailey Adrian J
Published: June 2006

Drawing upon studies of subnational (internal) family migration, in this paper we link international family migration to differential labour-market participation in Great Britain. We extend Kofman's fourfold categorisation of international family migration processes to develop a typology of scenarios that acknowledge the important role of the family. We match scenarios to different out-comes using a subsample of partnered migrants from the Sample of Anonymised Records (SAR) of the 1991 Census. In line with subnational family migration literature, descriptive analyses of the SAR point to a ‘gender gap’ between the labour-market participation of partnered men and partnered women moving into Great Britain between 1990–1991, with males twice as likely to be attached to the labour force compared with women. We contribute to debates on changing family organisation and employment returns to international migration by arguing that the magnitude of this gender gap varies across migration scenario and family structure. In this paper we stress the need for more interchange between international and subnational family-migration scholarship, and provide valuable entrees for analyses of the forthcoming microdata of the 2001 Census.
The Embeddedness of Global Production Networks: The Impact of Crisis in Fiji's Garment Export Sector
Authors: Weller Sally
Published: June 2006

In this paper the author explores how changing geopolitical conditions reconfigure network embeddedness and theorises the conditions of network disconnection and transformation. Through a case study of the changes in interfirm relationships within the Fiji–Australia garment-production network after Fiji's 2000 political coup d'état, the author develops a relational and dynamic view of embeddedness, highlighting its multifaceted and multiscalar character and emphasising the interrelationships between embeddedness, trust, and power.
Offshoring the Financial Services Industry: Implications for the Evolution of Indian IT Clusters
Authors: Grote Michael H , Täube Florian A
Published: June 2006

The authors explore the opportunities for existing Indian IT clusters to upgrade and undertake financial research activities. Wholesale financial activity and the accompanying financial research in banks are still highly concentrated in Western financial centers. Increasing competition in the financial services industry, as well as regulatory pressure, place the options of outsourcing and offshoring activities, especially research, to low-cost locations high on the agenda of financial institutions. For the first time, complex tasks at the core of financial activity are being offshored, which makes this an interesting case for a lot of other industries and their spatial economic organization in an ever-globalizing world. Will there be a World Financial Research Centre in Mumbai? With the aid of qualitative interview data as well as a quantitative analysis, the authors argue that research activities are locally embedded in Western financial centers to an extent that such a development is not likely. Two different research activities, country analysis and institutional equity analysis, are examined. The analysis suggests, however, that there is a certain potential for some research activities to be relocated to India. So far, investments take place in a very few existing IT clusters which have already gained a reputation in the financial community.
Sustainable Land Reuse: The Influence of Different Stakeholders in Achieving Sustainable Brownfield Developments in England
Authors: Dair Carol M , Williams Katie
Published: June 2006

The UK government has made the sustainable reuse of land a strong policy aim in its sustainable development and planning strategies. However, in this paper we present research into recent urban brownfield redevelopments in England that shows that many aspects of sustainability are currently not being considered in practice. To explain this, we focus on the role of different stakeholders involved in brownfield development and critically examine their actions and decisions. We establish which stakeholder types (for example, architects, planners, councillors, developers, investors) are more likely to attempt to introduce sustainability into development projects and which are more successful in meeting their agendas. We conclude by identifying five reasons for variation in the achievement of sustainability in brownfield development.
Wasted Density? The Impact of Toronto's Residential-Density-Distribution Policies on Public-Transit Use and Walking
Authors: Filion Pierre , McSpurren Kathleen , Appleby Brad
Published: June 2006

Although the Toronto metropolitan region performs well relative to its North American counterparts in terms of density and public-transit use, it does not derive as much walking and public-transit patronage benefit from its high-residential-density areas as it could. The impact of residential density on journey patterns is limited by an imperfect juxtaposition of density and public-transit service peaks. Another impediment is the difficulty of associating density with other variables needed for it to translate into increased walking and public-transit modal shares. We attribute this situation to insufficient planning capacity owing in large part to generalized neighbourhood opposition to high-density residential developments and disagreement between levels of government. In this paper we both narrate events of relevance to the distribution of high residential density over the last five decades and analyze present relationships between high-density areas and journey patterns. We conclude by discussing the possibility of achieving residential-density layouts and distributions that are more conducive to walking and public-transit use than the tower-in-the-park model and the scattering of high-density pockets, both of which predominate in Toronto.
Making Connections: Global Production Networks, Standards, and Embeddedness in the Mobile-Telecommunications Industry
Authors: Hess Martin , Coe Neil M
Published: June 2006

The authors investigate the contemporary restructuring of the mobile-telecommunications industry with the use of a global production networks (GPNs) perspective. After a brief conceptual discussion of GPN, standard setting and embeddedness, their analysis proceeds in four further stages. First, they consider how technological change has driven the development of complex mobile telecommunications GPNs in a sector previously characterised by relatively linear and simple value chains. Second, they show how processes of deregulation and privatisation over the past two decades have enabled the internationalisation of mobile telecommunications provision. Third, they explore the delicate power balance between embedded state and corporate actors in telecommunications GPNs through a consideration of the changing bases of standard setting in the industry. Despite ongoing processes of globalisation, the continuing importance of national policies and strategies is clear. Fourth, they demonstrate the continuing importance and differentiating role of embeddedness in the transformation of corporate mobile telecommunication GPNs. In sum, it is argued that the mobile-telecommunications sector should be understood as a constellation of multiscalar manufacturing and distribution networks connecting together firms, organisations, and customers in geographically uneven ways.
Inner retinal photoreception independent of the visual retinoid cycle
Authors: Tu Daniel C. , Owens Leah A. , Anderson Lauren , Golczak Marcin , Doyle Susan E. , McCall Maureen , Menaker Michael , Palczewski Krzysztof , Van Gelder Russell N.
Published: June 2006

Mice lacking the visual cycle enzymes RPE65 or lecithin-retinol acyl transferase (Lrat) have pupillary light responses (PLR) that are less sensitive than those of mice with outer retinal degeneration (
rd/rd
or
rdta
). Inner retinal photoresponses are mediated by melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs), suggesting that the melanopsin-dependent photocycle utilizes RPE65 and Lrat. To test this hypothesis, we generated
rpe65
−/−
; rdta
and
lrat
−/−
; rd/rd
mutant mice. Unexpectedly, both
rpe65
−/−
; rdta
and
lrat
−/−
; rd/rd
mice demonstrate paradoxically increased PLR photosensitivity compared with mice mutant in visual cycle enzymes alone. Acute pharmacologic inhibition of the visual cycle of melanopsin-deficient mice with
all-trans
-retinylamine results in a near-total loss of PLR sensitivity, whereas treatment of
rd/rd
mice has no effect, demonstrating that the inner retina does not require the visual cycle. Treatment of
rpe65
−/−
; rdta
with 9-
cis
-retinal partially restores PLR sensitivity. Photic sensitivity in P8
rpe65
−/−
and
lrat
−/−
ipRGCs is intact as measured by
ex vivo
multielectrode array recording. These results demonstrate that the melanopsin-dependent ipRGC photocycle is independent of the visual retinoid cycle.
Functional conservation of cold shock domains in bacteria and higher plants
Authors: Nakaminami Kentaro , Karlson Dale T. , Imai Ryozo
Published: June 2006

In
Escherichia coli
, a family of cold shock proteins (CSPs) function as transcription antiterminators or translational enhancers at low temperature by destabilizing RNA secondary structure. A wheat nucleic acid-binding protein (WCSP1) was found to contain a cold shock domain (CSD) bearing high similarity to
E. coli
cold shock proteins. In the present study, a series of mutations were introduced into WCSP1, and its functionality was investigated by using
in vivo
and
in vitro
assays in the context of functional conservation with
E. coli
CSPs. Constitutive expression of WT
WCSP1
in an
E. coli
cspA
,
cspB
,
cspE
,
cspG
quadruple deletion mutant complemented its cold-sensitive phenotype, suggesting that WCSP1 shares a function with
E. coli
CSPs for cold adaptation. In addition, transcription antitermination activity was demonstrated for WCSP1 by using an
E. coli
strain that has a hairpin loop upstream of a chloramphenicol resistance gene.
In vitro
dsDNA melting assays clearly demonstrated that WCSP1 melts dsDNA, an activity that was positively correlated to the ability to bind ssDNA. When mutations were introduced at critical residues within the consensus RNA binding motifs (RNP1 and RNP2) of WCSP1, it failed to melt dsDNA. Studies with WCSP1-GFP fusion proteins documented patterns that are consistent with ER and nuclear localization.
In vivo
and
in vitro
functional analyses, coupled with subcellular localization data, suggest that WCSP1 may function as a RNA chaperone to destabilize secondary structure and is involved in the regulation of translation under low temperature.
H2AX phosphorylation within the G
1
phase after UV irradiation depends on nucleotide excision repair and not DNA double-strand breaks
Authors: Marti Thomas M. , Hefner Eli , Feeney Luzviminda , Natale Valerie , Cleaver James E.
Published: June 2006

The variant histone H2AX is phosphorylated in response to UV irradiation of primary human fibroblasts in a complex fashion that is radically different from that commonly reported after DNA double-strand breaks. H2AX phosphorylation after exposure to ionizing radiation produces foci, which are detectable by immunofluorescence microscopy and have been adopted as clear and consistent quantitative markers for DNA double-strand breaks. Here we show that in contrast to ionizing radiation, UV irradiation mainly induces H2AX phosphorylation as a diffuse, even, pan-nuclear staining. UV induced pan-nuclear phosphorylation of H2AX is present in all phases of the cell cycle and is highest in S phase. H2AX phosphorylation in G
1
cells depends on nucleotide excision repair factors that may expose the S-139 site to kinase activity, is not due to DNA double-strand breaks, and plays a larger role in UV-induced signal transduction than previously realized.
The complete genome sequence of a chronic atrophic gastritis
Helicobacter pylori
strain: Evolution during disease progression
Authors: Oh Jung D. , Kling-Bäckhed Helene , Giannakis Marios , Xu Jian , Fulton Robert S. , Fulton Lucinda A. , Cordum Holland S. , Wang Chunyan , Elliott Glendoria , Edwards Jennifer , Mardis Elaine R. , Engstrand Lars G. , Gordon Jeffrey I.
Published: June 2006

Helicobacter pylori
produces acute superficial gastritis in nearly all of its human hosts. However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition characterized in part by diminished numbers of acid-producing parietal cells and increased risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic mouse model with an engineered ablation of parietal cells to show that loss of parietal cells provides an opportunity for a
H. pylori
isolate from a patient with ChAG (HPAG1) to bind to, enter, and persist within gastric stem cells. This finding raises the question of how ChAG influences
H. pylori
genome evolution, physiology, and tumorigenesis. Here we describe the 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its predicted ORFs, were used for whole-genome genotyping of additional
H. pylori
ChAG isolates obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome transcriptional profiling of HPAG1’s response to acid during
in vitro
growth indicates that genes encoding components of metal uptake and utilization pathways, outer membrane proteins, and virulence factors are among those associated with
H. pylori
’s adaptation to ChAG.
A
Caenorhabditis elegans
tissue model of radiation-induced reproductive cell death
Authors: Weidhaas J. B. , Eisenmann D. M. , Holub J. M. , Nallur S. V.
Published: June 2006

We have developed a tissue model of radiation-induced reproductive cell death in the nematode
Caenorhabditis elegans
. Reproductive cell death is the primary mode of death in tissue multipotential precursor cells, or “clonogens,” the targets of cytotoxic therapy, whose elimination results in normal tissue damage as well as solid-tumor eradication. Through extensive morphologic and genetic analysis, we have confirmed that cell death in this model represents reproductive cell death in isolation from apoptotic cell death, affording the opportunity to define the genetic pathways required for protection from reproductive cell death. We have additionally found that the DNA damage response pathway is necessary for protection from reproductive cell death, supporting the long-held tenet that DNA damage is the cause of reproductive cell death and further validating this model. This genetic tissue model provides a valuable tool for oncology-based research and affords a platform to broaden our insight into responses to cytotoxic therapy in tissues.
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
Authors: Schwer Bjoern , Bunkenborg Jakob , Verdin Regis O. , Andersen Jens S. , Verdin Eric
Published: June 2006

We report that human acetyl-CoA synthetase 2 (AceCS2) is a mitochondrial matrix protein. AceCS2 is reversibly acetylated at Lys-642 in the active site of the enzyme. The mitochondrial sirtuin SIRT3 interacts with AceCS2 and deacetylates Lys-642 both
in vitro
and
in vivo
. Deacetylation of AceCS2 by SIRT3 activates the acetyl-CoA synthetase activity of AceCS2. This report identifies the first acetylated substrate protein of SIRT3. Our findings show that a mammalian sirtuin directly controls the activity of a metabolic enzyme by means of reversible lysine acetylation. Because the activity of a bacterial ortholog of AceCS2, called ACS, is controlled via deacetylation by a bacterial sirtuin protein, our observation highlights the conservation of a metabolic regulatory pathway from bacteria to humans.
Spontaneous neuronal activity distinguishes human dorsal and ventral attention systems
Authors: Fox Michael D. , Corbetta Maurizio , Snyder Abraham Z. , Vincent Justin L. , Raichle Marcus E.
Published: June 2006

On the basis of task-related imaging studies in normal human subjects, it has been suggested that two attention systems exist in the human brain: a bilateral dorsal attention system involved in top-down orienting of attention and a right-lateralized ventral attention system involved in reorienting attention in response to salient sensory stimuli. An important question is whether this functional organization emerges only in response to external attentional demands or is represented more fundamentally in the internal dynamics of brain activity. To address this question, we examine correlations in spontaneous fluctuations of the functional MRI blood oxygen level-dependent signal in the absence of task, stimuli, or explicit attentional demands. We identify a bilateral dorsal attention system and a right-lateralized ventral attention system solely on the basis of spontaneous activity. Further, we observe regions in the prefrontal cortex correlated with both systems, a potential mechanism for mediating the functional interaction between systems. These findings demonstrate that the neuroanatomical substrates of human attention persist in the absence of external events, reflected in the correlation structure of spontaneous activity.
Cep55, a Microtubule-bundling Protein, Associates with Centralspindlin to Control the Midbody Integrity and Cell Abscission during Cytokinesis
Authors: Zhao Wei-meng , Seki Akiko , Fang Guowei
Published: June 2006

We report here an efficient functional genomic analysis by combining information on the gene expression profiling, cellular localization, and loss-of-function studies. Through this analysis, we identified Cep55 as a regulator required for the completion of cytokinesis. We found that Cep55 localizes to the mitotic spindle during prometaphase and metaphase and to the spindle midzone and the midbody during anaphase and cytokinesis. At the terminal stage of cytokinesis, Cep55 is required for the midbody structure and for the completion of cytokinesis. In Cep55-knockdown cells, the Flemming body is absent, and the structural and regulatory components of the midbody are either absent or mislocalized. Cep55 also facilitates the membrane fusion at the terminal stage of cytokinesis by controlling the localization of endobrevin, a v-SNARE required for cell abscission. Biochemically, Cep55 is a microtubule-associated protein that efficiently bundles microtubules. Cep55 directly binds to MKLP1 in vitro and associates with the MKLP1-MgcRacGAP centralspindlin complex in vivo. Cep55 is under the control of centralspindlin, as knockdown of centralspindlin abolished the localization of Cep55 to the spindle midzone. Our study defines a cellular mechanism that links centralspindlin to Cep55, which, in turn, controls the midbody structure and membrane fusion at the terminal stage of cytokinesis.
Transcript mapping with high-density oligonucleotide tiling arrays
Authors: Huber Wolfgang , Toedling Joern , Steinmetz Lars M.
Published: June 2006

Motivation: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization signal along genomic coordinates to accurately determine transcript boundaries and the adjustment of the sequence-dependent response of the oligonucleotide probes to achieve quantitative comparability of the signal between different probes.

Results: We describe a dynamic programming algorithm for finding a globally optimal fit of a piecewise constant expression profile along genomic coordinates. We developed a probe-specific background correction and scaling method that employs empirical probe response parameters determined from reference hybridizations with no need for paired mismatch probes. This combined analysis approach allows the accurate determination of dynamical changes in transcription architectures from hybridization data and will help to study the biological significance of complex transcriptional phenomena in eukaryotic genomes.

Availability: R package tilingArray at .

Contact:  huber@ebi.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
A reference database for circular dichroism spectroscopy covering fold and secondary structure space
Authors: Lees Jonathan G. , Miles Andrew J. , Wien Frank , Wallace B. A.
Published: June 2006

Motivation: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined.

This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.

Contact:  b.wallace@mail.cryst.bbk.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Additional Gene Ontology structure for improved biological reasoning
Authors: Myhre Simen , Tveit Henrik , Mollestad Torulf , Lægreid Astrid
Published: June 2006

Motivation: The Gene Ontology (GO) is a widely used terminology for gene product characterization in, for example, interpretation of biology underlying microarray experiments. The current GO defines term relationships within each of the independent subontologies: molecular function, biological process and cellular component. However, it is evident that there also exist biological relationships between terms of different subontologies. Our aim was to connect the three subontologies to enable GO to cover more biological knowledge, enable a more consistent use of GO and provide new opportunities for biological reasoning.

Results: We propose a new structure, the Second Gene Ontology Layer, capturing biological relations not directly reflected in the present ontology structure. Given molecular functions, these paths identify biological processes where the molecular functions are involved and cellular components where they are active. The current Second Layer contains 6271 validated paths, covering 54% of the molecular functions of GO and can be used to render existing gene annotation sets more complete and consistent. Applying Second Layer paths to a set of 4223 human genes, increased biological process annotations by 24% compared to publicly available annotations and reproduced 30% of them.

Availability: The Second GO is publicly available through the GO Annotation Toolbox (GOAT.no):

Contact:  astrid.lagreid@ntnu.no
Increasing confidence of protein interactomes using network topological metrics
Authors: Chen Jin , Hsu Wynne , Lee Mong Li , Ng See-Kiong
Published: June 2006

Motivation: Experimental limitations in high-throughput protein–protein interaction detection methods have resulted in low quality interaction datasets that contained sizable fractions of false positives and false negatives. Small-scale, focused experiments are then needed to complement the high-throughput methods to extract true protein interactions. However, the naturally vast interactomes would require much more scalable approaches.

Results: We describe a novel method called IRAP* as a computational complement for repurification of the highly erroneous experimentally derived protein interactomes. Our method involves an iterative process of removing interactions that are confidently identified as false positives and adding interactions detected as false negatives into the interactomes. Identification of both false positives and false negatives are performed in IRAP* using interaction confidence measures based on network topological metrics. Potential false positives are identified amongst the detected interactions as those with very low computed confidence values, while potential false negatives are discovered as the undetected interactions with high computed confidence values. Our results from applying IRAP* on large-scale interaction datasets generated by the popular yeast-two-hybrid assays for yeast, fruit fly and worm showed that the computationally repurified interaction datasets contained potentially lower fractions of false positive and false negative errors based on functional homogeneity.

Availability: The confidence indices for PPIs in yeast, fruit fly and worm as computed by our method can be found at our website

Contact:  skng@i2r.a-star.edu.sg

Supplementary information: Supplementary data are available at Bioinformatics online.