bluuebunny/crossref_metadata_2025 huggingface dataset:
Instabilities in multicomponent cold magnetized accretion disks
Authors: Nekrasov A. K.
Published: June 2007

New instabilities in multicomponent cold magnetized accretion disks are found using not the magnetohydrodynamics (MHD) framework but the equations of motion and continuity for each disk component and Maxwell’s equations, where the magnetic field perturbations are substituted by the electric field perturbations. The stationary velocities of magnetized charged particles are taken to be not the Keplerian velocity, as it is adopted in the astrophysical literature using the MHD approach for studying disks, but as the electric and gravitational drifts in the external magnetic field (at the neglect of collisions). The compressibility is taken into account. There are considered axisymmetric as well as nonaxisymmetric perturbations in the form of columns and spokes. The growth rates of instabilities being found can be considerably larger than the growth rate of the well-known magnetorotational instability studied in the MHD framework.
Stability of arbitrary electron velocity distribution functions to electromagnetic modes
Authors: Tzoufras M. , Ren C. , Tsung F. S. , Tonge J. W. , Mori W. B. , Fiore M. , Fonseca R. A. , Silva L. O.
Published: June 2007

The stability of general electron distribution functions to purely electromagnetic modes is considered, so as to generalize the well-known stability analysis for bi-Gaussian distribution functions. The expansion of an arbitrary nonrelativistic distribution function into a modified version of Hermite–Gaussian modes yields the dispersion relation for electromagnetic modes in a compact form that depends on the coefficients of the expansion as well as the well-known plasma dispersion function and its derivatives. The coefficients of the expansion that enter the dispersion relation depend only on the zeroth and second moments from the direction of high temperature. The general dispersion relation is solved analytically for the frequency in the low anisotropy (kinetic) limit. Purely imaginary solutions can be found for distribution functions symmetric in the direction of the wavenumber. If, in addition to being symmetric, the distribution function is separable, the only quantity from the high-temperature direction that enters the equation for the frequency of the electromagnetic wave is the variance.
Revisiting the calculation of condensed Fukui functions using the quantum theory of atoms in molecules
Authors: Otero Nicolás , Mandado Marcos , Mosquera Ricardo A.
Published: June 2007

The analysis of previously reported shortcomings of the condensed Fukui functions obtained making use of the quantum theory of atoms in molecules indicates these drawbacks are due to the inadequacy of the definition employed to compute them and not to the partitioning. A new procedure, which respects the mathematical definition and solves these problems, is presented for the calculation of condensed Fukui functions for atomic basins defined according to the quantum theory of atoms in molecules. It is tested in a set of 18molecules, which includes the most controversial reported cases.
Spontaneous thermal magnetic field fluctuation
Authors: Yoon Peter H.
Published: June 2007

In recent days, the relativistic version of the classic Weibel instability received renewed attention for its potential role as a mechanism to generate cosmic magnetic fields. However, one of the key conceptual foundations in association with the Weibel instability has not been addressed in the literature. Namely, the spontaneous emission of magnetic field fluctuation, which is supposed to provide the seed perturbation for the Weibel instability, has not been adequately discussed. The present Brief Communication addresses this issue.
Ellipticity of axisymmetric equilibria with flow and pressure anisotropy in single-fluid and Hall magnetohydrodynamics
Authors: Ito Atsushi , Ramos Jesús J. , Nakajima Noriyoshi
Published: June 2007

The ellipticity criteria for the partial differential equations of axisymmetric single-fluid and Hall magnetohydrodynamic (MHD) equilibria with flow and pressure anisotropy are investigated. The MHD systems are closed with cold ions and electron pressures derived from their parallel heat flux equations, a closure that reproduces the corresponding kinetic dispersion relation. In the single-fluid model, which differs from the double-adiabatic Chew–Goldberger–Low model, it is verified that the elliptic region boundaries occur at poloidal flow velocities equal to wave velocities from the kinetic dispersion relation. For Hall magnetohydrodynamics, a set of anisotropic-pressure equilibrium equations is derived and an ellipticity condition corresponding to a poloidal flow velocity slightly smaller than the ion sound velocity is obtained.
Energy-consistent pseudopotentials for quantum Monte Carlo calculations
Authors: Burkatzki M. , Filippi C. , Dolg M.
Published: June 2007

The authors present scalar-relativistic energy-consistent Hartree-Fock pseudopotentials for the main-group elements. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. They demonstrate their transferability through extensive benchmark calculations of atomic excitation spectra as well as molecular properties. In particular, they compute the vibrational frequencies and binding energies of 26 first- and second-row diatomic molecules using post-Hartree-Fock methods, finding excellent agreement with the corresponding all-electron values. They also show their pseudopotentials give superior accuracy than other existing pseudopotentials constructed specifically for QMC. Finally, valence basis sets of different sizes (VnZ with n=D,T,Q,5 for first and second rows, and n=D,T for third to fifth rows) optimized for our pseudopotentials are also presented.
Nonlinear energy absorption of rare gas clusters in intense laser field
Authors: Davis J. , Petrov G. M. , Velikovich A.
Published: June 2007

The energy absorption of rare gas clusters irradiated by an intense ultrashort laser pulse is studied numerically. Various mechanisms of collisionless energy absorption were evaluated and discussed. The molecular dynamics simulations results suggest that both the linear and nonlinear resonance absorption mechanisms are marginally relevant. A capacitor model is considered that links the energy absorption to outer electron ionization and volume distribution of charges, rather than oscillation of electrons and transition through a resonance. It predicts correctly the absolute absorbed energy, as well as the dependence of the absorbed energy versus number of atoms per cluster.
Proton momentum distribution in water: an open path integral molecular dynamics study
Authors: Morrone Joseph A. , Srinivasan Varadharajan , Sebastiani Daniel , Car Roberto
Published: June 2007

Recent neutron Compton scattering experiments have detected the proton momentum distribution in water. The theoretical calculation of this property can be carried out via “open” path integral expressions. In this work, present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize a flexible, single point charge empirical force field to model the system’s interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.
Photoluminescence characteristics of InAs self-assembled quantum dots in InGaAs∕GaAs quantum well
Authors: Kong Lingmin , Wu Zhengyun , Feng Zhe Chuan , Ferguson Ian T.
Published: June 2007

Three different InAs quantum dots (QDs) in an InGaAs∕GaAs quantum well were formed and investigated by time-resolved and temperature dependent photoluminescence (PL). A strong PL signal emitting at ∼1.3μm can be obtained at room temperature with a full width at half maximum of only 28meV. Dots-in-a-well structures result in strong stress release and large size InAs QDs which lead to narrowing and redshifting of PL emissions, enhancement of carrier migration, increasing carrier density in QDs, achievement of good PL lifetime stability on temperature, and improving the QD quality.
Structural, morphological, and optical properties of AlGaN/GaN heterostructures with AlN buffer and interlayer
Authors: Çörekçi S. , Öztürk M. K. , Akaoğlu B. , Çakmak M. , Özçelik S. , Özbay E.
Published: June 2007

Al x Ga 1 − x N ∕ GaN   ( x ∼ 0.3 ) heterostructures with and without a high-temperature (HT) AlN interlayer (IL) have been grown on sapphire (Al2O3) substrates and AlN buffer/Al2O3 templates by metal organic chemical vapor deposition. The effects of an AlN buffer layer (BL) grown on an Al2O3 substrate and an AlN IL grown under the AlGaN ternary layer (TL) on structural, morphological, and optical properties of the heterostructures have been investigated by high-resolution x-ray diffraction, spectroscopic ellipsometry, atomic force microscopy, and photoluminescence measurements. The AlN BL improves the crystal quality of the AlGaN TL. Further improvement is achieved by inserting an AlN IL between GaN BL and AlGaN TL. However, experimental results also show that a HT AlN IL leads to relatively rough surfaces on AlGaN TLs, and an AlN IL changes the strain in the AlGaN TL from tensile to compressive type. In addition, an AlN BL improves the top surface quality of heterostructures.
On the induced microstructure changes of the amorphous carbon nitride films during annealing
Authors: Lejeune M. , Durand-Drouhin O. , Charvet S. , Zeinert A. , Benlahsen M.
Published: June 2007

The analysis of the stress release and structural changes caused by postdeposition thermal annealing of amorphous carbon nitride thin films (a-CNx) has been carried out. The a-CNx films were deposited on Si (100) using reactive radio frequency (rf) magnetron sputtering of a high-purity graphite target in a pure nitrogen plasma under various different rf powers. Combined Fourier transform infrared (FTIR), Raman spectroscopy, transmission spectroscopy, photothermal deflexion spectroscopy, and residual stress measurements were used to fully characterize the films. Annealing of the samples in vacuum at temperature up to 600°C produces changes in their structural properties and the intrinsic stress. These changes are found to be strongly dependent on both the deposition conditions and microstructure changes occurring within the films during heating. FTIR spectra showed the existence of N–C sp3, NC sp2, and CN triple bonds in the deposited films. The analysis of the spectra versus annealing temperature (TA) reveals that the major microstructure changes are the reorganization of the C–N and C–C configurations, without significant densification of the deposited films. The Raman features combined to the optical measurements reveal that this progressive graphitization of the material, with increasing TA, is accompanied by a higher disorder form of C sp2 sites. These results are used to describe the stress variation that accompanies the nitrogen evolution within the deposited films.
Electronic transport under high electric fields in Sr2IrO4
Authors: Fisher B. , Genossar J. , Knizhnik A. , Patlagan L. , Reisner G. M.
Published: June 2007

We report measurements of conductivity under high electric fields of polycrystalline Sr2IrO4 at various temperatures, motivated by an earlier report on negative differential resistivity of a single crystal of this material. While our dc I-V characteristics are strongly nonlinear, the pulsed characteristics show almost negligible nonlinearity up to fields of ∼500V∕cm. We report also on low-field electronic transport measurements (resistivity and thermopower) as function of temperature, which are in qualitative agreement with recently published results.
Temperature dependence of the A1(LO) and E2 (high) phonons in hexagonal InN nanowires
Authors: Song B. , Jian J. K. , Wang G. , Bao H. Q. , Chen X. L.
Published: June 2007

The frequencies and dampings of the zone-center optical phonon modes of A1(LO) (longitudinal-optical) and E2 (high) in wurtzite InN nanowires have been investigated by micro-Raman scattering in the temperature range from 80 to 300 K. Our results reveal that the phonon frequencies decrease and the linewidths broaden with increasing temperature. The obtained experimental data of the frequencies and linewidths at various temperatures can be well described by an empirical model which takes into account the contribution of the thermal expansion of lattice and symmetric decay of phonons into two and three identical phonons with lower energy. The results show that decay into two phonons is the probable channel for the A1(LO) mode and three-phonon decay dominates the E2 (high) mode.
Fabrication and characterization of an electrically variable, nanospring based interferometer
Authors: Dice G. D. , Brett M. J. , Wang D. , Buriak J. M.
Published: June 2007

The authors report on an electrically variable Fabry-Pérot interferometer constructed from the organic material tris(8-hydroxyquinoline) aluminum (Alq3). A two-turn helical Alq3 film with a 300nm pitch is deposited via glancing angle deposition. Electrostatic compression of the nanosprings between parallel, partially reflective mirrors controls the peak transmission wavelength. Contact mode atomic force microscope measurements using a conductive tip indicate a spring compression of 1.2nm when a voltage of 6V is applied across the structure. Spectroscopic measurements show a 1.6nm shift in the peak transmission wavelength. These results demonstrate precise control of the transmission wavelength of an electrically variable nanometer scaled interferometer.
Nanometer spaced electrodes using selective area atomic layer deposition
Authors: Gupta R. , Willis B. G.
Published: June 2007

Nanoelectrodes with spacing controlled between 1 and 10nm with subnanometer increment have been achieved using atomic layer deposition. Field emission and metal-vacuum-metal tunneling are used to characterize the electrode properties in situ during growth. The current-voltage data is modeled and gives electrode spacing of 1.0±0.2nm, a barrier height of 4.5eV, and electrode radius of 10nm. Temperature variation from 26to235°C changes the spacing by 0.05nm, as calculated from electrical data. This is close to 0.1nm expected from thermal expansion. Exposing to air reduces the barrier height to 2.15eV, which is explained by the growth of a thin metal oxide layer.
Electrical characteristics of single and doubly connected Ni silicide nanowire grown by plasma-enhanced chemical vapor deposition
Authors: Kim Joondong , Shin Dong Hun , Lee Eung-Sug , Han Chang-Soo , Park Yun Chang
Published: June 2007

Ni silicide nanowires were grown by plasma-enhanced chemical vapor deposition at 350°C. Transmission electron microscope analysis showed that Ni silicide nanowire has a single crystalline Ni3Si2 structure. The nanowire alignment was controlled by dielectrophoretic method and two nanowires were placed onto Pt electrodes under an ac biasing of 10Vp-p at 100kHz. The electric characteristics of the nanowire were obtained from double connection and single connection of 5.07 and 10.44kΩ, respectively. The resistivity values were obtained to be 183 and 208μΩcm, showing a uniform performance of the connection.
Noise in MgO barrier magnetic tunnel junctions with CoFeB electrodes: Influence of annealing temperature
Authors: Scola J. , Polovy H. , Fermon C. , Pannetier-Lecœur M. , Feng G. , Fahy K. , Coey J. M. D.
Published: June 2007

Low frequency noise has been measured in magnetic tunnel junctions with MgO barriers and magnetoresistance values up to 235%. The authors investigated the noise for different degrees of crystallization and CoFeB∕MgO interface quality depending on the annealing temperature. The authors report an extremely low 1∕f noise, compared to magnetic junctions with Al2O3 barriers. The origin of the low frequency noise is discussed and it is attributed to localized charge traps with the MgO barriers.
Magnetic and magnetotransport properties of (AlGaN∕GaN):Mg∕(GaMnN) heterostructures at room temperature
Authors: Mahros Amr M. , Luen M. O. , Emara A. , Bedair S. M. , Berkman E. A. , El-Masry N. A. , Zavada J. M.
Published: June 2007

Dilute magnetic semiconductor films (GaMnN) are highly resistive, making transport measurements difficult to achieve. However, when GaMnN films are sandwiched between p-type doped (AlGaN∕GaN) strained-layer superlattices, holes from the superlattice interact with the Mn3+∕2+ ions and transport measurements were realized. The authors have found also that the ferromagnetic properties of GaMnN critically depend on the level of p-type doping in the superlattice. They report anomalous Hall effect measurements in this (AlGaN∕GaN):Mg∕(GaMnN) multilayered structure. The current results also demonstrate the role of carriers, especially holes, in mediating the ferromagnetic properties of GaMnN dilute magnetic semiconductor films.
Spontaneous aggregation of pentacene molecules and its influence on field effect mobility
Authors: Yoshikawa Genki , Sadowski Jerzy T. , Al-Mahboob Abdullah , Fujikawa Yasunori , Sakurai Toshio , Tsuruma Yuki , Ikeda Susumu , Saiki Koichiro
Published: June 2007

The authors have found that pentacene molecules deposited on SiO2 substrates treated with self-assembled monolayers, such as hexamethyldisilazane or octadecyltrichlorosilane, aggregate spontaneously. In situ, real-time low-energy electron microscopy investigation of the morpho-logical changes in pentacene films deposited under ultrahigh vacuum reveals that the balance between pentacene film and substrate surface energies is an origin of this aggregation. With in situ atomic force microscopy - field effect transistor measurements, the authors demonstrate that field effect mobility is critically affected by this aggregation.
Evidence for a pressure-induced phase transition of amorphous to amorphous in two lanthanide-based bulk metallic glasses
Authors: Liu X. R. , Hong S. M.
Published: June 2007

The in situ electrical resistance measurement and differential thermal analysis have been carried out for La68Al10Cu20Co2 and Nd60Al10Ni10Cu20 bulk metallic glasses under pressure up to 4GPa. The authors observed a clear drop of electrical resistance in the La- and Nd-based glasses at 1.44 and 1.17GPa at room temperature, respectively, and the sudden change is reversible with decompression. The differential thermal analysis revealed an endothermic process involved in the transition during compression and an exothermic process upon decompression. These results are strongly suggestive of an amorphous to amorphous phase transition induced by pressure in the two bulk metallic glasses.
Temperature dependence of elastic moduli in bulk metallic glasses down to liquid nitrogen temperature
Authors: Yu Peng , Wang R. J. , Zhao D. Q. , Bai H. Y.
Published: June 2007

Temperature dependences of elastic moduli for representative bulk metallic glasses (BMGs) are in situ studied by the ultrasonic method down to liquid nitrogen temperature. The elastic moduli display a monotonous increase with the decreasing temperature, and the temperature dependences of the elastic moduli can be well described by the Varshni expression for various BMGs. The elastic Grüneisen parameters, the molar specific heat, and the Debye temperature in low temperature limit are obtained for the BMGs and compared to those of nonmetallic glasses. The results might provide useful information for understanding the unique properties of the BMGs
Electroclinic effect in a chiral smectic C siloxane material
Authors: Jang J. N. , Davey A. B. , Crossland W. A.
Published: June 2007

The authors have proposed that the electroclinic effect can explain the mechanism of layer rotation in the chiral smectic C phase. In this work, they investigate the soft mode in the chiral smectic C phase with three different experiments: dielectric permittivity measurements, light transmission measurements, and direct tilt angle measurements. They could clearly identify the electroclinic effect in the chiral smectic C phase in the experiments, which was very small compared to that of the SmA* phase.
Low-resistivity Au∕Ni Ohmic contacts to Sb-doped p-type ZnO
Authors: Mandalapu L. J. , Yang Z. , Liu J. L.
Published: June 2007

Au ∕ Ni contacts were fabricated on Sb-doped p-type ZnO film, which was grown on n-type Si (100) substrate with a thin undoped ZnO buffer layer by molecular beam epitaxy. As-deposited contacts were rectifying while Ohmic behavior was achieved after thermally annealing the contacts in nitrogen environment. Contact resistance was determined by linear transmission line method and it decreased with the increase of annealing temperature. Low specific contact resistivity of 3.0×10−4Ωcm2 was obtained for sample annealed at 800°C for 60s. Secondary ion mass spectroscopy was used to analyze elemental profiles of the contacts before and after annealing. Zn vacancies created by outdiffusion of Zn are believed to couple with activated Sb atoms to increase the surface hole concentration enabling Ohmic contact formation.
Enhancement of temperature dependent mechanism by internanotube junctions
Authors: Hsu Ching-Tung , Hsu Wen-Kuang
Published: June 2007

When individual carbon nanotubes aggregate, the nanotube bundles behave as excellent thermal sensors and radiators. This is due to enhanced temperature dependent mechanism by internanotube junctions which act as thermal reservoirs.
Development and Design of Large Infrastructure Projects: Disregarded Alternatives and Issues of Spatial Planning
Authors: Priemus Hugo
Published: June 2007

The Dutch Parliamentary Commission on Infrastructural Projects has conducted a parliamentary inquiry into the decisionmaking process and implementation control in two major infrastructural projects: the Betuwe Freight Line between Rotterdam and Germany, and the HSL - Zuid— the high-speed rail link which will connect Amsterdam with Belgium and France. The commission proposes a new assessment framework which gives parliament better control of the decisionmaking process for future large projects. In this contribution I discuss the development and design of large infrastructure projects, including the way the territorial impact of these projects is mitigated. I observe that problems are often approached from extremely narrow terms of reference, from one favourite solution, whereby countless potentially worthwhile alternative solutions are dismissed out of hand or enter the picture too late. In addition, problems concerning the mitigation of territorial impacts of infrastructure are misjudged in the beginning, and lead to cost overruns at a later stage. There is too much focus on the infrastructure track and not enough focus on area development. Also, the operation of the infrastructure project is misjudged and attention is too narrowly focused on the investment aspects of the project. I formulate some lessons for the future, not only for the Netherlands, but also for other modern countries. The timely generation and acknowledgement of infrastructure alternatives enhances the democratic process and quality of public decisionmaking.
Cost — Benefit Analysis and Large-Scale Infrastructure Projects: State of the Art and Challenges
Authors: Vickerman Roger
Published: June 2007

In this paper I review the problems surrounding the use of cost-benefit analysis (CBA) in the appraisal of large-scale infrastructure projects. I define the requirements of a best-practice transport CBA and show the difficulties in achieving these for large-scale projects. The main difficulties discussed are those of forecasting over long time periods, dealing with imperfect competition in transport-using sectors to obtain estimations of wider transport benefits, introducing private finance and appraising network effects. I conclude that CBA can remain a valuable tool as part of the appraisal process but that the inputs to a CBA have to be carefully assessed, and complementary approaches, such as computable general equilibrium modelling, have a useful role to play for very large or network projects.
Building a City in Vitro: The Experiment and the Simulation Model
Authors: Hatna Erez , Benenson Itzhak
Published: June 2007

All current urban models accept the ‘first-order recursion’ view, namely, that the state of an urban system at time t is sufficient for predicting its state at t + 1. This assumption is not at all evident in the case of urban development, where the behavior of developers and planners is defined by the complex interaction between long-term and short-term plan guidelines, local spatial and temporal conditions, and individual entrepreneurial activity and cognition. In this paper we validate the first-order recursion approach in an artificial game environment: thirty geography students were asked to construct a ‘city’ on the floor of a large room, with each student using the same set of fifty-two building mock-ups. Based on the analysis of game outcomes, the first-order recursive set of behavioral rules shared by all the participants is estimated and further employed for computer generation of artificial cities. Comparison between the human-built and model patterns reveals that the constructed set of rules is sufficient for representing the dynamics of the majority of experimental patterns; however, the behavior of some participants differs and we analyze these differences. We consider this experiment as a preliminary yet important step towards the adequate modeling of decision-making behavior among real developers and planners.
Oxidation of Aromatic Alkynes with Nitrate Radicals (NO3•): An Experimental and Computational Study on a Synthetically Highly Versatile Radical
Authors: Wille Uta , Andropof Jilliarne
Published: June 2007

Addition of electro- and photochemically generated nitrate radicals, NO3•, to the C≡C triple bond of aromatic alkynes 9a–9h leads to formation of 1,2-diketones 10a–10h. Surprisingly, benzophenones 11a–11h are obtained as by-products, which formally result from loss of a carbon atom. Density functional studies performed with the BHandHLYP method in combination with various basis sets revealed that 1,2-diketones result from 5-endo cyclization of the initially formed vinyl radical and loss of NO•. The key step to benzophenone formation is a γ-cleavage at the stage of the vinyl radical with release of NO2•, followed by Wolff rearrangement of the resulting α-oxo carbene.
Multisegmented Block Copolymers by 'Click' Coupling of Polymers Prepared by ATRP
Authors: Golas Patricia L. , Tsarevsky Nicolay V. , Sumerlin Brent S. , Walker Lynn M. , Matyjaszewski Krzysztof
Published: June 2007

Multisegmented block copolymers were prepared by the step-growth click coupling of well-defined block copolymers synthesized by atom transfer radical polymerization (ATRP). α,ω-Diazido-terminated polystyrene-block-poly(ethylene oxide)-block-polystyrene was coupled with propargyl ether in N,N-dimethylformamide in the presence of a CuBr/N,N,N´,N´´,N´´-pentamethyldiethylenetriamine catalyst. The preparation of multisegmented block copolymers was also demonstrated by the click coupling of propargyl ether with another diazido-terminated triblock copolymer, poly(n-butyl acrylate)-block-poly(methyl methacrylate)-block-poly(n-butyl acrylate), and a diazido-terminated pentablock copolymer, polystyrene-block-poly(n-butyl acrylate)-block-poly(methyl methacrylate)-block-poly(n-butyl acrylate)-block-polystyrene. The formation of a product of higher molecular weight and broader molecular weight distribution was verified by triple-detection size exclusion chromatography, which revealed that typically five to seven block copolymers were linked together during the click reaction. Differential scanning calorimetry and dynamic mechanical analysis revealed that the amphiphilic block copolymer behaves as a viscoelastic fluid, while its corresponding multiblock copolymer is an elastic material. The multisegmented block copolymers with partially miscible segments exhibit higher glass transition temperatures than their precursors.
Synthesis and Surface Assembly of Ruthenium Bipyridine Complexes
Authors: Marin Veronica , Wouters Daan , Hoeppener Stephanie , Holder Elisabeth , Schubert Ulrich S.
Published: June 2007

Disulfide-functionalized bipyridine and the corresponding thiol derivative were prepared starting from xanthogenate-functionalized bipyridine. The reduction of the xanthogenate by hydrazine led to the formation of a mixture of thiol and disulfide-functionalized bipyridines that could be separated by size exclusion chromatography. The chelating properties of the bipyridine units were used to prepare fluorescent heteroleptic ruthenium complexes, whereas the thiol or disulfide group on the other end of the molecule was used to anchor the individual ligands as well as the formed complexes to solid substrates. Scanning tunnelling microscopy was used to visualize the assembly of these species on a flat gold(111) substrate.
Anhydrous Magnesium Sulfate Mediated Solvent-Free Synthesis of Dihydropyrimidin-2(1H)-ones at Ambient Temperature
Authors: Pore D. M. , Desai U. V. , Thopate T. S. , Wadgaonkar P. P.
Published: June 2007

An anhydrous magnesium sulfate mediated solvent-free protocol is described for the synthesis of dihydropyrimidinones (Biginelli compounds) at ambient temperature.
Effect of Redundant Chain Packing on the Uptake of Calcium Phosphate in Poly(2-Hydroxyethyl Methacrylate) Hydrogels
Authors: Chirila Traian V. , Hill Anita J. , Richens David T.
Published: June 2007

A method is described that allows reduction of the amount of calcium phosphate phases deposited spontaneously inside poly(2-hydroxyethyl methacrylate) (PHEMA), a hydrogel of biomedical importance. PHEMA homo-interpenetrating polymer networks (homo-IPNs) were synthesized and then treated in a calcifying solution. A reduction of calcium uptake of 58 to 75% was measured by ICP emission spectroscopy in the IPNs as compared to the PHEMA homopolymer (the parent network). The effect was rationalized in terms of reduction of the free volume available for the penetration and transport of Ca2+ and phosphate ions as a result of redundant chain packing through formation of IPNs.
Predicting fate from early connectivity in a social network
Authors: McDonald David B.
Published: June 2007

In the long-tailed manakin (
Chiroxiphia linearis
), a long-lived tropical bird, early connectivity within a social network predicts male success an average of 4.8 years later. Long-tailed manakins have an unusual lek mating system in which pairs of unrelated males, at the top of complex overlapping teams of as many as 15 males, cooperate for obligate dual-male song and dance courtship displays. For as long as 8 years before forming stable “alpha–beta” partnerships, males interact with many other males in complex, temporally dynamic social networks. “Information centrality” is a network connectivity metric that accounts for indirect as well as shortest (geodesic) paths among interactors. The odds that males would rise socially rose by a factor of five for each one-unit increase in their early information centrality. Connectivity of males destined to rise did not change over time but increased in males that failed to rise socially. The results suggest that network connectivity is important for young males (ages 1–6) but less so for older males of high status (ages 10–15) and that it is difficult to explain present success without reference to social history.
Oliver Rando: Taking chromatin analysis to the genomic scale
Authors: Williams Ruth
Published: June 2007

Oliver Rando uses microarrays to uncover the chromatin rules of genome usage.
β1 integrin activates Rac1 in Schwann cells to generate radial lamellae during axonal sorting and myelination
Authors: Nodari Alessandro , Zambroni Desirée , Quattrini Angelo , Court Felipe A. , D'Urso Alessandra , Recchia Alessandra , Tybulewicz Victor L.J. , Wrabetz Lawrence , Feltri M. Laura
Published: June 2007

Myelin is a multispiraled extension of glial membrane that surrounds axons. How glia extend a surface many-fold larger than their body is poorly understood. Schwann cells are peripheral glia and insert radial cytoplasmic extensions into bundles of axons to sort, ensheath, and myelinate them. Laminins and β1 integrins are required for axonal sorting, but the downstream signals are largely unknown. We show that Schwann cells devoid of β1 integrin migrate to and elongate on axons but cannot extend radial lamellae of cytoplasm, similar to cells with low Rac1 activation. Accordingly, active Rac1 is decreased in β1 integrin–null nerves, inhibiting Rac1 activity decreases radial lamellae in Schwann cells, and ablating Rac1 in Schwann cells of transgenic mice delays axonal sorting and impairs myelination. Finally, expressing active Rac1 in β1 integrin–null nerves improves sorting. Thus, increased activation of Rac1 by β1 integrins allows Schwann cells to switch from migration/elongation to the extension of radial membranes required for axonal sorting and myelination.
Essential and distinct roles for cdc42 and rac1 in the regulation of Schwann cell biology during peripheral nervous system development
Authors: Benninger Yves , Thurnherr Tina , Pereira Jorge A. , Krause Sven , Wu Xunwei , Chrostek-Grashoff Anna , Herzog Dominik , Nave Klaus-Armin , Franklin Robin J.M. , Meijer Dies , Brakebusch Cord , Suter Ueli , Relvas João B.
Published: June 2007

During peripheral nervous system (PNS) myelination, Schwann cells must interpret extracellular cues to sense their environment and regulate their intrinsic developmental program accordingly. The pathways and mechanisms involved in this process are only partially understood. We use tissue-specific conditional gene targeting to show that members of the Rho GTPases, cdc42 and rac1, have different and essential roles in axon sorting by Schwann cells. Our results indicate that although cdc42 is required for normal Schwann cell proliferation, rac1 regulates Schwann cell process extension and stabilization, allowing efficient radial sorting of axon bundles.
TGF-β signaling is essential for joint morphogenesis
Authors: Spagnoli Anna , O'Rear Lynda , Chandler Ronald L. , Granero-Molto Froilan , Mortlock Douglas P. , Gorska Agnieszka E. , Weis Jared A. , Longobardi Lara , Chytil Anna , Shimer Kimberly , Moses Harold L.
Published: June 2007

Despite its clinical significance, joint morphogenesis is still an obscure process. In this study, we determine the role of transforming growth factor β (TGF-β) signaling in mice lacking the TGF-β type II receptor gene (Tgfbr2) in their limbs (Tgfbr2PRX-1KO). In Tgfbr2PRX-1KO mice, the loss of TGF-β responsiveness resulted in the absence of interphalangeal joints. The Tgfbr2Prx1KO joint phenotype is similar to that in patients with symphalangism (SYM1-OMIM185800). By generating a Tgfbr2–green fluorescent protein–β–GEO–bacterial artificial chromosome β-galactosidase reporter transgenic mouse and by in situ hybridization and immunofluorescence, we determined that Tgfbr2 is highly and specifically expressed in developing joints. We demonstrated that in Tgfbr2PRX-1KO mice, the failure of joint interzone development resulted from an aberrant persistence of differentiated chondrocytes and failure of Jagged-1 expression. We found that TGF-β receptor II signaling regulates Noggin, Wnt9a, and growth and differentiation factor-5 joint morphogenic gene expressions. In Tgfbr2PRX-1KO growth plates adjacent to interphalangeal joints, Indian hedgehog expression is increased, whereas Collagen 10 expression decreased. We propose a model for joint development in which TGF-β signaling represents a means of entry to initiate the process.
Quantitative analysis of an anaphase B switch: predicted role for a microtubule catastrophe gradient
Authors: Cheerambathur Dhanya K. , Civelekoglu-Scholey Gul , Brust-Mascher Ingrid , Sommi Patrizia , Mogilner Alex , Scholey Jonathan M.
Published: June 2007

Anaphase B in Drosophila embryos is initiated by the inhibition of microtubule (MT) depolymerization at spindle poles, which allows outwardly sliding interpolar (ip) MTs to drive pole–pole separation. Using fluorescence recovery after photobleaching, we observed that MTs throughout the preanaphase B spindle are very dynamic and display complete recovery of fluorescence, but during anaphase B, MTs proximal to the poles stabilize and therefore display lower recovery than those elsewhere. Fluorescence microscopy of the MT tip tracker EB1 revealed that growing MT plus ends localize throughout the preanaphase B spindle but concentrate in the overlap region of interpolar MTs (ipMTs) at anaphase B onset. None of these changes occurred in the presence of nondegradable cyclin B. Modeling suggests that they depend on the establishment of a spatial gradient of MT plus-end catastrophe frequencies, decreasing toward the equator. The resulting redistribution of ipMT plus ends to the overlap zone, together with the suppression of minus-end depolymerization at the poles, could constitute a mechanical switch that initiates spindle elongation.
Organization of chromatin and histone modifications at a transcription site
Authors: Müller Waltraud G. , Rieder Dietmar , Karpova Tatiana S. , John Sam , Trajanoski Zlatko , McNally James G.
Published: June 2007

According to the transcription factory model, localized transcription sites composed of immobilized polymerase molecules transcribe chromatin by reeling it through the transcription site and extruding it to form a surrounding domain of recently transcribed decondensed chromatin. Although transcription sites have been identified in various cells, surrounding domains of recently transcribed decondensed chromatin have not. We report evidence that transcription sites associated with a tandem gene array in mouse cells are indeed surrounded by or adjacent to a domain of decondensed chromatin composed of sequences from the gene array. Formation of this decondensed domain requires transcription and topoisomerase IIα activity. The decondensed domain is enriched for the trimethyl H3K36 mark that is associated with recently transcribed chromatin in yeast and several mammalian systems. Consistent with this, chromatin immunoprecipitation demonstrates a comparable enrichment of this mark in transcribed sequences at the tandem gene array. These results provide new support for the pol II factory model, in which an immobilized polymerase molecule extrudes decondensed, transcribed sequences into its surroundings.
Myelination: all about Rac ‘n’ roll
Authors: Chan Jonah R.
Published: June 2007

During the development of the peripheral nervous system, Schwann cells select individual axons from a nerve bundle and establish a one-to-one relationship through a process termed “radial sorting”. Recent findings identify the Rho family GTPase Rac1 as the downstream effector molecule responsible for process extension and lamellipodia formation in Schwann cells, allowing for proper radial sorting and myelination. These findings begin to shed light on our understanding of the distinct and yet essential molecular mechanisms involved in developmental processes preceding myelination.
Rhizobacteria-Induced Priming inArabidopsisIs Dependent on Ethylene, Jasmonic Acid, andNPR1
Authors: Ahn Il-Pyung , Lee Sang-Woo , Suh Seok-Cheol
Published: June 2007

A nonpathogenic rhizobacterium, Pseudomonas putida LSW17S, elicited systemic protection against Fusarium wilt and pith necrosis caused by Fusarium oxysporum f. sp. lycopersici and P. corrugata in tomato (Lycopersicon esculentum L.). LSW17S also confers disease resistance against P. syringae pv. tomato DC3000 (DC3000) on Arabidopsis ecotype Col-0. To investigate mechanisms underlying disease protection, expression patterns of defense-related genes PR1, PR2, PR5, and PDF1.2 and cellular defense responses such as hydrogen peroxide accumulation and callose deposition were investigated. LSW17S treatment exhibited the typical phenomena of priming. Strong and faster transcription of defense-related genes was induced and hydrogen peroxide or callose were accumulated in Arabidopsis treated with LSW17S and infected with DC3000. In contrast, individual actions of LSW17S and DC3000 did not elicit rapid molecular and cellular defense responses. Priming by LSW17S was translocated systemically and retained for more than 10 days. Treatment with LSW17S reduced pathogen proliferation in Arabidopsis ecotype Col-0 expressing bacterial NahG; however, npr1, etr1, and jar1 mutations impaired inhibition of pathogen growth. Cellular and molecular priming responses support these results. In sum, LSW17S primes Arabidopsis for NPR1-, ethylene-, and jasmonic acid-dependent disease resistance, and efficient molecular and cellular defense responses.
Promoters of OrthologousGlycine maxandLotus japonicusNodulation Autoregulation Genes Interchangeably Drive Phloem-Specific Expression in Transgenic Plants
Authors: Nontachaiyapoom Sureeporn , Scott Paul T. , Men Artem E. , Kinkema Mark , Schenk Peer M. , Gresshoff Peter M.
Published: June 2007

The nodule autoregulation receptor kinase (GmNARK) of soybean (Glycine max) is essential for the systemic auto-regulation of nodulation. Based on quantitative reverse-transcriptase polymerase chain reaction, GmNARK is expressed to varying levels throughout the plant; the transcript was detected at high levels in mature leaves and roots but to a lesser extent in young leaves, shoot tips, and nodules. The transcript level was not significantly affected by Bradyrhizobium japonicum during the first week following inoculation. In addition, the activities of the promoters of GmNARK and Lotus japonicus HAR1, driving a β-glucuronidase (GUSPlus) reporter gene, were examined in stably transformed L. japonicus and transgenic hairy roots of soybean. Histochemical GUS activity in L. japonicus plants carrying either a 1.7-kb GmNARKpr∷GUS or 2.0-kb LjHAR1pr∷GUS construct was clearly localized to living cells within vascular bundles, especially phloem cells in leaves, stems, roots, and nodules. Phloem-specific expression also was detected in soybean hairy roots carrying these constructs. Our study suggests that regulatory elements required for the transcription of these orthologous genes are conserved. Moreover, rapid amplification of 5′ cDNA ends (5′ rapid amplification of cDNA ends) revealed two major transcripts of GmNARK potentially originating from two TATA boxes. Further analysis of the GmNARK promoter has confirmed that these two TATA boxes are functional. Deletion analysis also located a region controlling phloem-specific expression to a DNA sequence between 908 bp and 1.7 kb upstream of the translation start site of GmNARK.
The Transcriptional Response of Hybrid Poplar (Populus trichocarpa x P. deltoids) to Infection by Melampsora medusae Leaf Rust Involves Induction of Flavonoid Pathway Genes Leading to the Accumulation of Proanthocyanidins
Authors: Miranda Manoela , Ralph Steven G. , Mellway Robin , White Rick , Heath Michele C. , Bohlmann Jörg , Constabel C. Peter
Published: June 2007

The transcriptional response of hybrid poplar (Populus trichocarpa × P. deltoids) to poplar leaf rust (Melampsora medusae) infection was studied using the Populus 15.5K cDNA microarray. Pronounced changes in the transcriptome were observed, with approximately 20% of genes on the array showing either induction or repression of transcription within the 9-day infection timecourse. A small number of pathogen-defense genes encoding PR-1, chitinases, and other pathogenesis-related proteins were consistently upregulated throughout the experimental period, but most genes were affected only at individual timepoints. The largest number of changes in gene expression was observed late in the infection at 6 to 9 days postinoculation (dpi). At these timepoints, genes encoding enzymes required for proanthocyanidin (condensed tannin) synthesis were upregulated dramatically. Phytochemical analysis confirmed that, late in the infection, proanthocyanidin levels increased in infected leaves. Strongly M. medusae-repressed genes at 9 dpi included previously characterized wound- and herbivore-induced defense genes, which suggests antagonism between the tree responses to insect feeding and M. medusae infection. In this highly compatible plant-pathogen interaction, we postulate that the biotrophic pathogen evades detection and suppresses early host responses.
Sucrose-Mediated Priming of Plant Defense Responses and Broad-Spectrum Disease Resistance by Overexpression of the Maize Pathogenesis-Related PRms Protein in Rice Plants
Authors: Gómez-Ariza Jorge , Campo Sonia , Rufat Mar , Estopà Montserrat , Messeguer Joaquima , Segundo Blanca San , Coca María
Published: June 2007

Expression of pathogenesis-related (PR) genes is part of the plant's natural defense response against pathogen attack. The PRms gene encodes a fungal-inducible PR protein from maize. Here, we demonstrate that expression of PRms in transgenic rice confers broad-spectrum protection against pathogens, including fungal (Magnaporthe oryzae, Fusarium verticillioides, and Helminthosporium oryzae) and bacterial (Erwinia chrysanthemi) pathogens. The PRms-mediated disease resistance in rice plants is associated with an enhanced capacity to express and activate the natural plant defense mechanisms. Thus, PRms rice plants display a basal level of expression of endogenous defense genes in the absence of the pathogen. PRms plants also exhibit stronger and quicker defense responses during pathogen infection. We also have found that sucrose accumulates at higher levels in leaves of PRms plants. Sucrose responsiveness of rice defense genes correlates with the pathogen-responsive priming of their expression in PRms rice plants. Moreover, pretreatment of rice plants with sucrose enhances resistance to M. oryzae infection. Together, these results support a sucrose-mediated priming of defense responses in PRms rice plants which results in broad-spectrum disease resistance.
The Rhizobium leguminosarum bv. trifolii RosR: Transcriptional Regulator Involved in Exopolysaccharide Production
Authors: Janczarek Monika , Skorupska Anna
Published: June 2007

The acidic exopolysaccharide is required for the establishment of symbiosis between the nitrogen-fixing bacterium Rhizobium leguminosarum bv. trifolii and clover. Here, we describe RosR protein from R. leguminosarum bv. trifolii 24.2, a homolog of transcriptional regulators belonging to the family of Ros/MucR proteins. R. leguminosarum bv. trifolii RosR possesses a characteristic Cys2His2 type zincfinger motif in its C-terminal domain. Recombinant (His)6RosR binds to an RosR-box sequence located upstream of rosR. Deletion analysis of the rosR upstream region resulted in identification of two -35 to -10 promoter sequences, two conserved inverted palindromic pentamers that resemble the cAMP-CRP binding site of Escherichia coli, inverted repeats identified as a RosR binding site, and other regulatory sequence motifs. When assayed in E. coli, a transcriptional fusion of the cAMP-CRP binding site containing the rosR upstream region and lacZ gene was moderately responsive to glucose. The sensitivity of the rosR promoter to glucose was not observed in E. coli ΔcyaA. A rosR frame-shift mutant of R. leguminosarum bv. trifolii formed dry, wrinkled colonies and induced nodules on clover, but did not fix nitrogen. In the rosR mutant, transcription of pssA-lacZ fusion was decreased, indicating positive regulation of the pssA gene by RosR. Multiple copies of rosR in R. leguminosarum bv. trifolii 24.2 increased exopolysaccharide production.