bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of lead atom with atmospheric dioxygen and ozone: Quantic study of the structure and the stability of resulting Pb(On) (n=1,2,3) compounds
Authors: Benjelloun Adil Touimi , Daoudi Abdelali , Chermette Henry
Published: April 2005

Lead reaction with oxygen and ozone molecules is of a great importance for the study of the impact of this metal in the atmosphere medium. Stable species, intermediates, and transition states of possible resulting complexes have been studied with the three parameter hybrid B3LYP exchange-correlation DFT method, and coupled cluster with single, double, and triple excitation methods. Geometry, and spectroscopic and thermodynamic properties obtained for the different species are presented, discussed, and compared to available experimental data. On the basis of the knowledge of the thermal dissociation enthalpies and the absorbed wave length edges calculated for each species, we have drawn the most probable oxygenated complexes present in the atmosphere.
The redistribution of oxygen at AlOx∕CoFe interface of magnetic tunnel junctions through thermal treatment
Authors: Lee Donkoun , Hong Jongill
Published: April 2005

In an examination of the chemical structures of the AlOx∕Co90Fe10 interface, we confirmed that thermal treatment affects the redistribution of oxygen at the interface and that this leads to an increase in the tunneling barrier height of magnetic tunnel junctions. The as-deposited Al oxide barrier with a thickness of ∼13Å was oxygen-deficient AlOx, but most of it turned into Al2O3, the thermodynamically stable stoichiometric phase, through annealing. This enrichment of oxygen is likely responsible for the observed improvement. The near-edge x-ray absorption fine structure spectra of Co and Fe proved the fact that after bonding with Co and Fe in the underlying CoFe layer, the oxygen diffused back into the barrier and thereby enriched the barrier to the point where it mostly consisted of Al2O3. Our results confirm that controlling the chemical structures at the interface is a key to modify the properties of magnetic tunnel junctions.
Anisotropic resistivity in plasma-sprayed silicon thick films
Authors: Kharas Boris Dave , Sampath Sanjay , Gambino Richard J.
Published: April 2005

Silicon thick films deposited by thermal plasma spray are of interest as inexpensive electronic materials for conformal meso-scale electronics applications. In addition they also serve as a model system for the investigation of electrical properties of coatings with layered anisotropy. In this study impedance spectroscopy was used to measure the complex resistivity of free-standing 64μm-thick polycrystalline silicon films deposited by thermal plasma spraying in an atmospheric ambient. Impedance spectroscopy measurements were taken in the through-thickness (across-splat) and edge-to-edge (in-splat) directions and revealed a resistivity difference of approximately 7.5±0.23 between the two directions. The complex resistivity results are explained on the basis of a brick-layer type model, associated with the layered splat microstructure obtained from cross-sectional transmission electron microscope imaging of the films. In addition a circuit-based model made up of parallel, resistor-capacitor elements in series, and Cole–Cole and Davidson–Cole impedance functions were used to fit the impedance data to extract material parameters and contributions from the grains and splat boundaries. Furthermore, thermal processing and phosphorus doping is shown to lead to higher and lower resistivity, respectively, in the films.
Color tunable metal-cavity organic light-emitting diodes with fullerene layer
Authors: Han Sijin , Huang Changjun , Lu Zheng-Hong
Published: April 2005

Three primary colors, red, green, and blue have been obtained from a single-emission layer organic light-emitting diode (OLED) through optical design using a half-wavelength all-metal-cavity device. Fullerene is used as an electron transport layer to further enhance the electrical performance of the cavity device and the optical tuning of the cavity OLED. This fullerene layer results in a ∼2V driving voltage reduction and a ∼20% increase in power efficiency, as compared with traditional cavity OLED with Alq as the electron transport layer. The emissive spectra for the cavity OLEDs are well predicted by the Fabry–Perot cavity theory. The spectral narrowing and intensity enhancement at the resonance wavelength have been observed and are explained by the redistribution of optical-mode density inside the microcavity. Schemes to tune the emissive color by varying the cavity length through variations of indium tin oxide thickness, hole transport layer thickness, and electron transport thickness, individually or collectively, have been proposed and demonstrated.
Neutron and photon transport in seagoing cargo containers
Authors: Pruet J. , Descalle M.-A. , Hall J. , Pohl B. , Prussin S. G.
Published: April 2005

Factors affecting sensing of small quantities of fissionable material in large seagoing cargo containers by neutron interrogation and detection of β-delayed photons are explored. The propagation of variable-energy neutrons in cargos, subsequent fission of hidden nuclear material and production of the β-delayed photons, and the propagation of these photons to an external detector are considered explicitly. Detailed results of Monte Carlo simulations of these stages in representative cargos are presented. Analytical models are developed both as a basis for a quantitative understanding of the interrogation process and as a tool to allow ready extrapolation of our results to cases not specifically considered here.
Properties of radio-frequency-sputter-deposited GaN films in a nitrogen∕hydrogen mixed gas
Authors: Miyazaki Takayuki , Takada Kouhei , Adachi Sadao , Ohtsuka Kohji
Published: April 2005

GaN films have been deposited by reactive sputtering in nitrogen gas at pressures from 0.08 to 2.70 Pa with and without the addition of hydrogen gas. X-ray diffraction (XRD), Fourier transform infrared (FTIR), optical absorption, and photoluminescence (PL) spectroscopy have been used to characterize the sputter-deposited GaN films. The XRD pattern reveals that the GaN films deposited in nitrogen gas at pressures lower than 0.53 Pa are polycrystals with the (0001) texture (α-GaN), while those deposited at or above 1.07 Pa display mixed crystalline orientations or an amorphous-like nature. The GaN:H films deposited in nitrogen∕hydrogen mixed gas, on the other hand, show an amorphous or amorphous-like nature. The FTIR spectra indicate that the GaN:H films show peaks arising from hydrogen-related bonds at ∼1000 and ∼3200cm−1, in addition to the GaN absorption band at ∼555cm−1. The optical absorption spectra at 300 K indicate the fundamental absorption edges at ∼3.38 and ∼3.7eV for the highly oriented α-GaN and amorphous GaN:H films, respectively. PL emission has been observed from sputter-deposited α-GaN films at temperatures below 100 K. The GaN:H films also show strong band-edge and donor-acceptor pair emissions. The PL emission in the GaN:H film may arise from crystalline GaN particles embedded in the amorphous GaN matrix.
Synthesis and thermoelectric properties of p-type- and n-type-filled skutterudite RyMxCo4−xSb12(R:Ce,Ba,Y;M:Fe,Ni)
Authors: Tang Xinfeng , Zhang Qingjie , Chen Lidong , Goto Takashi , Hirai Toshio
Published: April 2005

Single-phase RyMxCo4−xSb12(x=0–3.0,y=0–0.7) compounds filled by Ce, Ba, and Y, and substituted by Fe and Ni are synthesized by using the solid-state reaction method and melting reaction method. The structure and the thermoelectric properties of RyMxCo4−xSb12 are investigated systematically. The thermal parameter (B) of Ba and Ce filled in Sb-icosahedron voids in the skutterudite structure is larger than that of Sb and Co (Fe). The maximum filling fraction of Ce and Ba (ymax) for RyFexCo4−xSb12 increases with the increasing Fe content, and it is found that the maximum filling fraction of Ba (ymax) is greater than that of CeyFexCo4−xSb12. The filling atoms Ba, Ce, and Y in Sb-icosahedron voids can reduce the lattice thermal conductivity of RyMxCo4−xSb12 compounds remarkably, and the lattice thermal conductivity decreases in the order of ionic radii decreasing of Ba2+, Ce3+, and Y3+. When Ce and Ba filing fraction is 0.3–0.4, the lattice thermal conductivity of RyFexCo4−xSb12 compounds reaches a minimum value. The lattice thermal conductivity can be greatly reduced by substituting Co with Fe or Ni, and compared with Fe substitution, the substituted atoms Ni are more effective in reducing the lattice thermal conductivity. The filling atoms Ba, Ce, and Y, and the substituted atoms Fe and Ni influence electrical transport properties of RyMxCo4−xSb12 compounds significantly. The carrier concentration and electrical conductivity of p-type RyFexCo4−xSb12 increase with the increasing Fe content but decrease with the increasing R filling fraction. At the same carrier concentration, electrical conductivity of p-type BayFexCo4−xSb12 is larger than that of p-type CeyFexCo4−xSb12. Electrical conductivity of n-type BayNixCo4−xSb12 increases with the increasing Ni content remarkably. The Seebeck coefficient of p-type RyFexCo4−xSb12 increases with the increasing Ce and Ba filling fraction and with the decreasing Fe content, and Seebeck coefficient of n-type BayNixCo4−xSb12 decreases with the increasing Ni content. In the present study, the obtained maximum ZT values reach 1.1 and 1.25 for p-type Co-rich Ce0.28Fe1.5Co2.5Sb12 (at 750K) and n-type Ba0.30Ni0.05Co3.95Sb12 (at 900K), respectively.
Electron and ion inertia effects on current-driven collisional dust acoustic, dust ion acoustic, and ion acoustic instabilities
Authors: Merlino Robert L. , D’Angelo Nicola
Published: April 2005

Ion acoustic waves can be excited by electrons drifting relative to the ions in a plasma. This relative drift can be produced, in a collisional plasma, by a static electric field. In the analysis of this instability, which occurs for frequencies well below the ion plasma frequency, the electron inertia term in the momentum equation is typically neglected. A similar assumption has been employed in the investigation of the dust ion acoustic instability in a collisional dusty plasma. In the study of the collisional current driven dust acoustic instability, both the electron and ion inertial terms were neglected. It is shown here that the inclusion of the appropriate inertia terms can result in significant differences in the growth rates for these instabilities. The cases studied, including the inertia terms, led to a decrease in the critical electric fields necessary to excite the current driven dust acoustic, dust ion acoustic, and ion acoustic instabilities.
Absolute detection efficiency of space-based ion mass spectrometers and neutral atom imagers
Authors: Funsten H. O. , Harper R. W. , McComas D. J.
Published: April 2005

Space-based ion mass spectrometers and neutral atom imagers often utilize a thin foil for generation of secondary electrons and employ a coincidence measurement between detection of the secondary electrons and detection of the primary ion or neutral atom, allowing unambiguous detection of the particle in a large noise background and determination of properties of the particle using time-of-flight measurement. We demonstrate a simple and straightforward method for laboratory calibration and in situ quantification and monitoring of the absolute detection probabilities of the detectors and the absolute detection efficiency of the detector subsystem without knowledge of the incident particle flux.
Effect of large-scale coherent structures on subgrid-scale stress and strain-rate eigenvector alignments in turbulent shear flow
Authors: Kang Hyung Suk , Meneveau Charles
Published: April 2005

A numerical and experimental study is performed of the effects of coherent structures on inertial range stress-strain tensor alignments. Data from two turbulent shear flows, namely, Kolmogorov flow at moderate Reynolds number and the intermediate cylinder wake at higher Reynolds number, are considered. Both flows exhibit large-scale coherent structures, consisting of vortices separated by straining regions. These different regions are analyzed using conditional phase averaging. The phase-averaged results, both from direct numerical simulation and experiments, reveal that the most likely angle between the most extensive strain-rate and negative stress eigenvectors is about 45° at the vortex centers. The most likely angle decreases to between 0° and 20° near the saddle points that occur between the vortices. By subtracting a similarity type term (such as a Leonard stress) from the subgrid scale stress tensor, the remainder stress is shown to align much better with the strain-rate tensor, under all conditions including the vortex centers. It is concluded that while large-scale coherent structures can affect small-scale stress-strain rate alignments directly, the effect occurs primarily through the Leonard-type stresses and is thus straightforward to account for in large eddy simulations using mixed models. More detailed investigation of the eigenvector alignments between the strain rate and the decomposed negative nonlinear model terms −S2, SΩ+ΩS, and Ω2 (where S and Ω are the strain–rate and rotation tensors, respectively) highlights the relevance of each of these terms in different regions of the large-scale coherent structures.
Equilibrium properties and exact solutions for two-dimensional nonlinear force-free magnetic fields with mass flow
Authors: Khater A. H. , Moawad S. M.
Published: April 2005

The steady state equilibrium properties of force-free magnetic fields (FFMFs) with mass flow in Cartesian geometry and invariant in a given direction are investigated. For constant Mach number (defined in Sec. II) flows, several classes of exact analytic solutions associated with solitonlike, antisolitonlike, kinklike, and antikinklike configurations are obtained. For nonconstant Mach number flows, it is shown that the equilibrium flow is impossible in some cases of FFMFs, and exact equilibria can be obtained in the other cases. The magnetic surfaces have a circular cross section for two-dimensional flows.
Second order superintegrable systems in conformally flat spaces. II. The classical two-dimensional Stäckel transform
Authors: Kalnins E. G. , Kress J. M. , Miller W.
Published: April 2005

This paper is one of a series that lays the groundwork for a structure and classification theory of second order superintegrable systems, both classical and quantum, in conformally flat spaces. Here we study the Stäckel transform (or coupling constant metamorphosis) as an invertible mapping between classical superintegrable systems on different spaces. Through the use of this tool we derive and classify for the first time all two-dimensional (2D) superintegrable systems. The underlying spaces are exactly those derived by Koenigs in his remarkable paper giving all 2D manifolds (with zero potential) that admit at least three second order symmetries. Our derivation is very simple and quite distinct. We also show that every superintegrable system is the Stäckel transform of a superintegrable system on a constant curvature space.
Cantilever tilt compensation for variable-load atomic force microscopy
Authors: Cannara Rachel J. , Brukman Matthew J. , Carpick Robert W.
Published: April 2005

In atomic force microscopy (AFM), typically the cantilever’s long axis forms an angle with respect to the plane of the sample’s surface. This has consequences for contact mode experiments because the tip end of the cantilever, which is constrained to move along the surface, displaces longitudinally when the applied load varies. As a result, the AFM tip makes contact with a different point on the surface at each load. These different positions lie along the projection of the lever’s long axis onto the surface. When not constrained by static friction, the amount of tip-displacement is, to first order, proportional to the load and is shown to be substantial for typical AFM and cantilever geometries. The predictions are confirmed experimentally to within 15% or better. Thus, care should be taken when performing load-dependent contact mode experiments, such as friction versus load, elasticity versus load, or force versus displacement measurements, particularly for heterogeneous or topographically-varying samples. We present a simple method to reliably and precisely compensate for in-plane tip displacement that depends only on the range of vertical motion used to vary the load. This compensation method should be employed in any load-varying AFM experiment that requires the tip to scan the same line or to remain at the same point at each load.
Multipoint focus-detecting method for measurement of biological nonsmooth surface topography
Authors: Hu Yao , Zeng Lijiang
Published: April 2005

To measure the 3D characteristic of biological nonsmooth surface, a multipoint focus-detecting method based on the light splitting effect of crossed grating was developed. The surface profile is obtained by analyzing the variation in spot size on it rather than in light intensity used in conventional confocal method. Thus the influence of surface reflectivity variation could be reduced. The system is simple and the lateral resolution could be adjusted by changing the moving step of the stage on which the sample lies. Currently the axial uncertainty is about 20μm. The profile of fish scales was measured and the uncertainties were analyzed.
Simple method to surface slope error characterization using x-ray optics
Authors: Gavinho L. , Cusatis C. , Mazzaro I. , Tirao G.
Published: April 2005

This work shows a method to characterize nearly flat reflective surfaces. Slope error on the mirror surface under the total reflection condition of x rays is measured by perfect crystal rocking curve profile widening. The experiment was performed using a conventional x-ray tube and a simple optical setup. The sensitivity was sufficient to detect at least a slope error of 7μrad, typical quality for synchrotron mirrors. It is shown that this technique can also be used to characterize roughness and curvature. The method proposed here is an alternative to the traditional techniques for surface characterization and has the advantages of simplicity, versatility and sensitivity, and the synchrotron mirror quality can be evaluated under similar conditions as those for the designed operation.
Logarithmic pulse generator for long-term creep and relaxation testing
Authors: Oza Ashish L. , McCabe Ronald P. , Vanderby Ray , Lakes Roderic S.
Published: April 2005

An existing logarithmic time base pulse generator design has been modified to collect data for creep and relaxation tests over at least 14decades of logarithmic time increments. Creep and relaxation studies of materials, which do not obey time temperature superposition, are done over many factors of ten (decades) of time. To acquire and store data efficiently one employs logarithmic sampling intervals. This device can trigger a data acquisition system to gather the data logarithmically. It generates trigger pulses accurately over 14decades of time.
Refractory clad transient internal probe for magnetic field measurements in high temperature plasmas
Authors: Kim Hyundae , Cellamare Vincent , Jarboe Thomas R. , Mattick Arthur T.
Published: April 2005

The transient internal probe (TIP) is a diagnostic for local internal field measurements in high temperature plasmas. A verdet material, which rotates the polarization angle of the laser light under magnetic fields, is launched into a plasma at about 1.8km∕s. A linearly polarized Ar+ laser illuminates the probe in transit and the light retroreflected from the probe is analyzed to determine the local magnetic field profiles. The TIP has been used for magnetic field measurements on the helicity injected torus where electron temperature Te⩽80eV. In order to apply the TIP in higher temperature plasmas, refractory clad probes have been developed utilizing a sapphire tube, rear disc, and a MgO window on the front. The high melting points of these refractory materials should allow probe operation at plasma electron temperatures up to Te∼300eV. A retroreflecting probe has also been developed using “catseye” optics. The front window is replaced with a plano-convex MgO lens, and the back surface of the probe is aluminized. This approach reduces spurious polarization effects and provides refractory cladding for the probe entrance face. In-flight measurements of a static magnetic field demonstrate the ability of the clad probes to withstand gun-launch acceleration, and provide high accuracy measurements of magnetic field.
Strong 1.3–1.6μm light emission from metamorphic InGaAs quantum wells on GaAs
Authors: Tångring I. , Wang S. M. , Gu Q. F. , Wei Y. Q. , Sadeghi M. , Larsson A. , Zhao Q. X. , Akram M. N. , Berggren J.
Published: April 2005

We demonstrate strong 1.3–1.6μm photoluminescence (PL) from InGaAs quantum wells (QWs) grown on alloy graded InGaAs buffer layers on GaAs by molecular beam epitaxy. The epistructures show quite smooth surfaces with an average surface roughness less than 2nm. The PL intensity is comparable with those from InAs quantum dots and InGaAs QWs on GaAs, and InGaAsP QWs on InP at similar wavelengths, but stronger than those from GaInNAs QWs (at least 10 times higher at around 1.5–1.6μm). The excellent optical quality implies that the metamorphic approach could be a promising alternative to GaInNAs(Sb) QWs for 1.55μm lasers on GaAs.
Optical observation of donor-bound excitons in hydrogen-implanted ZnO
Authors: Lee J.-K. , Nastasi M. , Hamby D. W. , Lucca D. A.
Published: April 2005

The optical and structural properties of H or He implanted ZnO were investigated using low temperature photoluminescence (PL) and infrared spectroscopy (IR). H implantation is shown to influence the relative luminescence intensities of the donor bound excitons, enhancing the 3.361 eV peak, and changing the overall intensity of the PL spectrum. PL from He implanted ZnO is used to demonstrate that implantation damage is partially responsible for the variations observed in the PL of H implanted ZnO. IR spectra show that the increase in the relative intensity of the 3.361 eV peak coincides with an appearance of the H vibrational mode in the ZnO lattice. Our results indicate that the implanted H forms O–H bonds at Zn vacancies, and that it is these defect complexes which give rise to the shallow donors participating in the observed bound-exciton luminescence at 3.361 eV.
All-MgB2 Josephson tunnel junctions
Authors: Ueda K. , Saito S. , Semba K. , Makimoto T. , Naito M.
Published: April 2005

Sandwich-type all-MgB2 Josephson tunnel junctions (MgB2∕AlOx∕MgB2) have been fabricated with as-grown MgB2 films formed by molecular-beam epitaxy. The junctions exhibit substantial superconducting current (IcRN product ∼0.8mV at 4.2 K), a well-defined superconducting gap (Δ=2.2–2.3mV), and clear Fraunhofer patterns. The superconducting gap voltage of Δ agrees well with the smaller gap in the multigap scenario. The results demonstrate that MgB2 has great promise for superconducting electronics that can be operated at T∼20K.
Polar behavior in Mn-doped SrTiO3 ceramics
Authors: Tkach A. , Vilarinho P. M. , Kholkin A. L.
Published: April 2005

Polar behavior was found in Sr1−xMnxTiO3(x=0.005–0.02) ceramic system. Radio-frequency dielectric measurements showed a diffuse maximum at 25–65 K shifting to higher temperatures with increasing measurement frequency and amount of Mn. The observation of hysteretic behavior in the P versus E curves shows the existence of a polar state at low temperatures. The hysteresis response slowly degenerates into just nonlinearity as the temperature increases. The observed relaxor-type dielectric behavior is attributed to the formation of electric dipoles and corresponding random fields due to the off-center position of Mn2+ ion at the Sr site of highly polarizable SrTiO3 lattice.
Metal nanoparticles-embedded three-dimensional microstructures created by single-beam holography
Authors: Yang Yi , Wang Guo Ping , Xie Jiang , Zhang Suhuai
Published: April 2005

Silver nanoparticles-embedded three-dimensional (3D) dielectric microstructures are demonstrated with a single-beam holographic technique. By using a top-cut triangular prism to split an incident plane wave into four umbrellalike beams and then to automatically combine the four beams in Ag+-doped dielectric matrices, a 3D microstructure with periodically embedded Ag nanoparticles is encoded. Our method can be used to create any 3D microstructures in various materials and hence provide a robust way for photonic crystal fabrications, label-free 3D biological imaging, and optical integration etc.
Propagation of shear bands in Ti66.1Cu8Ni4.8Sn7.2Nb13.9 nanostructure-dendrite composite during deformation
Authors: Kim K. B. , Das J. , Baier F. , Eckert J.
Published: April 2005

During deformation of Ti66.1Cu8Ni4.8Sn7.2Nb13.9 nanostructure-dendrite composite, primary and secondary shear bands form under perpendicular orientation. Detailed investigation of the microstructure of deformed specimens reveals deformed body-centered-cubic (bcc) β-Ti dendrites forming a stepped morphology at the interfaces between the bcc β-Ti dendrites and the nanostructured matrix, consisting of hexagonal close packed (hcp) α-Ti and body-centered-tetragonal (bct) Ti2Cu phases. In the nanostructured matrix, the primary shear bands pass through coherent grain boundaries between the hcp α-Ti and the bct Ti2Cu phases. In contrast, the secondary shear bands in the nanostructured matrix are arrested by sandwiched nanoscale grains of the hcp α-Ti and bct Ti2Cu phases.
Selective metallization of internal walls of hollow structures inside glass using femtosecond laser
Authors: Sugioka Koji , Hongo Tomohiro , Takai Hiroshi , Midorikawa Katsumi
Published: April 2005

The selective metallization of glass is demonstrated by femtosecond laser direct writing in an electroless plating solution. The multiphoton absorption of a femtosecond laser by transparent glass makes it possible to selectively deposit copper thin films on the internal walls of hollow microstructures fabricated inside the glass. We regard the mechanism of this process as the reducing reaction of metal ions in the electroless plating solution by the free electrons generated in the glass by the multiphoton absorption of the femtosecond laser.
A coiled-coil interaction mediates cauliflower mosaic virus cell-to-cell movement
Authors: Stavolone Livia , Villani Maria Elena , Leclerc Denis , Hohn Thomas
Published: April 2005

The function of the virion-associated protein (VAP) of cauliflower mosaic virus (CaMV) has long been only poorly understood. VAP is associated with the virion but is dispensable for virus morphogenesis and replication. It mediates virus transmission by aphids through simultaneous interaction with both the aphid transmission factor and the virion. However, although insect transmission is not fundamental to CaMV survival, VAP is indispensable for spreading the virus infection within the host plant. We used a GST pull-down technique to demonstrate that VAP interacts with the viral movement protein through coiled-coil domains and surface plasmon resonance to measure the interaction kinetics. We mapped the movement protein coiled-coil to the C terminus of the protein and proved that it self-assembles as a trimer. Immunogold labeling/electron microscopy revealed that the VAP and viral movement protein colocalize on CaMV particles within plasmodesmata. These results highlight the multifunctional potential of the VAP protein conferred by its efficient coiled-coil interaction system and show a plant virus possessing a surface-exposed protein (VAP) mediating viral entry into host cells.
Ab initio
molecular dynamics and quasichemical study of H
+
(aq)
Authors: Asthagiri D. , Pratt L. R. , Kress J. D.
Published: April 2005

The excess proton in water, H
+
(aq), plays a fundamental role in aqueous solution chemistry. Its solution thermodynamic properties are essential to molecular descriptions of that chemistry and for validation of dynamical calculations. Within the quasichemical theory of solutions those thermodynamic properties are conditional on recognizing underlying solution structures. The quasichemical treatment identifies H
3
O
+
and H
2
O
5
+
as natural inner-shell complexes, corresponding to the cases of
n
= 1, 2 water molecule ligands, respectively, of a distinguished H
+
ion. A quantum-mechanical treatment of the inner-shell complex with both a dielectric continuum and a classical molecular dynamics treatment of the outer-shell contribution identifies the latter case (the Zundel complex) as the more numerous species.
Ab initio
molecular dynamics simulations, with two different electron density functionals, suggest a preponderance of Zundel-like structures, but a symmetrical ideal Zundel cation is not observed.
Aneuploid neurons are functionally active and integrated into brain circuitry
Authors: Kingsbury M. A. , Friedman B. , McConnell M. J. , Rehen S. K. , Yang A. H. , Kaushal D. , Chun J.
Published: April 2005

The existence of aneuploid cells within the mammalian brain has suggested the influence of genetic mosaicism on normal neural circuitry. However, aneuploid cells might instead be glia, nonneural, or dying cells, which are irrelevant to direct neuronal signaling. Combining retrograde labeling with FISH for chromosome-specific loci, distantly labeled aneuploid neurons were observed in expected anatomical projection areas. Coincident labeling for immediate early gene expression indicated that these aneuploid neurons were functionally active. These results demonstrate that functioning neurons with aneuploid genomes form genetically mosaic neural circuitries as part of the normal organization of the mammalian brain.
Indirubin derivatives inhibit Stat3 signaling and induce apoptosis in human cancer cells
Authors: Nam Sangkil , Buettner Ralf , Turkson James , Kim Donghwa , Cheng Jin Q. , Muehlbeyer Stephan , Hippe Frankie , Vatter Sandra , Merz Karl-Heinz , Eisenbrand Gerhard , Jove Richard
Published: April 2005

Stat3 protein has an important role in oncogenesis and is a promising anticancer target. Indirubin, the active component of a traditional Chinese herbal medicine, has been shown previously to inhibit cyclin-dependent kinases, resulting in cell cycle arrest. Here, we show that the indirubin derivatives E564, E728, and E804 potently block constitutive Stat3 signaling in human breast and prostate cancer cells. In addition, E804 directly inhibits Src kinase activity (IC50= 0.43 μM) in anin vitrokinase assay. Levels of tyrosyl phosphorylation of c-Src are also reduced in cultured cells 30 min after E804 treatment. Tyrosyl phosphorylation of Stat3, which is known to be phosphorylated by c-Src, was decreased, and constitutive Stat3 DNA binding-activity was suppressed in cells 30 min after E804 treatment. The antiapoptotic proteins Mcl-1 and Survivin, which are encoded in target genes of Stat3, were down-regulated by indirubin derivatives, followed by induction of apoptosis. These results demonstrate that E804 directly blocks the Src-Stat3 signaling pathway, suggesting that the antitumor activity of indirubin compounds is at least partially due to inhibition of this pathway.
Identifying photoreceptors in blind eyes caused by
RPE65
mutations: Prerequisite for human gene therapy success
Authors: Jacobson Samuel G. , Aleman Tomas S. , Cideciyan Artur V. , Sumaroka Alexander , Schwartz Sharon B. , Windsor Elizabeth A. M. , Traboulsi Elias I. , Heon Elise , Pittler Steven J. , Milam Ann H. , Maguire Albert M. , Palczewski Krzysztof , Stone Edwin M. , Bennett Jean
Published: April 2005

Mutations in
RPE65
, a gene essential to normal operation of the visual (retinoid) cycle, cause the childhood blindness known as Leber congenital amaurosis (LCA). Retinal gene therapy restores vision to blind canine and murine models of LCA. Gene therapy in blind humans with LCA from
RPE65
mutations may also have potential for success but only if the retinal photoreceptor layer is intact, as in the early-disease stage-treated animals. Here, we use high-resolution
in vivo
microscopy to quantify photoreceptor layer thickness in the human disease to define the relationship of retinal structure to vision and determine the potential for gene therapy success. The normally cone photoreceptor-rich central retina and rod-rich regions were studied. Despite severely reduced cone vision, many
RPE65
-mutant retinas had near-normal central microstructure. Absent rod vision was associated with a detectable but thinned photoreceptor layer. We asked whether abnormally thinned
RPE65
-mutant retina with photoreceptor loss would respond to treatment. Gene therapy in
Rpe65
-/-
mice at advanced-disease stages, a more faithful mimic of the humans we studied, showed success but only in animals with better-preserved photoreceptor structure. The results indicate that identifying and then targeting retinal locations with retained photoreceptors will be a prerequisite for successful gene therapy in humans with
RPE65
mutations and in other retinal degenerative disorders now moving from proof-of-concept studies toward clinical trials.
Synaptic vesicle recycling studied in transgenic mice expressing synaptopHluorin
Authors: Li Zhiying , Burrone Juan , Tyler William J. , Hartman Kenichi N. , Albeanu Dinu F. , Murthy Venkatesh N.
Published: April 2005

Synaptic vesicles are recycled locally within presynaptic specializations. We examined how vesicles are reused after endocytosis, using transgenic mice expressing the genetically encoded fluorescent indicator synaptopHluorin in subsets of neurons. At both excitatory and inhibitory synapses in cultured hippocampal neurons, newly endocytosed vesicles did not preferentially enter the releasable pool of vesicles. Rather, they entered the reserve pool first and subsequently the readily releasable pool over a period of several minutes. All vesicles in the recycling pool could be accessed by spaced stimuli, arguing against preferential local reuse of the readily releasable vesicles. Interestingly, nearly half the vesicles at excitatory synapses, and a third at inhibitory synapses, could not be recruited for release even by sustained stimuli. We conclude that, at presynaptic terminals in the hippocampus, most vesicles vacate release sites after exocytosis and are replaced by existing vesicles from the reserve pool, placing constraints on kiss-and-run recycling.
G protein-coupled lysophosphatidic acid receptors stimulate proliferation of colon cancer cells through the β-catenin pathway
Authors: Yang Ming , Zhong Wendy W. , Srivastava Neelam , Slavin Anthony , Yang Jianxin , Hoey Timothy , An Songzhu
Published: April 2005

Recent studies suggest that lysophosphatidic acid (LPA) and its G protein-coupled receptors (GPCRs) LPA
1
, LPA
2
, or LPA
3
may play a role in the development of several types of cancers, including colorectal cancer. However, the specific receptor subtype(s) and their signal-transduction pathways responsible for LPA-induced cancer cell proliferation have not been fully elucidated. We show by specific RNA interference (RNAi) that LPA
2
and LPA
3
but not LPA
1
are targets for LPA-induced proliferation of HCT116 and LS174T colon cancer cells. We determined that LPA-induced colon cancer cell proliferation requires the β-catenin signaling pathway, because knockdown of β-catenin by RNAi abolished LPA-induced proliferation of HCT116 cells. Moreover, LPA activates the main signaling events in the β-catenin pathway: phosphorylation of glycogen synthase kinase 3β (GSK3β), nuclear translocation of β-catenin, transcriptional activation of T cell factor (Tcf)/lymphoid-enhancer factor (Lef), and expression of target genes. Inhibition of conventional protein kinase C (cPKC) blocked the effects, suggesting its involvement in LPA-induced activation of the β-catenin pathway. Thus, LPA
2
and LPA
3
signal the proliferation of colon cancer cells through cPKC-mediated activation of the β-catenin pathway. These results link LPA and its GPCRs to cancer through a major oncogenic signaling pathway.
Glutamate induces the rapid formation of spine head protrusions in hippocampal slice cultures
Authors: Richards David A. , Mateos José Maria , Hugel Sylvain , de Paola Vincenzo , Caroni Pico , Gähwiler Beat H. , McKinney R. Anne
Published: April 2005

Synaptic plasticity at neuronal connections has been well characterized functionally by using electrophysiological approaches, but the structural basis for this phenomenon remains controversial. We have studied the dynamic interactions between presynaptic and postsynaptic structures labeled with FM 4-64 and a membrane-targeted GFP, respectively, in hippocampal slices. Under conditions of reduced neuronal activity (1 μM tetrodotoxin), we observed extension of glutamate receptor-dependent processes from dendritic spines of CA1 pyramidal cells to presynaptic boutons. The formation of these spine head protrusions is blocked by α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor antagonists and by agents that reduce the release of glutamate from presynaptic terminals. Moreover, spine head protrusions form in response to exogenously applied glutamate, with clear directionality toward the glutamate electrode. Our results suggest that spontaneously released glutamate is sufficient to activate nearby spines, which can then lead to the growth of new postsynaptic processes connecting to a presynaptic site. Spines thus can compare their recent history with that of neighboring synapses and modify local connectivity accordingly.
A comparison of conventional and alternative agroecosystems using alfalfa (Medicago sativa) and winter wheat (Triticum aestivum)
Authors: Skelton Laura E. , Barrett Gary W.
Published: April 2005

Natural systems agriculture is based on an understanding that natural systems are self-sustaining due to regulatory mechanisms and processes that help to ensure the long-term maintenance of the ecosystem. An agroecosystem modeled after nature should encompass greater stability and biodiversity at all levels of organization than an agroecosystem based on conventional agricultural practices. The main objective of this study was to determine whether agroecosystems modeled after nature exhibit advantages over conventional agroecosystems. Five treatments were examined: winter wheat (Triticum aestivumL.) monoculture, alfalfa (Medicago sativaL.) monoculture, strip-cropped alfalfa and wheat, and two alfalfa–wheat intercrops (one no-till and one conservation-till). Indicators of ecosystem function studied included primary productivity, soil fertility, plant nitrogen (N) concentration, and abundances of arthropod pests and predators. No fertilizers or pesticides were used prior to or during this investigation. Monoculture, strip-crop and conservation-till treatments produced significantly higher yields than no-till intercropped alfalfa and wheat. Although yields from the no-till intercrop were low, wheat protein values were comparable to other treatments. Soil N concentrations tended to be high in treatments containing alfalfa. Insect pests preferred alfalfa and were, therefore, often more abundant in treatments containing high percentages of alfalfa, as were predators such as spiders. Researching alternatives to monoculture agroecosystems, such as the intercrop systems in this study, may provide us insight into a true natural systems agriculture.
Meeting the challenge of disease management in perennial grain cropping systems
Authors: Cox C.M. , Garrett K.A. , Bockus W.W.
Published: April 2005

Perennial grain production will likely present unique challenges for managing diseases that affect the productivity and longevity of crops being considered. Typical cultural practices effective at reducing soil- and residue-borne pathogens, such as annual crop rotations, delayed fall planting, and tillage, are not feasible in perennial systems. Consequently, soil- and residue-borne pathogens, and pathogens such as root colonizers and viruses that survive in live tissue, may increase in importance in a perennial grain crop. Resistance genes will undeniably be important defenses against disease. However, it is seldom, if ever, possible to incorporate within a single cultivar resistance to all existing and future important diseases. Furthermore, genes vulnerable to ‘boom and bust’ cycles are generally short-lived when deployed in monocultures. For these reasons, the use of mixtures of crop cultivars or species that vary in resistance functions will likely be an important strategy for managing diseases and pests of perennial grains. Burning of plant residue, a natural phenomenon in native perennial grass systems, may also be an effective disease management strategy. The successful implementation of these management tools may reduce or eliminate the risk that perennial grain crops will become pathogen refugia that affect neighboring annual plantings and the productivity of perennial plants.
Perennial grain crops: A synthesis of ecology and plant breeding
Authors: DeHaan L.R. , Van Tassel D.L. , Cox T.S.
Published: April 2005

Perennial grain crops would address many agricultural problems, including soil erosion, nutrient loss and pesticide contamination. Doubts about the possibility of perennial grain crops rest upon two assumptions: (1) that the relationship between yield and longevity is a fixed function that cannot be influenced by selection, mutation or environmental changes; and (2) that yield and longevity trade off in a bivariate manner to the exclusion of all other traits. These assumptions are consistent with the phenotypic trade-off model, but recent research suggests that a quantitative genetic model is a more appropriate approach to trade-offs. In the quantitative genetic model, environmental and genetic changes can result in increases in two traits simultaneously even when a trade-off, or negative correlation, exists between the two traits. Empirical evidence that the trade-off between perenniality and reproductive allocation is not fixed comes from wild, herbaceous perennials that can produce more than 2000 kg seed ha−1 in the temperate zone, and herbaceous perennial crops that produce on average 8900 kg fruit ha−1 in the tropics. Ecological literature suggests that most perennials produce small amounts of seed relative to their vegetative growth not as a physiological absolute, but rather as a result of natural selection in a stable, competitive environment favoring longevity. By selecting strongly for seed yield in a population of perennial plants, the plant breeder can likely achieve that which is rare in nature—a high seed-yielding perennial plant. The same general methodologies that have allowed annual grain breeders to increase grain yield and push many combinations of negatively correlated traits to levels of expression not seen in nature are available to the perennial grain breeder. Perennial grain breeders are integrating ecological principles and traditional plant breeding methods in their efforts to develop perennial grain wheat (Triticum spp.), sorghum (Sorghum spp.), sunflower (Helianthus spp.), Illinois bundleflower (Desmanthus illinoensis) and rice (Oryza spp.).
Delayed, asynchronous, and reversible T-lineage specification induced by Notch/Delta signaling
Authors: Taghon Tom N. , David Elizabeth-Sharon , Zúñiga-Pflücker Juan Carlos , Rothenberg Ellen V.
Published: April 2005

Using the OP9-DL1 system to deliver temporally controlled Notch/Delta signaling, we show that pluripotent hematolymphoid progenitors undergo T-lineage specification and B-lineage inhibition in response to Notch signaling in a delayed and asynchronous way. Highly enriched progenitors from fetal liver require ≥3 d to begin B- or T-lineage differentiation. Clonal switch-culture analysis shows that progeny of some single cells can still generate both B- and T-lineage cells, after 1 wk of continuous delivery or deprivation of Notch/Delta signaling. Notch signaling induces T-cell genes and represses B-cell genes, but kinetics of activation of lineage-specific transcription factors are significantly delayed after induction of Notch target genes and can be temporally uncoupled from the Notch response. In the cells that initiate T-cell differentiation and gene expression most slowly in response to Notch/Delta signaling, Notch target genes are induced to the same level as in the cells that respond most rapidly. Early lineage-specific gene expression is also rapidly reversible in switch cultures. Thus, while necessary to induce and sustain T-cell development, Notch/Delta signaling is not sufficient for T-lineage specification and commitment, but instead can be permissive for the maintenance and proliferation of uncommitted progenitors that are omitted in binary-choice models.
TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs
Authors: Bachman Nurjana , Gelbart Marnie E. , Tsukiyama Toshio , Boeke Jef D.
Published: April 2005

Retrotransposons are RNA elements that reverse transcribe their RNA genomes and make a cDNA copy that is inserted back into a new genomic location by the element-encoded integrase protein. Ty1 is a long terminal repeat (LTR) retrotransposon in Saccharomyces cerevisiae that inserts into an ∼700-bp integration window upstream of tRNA genes with a periodicity of ∼80 bp. ATP-dependent chromatin remodeling by Isw2 upstream of tRNA genes leads to changes in chromatin structure and Ty1 integration site selection. We show that the N terminus of Bdp1p, a component of the RNA polymerase III transcription factor TFIIIB, is required for periodic integration of Ty1 into the integration window. Deletion of the Bdp1p N terminus and mutation of ISW2 result in similar disruption of nucleosome positioning upstream of some tRNA genes, and the N-terminal domain of Bdp1p is required for targeting of Isw2 complex to tRNA genes. This study provides the first example for recruitment of an ATP-dependent chromatin-remodeling factor by a general transcription factor in vivo.
The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation
Authors: Thomson Nicholas R. , Yeats Corin , Bell Kenneth , Holden Matthew T.G. , Bentley Stephen D. , Livingstone Morag , Cerdeño-Tárraga Ana M. , Harris Barbara , Doggett Jon , Ormond Doug , Mungall Karen , Clarke Kay , Feltwell Theresa , Hance Zahra , Sanders Mandy , Quail Michael A. , Price Claire , Barrell Bart G. , Parkhill Julian , Longbottom David
Published: April 2005

The obligate intracellular bacterial pathogen Chlamydophila abortus strain S26/3 (formerly the abortion subtype of Chlamydia psittaci) is an important cause of late gestation abortions in ruminants and pigs. Furthermore, although relatively rare, zoonotic infection can result in acute illness and miscarriage in pregnant women. The complete genome sequence was determined and shows a high level of conservation in both sequence and overall gene content in comparison to other Chlamydiaceae. The 1,144,377-bp genome contains 961 predicted coding sequences, 842 of which are conserved with those of Chlamydophila caviae and Chlamydophila pneumoniae. Within this conserved Cp. abortus core genome we have identified the major regions of variation and have focused our analysis on these loci, several of which were found to encode highly variable protein families, such as TMH/Inc and Pmp families, which are strong candidates for the source of diversity in host tropism and disease causation in this group of organisms. Significantly, Cp. abortus lacks any toxin genes, and also lacks genes involved in tryptophan metabolism and nucleotide salvaging (guaB is present as a pseudogene), suggesting that the genetic basis of niche adaptation of this species is distinct from those previously proposed for other chlamydial species.
A Review of Productivity
Authors: Burgess Thomas F.
Published: April 2005

Considers the difficulties involved in applying the superficially
simple concept of productivity as total output divided by total input.
Discusses the systems view of productivity, the economists′ approach to
productivity, the UK productivity record, measuring organizational
performance in public and private sectors, individual productivity and
attitudes to productivity. Concludes that the assumptions on which
productivity analysis is based should always be questioned to avoid
misapplication.