bluuebunny/crossref_metadata_2025 huggingface dataset:
Mean potential phase space theory of chemical reactions
Authors: Larrégaray P. , Bonnet L. , Rayez J.-C.
Published: August 2007

A nonconventional application of phase space theory to the insertion reactions A+H2, with A=C(D1) and S(D1), is presented. Instead of approximating the potential energies of interaction between separated fragments by their isotropic long-range contributions, as in the original theory, the latter are replaced by the accurate potential energies averaged with respect to Jacobi angles. The integral and differential cross sections obtained from this mean potential phase space theory (MPPST) turn out to be in very satisfying agreement with the benchmark predictions of the time-independent and time-dependent statistical quantum methods. The formal and numerical simplicity of MPPST with respect to any approach combining statistical assumptions and dynamical calculations makes it a promising tool for studying indirect polyatomic reactions.
Monitoring of the laser microdrilling of glass by the optodynamic method
Authors: Petkovsek Rok , Mozina Janez
Published: August 2007

During the pulsed-laser microdrilling process using nanosecond pulses, a plasma and a shockwave develop. In order to study their formation and propagation and investigate the possibilities for monitoring the process, we have developed a highly automated experimental setup utilizing two types of detectors: A high-speed beam-deflection probe and a camera equipped with a liquid-crystal light attenuator mounted on an optical microscope. By analyzing the data from both detectors we were able to develop a technique for the online monitoring of hole-depth during the pulsed-laser microdrilling process for glass. It is based on time-of-flight measurements of the shockwave and simultaneous determination of its source size.
Influence of the optical control in the lateral transport of carriers in InGaAs∕GaAs one-side modulation-doped quantum wells
Authors: da Cunha J. F. R. , da Silva S. W. , Morais P. C. , Lamas T. E. , Quivy A. A.
Published: August 2007

The effects of optically exciting n-type and p-type one-side modulation-doped InGaAs∕GaAs quantum well structures were investigated by scanning the photoluminescence intensity profile on the sample’s surface. An undoped quantum well was used as reference. Photoluminescence and carrier diffusion length measurements were carried out at increasing optical excitation densities. We found that the excitation density dependence of the carrier diffusion length in doped samples is quite different from that of the undoped sample. This difference is discussed in terms of the reduction of band bending∕band-gap renormalization and carrier lifetime change due to the reduction of the two-dimensional carries gas density inside the quantum well upon intense laser illumination.
Density functional study of the interaction between small Au clusters, Aun (n=1–7) and the rutile TiO2 surface. I. Adsorption on the stoichiometric surface
Authors: Chrétien Steeve , Metiu Horia
Published: August 2007

This is the first paper in a series of four dealing with the adsorption site, electronic structure, and chemistry of small Au clusters, Aun (n=1–7), supported on stoichiometric, partially reduced, or partially hydroxylated rutile TiO2(110) surfaces. Analysis of the electronic structure reveals that the main contribution to the binding energy is the overlap between the highest occupied molecular orbitals of Au clusters and the Kohn-Sham orbitals localized on the bridging and the in-plane oxygen of the rutile TiO2(110) surface. The structure of adsorbed Aun differs from that in the gas phase mostly because the cluster wants to maximize this orbital overlap and to increase the number of Au–O bonds. For example, the equilibrium structures of Au5 and Au7 are planar in the gas phase, while the adsorbed Au5 has a distorted two-dimensional structure and the adsorbed Au7 is three-dimensional. The dissociation of an adsorbed cluster into two adsorbed fragments is endothermic, for all clusters, by at least 0.8eV. This does not mean that the gas-phase clusters hitting the surface with kinetic energy greater than 0.8eV will fragment. To place enough energy in the reaction coordinate for fragmentation, the impact kinetic energy needs to be substantially higher than 0.8eV. We have also calculated the interaction energy between all pairs of Au clusters. These interactions are small except when a Au monomer is coadsorbed with a Aun with odd n. In this case the interaction energy is of the order of 0.7eV and the two clusters interact through the support even when they are fairly far apart. This happens because the adsorption of a Aun cluster places electrons in the states of the bottom of the conduction band and these electrons help the Au monomer to bind to the five-coordinated Ti atoms on the surface.
Scattering properties and scattering kernel based on the molecular dynamics analysis of gas-wall interaction
Authors: Yamamoto Kyoji , Takeuchi Hideki , Hyakutake Toru
Published: August 2007

The scattering behaviors of nitrogen molecules reflected at a platinum surface are studied by the molecular dynamics method for the gas-surface interaction. The platinum surface is assumed to physically adsorb xenon molecules. Distributions of molecular velocities after reflection are obtained for the impinging molecules with specified velocities within a small range. The scattering distribution shows a bimodal behavior consisting of diffuse reflection and a distribution shifting to the velocity distribution of the impinging molecules. Comparison between the present scattering distribution and the Cercignani-Lampis-Lord scattering kernel shows large differences. A simple scattering kernel using a bimodal distribution is proposed assuming mutual independence of distributions in each velocity component and is compared favorably to the present scattering distribution. In addition, the scattering kernel of the rotational energy of the molecule is discussed.
Nanostripes in (Nd0.33Eu0.28Gd0.38)Ba2Cu3Ox superconductors
Authors: Koblischka M. R. , Winter M. , Koblischka-Veneva A. , Muralidhar M. , Mücklich F. , Hartmann U.
Published: August 2007

Nanostripes are observed in melt-textured, Gd-enriched light-rare-earth (LRE)-based ternary (Nd0.33Eu0.28Gd0.38)Ba2Cu3Ox (NEG-38) superconductors. Employing atomic force microscopy/scanning tunneling microscopy topographic scans together with electron backscatter diffraction (EBSD) analysis, the authors determine the direction of the nanostripes with respect to the twin structure. Details of the topography measurements and of the EBSD maps reveal that the nanostripes are composed of nanoclusters of the LRE-rich phase. The nanostripes in the NEG-38 samples have a periodicity of about 40–60nm, and in lateral direction between 300 and 500nm. The role of these nanostripes for flux pinning in these compounds is discussed.
Controlled vortex core switching in a magnetic nanodisk by a rotating field
Authors: Kravchuk Volodymyr P. , Sheka Denis D. , Gaididei Yuri , Mertens Franz G.
Published: August 2007

The control of the vortex state magnetic nanoparticle by ultrafast magnetic fields is studied theoretically. Using the micromagnetic simulations for the Permalloy nanodisk we demonstrate that the vortex core magnetization can be irreversible switched by the alternating field, rotating in the disk plane, with the frequency about 10 GHz and intensity about 20 mT. We propose an analytical picture of such phenomena involving the creation and annihilation of vortex-antivortex pairs and calculate the phase diagram of the fields parameters leading to the switching.
Deposition of nanocrystalline silicon films at room temperature
Authors: Mani Radhika C. , Pavel Ioana , Aydil Eray S.
Published: August 2007

Bond rearrangements, facilitated by H insertion into strained Si–Si bonds have been shown to result in H-induced crystallization of amorphous silicon films. Whether such H-induced rearrangements can lead to synthesis of nanocrystalline films at room temperature has remained an open question. In this article, the authors demonstrate the deposition of thin films containing nanocrystals of silicon using inductively coupled SiH4/H2 plasma at room temperature. Real time in situ spectroscopic ellipsometry and ex situ transmission electron microscopy revealed that the silicon nanocrystals nucleate below the surface, and grow beneath an amorphous silicon crust. This observation validates the hydrogen-induced crystallization model. Analysis of the crystal size distribution shows that the distribution depends on the growth duration rather than the substrate temperature. Observation of crystals as large as 100–150 nm at room temperature indicates that silicon nanocrystals not only nucleate but also grow substantially in the bulk even at room temperature.
Intrinsic dielectric and spectroscopic behavior of perovskite Ba(Ni1∕3Nb2∕3)O3–Ba(Zn1∕3Nb2∕3)O3 microwave dielectric ceramics
Authors: Lin I. N. , Chia C. T. , Liu H. L. , Cheng H. F. , Freer R. , Barwick M. , Azough F.
Published: August 2007

Ceramics of 0.35Ba(Ni1∕3Nb2∕3)O3–0.65Ba(Zn1∕3Nb2∕3)O3 were prepared by the mixed oxide route. The effect of the cooling rate (2 °C–240 °C∕h) after sintering on the microwave dielectric properties of the ceramics was examined. While the extrinsic factors, such as porosity and secondary phases, markedly influence the dielectric properties in the low-frequency regime, they have minimal effect on these properties in the high-frequency regime. The mechanisms involved in modifying the high-frequency dielectric properties of the materials were investigated by Fourier transform infrared and Raman spectroscopy, in conjunction with the Rietveld analysis of x-ray diffraction (XRD) spectra. A reduction in the cooling rate after sintering results in an increase in the high-frequency Q×f (product of dielectric Q value and measurement frequency) from 42 to 58 THz in the high-frequency regime (∼1.5 THz). Such behavior correlates very well with the increase in the B-site occupancy by Nb (deduced from the Rietveld analyses of XRD spectra) and the increase in the coherency of the lattice vibration (deduced from the reduction in the full-width-at-half-maximum of the A1g(O) Raman mode). In contrast, the cooling rate after sintering has very limited effect on the relative permittivity (varying from 40.8 to 41.9 at 1.5 THz), which is in accord with the phenomenon that the cell volume and the Raman shift of A1g(O) Raman mode are essentially independent of the cooling rate.
Focused ion beam induced synthesis of a porous antimony nanowire network
Authors: Schoendorfer Christoph , Lugstein Alois , Hyun Youn-Joo , Bertagnolli Emmerich , Bischoff Lothar , Nellen Philipp M. , Callegari Victor , Pongratz Peter
Published: August 2007

We present a focused ion beam-based approach for the synthesis of an antimony nanofiber network. The nanofibers, with a homogeneous distribution of diameters of about 25 nm and lengths up to several microns, are synthesized in a self-assembling process without any additional material source at room temperature. It is possible to recrystallize the as-grown amorphous nanofibers by moderate rapid thermal annealing at 473 K. These results have been verified by means of scanning electron microscopy, Auger electron spectroscopy, high-resolution transmission electron microscopy, selected area electron diffraction, and energy dispersive x-ray analysis. As this approach is not limited solely to the material discussed here, other substrates (e.g., GaSb and Ge) and ion sources should extend this method to other materials, which offers a great potential for future nanoscale devices and applications.
Terahertz time-domain spectroscopy of silicate glasses and the relationship to material properties
Authors: Naftaly M. , Miles R. E.
Published: August 2007

Terahertz (THz) time-domain transmission spectroscopy was used to obtain the absorption coefficients and refractive indices of silica, Pyrex, and seven different Schott glasses. The refractive indices were analyzed using the Clausius–Mossotti equation, and the absorption coefficients in terms of the power-law model of far-infrared absorption. Relationships were observed between THz absorption and refractive indices on the one hand, and glass properties on the other. THz transmission data have been shown to provide a useful insight into glass structure.
Partial recovery of potentials in generalized nonlinear Schrödinger equations on the line
Authors: Serov Valery , Harju Markus
Published: August 2007

The inverse Born approximation method is applied to inverse scattering problems for two one-dimensional nonlinear Schrödinger equations. We prove that all jumps and singularities of the unknown function are recovered from the Born function sequence. In particular, one can locate any bounded interval on the line. The result is based on the accurate determination of the first nonlinear term of the Born sequence.
Low temperature aging effects on the formation of Sn nanoclusters in SiO2∕Si films and interfaces
Authors: Kremer Felipe , Lopes João M. J. , Zawislak Fernando C. , Fichtner Paulo F. P.
Published: August 2007

The formation of Sn nanocrystals (NCs) in ion implanted SiO2∕Si films is investigated using Rutherford backscattering spectrometry and transmission electron microscopy. Low temperature and long time aging treatments followed by high temperature thermal annealings lead to the formation of a dense bidimensional NC array located at the SiO2∕Si interface. This behavior is discussed considering the formation of small Sn clusters with a significantly improved thermal stability. The present experimental results are in good agreement with recent theoretical predictions that small Sn clusters can have their melting temperature enhanced in more than 1000°C.
Effective removal of field-emitting sites from metallic surfaces by dry ice cleaning
Authors: Dangwal Arti , Müller Günter , Reschke Detlef , Floettmann Klaus , Singer Xenia
Published: August 2007

Systematic results of the field emission properties of polycrystalline copper and niobium and single-crystal Nb are reported. Dry ice cleaning (DIC) is found to suppress enhanced field emission from metallic surfaces. The cleaning effect on the emitting sites was investigated by means of field emission scanning microscopy up to fields of 250 MV/m and high-resolution scanning electron microscopy with energy dispersive x-ray analysis. The number density of emitters at given fields was drastically reduced by dry ice cleaning. Current-voltage measurements and derived Fowler-Nordheim parameters are partially discussed with respect to the morphology and impurity content of localized emitters. No emission from grain boundaries on large-grain Nb samples was observed. The microscopy results prove the effective removal of field-emitting particulates down to 400 nm as well as the partial smoothing of surface protrusions by DIC.
Self-suppression of reset induced triggering in picosecond SPAD timing circuits
Authors: Rech I. , Resnati D. , Gulinatti A. , Ghioni M. , Cova S.
Published: August 2007

We present a new photon timing circuit that achieves a time resolution of 35ps full width at half maximum with single photon avalanche diodes having active area diameters up to 200μm. The timing circuit is based on a double avalanche current sensing network that makes it particularly suited to operation at high photon counting rates. Thanks to its self-adjusting capabilities, no trimming is needed even when changing the photodetector operating conditions over a wide range.
Preparation of La68Al10Cu20Co2 bulk metallic glass by rapid compression
Authors: Liu X. R. , Hong S. M. , Lü S. J. , Shen R.
Published: August 2007

Melt of La68Al10Cu20Co2 alloy was solidified by rapid compression within 20msto5.5GPa at 733K. The structural analysis demonstrates that the recovered alloy is a fully glassy structure indicating that the method is an effective way for preparing bulk metallic glass. Differential scanning calorimetry analysis indicates the glass-forming ability of the alloy is enhanced according to the reduced glass transition temperature. It is found that exist markedly differences in thermodynamic and mechanical properties between the metallic glasses prepared by melt quenching and rapid compression.
Multiplexing surface plasmon polaritons on nanowires
Authors: Imre A. , Vlasko-Vlasov V. K. , Pearson J. , Hiller J. M. , Welp U.
Published: August 2007

The authors demonstrate a plasmonic device that generates and steers tightly focused plasmon beams between neighboring subwavelength metal-strip waveguides. By introducing a controlled phase shift into the plasmon condenser, they shifted the focused plasmon spot by microns with nanometer accuracy and realized the multiplexer functionality.
Processing and properties of Yb-doped BiFeO3 ceramics
Authors: Yan Z. , Wang K. F. , Qu J. F. , Wang Y. , Song Z. T. , Feng S. L.
Published: August 2007

The authors prepared Yb-doped bismuth iron oxide ceramics (Bi1−xYbxFeO3, with 0⩽x⩽0.20) by rapid liquid phase sintering method and investigated the material’s structures and electrical properties. The x-ray diffraction measurements showed that the doping of Yb has induced noticeable lattice distortion in the ceramics, and a largest distortion was observed when the concentration of Yb was 15%. By doping electrical resistivity, ferroelectric and dielectric properties of the ceramics were improved. Among all samples, BiFeO3 doped with 15% Yb was found to have the smallest leakage current density (<10−7A∕cm2) and the largest remnant polarization (8.5μC∕cm2).
Epitaxial growth of nonpolar AlN films on ZnO substrates using room temperature grown GaN buffer layers
Authors: Ueno Kohei , Kobayashi Atsushi , Ohta Jitsuo , Fujioka Hiroshi , Amanai Hidetaka , Nagao Satoru , Horie Hideyoshi
Published: August 2007

The authors have grown nonpolar AlN layers on m-plane ZnO substrates using pulsed laser deposition and investigated their structural properties. The direct growth of AlN on ZnO substrates at 750°C results in the formation of polycrystalline materials due to significant interfacial reactions between AlN and ZnO. On the other hand, m-plane AlN was grown epitaxially on the ZnO substrates by using a GaN buffer layer prepared at room temperature (RT). The full width at half maximum value for AlN 11¯00 x-ray rocking curve was determined to be 468arcsec. Grazing incidence angle x-ray reflectivity measurements revealed that the heterointerface between AlN and RT GaN is quite abrupt. X-ray diffraction measurements revealed that the in-plane epitaxial relationship is ⟨0001⟩AlN‖⟨0001⟩GaN‖⟨0001⟩ZnO. These results indicate that the use of the RT GaN buffer layer makes it possible to take full advantage of small lattice mismatches and the wurtzite structure of the ZnO substrates.
Current induced switching of vortex polarity in magnetic nanodisks
Authors: Sheka Denis D. , Gaididei Yuri , Mertens Franz G.
Published: August 2007

It is shown that the vortex polarity can be irreversibly switched by injecting a spin-polarized direct electrical current, which flows perpendicular to the disk plane. Intensive numerical spin-lattice simulations demonstrate that the switching process involves a vortex-antivortex pair creation. This differs from magnets with no dipolar interaction, where the spin dc acts similar to a static magnetic field.
Dresselhaus effect in bulk wurtzite materials
Authors: Wang Wan-Tsang , Wu C. L. , Tsay S. F. , Gau M. H. , Lo Ikai , Kao H. F. , Jang D. J. , Chiang Jih-Chen , Lee Meng-En , Chang Yia-Chung , Chen Chun-Nan , Hsueh H. C.
Published: August 2007

The spin-splitting energies of the conduction band for ideal wurtzite materials are calculated within the nearest-neighbor tight-binding method. It is found that ideal wurtzite bulk inversion asymmetry yields not only a spin-degenerate line (along the kz axis) but also a minimum-spin-splitting surface, which can be regarded as a spin-degenerate surface in the form of bkz2−k‖2=0 (b≈4) near the Γ point. This phenomenon is referred to as the Dresselhaus effect (defined as the cubic-in-k term) in bulk wurtzite materials because it generates a term γwz(bkz2−k‖2)(σxky−σykx) in the two-band k∙p Hamiltonian.
First-principles calculations for the elastic properties of nanostructured superhard TiN∕SixNy superlattices
Authors: Wang Sanwu , Gudipati R. , Rao A. S. , Bostelmann T. J. , Shen Y. G.
Published: August 2007

The authors report the first-principles density-functional calculations for the structure and the elastic properties of superlattices containing nanoscale crystalline titanium nitride (TiN) and thin layer of silicon nitride. The authors found that the elastic properties are strongly dependent on the size of the components. Superlattices with TiN thickness smaller than 2.5nm have far smaller values of bulk and shear moduli than bulk crystalline TiN, while ∼3nm TiN can make the superlattice have the elastic properties close to those of crystalline TiN.
Antiferroelectriclike polarization behavior in compositionally varying (1−x) Pb(Mg1∕3Nb2∕3)O3–(x) PbTiO3 multilayers
Authors: Ranjith R. , Krupanidhi S. B.
Published: August 2007

Compositionally varying multilayers of (1−x) Pb(Mg1∕3N2∕3)O3–(x) PbTiO3 were fabricated using pulsed laser ablation technique. An antiferroelectriclike polarization hysteresis was observed in these relaxor based multilayer systems. The competition among the intrinsic ferroelectric coupling in the relaxor ferroelectrics and the antiferroelectric coupling among the dipoles at the interface gives rise to an antiferroelectriclike polarization behavior. An increment in the coercive field and the applied field corresponding to the polarization flipping at low temperatures, provide further insight on the competition among the long-range ferroelectric interaction and the interfacial interaction in the polarization behavior of these relaxor multilayers.
Application of ac tomography to crack identification
Authors: Saguy H. , Rittel D.
Published: August 2007

The depth of penetration of alternating currents in conductors depends on their frequency and material properties. A tomographiclike technique was proposed, in which the frequency is systematically varied to detect and size flaws (emerging and hidden) in electrical conductors, based on an analysis of the skin effect [Saguy and Rittel, Appl. Phys. Lett. 89, 094107 (2006); 87, 084103 (2005)]. Initial results were reported for notched specimens [Saguy and Rittel, NDT & E Int. 40, 505 (2007)] This letter presents experimental results on the detection of actual sharp fatigue cracks, differing from notches in terms of sharpness and partial conduction through the crack flanks. The results show that hidden cracks with arbitrary crack-front shape can be accurately identified.
Magnetic force microscopy study of microwave-assisted magnetization reversal in submicron-scale ferromagnetic particles
Authors: Nozaki Y. , Ohta M. , Taharazako S. , Tateishi K. , Yoshimura S. , Matsuyama K.
Published: August 2007

Changes in magnetic-domain configurations caused by the application of radio-frequency (rf) fields ranging from 3to18GHz were observed using magnetic force microscope. rf fields barely altered the magnetization of Co particles with scattered large crystalline anisotropy; however, for NiFe particles, magnetization switching occurred when the rf approached the natural ferromagnetic-resonance frequency of 5.92GHz. However, the reduction of the switching field fluctuated widely among the particles. Scattering of the effective energy barrier to thermal fluctuations caused by an applied rf field can explain the stochastic switching properties.
Direct real-time observation of catastrophic optical degradation in operating semiconductor lasers using scanning tunneling microscopy
Authors: Cobley R. J. , Teng K. S. , Brown M. R. , Wilks S. P. , Rees P.
Published: August 2007

Cross-sectional scanning tunneling microscopy is performed on operating semiconductor quantum well laser devices to reveal real time changes in device structure. Low and nominally doped capping regions adjacent to the quantum well active region are found to heat under normal operating conditions. The increase in anion-vacancy defect formation and the generation of surface states pins the Fermi level at the surface and begins the process of catastrophic optical degradation which eventually destroys the device. The technique has implications for the study of defect generation and in-operation changes in all nanostructures.
Magnetocaloric effect in Ho5Pd2: Evidence of large cooling power
Authors: Samanta Tapas , Das I. , Banerjee S.
Published: August 2007

The study of magnetocaloric effect has been performed on polycrystalline Ho5Pd2 compound, which undergoes magnetic field-induced first order metamagnetic transition from antiferromagnetic to ferromagnetic state below antiferromagnetic transition temperature. A large magnetic entropy change associated with the field-induced metamagnetic transition has been observed over a wide temperature range. The evaluated value of relative cooling power is 6.32J∕cm3 for a magnetic field change of 5T, which is even larger than that for reported best known magnetic refrigerant materials irrespective of the temperature range.
Half-metallic sp-electron ferromagnets in rocksalt structure: The case of SrC and BaC
Authors: Gao G. Y. , Yao K. L.
Published: August 2007

First-principles calculations are employed to study the structural and magnetic properties of SrC and BaC in four different phases: rocksalt, CsCl, zinc blende, and NiAs. The obtained results indicate that both compounds show half-metallic behavior in all phases except the CsCl-type structure. Among them the rocksalt structure is found to be the most stable one with a robust half-metallic characteristic with respect to the lattice compression and expansion. The magnetic phase transition temperature Tc of the rocksalt phase is calculated employing both the mean-field approximation and the random-phase approximation. The predicted Tc values of both compounds are considerably above room temperature.
Control of open-circuit voltage in organic photovoltaic cells by inserting an ultrathin metal-phthalocyanine layer
Authors: Kinoshita Yoshiki , Hasobe Taku , Murata Hideyuki
Published: August 2007

The authors develop organic photovoltaic cells with multicharge separation (MCS) interfaces by inserting a very thin layer of metal phthalocyanine. The devices with MCS interface allow one to control short-circuit current density (Jsc) and open-circuit voltage (Voc). The power conversion efficiency (ηp) of the device with MCS interface (Cu-phthalocyanine/C60andpentacene∕C60) is enhanced compared with that of the device with single charge separation interface (pentacene/C60). The enhancement of ηp is attributable to the increase in Voc with maintaining the Jsc. By using Zn-phthalocyanine, which possesses longer excited lifetime compared with Cu-phthalocyanine, both Jsc and Voc have been improved simultaneously and the ηp reaches 2.04%.
Highly textured, magnetic Fe(1+x)S nanorods grown on silicon
Authors: Soon Jia Mei , Goh Lai Yoong , Loh Kian Ping , Foo Yong Lim , Ming Lin , Ding Jun
Published: August 2007

Highly textured nanorods of iron sulfide Fe(1+x)S (0.1<x<0.2) were deposited on silicon by chemical vapor deposition using the single source precursor iron(III) N,N-diethyldithiocarbamate. The evaporation of this precursor in vacuum, followed by its thermal decomposition on silicon substrate, resulted in the growth of iron-rich iron sulfide semiconductor. Magnetic profiling of the iron-rich Fe(1+x)S rods grown on silicon revealed a Curie temperature of 360°C; the in-plane:out-of-plane magnetic saturation ratio is 4:1, with a saturation magnetization of 19.7emu∕g.
Single bump, two-color quantum dot camera
Authors: Varley E. , Lenz M. , Lee S. J. , Brown J. S. , Ramirez D. A. , Stintz A. , Krishna S. , Reisinger Axel , Sundaram Mani
Published: August 2007

The authors report a two-color, colocated quantum dot based imaging system used to take multicolor images using a single focal plane array (FPA). The dots-in-a-well (DWELL) detectors consist of an active region composed of InAs quantum dots embedded in In.15Ga.85As quantum wells. DWELL samples were grown using molecular beam epitaxy and fabricated into 320×256 focal plane arrays with indium bumps. The FPA was then hybridized to an Indigo ISC9705 readout circuit and tested. Calibrated blackbody measurements at a device temperature of 77K yield midwave infrared and long wave infrared noise equivalent difference in temperature of ∼55 and 70mK.
A comprehensive archaeological map of the world's largest preindustrial settlement complex at Angkor, Cambodia
Authors: Evans Damian , Pottier Christophe , Fletcher Roland , Hensley Scott , Tapley Ian , Milne Anthony , Barbetti Michael
Published: August 2007

The great medieval settlement of Angkor in Cambodia [9th–16th centuries Common Era (CE)] has for many years been understood as a “hydraulic city,” an urban complex defined, sustained, and ultimately overwhelmed by a complex water management network. Since the 1980s that view has been disputed, but the debate has remained unresolved because of insufficient data on the landscape beyond the great temples: the broader context of the monumental remains was only partially understood and had not been adequately mapped. Since the 1990s, French, Australian, and Cambodian teams have sought to address this empirical deficit through archaeological mapping projects by using traditional methods such as ground survey in conjunction with advanced radar remote-sensing applications in partnership with the National Aeronautics and Space Administration (NASA)/Jet Propulsion Laboratory (JPL). Here we present a major outcome of that research: a comprehensive archaeological map of greater Angkor, covering nearly 3,000 km
2
, prepared by the Greater Angkor Project (GAP). The map reveals a vast, low-density settlement landscape integrated by an elaborate water management network covering >1,000 km
2
, the most extensive urban complex of the preindustrial world. It is now clear that anthropogenic changes to the landscape were both extensive and substantial enough to have created grave challenges to the long-term viability of the settlement.
Human and animal cognition: Continuity and discontinuity
Authors: Premack David
Published: August 2007

Microscopic study of the human brain has revealed neural structures, enhanced wiring, and forms of connectivity among nerve cells not found in any animal, challenging the view that the human brain is simply an enlarged chimpanzee brain. On the other hand, cognitive studies have found animals to have abilities once thought unique to the human. This suggests a disparity between brain and mind. The suggestion is misleading. Cognitive research has not kept pace with neural research. Neural findings are based on microscopic study of the brain and are primarily cellular. Because cognition cannot be studied microscopically, we need to refine the study of cognition by using a different approach. In examining claims of similarity between animals and humans, one must ask: What are the dissimilarities? This approach prevents confusing similarity with equivalence. We follow this approach in examining eight cognitive cases—teaching, short-term memory, causal reasoning, planning, deception, transitive inference, theory of mind, and language—and find, in all cases, that similarities between animal and human abilities are small, dissimilarities large. There is no disparity between brain and mind.
Wordom: a program for efficient analysis of molecular dynamics simulations
Authors: Seeber Michele , Cecchini Marco , Rao Francesco , Settanni Giovanni , Caflisch Amedeo
Published: August 2007

Summary: Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules and efficient handling of large sets of trajectories.

Availability: The Wordom program is distributed with full source code (in the C language) and documentation for usage and further development as a platform-independent package under a GPL license from http://www.biochem-caflisch.unizh.ch/wordom/

Contact:  caflisch@bioc.unizh.ch
Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach
Authors: Buendia Patricia , Narasimhan Giri
Published: August 2007

Motivation: Traditional phylogenetic methods assume tree-like evolutionary models and are likely to perform poorly when provided with sequence data from fast-evolving, recombining viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is proposed here, referred to as the Sliding MinPD method, that reconstructs evolutionary networks for serially-sampled sequences in the presence of recombination.

Results: Sliding MinPD combines distance-based phylogenetic methods with automated recombination detection based on the best-known sliding window approaches to reconstruct serial evolutionary networks. Its performance was evaluated through comprehensive simulation studies and was also applied to a set of serially-sampled HIV sequences from a single patient. The resulting network organizations reveal unique patterns of viral evolution and may help explain the emergence of disease-associated mutants and drug-resistant strains with implications for patient prognosis and treatment strategies.

Availability: From website http://biorg.cis.fiu.edu/SlidingMinPD

Contact:  giri@cis.fiu.edu

Supplementary information:  http://biorg.cis.fiu.edu/SlidingMinPD
Direct Extraction of Volatiles of Rice During Cooking Using Solid‐Phase Microextraction
Authors: Zeng Zhi , Zhang Han , Chen Jie Yu , Zhang Tao , Matsunaga Ryuji
Published: August 2007

An apparatus that allows extraction and enrichment of flavor volatiles of rice during cooking using solid‐phase microextraction (SPME) was designed and tested in the Japanese rice cultivar Akitakomachi. Because it is a solvent‐free technique, no solvent contaminants were extracted during sampling. This technique enables one to place the fiber of SPME in the effluent of the flavor volatiles of the rice during cooking and it can also be used for simultaneous extraction of those volatiles in the course of the cooking process. Therefore, variations in the composition and amount of volatile compounds of rice during cooking can be determined. The overall flavor volatiles of rice during cooking have been analyzed by using this SPME method. Compounds that have been previously highlighted as flavor volatile markers, such as volatiles from oxidative degradation of lipids, products from thermal decomposition, and fatty acids existing in rice, were extracted directly by SPME in conjunction with this apparatus.
Chromosomal rearrangement interferes with meiotic X chromosome inactivation
Authors: Homolka David , Ivanek Robert , Capkova Jana , Jansa Petr , Forejt Jiri
Published: August 2007

Heterozygosity for certain mouse and human chromosomal rearrangements is characterized by the incomplete meiotic synapsis of rearranged chromosomes, by their colocalization with the XY body in primary spermatocytes, and by male-limited sterility. Previously, we argued that such X–autosomal associations could interfere with meiotic sex chromosome inactivation. Recently, supporting evidence has reported modifications of histones in rearranged chromosomes by a process called the meiotic silencing of unsynapsed chromatin (MSUC). Here, we report on the transcriptional down-regulation of genes within the unsynapsed region of the rearranged mouse chromosome 17, and on the subsequent disturbance of X chromosome inactivation. The partial transcriptional suppression of genes in the unsynapsed chromatin was most prominent prior to the mid-pachytene stage of primary spermatocytes. Later, during the mid-late pachytene, the rearranged autosomes colocalized with the XY body, and the X chromosome failed to undergo proper transcriptional silencing. Our findings provide direct evidence on the MSUC acting at the mRNA level, and implicate that autosomal asynapsis in meiosis may cause male sterility by interfering with meiotic sex chromosome inactivation.
A novel olfactory receptor gene family in teleost fish
Authors: Saraiva Luis R. , Korsching Sigrun I.
Published: August 2007

While for two of three mammalian olfactory receptor families (OR and V2R) ortholog teleost families have been identified, the third family (V1R) has been thought to be represented by a single, closely linked gene pair. We identified four further V1R-like genes in every teleost species analyzed (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Tetraodon nigroviridis, Takifugu rubripes). In the phylogenetic analysis these ora genes (olfactory receptor class A-related) form a single clade, which includes the entire mammalian V1R superfamily. Homologies are much lower in paralogs than in orthologs, indicating that all six family members are evolutionarily much older than the speciation events in the teleost lineage analyzed here. These ora genes are under strong negative selection, as evidenced by very small dN/dS values in comparisons between orthologs. A pairwise configuration in the phylogenetic tree suggests the existence of three ancestral Ora subclades, one of which has been lost in amphibia, and a further one in mammals. Unexpectedly, two ora genes exhibit a highly conserved multi-exonic structure and four ora genes are organized in closely linked gene pairs across all fish species studied. All ora genes are expressed specifically in the olfactory epithelium of zebrafish, in sparse cells within the sensory surface, consistent with the expectation for olfactory receptors. The ora gene repertoire is highly conserved across teleosts, in striking contrast to the frequent species-specific expansions observed in tetrapod, especially mammalian V1Rs, possibly reflecting a major shift in gene regulation as well as gene function upon the transition to tetrapods.
Correspondence between shape and feeding habit changes throughout ontogeny of gilthead sea bream Sparus aurata L., 1758
Authors: Russo T. , Costa C. , Cataudella S.
Published: August 2007

The shape development through ontogeny of the gilthead sea bream Sparus aurata was studied by means of geometric morphometry and elliptic Fourier analysis. In parallel, observations are reported on the feeding habits of the same specimens until the end of the larval stage. Data for later stages were obtained from the literature. Sparus aurata underwent ontogenetic shifts in diet from zooplankton, selected by larvae, to mysids, errant polychaete, amphipods and isopods for juveniles, and finally to hard prey (decapods, gastropods and bivalves) in adults. The aims were: (1) to provide a complete description of shape development, from hatching to the adult stage, (2) to identify distinguishable morphological stages during ontogenesis, (3) to search for correspondence between morphological development and diet shifts, and (4) to examine the functional effect connecting shape changes to diet shifts and habitat selection. The growth trajectory obtained reflected a saturating curve made up by different sections. Each section corresponded to a developmental shape stage characterized by different allometric trends of different body regions. Indeed, these shape stages matched those based on widespread features of development. Furthermore, the size‐defined limits of the shape stages closely match the feeding shifts in the development of dietary behaviour of gilthead sea bream. The different constraints underpinning this pattern of covariation are discussed by showing that the growth profile of early stages is mainly determined by organogenesis of important apparati, whereas that of later stages seems optimized to improve feeding on hard prey in complex microhabitat and swimming abilities, and to reduce predation risk.
The influence of thermal parameters on the acclimation responses of pinfish Lagodon rhomboides exposed to static and decreasing low temperatures
Authors: Reber C. M. , Bennett W. A.
Published: August 2007

Pinfish Lagodon rhomboides acclimation rates were determined by modelling changes in critical thermal minimum (Tcrit min, ° C) estimates at set intervals following a temperature decrease of 3–4° C. The results showed that pinfish gained a total of 3·7° C of cold tolerance over a range of acclimation temperatures (Tacc, ° C) from (23–12° C), that cold tolerance increased with exposure time to the reduced temperature at all Tacc, but that the rate of cold tolerance accruement (mean 0·14° C day−1) was independent of Tacc. A highly significant (P < 0·001) multivariate predictive model was generated that described the acclimation rates and thermal tolerance of pinfish exposed to reduction in water temperature: log10Tcrit min= 0·41597 − 0·01704Tacc+ 0·04320Tplunge− 0·08376[log10 (t+ 1)], where Tplunge is plunge temperature (° C) and t is the time (days). A comparison of the present data, with acclimation rate data for other species, suggests that factors such as latitude or geographic range may play a more important role than ambient temperature in determining cold acclimation rates in fishes.
Sex ratio and sexual dimorphism of the anchovy Anchoa januaria (Actinopterygii, Engraulidae) in a tropical bay in south‐eastern Brazil
Authors: Santos J. N. S. , Araújo F. G. , Silva M. A. , Vasconcellos R. M.
Published: August 2007

Sex ratio and morphological traits of a very abundant anchovy Anchoa januaria were described in a tropical bay in south‐eastern Brazil. The aim was to test the hypothesis that sexual dimorphism occurs due to the different reproductive roles of the sexes. A fish sampling programme was carried out between September 1998 and August 1999 at six sites: four sandy beaches and two lower‐river sites. Population structure at river sites comprised adults only, ranging from 60 to 80 mm total length (LT), while at sandy beaches both juveniles and adults were found, ranging from 32 to 80 mm LT. Well‐balanced ‘spawning school’ at river sites during reproduction were detected, while female‐dominated schools occurred in the bay feeding areas. Males had relatively longer pectoral fins, slightly larger hearts and more somatic mass than females. Females outnumbered males at sizes >67 mm LT and had significantly longer intestines and heavier livers than males. The largest size reached by females was probably related to a higher growth rate as they have a larger intestinal absorbing area for nutrients. The prediction of higher energetic investment in reproduction by females that should have larger organs associated with food acquisition and processing to produce energy‐rich eggs was confirmed for A. januaria in Sepetiba Bay.
Effect of loss of heterozygosity of the c‐kit gene on prognosis after hepatectomy for metastatic liver gastrointestinal stromal tumors
Authors: Kikuchi Hirotoshi , Yamamoto Masayoshi , Hiramatsu Yoshihiro , Baba Megumi , Ohta Manabu , Kamiya Kinji , Tanaka Tatsuo , Suzuki Shohachi , Sugimura Haruhiko , Kitagawa Masatoshi , Kanai Toshikazu , Kitayama Yasuhiko , Kanda Tatsuo , Nishikura Ken , Konno Hiroyuki
Published: August 2007

The authors have previously reported that loss of heterozygosity (LOH) of the c‐kit gene could be responsible for the gain in high proliferative activity in some gastrointestinal stromal tumors (GIST), resulting in enhanced metastatic potential. In the present study, an attempt was made to identify the factors that might predict the postoperative prognosis of patients with metastatic liver GIST. The clinicopathologic or genetic features of resected liver GIST in 14 patients who had undergone a hepatectomy for metachronous liver metastases and who had not received adjuvant imatinib treatment were examined. LOH of the c‐kit gene was observed in seven of 12 metastatic liver GIST (58.3%), of which DNA suitable for testing could be extracted. Ten patients had recurrence after hepatectomy and four had none. The median post‐recurrent disease‐free survival (PRDFS) after hepatectomy was 27.5 months (range 8–104). The tumor‐specific PRDFS was examined using clinicopathologic features, c‐kit mutation and LOH of the c‐kit gene. No single clinicopathologic or genetic finding was significantly associated with PRDFS. However, patients with ‘Ki67 labeling index <5% and LOH(–)’ had a significantly longer PRDFS than those with ‘Ki67 ≥5% or LOH(+)’ (P = 0.032), and there was no correlation between the presence of LOH of the c‐kit gene and the Ki67 labeling index. LOH of the c‐kit gene in metastatic liver seems to be a common event, and LOH of the c‐kit gene in resected liver GIST may be a helpful factor in the prediction of the post‐recurrent prognosis of patients with liver metastasis. (Cancer Sci 2007; 98: 1734–1739)
Increased risk of larynx cancer in heterozygous carriers of the I171V mutation of the NBS1 gene
Authors: Ziólkowska Iwona , Mosor Maria , Wierzbicka Malgorzata , Rydzanicz Malgorzata , Pernak‐Schwarz Monika , Nowak Jerzy
Published: August 2007

The high incidence of multiple primary tumors (MPT) is a significant problem in head and neck tumor treatment. Recent studies suggest that carriers of heterozygous mutations in the NBS1 gene have an increased risk of malignant tumor development. The aim of our research was to assess the frequency of NBS1 mutations in patients with larynx cancer only (LC) and with MPT. The MPT group consisted of patients with one cancer localized to the larynx (primary or second) and another at another site. DNA from 175 patients with LC and 93 patients with MPT was analyzed using the single‐strand conformation polymorphism method and direct sequencing. We found nine carriers of the I171V mutation among these 268 cancer patients and only one carrier among 500 population controls (0.2%). Four carriers of the I171V mutation were detected among 175 LC patients (2.3%) and five among 93 patients with MPT (5.4%). The frequencies of the I171V mutation carriers in LC and MPT patients were significantly higher than in controls (odds ratio [OR] = 11.7, confidence interval [CI] 1.3–105.2, P = 0.0175 and OR = 28.35, CI 3.27–245.7, P = 0.0005, respectively). In one individual with LC, a novel molecular variant, c.1222 A > G (p.K408E), was identified. No carriers of R215W or 657del5 NBS1 mutations were found in the present study. These findings imply that heterozygous carriers of the I171V mutation are prone to the development of larynx cancer and may, in addition, display an increased risk of second tumors at other sites. (Cancer Sci 2007; 98: 1701–1705)