bluuebunny/crossref_metadata_2025 huggingface dataset:
The photoelectron spectrum of elusive cyclic-N3 and characterization of the potential energy surface and vibrational states of the ion
Authors: Babikov Dmitri , Mozhayskiy Vadim A. , Krylov Anna I.
Published: August 2006

A potential energy surface is constructed for the ground XA11 electronic state of cyclic-N3+ based on three-dimensional spline interpolation of ab initio points. The vibrational states of this molecular ion are calculated in the range up to 14500cm−1 using hyperspherical coordinates and the coupled-channel (sector-adiabatic) approach. All the vibrational states are analyzed and assigned. The Franck-Condon overlaps of these states with the vibrational states of the neutral are calculated to predict the photoelectron spectrum of cyclic-N3. Peak intensities are governed by the nodal structure of the vibrational wave functions and reflect the large geometric phase effect predicted for cyclic-N3. Experimental validation may shed light on the existence of this elusive molecule and confirm the magnitude of the geometric phase effect.
Observation and manipulation of paramagnetic oxygen vacancies in Co-doped TiO2 nanocrystals
Authors: Pan Dengyu , Xu Guoliang , Lv Liya , Yong Yuan , Wang Xiuwei , Wan Jianguo , Wang Guanghou , Sui Yunxia
Published: August 2006

Electron paramagnetic resonance measurements were presented to investigate paramagnetic oxygen vacancies (F+ centers) in Co-doped TiO2 nanocrystals. Surface and interior F+ centers were manipulated by washing or/and annealing. Anisotropic surface F+ centers are so instable as to be destroyed at high temperature, while isotropic interior F+ centers are rather stable even at 430°C. The correlation of ferromagnetism with F+ centers was observed, which provided direct experimental evidence for F+-center-mediated coupling in diluted magnetic oxides.
Experimental demonstration of negative magnetic permeability in the far-infrared frequency regime
Authors: Gundogdu T. F. , Tsiapa I. , Kostopoulos A. , Konstantinidis G. , Katsarakis N. , Penciu R. S. , Kafesaki M. , Economou E. N. , Koschny Th. , Soukoulis C. M.
Published: August 2006

Using transmission and reflection measurements in a five layer micrometer-scale split-ring resonator (SRR) system, fabricated by a photolithography procedure, the authors demonstrate the occurrence of a negative magnetic permeability regime in that system at ∼6THz. The transmission and reflection were measured using oblique incidence, resulting to a magnetic field component perpendicular to the SRR plane, which excites the resonant circular currents constituting the magnetic resonance.
Effects of strain on the electronic structures and TC’s of the La0.67Ca0.33MnO3 and La0.8Ba0.2MnO3 thin films deposited on SrTiO3
Authors: Chou Hsiung , Tsai M.-H. , Yuan F. P. , Hsu S. K. , Wu C. B. , Lin J. Y. , Tsai C. I. , Tang Y.-H.
Published: August 2006

The strain effects on the electronic structures of La0.67Ca0.33MnO3 (LCMO) and La0.8Ba0.2MnO3 (LBMO) thin films have been studied by O K-edge x-ray absorption near edge structure (XANES) spectroscopy. For LCMO, the first-principles calculations reveal that the features in the XANES spectra are associated with hybridized states between O 2p and Mn minority-spin 3d t2g and eg, La 5d∕Ca 3d, and Mn 4s∕Ca 4p states. An analysis of these features shows that the tensile strain decreases substantially La–O and Ca–O hybridization and TC for LCMO. For LBMO, the small compressive strain enhances slightly La–O and Ba–O hybridization and TC.
Design of a UHV-compatible rf plasma source and its application to self-assembled layers of CoPt3 nanoparticles
Authors: Gehl B. , Leist U. , Aleksandrovic V. , Nickut P. , Zielasek V. , Weller H. , Al-Shamery K. , Bäumer M.
Published: August 2006

A compact, versatile, and simple rf plasma source with capacitive coupling compatible to ultrahigh vacuum (UHV) requirements was designed and built to allow sequences of sample surface modification in plasma and surface preparation and analysis in vacuum without breaking the vacuum. The plasma source was operated at working pressures of less than 1 to a few millibars. Sample transfer to UHV was performed at pressures around 10−9mbar. For easy integration into an existing UHV setup, the sample recipient and transfer system were made to accept standard commercial sample holders. Preliminary experiments were performed by exposing monolayers of colloidal CoPt3 nanoparticles to oxygen and hydrogen plasmas. The structural and chemical effects of the plasma treatments were analyzed with scanning electron microscopy and x-ray photoelectron spectroscopy.
Assessing and managing laser system stability for quantum control experiments
Authors: Roth Matthias , Roslund Jonathan , Rabitz Herschel
Published: August 2006

Stable laser operation, which is essential for quantum control experiments as well as many other phase dependent processes, is investigated with respect to the influence of amplitude and spectral phase noise. Simulations are first performed and an easy to implement experimental method is presented to monitor the amplitude and phase stability of an ultrafast laser system. As an illustration of this stability assessment technique, the data monitoring is used to guide the identification and elimination of fluctuations in the laser amplification process. Through a number of practical alterations of the amplifier configuration, the stability of the laser system was greatly and consistently improved. Fluctuations on different time scales were eliminated, with special emphasis given to maintaining a stable spectral phase.
A size extensive energy functional derived from a double configuration interaction approach: The role of N representability conditions
Authors: Kollmar Christian
Published: August 2006

Starting from a configuration interaction (CI) approach including only doubly excited configurations, the corresponding energy functional is modified by introduction of a topological factor in the normalization condition of the CI coefficients in such a way that it gets inherently size extensive. Constraints imposed by N representability conditions on the modified functional are discussed and lead to a specific choice of the topological factor. The basic variable in the modified energy functional is the second-order reduced density matrix parametrized in terms of CI-like coefficients. Test calculations for a variety of small molecules show that the numerical results obtained with the new functional are in very good agreement with those obtained from coupled cluster singles doubles calculations.
A random-sampling high dimensional model representation neural network for building potential energy surfaces
Authors: Manzhos Sergei , Carrington Tucker
Published: August 2006

We combine the high dimensional model representation (HDMR) idea of Rabitz and co-workers [J. Phys. Chem. 110, 2474 (2006)] with neural network (NN) fits to obtain an effective means of building multidimensional potentials. We verify that it is possible to determine an accurate many-dimensional potential by doing low dimensional fits. The final potential is a sum of terms each of which depends on a subset of the coordinates. This form facilitates quantum dynamics calculations. We use NNs to represent HDMR component functions that minimize error mode term by mode term. This NN procedure makes it possible to construct high-order component functions which in turn enable us to determine a good potential. It is shown that the number of available potential points determines the order of the HDMR which should be used.
Nonstationarity of diffusion-controlled surface-wave-sustained discharges in a cw regime
Authors: Marinov K. , Shivarova A. , Stoev L.
Published: August 2006

The theory of the cw regime of maintenance of surface-wave-sustained gas discharges developed up to now is for discharge production at a given frequency. A generalization of this theory is presented here by considering discharge maintenance by a narrow-band signal, the actual situation in the experiments. Discharge production in a diffusion-controlled regime is treated within the fluid plasma theory. The set of the equations is for the interrelated variations along the discharge length of the time-dependent envelope of the electric field maintaining the plasma and for the time-dependent plasma characteristics (plasma density, electron temperature, power Θ absorbed on average by an electron). The numerical results presented for the time-space variations of wave-field amplitude and plasma density describe the nonstationary state of the cw regime of discharge maintenance. Detailed analysis with deterministic signals (Gaussian and super-Gaussian pulses) superimposed on a stationary cw-power level demonstrate different types of nonlinear effects—self-steepening and spontaneous modulation near the pulse edge—which are reminiscent of phenomena known from the nonlinear optics. The results for discharge maintenance by a high-frequency power modulated by a narrow-band low-amplitude Gaussian noise are discussed in terms of discharge stability/instability. Relevance to experimental finding in surface-wave-sustained discharge is commented on.
X-ray induced, substrate-carrier mediated deposition of metal on GaAs
Authors: Ma Qing , Divan R. , Mancini D. C. , Rosenberg R. A. , Quintana J. P. , Keane D. T.
Published: August 2006

A wet metal deposition process on GaAs surfaces is described. The process is induced by high energy x-ray photons and is mediated by photon-generated carriers through the photoelectrochemical mechanism similar to that for light-induced wet etching. The micrometer to submicrometer feature fabrication using this process is demonstrated.
In-phase evanescent coupling of two-dimensional arrays of defect cavities in photonic crystal vertical cavity surface emitting lasers
Authors: Raftery James J. , Lehman Ann C. , Danner Aaron J. , Leisher Paul O. , Giannopoulos Antonios V. , Choquette Kent D.
Published: August 2006

In-phase evanescent coupling in 2×1 and 2×2 arrays of defect cavities in photonic crystal (PhC) vertical cavity surface emitting lasers (VCSELs) is reported. Two-dimensional PhC patterns of air holes containing multiple defects are etched into the top distributed Bragg reflector of VCSELs. The resulting modification of the effective index and optical loss results in evanescent coupling between the multiple defect cavities of the PhC VCSEL. Far field measurements and simulations show good agreement and demonstrate the in-phase results.
Effect of asymmetric leads on critical switching current in magnetic nanopillars
Authors: Kurt H. , AlHajDarwish M. , Pratt W. P. , Bass J.
Published: August 2006

Manschot et al. [Appl. Phys. Lett. 85, 3250 (2004)] predicted that the critical current to switch the magnetizations in a ferromagnetic/nonmagnetic/ferromagnetic nanopillar from parallel to antiparallel could be reduced by up to a factor of 5 by pairing nonmagnetic leads with different effective resistances (resistivity times spin diffusion length). Comparing switching currents for Co∕Cu∕Co nanopillars with Pt and AgSn(5%) leads on alternate sides of the nanopillar did not give the large reduction predicted by Manschot et al. Possible reasons for this lack are discussed.
“Stick and slide” ferrofluidic droplets on superhydrophobic surfaces
Authors: Guo Zhi-Guang , Zhou Feng , Hao Jing-Cheng , Liang Yong-Min , Liu Wei-Min , Huck Wilhelm T. S.
Published: August 2006

The authors report the suspension and movement of ferrofluid droplets on superhydrophobic surfaces in the presence of strong external magnetic fields. The system allows the quantitative evaluation of friction between droplet and substrate surface. It represents an enabling example for the development of microferrofluidic devices and a breakthrough in the remote actuation of droplets on surfaces, which cannot be achieved using conventional microfluidics, or inkjet printing, electrowetting, or light-driven motion.
Compact system for high-speed velocimetry using heterodyne techniques
Authors: Strand O. T. , Goosman D. R. , Martinez C. , Whitworth T. L. , Kuhlow W. W.
Published: August 2006

We have built a high-speed velocimeter that has proven to be compact, simple to operate, and fairly inexpensive. This diagnostic is assembled using off-the-shelf components developed for the telecommunications industry. The main components are fiber lasers, high-bandwidth high-sample-rate digitizers, and fiber optic circulators. The laser is a 2W cw fiber laser operating at 1550nm. The digitizers have 8GHz bandwidth and can digitize four channels simultaneously at 20GS∕s. The maximum velocity of this system is ∼5000m∕s and is limited by the bandwidth of the electrical components. For most applications, the recorded beat frequency is analyzed using Fourier transform methods, which determine the time response of the final velocity time history. Using the Fourier transform method of analysis allows multiple velocities to be observed simultaneously. We have obtained high-quality data on many experiments such as explosively driven surfaces and gas gun assemblies.
Heterodyne interferometer with unequal path lengths
Authors: Kumar Deepak , Bellan Paul M.
Published: August 2006

Laser interferometry is an extensively used diagnostic for plasma experiments. Existing plasma interferometers are designed on the presumption that the scene and reference beam path lengths have to be equal, a requirement that is costly in both the number of optical components and the alignment complexity. It is shown here that having equal path lengths is not necessary, instead, what is required is that the path length difference be an even multiple of the laser cavity length. This assertion has been verified in a heterodyne laser interferometer that measures typical line-average densities of ∼1021∕m2 with an error of ∼1019∕m2.
Accelerating molecular simulations by reversible mapping between local minima
Authors: Uhlherr Alfred , Theodorou Doros N.
Published: August 2006

A new framework is presented for performing Monte Carlo simulations of condensed matter based on a recently developed bijective mapping between local energy minima. The framework is used to implement a range of new multiparticle Monte Carlo moves, which are investigated by simulating atomic Lennard-Jones fluids in the canonical and grand canonical ensembles. Important aspects of the simulation protocol and their effect on performance are analyzed in detail. Using the mapping accelerates the simulations by many orders of magnitude when compared to the equivalent moves without the mapping, and leads to particularly efficient configurational sampling at low temperatures and high densities. The method appears to be suitable for adapting to quantitative simulations of more complex molecular systems over long effective time scales.
High power gain-switched laser diode using a superfast GaAs avalanche transistor for pumping
Authors: Lanz Brigitte , Vainshtein Sergey , Kostamovaara Juha
Published: August 2006

Multiwatt single picosecond optical pulses were generated by gain-switched laser diodes using for pumping a superfast GaAs switch, which produces 1–10A current pulses with a duration comparable to the lasing delay. Good quantitative agreement was found between the measured and simulated optical responses and time-resolved spectra when lasing occurred before the trailing edge of the current pulse, while the measured single optical pulse generated near the trailing edge drastically exceeded that in the simulations. This difference is attributed to the effect of additional population of the quantum well by carriers accumulating earlier in the optical confinement region.
1.55
μ
m
emission from InAs∕GaAs quantum dots grown by metal organic chemical vapor deposition via antimony incorporation
Authors: Guimard Denis , Tsukamoto Shiro , Nishioka Masao , Arakawa Yasuhiko
Published: August 2006

The authors report a fabrication technique for redshifting the emission wavelength of InAs quantum dots (QDs) grown on GaAs substrate by metal organic chemical vapor deposition. By introducing an antimony irradiation step during the InAs QD growth, the authors have achieved ground-state emission at 1.55μm (and beyond) from InAs∕GaAs QDs capped by an In0.24Ga0.76As strain-reducing layer (SRL) at room temperature (RT). Photoluminescence intensity is strongly enhanced (×100) at RT compared to Sb-free QDs capped by a higher In-content SRL in which ground-state emission saturates at wavelengths shorter than 1.51μm.
Epitaxial growth of room-temperature ferrimagnetic semiconductor thin films based on the ilmenite-hematite solid solution
Authors: Hojo Hajime , Fujita Koji , Tanaka Katsuhisa , Hirao Kazuyuki
Published: August 2006

Epitaxial thin films composed of 0.7FeTiO3∙0.3Fe2O3 solid solution have been prepared on α-Al2O3 (0001) substrates by a pulsed laser deposition method, and their electrical and magnetic properties have been examined. A single phase of the ordered phase can be obtained under limited deposition conditions: oxygen partial pressure of 1.0×10−3Pa and substrate temperature of 600–700°C. The as-deposited film is semiconducting and ferrimagnetic below room temperature, while subsequent annealing in vacuum leads to the Curie temperature above room temperature. On the other hand, the thin films with the disordered phase appear to be antiferromagnetic and also insulating.
High-mobility transparent conductive Zr-doped In2O3
Authors: Koida T. , Kondo M.
Published: August 2006

Optical and electric properties in Zr-doped In2O3 epitaxial layers were systematically investigated. The films at Zr concentrations of 0.3–0.5at.% are found to be superior transparent conductive oxides in transparency in near infrared wavelength region and Hall mobility compared to Sn-doped In2O3. Maximum mobilities are over 100cm2∕Vs and corresponding carrier densities are approximately 1×1020cm−3. From the relationship between the values of Hall mobility and carrier concentration of the epilayers, a number and/or effects of multicharged and neutral scattering centers of electrons seem to be reduced.
Self-consistent study of single molecular transistor modulated by transverse field
Authors: Jiang F. , Zhou Y. X. , Chen H. , Note R. , Mizuseki H. , Kawazoe Y.
Published: August 2006

We use a self-consistent method to study the current of the single molecular transistor modulated by the transverse field in the level of the density functional theory and the nonequilibrium Green function method. The numerical results show that both the polyacene-dithiol molecules and the fused-ring thiophene molecules are the potential high-frequency molecular transistors controlled by the transverse field. The longer molecules of the polyacene-dithiol or the fused-ring thiophene are in favor of realizing the gate-bias controlled molecular transistor. The theoretical results suggest the related experiments.
Magnetoresistance in thin Permalloy film (10nm thick and 30–200nm wide) nanocontacts fabricated by e-beam lithography
Authors: García N. , Hao Cheng , Yonghua Lu , Muñoz M. , Chen Yifang , Cui Zheng , Lu Zhengqi , Zhou Yun , Pan Genhua , Pasa A. A.
Published: August 2006

In this letter the authors show spin dependent transport experiments in nanoconstrictions ranging from 30to200nm. These nanoconstrictions were fabricated by combined electron-beam lithography and thin film deposition techniques. Two types of geometries have been fabricated and investigated. They compare the experimental results with the theoretical estimation of the electrical resistance. Finally they show that the magnetoresistance for the different geometries does not scale with the resistance of the structure and obtain drops in voltage of 20mV at 20Oe.
Quasi-continuous-wave operation of an organic thin-film distributed feedback laser
Authors: Rabe T. , Gerlach K. , Riedl T. , Johannes H.-H. , Kowalsky W. , Niederhofer J. , Gries W. , Wang J. , Weimann T. , Hinze P. , Galbrecht F. , Scherf U.
Published: August 2006

The operation of organic thin-film distributed feedback lasers at repetition rates up to 5MHz is studied. The active organic medium consists of a highly efficient, modified poly(9,9-dioctylfluorene) derivative containing 12% of statistical intrachain 6,6′ -(2,2′-octyloxy-1,1′-binaphthalene) binaphthyl spacer groups. The threshold energy density of these pulsed optically pumped lasers remains virtually unaltered at elevated repetition rates up to 5MHz. Therefore, we conclude that on this time scale photoinduced absorption which might affect the waveguide loss or the overall quantum efficiency is negligible in our active polymer. These results state an organic solid-state laser operating at repetition rates in the megahertz range which for many applications can be considered as quasi-cw.
Nonlinear dynamics in thin-slice Nd:YAG ceramic lasers: Coupled local-mode laser model
Authors: Otsuka Kenju , Narita Tatsuro , Miyasaka Yoshihiko , Lin Chi-Ching , Ko Jing-Yuan , Chu Shu-Chun
Published: August 2006

The authors propose a coupled spatially distributed local-mode laser model for understanding self-induced high-speed modulations in Nd:YAG ceramic lasers with laser-diode end pumping, which critically depend on pump positions. In addition to complicated high-speed modulations, quasiperiodic and chaotic relaxation oscillations have been demonstrated experimentally and reproduced by numerical simulation of the model of coupled local-mode lasers. Q-switching-like periodic spiking pulsations have been also observed and reproduced numerically by assuming saturable absorber type of inclusions in grain boundaries.
Electron transport through individual Ge self-assembled quantum dots on Si
Authors: Chung Hung-Chin , Chu Wen-Huei , Liu Chuan-Pu
Published: August 2006

Electrical properties of self-assembled quantum dots have been the subject of intensive research due to quantum confinement. Here the authors report on the fabrication of Ge quantum dots (QDs) onto Si (100) by ultrahigh-vacuum ion beam sputtering and the electrical properties of individual QDs. Transmission electron microscopy images show that samples with completely incoherent or coherent semispherical islands can be produced under different ion energies. The current-voltage (I-V) characteristics with conductive atomic force microscopy at room temperature. exhibit linear behavior at low bias and nonlinear behavior at large bias from coherent islands, whereas the staircase structures are clearly observed in the I-V curve from incoherent islands, which are attributed to electron tunneling through the quantized energy levels of a single Ge QD.
Spin polarization of Co2FeSi full-Heusler alloy and tunneling magnetoresistance of its magnetic tunneling junctions
Authors: Gercsi Z. , Rajanikanth A. , Takahashi Y. K. , Hono K. , Kikuchi M. , Tezuka N. , Inomata K.
Published: August 2006

The authors report spin polarization (P) and tunneling magnetoresistance (TMR) of epitaxially grown Co2FeSi thin films on a MgO (001) substrate. A Heusler-type L21 structure was observed in the samples sputter deposited at 473K or above. The P value of the ordered film was measured as 0.49±0.02 by the point contact Andreev reflection (PCAR) technique. The TMR values obtained from the magnetic tunneling junction (MTJ) using the Co2FeSi electrode and Al-oxide barrier were 67.5% at 5K and 43.6% at 298K, respectively. The P value estimated from the TMR using Julliere’s model matches the spin polarization measured by the PCAR very well, indicating that the TMR value from the MTJ is governed by the intrinsic value of P of the electrode material for incoherent tunneling.
Negative differential resistance effect in organic devices based on an anthracene derivative
Authors: Chen Jiangshan , Xu Liling , Lin Jian , Geng Yanhou , Wang Lixiang , Ma Dongge
Published: August 2006

The authors observed a negative differential resistance (NDR) in organic devices consisting of 9,10-bis-(9,9-diphenyl-9H-fluoren-2-yl)-anthracene (DPFA) sandwiched between Ag and indium tin oxide electrodes. The large NDR shown in current-voltage characteristics is reproducible, resulting in that the organic devices can be electrically switched between a high conductance state (on state) and a low conductance state (off state). It can be found that the currents at both on to off states are space-charge limited and attributed to the electron traps at the Ag/DPFA interface. The large and reproducible NDR makes the devices of tremendous potential in low power memory and logic circuits.
Critical thickness for dislocation generation during ferroelectric transition in thin film on a compliant substrate
Authors: Zheng Yue , Wang Biao , Woo C. H.
Published: August 2006

The formation energy of misfit dislocations in a ferroelectric thin film grown on compliant substrate is calculated based on the Landau-Devonshire formalism and Timosheko’s method for thermal stresses. The critical thickness is shown to change significantly according to the polarization in the film, leading to serious concerns, particularly for thick substrates, in the device design stage.
Surface acoustic wave trapping in a periodic array of mechanical resonators
Authors: Laude Vincent , Robert Laurent , Daniau William , Khelif Abdelkrim , Ballandras Sylvain
Published: August 2006

The existence of two families of surface acoustic modes trapped by steep ridges on a piezoelectric substrate, shear horizontal and vertically polarized surface modes, is demonstrated experimentally using high aspect ratio interdigital transducers fabricated on lithium niobate. The experimental variation of the resonance frequencies of the various surface modes is obtained experimentally, and up to an order of magnitude slowing of surface waves is observed, with the phase velocity dropping from 4000 down to 450m∕s. It is argued that the observed resonances are surface modes trapped by the ridge electrodes.
Oscillating wave sensors based on ultrahigh-order modes in symmetric metal-clad optical waveguides
Authors: Chen Guang , Cao Zhuangqi , Gu Jianghua , Shen Qishun
Published: August 2006

An oscillating wave sensor that uses ultrahigh-order modes in symmetric metal-clad waveguide with submillimeter scale is investigated to measure minute changes in refractive index (RI) of aqueous solution. In the proposed sensor, the sample acts as the guiding layer where oscillating wave propagates. Owing to the concentrated power in the sensing region and the use of the very sensitive ultrahigh-order modes, it is demonstrated both theoretically and experimentally that its sensitivity is enhanced by one order of magnitude than that of evanescent wave sensor. The sensor also provides a wide detection range of RI from 1 to 2.0 or higher.
Extremely weak surface emission from (0001) c-plane AlGaN multiple quantum well structure in deep-ultraviolet spectral region
Authors: Kawanishi Hideo , Senuma Masanori , Yamamoto Mao , Niikura Eiichiro , Nukui Takeaki
Published: August 2006

We studied the anisotropic optical properties of c-plane AlxGa1−xN multiple quantum wells and m-plane AlxGa1−xN single layer grown on a SiC substrate. Very weak surface emission was detected from c-plane samples with x=0.66–0.76 (emission wavelength of 228–240nm), although strong surface emission was detected from c-plane samples with x=0–0.41 (280–365nm) and m-plane samples with x=0–0.76 (240–365nm). These results indicate that crystal-field splitoff hole valence band plays an important role in (E‖c) polarization and isotropic emissions from AlxGa1−xN with x≧0.5.
Noncontact excitation of quartz crystal resonator chips
Authors: Stevenson Adrian C. , Araya-Kleinsteuber Bernardita , Kioupritzi Eleftheria , Roque Ana C. A. , Lowe Christopher R.
Published: August 2006

The use of an acoustic wave device as a chemical sensing element is often limited by contact with wires and supports and by the need to control its fluidic environment. This letter describes the validation of a versatile noncontact configuration that makes use of a spiral coil antenna to electromagnetically excite miniature piezoelectric chips. Experimental evidence is provided to demonstrate that an AT cut quartz crystal resonator can be cleaved into chips that can be excited electromagnetically via coupling to the electric Y axis of the crystal. An unpredicted result was the superior coherence of chips at frequencies determined by their local thickness.
Study on photoluminescence from tris-(8-hydroxyquinoline)aluminum thin films and influence of light
Authors: Thangaraju K. , Kumar J. , Amaladass P. , Mohanakrishnan A. K. , Narayanan V.
Published: August 2006

Tris-(8-hydroxyquinoline)aluminum (Alq3), which is the most widely used material in organic electroluminescent devices, has been synthesized. Alq3 thin films have been deposited on glass and silicon substrates. The influence of light exposure on the optical properties of Alq3 thin films has been studied. It is confirmed that the photoluminescence (PL) of Alq3 thin film originates from its two geometrical isomers, namely, facial and meridional, which result from PL decay analysis (biexponential fit). It is also confirmed that the PL from both the isomers decreases for increasing light exposure time leading to the creation of luminescent quencher in Alq3 thin film.
Pygmoid Australomelanesian
Homo sapiens
skeletal remains from Liang Bua, Flores: Population affinities and pathological abnormalities
Authors: Jacob T. , Indriati E. , Soejono R. P. , Hsü K. , Frayer D. W. , Eckhardt R. B. , Kuperavage A. J. , Thorne A. , Henneberg M.
Published: August 2006

Liang Bua 1 (LB1) exhibits marked craniofacial and postcranial asymmetries and other indicators of abnormal growth and development. Anomalies aside, 140 cranial features place LB1 within modern human ranges of variation, resembling Australomelanesian populations. Mandibular and dental features of LB1 and LB6/1 either show no substantial deviation from modern
Homo sapiens
or share features (receding chins and rotated premolars) with Rampasasa pygmies now living near Liang Bua Cave. We propose that LB1 is drawn from an earlier pygmy
H. sapiens
population but individually shows signs of a developmental abnormality, including microcephaly. Additional mandibular and postcranial remains from the site share small body size but not microcephaly.
CaMKIIβ Association with the Actin Cytoskeleton Is Regulated by Alternative Splicing
Authors: O'Leary Heather , Lasda Erika , Bayer K. Ulrich
Published: August 2006

The Ca2+/calmodulin (CaM)-dependent protein kinase II (CaMKII)β has morphogenic functions in neurons not shared by the α isoform. CaMKIIβ contains three exons (v1, v3, and v4) not present in the CaMKIIα gene, and two of these exons (v1 and v4) are subject to differential alternative splicing. We show here that CaMKIIβ, but not α, mediated bundling of F-actin filaments in vitro. Most importantly, inclusion of exon v1 was required for CaMKIIβ association with the F-actin cytoskeleton within cells. CaMKIIβe, which is the dominant variant around birth and lacks exon v1 sequences, failed to associate with F-actin. By contrast, CaMKIIβ′, which instead lacks exon v4, associated with F-actin as full-length CaMKIIβ. Previous studies with CaMKIIβ mutants have indicated a role of nonstimulated kinase activity in enhancing dendritic arborization. Here, we show that F-actin–targeted CaMKIIβ, but not α, was able to phosphorylate actin in vitro even by nonstimulated basal activity in absence of Ca2+/CaM. In rat pancreatic islets and in skeletal muscle, the actin-associated CaMKIIβ′ and βM were the predominant variants, respectively. Thus, cytoskeletal targeting may mediate functions of CaMKIIβ variants also outside the nervous system.
Matrix-specific Suppression of Integrin Activation in Shear Stress Signaling
Authors: Orr A. Wayne , Ginsberg Mark H. , Shattil Sanford J. , Deckmyn Hans , Schwartz Martin A.
Published: August 2006

Atherosclerotic plaque develops at sites of disturbed flow. We previously showed that flow activates endothelial cell integrins, which then bind to the subendothelial extracellular matrix (ECM), and, in cells on fibronectin or fibrinogen, trigger nuclear factor-κB activation. Additionally, fibronectin and fibrinogen are deposited into the subendothelial ECM at atherosclerosis-prone sites at early times. We now show that flow activates ECM-specific signals that establish patterns of integrin dominance. Flow induced α2β1 activation in cells on collagen, but not on fibronectin or fibrinogen. Conversely, α5β1 and αvβ3 are activated on fibronectin and fibrinogen, but not collagen. Failure of these integrins to be activated on nonpermissive ECM is because of active suppression by the integrins that are ligated. Protein kinase A is activated specifically on collagen and suppresses flow-induced αvβ3 activation. Alternatively, protein kinase Cα is activated on fibronectin and mediates α2β1 suppression. Thus, integrins actively cross-inhibit through specific kinase pathways. These mechanisms may determine cellular responses to complex extracellular matrices.
Initiation of Protein Synthesis by Hepatitis C Virus Is Refractory to Reduced eIF2 · GTP · Met-tRNAiMetTernary Complex Availability
Authors: Robert Francis , Kapp Lee D. , Khan Shakila N. , Acker Michael G. , Kolitz Sarah , Kazemi Shirin , Kaufman Randal J. , Merrick William C. , Koromilas Antonis E. , Lorsch Jon R. , Pelletier Jerry
Published: August 2006

A cornerstone of the antiviral interferon response is phosphorylation of eukaryotic initiation factor (eIF)2α. This limits the availability of eIF2·GTP·Met-tRNAiMetternary complexes, reduces formation of 43S preinitiation complexes, and blocks viral (and most cellular) mRNA translation. However, many viruses have developed counterstrategies that circumvent this cellular response. Herein, we characterize a novel class of translation initiation inhibitors that block ternary complex formation and prevent the assembly of 43S preinitiation complexes. We find that translation driven by the HCV IRES is refractory to inhibition by these compounds at concentrations that effectively block cap-dependent translation in vitro and in vivo. Analysis of initiation complexes formed on the HCV IRES in the presence of inhibitor indicates that eIF2α and Met-tRNAiMetare present, defining a tactic used by HCV to evade part of the antiviral interferon response.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Authors: Stamatakis Alexandros
Published: August 2006

Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Γ yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets ≥4000 taxa it also runs 2–3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25 057 (1463 bp) and 2182 (51 089 bp) taxa, respectively.

Availability:  

Contact:  Alexandros.Stamatakis@epfl.ch

Supplementary information: Supplementary data are available at Bioinformatics online.
Dockground resource for studying protein–protein interfaces
Authors: Douguet Dominique , Chen Huei-Chi , Tovchigrechko Andrey , Vakser Ilya A.
Published: August 2006

Motivation: Public resources for studying protein interfaces are necessary for better understanding of molecular recognition and developing intermolecular potentials, search procedures and scoring functions for the prediction of protein complexes.

Results: The first release of the Dockground resource implements a comprehensive database of co-crystallized (bound–bound) protein–protein complexes, providing foundation for the upcoming expansion to unbound (experimental and simulated) protein–protein complexes, modeled protein–protein complexes and systematic sets of docking decoys. The bound–bound part of Dockground is a relational database of annotated structures based on the Biological Unit file (Biounit) provided by the RCSB as a separated file containing probable biological molecule. Dockground is automatically updated to reflect the growth of PDB. It contains 67 220 pairwise complexes that rely on 14 913 Biounit entries from 34 778 PDB entries (January 30, 2006). The database includes a dynamic generation of non-redundant datasets of pairwise complexes based either on the structural similarity (SCOP classification) or on user-defined sequence identity. The growing Dockground resource is designed to become a comprehensive public environment for developing and validating new methodologies for modeling of protein interactions.

Availability: Dockground is available at . The current first release implements the bound–bound part.

Contact:  douguet@cbs.cnrs.fr
MMM: a sequence-to-structure alignment protocol
Authors: Rai Brajesh K. , Madrid-Aliste Carlos J. , Fajardo J. Eduardo , Fiser András
Published: August 2006

Motivation: Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models.

Results: Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The alternatively aligned regions from the input alignment set are combined according to their fit in the structural environment of the template structure. The resulting, optimally spliced MMM alignment is used as input to an automated comparative modeling module to produce a full atom model.

Availability: The MMM server is freely accessible at

Contact:  andras@fiserlab.org
MARD: a new method to detect differential gene expression in treatment-control time courses
Authors: Cheng Chao , Ma Xiaotu , Yan Xiting , Sun Fengzhu , Li Lei M.
Published: August 2006

Motivation: Characterizing the dynamic regulation of gene expression by time course experiments is becoming more and more important. A common problem is to identify differentially expressed genes between the treatment and control time course. It is often difficult to compare expression patterns of a gene between two time courses for the following reasons: (1) the number of sampling time points may be different or hard to be aligned between the treatment and the control time courses; (2) estimation of the function that describes the expression of a gene in a time course is difficult and error-prone due to the limited number of time points. We propose a novel method to identify the differentially expressed genes between two time courses, which avoids direct comparison of gene expression patterns between the two time courses.

Results: Instead of attempting to ‘align’ and compare the two time courses directly, we first convert the treatment and control time courses into neighborhood systems that reflect the underlying relationships between genes. We then identify the differentially expressed genes by comparing the two gene relationship networks. To verify our method, we apply it to two treatment-control time course datasets. The results are consistent with the previous results and also give some new biologically meaningful findings.

Availability: The algorithm in this paper is coded in C++ and is available from

Contact:  lilei@usc.edu; chaochen@usc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Maximum likelihood of phylogenetic networks
Authors: Jin Guohua , Nakhleh Luay , Snir Sagi , Tuller Tamir
Published: August 2006

Motivation: Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative.

Results: In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree.

Availability: Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at

Contact:  tamirtul@post.tau.ac.il

Supplementary information: Supplementary data are available at Bioinformatics online.
TESD: a transposable element dynamics simulation environment
Authors: Deceliere Grégory , Letrillard Yann , Charles Sandrine , Biémont Christian
Published: August 2006

Various mathematical models have been used to explore the dynamics of transposable elements (TEs) within their host genomes. However, numerous factors can influence their dynamics, and we know only little about the dynamics of TEs when they first began to invade populations. In addition, the influence of population structuring has only recently been investigated. Transposable Element Simulator Dynamics, a population genomics simulation environment, has therefore been developed to provide a simple tool for analyzing the dynamics of TEs in a community based on (i) various TE parameters, such as the transposition and excision rates, the recombination rate and the coefficient of selection against TE insertions; and (ii) population parameters, such as population size and migration rates. The simulations can be used to illustrate the dynamic fate of TEs in structured populations, can be extended by using more specific molecular or demographic models, and can be useful for teaching population genetics and genomics.

Availability: TESD is distributed under GPL from the Pôle Bioinformatique Lyonnais (PBIL) web server at

Contact:  biemont@biomserv.univ-lyon1.fr
Will African Agriculture Survive Climate Change?
Authors: Kurukulasuriya Pradeep , Mendelsohn Robert , Hassan Rashid , Benhin James , Deressa Temesgen , Diop Mbaye , Eid Helmy Mohamed , Fosu K. Yerfi , Gbetibouo Glwadys , Jain Suman , Mahamadou Ali , Mano Renneth , Kabubo-Mariara Jane , El-Marsafawy Samia , Molua Ernest , Ouda Samiha , Ouedraogo Mathieu , Séne Isidor , Maddison David , Seo S. Niggol , Dinar Ariel
Published: August 2006

Measurement of the likely magnitude of the economic impact of climate change on African agriculture has been a challenge. Using data from a survey of more than 9,000 farmers across 11 African countries, a cross-sectional approach estimates how farm net revenues are affected by climate change compared with current mean temperature. Revenues fall with warming for dryland crops (temperature elasticity of −1.9) and livestock (−5.4), whereas revenues rise for irrigated crops (elasticity of 0.5), which are located in relatively cool parts of Africa and are buffered by irrigation from the effects of warming. At first, warming has little net aggregate effect as the gains for irrigated crops offset the losses for dryland crops and livestock. Warming, however, will likely reduce dryland farm income immedia-tely. The final effects will also depend on changes in precipitation, because revenues from all farm types increase with precipitation. Because irrigated farms are less sensitive to climate, where water is available, irrigation is a practical adaptation to climate change in Africa.
Incidence and Risk of Adverse Perioperative Events among Surgical Patients Taking Traditional Chinese Herbal Medicines
Authors: Lee Anna , Chui Po Tong , Aun Cindy S. T. , Lau Angel S. C. , Gin Tony
Published: August 2006

Background

The use of traditional Chinese herbal medicines (TCHMs) among the presurgical population is widespread, but their impact on perioperative patient care is unclear. The authors estimated the incidence and risk of TCHM-related perioperative events.

Methods

In a Hong Kong cohort study, 601 patients undergoing major elective surgery were asked about their Western medicine and TCHM use in the 2 weeks before surgery. Unanticipated perioperative events were noted by attending anesthesiologists, blinded to patients' use of specific TCHMs. Modified Poisson regression models were used to obtain the relative risk of combined endpoints of perioperative events associated with TCHM use.

Results

Of the 601 patients, 483 patients (80%) took self-prescribed TCHM, and 47 (8%) took TCHM by prescription (with or without self-prescribed TCHM) in the 2 weeks before surgery. The crude incidences of any combined endpoints of preoperative, intraoperative, and postoperative events were 23% (95% confidence interval, 19-26%), 74% (95% confidence interval, 71-78%), and 63% (95% confidence interval, 59-66%), respectively. Compared with nonusers, patients who took TCHM by prescription were more likely to have a preoperative event (adjusted relative risk, 2.21; 95% confidence interval, 1.14-4.29). The authors present four case reports to highlight the effect of TCHM by prescription on prolonged activated partial thromboplastin time and hypokalemia in the preoperative period. In contrast, there was no significant association between the use of any type of TCHM and the occurrence of either intraoperative or postoperative events.

Conclusions

The use of TCHM by prescription near the time of surgery should be discouraged because of the increased risk of adverse events in the preoperative period.