bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced green emission in ZnGa2O4:Mn thin film phosphors by Se doping
Authors: Jeong Jung Hyun , Moon Byung Kee , Seo Hyo Jin , Bae Jong Seong , Yi Soung-Soo , Kim Ill Won , Park Hong Lee
Published: August 2003

Mn-doped ZnGa2O4−xSex thin film phosphors have been grown using pulsed-laser ablation under various growth conditions. The structural characterization was carried out on a series of ZnGa2O4−xSex:Mn2+ films grown on MgO(100) substrates using Zn-rich ceramic targets. Zn-rich ceramic targets have been prepared to compensate the vaporization loss of Zn. The oxygen pressure was fixed at 100 mTorr and substrate temperatures were varied from 500 to 700 °C. The luminescence results indicated that MgO (100) is one of the most promised substrates for the growth of high-quality ZnGa2O4−xSex:Mn2+ films. In particular, the incorporation of Se into the ZnGa2O4 lattice induced a remarkable increase of photoluminescence. The highest green emission intensity was observed with ZnGa2O3.925Se0.075:Mn2+ films whose brightness was increased by a factor of 3.1 in comparison with that of ZnGa2O4:Mn2+ films. This phosphor may promise for application to the flat panel displays.
Quasiballistic transport in HgTe quantum-well nanostructures
Authors: Daumer V. , Golombek I. , Gbordzoe M. , Novik E. G. , Hock V. , Becker C. R. , Buhmann H. , Molenkamp L. W.
Published: August 2003

The transport properties of micrometer scale structures fabricated from high-mobility HgTe quantum wells have been investigated. A special photoresist and Ti masks were used, which allow for the fabrication of devices with characteristic dimensions down to 0.45 μm. Evidence that the transport properties are dominated by ballistic effects in these structures is presented. Monte Carlo simulations of semiclassical electron trajectories show good agreement with the experiment.
DNA size separation using artificially nanostructured matrix
Authors: Baba M. , Sano T. , Iguchi N. , Iida K. , Sakamoto T. , Kawaura H.
Published: August 2003

We have demonstrated two types of size separation of biomolecules using a nanostructured matrix artificially fabricated using electron-beam lithography: sieve-type separation using a regular pillar array structure and size exclusion chromatography (SEC) type separation using a structure with narrow and wide gaps. With these devices, samples of double-stranded DNA molecules (2, 5, and 10 k base pairs) were clearly separated into bands; smaller molecules eluted earlier in the sieve type while they eluted later in the SEC type. The nanostructured matrix enables various types of molecular separation by changing the design of the nanostructure. Moreover, it should be easy to integrate the matrix with other biomolecular fluidic devices because it does not require a filling medium.
Switchable optical polarizer based on electrochromism in stretch-aligned polyaniline
Authors: Andersson Peter , Berggren Magnus , Kugler Thomas
Published: August 2003

We report on the polarizing electrochromic (EC) effect of a conjugated polymer. This has been achieved in a planar flexible electrochemical device cell comprised of a patterned stretch-aligned thin film of polyaniline and an electrolyte, all made on a polyethylene foil substrate. The resulting device exhibits polarized absorption characteristics, of a dichroic ratio of 4, that can be controlled by the voltage applied. Also, thin flexible EC polarizers have been realized by combining two stretch-aligned polyaniline films with orthogonal stretching direction. In the resulting EC polarizer the orientation of the polarized absorption can be switched between two orthogonal directions, depending on the voltage applied.
Surface reconstructions of In-enriched InGaAs alloys
Authors: Millunchick J. Mirecki , Riposan A. , Dall B. J. , Pearson Chris , Orr B. G.
Published: August 2003

The atomic structure of In0.81Ga0.19As/InP alloy layers was examined using in situ scanning tunneling microscopy. The (2×3) reconstruction observed during growth by reflection high-energy electron diffraction represents a combination of surface structures, including a β2(2×4) commonly observed on GaAs(001) and InAs(001) surfaces, and a disordered (4×3) that is unique to alloy systems. The proposed (4×3) structure is comprised of both anion and cation dimers. Empty and filled states images show that the features reverse contrast with sample bias, in agreement with the model.
Coulomb blockade oscillation in a multiwalled carbon nanotube with internanotube tunnel junctions
Authors: Watanabe Eiichiro , Tsukagoshi Kazuhito , Kanai Dai , Yagi Iwao , Aoyagi Yoshinobu
Published: August 2003

Internanotube charge transport in a multiwalled carbon nanotube (MWNT) was investigated. We directly measured electrical transport from the outer nanotube to the inner nanotubes in a MWNT with two electrodes. The outer nanotubes between the two electrodes were disconnected, leaving the innermost nanotube, so that the current flows into the innermost nanotube via the internanotube junctions. The transport properties of this device clearly showed Coulomb blockade oscillation with a charging energy of 15 meV at 4.2 K. The observed Coulomb blockade oscillation was nonperiodic to the gate voltage, indicating that the multiple internanotube tunnel junctions were formed underneath the electrodes.
Pumping based on transverse electrokinetic effects
Authors: Gitlin Irina , Stroock Abraham D. , Whitesides George M. , Ajdari Armand
Published: August 2003

This work presents a strategy for microfluidic pumping based on transverse electro-osmotic flow in a channel with topographical features on one wall. In this channel, flow along the long axis is generated by an electric field applied across the channel. The pump operates at low (5–10 V) voltage and achieves pumping speeds up to ∼100 μm/s in submillimeter channels. The pump is straightforward to fabricate, contains no moving parts, and provides local control of the direction and strength of pumping. The performance of the pump scales favorably with decreasing size of a microchannel.
Tunable laser diodes by Stark effect
Authors: Le Thomas N. , Pelekanos N. T. , Hatzopoulos Z.
Published: August 2003

We demonstrate wavelength tuning of a laser diode (LD) by the quantum-confined Stark effect. This is achieved by introducing tunneling barriers in the LD active region, as a result of which significant space-charge fields are generated during current injection, modulating the gain spectrum of the “lasing” quantum well. In such a “modified” InGaAs/AlGaAs LD, we observed up to 5-nm Stark-tuning of the lasing wavelength in the 900-nm spectral region.
Optimized annealing conditions identified by analysis of radiative recombination in dilute Ga(As,N)
Authors: Mussler Gregor , Däweritz Lutz , Ploog Klaus H. , Tomm Jens W. , Talalaev Vadim
Published: August 2003

Rapid thermal annealing parameters for Ga(As,N) with 0.5% N are experimentally analyzed. The criteria taken into account are the relative intensity of the observed deep level photoluminescence, the intensity of edge luminescence contributions, and the luminescence decay time. For a 60 s treatment, we find an optimum annealing temperature of 850 °C with a clear tendency of lower optimum annealing temperatures for increasing N contents. Luminescence decay times of up to 400 ps for recombination of delocalized carrier pairs match well the lifetime region specific for direct III–V semiconductors and provide clear evidence of the type-I band alignment in the Ga(As,N) samples investigated.
Slow trap response of zirconium dioxide thin films on silicon
Authors: Harasek S. , Lugstein A. , Wanzenboeck H. D. , Bertagnolli E.
Published: August 2003

In this work, we explore the electrical properties of a metal–oxide–semiconductor system that incorporates a high-k zirconia dielectric with an equivalent oxide thickness of 3 nm deposited by metalorganic chemical vapor deposition. In general, the thin films examined exhibit excellent electrical properties. However, dynamic I–V measurements unveil the presence of trapping sites with response times up to 3 s. By applying a recently proposed model, this slow trap response can be consistently explained by traps located at the inner interface of a two-layer dielectric consisting of the high-k material itself and a transition layer in contact with the semiconductor. Trap energies are found to be distributed around two distinct levels.
Temporal pulse manipulation and ion generation in ultrafast laser ablation of silicon
Authors: Spyridaki M. , Koudoumas E. , Tzanetakis P. , Fotakis C. , Stoian R. , Rosenfeld A. , Hertel I. V.
Published: August 2003

The possibility of phase manipulation and temporal tailoring of ultrashort laser pulses provides new opportunities for optimal processing of materials. An experimental demonstration of the technique that shows the possibility to design excitation sequences tailored with respect to the material response is presented, laying the groundwork for adaptive optimization in material structuring. The technique is particularly suitable to generate controllable ion beams by ultrafast laser ablation. Silicon samples irradiated with multiple laser pulses separated by the phase-transformation time show increased ion emission efficiency with different energetic signatures correlated to a cleaner aspect of the laser-induced structures on the surface.
Dynamic response and hysteresis dispersion scaling of ferroelectric SrBi2Ta2O9 thin films
Authors: Pan B. , Yu H. , Wu D. , Zhou X. H. , Liu J.-M.
Published: August 2003

The dynamic hysteresis response of ferroelectric SrBi2Ta2O9 thin films versus periodically varying electric field over a frequency range of f=10−1–106 Hz and amplitude range of E0=15–158 kV/cm is measured utilizing the Sawyer–Tower method. The dynamic order parameter Q shows anomalous behavior against the field amplitude, and a single-peaked hysteresis dispersion is identified. The field response of hysteresis area 〈A〉 in the form of 〈A〉∝f2/3E02/3 over the low frequency range is evaluated, while the response over the high frequency range takes the form of 〈A〉∝f−1/3E02. We demonstrate that the hysteresis dispersion spectrum exhibits single-parameter scaling, and predicts a characteristic time for domain reversal that is inversely correlated to the field amplitude.
Self-assembled nanostructures through wavelength-controlled spinodal decomposition
Authors: Greaney P. Alex , Chrzan D. C. , Clemens B. M. , Nix W. D.
Published: August 2003

The self-assembly of nanostructured materials through controlled wavelength spinodal decomposition is explored using a simple model. The model assumes that a homogeneous alloy is deposited on a rigid, periodically strained substrate. A linear stability analysis establishes that the film will undergo spinodal decomposition with the dominant wavelength determined by the periodicity of the substrate strain.
Gate-controllable spin battery
Authors: Long Wen , Sun Qing-Feng , Guo Hong , Wang Jian
Published: August 2003

We propose a gate-controllable spin-battery for spin current. The spin battery consists of a lateral double quantum dot under a uniform magnetic field. A finite dc spin current is driven out of the device by controlling a set of gate voltages. Spin current can also be delivered in the absence of charge current. The proposed device should be realizable using present technology at low temperature.
Electrical properties of p–n junctions based on superlattices of AlN/AlGa(In)N
Authors: Kuryatkov V. , Zhu K. , Borisov B. , Chandolu A. , Gherasoiu Ìu. , Kipshidze G. , Chu S. N. G. , Holtz M. , Kudryavtsev Yu. , Asomoza R. , Nikishin S. , Temkin H.
Published: August 2003

Measurements of acceptor activation energy in p–n junctions based on superlattices of AlN (1.25 nm thick) and Al0.08Ga0.92(In)N (0.5 nm thick), with the average AlN content greater than 0.6, are reported. Structural characteristics of superlattices were determined using transmission electron microscopy and x-ray diffraction. p–n junctions in mesa-etched diodes exhibit low leakage current densities of 3×10−10 A/cm2 at near zero bias. Acceptor activation energy of 207±10 meV, obtained from the temperature dependence of the forward current, is very similar to that of uniform alloy of Al0.08Ga0.92N that constitutes the well material. The acceptor activation energy thus appears controlled by the well material and remains low despite high average AlN content and large band gap.
Dielectric relaxation in the Pb(Yb1/2Nb1/2)O3–PbTiO3 solid solution single crystal near the morphotropic phase boundary
Authors: Yasuda Naohiko , Inaba Hiroaki , Ohwa Hidehiro , Iwata Makoto , Terauchi Hikaru , Ishibashi Yoshihiro
Published: August 2003

The dielectric properties in 0.47Pb(Yb1/2Nb1/2)O3–0.53PbTiO3 (0.47PYN–0.53PT) single crystals near the morphotropic phase boundary (MPB) were investigated in the frequency range from 10 kHz to 1 MHz. Remarkable dielectric relaxation was observed along the polar 〈001〉 direction in the tetragonal 0.47PYN–0.53PT single crystal near the MPB. An increase of the dielectric relaxation time was observed as the Curie temperature was approached. The real part and the imaginary part of the complex relative permittivity obeys the Cole–Cole arc law, and the Debye type dielectric dispersion with the polydispersive type among the order-disorder type ferroelectrics was observed.
On mechanical properties of nanostructured meso-porous silicon
Authors: Populaire Ch. , Remaki B. , Lysenko V. , Barbier D. , Artmann H. , Pannek T.
Published: August 2003

Mechanical properties of meso-porous silicon are studied using topographic measurements and finite element simulations. Our approach is based on an original analysis of the strain at the free surface of porous silicon tub embedded in bulk Si regions allowing the determination of the Young’s modulus of the porous layers. In particular, the internal stress in the porous Si region is evaluated from the corresponding deformation of the monocrystalline Si adjacent region which mechanical parameters are well known. Moreover, a mechanical anisotropy of the columnar nanostructured porous Si is brought to the fore from the characteristic shape of the strained porous layer profile. Moderately oxidized, 70% in porosity, porous silicon patterns were investigated. Correlation of our measurements with x-ray data reported early in literature shows the macroscopic strain being close to the silicon lattice relative increase revealing an elastic deformation regime. The porous layers exhibit an unexpected low and strongly anisotropic Young’s modulus for all samples. Young’s modulus values of 1.5 and 0.44 GPa are found in parallel and perpendicular directions of the columnar structure, respectively. Finally, a phenomenological model for such a mechanical behavior taking into account porosity and percolation strength factor of the randomly arranged as-prepared and partially oxidized porous Si nanostructures is proposed.
Brillouin scattering study on relaxor ferroelectric Pb(Zn1/3Nb2/3)O3
Authors: Gorouya Yoshihiro , Tsujimi Yuhji , Iwata Makoto , Yagi Toshirou
Published: August 2003

The 90° Brillouin scattering experiment has been performed on a Pb(Zn1/3Nb2/3)O3 single crystal. The frequency shift and linewidth of the c33 pure longitudinal acoustic mode and the c44 pure transverse mode show bending anomalies near Tm=397 K, at which the low-frequency dielectric constant ε has a maximum value. In addition to the acoustic modes, a relaxational mode is found in the form of a central peak. The relaxation time τ of the mode has a temperature dependence similar to that of ε and shows a broad peak anomaly around Tm. The temperature dependence of τ can be analyzed by a modified superparaelectric model.
Composition-dependent crystallization of alternative gate dielectrics
Authors: van Dover R. B. , Green M. L. , Manchanda L. , Schneemeyer L. F. , Siegrist T.
Published: August 2003

We have investigated the crystallization of amorphous oxides that are considered likely candidates to replace amorphous SiO2 as the gate dielectric in advanced field-effect transistors. To avoid crystallization, the mole fraction of main-group oxide in the Zr–Si–O, Zr–Al–O, and Hf–Si–O systems must be greater than 83%, 65%, and 78%, respectively, leading to a maximum useful dielectric constant of only 6.9, 12.7, and 6.6, respectively. We conclude that the silicate systems are not likely to be useful as replacements for SiO2, while aluminates are more promising.
Shear-induced metallization of triamino-trinitrobenzene crystals
Authors: Riad Manaa M.
Published: August 2003

I report first principle density-functional calculations that demonstrate an insulator-metal transition based on the bending of covalent bonds in 1,3,5-triamino-2,4,6-trinitrobenzene, an organic molecular crystal. The critical shear angle responsible for the vanishing of the energy band gap is achieved at near constant volume via a 55° bending of the nitro group out of the molecular plane, accompanied by 0.1 Å stretch in the N–O bonds. The energy needed for inducing this motion is of the same order of magnitude as the energy band gap.
Resonant tunneling characteristics in SiO2/Si double-barrier structures in a wide range of applied voltage
Authors: Ikeda Hiroya , Iwasaki Masanori , Ishikawa Yasuhiko , Tabe Michiharu
Published: August 2003

We have found that current–voltage characteristics of resonant tunneling diodes (RTDs) with a structure of Al/upper-SiO2/p−-Si-well/lower-SiO2/n+-Si substrate are distinctly categorized by the kinetic energy of electrons in the Si well injected from the n+-Si substrate. For RTDs with a lower-SiO2-layer thickness below 4 nm, negative differential conductance is observed in accordance with our previous work [Y. Ishikawa, T. Ishihara, M. Iwasaki, and M. Tabe, Electron. Lett. 37, 1200 (2001)], where electrons have relatively low kinetic energies below 2.7 eV in the Si well. On the other hand, RTDs with a lower-SiO2 layer thicker than 5 nm have specific characteristics of a large current peak and a large hysteresis at higher kinetic energies above 2.9 eV, indicating that hot electrons are readily stored in the Si well, probably due to enhanced impact ionization scattering.
Continuous wave 2.9 μm dysprosium-doped fluoride fiber laser
Authors: Jackson Stuart D.
Published: August 2003

Single-mode room-temperature cw laser emission on the H13/26→H15/26 2.9 μm phonon terminated electronic transition of Dy3+ is demonstrated. The maximum output power of 0.275 W was generated at a slope efficiency of 4.5% (with respect to the absorbed pump power) when a Dy3+-doped ZBLAN fiber laser was tandem pumped with the ∼1100 nm output from a diode-cladding-pumped Yb3+-doped silica fiber laser.
In situ near-field imaging of magnetic domain patterns in ultrathin iron films
Authors: Meyer G. , Crecelius T. , Bauer A. , Mauch I. , Kaindl G.
Published: August 2003

We report on a scanning near-field optical microscope which operates in ultrahigh vacuum and allows magneto-optical Kerr-effect measurements at variable temperatures and in external magnetic fields with subwavelength lateral resolution. High magneto-optical contrast is achieved by combination with a Sagnac interferometer. In this way, magnetic domain patterns of ultrathin films of Fe/Cu(100), grown at 80 K, were studied in situ. A domain phase consisting of perpendicularly magnetized submicron wide stripes with directional order was observed.
Quantitative study of magnetic field distribution by electron holography and micromagnetic simulations
Authors: Beleggia M. , Schofield M. A. , Zhu Y. , Malac M. , Liu Z. , Freeman M.
Published: August 2003

The magnetic configuration of a submicrometer Ni88Fe12 permalloy island has been quantitatively mapped by off-axis electron holography. The two main contributions to the electron-optical phase shift, namely the phase shifts induced by the electrostatic and magnetic potentials, including fringing fields, were separated by inverting the specimen of 180° with respect to the electron beam and directly measuring the mean inner potential. A quantitative map of the projected magnetic induction in the sample was thereby retrieved and compared to results of micromagnetic and electromagnetic calculations, providing the minimum-energy configuration and the phase shift, respectively.
Preparation and basic properties of ferroelectric thin films having a superlattice structure of 2 Bi3TiNbO9 units–1 Bi4Ti3O12 unit
Authors: Shibuya Akira , Ikemori Shinichi , Wu W. B. , Noda Minoru , Okuyama Masanori
Published: August 2003

Natural-superlattice-structured ferroelectric thin films, Bi3TiNbO9–Bi4Ti3O12 (BTN–BIT), have been grown on Pt/TiO2/SiO2/Si and SrTiO3(001) single-crystal substrates by pulsed-laser deposition (PLD) using BTN–BIT (1 mol:1 mol) targets. BTN–BIT films show natural-superlattice peaks below 2θ=16° in x-ray diffraction patterns only when using an oxygen pressure of 0.05–0.07 Torr in the deposition. The c-axis lattice constant (8.300 nm) of BTN–BIT films suggests a natural superlattice structure consisting of iteration of two unit cells of Bi3TiNbO9 and one unit cell of Bi4Ti3O12. This 2–1 superlattice structure is different from that of BTN–BIT ceramics (2.909 nm), which is 1–1 superlattice. Natural-superlattice-structured BTN–BIT thin films having the 2–1 superlattice prepared at 550 °C exhibit superior ferroelectricity reflected by the value of 2Pr, which is 50 μC/cm2.
Te-free, Sb-based phase-change materials for high-speed rewritable optical recording
Authors: van Pieterson L. , van Schijndel M. , Rijpers J. C. N. , Kaiser M.
Published: August 2003

High-speed rewritable optical disks based on conventional (eutectic) Sb–Te phase-change materials have low archival life stability and high media noise. We propose Te-free, Sb-based phase-change materials for recording at linear velocities over 28 m/s. These materials combine good optical contrast, rapid crystallization, and high amorphous phase stability.
Ultrabroadband terahertz field detection by photoconductive antennas based on multi-energy arsenic-ion-implanted GaAs and semi-insulating GaAs
Authors: Liu Tze-An , Tani Masahiko , Nakajima Makoto , Hangyo Masanori , Pan Ci-Ling
Published: August 2003

The photoconductive antennas based on multi-energy arsenic-ion-implanted GaAs and semi-insulating GaAs are demonstrated to have a useful bandwidth beyond 20 THz for a gating laser pulse width of 15 fs. The bandwidth and signal-to-noise ratio are compared with those of reference photoconductive antennas based on low-temperature grown GaAs.
Hydrogen passivation of nitrogen in SiC
Authors: Gali A. , Deák P. , Son N. T. , Janzén E.
Published: August 2003

First-principles calculations carried out in 4H-SiC show that hydrogen may form stable complexes with substitutional nitrogen, passivating the shallow nitrogen donor. The complex is very stable with respect to isolated positive donors and negatively charged hydrogen interstitials, so reactivation is expected only at high temperature. The binding energy also increases the concentration of hydrogen, incorporated into 4H-SiC during growth or postgrowth hydrogenation.
Atomistic structure of the Si(100)–SiO2 interface: A synthesis of experimental data
Authors: Bongiorno Angelo , Pasquarello Alfredo
Published: August 2003

We construct atomistic models of the Si(100)–SiO2 interface in accord with available experimental data. Combining classical and first-principles simulation methods, we generate transition structures from crystalline silicon to disordered SiO2. The generation procedure accounts for the density of coordination defects, the amount and location of partially oxidized Si atoms, and the mass density profile, as measured in electron-spin-resonance, photoemission, and x-ray reflectivity experiments, respectively. A variety of model interfaces are obtained, differing by the degree of order in the transition region.
Chemical vapor deposition of Ge nanocrystals on SiO2
Authors: Baron T. , Pelissier B. , Perniola L. , Mazen F. , Hartmann J. M. , Rolland G.
Published: August 2003

We present a detailed study of the growth of Ge nanocrystals (NCs) on SiO2 by chemical vapor deposition. A two-step process was developed. First, Si nuclei are deposited on SiO2 using SiH4 as a gaseous precursor. Then, Ge NCs grow selectively on the Si nuclei previously formed. The density of the Ge NCs is adjustable in between 109 and 1012 cm−2. Their mean size varies between 5 and 50 nm. We have shown, combining grazing incidence x-ray diffraction and x-ray photoelectron spectroscopy, that pure Ge NCs are grown in a polycrystalline phase on a SiO2 surface.
Anomalous leakage current characteristics of Pt/(Ba0.75,Sr0.25)Ti1+yO3+z/Pt thin films grown by metalorganic chemical vapor deposition
Authors: Saha S. , Kaufman D. Y. , Streiffer S. K. , Auciello O.
Published: August 2003

The leakage and dielectric properties of a thickness series (90–480 nm) of {100} fiber-textured metalorganic chemical vapor deposited (Ba0.75Sr0.25)Ti1+yO3+z (BST) thin films on Pt/SiO2/Si were investigated. The permittivity demonstrated a suppressed temperature and electric field response that transitioned to a more bulk-like response with increasing thickness, consistent with earlier observations. At low fields the leakage currents showed a weak-field dependence and a monotonic increase with increasing temperature. In contrast, a positive temperature coefficient of resistance (PTCR) was observed in the leakage current behavior at high-field. The PTCR behavior was more pronounced for thicker BST films. The observed effect is contrasted with PTCR behavior in bulk BaTiO3 ceramics.
Differential expression in SAGE: accounting for normal between-library variation
Authors: Baggerly Keith A. , Deng Li , Morris Jeffrey S. , Aldaz C. Marcelo
Published: August 2003

Motivation: In contrasting levels of gene expression between groups of SAGE libraries, the libraries within each group are often combined and the counts for the tag of interest summed, and inference is made on the basis of these larger ‘pseudolibraries’. While this captures the sampling variability inherent in the procedure, it fails to allow for normal variation in levels of the gene between individuals within the same group, and can consequently overstate the significance of the results. The effect is not slight: between-library variation can be hundreds of times the within-library variation.

Results: We introduce a beta-binomial sampling model that correctly incorporates both sources of variation. We show how to fit the parameters of this model, and introduce a test statistic for differential expression similar to a two-sample t-test.

Contact: kabagg@mdanderson.org

Supplementary information http://bioinformatics.mdanderson.org/ Includes Matlab and R code for fitting the model.

* To whom correspondence should be addressed.
RankGene: identification of diagnostic genes
based on expression data
Authors: Su Yang , Murali T.M. , Pavlovic Vladimir , Schaffer Michael , Kasif Simon
Published: August 2003

Summary: RankGene is a program for analyzing gene expression data and computing diagnostic genes based on their predictive power in distinguishing between different types of samples. The program integrates into one system a variety of popular ranking criteria, ranging from the traditional t-statistic to one-dimensional support vector machines. This flexibility makes RankGene a useful tool in gene expression analysis and feature selection.

Availability: http://genomics10.bu.edu/yangsu/rankgene

Contact: murali@bu.edu

* To whom correspondence should be addressed.
MrBayes 3: Bayesian phylogenetic inference under mixed models
Authors: Ronquist Fredrik , Huelsenbeck John P.
Published: August 2003

Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.

Availability: http://morphbank.ebc.uu.se/mrbayes

Contact: fredrik.ronquist@ebc.uu.se

* To whom correspondence should be addressed.
AGenDA: homology-based gene prediction
Authors: Taher Leila , Rinner Oliver , Garg Saurabh , Sczyrba Alexander , Brudno Michael , Batzoglou Serafim , Morgenstern Burkhard
Published: August 2003

Summary: We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.

Availability: http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/

Contact: ltaher@TechFak.Uni-Bielefeld.DE

* To whom correspondence should be addressed.
PseuRECA: genome annotation and gene context analysis for
Pseudomonas aeruginosa PAO1
Authors: Weinel Christian , Ermolaeva Maria D. , Ouzounis Christos
Published: August 2003

Availability:The PseuRECA database is accesible at http://maine.ebi.ac.uk:8000/services/pseureca/

Contact: weinel.christian@mh-hannover.de

* To whom correspondence should be addressed.
Identification of functional links between genes using phylogenetic
profiles
Authors: Wu Jie , Kasif Simon , DeLisi Charles
Published: August 2003

Motivation: Genes with identical patterns of occurrence across the phyla tend to function together in the same protein complexes or participate in the same biochemical pathway. However, the requirement that the profiles be identical (i) severely restricts the number of functional links that can be established by such phylogenetic profiling; (ii) limits detection to very strong functional links, failing to capture relations between genes that are not in the same pathway, but nevertheless subserve a common function and (iii) misses relations between analogous genes. Here we present and apply a method for relaxing the restriction, based on the probability that a given arbitrary degree of similarity between two profiles would occur by chance, with no biological pressure. Function is then inferred at any desired level of confidence.

Results: We derive an expression for the probability distribution of a given number of chance co-occurrences of a pair of non-homologous orthologs across a set of genomes. The method is applied to 2905 clusters of orthologous genes (COGs) from 44 fully sequenced microbial genomes representing all three domains of life. Among the results are the following. (1) Of the 51 000 annotated intrapathway gene pairs, 8935 are linked at a level of significance of 0.01. This is over 30-fold greater than the 271 intrapathway pairs obtained at the same confidence level when identical profiles are used. (2) Of the 540 000 interpathway genes pairs, some 65 000 are linked at the 0.01 level of significance, some 12 standard deviations beyond the number expected by chance at this confidence level. We speculate that many of these links involve nearest-neighbor path, and discuss some examples. (3) The difference in the percentage of linked interpathway and intrapathway genes is highly significant, consistent with the intuitive expectation that genes in the same pathway are generally under greater selective pressure than those that are not. (4) The method appears to recover well metabolic networks. This is illustrated by the TCA cycle which is recovered as a highly connected, weighted edge network of 30 of its 31 COGs. (5) The fraction of pairs having a common pathway is a symmetric function of the Hamming distance between their profiles. This finding, that the functional correlation between profiles with near maximum Hamming distance is as large as between profiles with near zero Hamming distance, and as statistically significant, is plausibly explained if the former group represents analogous genes.

Contact: delisi@bu.edu
Pandit: a database of protein and associated nucleotide domains with
inferred trees
Authors: Whelan Simon , de Bakker Paul I. W. , Goldman Nick
Published: August 2003

Motivation: A large, high-quality database of homologous sequence alignments with good estimates of their corresponding phylogenetic trees will be a valuable resource to those studying phylogenetics. It will allow researchers to compare current and new models of sequence evolution across a large variety of sequences. The large quantity of data may provide inspiration for new models and methodology to study sequence evolution and may allow general statements about the relative effect of different molecular processes on evolution.

Results: The Pandit 7.6 database contains 4341 families of sequences derived from the seed alignments of the Pfam database of amino acid alignments of families of homologous protein domains (Bateman et al., 2002). Each family in Pandit includes an alignment of amino acid sequences that matches the corresponding Pfam family seed alignment, an alignment of DNA sequences that contain the coding sequence of the Pfam alignment when they can be recovered (overall, 82.9% of sequences taken from Pfam) and the alignment of amino acid sequences restricted to only those sequences for which a DNA sequence could be recovered. Each of the alignments has an estimate of the phylogenetic tree associated with it. The tree topologies were obtained using the neighbor joining method based on maximum likelihood estimates of the evolutionary distances, with branch lengths then calculated using a standard maximum likelihood approach.

Availability: The Pandit database is available for browsing and download via its home page at http://www.ebi.ac.uk/goldman-srv/pandit/

Contact: simon@ebi.ac.uk

* To whom correspondence should be addressed.
Greedy method for inferring tandem duplication history
Authors: Zhang Louxin , Ma Bin , Wang Lusheng , Xu Ying
Published: August 2003

Motivation: Genome analysis suggests that tandem duplication is an important mode of evolutionary novelty by permitting one copy of each gene to drift and potentially to acquire a new function. With more and more genomic sequences available, reconstructing duplication history has received extensive attention recently.

Results: An efficient method is presented for inferring the duplication history of tandemly repeated sequences based on the model proposed by Fitch (1977). We validate the method by using simulation results and real data sets of mucin genes, ZNF genes, and olfactory receptors genes. The agreement with conclusions drawn by other biological researchers strongly indicates that our method is efficient and robust.

Availability:The program is available by request.

Contact: matzlx@nus.edu.sg

* To whom correspondence should be addressed.
A hidden Markov model for progressive multiple alignment
Authors: Löytynoja Ari , Milinkovitch Michel C.
Published: August 2003

Motivation: Progressive algorithms are widely used heuristics for the production of alignments among multiple nucleic-acid or protein sequences. Probabilistic approaches providing measures of global and/or local reliability of individual solutions would constitute valuable developments.

Results: We present here a new method for multiple sequence alignment that combines an HMM approach, a progressive alignment algorithm, and a probabilistic evolution model describing the character substitution process. Our method works by iterating pairwise alignments according to a guide tree and defining each ancestral sequence from the pairwise alignment of its child nodes, thus, progressively constructing a multiple alignment. Our method allows for the computation of each column minimum posterior probability and we show that this value correlates with the correctness of the result, hence, providing an efficient mean by which unreliably aligned columns can be filtered out from a multiple alignment.

Availability: The software is freely available http://www.ulb.ac.be/sciences/ueg/

Contact: aloytyno@ulb.ac.be; mcmilink@ulb.ac.be.

* To whom correspondence should be addressed.
GenoMap, a circular genome data viewer
Authors: Sato Naoki , Ehira Shigeki
Published: August 2003

Summary: A Tcl/Tk-based application called GenoMap is described, a viewer for genome-wide map of microarray expression data within a circular bacterial genome. An interactive interface facilitates easy identification of the expressed region. This software is also used for drawing genome-wide quantitative data.

Availability: The program is freely available to academic users as a Tcl/Tk source code at http://www.molbiol.saitama-u.ac.jp/~naoki/GenoMap/

Contact: naokisat@molbiol.saitama-u.ac.jp
ESTWeb: bioinformatics services for EST sequencing projects
Authors: Paquola Apuã C. M. , Nishyiama Milton Y. , Reis Eduardo M. , da Silva Aline M. , Verjovski-Almeida Sergio
Published: August 2003

Summary: ESTWeb is an internet based software package designed for uniform data processing and storage for large-scale EST sequencing projects. The package provides for: (a) reception of sequencing chromatograms; (b) sequence processing such as base-calling, vector screening, comparison with public databases; (c) storage of data and analysis in a relational database, (d) generation of a graphical report of individual sequence quality; and (e) issuing of reports with statistics of productivity and redundancy. The software facilitates real-time monitoring and evaluation of EST sequence acquisition progress along an EST sequencing project.

Availability: http://bioinfo.iq.usp.br/estweb

Contact: verjo@iq.usp.br

Supplementary information: http://bioinfo.iq.usp.br/estweb

* To whom correspondence should be addressed.
QAlign: quality-based multiple alignments with dynamic
phylogenetic analysis
Authors: Sammeth M. , Rothgänger J. , Esser W. , Albert J. , Stoye J. , Harmsen D.
Published: August 2003

Summary: Integrating different alignment strategies, a layout editor and tools deriving phylogenetic trees in a ‘multiple alignment environment’ helps to investigate and enhance results of multiple sequence alignment by hand. QAlign combines algorithms for fast progressive and accurate simultaneous multiple alignment with a versatile editor and a dynamic phylogenetic analysis in a convenient graphical user interface.

Availability: QAlign is freely available over the internet at http://www.ridom.de/qalign/. The platform-independent JAVA technology used provides distributions for various operating systems and hardware architectures.

Contact: qalign@ridom.de

* To whom correspondence should be addressed.

† Present address: Genome Informatics, Department of Technology, Bielefeld University, 33594 Bielefeld, Germany.
Serial BLAST searching
Authors: Korf Ian
Published: August 2003

Motivation: The translating BLAST algorithms are powerful tools for finding protein-coding genes because they identify amino acid similarities in nucleotide sequences. Unfortunately, these kinds of searches are computationally intensive and often represent bottlenecks in sequence analysis pipelines. Tuning parameters for speed can make the searches much faster, but one risks losing low-scoring alignments. However, high scoring alignments are relatively resistant to such changes in parameters, and this fact makes it possible to use a serial strategy where a fast, insensitive search is used to pre-screen a database for similar sequences, and a slow, sensitive search is used to produce the sequence alignments.

Results: Serial BLAST searches improve both the speed and sensitivity.

Contact: ik1@sanger.ac.uk
A comparison of statistical methods for analysis of
high density oligonucleotide array data
Authors: Rajagopalan Dilip
Published: August 2003

Motivation: Gene expression profiling has become an invaluable tool in functional genomics. A wide variety of statistical methods have been employed to analyze the data generated in experiments using Affymetrix GeneChip® microarrays. It is important to understand the relative performance of these methods in terms of accuracy in detecting and quantifying relative gene expression levels and changes in gene expression.

Results: Three different analysis approaches have been compared in this work: non-parametric statistical methods implemented in Affymetrix Microarray Analysis Suite v5.0 (MAS5); an error-modeling based approach implemented in Rosetta Resolver® v3.1; and an intensity-modeling approach implemented in dChip v1.1. A Latin Square data set generated and made available by Affymetrix was used in the comparison. All three methods—Resolver, MAS5 and the version of dChip based on the difference between perfect match and mismatch intensities—perform well in quantifying gene expression. Presence calls made by MAS5 and Resolver perform well at high concentrations, but they cannot be relied upon at low concentrations. The performance of Resolver and MAS5 in detecting 2-fold changes in transcript concentration is superior to that of dChip. At a comparable false positive rate, Resolver and MAS5 are able to detect many more true changes in transcript concentration. Estimated fold changes calculated by all the methods are biased below the true values.

Contact: dilip.2.rajagopalan@gsk.com
Currency boards and Chinese banks in Malaya and the Philippines before World War II
Authors: Huff W. G.
Published: August 2003

This article examines the relationship between currency boards and the development of local Chinese deposit banking in Malaya and the Philippines before World War II. While in both countries Chinese banks filled an important gap in financial intermediation, the currency board system – an especially strict version of the classical gold standard – virtually ensured that these institutions remained small. Moreover, in the slump of the 1930s the currency board system's preclusion of a central bank and requirement to pay depositors in 100% metropolitan currency, together with the volatility of highly staple‐dependent export economies, pushed Chinese banks to the verge of bankruptcy or beyond. Examination of the 1930s crisis in South‐East Asia and the role of banks in it reveals more differences from than parallels with the 1990s experience.
Banking crises and the evolution of the regulatory framework in Hong Kong 1945–1970
Authors: Schenk Catherine R.
Published: August 2003

Hong Kong initially emerged relatively unscathed from the East Asian financial crisis of 1997–1998 and was able to defend the pegged exchange rate on which its status as an international financial centre depended. The soundness and transparency of the financial system is widely credited with allowing Hong Kong to avoid the worst excesses that brought down financial systems elsewhere. This article explores the evolution of the regulatory framework in the post‐war period, revealing the reluctance with which the state tightened its control over the banking system. This resulted in the combination of poor supervision and constraints on competition that contributed to further instability.
The Chinese silver standard economy and the 1929 Great Depression
Authors: Lai Cheng‐chung , Gau Joshua Jr‐Shiang
Published: August 2003

It is often argued that the silver standard insulated the Chinese economy from the Great Depression that prevailed in the gold standard countries during the period 1929–1935. Using econometric testing and counterfactual simulations, this article shows that if China had been on the gold standard (or on the gold‐exchange standard), the balance of trade of this semiclosed economy would have been ameliorated, but the general price level would have declined significantly. Due to limited statistics, two important variables (GDP and industrial production) are not included in the analysis, but the general argument that the silver standard was a lifeboat to the Chinese economy remains defensible.
Business responses to crisis in Indonesia: the 1930s and the 1990s
Authors: Lindblad J. Thomas
Published: August 2003

This article looks at the responses of foreign business firms to crisis in a comparative historical perspective. The focus is on Indonesia in the 1930s and the late 1990s. The main approach is one of case studies in order to gain an insight into strategies of adjustment to deteriorating business conditions. For the late 1990s, such information is supplemented by macroeconomic evidence covering a wider range of firms. The article reaffirms a basic resilience of foreign direct investment in times of economic crisis even when there is an overall economic decline, as in Indonesia in the 1990s. The capacity of foreign firms in Indonesia to adjust successfully was considerable both in the 1930s and the late 1990s. Yet, prospects for a swift recovery are far better in the latter case than in the former period, reflecting the different nature of the two crises.
The Indonesian economic crisis and the long road to recovery
Authors: Wie Thee Kian
Published: August 2003

This article provides a concise overview of the origins and impact of the 1997–1998 crisis on the Indonesian economy and the tardy process of recovery since. It is pessimistic about the current prospects for speedy recovery due to the inability of the politically weak governments, which succeeded the highly authoritarian Soeharto regime, to take the necessary steps needed to achieve full economic recovery. The article briefly compares this crisis with the economic crises that hit Indonesia during the early 1930s and mid‐1960s, and points to similarities as well as differences.
Foreign direct investment in crisis and recovery: lessons from the 1997–1998 Asian crisis
Authors: Athukorala Prema‐chandra
Published: August 2003

Is foreign direct investment more resilient at the onset of an economic crisis and the subsequent economic collapse in a host country compared to other forms of foreign capital inflows? Are affiliates of multinational enterprises in a crisis‐hit country better equipped to withstand a crisis and aid the recovery process by readjusting their investment, production and sales strategies compared to local firms? This article examines these issues in the context of the 1997–1998 economic crisis in Thailand, Malaysia, Indonesia, Korea and the Philippines. The findings suggest that foreign direct investment was a relatively stable source of foreign capital in the crisis context and that the affiliates of multinational enterprises were instrumental in ameliorating the severity of economic collapse and facilitating the recovery process.
Third generation management of technology intelligence processes
Authors: Lichtenthaler Eckhard
Published: August 2003

How have the technology intelligence approaches of large technology‐intensive companies changed in the last 30 years? This paper aims to answer this question through case study research in 26 leading European and North American companies in the pharmaceutical, telecommunication equipment and automobile/machinery industries. The empirical results show that technology intelligence approaches have closely followed the changes in R&D organization, project selection and technology planning. Three generations of technology intelligence management can be distinguished. Furthermore, the contingency factors for the location of technology intelligence within technology intensive companies are identified.