bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurement of the rate coefficient for collisional removal of O2(XΣg−3,υ=1) by O(P3)
Authors: Kalogerakis Konstantinos S. , Copeland Richard A. , Slanger Tom G.
Published: November 2005

We report a laboratory measurement of the rate coefficient for the collisional removal of O2(XΣg−3,υ=1) by O(P3) atoms. In the experiments, 266-nm laser light photodissociates ozone in a mixture of molecular oxygen and ozone. The photolysis step produces vibrationally excited O2(aΔg1) that is rapidly converted to O2(XΣg−3,υ=1–3) in a near-resonant electronic energy-transfer process with ground-state O2. In parallel, a large amount of O(D1) atoms is generated that promptly relaxes to O(P3). Under the conditions of the experiments, only collisions with the photolytically produced O(P3) atoms control the lifetime of O2(XΣg−3,υ=1), because its removal by molecular oxygen at room temperature is extremely slow. Tunable 193-nm laser light monitors the temporal evolution of the O2(XΣg−3,υ=1) population by detection of laser-induced fluorescence near 360 nm. The removal rate coefficient for O2(XΣg−3,υ=1) by O(P3) atoms is (3.2±1.0)×10−12cm3s−1(2σ) at a temperature of 315±15K(2σ). This result is essential for the analysis and correct interpretation of the 6.3-μm H2O(ν2) band emission in the Earth’s mesosphere and indicates that the deactivation of O2(XΣg−3,υ=1) by O(P3) atoms is significantly faster than the nominal values recently used in atmospheric models.
An eight-degree-of-freedom quantum dynamics study for the H2+C2H system
Authors: Wang Dunyou
Published: November 2005

An eight-degree-of-freedom (8DOF) time-dependent wave-packet approach has been developed to study the H2+C2H→H+C2H2 reaction system. The 8DOF model is obtained by fixing one of the Jacobi torsion angle in the nine-degree-of-freedom AB+CDE reaction system. This study is an extension of the previous seven-degree-of-freedom (7DOF) computation [J. Chem. Phys. 119, 12057 (2003)] of this reaction system. This study shows that vibrational excitations of H2 enhance the reaction probability, whereas the stretching vibrational excitations of C2H have only a small effect on the reactivity. Furthermore, the bending excitation of C2H, compared to the ground-state reaction probability, hinders the reactivity. A comparison of the rate constant between the 7DOF calculation and the present 8DOF results has been made. The theoretical and experimental results agree with each other very well when the present 8DOF results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.
Strain distribution in GaN∕AlN quantum-dot superlattices
Authors: Sarigiannidou E. , Monroy E. , Daudin B. , Rouvière J. L. , Andreev A. D.
Published: November 2005

The two-dimensional strain distribution in a GaN∕AlN quantum-dot (QD) superlattice is measured from high-resolution transmission electron microscopy images using the geometrical phase analysis. The results are compared to elastic theoretical calculations using a combination of Fourier transform and Green’s function techniques. The GaN∕AlN system appears to be a model system for a comparison between theory and experiments as interdiffusion between GaN and AlN is negligible. We verify that for the case of a three-dimensional system, such as a QD, the biaxial strain approximation is not valid. Furthermore, we demonstrate that the presence of QDs induces a modulation in the strain state of the AlN barriers which is the driving force for the vertical alignment of the GaN QDs in the AlN matrix.
Dynamic electrostriction of a Bose condensate and of a system of neutral atoms
Authors: Kosevich A. M.
Published: November 2005

It is shown that the condensate of a Bose gas of neutral atoms has electrical properties that are reflected in the dynamics of the condensate and do not reduce to a trivial polarization of the atomic gases in an external electric field. The concept of an isotropic atomic quadrupole moment whose distribution creates a distribution of the macroscopic electric potential 〈φ〉 in a system of neutral atoms is used. The nonuniform distribution of atoms that arises in a sound wave, for example, will produce an electric field whose behavior is determined by the dynamics of 〈φ〉.
Low-temperature thermal conduction and sound damping in a disordered quasi-one-dimensional crystal with a weakly dispersive branch of the vibrations
Authors: Chulkin E. P.
Published: November 2005

This paper discusses the question of how the weak localization of the low-energy acoustic vibrational mode, whose dispersion law has a large flat section, affects the propagation of sound and heat in a nonideal chainlike crystal. Analytical expressions are obtained for the thermal-conduction and sound-damping coefficients for the low-temperature region. The role of specific interference processes of phonon scattering at phonon-density fluctuations close to defects under conditions of weak interaction between the chains is analyzed. It is shown that, in the low-frequency region, where the dispersion law of the vibrational mode under consideration manifests quasi-one-dimensional properties, the renormalization of the thermal-conduction and sound-damping coefficients can be revealed experimentally when the atomic concentration of defects is c⩾5%. The nonstandard temperature dependence of the speed of sound is discussed.
Electric activity of vortices in superfluid He4
Authors: Natsik V. D.
Published: November 2005

The vortical motion of atoms in a quantum liquid is accompanied by their weak polarization under the action of centrifugal forces. Theoretical estimates of the effect give an electric field close to the axis of the vortex of about 300 V⋅cm−1 and a linear density of the bound charge in the core of about (3e)cm−1 (e is the charge of an electron).
Nucleation and growth of Pd clusters on (001) SrTiO3: Determination of diffusion and adsorption energies from cluster densities
Authors: Richter G. , Wagner T.
Published: November 2005

The nucleation and the growth of Pd on (001) SrTiO3 surfaces were studied by scanning tunneling microscopy. Between 500 and 700°C the Pd nucleated as three-dimensional clusters on the (001) SrTiO3 surface. The condensation regime for the nucleation of Pd clusters on SrTiO3 could be confined by Auger electron spectroscopy and transmission electron microscopy investigations. An approximation of Venables’s nucleation rate theory [J. A. Venables, Philos. Mag. 27, 697 (1973)] was used which holds for the initially incomplete and complete regimes of condensation. With this approximation, we could simultaneously extract the activation energies for the diffusion and adsorption, Ed and Ea, of Pd atoms on the (001) surface of SrTiO3. The results are compared with other metal-oxide systems, and some general trends of the nucleation behavior of metal clusters on oxide surfaces are discussed.
Effect of helium addition on discharge characteristics in a flat fluorescent lamp
Authors: Lee Seong-Eui , Lee Ho-Nyeon , Park Hyoung-Bin , Lee Kyo Sung , Choi Kyung Cheol
Published: November 2005

The discharge characteristics of a multielectrode dual coplanar in a mercury-free flat fluorescent lamp were investigated using brightness-efficiency measurement and the infrared (IR) spectrum and intensified charge coupled device (ICCD) characteristics. The level of brightness was above 14900cd∕m2 under the conditions of neon-–50% xenon–8% He gas composition, 150Torr pressure, and 20kHz alternating current pulse. The ICCD results revealed a faster and wider discharge with a Ne–50% Xe–8% He gas composition. The effect of adding helium (He) to Ne–50% Xe revealed a faster peak emission, as confirmed by ICCD images. From the gated IR emission spectrum, the intensity ratio of I823nm∕I828nm was ∼8% higher with Ne–50% Xe–8% He than with Ne–50% Xe under the same pressure and applied voltage conditions.
Change in spectra of mobility of small atmospheric ions during convection and diffusion
Authors: Maruyama Toshiro , Wakabayashi Makoto
Published: November 2005

The change in spectra of mobility of small atmospheric ions during molecular diffusion and convection in air has been studied experimentally. There occurs no change in mobility spectra for the molecular diffusion in windless air because both coefficients of adhesion and diffusion are proportional to the mobility. On the other hand, the mobility spectrum of ions changes during the convections due to the inverse proportionality of the lifetime to the mobility of ions. The mean lifetime of ions was experimentally obtained from the measured concentration distribution of ions in a round free jet. The results showed that the mobility spectrum of ions changes with increasing downstream distance due to a rapid dissipation of the ions of high mobility during the convections.
Micro-Raman and photoluminescence spectroscopies of horizontal Bridgman-grown AgGaSe2
Authors: Roy U. N. , Cui Y. , Miles R. , Burger A. , Goldstein Jonathan T. , Bell Zane W. , Carpenter Donald A.
Published: November 2005

Ag Ga Se 2 crystals grown by the horizontal Bridgman technique were studied by room-temperature micro-Raman scattering and low-temperature photoluminescence (PL) spectroscopies. The most intense Raman line observed had the frequency of 177cm−1, corresponding to the Γ1(W1) mode. The measurements were performed along the direction of growth of the boule and the line frequency was found to be almost constant within the experimental accuracy. The average full width at half maximum of the Γ1(W1) mode was found to be 4.6cm−1 and its insignificant variation along the ingot suggests its structural and compositional uniformities. At low temperature (8K), the main PL peak at 1.772eV is due to donor-acceptor-pair recombination. A doublet in the excitonic peak, observed at that temperature, suggests a reduced inhomogeneous broadening and the better crystallinity of the sample, when compared with the previous literature. The dispersion of the various PL peaks along the length of the ingot was also found negligible, which indicates the compositional homogeneity and the uniform distribution of the intrinsic defects.
Below band-gap optical absorption in GaxIn1−xSb alloys
Authors: Chandola A. , Kim H. J. , Dutta P. S. , Guha S. , Gonzalez L. , Kumar V.
Published: November 2005

The below band-gap optical-absorption characteristics of GaxIn1−xSb alloy system have been reported. The different dependencies of the hole and electron absorption mechanisms on wavelength result in significant changes of the absorption characteristics with alloy composition. In the undoped Ga-rich alloy compositions that are p type in nature (due to residual holes resulting from native defects), the inter-valence-band absorption has been found to be the dominant absorption mechanism. With decreasing Ga (increasing indium) mole fraction, the hole to electron ratio decreases for undoped samples. For such samples, absorption due to electrons becomes significant. With n-type extrinsic doping, intervalley transitions are seen for certain Ga-rich compositions, which also alter the absorption characteristics. The dependencies of various absorption mechanisms as a function of wavelength have been analyzed and discussed in this paper. Based on the theoretical analysis presented in this paper, one can calculate the extrinsic doping level necessary for each alloy composition in order to obtain high optical transparency necessary for infrared optical applications.
Experimental study of manifestations of resonance scattering of conduction electrons on transition-element impurities in mercury selenide
Authors: Okulov V. I. , Gergert A. V. , Govorkova T. E. , Korolyov A. V. , Lonchakov A. T. , Sabirzyanova L. D. , Paranchich S. Yu. , Andriyichuk M. D. , Romanyuk V. P.
Published: November 2005

An interpretation of the experimental data on the low-temperature conductivity and magnetic susceptibility of mercury selenide containing donor impurities of transition elements is developed on the basis of electron resonance scattering theory in the Friedel approach. Both existing data and results obtained in the present study, for solid solutions of chromium, cobalt, and gadolinium, are considered. The results of a fitting of the measured temperature dependence of the electron mobility in HgSe:Cr crystals and concentration dependence of the Curie constant in the impurity magnetic susceptibility of HgSe:Co crystals are analyzed to obtain quantitative confirmation of the idea that resonance donor levels of the impurities chromium and cobalt are present in the conduction band of the respective crystals. The resonance level widths are determined and are found to be an order of magnitude larger than those of iron. It is shown that the observed concentration maximum of the electron mobility in mercury selenide containing gadolinium impurities can be explained on the basis of resonance scattering theory, although the existing data are insufficient for justification of such an explanation of the origin of that maximum.
Doped-channel micro-Hall devices: Size and geometry effects
Authors: Kunets Vas. P. , Mazur Yu. I. , Salamo G. J. , Bierwagen O. , Masselink W. T.
Published: November 2005

Using a doped-channel Al0.3Ga0.7As-GaAs-In0.2Ga0.8As Greek-cross micro-Hall device as model structure, the size, and geometry effects on the absolute magnetic sensitivity and noise were investigated. The data show that although the absolute magnetic sensitivity is higher for devices with larger active areas, the self-heating effects at moderate and high electric fields are more detrimental for larger devices than for smaller ones. For this reason, the scaled absolute sensitivity is greater for smaller devices. The geometry is further optimized using finite element method simulations. Rounding the corners within the Greek-cross geometry results in lower peak electric fields and therefore a higher signal-to-noise sensitivity.
Loss of polarization in a hot-electron current through electron-electron scattering
Authors: Perrella A. C. , Mather P. G. , Buhrman R. A.
Published: November 2005

By utilizing the spin-dependent mean free paths in Co, a polarizer-analyzer system for hot electrons has been established, enabling ballistic electron emission microscopy to measure the effects of scattering on the spin-dependent transport of hot electrons. Through the gradual oxidation of Al, it is possible to controllably increase the scattering effects of a Cu–Al–Cu spacer layer. As scattering increases, the measured polarization exiting the spacer decreases. The effect is explained by a straightforward Auger-like hot-electron scattering process which conserves spin flux but reduces the polarization of a hot-electron current through generation of energetic electron-hole pairs.
Interface patterns between still gas and liquid in horizontal tubes
Authors: Turnau Jean-Rémi , Fabre Jean
Published: November 2005

The pattern of the interface between a liquid and a gas at rest in a small horizontal tube is investigated both experimentally and theoretically. The experimental study was carried out for different liquid fractions with air and fluids of various surface tension and contact angle. When the contact angle is zero, a hysteresis is observed at the transition between the stratified and bubble patterns. The theory shows that the bubble-to-stratified transition occurs when the energy of the stratified pattern becomes smaller than that of the bubble pattern, and that the stratified-to bubble-transition occurs when the energy of the linearly perturbed interface becomes smaller than the energy of the unperturbed one. The theory for the bubble-to-stratified transition is extended to nonzero contact angle. It shows that its influence is significant when it is greater than 90°. Experiments carried out with mercury confirm the theory.
Room-temperature ferromagnetism observed in Fe-doped NiO
Authors: Wang Jianfei , Cai Jingnan , Lin Yuan-Hua , Nan Ce-Wen
Published: November 2005

Here we report a kind of diluted magnetic semiconductor (DMS) system, i.e., Fe-doped NiO. Monophase Ni1−xFexO (x=0–0.02) was synthesized by using a chemical coprecipitation method and post-thermal decomposition processing. Pure NiO without Fe doped is antiferromagnetic. The results demonstrated the samples with Fe doped were ferromagnetic at room temperature, which is stronger than most DMS oxide systems, e.g., Mn or Ni-doped ZnO, and Co-doped TiO2 reported recently. The effect of Fe doping was discussed and relevant mechanism was proposed, by comparing with previous studies of finite size effect in NiO nanoparticles and other DMS systems.
Conducting and transparent single-wall carbon nanotube electrodes for polymer-fullerene solar cells
Authors: Pasquier Aurelien Du , Unalan Husnu Emrah , Kanwal Alokik , Miller Steve , Chhowalla Manish
Published: November 2005

We describe the use of single-wall carbon nanotube (SWNT) thin films as transparent and conducting electrodes for hole collection in poly(hexyl)thiophene-[6-6]phenyl-C61-butyric acid methyl ester (P3HT-PCBM) organic photovoltaics. We report a power conversion efficiency of 1%, with a fill factor of 0.3 and a short-circuit current of 6.5mA∕cm2 under 100mW∕cm2 polychromatic white light illumination measured in air. These values are comparatively higher than reference cells of similar thickness made on indium tin oxide (ITO) glass substrates. This is attributed to the three-dimensional nature of the interface between the SWNTs and the P3HT-PCBM nanocomposite. Our results indicate that solution processed SWNT thin films are a viable alternative to ITO for photovoltaic devices, eliminating an expensive vacuum deposition step in the fabrication of organic solar cells.
Chirped pulse compression in nonuniform plasma Bragg gratings
Authors: Wu Hui-Chun , Sheng Zheng-Ming , Zhang Jie
Published: November 2005

A nonuniform plasma Bragg grating with a monotonically increasing density-modulation profile can be naturally produced by two Gaussian laser pulses counterpropagating through a homogeneous plasma slab. Such a plasma grating exhibits a nonuniform photonic band gap with a monotonically increasing width. It can be used to compress a positively or negatively chirped pulse. Particle-in-cell simulations show that the compressed pulse has nearly no energy loss and the compression efficiency can exceed 90%.
Temperature-dependent luminescence of InP quantum dots coupled with an InGaP quantum well and of InP quantum dots in a quantum well
Authors: Zhang X. B. , Ryou J. H. , Dupuis R. D. , Walter G. , Holonyak N.
Published: November 2005

We report the temperature-dependent cathodoluminescence (CL) properties of (1) InP∕InAlGaP quantum dots (QDs) coupled to an InGaP quantum well (QW) through a thin InAlGaP barrier (or simply QW+QD), (2) InP QDs grown directly in the well (DWELL), and (3) a reference sample InP∕InAlGaP QDs. We found that with an increase in temperature, the CL peak of the reference sample shows a large redshift compared with the band gap shift of InP. This large redshift is due to the thermally activated carriers transferred from small QDs to large ones. Within the temperature range studied, this redshift of the CL peak is much larger in DWELL but is much smaller, and in some temperature range, the energy of CL peak is independent of temperature for QW+QD samples. We believe that the temperature-insensitive emission energy observed in QW+QD is caused by (1) thermalization of hot carriers in the QW and (2) nonuniform tensile strain in the QW created by the varying sizes of QDs on top of the QW.
Synthesis of a Novel Pyrrole Oxazole Analogue of the Insecticide Pirate
Authors: Loughlin Wendy A. , Murphy Michelle E. , Elson Kathryn E. , Henderson Luke C.
Published: November 2005

The pyrrole oxazole 4 is a novel analogue of the broad-spectrum insecticide and miticide pirate 2. The expedient synthesis of pyrrole oxazole 4 in six steps from pyrrole is reported using a synthetic route that could have potential for the solution-phase combinatorial synthesis of analogues. Preliminary biological evaluation of the protected pyrrole oxazole 4 (LD50 1.13 μg mL–1) and the deprotected pyrrole oxazole 5 (LD50 1.06 μg mL–1) for potential cytotoxicity was carried out.
Benzoyloxymethyl p-Toluenethiosulfonate: a Crystalline, Stable Synthetic Equivalent for +CH2S+
Authors: Kabir S. M. Humayun , Langler Richard F.
Published: November 2005

Benzoyloxymethyl p-toluenethiosulfonate has been developed as a reagent for the one-pot preparation of α-sulfide disulfides and the corresponding symmetrical bissulfide disulfides. The reagent is effective for systems bearing terminal aryl groups.
The Nickel(II)/2,4,6-Tris(2-pyridyl)-1,3,5-triazine System: Synthesis and Crystallographic Characterization of a Series of Complexes
Authors: Zibaseresht Ramin , Hartshorn Richard M.
Published: November 2005

A series of nickel(ii) complexes of 2,4,6-tris(2-pyridyl)-1,3,5-triazine (tpt) have been prepared and identified using crystallographic techniques. Changes in the reaction conditions result in complexes with metal–triazine ligand ratios of 2 : 1, 1 : 1, and 1 : 2 being isolated. The results of the structural studies show that different stereoisomers can be formed, and the structures have been examined in order to identify the stabilizing features that might have led to these particular compounds being formed in preference to others in such labile systems. Numerous π–π stacking and hydrogen-bonding interactions can be found within the lattices of the structures, but these are notably absent in the structure of [Ni(tpt)2](ClO4)2 7, the complex isolated when perchlorate ions are added to solutions of all the other compounds.
Some Stability and Stereochemical Considerations of Simple Bicyclo[4.2.0]octanols
Authors: Loughlin Wendy A. , Rowen Catherine C. , McCleary Michelle A.
Published: November 2005

Bicyclooctanols 3 and 4 were formed with control of the stereochemistry at C8 by using an aluminium enolate of cyclohexanone in 1,2-dimethoxyethane. Bicyclooctanols 1 and 3 were stable towards aqueous hydrochloric acid for short times (< 3.5 h), and ring open to a diastereomeric mix of monoalkylated 5 under protic or aprotic conditions in the presence of base (NaOH or lithium diisopropylamide). The rate of ring opening appears to be dependent on reaction temperature. Bicyclooctanols 1, 3, and 4 displayed remarkable stability when heated at reflux in benzene, whereas use of ethanol prompted stereoselective ring opening of 1 and 3 to give individual diastereomers of monoalkylated 5 and ring opening of 4 to give a 50 : 50 mix of diastereomers of 5. This unexpected result was attributed to the stereochemistry of the bicyclooctanol and placement of hydrogen-bonding sites.
An Efficient Two-Step Synthesis of Jensenone Isolated from Eucalyptus jensenii. Synthesis of Analogues and Evaluation as Antioxidants
Authors: Bharate Sandip B. , Chauthe Siddheshwar K. , Bhutani Kamlesh K. , Singh Inder P.
Published: November 2005

A phloroglucinol derivative, jensenone (1) isolated from leaves of Eucalyptus jensenii has been synthesized for the first time through a short and efficient two-step procedure starting from commercially available phloroglucinol. The methodology provides a simplified route to introduce diformyl moiety for synthesis of biologically active formylated phloroglucinol compounds such as antimalarial robustadials, cancer chemopreventive euglobals, and antifouling sideroxylonals. Several analogues of jensenone have also been synthesized and evaluated for antioxidant capacity.
The functional status of paraveinal mesophyll vacuoles changes in response to altered metabolic conditions in soybean leaves
Authors: Murphy Kimberly A. , Kuhle Rachel A. , Fischer Andreas M. , Anterola Aldwin M. , Grimes Howard D.
Published: November 2005

Antibodies raised against tonoplast intrinsic proteins (TIPs) were used to probe the functional status of the soybean [Glycine max (L.) Merr.] paraveinal mesophyll (PVM) vacuole during changes in nitrogen metabolism within the leaf. Young plants grown under standard conditions had PVM vacuoles characterised by the presence of γ-TIP, which is indicative of a lytic function. When plants were then subjected to shoot tip removal for a period of 15 d, forcing a sink-limited physiological condition, the γ-TIP marker diminished while the δ-TIP marker became present in the PVM vacuole, indicating the conversion of the PVM vacuole to a storage function. When the shoot tips were allowed to regrow, the γ-TIP marker again became dominant demonstrating the reversion of these PVM vacuoles back to a lytic compartment. The changes in TIP markers correlated with the accumulation of vegetative storage proteins and vegetative lipoxygenases, proteins implicated in nitrogen storage and assimilate partitioning. This research suggests that the PVM vacuole is able to undergo dynamic conversion between lytic and storage functions and further implicates this cell layer in assimilate storage and mobilisation in soybeans.
Managing soils to enhance the potential for bioremediation of water repellency
Authors: Roper Margaret M.
Published: November 2005

Water repellency can significantly reduce crop and pasture establishment and production in sandy soils. Management practices that increase the rate of water infiltration into dry soils following the first rains at the end of the dry season were investigated. In the laboratory, addition of water to water repellent soil and maintenance of warm moist conditions produced a gradual decline in water repellency. This was supported by results in the field which showed that under daily irrigation there was a gradual decline in water repellency over time. However, under dryland conditions, other mechanisms to increase water infiltration had to be found. In the laboratory, after the addition of lime and kaolinite clay, there was an initial rapid decline in repellency, indicative of a physical mechanism, followed by a more gradual decline suggesting a biological response. In the field, under dryland conditions, the addition of lime and kaolinite clay resulted in a reduction in water repellency, and in the case of lime, this effect increased with the size of application. Estimates of the numbers of wax-degrading bacteria in the treated soils, using a most-probable-number assay, showed at least a 10-fold increase in lime-treated sands, but not in the clay-treated sands. The results suggest that lime may provide a viable alternative for increasing the wettability of soils by physical mechanisms and by promoting microbial activity by bacteria responsible for wax degradation, resulting in more consistent plant germination and establishment, and increased crop yields.
Purkinje cell long-term depression is prevented by T-588, a neuroprotective compound that reduces cytosolic calcium release from intracellular stores
Authors: Kimura Tatsuo , Sugimori Mutsuyuki , Llinás Rodolfo R.
Published: November 2005

Long-term depression (LTD) of the parallel-fiber (PF) Purkinje synapse induced by four different experimental paradigms could be prevented in rat cerebellar slices by T-588, a neuroprotective compound. The paradigms consisted of pairing PF activation with climbing-fiber activation, direct depolarization, glutamic iontophoretic depolarization, or caffeine. In all cases, LTD was determined by patch-clamp recording of PF excitatory postsynaptic currents at the Purkinje cell somata. T-588 at 1 μM prevented the triggering of LTD reversibly and did not generate LTD on its own. Two-photon calcium-sensitive dye imaging demonstrated that T-588 reduces intracellular calcium concentration ([Ca
2+
]
i
) increase by blocking calcium release from intracellular stores. Because [Ca
2+
]
i
increase has been widely shown to trigger LTD and glutamate excitotoxicity, we propose that LTD may act as a neuroprotective mechanism. As such, LTD would serve to decrease glutamatergic-receptor sensitivity to limit deleterious [Ca
2+
]
i
increase rather than to act as a mechanism for cerebellar learning.
PCP: a program for supervised classification of gene expression profiles
Authors: Buturović Ljubomir J.
Published: November 2005

Summary: PCP (Pattern Classification Program) is an open-source machine learning program for supervised classification of patterns (vectors of measurements). The principal use of PCP in bioinformatics is design and evaluation of classifiers for use in clinical diagnostic tests based on measurements of gene expression. PCP implements leading pattern classification and gene selection algorithms and incorporates cross-validation estimation of classifier performance. Importantly, the implementation integrates gene selection and class prediction stages, which is vital for computing reliable performance estimates in small-sample scenarios. Additionally, the program includes automated and efficient model selection (optimization of parameters) for support vector machine (SVM) classifier. The distribution includes Linux and Windows/Cygwin binaries. The program can easily be ported to other platforms.

Availability: Free download at

Contact:  ljubomir@sfsu.edu
Pathway recognition and augmentation by computational analysis of microarray expression data
Authors: Novak Barbara A. , Jain Ajay N.
Published: November 2005

Motivation: We present a system, QPACA (Quantitative Pathway Analysis in Cancer) for analysis of biological data in the context of pathways. QPACA supports data visualization and both fine- and coarse-grained specifications, but, more importantly, addresses the problems of pathway recognition and pathway augmentation.

Results: Given a set of genes hypothesized to be part of a pathway or a coordinated process, QPACA is able to reliably distinguish true pathways from non-pathways using microarray expression data. Relying on the observation that only some of the experiments within a dataset are relevant to a specific biochemical pathway, QPACA automates selection of this subset using an optimization procedure. We present data on all human and yeast pathways found in the KEGG pathway database. In 117 out of 191 cases (61%), QPACA was able to correctly identify these positive cases as bona fide pathways with p-values measured using rigorous permutation analysis. Success in recognizing pathways was dependent on pathway size, with the largest quartile of pathways yielding 83% success. In cross-validation tests of pathway membership prediction, QPACA was able to yield enrichments for predicted pathway genes over random genes at rates of 2-fold or better the majority of the time, with rates of 10-fold or better 10–20% of the time.

Availability: The software is available for academic research use free of charge by email request.

Contact:  ajain@jainlab.org

Supplementary information: Data used in the paper may be downloaded from
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
Authors: Pei Jimin , Cai Wei , Kinch Lisa N. , Grishin Nick V.
Published: November 2005

Motivation: A number of methods have been developed to predict functional specificity determinants in protein families based on sequence information. Most of these methods rely on pre-defined functional subgroups. Manual subgroup definition is difficult because of the limited number of experimentally characterized subfamilies with differing specificity, while automatic subgroup partitioning using computational tools is a non-trivial task and does not always yield ideal results.

Results: We propose a new approach SPEL (specificity positions by evolutionary likelihood) to detect positions that are likely to be functional specificity determinants. SPEL, which does not require subgroup definition, takes a multiple sequence alignment of a protein family as the only input, and assigns a P-value to every position in the alignment. Positions with low P-values are likely to be important for functional specificity. An evolutionary tree is reconstructed during the calculation, and P-value estimation is based on a random model that involves evolutionary simulations. Evolutionary log-likelihood is chosen as a measure of amino acid distribution at a position. To illustrate the performance of the method, we carried out a detailed analysis of two protein families (LacI/PurR and G protein α subunit), and compared our method with two existing methods (evolutionary trace and mutual information based). All three methods were also compared on a set of protein families with known ligand-bound structures.

Availability: SPEL is freely available for non-commercial use. Its pre-compiled versions for several platforms and alignments used in this work are available at

Contact:  grishin@chop.swmed.edu.

Supplementary information: Supplementary materials are available at
Response to “Revisiting the Influence of Campaign Tone on Turnout in Senate Elections”
Authors: Fridkin Kim L. , Kenney Patrick J.
Published: November 2005

Robert Jackson and Jason Sides (2005) conclude in their article, Revisiting the Influence of Campaign Tone on Turnout in Senate Elections, “We are hard-pressed to conclude that respondents' political profiles condition the influence of campaign tone on their turnout behavior.… Kahn and Kenney's conclusions about differential citizen responsiveness to campaign negativity should not become part of accepted wisdom in this area of scholarship.” We disagree and our reasoning rests on three points: the measurement and operationalization of a key variable: mudslinging; the selection of an appropriate estimation strategy; and the employment of theoretical expectations to make sense of the central findings.
Mechanics of direct wafer bonding
Authors: Turner K.T , Spearing S.M
Published: November 2005

Direct wafer bonding is a manufacturing process that is used in the fabrication of electronic, optical and mechanical microsystems. The initial step in the process requires that the wafers are sufficiently smooth, flat and compliant such that short-range surface forces can elastically deform the wafers and bring the surfaces into complete contact. Analytical and computational mechanics models of this adhesion process as well as experiments that validate these models are presented in this work. An energy-based analysis is used to develop the models that allow acceptable limits of wafer-scale flatness variations to be predicted. The analytical models provide basic insight into the process while the finite-element-based model reported provides a method to analyse a broad range of realistic cases, including the bonding of wafers with etch patterns and arbitrary geometries. Experiments, in which patterned silicon wafers with different magnitudes of wafer-scale shape variations were bonded, were performed and the results demonstrate that the proposed models can accurately predict the size and shape of the bonded area based on the wafer geometry, elastic properties and work of adhesion.
How can automimicry persist when predators can preferentially consume undefended mimics?
Authors: Ruxton Graeme D , Speed Michael P
Published: November 2005

It is common for species that possess toxins or other defences to advertise these defences to potential predators using aposematic (‘warning’) signals. There is increasing evidence that within such species, there are individuals that have reduced or non-existent levels of defence but still signal. This phenomenon (generally called automimicry) has been a challenge to evolutionary biologists because of the need to explain why undefended automimics do not gain such as a fitness advantage by saving the physiological costs of defence that they increase in prevalence within the population, hence making the aposematic signal unreliable. The leading theory is that aposematic signals do not stop all predatory attacks but rather encourage predators to attack cautiously until they have identified the defence level of a specific individual. They can then reject defended individuals and consume the undefended. This theory has recently received strong empirical support, demonstrating that high-accuracy discrimination appears possible. However, this raises a new evolutionary problem: if predators can perfectly discriminate the defended from the undefended and preferentially consume the latter, then how can automimicry persist? Here, we present four different mechanisms that can allow non-trivial levels of automimics to be retained within a population, even in the extreme case where predators can differentiate defended from undefended individuals with 100% accuracy. These involve opportunity costs to the predator of sampling carefully, temporal fluctuation in predation pressure, predation pressure being correlated with the prevalence of automimicry, or developmental or evolutionary constraints on the availability of defence. These mechanisms generate predictions as to the conditions where we would expect aposematically signalling populations to feature automimicry and those where we would not.
Influence of density dependence on predator–prey seabird interactions at large spatio-temporal scales
Authors: Oro Daniel , Martínez-Abraín Alejandro , Paracuellos Mariano , Nevado Juan Carlos , Genovart Meritxell
Published: November 2005

Theoretical investigations of competitive dynamics have noted that numbers of predator and prey influence each other. However, few empirical studies have demonstrated how a life-history trait of the prey (such as fecundity) can be affected simultaneously by its own density and the density of predators. For instance, density dependence can reduce fecundity with increasing number of prey, while inverse density dependence or Allee effects may occur especially when the prey is a social organism. Here we analysed an intraguild predator–prey system of two seabird species at a large spatio-temporal scale. As expected, we found that fecundity of prey was negatively affected by predator density. Nevertheless, fecundity of prey also increased nonlinearly with its own density and strikingly with the prey–predator ratio. Small groups of prey were probably not able to defend their nests especially against large number of predators. At the highest prey densities (i.e. when anti-predator strategies should be most efficient), prey fecundity also lowered, suggesting the appearance of density dependence mediated by food competition. Allee effects and density dependence occurred across a broad range of population sizes of both the prey and the predator at several local populations facing different ecological environments.
Mitosis, stature and evolution of plant mating systems: low-Φ and high-Φ plants
Authors: Scofield Douglas G , Schultz Stewart T
Published: November 2005

There is a long-recognized association in plants between small stature and selfing, and large stature and outcrossing. Inbreeding depression is central to several hypotheses for this association, but differences in the evolutionary dynamics of inbreeding depression associated with differences in stature are rarely considered. Here, we propose and test the Φ model of plant mating system evolution, which assumes that the per-generation mutation rate of a plant is a function of the number of mitoses (Φ) that occur from zygote to gamete, and predicts fundamental differences between low-Φ (small-statured) and high-Φ (large-statured) plants in the outcomes of the joint evolution of outcrossing rate and inbreeding depression. Using a large dataset of published population genetic studies of angiosperms and conifers, we compute fitted values of inbreeding depression and deleterious mutation rates for small- and large-statured plants. Consistent with our Φ model, we find that populations of small-statured plants exhibit a range of mating systems, significantly lower mutation rates, and intermediate inbreeding depression, while large-statured plants exhibit very high mutation rates and the maximum inbreeding depression of unity. These results indicate that (i) inbred progeny typically observed in large-statured plant populations are completely lost prior to maturity in nearly all populations; (ii) evolutionary shifts from outcrossing to selfing are generally not possible in large-statured species, rather, large-statured species are more likely to evolve mating systems that avoid selfing such as self-incompatibility and dioecy; (iii) destabilization of the mating system—high selfing rate with high-inbreeding depression—might be a common occurrence in large-statured species; and (iv) large-statured species in fragmented populations might be at higher risk of extinction than previously thought. Our results help to unify and simplify a large and diverse field of research, and serve to emphasize the importance that developmental and genetic constraints play in the evolution of plant mating systems.
Colour-assortative mating among populations ofTropheus moorii, a cichlid fish from Lake Tanganyika, East Africa
Authors: Salzburger Walter , Niederstätter Harald , Brandstätter Anita , Berger Burkhard , Parson Walther , Snoeks Jos , Sturmbauer Christian
Published: November 2005

The species flocks of cichlid fishes in the East African Lakes Tanganyika, Malawi and Victoria are prime examples of adaptive radiation and explosive speciation. Several hundreds of endemic species have evolved in each of the lakes over the past several thousands to a few millions years. Sexual selection via colour-assortative mating has often been proposed as a probable causal factor for initiating and maintaining reproductive isolation. Here, we report the consequences of human-mediated admixis among differentially coloured populations of the endemic cichlid fishTropheus mooriifrom several localities that have accidentally been put in sympatry in a small harbour bay in the very south of Lake Tanganyika. We analysed the phenotypes (coloration) and genotypes (mitochondrial control region and five microsatellite loci) of almost 500 individuals, sampled over 3 consecutive years. Maximum-likelihood-based parenthood analyses and Bayesian inference of population structure revealed that significantly more juveniles are the product of within-colour-morph matings than could be expected under the assumption of random mating. Our results clearly indicate a marked degree of assortative mating with respect to the different colour morphs. Therefore, we postulate that sexual selection based on social interactions and female mate choice has played an important role in the formation and maintenance of the different colour morphs inTropheus, and is probably common in other maternally mouthbrooding cichlids as well.
Sex chromosomes and male ornaments: a comparative evaluation in ray-finned fishes
Authors: Mank Judith E , Hall David W , Kirkpatrick Mark , Avise John C
Published: November 2005

Theory predicts that the mechanism of genetic sex determination can substantially influence the evolution of sexually selected traits. For example, female heterogamety (ZZ/ZW) can favour the evolution of extreme male traits under Fisher's runaway model of sexual selection. We empirically test whether the genetic system of sex determination has played a role in the evolution of exaggerated male ornaments in actinopterygiian fishes, a clade in which both female-heterogametic and male-heterogametic systems of sex determination have evolved multiple times. Using comparative methods both uncorrected and corrected for phylogenetic non-independence, we detected no significant correlation between sex-chromosome systems and sexually selected traits in males. Results suggest that sex-determination mechanism is at best a relatively minor factor affecting the outcomes of sexual selection in ray-finned fishes.
Integrating life history and cross-immunity into the evolutionary dynamics of pathogens
Authors: Restif Olivier , Grenfell Bryan T
Published: November 2005

Models for the diversity and evolution of pathogens have branched into two main directions: the adaptive dynamics of quantitative life-history traits (notably virulence) and the maintenance and invasion of multiple, antigenically diverse strains that interact with the host's immune memory. In a first attempt to reconcile these two approaches, we developed a simple modelling framework where two strains of pathogens, defined by a pair of life-history traits (infectious period and infectivity), interfere through a given level of cross-immunity. We used whooping cough as a potential example, but the framework proposed here could be applied to other acute infectious diseases. Specifically, we analysed the effects of these parameters on the invasion dynamics of one strain into a population, where the second strain is endemic. Whereas the deterministic version of the model converges towards stable coexistence of the two strains in most cases, stochastic simulations showed that transient epidemic dynamics can cause the extinction of either strain. Thus ecological dynamics, modulated by the immune parameters, eventually determine the adaptive value of different pathogen genotypes. We advocate an integrative view of pathogen dynamics at the crossroads of immunology, epidemiology and evolution, as a way towards efficient control of infectious diseases.
Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount
Authors: Kuwabara Tomohiko , Minaba Masaomi , Iwayama Yukihiro , Inouye Isao , Nakashima Miwako , Marumo Katsumi , Maruyama Akihiko , Sugai Akihiko , Itoh Toshihiro , Ishibashi Jun-ichiro , Urabe Tetsuro , Kamekura Masahiro
Published: November 2005

A cell-fusing hyperthermophilic archaeon was isolated from hydrothermal fluid obtained from Suiyo Seamount of the Izu-Bonin Arc. The isolate, TS1T, is an irregular coccus, usually 0·5–2 μm in diameter and motile with a polar tuft of flagella. Cells in the exponential phase of growth fused at room temperature in the presence of DNA-intercalating dye to become as large as 5 μm in diameter. Fused cells showed dark spots that moved along in the cytoplasm. Large cells with a similar appearance were also observed upon culture at 87 °C, suggesting the occurrence of similar cell fusions during growth. Transmission electron microscopy revealed that cells in the exponential phase possessed a thin and electron-lucent cell envelope that could be lost subsequently during culture. The fragile cell envelope must be related to cell fusion. The cells grew at 57–90 °C, pH 5·2–8·7 and at NaCl concentrations of 1·5–4·5 %, with the optima being 87 °C, pH 6·5 and 2·5 % NaCl. The isolate was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 53·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate was closely related to Thermococcus species. However, no significant DNA–DNA hybridization was observed between genomic DNA of strain TS1T and phylogenetically related Thermococcus species. We propose that isolate TS1T represents a novel species, Thermococcus coalescens sp. nov., with the name reflecting the cell fusion activity observed in the strain. The type strain is TS1T (=JCM 12540T=DSM 16538T).
Spiroplasma penaei sp. nov., associated with mortalities in Penaeus vannamei, Pacific white shrimp
Authors: Nunan Linda M. , Lightner Donald V. , Oduori Marietta A. , Gasparich Gail E.
Published: November 2005

A new bacterial strain, designated SHRIMPT, isolated from the haemolymph of the Pacific white shrimp, Penaeus vannamei, was serologically distinct from other spiroplasmas. Cells of this strain were helical in form and variable in length. Examination by electron microscopy revealed wall-less cells delineated by a single cytoplasmic membrane. The organisms grew well in M1D media supplemented with 2 % NaCl. Strain SHRIMPT grew at temperatures of 20–37 °C, with optimum growth occurring at 28 °C. The strain catabolized glucose and hydrolysed arginine, but did not hydrolyse urea. The G+C content of the DNA was 29±1 mol%. Strain SHRIMPT (=ATCC BAA-1082T=CAIM 1252T) is designated the type strain of a novel species, Spiroplasma penaei sp. nov., which represents a new subgroup (I-9) of the group I spiroplasmas.