bluuebunny/crossref_metadata_2025 huggingface dataset:
Well width dependence of disorder effects on the optical properties of AlGaN∕GaN quantum wells
Authors: Friel I. , Thomidis C. , Moustakas T. D.
Published: October 2004

We report on a temperature-dependent photoluminescence study of disorder effects on the optical properties of Al0.2Ga0.8N∕GaN multiple quantum wells as a function of the well width. It is found that the disorder-induced inhomogeneous broadening of the excitonic density of states increases with decreasing well width. A nonmonotonic temperature variation of the photoluminescence peak energy is observed, and interpreted as a crossover from a thermal to a nonthermal (trapped) distribution of recombining excitons amongst the band-tail states. The luminescence is quenched by two thermally activated mechanisms, and the dependence of the activation energies with well width is accounted for.
How well does total electron yield measure x-ray absorption in nanoparticles?
Authors: Fauth K.
Published: October 2004

The possibility to quantitatively analyze total electron yield (TEY) spectra as a measure of the x-ray absorption cross section from supported magnetic nanoparticles is explored by a combination of experiments and Monte Carlo simulations. Unless the particles are very small, it is found that saturation effects are important and can lead to a severe underestimation of the magnetic moments, when the magneto-optical sum rules are straightforwardly applied to experimental data. However, unlike for planar samples the possibility to examine and correct the saturation effects by varying the x-ray angle of incidence is not given, the absorption profiles are largely unaffected in their shape. The Monte Carlo simulations, appropriately conducted for the material under investigation, provide an estimate of the saturation effects occurring in nanoparticle TEY data.
Capillary filling speed of water in nanochannels
Authors: Tas N. R. , Haneveld J. , Jansen H. V. , Elwenspoek M. , van den Berg A.
Published: October 2004

The capillary filling speed of water in nanochannels with a rectangular cross section and a height on the order of 100nm has been measured over a length of 1cm. The measured position of the meniscus as a function of time qualitatively follows the Washburn model. Quantitatively, however, there is a lower than expected filling speed, which we attribute to the electro-viscous effect. For demineralized water in equilibrium with air the elevation of the apparent viscosity amounts up to 24±11% in the smallest channels (53nm height). When using a 0.1M NaCl (aq) solution the elevation of the apparent viscosity is significantly reduced.
Microstructure and piezoelectric properties of sub-80 nm high polycrystalline SrBi2Ta2O9 nanostructures within well-ordered arrays
Authors: Ma Wenhui , Hesse Dietrich
Published: October 2004

Well-ordered arrays of sub-80 nm high SrBi2Ta2O9 nanostructures were fabricated on SrTiO3:Nb (111) single-crystal substrates by latex sphere lithography. The as-prepared nanostructures have a pyramid-like shape with around 220 nm lateral dimension at half their height. After annealing, the pyramid-like shape changes due to the formation of nano-sized SrBi2Ta2O9 grains of high crystal anisotropy in the individual nanostructures. Microstructure and piezoelectric properties of the nanostructures were investigated by cross-sectional transmission electron microscopy and piezoresponse force microscopy, respectively. Scattering in piezoelectric strain constants d33 was observed, probably arising from varying orientations, high anisotropy, and interfacial diffusion layer of the polycrystalline SrBi2Ta2O9 nanostructures on SrTiO3. The d33 increases continuously with dc bias and reaches 8pm∕V at a bias of 20 V. The size effect on piezoelectric properties of SrBi2Ta2O9 was found to be much less severe than that in BaTiO3. The acquired piezoresponse hysteresis loops proved that 30 nm high SrBi2Ta2O9 nanostructures are still ferroelectric.
Development of phase-slip centers in superconducting Sn nanowires
Authors: Michotte S. , Piraux L. , Boyer F. , Ladan F. R. , Maneval J. P.
Published: October 2004

By electrodeposition of tin inside the pores of a polycarbonate template, nanowires were grown, out of which a single one was contacted electrically so as to form a quasi-one-dimensional superconductor (diameter: 50nm). A resistive phase-slip center appears as a response to a pulse of supercritical current. Measuring its resistance, and its time of nucleation, gives access to the electron inelastic lifetime, and to the gap relaxation time, respectively, both in the nanosecond range. Finally, the threshold current for passage into the fully normal state indicates a good thermal contact with the polycarbonate matrix.
Laboratory air bubble generation of various size distributions
Authors: Puleo Jack A. , Johnson Rex V. , Kooney Tim N.
Published: October 2004

Air bubble size in aqueous environments is an important factor governing natural processes ranging from fluid/atmosphere gas transfer to noise production. Bubbles are also known to affect various scientific instruments. In this study we investigate the production capability of eight inexpensive bubble generators using optical imaging techniques. Specific emphasis is directed towards determining bubble size and distribution for a given device, flow conditions, and type of water used (fresh vs salt). In almost all cases tested here, bubbles produced in salt water were more numerous, and smaller than for the same bubbler and conditions in fresh water. For porous media, the finer the pore size, the smaller the bubble produced with some variation depending on thickness of material containing the pore and water type. While no single generator tested was capable of spanning all the bubble sizes observed (100 to 6000 microns), the data contained herein will enable proper choice of bubbler or combinations thereof for future studies depending on the size and distribution of bubbles required.
Increased terahertz emission from thermally treated GaSb
Authors: Winnerl S. , Sinning S. , Dekorsy T. , Helm M.
Published: October 2004

We report on the terahertz (THz) emission from GaSb surfaces with modified surface stochiometry. While very weak emission is observed from virgin GaSb wafers, the emission is significantly increased by a single thermal treatment of the wafers. Optimum emission is observed for 500 °C thermal annealing. The reason for the THz emission is a surface electric field induced by thermal decomposition of the surface, as corroborated by Raman spectroscopy.
Diagram of the states in arrays of iron nanocylinders
Authors: Porrati F. , Huth M.
Published: October 2004

The magnetic states of two-dimensional cylinder arrays of iron are studied as function of thickness, diameter, and separation by means of numerical micromagnetics. The corresponding diagram of the states for cylinders with thickness and diameter in the nanoscale regime is presented. The diagram is composed of regions with a single minimum of the free energy, relevant for applications, and regions with multiple minima. The effect of the magnetostatic coupling is highlighted by comparing the state diagram for cylinders with 10nm perimetrical separation with the one for isolated cylinders.
Growth and magnetic properties of MnO2−δ nanowire microspheres
Authors: Yang J. B. , Zhou X. D. , James W. J. , Malik S. K. , Wang C. S.
Published: October 2004

We report the synthesis of MnO2−δ microspheres using hydrothermal and conventional chemical reaction methods. The microspheres of MnO2−δ consist of nanowires having a diameter of 20–50nm and a length of 2–8μm. The value of oxygen vacancy δ estimated from x-ray photoelectron spectrum is 0.3. The magnetization versus temperature curve indicates a magnetic transition at about 13K. It is found that a parasitic ferromagnetic component is imposed on the antiferromagnetic structure of MnO2−δ, which might result from distortion of the lattice structure due to oxygen vacancies. The magnetic transition temperature TN is about 10K lower than that of the bulk MnO2 single crystal.
Thiolation of single-wall carbon nanotubes and their self-assembly
Authors: Plank N. O. V. , Cheung R. , Andrews R. J.
Published: October 2004

A method for the thiolation of single-wall carbon nanotubes has been developed by exposing a sulfur/carbon nanotubes mixture to an argon/hydrogen gaseous plasma. X-ray photoelectron spectroscopy provides evidence of the existence of sulfur attached to carbon on the carbon nanotubes samples and Raman spectroscopy results show that the carbon nanotubes’ structure has been preserved after the treatment. One added advantage of the reported method is that excess oxygen is not present on the nanotubes. The thiolated carbon nanotubes are shown to self-assemble onto gold electrodes. Our method for thiolating carbon nanotubes provides a reliable and simple way for preparing functionalized tubes for nanoelectronic circuits based on carbon nanotubes.
Leaky surface acoustic waves in Z-LiNbO3 substrates with epitaxial AIN overlays
Authors: Bu G. , Ciplys D. , Shur M. S. , Namkoong G. , Doolittle W. A. , Hunt W. D.
Published: October 2004

The properties of leaky surface acoustic waves (LSAW) in MBE grown AIN layer on Z-cut LiNbO3 structures have been studied by numerical simulation and experimental measurements and compared with those of Rayleigh waves in the same structure. In the range of AIN layer thicknesses studied (0<kh<0.145) the measured velocity of LSAW propagating along the X axis of LiNbO3 substrate was essentially constant at around 4400m∕s. The measured electromechanical coupling coefficients (K2) for the LSAW are roughly 1/4 of the predicted values, which might be due to the strong attenuation of the leaky wave unaccounted for during the parameter extraction. The thin AIN film slightly improved the measured temperature coefficient of frequency for the LSAW over that attained for the Z-cut, X-propagating LiNbO3 substrate alone.
Effect of strain-compensation in stacked 1.3μm InAs∕GaAs quantum dot active regions grown by metalorganic chemical vapor deposition
Authors: Nuntawong N. , Birudavolu S. , Hains C. P. , Huang S. , Xu H. , Huffaker D. L.
Published: October 2004

We have introduced tensile layers embedded in a GaAs matrix to compensate compressive strain in stacked 1.3μm InAs quantum dot (QD) active regions. The effects of the strain compensation are systematically investigated in five-stack and ten-stack QD structures where we have inserted InxGa1−xP (x=0.30 or 0.36) layers. High-resolution x-ray diffraction spectra quantify the overall strain in each sample and indicate >35% strain reduction can be accomplished. Both atomic force and transmission electron microscope images confirm that strain compensation improves material crystallinity and QD uniformity. With aggressive strain compensation, room temperature QD photoluminescence intensity is significantly increased demonstrating a reduced defect density.
Size effect and strain rate sensitivity in benzocyclobutene film
Authors: Liu D.-L. , Lu T.-M. , Wang G.-C. , Picu R. C.
Published: October 2004

The mechanical properties of benzocyclobutene film are investigated at the nanoscale by nano-indentation using atomic force microscopy (AFM). The force versus indentation depth data were collected with two different AFM tips of radii ∼20 and ∼380nm. A strong size effect of the plastic flow stress was observed as the radius of the indenter tip was reduced. More important, the material exhibited pronounced strain rate sensitivity when probed at the nanoscale, while it was rate insensitive at larger scales. These two size effects were quantified by analytic and finite element modeling.
Efficient radiative recombination from ⟨112¯2⟩ -oriented InxGa1−xN multiple quantum wells fabricated by the regrowth technique
Authors: Nishizuka K. , Funato M. , Kawakami Y. , Fujita Sg. , Narukawa Y. , Mukai T.
Published: October 2004

In x Ga 1 − x N multiple quantum wells (QWs) with [0001], ⟨112¯2⟩, and ⟨112¯0⟩ orientations have been fabricated by means of the regrowth technique on patterned GaN template with striped geometry, normal planes of which are (0001) and {112¯0}, on sapphire substrates. It was found that photoluminescence intensity of the {112¯2} QW is the strongest among the three QWs, and the internal quantum efficiency of the {112¯2} QW was estimated to be as large as about 40% at room temperature. The radiative recombination lifetime of the {112¯2} QW was about 0.38ns at low temperature, which was 3.8 times shorter than that of conventional [0001]-oriented InxGa1−xN QWs emitting at a similar wavelength of about 400nm. These findings strongly suggest the achievement of stronger oscillator strength owing to the suppression of piezoelectric fields.
Time response characteristics of an oxide-confined GaAs∕AlGaAs resonant cavity-enhanced photodetector
Authors: Estacio E. , Alonzo C. , Samson A. , Garcia A. , Somintac A. , Salvador A.
Published: October 2004

This work compares the speed characteristics of a ∼135-μm-diam GaAs∕AlGaAs resonant cavity-enhanced (RCE) detector-emitter device with its laterally oxidized ∼80-μm-diam counterpart. The full width at half-maximum of the photocurrent spectrum exhibited no degradation in wavelength selectivity. Moreover, oxide confinement caused no current bottleneck that was inferred to adversely affect the device speed. The measured pulse responses were 65 and 75ps for the unoxidized and oxidized devices, respectively. Oxide-confined RCE photodetectors show relevant application in concentric hybrid RCE vertical cavity laser devices, this work deals with the speed characteristics of laterally oxidized resonant cavity-enhanced devices.
Heating of a particulate by radio-frequency electric and magnetic fields
Authors: Bosman Herman , Tang Wilkin , Lau Y. Y. , Gilgenbach R. M.
Published: October 2004

With the use of a highly symmetrical model, the heating of a spherical particulate by a predominantly radio-frequency electric field and by a predominantly rf magnetic field is solved exactly using the Maxwell equations. It is found that, in general, heating by the rf magnetic field is dominant whenever δ<a, where δ is the resistive skin depth and a is the radius of the particulate, which may either be nonmagnetic or magnetic. The known analytic scaling laws in the various regimes are recovered, from the static case to very high frequency, subject to λ⪢a, where λ is the free space wavelength of the rf field. The analysis may form a theoretical basis in the heating phenomenology of particulates.
Imaging of μm wavelength collective cavity resonances in Bi2Sr2CaCu2O8+x intrinsic Josephson junction stacks under microwave irradiation
Authors: Clauss Tobias , Uchida Takashi , Mößle Michael , Koelle Dieter , Kleiner Reinhold
Published: October 2004

We have used low-temperature scanning electron microscopy to image the electromagnetic field distribution in microstructured Bi2Sr2CaCu2O8+x intrinsic Josephson junction stacks under microwave irradiation. Even for microwave frequencies below 10GHz, standing waves along the stack with wavelengths of order 10μm can be observed. The data, together with numerical simulations based on coupled sine-Gordon equations, strongly indicate that the standing waves are due to collective Josephson plasma cavity resonances, with a large number of junctions oscillating in phase. The resonance frequencies are estimated to be of order 100–500GHz, that is, much higher than the drive frequency. We suggest that, under the low-frequency microwave irradiation, fluxon∕antifluxon pairs form, in turn exciting the high-frequency collective cavity resonances.
Differential ellipsometric surface plasmon resonance sensors with liquid crystal polarization modulators
Authors: Hooper I. R. , Sambles J. R.
Published: October 2004

Differential ellipsometric interrogation of surface plasmon (SP) resonances is a technique that gives ultrahigh sensitivity to refractive index changes, and it may provide the basis for chemical and biological sensors. In this study, a liquid crystal polarization modulator has been developed to provide such a differential technique. A refractive index sensitivity of 2×10−7 refractive index units is demonstrated, which is at least as sensitive as more established SP sensing techniques. The use of a liquid crystal modulator allows for low-voltage signal modulation and also feedback locking to zero. Possibly more important, it leads to pixelization for array sensing and for potential imaging.
Organic thin-film transistors with nanocomposite dielectric gate insulator
Authors: Chen Fang-Chung , Chu Chih-Wei , He Jun , Yang Yang , Lin Jen-Lien
Published: October 2004

High-performance organic thin-film transistors (OTFTs) with a nanoparticle composite dielectric layer have been demonstrated. The dielectric layer consists of cross-linked poly-4-vinylphenol (PVP) and high-dielectric titanium dioxide (TiO2) nanoparticles. Because of the nanosize of TiO2, it disperses well in the organic solvent, which makes it possible to use solution-processable methods to prepare the dielectric layer. OTFTs with pentacene as the semiconducting layers have been demonstrated; it was found that the OTFTs with the nanocomposite dielectric layer have higher field-induced current than that of conventional devices because the dielectric constant of the gate insulator is increased. This finding opens an interesting direction for the preparation of high-performance OTFTs without complicated sputtering of high-κ dielectric materials.
Subpicosecond exciton spin relaxation in GaN
Authors: Kuroda T. , Yabushita T. , Kosuge T. , Tackeuchi A. , Taniguchi K. , Chinone T. , Horio N.
Published: October 2004

The spin-relaxation process of A-band exciton in GaN is observed by spin-dependent pump and probe reflectance measurement with subpicosecond time resolution. The spin-relaxation times at 150−225K are 0.47−0.25ps. These are at least one order of magnitude shorter than those of the other III-V compound semiconductors. The spin-relaxation time τs is found to be proportional to T−1.4, where T is the temperature.
Direct optical observation of compositional fluctuation in GaAs1−xNx by near-field photoluminescence spectroscopy and microscopy with high spatial resolution
Authors: Matsuda K. , Saiki T. , Yamada T. , Ishizuka T.
Published: October 2004

We describe imaging spectroscopy of GaAs1−xNx∕GaAs single quantum wells using low-temperature near-field scanning optical microscope with a high spatial resolution of 35nm. In near-field photoluminescence spectra of a GaAs1−xNx∕GaAs(x=0.7%) quantum well, the narrow spectral peaks with a point emission spatial profile (localized exciton emission) come from local N-rich regions (spontaneous N clusters), and the broad peaks with spatial extension (delocalized exciton emission) are random alloy regions. Localized exciton emissions due to spontaneous N clusters are also observed in GaAs1−xNx with a higher N concentration (x=1.2%).
Negative differential Rashba effect in two-dimensional hole systems
Authors: Habib B. , Tutuc E. , Melinte S. , Shayegan M. , Wasserman D. , Lyon S. A. , Winkler R.
Published: October 2004

We demonstrate experimentally and theoretically that two-dimensional (2D) heavy-hole systems in single heterostructures exhibit a decrease in spin–orbit interaction-induced spin splitting with an increase in perpendicular electric field. Using front and back gates, we measure the spin splitting as a function of applied electric field while keeping the density constant. Our results are in contrast to the more familiar case of 2D electrons where spin splitting increases with electric field.
Stress in hard metal films
Authors: Janssen G. C. A. M. , Kamminga J.-D.
Published: October 2004

In the absence of thermal stress, tensile stress in hard metal films is caused by grain boundary shrinkage and compressive stress is caused by ion peening. It is shown that the two contributions are additive. Moreover tensile stress generated at the grain boundaries does not relax by ion bombardment. In polycrystalline hard metal films the grain structure evolves during growth, leading to wider grains higher up in the film. The tensile component of the stress in the film is generated at the grain boundaries and therefore depends on film thickness. The effect of ion bombardment is independent of grain size, therefore compressive stress does not depend on film thickness. As a result in polycrystalline films deposited under a bias voltage a stress gradient exists from tensile at the interface to compressive at the top of the film.
High resolution x-ray absorption spectroscopy using a laser plasma radiation source
Authors: Vogt Ulrich , Wilhein Thomas , Stiel Holger , Legall Herbert
Published: October 2004

In this article we present a setup of a spectrometer for near edge x-ray absorption spectroscopy at the carbon K-edge (284 eV). The spectrometer works with a laser produced plasma as x-ray source and a single x-ray optical element in grazing incidence configuration called off-axis reflection zone plate. Using different sample foils we were able to demonstrate a spectral resolution of E/ΔE≈600. The positions of specific absorption peaks are in agreement with data measured at synchrotron sources. Since the off-axis zone plate is a focusing system, the x-ray flux in the detector plane is high enough to record an absorption spectrum on a charge-coupled device detector with a single shot. In the single shot modus a spectrum can be recorded before a sample degradation takes place. This will enable time-resolved experiments using pump-probe techniques.
Design for a multifrequency high magnetic field superconducting quantum interference device-detected quantitative electron paramagnetic resonance probe: Spin-lattice relaxation of cupric sulfate pentahydrate (CuSO4⋅5H2O)
Authors: Cage Brant , Russek Stephen
Published: October 2004

We have designed a spectrometer for the quantitative determination of electron paramagnetic resonance (EPR) at high magnetic fields and frequencies. It uses a superconducting quantum interference device (SQUID) for measuring the magnetic moment as a function of the applied magnetic field and microwave frequency. We used powdered 2,2-diphenyl-1-picrylhydrazyl to demonstrate resolution of g-tensor anisotropy to 1 mT in a magnetic field of 3 T with a sensitivity of 1014 spins per 0.1 mT. We demonstrate multifrequency operation at 95 and 141 GHz. By use of an aligned single crystal of cupric sulfate pentahydrate (chalcanthite) CuSO4⋅5H2O, we show that the spectrometer is capable of EPR line shape analysis from 4 to 200 K with a satisfactory fit to a Lorentzian line shape at 100 K. Below 100 K, we observed line-broadening, g shifts, and spectral splittings, all consistent with a known low-dimensional phase transition. Using SQUID magnetometry and a superconducting magnet, we improve by an order of magnitude the sensitivity and magnetic field range of earlier power saturation studies of CuSO4⋅5H2O. We were able to saturate up to 70% of the magnetic moment with power transfer saturation studies at 95 GHz, 3.3 T, and 4 K and obtained the spin-lattice relaxation time, T1=1.8 ms, of CuSO4⋅5H2O at 3.3 T and 4 K. We found an inverse linear dependence of T1, in units of seconds (s) at 3.3 T between 4 and 2.3 K, such that T1=0.016⋅K⋅s⋅τ−1−0.0022⋅s, where τ is the absolute bath temperature. The quantitative determination of EPR is difficult with standard EPR techniques, especially at high frequencies or fields. Therefore this technique is of considerable value.
Determination of groove spacings for concave diffraction gratings
Authors: Hu Zhongwen , Liu Zuping , Wang Qiuping
Published: October 2004

A long trace profiler (LTP) based method has been reported to measure the groove density of a concave grating with a curvature radius 14346.8 mm. It is appropriate for gratings with a sufficiently large curvature radius. Measurements of the groove density of a concave or convex grating with a small curvature radius could be problematic. A system based on a diffraction method and developed to check the groove variation of variable line spacing (VLS) gratings was used to measure a concave grating at NSRL recently and is the subject of this paper. For a grating with a small radius of curvature, the off-axis errors become dominant factors determining the system uncertainty. The errors are evaluated, and a correction algorithm is developed. A commercially available concave grating with a curvature radius of 750 mm was measured. The maximum relative groove density error (ΔN/N) was 3×10−5.
Investigation of self-organized criticality behavior of edge plasma transport in Torus experiment of technology oriented research
Authors: Xu Y. H. , Jachmich S. , Weynants R. R. , Huber A. , Unterberg B. , Samm U.
Published: October 2004

The self-organized criticality (SOC) behavior of the edge plasma transport has been studied using fluctuation data measured in the plasma edge and the scrape-off layer of Torus experiment of technology oriented research tokamak [H. Soltwisch et al., Plasma Phys. Controlled Fusion 26, 23 (1984)] before and during the edge biasing experiments. In the “nonshear” discharge phase before biasing, the fluctuation data clearly show some of the characteristics associated with SOC, including similar frequency spectra to those obtained in “sandpile” transport and other SOC systems, slowly decaying long tails in the autocorrelation function, values of Hurst parameters larger than 0.5 at all the detected radial locations, and a radial propagation of avalanchelike events in the edge plasma area. During the edge biasing phase, with the generation of an edge radial electric field Er and thus of Er×B flow shear, contrary to theoretical expectation, the Hurst parameters are substantially enhanced in the negative flow shear region and in the scrape-off layer as well. Concomitantly, it is found that the local turbulence is well decorrelated by the Er×B velocity shear, consistent with theoretical predictions.
Spring wetlands in seasonally arid Queensland: floristics, environmental relations, classification and conservation values
Authors: Fensham R. J. , Fairfax R. J. , Sharpe P. R.
Published: October 2004

The vegetation and environmental setting of permanent spring wetlands are described from a survey of 269 spring complexes throughout seasonally arid Queensland. Wetlands associated with springs in the western and southern discharge areas of the Great Artesian Basin are floristically distinct from other spring wetlands. Ordination analysis suggests that the biogeographic regions and the broad geological substrates that support spring wetlands provide a meaningful representation of floristic range. An existing classificatory system that defines ‘regional ecosystems’ on the basis of the biogeographic region and broad geological substrate is adopted to define 15 spring-wetland types in seasonally arid Queensland. The conservation value of the springs is assessed by a scheme that weights plant species populations on the basis of their endemicity and isolation from other populations, demonstrating that both Great Artesian Basin and non-Great Artesian Basin springs have similar conservation values.
Programinis burmitis gen. et sp. nov., and P. laminatus sp. nov., Early Cretaceous grass-like monocots in Burmese amber
Authors: Poinar, Jr. George O.
Published: October 2004

The remains of a spikelet and a leaf of an Early Cretaceous grass-like monocot in Burmese amber are described as Programinis burmitis gen. et sp. nov., and P.�laminatus sp. nov., respectively. The laterally compressed spikelet of P.�burmitis has two basal sterile glumes, a series of lemmas and paleas and remains of stamens and a gynoecium. Adjacent to the spikelet are spherical, monoporate pollen grains. The epidermis of the leaf fragment of P.�laminatus contains numerous stomata with well-defined, sausage-shaped guard cells with elongate nuclei, rows of epidermal cells with long and short cells and spherical and elliptical silica-like bodies in cuboid epidermal cells. Unpointed papillae and uniseriate bicellular microhairs, both raised, occur on the leaf surface. Programinis burmitis and P.�laminatus are considered early bambusoid types that grew in tropical, forested habitats. Their discovery suggests that true grasses may have evolved in South-east Asia, since the Burmese amber mines are located on the Burma Plate, part of Laurasia.
A reassessment of the genus Haeckeria (Asteraceae: Gnaphalieae), with definition of new species in Cassinia
Authors: Orchard A. E.
Published: October 2004

Variation in the species hitherto known as Haeckeria ozothamnoides F.Muell. is discussed. This taxon has well-developed paleae between the florets, and many collections show development of a pappus. These characters, along with others such as leaf anatomy and morphology, strongly distinguish H. ozothamnoides s. lat. from Haeckeria s. str. and place it in Cassinia. The taxon is also shown to comprise three closely related species, which are here described as Cassinia ozothamnoides (F.Muell.) Orchard, comb. nov., C.�scabrida Orchard, sp. nov. and C.�venusta Orchard, sp. nov. The history, taxonomy, relationships and classification of Haeckeria is reviewed, and the genus and its two remaining species, H.�cassiniiformis and H.�punctulata, are described. All five species are illustrated and their distributions mapped.
Multiple origins of the endemic Australian Macrobrachium (Decapoda : Palaemonidae) based on 16S rRNA mitochondrial sequences
Authors: Murphy Nicholas P. , Austin Christopher M.
Published: October 2004

The evolutionary relationships of the freshwater prawn genus Macrobrachium are obscure. Members of this genus are widely distributed across tropical and subtropical regions. The phylogenetic relationships among the seven endemic and six non-endemic Australian Macrobrachium, along with five non-Australian species, were inferred from the mitochondrial 16S rRNA gene sequences. Methods of analysis yielded phylogenetic trees of differing topologies; however, none supported a monophyletic origin for endemic Australian Macrobrachium. Enforced monophyly of a single origin of endemic Macrobrachium was statistically tested and rejected. These results support the view that the endemic Australian Macrobrachium arose from multiple origins. Previous biogeographical hypotheses related to the radiation of Macrobrachium into Australia are re-examined in the context of these results.
Influence of season and weather on activity patterns of the numbat (Myrmecobius fasciatus) in captivity
Authors: Cooper C. E. , Withers P. C.
Published: October 2004

To separate the influence of weather from predation pressure and food availability, and to aid in the interpretation of activity data for wild numbats, we examined the influence of season and weather on the activity of captive numbats. Unlike other Australian marsupials, numbats are exclusively diurnal, being active for an average of 21.2% of the 24 h day. However, in the present study, activity duration varied seasonally, with numbats being active for longer periods in summer (39–65% of the available daylight) than winter (17–59%). During winter, captive numbats were active for shorter periods than wild numbats (presumably because captive numbats don't have to forage for food); however, they did not cease activity in the middle of the day during summer (suggesting that the inactivity of wild numbats at midday during summer is a response to food availability rather than a thermoregulatory response). Captive numbats were more active in summer than in winter, which may reflect their summer breeding season. Environmental conditions significantly affected daily activity, with low levels of activity recorded on days of low light intensity and high relative humidity. The majority of numbat activity occurred at ambient temperatures below thermoneutrality (<30°C). The associated costs of thermoregulation for active numbats were calculated, from activity time, to be higher in winter (0.586 mL O2 g–1 h–1) than in summer (0.274 mL O2�g–1�h–1).
Overwintering ecology of Chrysophtharta agricola: mechanisms of reproductive diapause induction and termination
Authors: Nahrung H. F. , Allen G. R.
Published: October 2004

Reproductive diapause is common in the Chrysomelidae, and allows 'escape in time' of conditions unfavourable for growth and development. Chrysophtharta agricola (Chapuis) (Coleoptera : Chrysomelidae), which undergoes one or two generations per year, spends 7–8 months in reproductive diapause, emerging in spring to feed and oviposit. We manipulated photoperiod and temperature to test their effects on induction and termination of diapause in the laboratory; we also conducted field studies for validation of results, and to examine patterns of voltinism as determined by the onset of diapause. A critical photoperiod of between 12 and 16 h of light was required to initiate diapause in the laboratory and field, although 55% of beetles entered diapause in response to low temperature (9°C) alone. At short photoperiods (8L : 16D), high temperature (21°C) subverted diapause in 20% of adults. Therefore, voltinism in C. agricola is a seasonally plastic trait dependent on emergence time of teneral adults. Diapause termination was primarily influenced by temperature, although photoperiod had an effect at low temperatures. Beetles accumulated day-degrees (DD) during overwintering, with beetles collected later terminating diapause sooner than those collected earlier (total DD was similar). Diapause termination is, therefore, dependent on DD accumulation above the threshold temperature (6.7°C), rather than a specific environmental cue. Results are discussed in ecological and applied contexts, and provide the ability to predict the population phenology of C. agricola. Seasonal plasticity, as demonstrated here, allows insects to balance resource availability, reproductive strategy and climatic tolerance.
Molecular phylogeny of blindsnakes (Ramphotyphlops) from western Australia and resurrection of Ramphotyphlops bicolor (Peters, 1857)
Authors: Rabosky D. L. , Aplin K. P. , Donnellan S. C. , Hedges S. B.
Published: October 2004

Blindsnakes (Typhlopidae) represent one of the least known elements of the Australian herpetofauna. Mitochondrial DNA sequence data and morphology are used here to show that a widespread species of Australian blindsnake, Ramphotyphlops australis, comprises two distinct species. Ramphotyphlops bicolor (new combination) is resurrected from synonymy with R. australis and redescriptions are provided for both species. Mitochondrial DNA sequence variation within R. australis indicates that the central and south-coast populations are more closely related to each other than either is to the morphologically distinctive populations at the northern edge of the species' range. Observed levels of differentiation suggest historical isolation of populations from the Kalbarri/Shark Bay region of the western Australian coastline. However, lack of concordance between mitochondrial haplotype phylogeny and morphology for several individuals might reflect limited gene flow between the northern and south–central populations. We note that many taxa show restricted distributions or range disjunctions along the central Western Australian coastal margin, and we discuss possible models to explain population fragmentation in this region. Pliocene–Pleistocene sea-level fluctuations along the western Australian coast could have isolated sand plain communities in the Kalbarri/Shark Bay region from similar communities further south near Geraldton, possibly underlying the phylogeographic pattern in R. australis. Data from additional taxa will be needed to fully evaluate this hypothesis.
Effects of dietary fat and carbohydrate on appetite vary depending upon site and structure
Authors: French Stephen
Published: October 2004

The present review summarises the effects of different carbohydrate and fat structures on food intake and appetite and the differences in response at various levels of processing of macronutrients. Several physico-chemical properties of carbohydrate and fat molecules appear to influence the short-term satiating properties. However, long-term substantiation of these findings expressed in terms of food intake or body weight is not currently available. Such studies will be required to make clear recommendations regarding dietary composition to aid satiety.
Protein, amino acids and the control of food intake
Authors: Tome Daniel
Published: October 2004

The influence of protein and amino acid on the control of food intake and the specific control of protein and amino acid intakes remains incompletely understood. The most commonly accepted conclusions are: (1) the existence of an aversive response to diets deficient in or devoid of protein or deficient in at least one essential amino acid; (2) the existence of a mechanism that enables attainment of the minimum requirement for N and essential amino acids by increasing intake of a low-protein diet; (3) a decrease in the intake of a high-protein diet is associated with different processes, including the high satiating effect of protein. Ingested proteins are believed to generate pre- and post-absorptive signals that contribute to the control of gastric kinetics, pancreatic secretion and food intake. At the brain level, two major afferent pathways are involved in protein and amino acid monitoring: the indirect neuro-mediated (mainly vagus-mediated) pathway and the direct blood pathway. The neuro-mediated pathway transfers pre-absorptive and visceral information. This information is for the main part transferred through the vagus nerve that innervates part of the oro-sensory zone: the stomach, the duodenum and the liver. Other information is directly monitored in the blood. It is likely that the system responds precisely when protein and essential amino acid intake is inadequate, but in contrast allows a large range of adaptive capacities through amino acid degradation and substrate interconversion.
Energy balance and body-weight stability: impact of gene–environment interactions
Authors: Tremblay Angelo , Pérusse Louis , Bouchard Claude
Published: October 2004

Studies of monozygotic twins in the context of overfeeding and energy deficit experiments have shown that gene–environment interactions affect energy balance. From a clinical standpoint, this implies that some individuals are more susceptible to body-weight gain or loss than others because of genetic differences. This opens new perspectives in predictive medicine. In the future, health professionals should be able to count on early diagnosis of individuals at risk for developing long-term metabolic problems and obesity or for not responding adequately to clinical interventions. However, before predictive medicine is in a position to contribute significantly to prevention or treatment of patients, an enormous amount of work has to be done to identify all genetic and environmental factors of relevance, and their network of interactions.
A Small C-Terminal Sequence of Aurora B Is Responsible for Localization and Function
Authors: Scrittori Laetitia , Skoufias Dimitrios A. , Hans Fabienne , Gerson Véronique , Sassone-Corsi Paolo , Dimitrov Stefan , Margolis Robert L.
Published: October 2004

Aurora B, a protein kinase required in mitosis, localizes to inner centromeres at metaphase and the spindle midzone in anaphase and is required for proper chromosome segregation and cytokinesis. Aurora A, a paralogue of Aurora B, localizes instead to centrosomes and spindle microtubules. Except for distinct N termini, Aurora B and Aurora A have highly similar sequences. We have combined small interfering RNA (siRNA) ablation of Aurora B with overexpression of truncation mutants to investigate the role of Aurora B sequence in its function. Reintroduction of Aurora B during siRNA treatment restored its localization and function. This permitted a restoration of function test to determine the sequence requirements for Aurora B targeting and function. Using this rescue protocol, neither N-terminal truncation of Aurora B unique sequence nor substitution with Aurora A N-terminal sequence affected Aurora B localization or function. Truncation of unique Aurora B C-terminal sequence from terminal residue 344 to residue 333 was without effect, but truncation to 326 abolished localization and function. Deletion of residues 326-333 completely abolished localization and blocked cells at prometaphase, establishing this sequence as critical to Aurora B function. Our findings thus establish a small sequence as essential for the distinct localization and function of Aurora B.
Cellular Distribution and Functions of Wild-Type and Constitutively ActivatedDictyosteliumPakB
Authors: de la Roche Marc , Mahasneh Amjad , Lee Sheu-Fen , Rivero Francisco , Côté Graham P.
Published: October 2004

Dictyostelium PakB, previously termed myosin I heavy chain kinase, is a member of the p21-activated kinase (PAK) family. Two-hybrid assays showed that PakB interacts with Dictyostelium Rac1a/b/c, RacA (a RhoBTB protein), RacB, RacC, and RacF1. Wild-type PakB displayed a cytosolic distribution with a modest enrichment at the leading edge of migrating cells and at macropinocytic and phagocytic cups, sites consistent with a role in activating myosin I. PakB fused at the N terminus to green fluorescent protein was proteolyzed in cells, resulting in removal of the catalytic domain. C-terminal truncated PakB and activated PakB lacking the p21-binding domain strongly localized to the cell cortex, to macropinocytic cups, to the posterior of migrating cells, and to the cleavage furrow of dividing cells. These data indicate that in its open, active state, the N terminus of PakB forms a tight association with cortical actin filaments. PakB-null cells displayed no significant behavioral defects, but cells expressing activated PakB were unable to complete cytokinesis when grown in suspension and exhibited increased rates of phagocytosis and pinocytosis.
An enzyme mechanism language for the mathematical modeling of metabolic pathways
Authors: Yang Chin-Rang , Shapiro Bruce E. , Mjolsness Eric D. , Hatfield G. Wesley
Published: October 2004

Motivation: As a first step toward the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways.

Results: We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association–dissociation reactions that are translated by Cellerator into ordinary differential equations that are numerically solved by Mathematica™. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.

Availability: A Mathematica™ executable kMech.m file is available at the University of California, Irvine, Institute for Genomics and Bioinformatics website, http://www.igb.uci.edu/servers/sb.html. Cellerator, free of charge to academic, US government, and other non-profit organizations, can be obtained at the Cellerator website, (http://www-aig.jpl.nasa.gov/public/mls/cellerator/feedback.html).

Contact: Biology correspondence should be addressed to gwhatfie@uci.edu. Computation correspondence should be addressed to emj@uci.edu.

Supplementary information:  http://www.igb.uci.edu/servers/sb.html.
Profile-based detection of microRNA precursors in animal genomes
Authors: Legendre Matthieu , Lambert André , Gautheret Daniel
Published: October 2004

Motivation: MicroRNAs (miRNA) are essential 21–22 nt regulatory RNAs produced from larger hairpin-like precursors. Local sequence alignment tools such as BLAST are able to identify new members of known miRNA families, but not all of them. We set out to estimate how many new miRNAs could be recovered using a profile-based strategy such as that implemented in the ERPIN program.

Results: We constructed alignments for 18 miRNA families and performed ERPIN searches on animal genomes. Results were compared to those of a WU-BLAST search at the same E-value cutoff. The two combined approaches produced 265 new miRNA candidates that were not found in miRNA databases. About 17% of hits were ERPIN specific. They showed better structural characteristics than BLAST-specific hits and included interesting candidates such as members of the miR-17 cluster in Tetraodon. Profile-based RNA detection will be an important complement of similarity search programs in the completion of miRNA collections.

Contact:  gautheret@esil.univ-mrs.fr
Statistical analysis of domains in interacting protein pairs
Authors: Nye Tom M. W. , Berzuini Carlo , Gilks Walter R. , Babu M. Madan , Teichmann Sarah A.
Published: October 2004

Motivation: Several methods have recently been developed to analyse large-scale sets of physical interactions between proteins in terms of physical contacts between the constituent domains, often with a view to predicting new pairwise interactions. Our aim is to combine genomic interaction data, in which domain–domain contacts are not explicitly reported, with the domain-level structure of individual proteins, in order to learn about the structure of interacting protein pairs. Our approach is driven by the need to assess the evidence for physical contacts between domains in a statistically rigorous way.

Results: We develop a statistical approach that assigns p-values to pairs of domain superfamilies, measuring the strength of evidence within a set of protein interactions that domains from these superfamilies form contacts. A set of p-values is calculated for SCOP superfamily pairs, based on a pooled data set of interactions from yeast. These p-values can be used to predict which domains come into contact in an interacting protein pair. This predictive scheme is tested against protein complexes in the Protein Quaternary Structure (PQS) database, and is used to predict domain–domain contacts within 705 interacting protein pairs taken from our pooled data set.

Contact:  thomas.nye@mrc-bsu.cam.ac.uk
LabArray: real-time imaging and analytical tool for microarrays
Authors: Ng Johnson Kian-Kok , Liu Wen-Tso
Published: October 2004

Summary: Microarrays have been used to perform high-throughput genetic analyses such as single-nucleotide polymorphisms detection and microbial genome analysis. Some of these analyses require real-time monitoring of the hybridization signals with respect to a varying experimental condition, such as temperature. However, current microarray imaging and analysis packages typically do not possess such real-time capabilities. Therefore, microarray image analyses are often time-consuming and labour-intensive. LabArray was developed to expedite such processes by enabling real-time monitoring of microarray signals.

Availability: LabArray is available at http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm

Contact:  cveliuwt@nus.edu.sg

Supplementary information: Screenshots and instructions for use are available at the above website.
COPS—Cis/transpeptide bond conformation prediction of amino acids on the basis of secondary structure information
Authors: Pahlke Doreen , Leitner Dietmar , Wiedemann Urs , Labudde Dirk
Published: October 2004

Summary: COPS predicts for all 20 naturally occurring amino acids whether the peptide bond in a protein is in cis or trans conformation. The algorithm is based only on secondary structure information of amino acid triplets without considering the amino acid sequence information. Conformation parameters are derived from solved 3D structures deposited in the PDB and led to propensities based on modified Chou–Fasman parameters. COPS analyses amino acid triplets taking only their respective secondary structure into consideration and upon application of a set of rules utilizing the conformation parameters, the N-terminal peptide bond conformation of the middle residue is predicted. COPS was tested on a random selection of protein datasets.

Availability: The COPS program and further information are freely available from the FMP website at http://www.fmp-berlin.de/nmr/cops

Contact:  labudde@fmp-berlin.de